@article {pmid42219571,
year = {2026},
author = {Rossini, L and Benhamouche, O and Garone, E},
title = {Optimal control and multitrophic physiologically-based models: The binomial for successful decision support systems in insect pest management.},
journal = {Pest management science},
volume = {82},
number = {9},
pages = {9285-9292},
pmid = {42219571},
issn = {1526-4998},
support = {//European Commission/ ; },
mesh = {Animals ; *Insect Control/methods/economics ; *Decision Support Techniques ; *Insecta/physiology ; Models, Theoretical ; Crops, Agricultural/growth & development ; Agroecology ; },
abstract = {BACKGROUND: Agroecosystems can be viewed as dynamic systems that receive inputs through agronomic practices, generate yield as an output, and whose economic profitability depends on balancing production costs and revenues. Pests and pathogens reduce crop yield and often require growers to apply additional inputs, thereby increasing production costs. According to integrated pest management (IPM), however, maximising yield while minimising costs does not mean eradicating bio-aggressors from the field but corresponds to maintain pest populations below economic thresholds. This objective can be achieved by identifying the optimal timing for control actions through decision support systems (DSSs) as, from a mathematical perspective, IPM can be formulated as an optimal control problem: the objective function accounts for economic returns and production costs, including treatments, and is driven by plant-pest dynamics.<br><br>RESULTS: We introduced the essential concepts of an optimal control problem that faithfully fits the IPM guidelines. Multitrophic models account the interaction between plant and pest, while the effect of control actions relates to the objective function of the problem: the total economic income of the farm depends on the number of treatments and the timing of their application. Simulations showed both that lower pest population does not correspond to the maximum profit and that a good timing in the application can have almost the same effect of repeated treatments.<br><br>CONCLUSION: This study revises the concept of DSS through optimal control applied to pest populations, pointing out that multitrophic models are fundamental to fit the IPM guidelines of economic and environmental sustainability. &#xa9; 2026 The Author(s). Pest Management Science published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.},
}
@article {pmid42533338,
year = {2026},
author = {Kouba, M and Stehlíková Sovadinová, S and Tulis, F and Ševčík, M and Bartošová, J and Korpimäki, E and Bartoš, L},
title = {Publisher Correction: Sibling cooperation in boreal owls during the post-fledging dependence period.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {},
doi = {10.1186/s12915-026-02702-8},
pmid = {42533338},
issn = {1741-7007},
}
@article {pmid42303211,
year = {2026},
author = {Li, L and He, L and Jia, Z and Li, Q and Li, J and Yang, Q and Zheng, Y},
title = {Comparative physiological and multi-omics responses reveal divergent drought-response patterns in two Melilotus species.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {371},
number = {},
pages = {113283},
doi = {10.1016/j.plantsci.2026.113283},
pmid = {42303211},
issn = {1873-2259},
mesh = {Multiomics ; Drought Resistance ; *Melilotus/physiology/genetics/metabolism ; *Droughts ; Metabolomics ; Transcriptome ; Stress, Physiological ; Species Specificity ; },
abstract = {Melilotus albus and M. officinalis are closely related legume species with potential value as stress-resilient resources for dry and marginal environments. However, whether they exhibit similar physiological and multi-omics response organization under continuous drought remains unclear. In this study, physiological, transcriptomic, and metabolomic analyses were integrated to compare drought-tolerant and drought-sensitive accessions of the two species at 0, 4, and 8 d of continuous drought. Both species showed coordinated changes in osmolyte accumulation, antioxidant defense, photosystem adjustment, and secondary metabolic remodeling, but differed in response rhythm and regulatory emphasis. Across the selected accession pairs, M. albus was mainly associated with sustained soluble sugar accumulation and relatively moderate photosystem changes, whereas M. officinalis showed a clearer tendency toward POD-associated defense and photoprotective adjustment. Comparative analyses across physiological and omics layers suggested that drought-response divergence became more clearly concentrated at the middle stage within the sampled period. Integrative analysis further indicated that phenylpropanoid- and flavonoid-related remodeling represented a major shared response direction in both species. However, this shared direction was organized differently, with M. albus showing changes across the phenylpropanoid backbone and multiple flavonoid-related branches, whereas M. officinalis showed a more focused pattern involving lignin-related and selected flavonol-related branches. These findings suggest that closely related Melilotus resources may differ in temporal coordination and secondary metabolic organization under continuous drought, providing useful information for understanding their response characteristics in dry and marginal environments.},
}
@article {pmid42314817,
year = {2026},
author = {Ruan, G and Ai, X and Sun, S and Qian, J and Song, G and Mi, W and Wan, D and Bi, Y},
title = {Time-resolved multi-omics reveals molecular dynamics of Synechocystis sp. PCC 6803 to cadmium stress.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {406},
number = {},
pages = {128590},
doi = {10.1016/j.envpol.2026.128590},
pmid = {42314817},
issn = {1873-6424},
mesh = {*Cadmium/toxicity ; *Synechocystis/drug effects/physiology/metabolism/genetics ; Multiomics ; Stress, Physiological ; Proteomics ; Molecular Dynamics Simulation ; },
abstract = {Cadmium pollution posed a serious threat to eco-environmental security, but molecular variation in microalgae induced by cadmium remains unknown. To address this, we screened the molecular dynamics in Synechocystis sp. PCC 6803 exposed to an environmentally relevant Cd[2+] concentration (0.05 mg L[-1]) over 0-144 h. Differential express genes/proteins (DEGs/DEPs) and expression levels divided the exposure process into two stages. The response phase (0-24 h) was characterized by the rapid, transient, and highly specific gene/protein activation; the top uniquely DEGs/DEPs included nrsA (cation-efflux), PsbA1/T (Photosystem II protein) and Ssl1911 (glutamine synthetase) were defined as stage-specific molecular signatures. Their expression peaked before 24 h and showed no significant change thereafter. The adaptive phase (24-144 h) was characterized by the sustained and synergistic proteomic dynamic regulation, 145 co-expressed DEPs were identified, cadmium influx-associated transporters (MntCAB/FeoB) were suppressed, efflux systems (Slr0944/ZiaA) were induced coupled with enhanced central carbon metabolism (carbon fixation, oxidative phosphorylation, TCA cycle) and elevated antioxidant enzyme activity (Slr1516). It was concluded DEGs/DEPs involved in photosynthetic processes and antioxidant defense changed significantly within 24 h. These changes were followed by adaptive mechanisms, including down-regulating inward Cd[2+] transporters while simultaneously up-regulating efflux pumps, as well as enhancing energy metabolism and antioxidant capacity. This dynamic pattern provided insight into the interaction between cyanobacterial cells and cadmium ions.},
}
@article {pmid42413877,
year = {2026},
author = {Liao, S and Ji, J and Jiang, N and Ally, MS and Zhou, B and Jiang, T},
title = {Multi-omics analysis reveals defense mechanisms of Pinus sylvestris var. mongolica Litv. in response to Diplodia sapinea.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {371},
number = {},
pages = {113308},
doi = {10.1016/j.plantsci.2026.113308},
pmid = {42413877},
issn = {1873-2259},
mesh = {*Pinus sylvestris/microbiology/genetics/immunology/metabolism ; Multiomics ; *Ascomycota/physiology ; *Plant Diseases/microbiology/immunology ; Transcriptome ; Proteomics ; Plant Proteins/metabolism/genetics ; Gene Expression Profiling ; Metabolomics ; *Disease Resistance/genetics ; },
abstract = {Shoot blight, caused by Diplodia sapinea, severely threatens the growth and ecological functions of Pinus sylvestris var. mongolica Litv. Although this disease has caused increasing concern, the integrated molecular defense mechanisms of P. sylvestris var. mongolica in response to D. sapinea infection remain unclear. Understanding the molecular defense mechanisms of P. sylvestris var. mongolica is crucial for the development of targeted and environmentally sustainable strategies to manage this disease. Therefore, this study aimed to explore the molecular defense mechanisms of P. sylvestris var. mongolica in responses to D. sapinea infection through integrated analyses of second- and third-generation transcriptomics, proteomics, and metabolomics. A total of 264,852 high-quality full-length transcripts were acquired. Among these, 21,358 differentially expressed genes (DEGs) with known functions, 303 differentially expressed proteins (DEPs), and 675 differentially accumulated metabolites (DAMs) were identified. DEGs and DEPs analyses indicated significant increase of chitinases, peroxidases, and pathogenesis-related (PR) proteins. DAMs were categorized into lipids and lipid-like molecules, as well as phenylpropanoids and polyketides. KEGG analysis revealed that DEGs, DEPs and DAMs were mainly involved in phenylpropanoid biosynthesis, flavonoid biosynthesis, glutathione metabolism, and plant hormone signal transduction. Importantly, the phenylpropanoid-flavonoid biosynthesis pathway showed a notable accumulation of antimicrobial flavonoid metabolites. In vitro antifungal tests further confirmed that phloretin effectively inhibited the growth of D. sapinea. Overall, multi-omics data integration uncovers a complex defense system in P. sylvestris var. mongolica, characterized by direct antifungal activity mediated by chitinases and PR proteins, detoxification and redox homeostasis facilitated by glutathione metabolism, and the production of antimicrobial flavonoids. These results highlight PAL, CHS, GSTs, chitinases, and PR proteins as potential candidate targets for improving defense-related traits against shoot blight in P. sylvestris var. mongolica.},
}
@article {pmid42533155,
year = {2026},
author = {Haylock, KA and Parrini, F and Strauss, WM and Beytell, P and Moeller, CH and Hetem, RS},
title = {Vegetation greenness and heat load drive the movements of a water-dependent, selective grazer.},
journal = {Oecologia},
volume = {208},
number = {8},
pages = {},
pmid = {42533155},
issn = {1432-1939},
mesh = {Animals ; *Antelopes/physiology ; Climate Change ; Ecosystem ; Geographic Information Systems ; *Hot Temperature ; Namibia ; *Herbivory ; },
abstract = {Low-density, selective grazers with restricted habitat requirements may be particularly vulnerable to extinction under hotter, drier conditions expected across Africa's drylands with climate change. We evaluated how spatiotemporal variation in vegetation greenness and environmental heat load influenced movements of sable antelope, a water-dependent African grazer with selective resource requirements. We recorded hourly Global Positioning System (GPS) locations of 10 sable antelopes (Hippotragus niger) in Bwabwata National Park, Namibia, for up to 24 months, with concurrent hourly measurements of environmental heat load. As conditions became hotter and vegetation became browner during the dry season, home ranges increased in size and elongated towards the Kavango River. The 24-hour mean hourly displacement distance of sable antelopes increased in response to increased heat load and brown vegetation exposure, primarily due to more frequent long-distance movements to the Kavango River during the late dry season. Using Hidden Markov Models (HMMs), we identified four behavioural states of movement from GPS movement tracks: resting, foraging, local movement, and relocating. The relocating state, which was generally associated with directed movements to surface water, predominated during the late dry season. Sable antelopes increased both relocating and local movements, while decreasing foraging when exposed to high heat loads and brown vegetation. As conditions become increasingly hotter and drier, and resource availability becomes more unpredictable in space and time, species with specific resource requirements may face increased risk of extirpation, as walking farther to meet water requirements may compromise their already precarious energy balance during periods of resource limitation.},
}
@article {pmid42525642,
year = {2026},
author = {Dóris, B and Savogin Andraus, G and da Silva Seunaraine, R and Nabor de Cássia Silva, D and da Silva Teixeira, N and Siegel Guerra, B and Proença de Moraes, T and Lenci Marques, G},
title = {Association between climatic variables and cardiovascular hospitalizations in Brazil: An ecological study.},
journal = {PLOS global public health},
volume = {6},
number = {7},
pages = {e0005294},
pmid = {42525642},
issn = {2767-3375},
abstract = {Cardiovascular disease is the leading cause of death worldwide, and external factors such as ambient temperature can predispose to cardiovascular events. Brazil, a country with continental dimensions and diverse climates, lacks a recent study comparing cardiovascular hospitalization rates with climatic data across the Brazilian states. This study aimed to describe and relate the hospitalization counts of cardiovascular events, including acute myocardial infarction, stroke, and heart failure, to climatic data. Data were obtained from the Department of Informatics of the Unified Health System and the National Meteorology Institute from 2010 to 2024. We recorded a total of 2,917,900 hospitalizations for cardiovascular diseases across 103 cities in Brazil where complete climatic data were available. The hospitalization rates per 100,000 inhabitants ranged from 0.007 in the state of Maranhão to 0.023 in Rio Grande do Sul. We observed a lower relative risk of hospitalization for cardiovascular diseases in regions with a higher ambient temperature, with the temperature range up to 19°C having the highest risk. No difference in hospitalization risk was observed between the temperate and tropical climate regions. This study highlights the importance of public measures for cardiovascular event prevention during periods of lower temperature throughout the year.},
}
@article {pmid42529102,
year = {2026},
author = {Zhang, Z and He, L and Chen, B and Zhang, H},
title = {Mapping therapy-responsive immune ecotypes in clear cell renal cell carcinoma through integrative omics.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1893607},
pmid = {42529102},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Renal Cell/immunology/therapy/genetics/metabolism/drug therapy ; *Kidney Neoplasms/immunology/therapy/genetics/drug therapy/metabolism ; Tumor Microenvironment/immunology ; Immunotherapy/methods ; Biomarkers, Tumor ; Multiomics ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; },
abstract = {Clear cell renal cell carcinoma (ccRCC) is a kidney cancer in which immune activity is closely intertwined with von Hippel-Lindau (VHL) loss, hypoxia-inducible factor (HIF) signaling, angiogenesis, hypoxia, and metabolic adaptation. Although immune checkpoint inhibitor (ICI)-based regimens have changed the treatment landscape of advanced ccRCC, only a subset of patients achieve durable benefit. Commonly used biomarkers, such as programmed death-ligand 1 (PD-L1) expression, tumor mutation burden (TMB), and broad inflammatory gene signatures, have not been sufficient to explain this variation or to guide routine treatment selection. One reason is that immune infiltration in ccRCC is not synonymous with effective antitumor immunity. A tumor rich in CD8+ T cells may still be resistant if these cells are exhausted, metabolically restricted, spatially separated from tumor nests, or surrounded by suppressive myeloid, stromal, and vascular programs. Therefore, the key issue is not simply whether a tumor is immunologically "hot" or "cold," but which part of the antitumor response has failed. In this Mini Review, we discuss ccRCC immunotherapy response from an immune-ecological perspective. We focus on several treatment-relevant immune states, including T-cell-inflamed but dysfunctional tumors, myeloid-dominant suppressive tumors, angiogenesis- and hypoxia-skewed tumors, and immune-excluded tumors. We also consider how bulk transcriptomics, single-cell and spatial profiling, T-cell receptor sequencing, proteomics, metabolomics, and longitudinal liquid biopsy may help define these ecotypes and capture treatment-induced remodeling. This perspective may support more refined patient stratification and more mechanism-matched immunotherapy strategies in ccRCC.},
}
@article {pmid42529136,
year = {2026},
author = {Huang, L and Lin, N and Li, H and Hu, Y},
title = {Spatially organized macrophage-T-cell crosstalk in cervical cancer: insights from single-cell and spatial omics.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1896004},
pmid = {42529136},
issn = {1664-3224},
mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/immunology/pathology/metabolism ; *Macrophages/immunology/metabolism ; Tumor Microenvironment/immunology ; *T-Lymphocytes/immunology/metabolism ; *Cell Communication/immunology ; Multiomics ; Animals ; Single-Cell Analysis ; Human Papillomavirus Viruses/immunology ; Papillomavirus Infections/immunology ; Spatial Transcriptomics ; },
abstract = {Immunotherapy has transformed the therapeutic landscape of advanced cervical cancer, yet clinical benefit remains limited by a highly heterogeneous and immunosuppressive tumor microenvironment. Traditional paradigms, including binary M1/M2 macrophage polarization and models that interpret T-cell dysfunction solely through checkpoint expression, are insufficient to capture the localized intercellular dynamics that drive immune evasion. Recent advances in single-cell and spatial multi-omics have fundamentally reshaped our understanding of this landscape. In this review, we synthesize emerging high-dimensional atlases to reframe macrophage-T-cell crosstalk from simple ligand-receptor interactions into a spatially organized ecological model. We highlight the paradigm shift toward highly resolved myeloid programs, particularly SPP1[+] and C1QC[+] macrophage states, and discuss how these programs interact with stromal barriers, regulatory T cells, and metabolic checkpoints to restrict, exclude, or functionally constrain effector T cells within suppressive niches. Crucially, we position persistent high-risk human papillomavirus infection not merely as an initiating carcinogenic trigger, but as an upstream and continuous programmer that rewires innate immune sensing, including context-dependent cGAS-STING-related circuits, to stabilize local immune tolerance throughout disease progression. Finally, we propose translational strategies for distilling complex multi-omic atlases into pathology-compatible prognostic and predictive biomarker signatures. Ultimately, by deciphering these spatially organized networks, this review aims to provide actionable translational insights for targeting macrophage vulnerabilities, guiding biomarker-driven combinatorial immunotherapies, and overcoming immune resistance in cervical cancer.},
}
@article {pmid42530538,
year = {2026},
author = {Ueda, N and Nakamura, M and Ojima, T and Miura, A and Nagahata, T and Kondo, I and Hayakawa, T and Kadota, A and Kondo, K and Yoshita, K and Okuda, N and Okayama, A and Miura, K and Okamura, T and , },
title = {Association of protein intake per kilogram body weight with decline in activities of daily living and death in the older Japanese population: NIPPON DATA90.},
journal = {Nutrition and health},
volume = {},
number = {},
pages = {2601060261464039},
doi = {10.1177/02601060261464039},
pmid = {42530538},
issn = {2047-945X},
abstract = {BackgroundThe aging population in Japan highlights the public health need to maintain functional abilities, with activities of daily living (ADL) being essential for healthy aging.AimWe prospectively examined the association between protein intake (g/BWkg/day) and the ADL decline or death risk among older Japanese adults.MethodsData from 1773 Japanese adults aged ≥65 years in the NIPPON DATA90 cohort were analyzed. Protein intake was assessed using data from the 1990 National Nutrition Survey of Japan, and individual intakes were estimated from household dietary records. Protein intake (g/BWkg/day) was categorized into sex-specific quartiles. ADL decline was defined as requiring assistance in ≥1 of ADL tasks during follow-up surveys (1995-2012). Logistic regression was used to estimate odds ratios for ADL decline or death by survey year, and Cox proportional hazards models examined hazard ratios for time-to-event ADL decline or death.SummaryDuring follow-up, 515 participants experienced ADL decline, and 1015 died. Among women, moderate protein intake (second quartile, 1.15-1.38 g/BWkg/day) was associated with a 35% lower risk of ADL decline (adjusted hazard ratio 0.65) compared with the lowest quartile. A similar pattern was observed for the combined outcome of ADL decline or death, whereas higher intake levels did not show additional benefit. No clear association was observed among men. These findings suggest that moderate protein intake was associated with the lowest risks of ADL decline and death, particularly among women. Adequate, but not excessive, protein consumption may help support functional health in older Japanese adults.},
}
@article {pmid42104558,
year = {2026},
author = {Luo, X and Lei, Z and Fang, D and Chen, H and Qian, L and Jin, C and Wang, X and Liu, X and Liu, H and Wang, Y},
title = {Integrated multi-omics decipher the complex nodule microbiota and distinct Frankiaceae symbiotic traits in wild actinorhizal plants.},
journal = {The New phytologist},
volume = {251},
number = {5},
pages = {2832-2851},
doi = {10.1111/nph.71234},
pmid = {42104558},
issn = {1469-8137},
support = {32300265//Young Scientists Fund of the National Natural Science Foundation of China/ ; },
mesh = {*Symbiosis/genetics ; Multiomics ; *Root Nodules, Plant/microbiology ; *Microbiota/genetics ; Phylogeny ; Frankia/genetics ; Fabaceae/microbiology ; Transcriptome/genetics ; },
abstract = {Actinorhizal plants are ecologically important pioneer species in temperate regions, capable of nitrogen-fixing root nodule symbiosis with Frankiaceae bacteria. Despite their significance within the nitrogen-fixing clades (NFC), multi-omics studies of actinorhizal symbiosis remain scarce. We profiled prokaryotic communities in the rhizosphere, root, and/or nodule compartments from five phylogenetically representative actinorhizal species, three legumes, and four nonnodulated NFC species using 16S rDNA sequencing. Transcriptomic and metagenomic analyses were performed on actinorhizal roots and nodules, respectively. Metagenome-assembled genomes revealed four novel Frankiaceae species. Frankiae relative abundance levels in nodules were generally lower than rhizobia in legumes. Actinorhizal nodules harbour diverse bacterial taxa, which exhibit predominantly positive interactions, with Frankiae forming a tightly interacting subgroup. Actinorhizal plants engage actively with soil microbiota, recruiting a specific rhizosphere community enriched with beneficial microbes, including ammonia-oxidising archaea. Many symbiotic mechanisms in nodulating host plants are conserved and derived from pre-existing molecular modules. Our analysis suggests the phosphoinositide signalling likely functions in actinorhizal symbiotic signal transduction. However, Frankiae exhibit fundamentally different symbiotic functional characteristics compared to rhizobia, reflecting less intimate symbiosis, which might favour the life-history strategies of temperate perennial actinorhizal plants.},
}
@article {pmid42335476,
year = {2026},
author = {Valentino, V and De Filippis, F and Ercolini, D},
title = {Fermented foods: lessons learned from metagenomics.},
journal = {Current opinion in biotechnology},
volume = {100},
number = {},
pages = {103545},
doi = {10.1016/j.copbio.2026.103545},
pmid = {42335476},
issn = {1879-0429},
mesh = {*Metagenomics/methods ; *Fermented Foods/microbiology ; *Food Microbiology ; Fermentation ; Microbiota ; Multiomics ; Probiotics ; },
abstract = {Thanks to the standard microbiology protocols of isolation and culturing, hundreds of strains have been isolated from fermented foods throughout the last decades, and phenotypic traits linked with pro-technological properties and health claims have been investigated. However, culture-independent metagenomic analyses have revealed an unexpected microbial diversity in foods fermented spontaneously or by undefined starter cultures. Here, we report the most groundbreaking advancements in the understanding of fermented foods ecology by presenting case studies where metagenomics has been applied, contributing to identifying novel species in silico or to deciphering the microbiome structure associated with spontaneous fermentations. We also highlight the potential of metagenomics in supporting the identification of potential probiotics and discuss the future ahead, particularly focusing on the integration of multi-omics approaches.},
}
@article {pmid42398853,
year = {2026},
author = {Zhang, L and Yuan, M and Duan, D and Li, C and Ma, Y and Li, J and Zhou, C and Zhang, J and Zhang, H and Zhang, S},
title = {Integrated multi-omics analyses reveal impaired energy homeostasis underlying tongue-rolling behavior in dairy cattle.},
journal = {Veterinary journal (London, England : 1997)},
volume = {318},
number = {},
pages = {106768},
doi = {10.1016/j.tvjl.2026.106768},
pmid = {42398853},
issn = {1532-2971},
mesh = {Animals ; Cattle/physiology ; *Energy Metabolism ; *Homeostasis ; Multiomics ; *Tongue/physiology ; Female ; *Behavior, Animal ; Blood Glucose ; },
abstract = {Tongue rolling in cattle is a stereotypic behavior with poorly understood biological basis. Here, we show that it is not associated with alterations in blood mineral status, but is characterized by significantly reduced serum glucose, indicating impaired energy homeostasis. Multi-omics analyses revealed coordinated molecular changes, with transcriptomic enrichment in Rap1 and Ras signaling pathways and proteomic enrichment in lipid metabolism and energy-related processes. Key regulators of glucose homeostasis (RAP1A/B) and fatty acid oxidation (e.g., MCAD) were upregulated, suggesting adaptive metabolic reprogramming. Despite activation of compensatory pathways, reduced glucose availability persisted. These findings indicate that tongue rolling represents a metabolic phenotype driven by chronic energy imbalance and dysregulated energy-sensing pathways, rather than a consequence of isolated nutritional deficiency.},
}
@article {pmid42442320,
year = {2026},
author = {Sabater, C and Calvete-Torre, I and Vázquez, X and Cobo-Díaz, JF and Álvarez-Ordoñez, A and Ruas-Madiedo, P and Ruiz, L and Margolles, A},
title = {Metagenomics to assess authenticity and traceability of Asturian Gamonéu PDO cheese: A multi-omic study.},
journal = {International journal of food microbiology},
volume = {460},
number = {},
pages = {111939},
doi = {10.1016/j.ijfoodmicro.2026.111939},
pmid = {42442320},
issn = {1879-3460},
mesh = {*Cheese/microbiology/analysis ; Spain ; *Metagenomics/methods ; Volatile Organic Compounds/analysis ; Food Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Multiomics ; Machine Learning ; Microbiota ; },
abstract = {Cheese is one of the most widely consumed fermented foods in Europe. The Principality of Asturias (northern Spain) has a broad tradition in cheese making including four cheeses under Protected Designation of Origin (PDO) status (Cabrales, Gamonéu, Casín and Afuega'l Pitu). The added value of PDO food products increases the risk of fraudulently copied cheeses reaching the market. The aim of this work was to develop a novel microbiome-based method contributing to the assessment of the authenticity of Gamonéu PDO cheese. For this purpose, cheese metagenomes and volatile organic compounds (VOCs) profiles were integrated using machine learning (ML) algorithms. Computational models accurately discriminated between samples from 9 Gamonéu PDO cheese producers, as well as between cheeses ripened in different natural caves. Furthermore, they allowed distinguishing PDO and non-PDO Gamonéu-like cheeses produced in the same area. Potential microbial markers of the geographical origin of Gamonéu PDO cheese included Debaryomyces hansenii, Lacticaseibacillus paracasei and Penicillium roqueforti (more abundant in non-PDO cheeses), and Brachybacterium faecium (more abundant in PDO cheeses). Computational models presented in this work may contribute to improving existing traceability methods in the field of fermented foods and may be applied to a wide range of cheese varieties.},
}
@article {pmid42442452,
year = {2026},
author = {Pastore, EP and De Rango, F},
title = {The noncomputability of immune reaction complexity: Algorithmic information gaps under effective constraints.},
journal = {Bio Systems},
volume = {267},
number = {},
pages = {105878},
doi = {10.1016/j.biosystems.2026.105878},
pmid = {42442452},
issn = {1872-8324},
mesh = {*Algorithms ; Humans ; *Models, Immunological ; *Adaptive Immunity/immunology ; Immunoinformatics ; Animals ; },
abstract = {Adaptive immune responses must turn variable antigenic contexts into valid molecular actions under constraints of recognition, specificity, tolerance, and execution. We study the informational difficulty of this task by representing an instance x together with candidate responses r, accepted when a validity predicate V(x,r) holds. A fixed input-blind executor receives only a self-delimiting advice string and outputs a candidate response. The minimum feasible realizer complexity M(x)=minr:V(x,r)=1K(r) measures the shortest description of any response valid for x. We define the Normalized Advice Quantile (NAQ) as the percentile rank of M(x) within a reference pool, giving a scale-free measure of relative response difficulty. The Exact Realizer Identity shows that the minimum advice needed by an input-blind executor equals M(x) up to an additive constant. Feature maps split this burden into a description term and a selection term, separating the cost of specifying a response class from the cost of finding a concrete realization. We derive computability separations, resource-bounded variants, and an operational converse linking high-NAQ mass to advice and memory requirements. Finally, empirical NAQ may be approximated through calibrated code-length or compressor-based proxies, with sampling error controlled by the Dvoretzky-Kiefer-Wolfowitz inequality.},
}
@article {pmid42484287,
year = {2026},
author = {Sun, Y and Su, W and Zhu, S and Yan, S and Shi, X and Shang, J and Liu, JX},
title = {MRGBMDAT: a multi-relational graph encoder network with bilinear fusion for miRNA-disease association type prediction.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {8},
pages = {},
doi = {10.1093/bioinformatics/btag534},
pmid = {42484287},
issn = {1367-4811},
support = {62472250//National Natural Science Foundation of China/ ; 62473179//National Natural Science Foundation of China/ ; 2025CXGC010113//Key R&amp;D Program of Shandong Province, China/ ; },
mesh = {*MicroRNAs/genetics ; *Computational Biology/methods ; Graph Neural Networks ; Humans ; Algorithms ; *Software ; },
abstract = {MOTIVATION: MicroRNAs (miRNAs) are key post-transcriptional regulators involved in diverse biological processes, and their dysregulation is closely associated with the onset and progression of many diseases. Accurate prediction of miRNA-disease association types is therefore essential for understanding disease mechanisms and advancing precision medicine. Although computational methods provide efficient alternatives to wet-lab experiments, existing approaches often focus on binary association prediction, inadequately integrate local semantic dependencies and global topological structures, and suffer from class imbalance.<br><br>RESULTS: To address these limitations, we propose MRGBMDAT, a multi-relational graph encoder network with bilinear fusion for miRNA-disease association type prediction. Specifically, a multi-relational graph convolution module with bidirectional cross-attention captures global topological structures, while a local subgraph sampling module extracts local semantic dependencies. A bilinear fusion decoder with element-wise attention jointly models their linear and nonlinear interactions. In addition, an iterative feature similarity-based negative sample selection strategy is introduced to alleviate class imbalance. Experimental results on the HMDD v3.2 dataset demonstrate that MRGBMDAT significantly outperforms five state-of-the-art methods across multiple evaluation metrics, exhibiting strong discriminative power and generalization capability.<br><br>The source code is publicly available at https://github.com/CDMBlab/MRGBMDAT.},
}
@article {pmid42508330,
year = {2026},
author = {Lei, Z and Zhang, Y and Huang, J and Zhou, R},
title = {Defined synthetic microbial communities improve process controllability and inter-site reproducibility in high-temperature Daqu production.},
journal = {International journal of food microbiology},
volume = {460},
number = {},
pages = {111982},
doi = {10.1016/j.ijfoodmicro.2026.111982},
pmid = {42508330},
issn = {1879-3460},
mesh = {Fermentation ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Hot Temperature ; *Microbiota ; Reproducibility of Results ; *Food Microbiology ; Multiomics ; },
abstract = {High-temperature Daqu (HTD), the core starter for sauce-flavor Baijiu, is highly susceptible to quality fluctuations because it is produced through open solid-state fermentation and depends on heterogeneous Muqu. Here, we evaluated whether defined synthetic microbial communities (SynMCs) could improve process controllability and inter-site reproducibility during HTD production. SynMC biofortification reduced physicochemical variability and reshaped microbial community succession in a stage- and composition-dependent manner. Among the tested designs, inter-kingdom community, particularlySynMC4 and SynMC6, showed comparatively stable physicochemical performance and higher pyrazine accumulation. Integrated multi-omics analysis associated pyrazine enrichment with coordinated shifts in specific low-abundance taxa, suggesting that rare members may participate in VOC differentiation under SynMC regulation. Ecological analyses further indicated that SynMCs altered the balance between stochastic and deterministic assembly and reorganized co-occurrence networks by modifying connectivity and modularity, although these effects varied across fermentation stages and subcommunities. Cross-site validation showed that SynMC6 exerted partially consistent regulatory effects on bacterial communities across geographically independent production systems, while the magnitude and specific metabolic outcomes remained site-dependent. These findings provided an application-oriented basis for improving HTD standardization and highlight the need to incorporate both abundant and rare taxa into further SynMC design.},
}
@article {pmid42517546,
year = {2026},
author = {Windram, F and Kelly, S and Modrak, S and Dietrich, I and Minetti, C and Mansfield, KL and Seelig, F and Fisher, AM and Vollans, M and Billows, N and Ahmed, F and Shocket, M and Campino, S and Tytheridge, S and Gandy, SL and Gonzalez, E and Medlock, JM and Baylis, M and Hughes, GL and Ewing, DA and Purse, BV and Kirby, G and Strode, C and Folly, AJ and Starns, D and Ferguson, H and Smith-Mullally, S and Roberts, H and Jones, CM and Vineer, HR and England, M and Sanders, C and Pawar, S and Pearse, WD and White, SM and Jones, RT and Cator, LJ},
title = {Come together: Data sharing to support one health responses to vector-borne disease threats.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.70096},
pmid = {42517546},
issn = {1365-2915},
support = {BB/Y008766/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //Defra/ ; },
abstract = {Vector-borne diseases (VBDs) are an increasing threat to animal and human health worldwide. Due to the complexity of VBD transmission and ecology, informing responses to VBDs can be challenging. A One Health approach provides a powerful framework for addressing these threats, but its effectiveness depends on timely access to and integration of diverse and often fragmented data categories. Here we outline three key community actions: applying global metadata and data standards, depositing data into global repositories and responsible shared data usage, which can enhance VBD data sharing. We highlight how these data-sharing practices allow for the development of new informatic infrastructure, established by the One Health VBD Hub project, to facilitate analyses and ultimately enhance our ability to provide timely responses to endemic and emerging VBD threats.},
}
@article {pmid42518859,
year = {2026},
author = {Yan, L and Yang, H and Feng, H and Qi, F and Kong, F and Yu, Q and Zhu, W and Zhang, J and Liu, C and Zhang, Z},
title = {Paired comparison of tumor core and airway lumen (BALF) microbiomes in lung adenocarcinoma: deciphering specific Bacillus enrichment and immunomodulation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1768287},
pmid = {42518859},
issn = {2235-2988},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Adenocarcinoma of Lung/microbiology/immunology/pathology ; *Lung Neoplasms/microbiology/immunology/pathology ; RNA, Ribosomal, 16S/genetics ; *Immunomodulation ; Tumor Microenvironment/immunology ; Male ; *Bacillus/isolation &amp; purification/genetics/classification/immunology ; Female ; Middle Aged ; Aged ; Lung/microbiology ; Computational Biology ; },
abstract = {BACKGROUND: Lung adenocarcinoma (LUAD) is the leading cause of cancer mortality. While the lung microbiome influences tumorigenesis, the spatial heterogeneity between the airway reservoir (bronchoalveolar lavage fluid, BALF) and the actual intratumoral niche remains underexplored. Understanding this distinction is critical for identifying true tumor-resident drivers.<br><br>METHODS: Paired tumor tissue and BALF samples were collected from 77 LUAD patients. 16S rRNA gene sequencing targeting V3-V4 regions was performed to characterize microbial diversity. Host transcriptomics were integrated to explore host-microbe interactions. Bioinformatics analyses utilized UPARSE for OTU clustering, PICRUSt2 for functional prediction, and CIBERSORTx for immune cell deconvolution. Differential abundance was assessed using LEfSe and Random Forest algorithms to identify discriminatory biomarkers.<br><br>RESULTS: Comparative analysis revealed distinct ecological architectures, with tumor tissues exhibiting significantly reduced alpha-diversity compared to BALF. The genus Bacillus was identified as a key tumor-enriched biomarker (LDA > 2.0), distinct from airway colonizers. Clinically, elevated Bacillus abundance significantly correlated with tumor invasiveness. Immunologically, Bacillus load was inextricably linked to an immunosuppressive microenvironment, characterized by the upregulation of inhibitory checkpoints (VSIR, TIGIT, PD-L1) and a reduction in M1 macrophage infiltration. Functional analysis suggested Bacillus involvement in metabolic pathways facilitating tumor adaptation.<br><br>CONCLUSION: This study delineates the spatial disparity between intratumoral and airway microbiomes, identifying Bacillus as a potential driver of malignant progression and immune evasion. Targeting intratumoral microbiota offers novel diagnostic and therapeutic avenues for lung cancer.},
}
@article {pmid42519882,
year = {2026},
author = {Bán, M},
title = {RUM/FILH: a standardized operational capability model for biodiversity databases.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {42519882},
issn = {1758-0463},
mesh = {*Biodiversity ; *Databases, Factual/standards ; },
abstract = {The increasing reliance of biodiversity research on large-scale databases has brought significant progress in data accessibility but also new challenges in data comparability, reliability, and interpretability. While global platforms, such as GBIF and iNaturalist standardize and disseminate vast quantities of biodiversity information, they cannot fully meet the needs of users relying on local or thematic data sources. In this paper, we propose a unified service capability model, the RUM/FILH model, that provides a transparent, comparable framework for describing database functionalities and data management quality. The RUM model distinguishes three essential data-related services: Read, Upload, and Modify, while the FILH extension integrates FAIR principles and data history accessibility. This combined system enables both users and database administrators to assess interoperability, metadata quality, and licensing conditions quickly and consistently. We demonstrate the applicability of the RUM/FILH model across biodiversity databases of different scales, including international aggregators and community-based platforms. The proposed capability model enhances trust, transparency, and collaboration across distributed data infrastructures, supporting the development of a more coherent and sustainable global biodiversity informatics network.},
}
@article {pmid42520707,
year = {2026},
author = {Fang, J and Su, M and Li, Y and Gui, Y and Ai, Y and Joseph, O and Cao, T and He, S and Yang, M},
title = {Controlling filamentous cyanobacterial blooms requires adaptive, weather-informed strategy.},
journal = {Water research},
volume = {306},
number = {},
pages = {126505},
doi = {10.1016/j.watres.2026.126505},
pmid = {42520707},
issn = {1879-2448},
abstract = {The global expansion of filamentous cyanobacteria threatens water security due to their production of toxins and taste-and-odor compounds. As subsurface dwellers, filamentous cyanobacteria are resistant to conventional nutrient and flocculation controls, exposing a management gap. We developed an adaptive, forecast-guided framework that integrates predictive modeling with precision sediment resuspension (SR), in which SR-associated light attenuation likely contributes substantially to bloom suppression. A 2023-2024 survey of 40 reservoirs in eastern China showed filamentous dominance of over 80% biomass in half the systems. An XGBoost model (R[2] = 0.57) identified September-October as the highest-risk period, with over 80% of reservoirs affected. SR efficacy is light-dependent: it suppresses growth under low irradiance but can promote it under high light if shading shifts irradiance into the optimal range for filamentous taxa. We optimized SR through modulated sediment flux (0.1-5.2 g l[-1]) to dynamically attenuate light in response to real-time forecasts. Field validation confirmed forecast-guided SR effectively limited Pseudanabaena via light control. This ecology-based management provides a scalable framework for sustainable water security under changing climates.},
}
@article {pmid42523298,
year = {2026},
author = {Valtadoros, LE and Hicks, P and Yuan, H and Ahmadian, M and Johnson, KA and Krishnan, A},
title = {Large-scale automated detection reveals pervasive sex imbalance in biomedical research.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42523298},
issn = {2692-8205},
abstract = {Sex is a critical biological variable that impacts disease risk, progression, and treatment response across virtually every organ system. However, decades of biomedical research have relied primarily on male study subjects, leaving large gaps in our understanding of female-specific disease biology. Quantifying the extent of this imbalance across thousands of disease areas and millions of publicly available biological samples has remained computationally intractable. Here, we present a multimodal computational framework that infers the biological sex of ~230,000 publicly available human transcriptome samples and links inferred sex labels to disease terms extracted from ~9,000 associated study records and ~5,000 publication abstracts to quantify sex imbalance at scale. Applying this approach revealed that the majority of disease terms with the largest research-derived sex imbalance are skewed toward male representation, including areas with no known biological justification for that imbalance. After adjusting for global sex-specific disease prevalence to isolate biologically unjustified imbalance, up to 58% of all disease terms showed male-leaning association. Diseases including glioblastoma, cirrhosis, idiopathic pulmonary fibrosis, and schizophrenia emerged as critically understudied in females despite affecting both sexes comparably. These findings provide a principled, data-driven basis for prioritizing compensatory research efforts and offer a reusable framework for ongoing monitoring of sex representation in the biomedical literature.},
}
@article {pmid42525015,
year = {2026},
author = {Costa, EP and Nascimento, LFC},
title = {Childhood vaccination coverage and socioeconomic inequalities in the Northern region of Brazil.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {29},
number = {},
pages = {e260027},
pmid = {42525015},
issn = {1980-5497},
mesh = {Humans ; Brazil ; Cross-Sectional Studies ; *Vaccination Coverage/statistics &amp; numerical data ; Socioeconomic Disparities in Health ; Socioeconomic Factors ; Female ; Spatio-Temporal Analysis ; Infant ; },
abstract = {OBJECTIVE: To evaluate the spatio-temporal variation of childhood immunobiological vaccine coverage in the municipalities of the Northern region of Brazil, comparing cross-sectional data from 2018 and 2022, and its association with socioeconomic and maternal variables.<br><br>METHODS: This is a comparative ecological study with coverage data for seven immunobiologicals in the municipalities of the Northern region for the years 2018 and 2022. Data were obtained from the Department of Informatics of the Unified Health System. Spatial analysis (global, bivariate, and local Moran's Index) was used to verify the association between vaccine coverage and independent variables (GDP per capita, Brazilian Deprivation Index, maternal schooling, proportion of indigenous people, full-term births, and birth weight).<br><br>RESULTS: There was a widespread decline in vaccine coverage when comparing the two periods, except for the meningococcal C vaccine. Vaccination was positively associated with GDP per capita and maternal schooling, and negatively associated with the Deprivation Index, with these associations intensifying over the period. The spatial correlation between immunization and the proportion of the indigenous population, previously not significant, became strongly negative in 2022. Clusters of low immunization and socioeconomic vulnerability were identified mostly in the states of Par&#xe1; and Amazonas, and clusters of high immunization and better indicators in Tocantins and Rond&#xf4;nia.<br><br>CONCLUSION: The decline in childhood vaccination in the Northern region is a spatially structured phenomenon that reflects and deepens socioeconomic inequalities. The formation of vulnerability clusters, especially in areas near the Brazilian border, represents a risk for the re-emergence of vaccine-preventable diseases and demands territorially focused public health policies.},
}
@article {pmid42512875,
year = {2026},
author = {Dettori, M and Deiana, G and Palmieri, A and Arghittu, A and Castiglia, P and Piana, A and Campus, G},
title = {Rethinking Dengue Preparedness in the Era of Climate Change, Urbanisation, and Digital Health: A Structured Narrative Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {7},
pages = {},
pmid = {42512875},
issn = {1648-9144},
mesh = {Humans ; *Climate Change ; *Dengue/prevention &amp; control/epidemiology/transmission ; *Urbanization/trends ; Digital Health ; Public Health/methods ; Animals ; },
abstract = {Background and Objectives: Dengue is emerging as a multifaceted public health challenge that extends beyond traditional vector-borne disease frameworks. Climate change, rapid urbanisation, environmental transformation, global mobility, and digital ecosystems are progressively reshaping transmission dynamics, outbreak patterns, and preparedness needs worldwide. This narrative review aimed to examine dengue from an integrated public health perspective, focusing on climate-sensitive transmission, urban health, surveillance and preparedness, digital epidemiology, artificial intelligence (AI), and health communication. Materials and Methods: A structured narrative review was conducted through targeted literature searches in PubMed, Scopus, and Web of Science between April and May 2026. To this end, a series of separate thematic search strategies were developed to explore the principal conceptual domains addressed in the review. The synthesis was organised around five interconnected preparedness domains: climate change and environmental transformation; urbanisation and urban health; surveillance, vaccination, and integrated preparedness; digital health, artificial intelligence, and mathematical modelling; and health communication and community engagement. The retrieved literature was analysed using a thematic narrative synthesis approach. Results: The retrieved evidence indicated the progressive expansion and redefinition of dengue risk across both endemic and historically non-endemic regions. Climate variability, environmental transformation, rapid urbanisation, and increasing human mobility have emerged as interconnected drivers capable of influencing vector ecology, transmission dynamics, outbreak frequency, and healthcare system vulnerability. Urbanisation has been frequently associated with infrastructural inequalities, environmental degradation, inadequate water and waste management, and territorial conditions favourable to vector proliferation. The extant literature has also placed significant emphasis on the growing importance of integrated surveillance systems and early warning approaches combining epidemiological, environmental, climatic, entomological, and mobility-related data. Digital epidemiology, AI-based predictive models, and digital surveillance tools may contribute to strengthening outbreak forecasting and preparedness capacity, although important limitations related to data quality, interoperability, interpretability, and implementation remain. In parallel, misinformation, risk communication challenges, and digital communication ecosystems emerged as relevant factors influencing public perception, preventive behaviours, institutional trust, and adherence to public health interventions. Conclusions: Dengue is a systems-level public health challenge shaped by climate change, urbanisation, environmental disruption, human mobility, health-system preparedness, and digital ecosystems. Conventional vector-control strategies alone are unlikely to adequately address this growing complexity. Strengthening dengue preparedness should therefore be considered a broader indicator of public health resilience and long-term health-system adaptation.},
}
@article {pmid42513798,
year = {2026},
author = {Liu, S and Hao, W and Gao, G and Liu, Y and Guo, H and Zhou, Y and Lv, J and Liu, Y},
title = {Study on Kiln-Transformation Mechanism of 3D-Printed Body of Hejin Gray Pottery.},
journal = {Materials (Basel, Switzerland)},
volume = {19},
number = {14},
pages = {},
pmid = {42513798},
issn = {1996-1944},
abstract = {The firing of traditional gray pottery relies on complex physicochemical reactions governing its color, dimensional accuracy, and structural stability. Unclear kiln-transformation mechanisms restrict standardized and digital production of this Chinese intangible cultural heritage. Herein, direct ink writing (DIW) was used to fabricate Hejin gray pottery green bodies from local ternary raw materials. Thermodynamic calculations, TG-DTG/DSC, XRD, XRF, and atmosphere-controlled firing tests were combined to reveal coupled phase evolution and reduction color-forming mechanisms during sintering. Two interrelated kiln-transformation processes were identified. First, sequential mineral reconstruction occurs at four critical temperatures: free water loss at 119.8 °C, two-stage dehydroxylation of hydrous silicates at 270.5 °C and 767.9 °C, and CaCO3 decomposition at 547.9 °C. Uneven shrinkage and gas release at these temperatures induce cracking, blistering, and deformation of printed bodies. Micron-sized CaCO3 (equivalent radius ≈ 1.31 μm) exhibits high surface energy and significantly reduces its decomposition temperature, consistent with experimental observations. Second, reducing atmospheres trigger competitive phase formation. Distinct from the conventional Fe2O3 → Fe3O4 → FeO reduction pathway, Fe oxides preferentially react with abundant Al2O3 to form thermodynamically stable FeAl2O4 spinel, yielding uniform celadon-gray tones. The final color is nearly independent of 20-90 vol% CO, and air-isolated cooling below 600 °C is mandatory to prevent secondary oxidation and reddening. This work establishes a thermodynamic framework for DIW-printed Hejin gray pottery kiln transformation, clarifies microscale defect and color-evolution mechanisms, and offers theoretical guidance for atmosphere-controlled firing and digital mass production of heritage ceramics.},
}
@article {pmid42214893,
year = {2026},
author = {Li, X and Fu, X and Gao, X and Zuo, Q and Qin, S and Wu, J},
title = {Time spent in outdoor light is associated with the dynamic progression of mental disorder: A prospective study in the UK biobank.},
journal = {Public health},
volume = {257},
number = {},
pages = {106347},
doi = {10.1016/j.puhe.2026.106347},
pmid = {42214893},
issn = {1476-5616},
mesh = {Humans ; Prospective Studies ; United Kingdom/epidemiology ; *Sunlight/adverse effects ; *Mental Disorders/epidemiology ; Female ; Male ; Disease Progression ; Middle Aged ; UK Biobank ; Aged ; Time Factors ; Seasons ; },
abstract = {OBJECTIVES: Ecological studies have highlighted the role of sunlight in mental disorders (MD) development, yet evidence regarding individual-level sunlight exposure and its impact on the dynamic progression of MD remains limited.<br><br>STUDY DESIGN: Prospective cohort study.<br><br>METHODS: Data were obtained from the UK Biobank database. Self-report sunlight exposure was available from questionnaires. The restricted cubic spline (RCS) and Cox model were used to explore associations between sunlight exposure and first MD (FMD), MD multimorbidity (MDM), and all-cause death. The multistate model was performed to explore the effects of sunlight exposure on MD trajectories. Finally, seasonal and sex-specific associations between them were assessed.<br><br>RESULTS: 273,261 participants were included in this study, among whom 33,964 subjects developed FMD, 8306 subjects developed MDM, and 17,233 subjects developed deaths. The non-linear relationships between sunlight exposure on average and FMD, MDM, and death were noticed and the lowest risk was found at 1.5h/day. The multistate model found that >1.5h/day sunlight exposure was significantly associated with the increased risk of transitions from baseline to death and FMD, especially depression, dementia, and substance disorder compared to 1.5h/day. Excessive sunlight exposure was also significantly related to a higher risk of transitions from FMD to MDM, particularly from anxiety or dementia to MDM. Additionally, seasonal and sex-related effects of sunlight exposure on MD transitions were observed.<br><br>CONCLUSIONS: Appropriate sunlight exposure might play a critical part in MD progression. Our findings could provide evidence-based strategies for the adoption of sunlight exposure in the prevention and management of MDs.},
}
@article {pmid42485963,
year = {2026},
author = {Fu, Y and Chen, M and Zhang, X and Yu, G and Jiang, P and Liu, J and You, S},
title = {Multi-omics analysis of the rhizosphere effects and molecular mechanisms of Ageratum conyzoides linn. at different stages of Cd, Pb, and Zn co-stress.},
journal = {Journal of environmental management},
volume = {414},
number = {},
pages = {130461},
doi = {10.1016/j.jenvman.2026.130461},
pmid = {42485963},
issn = {1095-8630},
mesh = {*Rhizosphere ; Soil Pollutants ; Cadmium ; Biodegradation, Environmental ; Multiomics ; Zinc ; *Metals, Heavy ; Plant Roots ; },
abstract = {Ageratum conyzoides Linn. is a promising candidate for multi-metal remediation. This study examined the rhizosphere microecology and molecular regulation of A. conyzoides under Cd, Pb, and Zn co-stress after 21 and 50 days of exposure. The ethanol-extracted fraction was found to be the predominant form of Cd, Pb, and Zn in the roots, whereas the NaCl-, HCl-, and HAc-extracted fractions prevailed in the shoots. Heavy metals were mainly distributed in the cell wall and soluble fractions. Metabolome and microbiome analyses revealed dynamic changes in rhizosphere exudate metabolic profiles and bacterial community composition in the rhizosphere soil after 21 and 50 days of exposure to stress. After 21 days of stress, increased exudation of oxalic acid, L-valine, and L-glutamate was correlated with the enrichment of Clostridium_sensu_stricto_12 and norank_p_FCPU426. After 50 days of stress, significantly increased exudation of jasmonic acid, gibberellin A24, and 4-hydroxynonenal was correlated with the enrichment of Bauldia, Candidatus_Udaeobacter, and norank_f_Anaerolineaceae. Transcriptome analysis revealed that prolonged stress upregulated the expression of SEC61A2, Uggt, Ggt7, gss, and PRX1 in A. conyzoides leaves; the differentially expressed genes were found to be significantly enriched in the protein processing in the endoplasmic reticulum pathway and glutathione metabolic pathway. Overall, these findings provide a theoretical foundation for optimizing phytoremediation using A. conyzoides.},
}
@article {pmid42511722,
year = {2026},
author = {Zhang, Y and Huang, C and Liu, YE and Wang, Z and Wang, T and Zhang, Y and Lu, Q and Zeng, Y and Wang, S and Mai, B},
title = {Competitive Inhibition and Pathway Truncation During Biotransformation of Traditional and Novel Brominated Flame Retardants Using a Dehalogenimonas-Rich Consortium: Chemical and Microbiological Insights.},
journal = {International journal of molecular sciences},
volume = {27},
number = {14},
pages = {},
pmid = {42511722},
issn = {1422-0067},
support = {42577246, 42277242, 42207250//National Natural Science Foundation of China/ ; BK20221141//Natural Science Foundation of Jiangsu Province/ ; 2022ZZCX01K1//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Flame Retardants/metabolism ; Biotransformation ; *Halogenated Diphenyl Ethers/metabolism/chemistry ; Kinetics ; Biodegradation, Environmental ; },
abstract = {The ubiquitous co-contamination of traditional and novel brominated flame retardants (TBFRs and NBFRs) in anaerobic environments necessitates a comprehensive understanding of their combined environmental fate. This study investigated the anaerobic biotransformation of BDE 99 (a legacy aromatic TBFR) and β-TBCO (a cycloaliphatic NBFR) using a Dehalogenimonas-containing mixed culture (QY2-S1) under single- and co-exposure conditions. In a single-exposure system, QY2-S1 achieved efficient transformation of both substrates, with the observed first-order kinetic constants (kobs) of 1.31 ± 0.09 d[-1] and 2.35 ± 0.13 d[-1] for BDE 99 and β-TBCO, respectively. However, the corresponding kobs values decreased by approximately 3- to 5-fold in a co-exposure system, demonstrating pronounced reciprocal kinetic inhibition. Notably, while culture QY2-S1 maintained a unique ortho-regioselectivity for BDE 99, its stepwise debromination was truncated at the tetra-BDE stage during co-exposure. Absolute quantitative 16S rRNA sequencing identified Dehalogenimonas as the sole organohalide-respiring bacterium, with its abundance initially increasing in tandem with substrate transformation. However, the dehalogenation-coupled cell growth of Dehalogenimonas was significantly modulated by substrate type and combination, with its absolute biomass following the order of: single β-TBCO > co-exposure > single BDE 99. Collectively, these results suggest that the reciprocal kinetic inhibition and the truncation of the BDE 99 debromination pathway under co-exposure are collectively driven by the suppressed growth and substrate preference of Dehalogenimonas. This study provides critical insights for predicting ecological risks and developing bioremediation strategies for co-occurring BFRs in real-world scenarios.},
}
@article {pmid42511801,
year = {2026},
author = {Cheng, A and Ee, KP},
title = {Deciphering Stress Resilience in Black Pepper (Piper nigrum L.): From Current Advances to Emerging Opportunities.},
journal = {International journal of molecular sciences},
volume = {27},
number = {14},
pages = {},
pmid = {42511801},
issn = {1422-0067},
support = {FRGS/1/2024/STG01/UM/02/1//Ministry of Higher Education/ ; },
mesh = {*Piper nigrum/genetics/microbiology/physiology ; *Stress, Physiological ; Genomics/methods ; Microbiota ; Multiomics ; Plant Breeding ; },
abstract = {Black pepper (Piper nigrum Linn.), one of the world's most economically important spice crops, is increasingly challenged by climate-related stresses, emerging pests and diseases, and declining soil health, all of which threaten its productivity and sustainability. While previous reviews have predominantly focused on black pepper genomic resources, breeding strategies, and disease management, the integration of multi-omics technologies, microbiome science, and artificial intelligence (AI) to enhance its stress resilience has received comparatively limited attention. This review synthesizes recent advances in the molecular mechanisms underlying black pepper responses to biotic and abiotic stresses, with emphasis on omics approaches (such as genomics and transcriptomics), as well as the roles of beneficial microbial communities in enhancing stress tolerance, nutrient acquisition, and disease suppression. We further discuss emerging microbiome-assisted strategies, including the development of beneficial microbial consortia and targeted manipulation of microbial functions, for enhancing black pepper resilience under changing environmental conditions. In addition, we explore how AI-driven analytical approaches can integrate complex multi-omics and microbiome datasets to unravel the complex molecular networks governing black pepper-microbe interactions under stress conditions and accelerate precision breeding. By integrating genomics, microbial ecology, and AI, this review presents a systems-level framework for understanding and improving stress resilience in black pepper. This interdisciplinary perspective highlights new opportunities to accelerate the development of climate-resilient cultivars and advance sustainable black pepper production.},
}
@article {pmid42479765,
year = {2026},
author = {Fant, L and Macocco, I and Grilli, J},
title = {Eco-evolutionary dynamics lead to functionally robust and redundant communities.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1014437},
doi = {10.1371/journal.pcbi.1014437},
pmid = {42479765},
issn = {1553-7358},
mesh = {*Biological Evolution ; *Models, Biological ; *Ecosystem ; *Microbiota/physiology ; Computational Biology ; },
abstract = {Microbial communities are taxonomically diverse and variable: species presence and abundances widely fluctuate over time, space, and even across biological replicates under controlled experimental conditions. However, environmental conditions exert strong selection on the traits of community members and their functions. Similar environmental conditions are expected to produce functionally similar communities. This environmental selection, combined with taxonomic variability, leads to the influential concept of functional redundancy - the idea that many species can perform the same function, allowing communities with different species compositions to maintain identical functional profiles. Despite the centrality of functional redundancy in microbial ecology, we lack a theoretical understanding of its origin. Here we study the eco-evolutionary dynamics of communities interacting through competition and cross-feeding. We show that eco-evolutionary trajectories rapidly converge to a "functional attractor" - a functional composition uniquely determined by environmental conditions. Taxonomic composition follows non-reproducible dynamics while being constrained by the conservation of functional composition. Our framework provides a theoretical foundation for understanding functional robustness and redundancy in microbial communities.},
}
@article {pmid42508699,
year = {2026},
author = {Chopra, C and Kukkar, D and Kaur, H and Samudrala, R},
title = {QIIME2-based pooled re-analysis of 16s rRNA sequences reveals gut microbiota dysbiosis in diabetic nephropathy mouse models.},
journal = {Microbial pathogenesis},
volume = {219},
number = {},
pages = {108732},
doi = {10.1016/j.micpath.2026.108732},
pmid = {42508699},
issn = {1096-1208},
abstract = {Diabetic nephropathy (DN) is a progressive microvascular and renal disease that develops due to chronic suffering from diabetes. Growing research evidences have suggested the role of gut microbiota dysbiosis in advancement of DN. In this regard, our study executes pooled re-analysis of publicly available 16S rRNA sequencing datasets from murine models (38 DN, 37 healthy controls (HCs), and 33 diabetic mellitus (DM) samples) using the quantitative insights into microbial ecology 2 (QIIME2) platform to explore gut microbial alterations associated with disease progression. Following quality filtration, trimmomatic, and DADA2 assisted denoising, taxonomic classification was performed using the SILVA database, and alpha diversity was assessed through shannon, faith's PD, pielou's evenness, and observed feature indices. Firmicutes and Bacteroidota were found to be the dominant group, with minor contributions from Proteobacteria and Actinobacteriota. Controls showed the higher abundance of Faecalibacterium, Roseburia, and Blautia, whereas Escherichia-Shigella and Alistipes were elevated in DN groups. Alpha diversity analysis revealed insignificant differences in richness or evenness between DN and control samples, suggesting that disease-associated microbial variations are primarily driven by specific taxonomic shifts rather than overall diversity. These findings highlight the potential involvement of gut dysbiosis in DN pathophysiology and support the therapeutic relevance of targeting the gut-kidney axis.},
}
@article {pmid42511655,
year = {2026},
author = {Malik, WA and Afzal, M and Yousuf, S and Ma, L and Tian, X and Wang, L and Zhang, Y and Wang, H},
title = {Cracking the Hard Seed: Molecular Mechanisms and Multi-Omics Insights into Seed Dormancy and Germination in the Genus Astragalus.},
journal = {International journal of molecular sciences},
volume = {27},
number = {14},
pages = {},
pmid = {42511655},
issn = {1422-0067},
support = {2024B02015-2//Key Research and Development Program of Xinjiang Uygur Autonomous Region/ ; 2024SNGGGCC040//High-level Talents in Modern Agriculture and Animal Husbandry Development/ ; },
mesh = {*Plant Dormancy/genetics ; *Germination/genetics ; *Seeds/genetics/metabolism/physiology ; *Astragalus Plant/genetics/metabolism/physiology ; Multiomics ; Gene Expression Regulation, Plant ; Plant Growth Regulators/metabolism ; Gibberellins/metabolism ; },
abstract = {The genus Astragalus comprises one of the largest and most ecologically diverse groups of flowering plants and includes species of major medicinal, forage, and restoration value, particularly Astragalus membranaceus and allied taxa. However, effective germplasm utilization and large-scale cultivation remain constrained by strong seed dormancy, most commonly expressed as physical dormancy imposed by a water-impermeable seed coat. In some species, this coat-imposed barrier is further complicated by an additional physiological component, resulting in combinational dormancy. This review synthesizes current knowledge on the structural, molecular, and multi-omics basis of seed dormancy and germination in Astragalus, with emphasis on the dormancy-to-germination transition. We first examine the anatomical basis of hardseededness, including the palisade layer, light line, and associated seed-coat barrier domains, and discuss the likely contributions of phenylpropanoid, lignin, suberin, and cutin biosynthesis to the establishment of physical dormancy. We then summarize current understanding of hormone crosstalk, highlighting the central roles of abscisic acid and gibberellins together with ethylene, brassinosteroids, reactive oxygen species, and nitric oxide in regulating post-dormancy germination. Recent transcriptomic, metabolomic, and emerging integrative omics studies reveal that Astragalus germination involves not only reserve mobilization and energy activation but also early induction of characteristic secondary-metabolite pathways, particularly flavonoids and isoflavonoids, which distinguishes medicinal Astragalus seeds from many conventional crop seeds. Finally, we discuss current bottlenecks, including the limited availability of robust functional-genomics tools, and outline future directions involving CRISPR-based validation, epigenetic regulation, and marker-assisted breeding for improved germination uniformity and reduced hardseededness. This review provides a mechanistic framework for unlocking Astragalus seed dormancy and accelerating the conservation, breeding, and medicinal utilization of this important genus.},
}
@article {pmid42506960,
year = {2026},
author = {Yang, X and Zeng, M and Zhang, X and Liang, L and Lin, H},
title = {Anteroplacement of the Mucocutaneous Junction and Goblet Cell Expansion: Microanatomic Remodeling of the Human Eyelid Margin.},
journal = {Investigative ophthalmology &amp; visual science},
volume = {67},
number = {8},
pages = {54},
pmid = {42506960},
issn = {1552-5783},
mesh = {Humans ; Aged ; Adult ; Middle Aged ; Female ; *Goblet Cells/cytology/pathology ; Male ; *Eyelids/anatomy &amp; histology/pathology ; Aged, 80 and over ; *Meibomian Glands/pathology/cytology ; Aging/physiology ; Conjunctiva ; Cadaver ; *Mucous Membrane/anatomy &amp; histology ; Cell Count ; },
abstract = {PURPOSE: The mucocutaneous junction (MCJ) plays a vital role in maintaining ocular surface health and integrity. However, the corresponding histopathological changes of the MCJ in human eyelids remain unclear. This study aimed to investigate the pathological alterations of the MCJ and their relationship with meibomian gland (MG) morphology and advancing age.<br><br>METHODS: Tarsal plates (TPs) were obtained from 18 cadaveric donors aged 25 to 90 years. Infrared meibography was performed to evaluate MG morphology. Specimens were processed for histology and immunofluorescence to assess lid margin structures. Quantitative analyses of lid margin parameters, including the MCJ displacement, width of MCJ and lid wiper, goblet cell (GC) density in the lid wiper, and the presence of GCs at the MCJ and MG orifice (MGO) were conducted.<br><br>RESULTS: Histological analysis identified four progressive grades of MCJ displacement (0-3) in human eyelids, with the average grade increasing significantly with age. In eyelids with MCJ anteroplacement, palpebral conjunctival GC clusters were predominantly located near the anterior lid margin and occasionally extended into MGOs. The muscular conjunctival area ratio of the MG revealed spatially non-uniform distribution patterns in sagittal TP, and, importantly, correlated with the extent of the MCJ shift, indicating that MCJ anteroplacement involves reorganization of the MG within the TP.<br><br>CONCLUSIONS: Our findings suggest that conjunctivalization, accompanied by palpebral GC expansion at the MCJ and MGO, may be a function of age-related MCJ anteroplacement. MCJ anteroplacement and reorganization of the MG provides a plausible histopathological link among lid margin anatomy, MG morphology, and ocular surface ecology.},
}
@article {pmid42497768,
year = {2026},
author = {García, PIR and Dabalà, C and Coccon, F and Sfriso, A and Torresan, S and Comandini, P and Causio, S and Horneman, F and Federico, I and Giupponi, C},
title = {Combining participatory and GIS-based multi-criteria decision analysis for salt marsh restoration and rebuilding planning in the Venice lagoon.},
journal = {The Science of the total environment},
volume = {1048},
number = {},
pages = {182039},
doi = {10.1016/j.scitotenv.2026.182039},
pmid = {42497768},
issn = {1879-1026},
abstract = {The Venice Lagoon has experienced a long-term decline of salt marsh habitats due to sediment deficit, morphological deepening, increased hydrodynamic exposure, and human-induced alterations to lagoon processes. Identifying suitable locations for restoration is therefore a key challenge for lagoon management. This study applies a participatory GIS-based Multi-Criteria Decision Analysis (S-PMCA) to support the spatial prioritization of salt marsh restoration and rebuilding within the framework of the WaterLANDS and REST-COAST projects. The analysis combined stakeholder knowledge with spatially explicit environmental information. An initial set of criteria was reviewed through a pre-workshop survey involving 21 stakeholders and subsequently refined during a workshop attended by 43 participants. The final analysis incorporated six spatial criteria: distance from canals, wind fetch, proximity to existing salt marshes, historical salt marsh loss, seagrass protection, and water quality. Criteria were transformed into standardized suitability layers and weighted according to stakeholder preferences. Distance from canals received the highest average importance weight (21.4/100), whereas water quality received the lowest (13.8/100). Suitability maps were generated using an Ordered Weighted Averaging (OWA) approach and combined with a bathymetry-based proxy of restoration costs to perform a spatial cost-effectiveness assessment. Priority restoration areas were identified along lagoon margins and near the Malamocco-Marghera Canal, where wave attenuation potential, ecological connectivity, historical marsh presence, and favourable implementation conditions converge. By combining stakeholder preferences with morphodynamic conditions, ecological factors, and implementation costs, this study supports the identification of restoration areas that are both feasible and strategically relevant in the Venice Lagoon.},
}
@article {pmid42499149,
year = {2026},
author = {Owasitth, R and Chaisuparat, R and Lawpoolsri, S and Soparat, P and Detsomboonrat, P},
title = {Oral Potentially Malignant Disorders in Thailand: Regional Variations and Ecological Determinants.},
journal = {JDR clinical and translational research},
volume = {},
number = {},
pages = {23800844261454274},
doi = {10.1177/23800844261454274},
pmid = {42499149},
issn = {2380-0852},
abstract = {OBJECTIVES: To quantify the provincial heterogeneity incidence of oral potentially malignant disorders (OPMDs) and explore geographic disparities and ecological determinants in Thailand through Bayesian disease mapping.<br><br>METHODS: An observational ecological study analyzed clinically diagnosed OPMDs from Thailand's national electronic health record database (2023 to 2024) except Bangkok. Spatial autocorrelation with spatial Bayesian hierarchical models were used to evaluate their associations with behavioral, socioeconomic, and oral-health determinants.<br><br>RESULTS: A total of 5,956 OPMDs diagnoses were identified across 76 provinces. The median age at diagnosis was 62 y, with females comprising 68.2%. Lichen planus (45.9%) and leukoplakia (39.5%) were the predominant subtypes. The age-standardized incidence rate was 1.9 per 100,000 (female: 2.5; male: 1.3), peaking at ages 60 to 69 y. Spatial analyses revealed high-risk clusters in northern Thailand and identified smokeless tobacco use, dentist density, and Gini coefficient as significant ecological predictors of the incidence of OPMDs.<br><br>CONCLUSIONS: This population-based analysis demonstrates spatial disparities in the incidence of OPMDs. Contextual social determinants of health including socioeconomic inequality, smokeless tobacco behaviors, and workforce availability contribute to variations in disease distribution at the population level. Strengthening the integration of big data analytics within oral health surveillance systems can enhance timely, evidence-informed decision-making and support the strategic refinement and resource optimization of Thailand's national oral cancer screening benefit package.Knowledge Transfer Statement:The results provide strategic insights for clinicians, public health professionals, and policymakers identifying high-risk geographic areas where preventive interventions and early detection efforts should be prioritized. By clarifying province-specific risk profiles, the study supports the development of targeted health promotion, prevention, and screening strategies aimed at reducing geographic inequalities and improving oral health outcomes.},
}
@article {pmid42506694,
year = {2026},
author = {Wei, X and Ren, P and Feng, J and Shi, J and Zhang, P and Li, H},
title = {Integrated Multi-Omics Analysis Reveals Complex Cytotoxicity-Associated Molecular Response Patterns of Representative Toxins from Four Classes of Lipophilic Algal Toxins in Neuro-2a Cells.},
journal = {Toxins},
volume = {18},
number = {7},
pages = {},
pmid = {42506694},
issn = {2072-6651},
support = {2024YFF0506903//China National Center for Biotechnology Development/ ; },
mesh = {*Marine Toxins/toxicity ; Animals ; Multiomics ; Polyether Toxins ; Oxocins/toxicity ; Proteomics ; Cell Survival/drug effects ; Macrolides/toxicity ; Mice ; *Pyrans/toxicity ; Okadaic Acid/analogs &amp; derivatives/toxicity ; Metabolomics ; Cell Line, Tumor ; Furans/toxicity ; Spiro Compounds/toxicity ; Transcriptome/drug effects ; Mollusk Venoms ; },
abstract = {Lipophilic marine toxins (LMTs) are important toxic risk factors in marine ecosystems and seafood safety, yet the comparative cytotoxicity-associated molecular responses of different LMT classes remain unclear. Here, Neuro-2a cells were exposed to four representative LMTs-dinophysistoxin-1 (DTX1), azaspiracid-3 (AZA3), yessotoxin (YTX), and pectenotoxin-2 (PTX2)-and acute cytotoxicity was evaluated together with integrated transcriptomic, proteomic, and metabolomic analyses. Cell viability assays showed a cytotoxic potency order of DTX1 > AZA3 > YTX > PTX2. Integrated multi-omics analysis revealed that DTX1, the most cytotoxic toxin, caused the broadest molecular perturbations, mainly involving mitochondrial energy metabolism, p53-mediated stress responses, and multilayered metabolic networks. AZA3 and YTX induced intermediate cytotoxicity and showed partially similar perturbation patterns, particularly affecting cytoskeleton-related, immune-related, and metabolism-related processes. In contrast, PTX2, the least cytotoxic toxin, produced more limited responses mainly involving tyrosine metabolism and the cGMP-PKG signaling network. Overall, molecular perturbation patterns generally corresponded to acute cytotoxic potencies, while each toxin exhibited distinct key pathways and functional modules. These findings provide a multi-omics basis for cytotoxic responses of representative LMT classes and guide subsequent functional validation.},
}
@article {pmid42419187,
year = {2026},
author = {Abbod, M},
title = {Computational framework integrating subtractive proteomics and structural bioinformatics to nominate candidate fungicide targets in Puccinia graminis f. sp. tritici.},
journal = {Computational biology and chemistry},
volume = {124},
number = {Pt 2},
pages = {109233},
doi = {10.1016/j.compbiolchem.2026.109233},
pmid = {42419187},
issn = {1476-928X},
mesh = {*Proteomics ; *Fungicides, Industrial/chemistry/pharmacology ; *Puccinia/drug effects/chemistry/metabolism ; *Computational Biology ; Molecular Docking Simulation ; *Fungal Proteins/metabolism/chemistry/antagonists &amp; inhibitors ; Triticum/microbiology ; },
abstract = {Puccinia graminis f. sp. tritici, the causal agent of wheat stem rust, continues to threaten global wheat production through recurring outbreaks and the erosion of host resistance and chemical control efficacy. This study aimed to identify candidate protein targets for fungicide development in P. graminis f. sp. tritici. An integrated subtractive proteomics pipeline was then applied, combining essentiality screening, pathway analysis, structural modeling, and exploratory molecular docking. A stringent filtering strategy excluding proteins homologous to Triticum aestivum, Homo sapiens, and beneficial microbes (Bacillus subtilis, Pseudomonas fluorescens, and Trichoderma harzianum) was applied, thereby maximizing selectivity while minimizing potential off-target ecological effects. From 36,348 proteins, four putative targets were identified: two β-glucan synthesis-associated KRE6 homologs, a cell wall α-1,3-glucan synthase (AGS1), and a Major Facilitator Superfamily (MFS) transporter. Guided by intrinsic disorder analysis, AlphaFold2 was used to generate high-quality 3D structural models of the prioritized targets. Network-based functional analysis linked these proteins to core cellular processes, while underscoring that their essentiality in P. graminis f. sp. tritici remains experimentally unconfirmed. Molecular docking with the antifungal agent poacic acid and the nucleotide sugar UDP-glucose suggested potential binding interactions within the predicted cavities. These exploratory simulations present preliminary evidence for plausible small-molecule binding pockets in the selected candidate targets. Collectively, this work provides a multi-layered computational framework for nominating and structurally characterizing candidate targets in wheat stem rust and generates testable hypotheses for future experimental work.},
}
@article {pmid42485614,
year = {2026},
author = {Zhang, J and Xu, W and Xing, J and Sun, Y and Huang, S and Su, X},
title = {CAM-Net: a context-aware network for identifying reliable microbial relations via optimal consortium.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {4},
pages = {},
pmid = {42485614},
issn = {1477-4054},
support = {2025Z154//Innovation Yongjiang 2035 Key R&amp;D Program/ ; 25-3-1-11-zyyd-jch//Qingdao Natural Science Foundation/ ; 32572519//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; Algorithms ; *Computational Biology/methods ; *Microbial Interactions ; },
abstract = {Microbes exist within complex community contexts, particularly for key functional species whose stable colonization critically depends on specific ecological partners. However, conventional microbial correlation analyses predominantly rely on isolated pairwise metrics (e.g. Spearman, SparCC, and FlashWeave), which ignore community-level dependencies. This limitation leads to spurious associations in large-scale datasets and obscures the true structure of microbial interactions. Here, we introduce CAM-Net, a context-aware framework that identifies a target microbe's optimal consortium, a fully connected network subset that accurately predicts its abundance. By constructing networks via multi-hop information propagation, CAM-Net effectively filters false positives from indirect associations and captures complex, context-dependent patterns that are inaccessible to traditional pairwise approaches. We evaluated CAM-Net on over 25 000 human gut microbiome samples using Akkermansia muciniphila and Lactobacillus acidophilus as representatives of indigenous and transient colonizers. CAM-Net identified a coherent and reproducible consortium for A. muciniphila, but only weak association structures for L. acidophilus, consistent with their ecological behaviors. In contrast, pairwise methods produced spurious associations for both species. Notably, despite substantial geographic heterogeneity, Alistipes shahii consistently emerged as a conserved core member of the A. muciniphila consortium, demonstrating the advantage of context-aware modeling. The source code is available at https://github.com/qdu-bioinfo/CAM-Net.},
}
@article {pmid42489682,
year = {2026},
author = {Jain, B and Bandodkar, AJ},
title = {Biodegradable and bioresorbable rechargeable batteries: chemistries, AI-driven material discovery, and emerging applications.},
journal = {Materials horizons},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6mh01006g},
pmid = {42489682},
issn = {2051-6355},
abstract = {Biodegradable and bioresorbable rechargeable batteries are emerging as key enabling technologies for transforming the manner in which electronic systems are powered when device retrieval, recycling, or long-term persistence is a challenge or undesirable. This review integrates recent advances in materials engineering and artificial intelligence for creating "green-by-design" secondary batteries that operate safely in the environment and on/within living organisms for a desired timeline before naturally disintegrating into non-toxic materials. The discussion first surveys sustainable chemistries and architectures that collectively enable rechargeable operation and degradation of spent batteries into benign ions and small molecules. Subsequent sections examine how established lithium-ion battery informatics can be repurposed for biodegradable alternatives. Specifically, these sections explore how workflows for property prediction, multi-objective optimization, and literature mining can integrate explicit constraints regarding battery lifetime and environmental toxicity. The review concludes by outlining grand challenges and research priorities required to transition biodegradable secondary batteries from laboratory exemplars into practical power sources intrinsically aligned with their biological and ecological contexts.},
}
@article {pmid42490563,
year = {2026},
author = {Mir, ZR and Pebsworth, P and Hardman, J and Ala'amri, S and Alahmari, A and Almalki, K and Boug, A},
title = {Effects of urban association on the movement ecology of hamadryas baboons (Papio hamadryas) in Saudi Arabia.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0354133},
pmid = {42490563},
issn = {1932-6203},
mesh = {Animals ; Saudi Arabia ; *Papio hamadryas/physiology ; Male ; Ecosystem ; Geographic Information Systems ; Humans ; Movement ; },
abstract = {Human-wildlife conflict involving primates is an emerging conservation concern in rapidly urbanizing regions. The hamadryas baboon (Papio hamadryas), the only native non-human primate of the Arabian Peninsula, increasingly exploits anthropogenic food sources, intensifying human-baboon conflict across southwestern Saudi Arabia. To examine how human-modified environments influence baboon spatial ecology; we fitted GPS collars to ten adult males representing groups that are regarded as living in urban, natural and semi-natural environments across five regions. Over nine months, we collected 13,962 location fixes and analyzed them using empirical variograms, home range analysis, and minimum daily path length estimates. Variogram analyses indicated that baboons living in a natural environment exhibited the greatest space-use extent, semi-natural individuals showed intermediate and more variable space-use dynamics, whereas baboons living in urban areas displayed restricted movement. Hamadryas baboons living in natural environments exhibited the largest home ranges with a median of 8.79 km2 (range: 6.19-13.86 km2) and minimum daily path lengths with median 3.33 km (range 0.02-20.6 km), whereas baboons living in urban areas maintained the smallest ranges with a median of 1.31 km2 (range: 1.24-1.79 km2) and the minimum daily path lengths with a median of 2.16 km (range: 0.01-4.85 km). The proportion of daytime spent in urban areas increased along the gradient, 7.2% (natural), 40.6% (semi-natural), and 55.0% (urban). These findings support the Resource Dispersion Hypothesis, suggesting that food predictability shapes baboon space use more than resource scarcity. The study strengthens ongoing conflict-mitigation efforts by providing insights into baboon movement patterns and supporting the ecological differentiation of natural, semi-natural, and urban baboon groups, thereby informing category-specific management interventions.},
}
@article {pmid42491029,
year = {2026},
author = {DeSalle, AJ and Agbajelola, VI and Ericsson, AC and Shyu, CR and Palaniappan, K and Shacham, E and Raghavan, RK},
title = {Seasonal variation in the bacterial microbiome of questing nymphal ticks in Missouri, United States.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1863755},
pmid = {42491029},
issn = {1664-302X},
abstract = {BACKGROUND: Seasonal environmental variation may influence the composition of tick-associated bacterial communities. This study assessed seasonal differences in the microbiome of questing nymphal ticks collected from Missouri, United States.<br><br>METHODS: Questing ticks were collected during early and late seasonal periods at a livestock-associated site in central Missouri. To minimize confounding by developmental stage, microbiome analyses were restricted to nymphal ticks. Bacterial communities were characterized using 16S rRNA gene sequencing. Alpha diversity (richness, Shannon, and Simpson indices), beta diversity (Jaccard and Bray-Curtis dissimilarities), and differential abundance analyses were performed. Community differences were evaluated using permutational multivariate analysis of variance (PERMANOVA).<br><br>RESULTS: Sequencing generated 984-101,293 reads per sample. Sequencing depth was strongly correlated with observed richness (R [2]&#x202f;=&#x202f;0.808, p&#x202f;=&#x202f;2&#x202f;&#xd7;&#x202f;10[-7]). Comparisons of non-rarefied and rarefied datasets revealed no significant differences between early- and late-season nymphal ticks in observed richness, Shannon diversity, or Simpson diversity (all p&#x202f;>&#x202f;0.05). In contrast, beta-diversity analyses identified significant differences in bacterial community membership between seasonal groups based on Jaccard dissimilarity (PERMANOVA: F&#x202f;=&#x202f;1.5, R [2]&#x202f;=&#x202f;0.066, p&#x202f;=&#x202f;0.0102), whereas Bray-Curtis dissimilarity showed a non-significant trend toward seasonal separation (F&#x202f;=&#x202f;2.2, R [2]&#x202f;=&#x202f;0.090, p&#x202f;=&#x202f;0.0834). Differential abundance analysis identified 18 amplicon sequence variants (ASVs) with raw p-values < 0.05, of which one Rickettsia-associated ASV remained significant following false discovery rate correction.<br><br>CONCLUSION: Seasonal differences in bacterial community composition were detected among nymphal ticks despite similar levels of microbial richness and alpha diversity. The enrichment of a Rickettsia-associated ASV in early-season ticks suggests that season may influence the occurrence of specific bacterial taxa within tick microbiomes. Further studies using higher-resolution sequencing and pathogen-specific approaches are needed to clarify the ecological significance of these seasonal patterns.},
}
@article {pmid42491558,
year = {2026},
author = {Gemeinholzer, B and Bonn, A and Ebert, B and Fischer, S and Güntsch, A and Holetschek, J and Johansson, VA and Friedrichs-Manthey, M and Röder, J and Schomburg, C and Steinthorsdottir, M and van Ommen Kloeke, E and de Boer, HJ},
title = {Experiences from national biodiversity data infrastructures in Europe: advancing data integration and community engagement.},
journal = {Bioscience},
volume = {76},
number = {7},
pages = {635-649},
pmid = {42491558},
issn = {0006-3568},
abstract = {The urgent need for comprehensive biodiversity data is driven by rapid biodiversity loss due to human activity. Drawing on insights from established national biodiversity data infrastructures in Europe, this article highlights eight key considerations for strengthening national data infrastructures-particularly in enhancing stakeholder engagement through improved data availability and accessibility. We emphasize the importance of collaboration among diverse stakeholders to enhance data sharing and integration. By utilizing technological advancements, implementing international standards for data interoperability under FAIR (Findable, Accessible, Interoperable, and Reusable) conditions, establishing robust communication strategies, and providing necessary training and legal guidance, these infrastructures can support effective data mobilization. Furthermore, promoting a culture of collaboration among stakeholders enhances the quality and applicability of biodiversity data for scientific research, policy, and conservation efforts. Our recommendations aim to ensure that national biodiversity data infrastructures effectively contribute to achieving the UN Global Biodiversity Framework targets and Sustainable Development Goals by encouraging strong partnerships and efficient data management practices.},
}
@article {pmid42496189,
year = {2026},
author = {Fernandes Erickson, M and Daluwatta Galappaththige, HSS and Mclean, DJ and Silva, DJA and Fulham, M and Wild, Z and Kelly, MBJ and Irving, CJ and Carlesso, D and Binns, GE and Silvasti, SA and Hämäläinen, L and O'Neill, LG and L'Herpiniere, K and Mappes, J and Kikuchi, DW and Rowland, HM and Power, M and White, TE and Kemp, DJ and Herberstein, ME},
title = {OzButterflies - a high quality open database of multispectral images and spectra of tropical to temperate Australian butterflies.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {42496189},
issn = {1758-0463},
support = {DP220102323//Australian Research Council/ ; FT170100417//Australian Research Council/ ; APSF22042//Australia and Pacific Science Foundation/ ; },
mesh = {Animals ; *Butterflies/genetics/anatomy &amp; histology ; Australia ; *Databases, Factual ; Wings, Animal/anatomy &amp; histology ; Female ; Male ; Electron Transport Complex IV/genetics ; },
abstract = {Butterflies have been a model system for studying the evolution of colour. This is partly due to their complex patterns that reflect human-visible (VIS) and ultraviolet (UV) light, which are perceived by conspecifics and predators. Many studies have sourced data from publicly available images, but most of these images only consider the visible spectrum of light. Including the UV spectrum is crucial for fully understanding the evolution of butterfly morphology and behavioural ecology. Here we provide standardized images (VIS and UV) of over 4 000 individuals from 16 communities of Australian butterflies. These communities represent different climates and urbanization levels spanning over 2 500 km. The dataset contains at least one individual of 125 different species from five families, constituting over one quarter of Australian butterfly diversity. In addition to photographs, we provide spectral measurements of butterfly wings for at least one individual of each species and sex, and Cytochrome Oxidase subunit 1 (CO1) sequences of 1 635 individuals. All these data are accessible in Zenodo and an associated R package simplifies the download of subsets of the database. This database will be of use to evolutionary biologists and ecologists interested in a broad range of topics related to phenotypic variation.},
}
@article {pmid42190858,
year = {2026},
author = {Qiu, J and Guo, X and Fan, G and Xu, H and Zhao, X and Xu, J},
title = {Integrated transcriptomic and metabolomic analysis of the toxic effects of PE microplastics on the Kumamoto oyster (Crassostrea sikamea).},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {308},
number = {},
pages = {110586},
doi = {10.1016/j.cbpc.2026.110586},
pmid = {42190858},
issn = {1532-0456},
mesh = {Animals ; *Transcriptome/drug effects ; *Microplastics/toxicity ; *Crassostrea/drug effects/metabolism/genetics ; Metabolomics ; Oxidative Stress/drug effects ; *Water Pollutants, Chemical/toxicity ; *Polyethylene/toxicity ; Hepatopancreas/drug effects/metabolism ; Multiomics ; Metabolome/drug effects ; Particle Size ; Biomarkers/metabolism ; },
abstract = {Microplastic pollution, particularly from polyethylene (PE), poses an increasing threat to coastal ecosystems, yet how particle size and exposure duration jointly regulate organismal responses remains poorly understood. Here, we investigated the size- and time-dependent toxic effects of PE-MPs (10 μm and 50 μm) on the Kumamoto oyster (Crassostrea sikamea) using an integrative framework combining physiological biomarkers (SOD, CAT, MDA), histopathology (gills and hepatopancreas), transcriptomics (gills), and metabolomics (hepatopancreas) during acute (1 day), short-term (7 days), and long-term (14 days) phases. Both PE-MP sizes induced significant oxidative stress and tissue injury in a time-dependent manner, with smaller particles casing more persistent oxidative stress, greater metabolic disturbance, and stronger immune suppression. Multi-omics analyses revealed a clear phase-dependent response pattern characterized by early defense activation, short-term metabolic reprogramming, and long-term functional suppression. Acute exposure activated oxidative stress responses, cytoskeletal remodeling, and particle clearance-related pathways, whereas short-term exposure was associated with metabolic reprogramming characterized by enhanced glycolysis and amino acid metabolism, suggesting increased energetic demands during stress responses. In contrast, long-term exposure resulted in coordinated suppression of immune, digestive, and lipid metabolic-related pathways, together with a metabolic shift toward long-term energy conservation. Overall, these findings suggest that PE-MPs exposure may induce coordinated physiological and metabolic adjustments associated with energy trade-offs under chronic stress conditions, highlighting the importance of particle size and exposure duration in ecological risk assessment for coastal and aquaculture environments.},
}
@article {pmid42475529,
year = {2026},
author = {Biondi, L and Gomes, N and Maior, RS and Silva, F and Silva, S and Soares, SC},
title = {Ecological context modulates the visual detection advantage for snakes.},
journal = {Cognition &amp; emotion},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/02699931.2026.2697201},
pmid = {42475529},
issn = {1464-0600},
abstract = {Research indicates that the human visual system is highly efficient at detecting snakes, yet less is known about how ecological visual contexts modulate this advantage. We conducted two experiments with university students (N = 58 each) to test whether background complexity influences snake-detection efficiency using a dual-task paradigm. In Experiment 1, stimuli were presented on a uniform grey background. Here, snakes were detected and visually fixated significantly faster than non-snake control animals, consistent with previous findings. Crucially, this advantage was not influenced by participants' self-reported fear of snakes or anxiety levels. In Experiment 2, the same stimuli were embedded in a complex leaf-litter background. Under these conditions, non-snake stimuli were detected earlier than snakes, and overall accuracy declined. This indicates that the snake detection advantage is sensitive to changes in perceptual and contextual conditions, which may attenuate or reverse the pattern observed under simplified settings. Subjective fear scores again showed no moderating effect. Overall, these findings are consistent with an evolved sensitivity to snake-related visual features, but show that this advantage is context-dependent and can be attenuated or even reversed under ecologically complex visual conditions, independently of self-reported fear. They underscore the necessity of incorporating ecological variables into threat-detection research.},
}
@article {pmid42475681,
year = {2026},
author = {Li, R and Wu, W and Yan, C and Li, JT},
title = {CNEwrap: a scalable toolkit with a novel algorithm for large-scale genome-wide accelerated conserved non-coding elements detection.},
journal = {Nucleic acids research},
volume = {54},
number = {14},
pages = {},
pmid = {42475681},
issn = {1362-4962},
support = {2023YFF1304800//National Key Program of Research and Development, Ministry of Science and Technology of China/ ; 32370449//National Natural Science Foundation of China/ ; 32400407//National Natural Science Foundation of China/ ; 32570585//National Natural Science Foundation of China/ ; 32270449//National Natural Science Foundation of China/ ; 32325011//National Natural Science Foundation of China/ ; 2024YFHZ0294//Sichuan Science and Technology Program/ ; 2026NSFSCZY0073//Sichuan Science and Technology Program/ ; 2025ZYD0163//Sichuan Science and Technology Program/ ; },
mesh = {*Algorithms ; Animals ; Humans ; *Conserved Sequence/genetics ; *Software ; Evolution, Molecular ; *Genomics/methods ; Phylogeny ; Sequence Alignment ; Genome ; Computational Biology/methods ; },
abstract = {Conserved non-coding elements (CNEs) are fundamental components of gene regulatory networks in eukaryotes, yet their reliable identification across large-scale genomes and systematic evaluation of their genetic variation remains technically challenging, limiting comprehensive insights into their functional roles. To address these challenges, CNEwrap (https://github.com/YanCCscu/CNEwrap) was developed as a streamlined and modular bioinformatics toolkit that integrates subprograms capable of performing diverse tasks ranging from whole-genome alignment to CNE scanning and accelerated evolution analysis. Designed for high-throughput, multi-species applications, CNEwrap enables efficient and accurate discovery of genome-wide CNEs and comparative analysis of their variation across diverse taxa. Specifically, we developed a novel algorithm, "EvoAcc," designed for assessing accelerated evolution of specific species in different scenarios from CNE alignments. The EvoAcc algorithm integrates nucleotide variation frequencies and phylogenetic relationships to reconcile global conservation with clade-specific divergence, outperforming PhyloAcc, PhyloP, and ForwardGenomics in simulated datasets, particularly in scenarios involving two or three accelerated lineages. In validation analyses of functional genomic fragments across mammal species, EvoAcc performed comparably to existing algorithms in detecting human-specific accelerated segments while exhibiting superior sensitivity for InDel mutations and recovering specific signals missed by other algorithms. Case studies further confirm that CNEwrap is broadly applicable within diverse evolutionary lineages. Collectively, the CNEwrap pipeline establishes a scalable and integrative framework for uncovering CNEs and their evolutionary dynamics, while the incorporated EvoAcc algorithm complements existing methodologies, deepening insights into conserved regulatory architectures across eukaryotic evolution.},
}
@article {pmid42476159,
year = {2026},
author = {, },
title = {Global, regional, and national burden of road injuries 1990-2023: a systematic analysis for the Global Burden of Disease Study 2023.},
journal = {The Lancet. Public health},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2468-2667(26)00141-6},
pmid = {42476159},
issn = {2468-2667},
abstract = {BACKGROUND: Road injuries are a leading cause of mortality and morbidity worldwide. Years of international efforts have aimed to strengthen policy engagement, including the 2020 UN General Assembly's proclamation of the Second Decade of Action for Road Safety (2021-30), targeting a 50% reduction in road traffic deaths and serious injuries by 2030. The aim of this study is to provide estimates to monitor progress and identify intervention gaps.<br><br>METHODS: As part of the Global Burden of Diseases, Injuries, and Risk Factors Study 2023, we estimated incidence, mortality, and morbidity of road injuries for 204 countries and territories from 1990 to 2023. Four road injury types and 47 nature-of-injury categories were examined. Morbidity and mortality data from clinical records, vital registration, and police reports were harmonised using meta-analytic techniques to ensure consistency and correct for systematic bias. Incidence was modelled with the meta-regression tool Disease Modelling-Meta-Regression version 2.1 and cause-specific mortality with the Cause of Death Ensemble model, both incorporating location-specific covariates to support interpolation. Years of life lived with disability (YLDs) were estimated from the prevalence and severity of the nature of road injury, and years of life lost (YLLs) from the number of cause-specific deaths multiplied by the standard life expectancy at the age of death. Disability-adjusted life-years (DALYs) were the sum of YLLs and YLDs. All metrics were calculated with 95% uncertainty intervals (UIs).<br><br>FINDINGS: In 2023, there were 50&#xb7;9 million (95% UI 46&#xb7;1-56&#xb7;1) road injury incident cases, 1&#xb7;34 million (1&#xb7;04-1&#xb7;58) deaths, and 75&#xb7;3 million (59&#xb7;8-89&#xb7;2) DALYs globally. Road injuries were the leading global cause of death among males aged 10-39 years. Between 1990 and 2023, age-standardised incidence decreased by 38&#xb7;3% (95% UI 36&#xb7;9-39&#xb7;7) and mortality decreased by 32&#xb7;3% (6&#xb7;1-49&#xb7;0), but progress varied widely by World Bank income group. Mortality in low-income countries (43&#xb7;8 [95% UI 31&#xb7;7-56&#xb7;0] deaths per 100&#x2008;000 population) was approximately six times higher than in high-income countries (7&#xb7;5 [7&#xb7;1-7&#xb7;9] deaths per 100&#x2008;000), despite the high-income countries showing the highest age-standardised incidence rates (858&#xb7;1 [95% UI 781&#xb7;9-947&#xb7;1] cases per 100&#x2008;000). In the past decade, many countries achieved notable reductions in road injuries, but others, including Ghana and the USA, saw increases. More severe injuries tended to occur in low-income and middle-income countries.<br><br>INTERPRETATION: Although global incidence, mortality, and DALY rates from road injuries have declined, progress remains uneven, with pronounced disparities across income groups reflecting systemic inadequacies in infrastructure, vehicle standards, enforcement, and post-crash care. Strengthening emergency response, improving road design, enforcing safety measures, and adapting policies to the evolving demographics remain essential.<br><br>FUNDING: Gates Foundation.},
}
@article {pmid42484728,
year = {2026},
author = {Karbasi, G and Ahmad, SA and Moradi, G and Danaee, M and Ishak, NH and Kunasekaran, P and Mohtar, MN},
title = {Validation of an mHealth adoption questionnaire for osteoporosis management in Iranian older adults at risk.},
journal = {Archives of osteoporosis},
volume = {21},
number = {1},
pages = {},
pmid = {42484728},
issn = {1862-3514},
mesh = {Humans ; *Osteoporosis/therapy ; *Telemedicine ; Surveys and Questionnaires ; Female ; Iran ; Aged ; Male ; Middle Aged ; Psychometrics ; Reproducibility of Results ; Digital Health ; Self Efficacy ; Health Literacy ; },
abstract = {BACKGROUND: With the increasing prevalence of osteoporosis among older adults and the growing need for effective self-management strategies, mobile health (mHealth) technologies may play an important role in supporting osteoporosis management. This study aimed to adapt and validate a culturally appropriate Persian questionnaire to assess mHealth adoption for osteoporosis management among Iranian adults aged ≥50 years, regardless of osteoporosis diagnosis status.<br><br>METHODS: A questionnaire was adapted from established theoretical frameworks, including the Unified Theory of Acceptance and Use of Technology (UTAUT), the Health Belief Model (HBM), self-efficacy, digital literacy, and technology anxiety. The instrument underwent cross-cultural adaptation and psychometric evaluation in two phases: (1) content validation and cognitive testing, and (2) construct validation using exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) with SmartPLS version 4.<br><br>RESULTS: The final instrument consisted of 54 items after removing poorly performing indicators. The measurement model demonstrated satisfactory psychometric properties, with average variance extracted (AVE) values ranging from 0.608 to 0.833 and composite reliability (CR) values between 0.866 and 0.950. Discriminant validity was supported by heterotrait-monotrait ratio (HTMT) values below the recommended threshold. Performance expectancy, self-efficacy, digital literacy, and perceived severity emerged as key&#xa0;determinants of mHealth adoption among older adults.<br><br>CONCLUSION: This study developed a culturally adapted Persian questionnaire with strong reliability and validity for assessing mHealth adoption in osteoporosis management among older adults. The instrument may help researchers, clinicians, and policymakers identify barriers to digital health engagement and design targeted interventions to improve mHealth adoption in ageing populations. The study designed and validated a culturally appropriate questionnaire to assess the acceptance of mHealth for osteoporosis management in Iranian adults over 50. Key predictors included performance expectancy, self-efficacy, and digital literacy. The findings support implementing tailored interventions to increase mHealth acceptance among older adults in resource-limited settings.},
}
@article {pmid40913400,
year = {2026},
author = {Zhong, H and Shi, Y and Kozlova, A and Moravcova, R and Rogalski, JC and Jamieson, A and Lansing, L and Moon, KM and Yuan, X and Gregoris, AS and Higo, H and Common, J and Conflitti, IM and Pepinelli, M and Tran, L and Cunningham, M and Jabbari, H and Bukhari, SA and French, SK and Polo, RO and Hoover, SE and Pernal, SF and Giovenazzo, P and Guarna, MM and Zayed, A and Foster, LJ},
title = {Omics Insights Into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology.},
journal = {Proteomics},
volume = {26},
number = {8},
pages = {41-57},
doi = {10.1002/pmic.70033},
pmid = {40913400},
issn = {1615-9861},
support = {AAFC J-002368//Government of Canada through Agriculture and Agri-Food Canada (AAFC) Genomics Research and Development Initiative (GRDI)/ ; LSARP #16420//Genome Canada/ ; OGI-185//Ontario Genomics Institute/ ; 374PRO//Life Sciences Institute, and Genome BC/ ; },
mesh = {Animals ; Bees/physiology/microbiology ; *Blueberry Plants ; Multiomics ; *Vaccinium macrocarpon ; Proteomics/methods ; Gastrointestinal Microbiome ; Agroecology ; Crops, Agricultural ; },
abstract = {Honey bees (Apis mellifera) are vital pollinators in fruit-producing agroecosystems like highbush blueberry (HBB) and cranberry (CRA). However, their health is threatened by multiple interacting stressors, including pesticides, pathogens, and nutritional changes. We tested the hypothesis that distinct agricultural ecosystems-with different combinations of agrochemical exposure, pathogen loads, and floral resources-elicit ecosystem-specific, tissue-level molecular responses in honey bees. We conducted an integrated multi-omics analysis using RNA-sequencing (RNA-seq), proteomics, and gut microbiome profiling across three key tissue types (head, abdomen, and gut) of honey bees collected from two agroecosystems over two field seasons. Quantification was performed for pesticide residues, pathogen loads (Nosema spp., Varroa destructor, and multiple viruses), and gut microbiota. Weighted gene co-expression network analysis (WGCNA) revealed tissue-specific protein modules with ecosystem-associated patterns, which differed from RNA co-expression networks. Microbiome composition also varied, with key genera like Gilliamella, Snodgrassella, and Bartonella correlating with metabolic modules. These findings underscore the complex, environment-dependent impacts of agroecosystem conditions on bee health. Our study provides a system-level understanding of how combined pesticide, pathogen, and parasitic stressors, mediated by diet and microbiome, shape molecular phenotypes in honey bees-informing strategies for pollinator protection in managed landscapes. SUMMARY: This study provides a comprehensive multi-omics analysis of honey bees foraging in blueberry and cranberry agroecosystems, offering novel insights into the molecular mechanisms underlying pollinator health in managed crop environments. By integrating transcriptomic, proteomic, and microbiome profiling across key tissues-head, abdomen, and gut-we reveal how environmental stressors, including pesticide exposure, pathogen infections, and parasitic infestations (e.g., Varroa destructor), differentially impact bee physiology and microbiome composition. Our findings highlight tissue-specific responses to these stressors, with distinct metabolic pathway alterations observed in each tissue. Proteomic and transcriptomic analyses uncovered dysregulated pathways linked to oxidative phosphorylation and protein synthesis, while microbiome analysis revealed crop-dependent shifts in gut bacterial communities, suggesting potential roles in pesticide detoxification and immune modulation. Notably, we identified key molecular biomarkers associated with stress adaptation, which may serve as early indicators of colony health deterioration. This research underscores the need for a system-level approach to understanding pollinator stress in agricultural landscapes. By elucidating the interactions between diet, pesticide residues, pathogen loads, and molecular stress responses, our study provides a foundation for targeted conservation strategies aimed at mitigating environmental risks and improving pollination sustainability in agroecosystems.},
}
@article {pmid42407216,
year = {2026},
author = {Zhang, B and Wang, X and Kuang, C and Wu, J and Hong, Y},
title = {Development of an integrated workflow (NosZRef) for rapid and accurate nosZ gene profiling and its application to oceanic ecosystems.},
journal = {Marine environmental research},
volume = {220},
number = {},
pages = {108247},
doi = {10.1016/j.marenvres.2026.108247},
pmid = {42407216},
issn = {1879-0291},
mesh = {Workflow ; *Ecosystem ; High-Throughput Nucleotide Sequencing ; Nitrous Oxide/metabolism ; Oceans and Seas ; *Bacteria/genetics ; Gene Expression Profiling ; Computational Biology ; },
abstract = {The widespread adoption of next-generation sequencing technologies and the rapid growth of publicly available sequence data have generated an unprecedented resource for investigating nitrous oxide (N2O) reducing microorganisms. However, the lack of standardized practices has hindered cross-study comparisons and limited our ability to thoroughly assess the community structure, diversity and biogeography of N2O-reducing microorganisms. To address these knowledge gaps, a bioinformatic workflow was developed to standardize the processing of nosZ gene datasets originating from high-throughput sequencing. We first manually curated and constructed a comprehensively annotated reference protein sequence database containing 3,361, 5,665, and 96 sequences from the NosZ-I, NosZ-II, and NosZ-III clades, respectively. Integrated with this database, we developed NosZRef, a fast, accurate and scalable analytical pipeline for nosZ gene profiling. With one single command, NosZRef provides users full-pipeline analysis from raw reads to statistical and visualization outputs. We employed NosZRef to profile nosZ genes across diverse depths in the Tara Oceans dataset, revealing that the three nosZ clades exhibit distinct depth-dependent distribution patterns and ecological strategies. In summary, NosZRef offers high specificity and comprehensive coverage for accurate profiling of N2O-reducing microorganisms in oceanic ecosystems from high-throughput sequencing data, providing a useful tool for investigating microbially mediated N2O reduction in oceanic environments. NosZRef is available at https://github.com/ZhangBaoshan668/NosZRef.},
}
@article {pmid42429456,
year = {2026},
author = {Flamholz, ZN and Mulay, SA and Leshyk, V and Caporaso, JG and Eisen, JA and Kelly, L and Lloyd, KG and Osburn, MR and Podar, M and Roux, S and Regberg, SAB and Ruff, SE and Tierney, B and Tighe, S and Trembath-Reichert, E and Venkateswaran, K and Woyke, T and Locken, KM and Sapers, HM and Whiteson, K},
title = {Exploring life's hidden majority: microbial dark matter symposium highlights.},
journal = {mSphere},
volume = {11},
number = {7},
pages = {e0058725},
pmid = {42429456},
issn = {2379-5042},
mesh = {Metagenomics ; *Microbiota ; Bacteria/genetics/classification ; Computational Biology ; Ecosystem ; },
abstract = {The Microbial Dark Matter Symposium held on August 28-29, 2025, in Laguna Beach, Orange County, CA, convened a multidisciplinary group of scientists to address the vast unknowns in microbial life-from uncultured taxa and uncharacterized proteins to elusive viruses and spacefaring microbes. Set against a scenic coastal backdrop, the symposium highlighted advances in single-cell genomics, proximity ligation sequencing, and artificial intelligence-ready bioinformatics, while also probing the limits of microbial persistence, metabolism, and ecological distribution. Sessions explored microbial dark matter from multiple dimensions: cultivability, where new strategies are enabling recovery of elusive microbes; functional ambiguity, where metagenomic dark zones are illuminated by computational annotation; and genomic representation, where single-cell methods bridge gaps left by shotgun community sequencing. Researchers shared breakthroughs in identifying atmospheric microbiomes, "dark oxygen" production in groundwater ecosystems, and microbial survival on the International Space Station. The symposium emphasized integration of methods, disciplines, and ecosystems, advancing a collective push to illuminate the microbial dark matter on Earth and beyond. By highlighting emerging tools, pressing questions, and cross-domain insights, the symposium underscored the need for collaborative, open, and adaptive approaches to study the microbial unknown. The meeting marks a pivotal moment in microbiology, where cultivating knowledge of the uncultivated promises transformative understanding of life, everywhere.},
}
@article {pmid42465418,
year = {2026},
author = {Sharma, J and Maldonado, B and Ungar, R and Adimoelja, A and Flores, JP and Gjorgjieva, T and Jones, K and Khan, A and Xue, D and Patel, R and Caggiano, C},
title = {Recommendations for the ethical and accurate use of population descriptors: a trainee-led survey of early-career researchers.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42465418},
issn = {2692-8205},
abstract = {Despite the importance of population descriptors in human genomics research, many scientists struggle to translate evolving ethical guidelines into their computational workflows. To characterize this gap between recommendations and implementation, we conducted a mixed-methods survey of early-career researchers to assess how they understand and implement the landmark 2023 NASEM report on the use of population descriptors in human genetics research. We show that while exposure to the report fosters ethical awareness, fundamental misconceptions about race and ancestry persist across academic disciplines, and trainees face structural bottlenecks, including legacy data constraints and a lack of technical confidence. To address this gap, we offer actionable, stakeholder-specific recommendations across the research lifecycle ranging from decision-support tools to "bring-your-own-data" workshops to leadership from academic journals, scientific societies, and trainee mentors. Ultimately, we argue that to promote scientific rigor and reduce bias in genetic discoveries, the scientific ecosystem must invest in the infrastructure necessary to empower the next generation of researchers.},
}
@article {pmid42470576,
year = {2026},
author = {Kamp, K and Yoo, L and Kale, T and Zhang, X and Malloy, C and Kahveci, I and Cordova, R and Hernandez, I and Tsai, CS and Pan, TD and Clark-Snustad, K and Lee, S and Levy, RL and Keefer, L and Heitkemper, M},
title = {Feasibility, Acceptability, and Preliminary Effects of a Nurse-Delivered Self-Management Program for Individuals with Inflammatory Bowel Disease: A Pilot Randomized Controlled Trial.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {42470576},
issn = {1573-2568},
support = {K23 NR020044/NR/NINR NIH HHS/United States ; P2C HD042828/HD/NICHD NIH HHS/United States ; T32016913/NR/NINR NIH HHS/United States ; UL1 TR002319/TR/NCATS NIH HHS/United States ; },
abstract = {PURPOSE: Individuals with inflammatory bowel disease experience persistent symptoms and disease challenges which may not be solved with medical management. Self-management interventions may support patients, but their feasibility, acceptability, and preliminary effectiveness should be evaluated prior to large-scale testing.<br><br>METHODS: We conducted a pilot randomized controlled trial with 2:1 allocation of a nurse-delivered, self-management program to usual care. Adults with a healthcare provider diagnosis of ulcerative colitis or Crohn's disease, aged 18-75&#xa0;years, currently reporting at least two symptoms were recruited. The self-management program included eight online modules plus weekly phone check-ins with a registered nurse. Feasibility and acceptability were measured using surveys and interviews. Secondary outcomes included patient activation, self-regulation, self-efficacy, functional impairment, quality of life, symptoms, and fecal calprotectin. Linear mixed models estimated the differences in change scores between groups from baseline to 3- and 6-month follow-up.<br><br>RESULTS: Fifty-five participants were randomized (n&#x2009;=&#x2009;36 self-management, n&#x2009;=&#x2009;19 usual care). Participants were on average 39.0&#xa0;years old (range: 20-73), 76.4% women, and 80% Crohn's disease. The self-management program demonstrated high satisfaction (91.1/100), feasibility (4.34/5), and acceptability (4.28/5). Compared with usual care, the self-management program produced the largest improvement in functional impairment (mean change&#x2009;-&#x2009;15.1 [95% CI&#x2009;-&#x2009;23.3,&#x2009;-&#x2009;6.8], with additional improvements in patient activation (10.3 [2.8, 17.9]), self-regulation (4.1 [1.1, 7.1]), and quality of life (4.6 [0.3, 8.9]). Symptom severity and fecal calprotectin were largely unchanged. Qualitative feedback emphasized the value of regular nurse check-ins, accountability, and applicability of the program beyond disease-specific concerns.<br><br>CONCLUSIONS: A nurse-delivered self-management program was feasible, acceptable, and led to meaningful changes in key intervention targets for inflammatory bowel disease management. High engagement supports potential for future testing in a fully powered trial and eventual integration into routine care.},
}
@article {pmid42470863,
year = {2026},
author = {Guan, Q and Ji, P and Guan, C and Chen, A and Tang, X and Wang, Y and Gong, T and Guo, K},
title = {A framework for constructing water ecological security patterns based on water provision service flow simulation.},
journal = {Journal of environmental management},
volume = {414},
number = {},
pages = {130488},
doi = {10.1016/j.jenvman.2026.130488},
pmid = {42470863},
issn = {1095-8630},
abstract = {Constructing a Water Ecological Security Pattern (WESP) is essential for mitigating water scarcity, yet existing methods are mostly based on static supply-demand assessments and fail to capture the spatial flow pathways of water resources between supply and demand areas. This results in WESPs lacking spatial connectivity and process integrity. To address these gaps, this study quantifies the supply and demand of water provision service and proposes a network model-based simulation approach for water provision service flows. The proposed method integrates the Least Cost Path (LCP) model with an Iterative Dynamic Allocation algorithm, enabling the joint consideration of landscape resistance and human demand in simulating the dynamic flow process of water provision service. The simulation results are used to identify key spatial elements for WESP construction in the Yellow River Delta (YRD), thereby providing a basis for establishing a WESP with dynamic connectivity. Analysis across three representative years indicates a persistent water deficit in the YRD. A growing spatial mismatch was observed, driven by declining supply in the north and surging demand in the south. The simulated flow network demonstrates a distinct "periphery-to-center" convergence, connecting coastal supply nodes to inland demand centers through 62 key flow pathways. Based on these dynamics, we proposed a WESP comprising "five zones, two corridors, three belts, and three cores". According to its structural characteristics, these spatial elements are further classified into four management zones, for which differentiated spatial regulation strategies are developed. These findings offer a novel, flow-based perspective for resolving supply-demand imbalances and enhancing regional water security.},
}
@article {pmid42471340,
year = {2026},
author = {Zeng, F and Song, C and Woolway, RI and Ke, L and Wang, J and Feng, D and Allen, GH and Lin, P and Liu, K and Chen, T and Zhan, P and Fan, C and Zhang, H and Huang, L and Pavelsky, TM},
title = {Human imprints on global riverfronts.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-75777-0},
pmid = {42471340},
issn = {2041-1723},
abstract = {Rivers are profoundly shaped by human activity along their water-land interfaces (riverfronts), yet the global distribution and drivers of these imprints remain poorly understood. Here we present a high-resolution global map of 7.52 million kilometers of riverfronts using satellite imagery and deep learning. We find that nearly 20% of global riverfronts are anthropogenically modified, primarily by agriculture (13.43%) and built-up areas (6.29%). A distinct modification belt spans parts of Africa and Eurasia, accounting for ~60% of global alterations, with imprint densities six times higher than elsewhere. This lateral fragmentation represents a pervasive human pressure that differs fundamentally from dam-induced longitudinal fragmentation, and is closely linked to deteriorating water quality and biodiversity threats. Environmental constraints and region-specific socio-economic dependencies further shape these spatial patterns. Our findings inform riverfront management and underscore the urgent need to reconcile development with the ecological integrity of these transitional zones.},
}
@article {pmid42473400,
year = {2026},
author = {Wang, Q and Xing, XT and Meng, F and Liu, PD and Liu, Y and Yang, Y and Huo, AD},
title = {[Prediction of Land Use and Ecological Network in Shandong Province by Coupling SD-PLUS-InVEST Model].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {7},
pages = {4846-4857},
doi = {10.13227/j.hjkx.202506065},
pmid = {42473400},
issn = {0250-3301},
abstract = {Under the background of "double carbon，" it is of great significance to study the land use change in Shandong Province to maintain the security of the ecosystem and build a sustainable ecological network. Based on the analysis of land use data in 2010 and 2020， this study coupled the SD-PLUS model to simulate the land use evolution in 2030 and 2060 under three scenarios in CMIP6： low emission sustainable development scenario （SSP119）， medium emission baseline scenario （SSP245）， and high emission extreme scenario （SSP585）， and we then extracted the land use pattern. The InVEST model was used to evaluate the habitat quality， and the MSPA model and MCR model were further combined to construct the ecosystem network of Shandong Province. The results show that： ① From 2010 to 2020 （historical period）， land use was dominated by cultivated land but continued to decrease， with the dual-core expansion of construction land， the slight growth of forest land and water area， and the continuous reduction of grassland and unused land. From 2020 to 2060 （the future period）， under the SSP119 scenario， the cultivated land area will decrease to 64.01 %， the construction land will increase to 25.37 %， the forest land and water area will increase， and the grassland and unused land area will decrease. Under the SSP585 scenario， the decrease of cultivated land was the largest， and the proportion of construction land was the highest in the three scenarios. ② Changes in habitat quality： In the historical period， the pattern of "high in the east and low in the west" was presented， and the contribution of cultivated land was > 60 %. Under the SSP119 scenario in the future period， the high-value areas of mountainous and coastal areas in the central and western regions will be optimized， and the contribution of forest habitat will be the most obvious. Under the SSP245 scenario， the habitat in southwest Shandong Province and the Yellow River Delta was degraded and partially fragmented. Under the SSP585 scenario， the habitat quality in the plain area was degraded in a large area， and the contribution of various habitats decreased. ③ Ecological network construction： From 2010 to 2020， the ecological source area developed into the "East-Central-South" three poles， and the ecological network was gradually optimized. In the future， under the SSP119 scenario， the mountainous areas of central Shandong Province and Jiaodong Peninsula will form a dense network， and the corridors will be interwoven and connected. Under the SSP245 scenario， a buffer zone appears in the northwestern Shandong Plain， and the secondary corridor expands， but the Jiaoji Economic Belt is still dominated by the primary corridor. In the context of SSP585， the ecological source is fragmented， and the first-level corridor along Jiaoji is the core， and there are only sparse low-level corridors in southwestern Shandong Province.},
}
@article {pmid42475117,
year = {2026},
author = {Alexsandra, N and Mazaya, M and Prawira, AY and Surya Alwi, R},
title = {Molecular modeling of the stability of the interaction of Sunda porcupine (Hystrix javanica) quill protein homologs with vascular endothelial growth factor receptor 2 (VEGFR-2).},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/07391102.2026.2702491},
pmid = {42475117},
issn = {1538-0254},
abstract = {Porcupines (Hystrix spp.) are widely distributed rodents known not only for their ecological roles but also for their traditional medicinal applications. In Indonesia, quills from species like Hystrix javanica, Hystrix sumatraensis, and Hystrix brachyura are traditionally used to relieve pain and promote wound healing. Scientific studies have revealed that porcupine quills are rich in bioactive compounds, including keratin, peptides, flavonoids, and triterpenoids. Keratin, a structural protein abundant in epithelial cells extracted from porcupine quill, has been found to support various wound-healing processes, having antibacterial properties, and the ability to induce apoptosis in breast cancer cells. Meanwhile, the vascular endothelial growth factor receptor 2 (VEGFR-2) plays a crucial role in angiogenesis and tissue regeneration during the wound-healing process. This study employed exploratory structural bioinformatics to study the potential interaction between porcupine quill-derived homolog proteins and VEGFR-2 from our previous published work. Through protein-protein docking and molecular dynamics simulation, we predicted molecular recognition and binding affinity computationally. Keratin type II (P50446), Krt2 (B2RTP7), and Keratin isoform X1 (A0A6P5R3S8) demonstrated the most robust and stable interactions with VEGFR-2. Contrarily, Keratin type II (P04264) displayed comparatively greater structural fluctuations and weaker stability, suggesting less optimal and more flexible binding interactions with the receptor. Thus, this research provides preliminary hypothesis evidence of potential interactions between porcupine quill-derived proteins and VEGFR-2, supporting further experimental studies to determine whether these interactions have biological relevance in wound-healing processes.},
}
@article {pmid42475360,
year = {2026},
author = {Duane, D and Duggan, MT and Berlik, E and Dantzker, MS and Rice, AN and Freeman, LA},
title = {Multi-class, unsupervised detection and classification of biological and anthropogenic sounds in coral reefs.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1014516},
pmid = {42475360},
issn = {1553-7358},
mesh = {*Coral Reefs ; Animals ; Classification Algorithms ; *Unsupervised Machine Learning ; Acoustics ; Sound Spectrography/methods ; *Vocalization, Animal/classification/physiology ; Computational Biology ; Hawaii ; *Sound ; Autoencoder ; Clustering Algorithms ; Humans ; Environmental Monitoring/methods ; Anthropogenic Effects ; },
abstract = {Analyzing the complex and diverse soundscapes of ecosystems such as coral reefs remains a challenge for understanding environmental dynamics and processes. While machine learning techniques can significantly improve detection and classification capabilities, applications of traditional supervised learning to underwater acoustics are limited by the size and class-coverage of labeled datasets. Unsupervised machine learning offers the potential to detect and classify sounds without the guidance of human labels, including signals that were unknown to the human analyst. However, the majority of previously developed unsupervised approaches characterize reef soundscapes from correlative metrics without identifying specific sounds, and the few that detect individual signals have been trained on limited data (<10 days), which constrains the potential to generalize across datasets and geographical localities. Here, a convolutional autoencoder was built and trained on year-long acoustic datasets from four Hawaiian coral reefs, and latent embeddings were clustered using Gaussian mixture modeling. A total of 29 classes were automatically generated, and a manual review of samples in each class determined that nine of the classes corresponded to distinct biological and anthropogenic sounds. The classes were identified to be two call types from the damselfish, Dascyllus albisella, parrotfish feeding sounds, holocentrid calls, an unidentified fish sound, three humpback whale song units, and ship noise. The classifier was found to be robust against an independently-collected test dataset with D. albisella calls (AUC = 0.9) with no extra training on the labels. Diel, lunar, and seasonal trends were observed for all nine classes, including previously-unidentified responses of the holocentrid and unknown fish groups to lunar illumination. This work demonstrates the capability of unsupervised algorithms to cluster acoustic signals into identifiable biological and anthropogenic categories in order to examine and characterize ecological trends.},
}
@article {pmid42462070,
year = {2026},
author = {Li, CY and Jiao, ZZ and Zhang, LQ and Li, H and Wang, MY and Guo, WH and Wang, YX and Wang, Y},
title = {Application of Just-in-Time Adaptive Interventions in Dietary Health Management: Systematic Review.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e92139},
pmid = {42462070},
issn = {1438-8871},
mesh = {Humans ; Digital Health ; Telemedicine ; Digital Media ; },
abstract = {BACKGROUND: Just-in-time adaptive interventions (JITAIs) use real-time data to deliver personalized support at moments of heightened need and may improve dietary behaviors in real-world settings.<br><br>OBJECTIVE: The aim of this study is to systematically review the application, characteristics, and effectiveness of JITAIs in dietary health management.<br><br>METHODS: We included human studies evaluating JITAIs-based dietary interventions delivered through digital platforms that used real-time or near-real-time data to tailor intervention content, timing, or intensity. Eligible studies reported at least one behavioral, engagement, physiological, or clinical outcome; reviews, protocols, editorials, commentaries, and studies without outcome data were excluded. We searched PubMed, Embase, Scopus, CINAHL, Web of Science, ClinicalTrials.gov, WHO ICTRP (International Clinical Trials Registry Platform), and ISRCTN (International Standard Randomized Controlled Trial Number) from inception. The initial search was conducted on August 20, 2025, and updated on March 16, 2026; reference lists were also screened manually. Two reviewers independently screened studies and extracted data. Methodological quality was assessed using the 2018 Mixed Methods Appraisal Tool, and reporting quality was assessed using the Mobile Health Evidence Reporting and Assessment checklist. Because of substantial heterogeneity, findings were synthesized narratively. The review was registered in PROSPERO (International Prospective Register of Systematic Reviews; CRD420261285292).<br><br>RESULTS: Twenty studies involving 2948 participants were included. Target populations comprised individuals with overweight or obesity, chronic conditions, and eating disorders and the general population engaged in dietary management. Interventions were mainly delivered via smartphone apps, SMS text messaging, wearable-device feedback, and context-triggered notifications. More consistent benefits were observed for proximal behavioral and process outcomes, including fruit and vegetable intake, sodium-restriction behaviors, drinking automaticity, self-monitoring, eating-related behaviors, and responsiveness to prompts. Some studies also reported improvements in distal clinical outcomes, such as body weight, BMI, waist circumference, blood pressure, blood glucose, and selected biochemical indicators. However, these findings were inconsistent, and most studies did not show clear between-group advantages. Common implementation barriers included device incompatibility, variability in digital literacy, geolocation or signal limitations, and burden from frequent prompts.<br><br>CONCLUSIONS: JITAIs-based dietary interventions appear promising for supporting timely and individualized dietary behavior change, particularly for proximal behavioral outcomes, although evidence for sustained clinical effects remains inconsistent. This review contributes to the JITAIs literature by examining dietary health management as a distinct application domain and by synthesizing evidence that has otherwise been dispersed across broader reviews of digital behavior change and weight management. By integrating intervention characteristics, delivery approaches, triggering mechanisms, and effects across diverse populations, it clarifies methodological and implementation gaps and informs more standardized intervention design and reporting. These findings support the development of scalable, context-sensitive digital dietary interventions for clinical care, chronic disease self-management, weight management, and public health nutrition.},
}
@article {pmid42463295,
year = {2026},
author = {Chen, H and Wu, Y and Wang, X and Liang, D and Yang, Y and Xu, Y and Wu, W},
title = {Multi-Omics Reveal Extracellular Electron Transfer Mechanism Under Deep-Sea High Salinity.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70376},
pmid = {42463295},
issn = {1462-2920},
support = {25ZR1402191//Natural Science Foundation of Shanghai Municipality/ ; 52500086//National Natural Science Foundation of China/ ; 42106046//National Natural Science Foundation of China/ ; 42376047//National Natural Science Foundation of China/ ; },
mesh = {Electron Transport ; *Shewanella/metabolism/genetics ; *Salinity ; *Seawater/microbiology ; Multiomics ; Bacterial Proteins/genetics/metabolism ; Riboflavin/metabolism ; Citric Acid Cycle ; },
abstract = {Microorganism-mineral interaction is crucial for understanding the degradation of organic matter involved in the electron exchange in marine sediments. Widespread metal-reducing bacteria Shewanella spp. have a unique ability of extracellular electron transfer (EET); however, their EET activity and underlying mechanisms under high-salinity stress in the deep sea remain poorly explored. Here, we studied the EET process and the underlying metabolic mechanism based on a deep-sea bacterium Shewanella piezotolerans WP3. S. piezotolerans WP3 has comparable electroactivity to the model strain S. oneidensis MR-1, achieving a maximum current density of 9.7 ± 0.7 μA/cm[2] at 0.6 V vs. Ag/AgCl. Multiheme-cytochrome OmcA-MtrCAB complex contributed to the direct EET, with mtrB, mtrA and omcA-1 upregulated and the redundant omcA genes (i.e., omcA-4, omcA-3) exhibiting low expression. Riboflavin, synthesised from guanosine triphosphate under high-salinity conditions, was secreted to facilitate EET. Enhanced glycolysis and TCA cycle activities under high anode potential (0.6 V) were confirmed by the downregulation of intermediate metabolites (e.g., phosphoenolpyruvate) and the upregulation of corresponding genes (e.g., pyk), supporting the high energy yield for the EET process. Our findings provide new insights into the EET mechanisms of marine Shewanella, paving the way for the development of bioelectronic sensors and biotechnology applications in high-salinity wastewater.},
}
@article {pmid42463489,
year = {2026},
author = {Gao, Z and Wu, J and Lucaci, AG and Ouyang, J and Wang, L and Ryon, KA and Elhaik, E and Probst, AJ and Rodó, X and Velavan, TP and Chasapi, A and Ouzounis, CA and Oliveira, M and Dias-Neto, E and Osuolale, O and Poulsen, M and Meleshko, D and Bhattacharyya, M and Ugalde, JA and Tull, A and Rubins, KH and Sierra, MA and Tierney, BT and Prithiviraj, B and Sharma, NK and Munteanu, V and Mangul, S and Kurt, KC and Ushio, M and Mazur-Panasiuk, N and Kopera, K and Marszałek, K and Kowalski, M and Toscan, RB and Branicki, W and Pyrć, K and Łabaj, PP and Subramanian, B and Frolova, A and Burkhart, JG and Deng, Y and Udekwu, KI and Schriml, LM and Hazrin-Chong, NH and Suzuki, H and Lee, PKH and Camargo, AP and Kyrpides, NC and Liu, D and Wang, LF and Mason, CE and Shi, T and , },
title = {Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42463489},
issn = {2041-1723},
support = {32370720//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Virome/genetics ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; RNA, Viral/genetics ; Cities ; Animals ; },
abstract = {RNA viruses represent an integral component of human-associated environments and human health. However, the ecology of environmental RNA viruses remains largely unexplored. Here, we analyzed 2922 metatranscriptomic samples collected from urban and surrounding environments-including human-dense settings (e.g., transit hubs, hospitals, banks), alongside peri-urban settings - across 102 cities in 31 countries and constructed the Urban &amp; Peri-urban RNA Virus Atlas (UPVAtlas), comprising 54,945 RNA viruses, 77% of which had not been previously observed. Phylogenetic reconstruction based on RNA-dependent RNA polymerases from UPVAtlas greatly expanded the evolutionary diversity of RNA viruses, leading to the identification of two potential candidate phyla, one candidate class, and several unclassified clades. Host association analyses further revealed the ecological complexity of environmental RNA viruses, with the diversity of vertebrate-related and ESKAPE pathogen-related viruses underscoring the importance of continued monitoring of urban environments for tracking RNA viral prevalence and dynamics, with direct relevance to future public health.},
}
@article {pmid42463898,
year = {2026},
author = {Siepe, BS and Haslbeck, JMB and Kloft, M and Büchner, A and Zhang, Y and Fried, EI and Heck, DW},
title = {Introducing openESM: A database of openly available experience sampling datasets.},
journal = {Behavior research methods},
volume = {58},
number = {8},
pages = {},
pmid = {42463898},
issn = {1554-3528},
support = {VENI grant number 221G.110//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWO gravitation grant number 024.004.016//Dutch Research Council and the Dutch Ministry of Education, Culture and Science/ ; European Union's Horizon 2020 research and innov//H2020 European Research Council/ ; Doctoral Scholarship//German Academic Scholarship Foundation/ ; },
mesh = {Humans ; *Databases, Factual ; *Ecological Momentary Assessment ; Internet ; },
abstract = {Experience sampling via mobile devices enables unprecedented insights into daily life. However, individual studies often cannot answer research questions conclusively, and open data are scattered across repositories in different formats. This impedes research into robustness, generalizability, and heterogeneity. We address this issue by introducing openESM, an open-source database of openly available experience sampling datasets in a harmonized format. The growing database currently comprises 60 datasets with more than 16,000 participants and more than 740,000 observations. Metadata can be searched via our website (openesmdata.org) to select and download datasets via packages in R and Python. We demonstrate the potential of openESM through an analysis of within-person correlations of positive and negative affect in 39 datasets, providing evidence for a large negative momentary correlation (- 0.49 , 95% CI: [ - 0.54 , - 0.42 ]). We end by discussing the design principles that will allow openESM to become a continuously evolving community resource for cumulative experience sampling research.},
}
@article {pmid42465405,
year = {2026},
author = {Hunt, M and Torres, MDT and Alikhan, NF and Anderson, D and Andreani, ML and Blom, J and Bouras, G and Brinkman, FSL and Carroll, LM and Croxen, MA and Floto, RA and Hall, MB and Hawkey, J and Horsfield, ST and Jia, B and Lacey, JA and Lee, HS and Lima, L and MacAlasdair, N and Mallawaarachchi, S and Matlock, W and Moustafa, AM and Petit, R and Ramnath, V and Raghuram, V and Russell, MJ and Sanderson, T and Saratto, T and Schwengers, O and Seemann, T and Shaw, LP and Shen, W and Thomson, N and Tonkin-Hill, G and Toussaint, J and Viet, TL and von Wachsmann, J and Wan, F and Weimann, A and Wheatley, RM and Wiatrak, M and Xie, O and de la Fuente-Nunez, C and Lees, JA and Iqbal, Z},
title = {AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42465405},
issn = {2692-8205},
abstract = {Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not uniformly assembled, quality controlled, annotated or searchable at scale. Here we present AllTheBacteria, an open, community-built resource that transforms public bacterial short-read whole-genome sequencing reads into a uniformly processed discovery platform. The current analysed release contains 2,440,377 high-quality bacterial and archaeal genomes from 11,273 species, together with standardized taxonomic assignments, genome annotations, antimicrobial resistance calls, antiphage-defence annotations, protein structure predictions and AI-ready sequence tables. We show that this infrastructure enables applications that would otherwise be impractical, from global sequence search and outbreak contextualization to pangenome method development, antimicrobial resistance reservoir mapping and antiphage-defence ecology. As a stringent experimental demonstration, we mined 3,919,096 encrypted peptide fragments from AllTheBacteria proteomes using our deep learning model APEX 1.1, identifying 1,867 candidates with predicted antimicrobial activity. We synthesized 24 representative peptides and tested them against 20 clinically relevant bacterial strains, including antibiotic-resistant pathogens. Multiple peptides showed low-micromolar activity, membrane-responsive conformational transitions and selective envelope perturbation. A lead molecule, ATB20, reduced Acinetobacter baumannii burden in a murine skin abscess model with efficacy comparable to polymyxin B and no overt toxicity. Together, these results establish AllTheBacteria as both a foundational community resource for microbiology and a renewable engine for AI-guided antimicrobial discovery.},
}
@article {pmid42098178,
year = {2026},
author = {Brant, CO and Silvis, S and Bennion, DH and Castiglione, C and Tyrrell, K and Hannahs, K and Slattery, M and Bunnell, D and Honsey, A and Tingley, R and King, K and Alofs, KM and Ackiss, A and Bronte, CR and Smith, J and Herbert, M},
title = {Two hundred years of historical spawning and nursery data for coregonine fishes in the Laurentian Great Lakes.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42098178},
issn = {2052-4463},
mesh = {*Salmonidae ; *Lakes ; *Conservation of Natural Resources ; Ecosystem ; Great Lakes Region ; Databases, Factual ; Species Specificity ; Animals ; },
abstract = {Historical data can provide critical ecological information for species across the globe, many of which are facing unprecedented rates of ecosystem change. Yet, historical information related to freshwater species, especially fishes, remains scattered, often in original formats, and underutilized for informing conservation and restoration activities. Here, we present a Data Descriptor called Coregonine Spawning History (CORHIST), a database designed to house diverse data related to past spawning and nursery areas for fishes in the family Salmonidae, subfamily Coregoninae (ciscoes and whitefishes), in the Laurentian Great Lakes and their tributaries. Data for 11 species of coregonines historically occurring in the Great Lakes are included in CORHIST. Over 3,400 occurrence records at the coordinate scale have been entered, over 2,200 of which are for Cisco (Coregonus artedi) and Lake Whitefish (C. clupeaformis)-two focal species for which there is either multinational conservation interest or restoration efforts underway in the Laurentian Great Lakes. CORHIST is already proving useful for several studies developing habitat suitability models and delineating spatial units for conservation or restoration planning.},
}
@article {pmid42364172,
year = {2026},
author = {Zhang, H and Liu, P and Chen, Y and Lv, J and Zhang, X and Zhang, J and Sun, Y and Wang, C and Wei, S and Wang, X and Gao, S and Qian, X and Jia, H and Tiedje, JM},
title = {Density-mediated freshwater plastisphere microbiomes preferentially degrade conventional rather than biodegradable microplastics.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag167},
pmid = {42364172},
issn = {1751-7370},
support = {2024ZY-JCYJ-02-25//Dryland Agriculture Shaanxi Laboratory Foundation/ ; 241111320200//Key R&amp;D projects in Henan Province/ ; 2025SF-YBXM-523//Key R&amp;D Program of Shaanxi Province/ ; 2024YFC3713900//National Key R&amp;D Program of China/ ; 42107434//National Natural Science Foundation of China/ ; 42477394//National Natural Science Foundation of China/ ; },
mesh = {*Microplastics/metabolism ; Biodegradation, Environmental ; *Fresh Water/microbiology ; Polyesters/metabolism ; *Microbiota ; *Bacteria/metabolism/classification/genetics ; *Polypropylenes/metabolism ; *Biodegradable Plastics/metabolism ; Biofilms/growth &amp; development ; Multiomics ; },
abstract = {The escalating demand for plastics leads to ubiquitous microplastic (MP) pollution worldwide. Existing evidence suggests that biodegradable MPs degrade faster than conventional MPs in aquatic environments. Here, we demonstrate the greater biodegradability of conventional polypropylene (PP) over biodegradable polylactic acid (PLA) in freshwater based on field survey, mesocosm experiment, co-culture assay, and multi-omics analysis. The biodegradation rate is 3.3-fold higher for PP compared to PLA, and this difference is more pronounced between photoaged MPs (5.7-fold). The unexpected superior biodegradability of PP is supported by a greater diversity of MP-degrading bacteria in PP biofilm (predominantly aerobes) than in PLA biofilm (mainly facultative and obligate anaerobes). The inferior biodegradability of PLA is attributed to microbial growth constraints in the plastisphere driven by oxic-to-hypoxic/anoxic transition, oxygen-containing functional group detachment from the polymer, and lactide accumulation during long-term biodegradation. Our findings reveal previously overlooked but important environmental fates and impacts of biodegradable plastics against increasing substitution of conventional plastics with biodegradable alternatives.},
}
@article {pmid42458931,
year = {2026},
author = {Vinay, KL and Goyal, N and Warudkar, A and Arvind, C and Robin, VV},
title = {Genome Assemblies for Seven Families of Birds From the Global South.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70162},
pmid = {42458931},
issn = {1755-0998},
support = {//Rohini Nilekani Philanthropies Foundation/ ; //Indian Institute of Science Education and Research Tirupati/ ; },
mesh = {Animals ; *Birds/genetics/classification ; *Genome ; India ; Sequence Analysis, DNA ; Computational Biology/methods ; Genomics/methods ; },
abstract = {Tropical regions are biodiversity-rich, yet remain underrepresented in the availability of genomic resources, as is evident in the Western Ghats of India, a biodiversity hotspot with high endemism. Here, we present high-quality, de novo genome assemblies for seven birds, representing seven families distributed in the Western Ghats: Black-naped Monarch (Monarchidae: Hypothymis azurea), Indian Yellow Tit (Paridae: Machlolophus aplonotus), Brown-cheeked Fulvetta (Leiothrichidae: Alcippe poioicephala), Malabar Trogon (Trogonidae: Harpactes fasciatus), Blue-bearded Bee-eater (Meropidae: Nyctyornis athertoni), Malabar Whistling-Thrush (Muscicapidae: Myophonus horsfieldii), Orange-headed Thrush (Turdidae: Geokichla citrina). Using a hybrid Oxford Nanopore long reads-Illumina short reads approach, we assembled genomes with sizes ranging from 1.03 to 1.13 Gbp. All assemblies demonstrated high contiguity and completeness (BUSCO scores > 97%, UCEs > 4799). Repeat masking identified ~10% of the genomes as interspersed repeats. Of the predicted protein-coding genes, an average of 9619 per species received high-confidence functional annotation hits. Comparative analysis showed our assemblies had significantly higher contiguity than the median of existing avian genomes on NCBI (Wilcoxon test, p = 0.00226). Our genome assemblies fill a key geographic and taxonomic gap in the genomic data and provide a foundational resource for evolutionary and ecological research in the Old-World tropics.},
}
@article {pmid42459996,
year = {2026},
author = {Filippova, N and Bulyonkova, TM and Zvyagina, E and Ageev, D and Rudykina, E and Mingalimova, A},
title = {Cortinarius barcoding database of Western Siberia and adjacent areas.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e196734},
pmid = {42459996},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Cortinarius (Pers.) Grays. is a highly diverse and ecologically crucial group of ectomycorrhizal fungi in boreal forests. Despite a long history of mycological study in Russia, a comprehensive, molecularly validated inventory of its diversity in Western Siberia has been lacking. Global genetic resources are essential for modern fungal research, yet such a curated, regional dataset for this complex genus has not been previously available for this region.<br><br>NEW INFORMATION: This paper describes a curated database of 624 Cortinarius specimens from Western Siberia and adjacent regions, resulting in 624 high-quality ITS sequences. The dataset includes detailed collection metadata, morphological descriptions and photographic documentation, all standardised and linked to DNA sequence data originally managed in Specify 7. The sequences were processed through a rigorous bioinformatics pipeline with strict quality controls and assigned provisional taxonomy using a defined BLAST protocol against international reference databases. The complete dataset, including raw sequences, specimen data and collection images, has been deposited in international repositories (Global Biodiversity Information Facility (GBIF) (https://doi.org/10.15468/4v8km8), Sequence Reads Archive (SRA) and GenBank), providing a foundational resource for future taxonomic, phylogenetic and ecological studies on this key fungal genus in Western Siberia.},
}
@article {pmid42460566,
year = {2026},
author = {Mortazavi, S and Alazaiza, MYD and Nikolova, MP and Naeijian, F and Choi, H and Sillanpää, M},
title = {Review on magnetic chitosan nanomaterials as sustainable adsorbents for water pollution control.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {94},
number = {1},
pages = {198-214},
pmid = {42460566},
issn = {0273-1223},
support = {BG16RFPR002-1.014-0004//Centre of Excellence "Universities for Science, Informatics and Technologies in e-Society" (UNITe), funded by the Ministry of Innovation and Growth of the Republic of Bulgaria under the Program "Research, Innovation and Digitalization for Smart Transformation" (PRIDST) and co-funded by the European Union through the ERDF/ ; },
mesh = {*Chitosan/chemistry ; Adsorption ; *Water Purification/methods ; Water Pollutants, Chemical/chemistry ; *Water Pollution/prevention &amp; control ; *Nanostructures/chemistry ; Magnetics ; },
abstract = {Adsorption stands out for its simplicity, cost-effectiveness, and high efficiency in removing a wide range of contaminants. However, traditional adsorbents often suffer from limited capacity, selectivity, and reusability. In response to these limitations, a significant research effort has recently focused on developing magnetic chitosan nanomaterials (MCNMs), which combine the inherent biodegradability and biocompatibility of chitosan with magnetic responsiveness for easy separation and reusability. Previous articles reviewed general MCNMs, primarily focusing on their adsorption mechanisms and performance in removing specific pollutants. This review comprehensively discusses recent advances in nanoscale modification of the materials and their applications for enhanced treatment of water containing various heavy metals and pharmaceuticals. A detailed comparison is provided between conventional chitosan materials and their magnetic nano-engineered counterparts (MCNMs), emphasizing improvements in adsorption capacity, kinetics, and regeneration potential. This review also highlights key factors that govern adsorption efficacy, such as pH, surface modification, and pollutant type. By reviewing current trends and challenges in the field, this work aims to guide future research toward the design of more efficient and sustainable water treatment systems, offering a forward-looking perspective on the potential of MCNMs for real-world water and wastewater treatment applications.},
}
@article {pmid42429454,
year = {2026},
author = {Di Leo, D and Nilsson, E and Westmeijer, G and Pinhassi, J and Lundin, D},
title = {nf-core/magmap: Map metatranscriptomes to large collections of genomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {7},
pages = {},
doi = {10.1093/bioinformatics/btag501},
pmid = {42429454},
issn = {1367-4811},
support = {//Linnaeus University/ ; 2019-00242//Swedish Research Council VR Swedish Biodiversity Data Infrastructure (SBDI)/ ; 2023-00184//Swedish Research Council VR Swedish Biodiversity Data Infrastructure (SBDI)/ ; 2023-03401//Swedish Research Council VR/ ; //Swedish strong research environment EcoChange/ ; 23-0228//Kempe Foundation/ ; //National Academic Infrastructure for Supercomputing in Sweden (NAISS)/ ; 2025/22-936//NAISS/ ; 2025/6-241, NAISS 2025/22-489//NAISS/ ; 2025/23-189//NAISS/ ; 2022-06725//Swedish Research Council/ ; },
mesh = {*Software ; *Metagenomics/methods ; *Chromosome Mapping/methods ; *Genome ; Databases, Genetic ; *Metagenome ; },
abstract = {SUMMARY: The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes.<br><br>The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).},
}
@article {pmid42424959,
year = {2026},
author = {Khan, S and Zeb, A and Ullah, K and Shi, R and Zhao, Y and Tariq, H and Baig, AM and Li, X and Iqbal, H and Hussain, S and Wu, Z and Liu, W},
title = {Unraveling jasmonic acid-mediated mitigation of 6PPD toxicity in tomato plants using multi-omics approaches.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142926},
doi = {10.1016/j.jhazmat.2026.142926},
pmid = {42424959},
issn = {1873-3336},
mesh = {*Cyclopentanes/pharmacology ; *Oxylipins/pharmacology ; *Solanum lycopersicum/drug effects/metabolism/genetics/growth &amp; development ; Multiomics ; Metabolomics ; Molecular Docking Simulation ; Oxidative Stress/drug effects ; *Plant Growth Regulators/pharmacology ; Photosynthesis/drug effects ; },
abstract = {The widespread application of the tire antioxidant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) has driven the pervasive environmental occurrence of its toxic quinone transformation product, 6PPD-quinone, raising significant ecological concerns and necessitating effective mitigation strategies. However, despite the widespread use of external biomass-based remediation strategies for environmental cleanup, internal physiological mitigation approaches to alleviate 6PPD induced phytotoxicity in plants are still lacking. Herein, we establish a multi-level phytoprotection framework, investigating the protective role of foliar-applied jasmonic acid (JA) against 6PPD toxicity in tomato plants through the integration of physiological assessments, multi omics (transcriptomics and metabolomics) analyses and molecular docking simulation. Physiological results revealed that 6PPD exposure triggered severe oxidative stress, inhibiting plant growth and impairing photosynthetic functions. Exogenous JA application effectively mitigated these adverse effects and restored physiological homeostasis. Integrated omics analyses revealed that JA mediated a comprehensive reprogramming of the plant's metabolic and transcriptional landscape to counteract 6PPD toxicity. Specifically, JA redirected metabolic flux by enhancing carbohydrate metabolism to fuel defense responses, while transcriptionally reallocating resources from growth-related processes toward the activation of specialized metabolic pathways, particularly flavonoid biosynthesis. Molecular docking further demonstrated that JA possessed a high binding affinity for key enzymes (e.g., chalcone synthase) in the flavonoid biosynthesis pathway, providing a mechanistic basis for its regulatory role. These findings highlight a promising internal defense strategy, warranting further validation under field conditions and across a broader range of crops and organic contaminants.},
}
@article {pmid42452269,
year = {2026},
author = {Pieroni, A and Alrhmoun, M and Ullah, I and Hajdari, A and Bajrami, A and Kalle, R and Sulaiman, N and Sõukand, R},
title = {Continuity and Change in the Arbëreshë Wild Food Plant Foraging in Inland Southern Italy.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
pmid = {42452269},
issn = {2223-7747},
abstract = {This study investigates the ethnobiology of wild food plants in Arbëreshë (Albanian-speaking) and neighbouring Calabrian communities in north-eastern Calabria, inland southern Italy. It examines how traditional ecological knowledge, plant use patterns, and cultural perceptions are represented across two datasets, contributing to the understanding of biocultural dynamics in Mediterranean rural contexts. Fieldwork was conducted through forty-six semi-structured interviews in five villages in north-eastern Calabria, Southern Italy. Data were compared with an ethnobotanical dataset collected in the Vulture area (northern Lucania, southern Italy) during 2000-2001. The comparison is treated as cross-spatial and diachronic at the level of observed ethnobotanical records. Because the study areas differ in ecological and socio-economic conditions, comparisons are presented as descriptive contrasts rather than as direct temporal change. Taxa were classified by citation frequency, and comparisons were conducted at genus level to describe patterns of presence and variation in reported wild plant use. A total of 82 wild food taxa were documented. The dataset was dominated by vascular plants, with frequent representation of the families Asteraceae, Brassicaceae, Apiaceae, and Lamiaceae. Arbëreshë participants reported 60 genera, including seven genera not recorded in the comparative dataset (Asphodeline, Pimpinella, Hirschfeldia, Silene, Bellevalia, Leontodon, and Crocus). Calabrian participants reported 28 genera, including three not recorded among Arbëreshë participants (Clinopodium, Suillus, and Urospermum). Twenty-one genera were present in both datasets. Differences in citation frequency and genus composition are observed between datasets, with variation across groups and contexts. The results show a shared set of commonly reported wild food taxa across datasets, alongside variation in less frequently reported genera. The findings describe differences in ethnobotanical records across communities and time-separated datasets, reflecting combined influences of ecological context, sampling conditions, and local knowledge practices.},
}
@article {pmid42455829,
year = {2026},
author = {Calahorro, F and Fouladi, P and Pandini, A and Khushi, M and Gaihre, Y and Bury, NR},
title = {Binding Affinity Ranking at the Molecular Initiating Event (BARMIE): An open-source computational pipeline for the rapid screening of chemical interactions with steroid receptors from many species.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0353622},
pmid = {42455829},
issn = {1932-6203},
mesh = {Animals ; *Receptors, Glucocorticoid/metabolism/chemistry ; Protein Binding ; Ligands ; *Receptors, Steroid/metabolism/chemistry ; Hydrocortisone/metabolism/chemistry ; Oncorhynchus mykiss/metabolism ; Binding Sites ; Glucocorticoids/metabolism/chemistry ; *Computational Biology/methods ; Computer Simulation ; Fishes/metabolism ; },
abstract = {A challenge in ecological risk assessment is identifying the chemicals that pose the greatest threat and determining which species are most vulnerable to them. To help address this, this study has developed an in-silico open-source tool called BARMIE (Binding Affinity Ranking at the Molecular Initiating Event) to rapidly predict the chemical binding affinity of steroid receptor proteins to synthetic steroids to identify potentially vulnerable species and chemicals of concern. BARMIE was used to screen 163 teleost fish glucocorticoid receptors (GRs) for binding to the natural ligand cortisol and to 10 synthetic glucocorticoid drugs (GCs) designed to interact within the ligand-binding pocket (LBP) of GRs. BARMIE identified species from the superorder Protacanthopterygii with high-affinity GRs to synthetic GCs (e.g., vulnerable species).. BARMIE was also used to screen binding profiles of compounds in the Medicine for Malaria Venture Global Health Priority Box to rainbow trout GRs (rtGR1 and rtGR2). Of the 178 compounds, 24 and 36 bind within the LBP of rtGR1 and rtGR2, respectively. For 30 of these compounds, transactivation activity was assessed at 1µM in the presence or absence of 1µM cortisol and confirmed 2 compounds with agonistic properties (e.g., chemicals of concern) that would require further in vitro and/or in vivo studies to assess the environmental risk. BARMIE can rapidly generate predicted binding affinities for 100's of species and chemicals as a first screen in environmental risk assessment to provide information on which substances to prioritise in downstream tests.},
}
@article {pmid42457409,
year = {2026},
author = {Liang, LW and Fatimah, A and Qian, Q and Zhang, T and Wang, XY and Zhang, FY and Xiao, Q and Guo, ZG and Jiang, AL and Zhao, XY and Wu, XG and Du, MX and Yu, JY and Liu, HC and Chen, YH and Jiang, JP and Liao, ZY},
title = {Global Camera Trapping Inventory (GCTI) v.1.0: A worldwide inventory of camera-trapping studies for spatial biodiversity analysis.},
journal = {Zoological research},
volume = {47},
number = {4},
pages = {1097-1105},
doi = {10.24272/j.issn.2095-8137.2025.340},
pmid = {42457409},
issn = {2095-8137},
mesh = {*Biodiversity ; Animals ; *Photography ; Conservation of Natural Resources/methods ; *Databases, Factual ; },
abstract = {Camera traps have significantly advanced biodiversity monitoring by enabling standardized, noninvasive detection of medium- and large-sized wildlife across broad spatial scales. However, the lack of data sharing within the camera-trapping community, particularly during the early development of the field, has restricted the availability of public species-occurrence records and limited the integration of camera-trap evidence into global spatial analyses. Data sensitivity, especially for threatened species, has further constrained open access to study-level geographic records. To address this gap, the Global Camera Trapping Inventory (GCTI) v.1.0 was developed to compile project-level spatial information from 970 camera-trapping studies indexed in the Web of Science (WoS) and China National Knowledge Infrastructure (CNKI) between 1990 and 2023. The database includes an Excel file with 22 fields documenting study design, survey methods, recorded taxa, and associated metadata, together with three shapefile formats that capture geographic information at complementary spatial resolutions. The GCTI database was established to strengthen open, collaborative data sharing in biodiversity monitoring while preserving the spatial structure needed for research synthesis. By providing project-level shapefiles linked to specific regions and species, GCTI offers a spatially explicit resource for biodiversity, conservation, ecology, and biogeography research. Compared with existing platforms such as Wildlife Insights and eMammal, GCTI provides data suitable for meta-analyses, literature reviews, and spatial overlap analyses with global biodiversity resources, such as GBIF and the IUCN Red List. To facilitate data access and application, an interactive web platform was developed to enable online searching, visualization, and download (https://biodiversityoptimization.shinyapps.io/gcti_v1/).},
}
@article {pmid42151184,
year = {2026},
author = {Ma, F and Huang, H and Yang, Q and Altermatt, F and Hong, P and Luo, M and Wang, S},
title = {Biodiversity and habitat complexity buffer the destabilizing effects of anthropogenic activities on riverine fish communities.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42151184},
issn = {2041-1723},
support = {32588202//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32425036//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32301349//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Humans ; *Anthropogenic Effects ; *Biodiversity ; Datasets as Topic ; *Fishes ; Latent Class Analysis ; Population Dynamics ; *Rivers ; Spatial Analysis ; Temperature ; Conservation of Natural Resources ; },
abstract = {Riverine fish communities are essential for the functioning of aquatic ecosystems and provide important ecosystem services for fisheries. Yet, anthropogenic environmental changes pose threats to fish communities and result in population collapses and reduced yields, underscoring the need to understand their stability from local to regional scales. In this study, we leverage long-term observational data of riverine fish communities in 108 hydrological basins across the globe to determine how anthropogenic activity, biodiversity, and habitat complexity jointly influence riverine fish community stability (i.e., temporal invariability of total fish abundance) at the site and basin scales. Our analyses show that anthropogenic activities represented by human footprint index decrease fish community stability across spatial scales; however, biodiversity and habitat complexity buffer these destabilizing effects by providing insurance effects at both site and basin scales. Specifically, biodiversity has consistently stabilizing effects across scales through enhancing the asynchrony within and/or among fish communities. At the basin scale, greater habitat area increases gamma stability by enhancing spatial community asynchrony. Our findings underscore the importance of conserving both fish biodiversity and habitat complexity to sustain the stability of riverine fish communities in the Anthropocene.},
}
@article {pmid42364396,
year = {2026},
author = {Wang, LM and Montanari, A and Gal, N and Chaix, B and Birenboim, A},
title = {Temporal patterns of smartphone-mediated digital engagement and mental health symptomatology.},
journal = {Acta psychologica},
volume = {268},
number = {},
pages = {107259},
doi = {10.1016/j.actpsy.2026.107259},
pmid = {42364396},
issn = {1873-6297},
mesh = {Humans ; *Smartphone/statistics &amp; numerical data ; Female ; Male ; *Anxiety/psychology ; Adult ; *Depression/psychology ; Ecological Momentary Assessment ; Digital Media ; Young Adult ; Middle Aged ; Media Exposure ; Time Factors ; Digital Health ; Mental Health ; },
abstract = {Current ubiquitous information and communication technologies are reshaping human behaviours and could have profound implications for mental health. To investigate the dynamic patterns of daily interactions with the digital environment-particularly via smartphones-a novel, ecological approach is implemented which incorporates the use of innovative sensors. Data was collected from 31 healthy individuals from the general population living in Jerusalem who were tracked using objective smartphone logs of digital activity and daily self-reports of anxiety and depression symptoms. Significant associations were found between temporal patterns of smartphone usage and momentary anxiety symptomatology. Higher levels of overall phone usage in the morning hours were a significant predictor of anxiety while high levels of phone usage in the rest of the day were associated with decreased anxiety symptoms. A more nuanced analysis of usage types revealed that high levels of social and process-related digital activity in the morning were associated with a reduction in anxiety symptoms, with evidence of a dose-response relationship. These findings highlight the importance of context, user motivation, and the complex relationship between smartphone usage and mental health which warrant further research.},
}
@article {pmid42449219,
year = {2026},
author = {Qu, S and Xu-Ri, and Yu, J and Shama, R and Lei, H and Tian-Liang, and Bayarsaikhan, S and Jukov, A and Tsendeekhuu, M and Vanjil, G and Borjigidai, A},
title = {Climatic controls on water-use efficiency and nitrogen acquisition of Astragalus on southwestern Tibetan Plateau.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09356-2},
pmid = {42449219},
issn = {1471-2229},
support = {U21A20185//National Natural Science Foundation of China/ ; 2019QZKK0606//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2022YFE0119300//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: The southwestern Tibetan Plateau (TP) is characterized by cold and dry alpine grasslands, yet how plants and soil nitrogen cycles adapt to conditions that are drier and colder than other parts of the TP remain unclear. We measured δ[13]C and δ[15]N in Astragalus, a widespread N-fixing legume, and soils along a 3500-5000 m transect in the southwestern TP.<br><br>RESULTS: Plant &#x3b4;[13]C and inferred intrinsic water-use efficiency (iWUE, 85.6-114.2&#xa0;&#x3bc;mol CO2 mol[-1] H2O) were primarily controlled by growing-season temperature (GST), with SEM showing a significant direct effect of GST on iWUE (standardized path coefficient&#x2009;=&#x2009;0.45, p&#x2009;<&#x2009;0.01). Conversely, soil &#x3b4;[15]N (2.8&#x2030; to 11.3&#x2030;) was negatively associated with mean annual precipitation (MAP; R[2]&#x2009;=&#x2009;0.26, p&#x2009;<&#x2009;0.01), while plant-soil &#x394;[15]N was mainly driven by mean annual precipitation (MAP, R[2]&#x2009;=&#x2009;0.24, p&#x2009;<&#x2009;0.01). These &#x394;[15]N patterns may reflect shifts in the relative contribution of atmospheric N2 fixation and soil N uptake by Astragalus, as inferred from isotopic evidence.<br><br>CONCLUSIONS: These results suggest potential responses of plant carbon-water coupling and isotope-inferred N acquisition under future warming and drying in high-elevation ecosystems.},
}
@article {pmid42451887,
year = {2026},
author = {Matyjas-Zgondek, E and Kulpiński, P and Skiba, E and Popczyk, M and Swinarew, AS},
title = {Long-Lasting Photocatalytic and Antimicrobial Activity of Cotton Dishcloths Finished with TiO2 Nanoparticles and Zinc Pyrithione.},
journal = {Materials (Basel, Switzerland)},
volume = {19},
number = {13},
pages = {},
pmid = {42451887},
issn = {1996-1944},
abstract = {This study assesses the durability of self-cleaning and antimicrobial activities of dishcloths made of 100% cotton woven fabric modified with TiO2 nanoparticles (NPs) and zinc pyrithione particles (ZnPt). The self-cleaning properties were measured as the ability to decompose staining particles via photocatalytic action under UV/VIS light irradiation and confirmed by colour measurements (K/S values, colour differences, and colour changes ΔL*, Δa*, Δb*). The SEM micrographs confirmed the long-term durability of the modification process, and ICP-OES analysis confirmed the presence of Ti and Zn elements on and within the fabric. The amounts of TiO2 and ZnPt decreased by 2.2-2.5 times after the first 5 washings and by 2.1-1.2 times after the subsequent 45 washings. Antimicrobial activity was tested against Staphylococcus aureus ATCC 6538, Escherichia coli ATCC 11229 and Candida albicans ATCC 10231. The results indicate that the material maintains excellent self-cleaning properties and good antimicrobial activity for up to 50 washings; however, activity against E. coli remains weak after 30 and 50 washings.},
}
@article {pmid41678595,
year = {2026},
author = {Davis, KP and Eaton, MJ and Bjerre, ER and White, HM and Boal, CW and Herner-Thogmartin, JH and Robinson, OJ and Lawson, AJ},
title = {Constructed value of information with iterative scoring and parametric uncertainty to identify management-relevant research priorities for a declining raptor species.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {40},
number = {4},
pages = {e70227},
pmid = {41678595},
issn = {1523-1739},
support = {G22AC00121//U.S. Geological Survey/U.S. Fish and Wildlife Service Science Support Partnership Program/ ; },
mesh = {Animals ; *Conservation of Natural Resources/methods ; Uncertainty ; *Falconiformes/physiology ; *Decision Support Techniques ; Population Dynamics ; },
abstract = {Constructed value of information (CVoI) is an expert elicitation decision-analytic tool used to prioritize sources of uncertainty based on their potential to improve decision outcomes if resolved. Despite increased application of CVoI, the robustness of CVoI prioritization of sources of uncertainty relative to differences in expert elicitation and scoring methods has not been evaluated. We engaged a group of species experts in a decision-analytic process to elicit uncertainties, framed as alternative hypotheses, about current population declines of the American kestrel (Falco sparverius) in the United States. Participants scored 13 hypotheses across 3 CVoI criteria, which are defined as constructed scales. Rather than experts selecting a single score per criterion, we used a likelihood point method to incorporate parametric uncertainty in the scoring process, in which experts were given 100 points to distribute across possible score categories within the criterion-specific constructed scale. Experts provided scores over 2 scoring rounds, with an opportunity to review and discuss initial scores between rounds. We used a Shannon entropy calculation to quantify how evenly participants allotted their points. We used simulation to evaluate the robustness of our prioritization results relative to a scoring method in which participants selected a single score category for each criterion. Participants often spread their points across 2 adjacent scores, reflecting parametric uncertainty. For one third of the hypothesis-scoring round combinations, the prioritization results differed in approximately 50% of simulations. The highest scoring hypotheses related to how the use of artificial versus natural nest cavities affects fecundity or survival, whether winter roosting sites are a limiting factor for population growth, and whether gamebird habitat management may benefit kestrel populations. Our CVoI prioritization framework can be used to develop collaborative research that is directly relevant to a management decision and is an advance in eliciting more representative expert beliefs.},
}
@article {pmid41814567,
year = {2026},
author = {Pelage, L and Brunel, A and Fache, E and Frédou, T and Lanco, S and Lucena-Frédou, F and Bertrand, A},
title = {Guiding stakeholder negotiations in data-poor coastal planning with open-access spatial data.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {40},
number = {4},
pages = {e70248},
pmid = {41814567},
issn = {1523-1739},
support = {734271//Horizon 2020/ ; },
mesh = {*Conservation of Natural Resources/methods ; Brazil ; Fisheries ; *Negotiating ; *Ecosystem ; Tourism ; Decision Support Techniques ; Satellite Imagery ; },
abstract = {Negotiating conservation priorities in highly anthropic ecosystems requires approaches that promote cooperation and cost bargaining among stakeholders. In data-poor contexts, such negotiations are hindered by limited information and conflicting interests. We developed a transparent and reproducible prioritization framework, combining open-access satellite imagery with a decision-support tool, to inform participatory coastal planning. Although illustrated in northeast Brazil, a data-poor region where coastal conflicts between tourism and fisheries are acute, the framework was designed to be broadly applicable to similar coastal social-ecological systems. It generates visualizations that help stakeholders explore trade-offs in three dimensions: defining a conservation target; debating the location of coastal candidate areas that balance habitat protection with minimizing impacts on tourism and fishing activities; and deliberating the degree of restriction within each candidate area based on conservation and socioeconomic considerations. We applied this approach to design five alternative spatial planning scenarios. Three were based on composite tourism and fisheries indices ("neutral", "avoid fisheries areas", and "avoid tourism areas"), and two focused on specific practices ("all specific activities" and "do not exclude small-scale"). These scenarios revealed where restrictions can be applied or relaxed to achieve conservation objectives while maintaining essential local livelihoods. By highlighting the limitations of existing conservation units and promoting inclusive, transparent decision-making, our method provides a practical means to focus stakeholder negotiations. More broadly, the framework offers a scalable and transferable approach for equitable, multisectoral conservation planning in other data-poor coastal regions facing similar trade-offs.},
}
@article {pmid42349033,
year = {2026},
author = {Cárdenas-Conejo, Y},
title = {GenomoBase: A comprehensive resource for the family Genomoviridae.},
journal = {Virology},
volume = {623},
number = {},
pages = {111018},
doi = {10.1016/j.virol.2026.111018},
pmid = {42349033},
issn = {1096-0341},
mesh = {*DNA Viruses/genetics/classification/isolation &amp; purification ; *Genome, Viral ; Metagenomics ; Animals ; Metagenome ; *Databases, Genetic ; Phylogeny ; },
abstract = {The family Genomoviridae comprises circular single-stranded DNA viruses reported from fungi, plants, animals and environmental samples. Although metagenomics has accelerated their discovery, genomic sequences, annotations and metadata remain dispersed across repositories. Here we present GenomoBase (https://www.genomobase.org), a curated resource that integrates genomic, ecological and bibliographic data for all 237 ICTV-recognized genomovirus species. GenomoBase incorporates Serratus-filtered SRA screening outputs, enabling prioritization of metagenomes for targeted re-analysis. As a proof of concept, a targeted bait-and-assemble workflow of one prioritized SRA run reconstructed two candidate complete circular genomovirus genomes from metagenomic reads, both below the 78% species demarcation threshold for genomoviruses. Overall, GenomoBase supports comparative analyses and taxonomically informed exploration of public metagenomes.},
}
@article {pmid42442356,
year = {2026},
author = {Nguyen, TN and Cosgrove, EJ and Chen, N and Lehr, N and Lokey, MG and Beaudry, FEG and Fitzpatrick, SW and Bowman, R and Miller, KE and Fitzpatrick, JW and Clark, AG},
title = {Florida scrub-jay genomes across space and time reveal impacts of population decline and reduced gene flow.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.06.044},
pmid = {42442356},
issn = {1879-0445},
abstract = {Whole-genome sequencing is proving to be highly informative about the past demography of free-living populations, and in the context of endangered species, it can provide a quantification of the genetic risk posed by reduced genetic diversity and inbreeding. Prior to 1920, the Florida scrub-jay (Aphelocoma coerulescens) was more numerous across peninsular Florida, but with the expansion of agriculture and human habitation, its population has declined by 95%, resulting in fragmentation into semi-isolated subpopulations. By sequencing 241 individuals sampled from five different regions and across two time points, this study quantifies a greater loss of genetic diversity and greater levels of inbreeding in smaller and more isolated subpopulations. Consistent with population genetics theory, a reduction in population size results in a dramatic loss of rare alleles, skewing the site frequency spectrum far from the expected equilibrium. Increased inbreeding in the smaller, more remote subpopulations is especially evident in the increased size and number of runs of homozygosity. The Florida scrub-jay displays limited dispersal, and habitat fragmentation has greatly reduced the magnitude of gene flow in the past 30 years, resulting in further decline of genetic diversity, especially in the peripheral populations. Analysis of these data is informative in guiding conservation efforts to retain genetic diversity and minimize the consequences of inbreeding in the Florida scrub-jay.},
}
@article {pmid42443342,
year = {2026},
author = {Zhuang, Y and He, G and Xi, W and Zhang, J and Wang, R and Jin, T and Zhu, Y and Fu, J},
title = {Environmental space similarity model maps dry red soil under limited samples in the Yuanmou Dry Hot Valley.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61912-w},
pmid = {42443342},
issn = {2045-2322},
support = {202304BT090025-04//Yunnan Provincial Science and Technology Department, Yunnan Innovation Guidance and Cultivation Program for Science and Technology Enterprises - "Building Yuanmou County as a Science and Technology Innovation County for Rural Revitalization" Project/ ; 202205AK070026-01//Yunnan Key Laboratory of Soil Erosion Prevention and Green Development/ ; 202202AD080010//Major scientific and technological projects of Yunnan Province: Research on Key Technologies of ecological environment monitoring and intelligent management of natural resources in Yunnan/ ; KLMHER-K25//Supported by "the Open Funds of the Key Laboratory of Mountain Hazards and Engineering Resilience, Chinese Academy of Sciences"/ ; 202305AS350003//Yunnan Province Innovation Team Project/ ; },
abstract = {Obtaining sufficient field observations for natural resources in complex mountainous environments is often constrained by limited soil samples. Geographic environmental similarity may provide a useful basis for spatial inference under small-sample conditions. Here we infer the spatial distribution of dry-red soil in the Yuanmou Dry-Hot Valley, China. Field surveys produced a training set (n = 72) and an independent validation set (n = 46; dry-red soil/non-dry-red soil = 1:1). After screening covariates related to soil, terrain, climate, and vegetation, we quantified environmental similarity among samples and computed a composite similarity score. Using stratified repeated random splitting on the independent validation set, we calibrated the classification threshold, built an Environmental Similarity Model (ESM), and generated an uncertainty layer for interpretation and extrapolation-risk identification. Results show that (1) dry-red soil is mainly distributed in basins and valley areas; (2) the ESM showed relatively strong performance on the independent validation set within the present study area (mean AUC = 0.946, Accuracy = 0.867, Recall = 0.870, F1-score = 0.862), exceeding the benchmark machine-learning models under the current validation design (mean AUC = 0.654-0.809, Accuracy = 0.589-0.707); and (3) the uncertainty layer identifies environmentally under-represented areas with higher extrapolation risk, which may support prioritized supplementary sampling and iterative updating. Overall, these results suggest that the ESM provides an interpretable option for dry-red soil inference under the present small-sample and heterogeneous environmental setting.},
}
@article {pmid42443631,
year = {2026},
author = {Flannery, JL and Engelhard, MM and Kansagra, S and Kollins, SH and Krystal, A and Lunsford-Avery, JR},
title = {Leveraging convenient wearable technology to assess adolescent sleep: physical and behavioral health correlates of single-channel sleep electroencephalogram in a community sample of youth.},
journal = {Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine},
volume = {22},
number = {1},
pages = {},
pmid = {42443631},
issn = {1550-9397},
support = {5T32-MH132515-02//National Institute of Health Sciences/ ; },
mesh = {Humans ; Female ; Adolescent ; Male ; *Electroencephalography/instrumentation/methods ; *Wearable Electronic Devices ; Child ; *Sleep Wake Disorders/diagnosis/physiopathology ; Sleep Duration ; Digital Health ; },
abstract = {STUDY OBJECTIVES: Sleep disturbances during adolescence heighten risk for physical and behavioral health problems, yet sleep physiological markers critical to health outcomes are rarely assessed in pediatric care. Wearable single-channel electroencephalography (EEG) devices may offer scalable, ecologically valid methods for assessing sleep physiology in home settings. This study evaluated whether single-channel sleep-EEG metrics were associated with physical and behavioral health in adolescents.<br><br>METHODS: Eighty-five community-derived adolescents (ages 11-17, 50% female) completed seven consecutive nights of at-home, single-channel sleep-EEG, physical health assessments (i.e., body mass index and blood pressure), and subjective sleep and behavioral health measures. Parents provided psychiatric diagnosis history.<br><br>RESULTS: Odds of being overweight/obese decreased with greater REM duration (-&#x2009;2.72% per minute) and higher REM percentage (-&#x2009;100% per 1%). Odds of hypertension decreased with greater time spent in stage 3 (N3) (-&#x2009;4.78% per minute). Multivariate analyses showed reduced N3 sleep was associated with parent-reported ADHD symptoms, whereas shorter total sleep time, lower sleep efficiency (SE), and longer sleep onset latency (SOL) were associated with higher adolescent-reported ADHD and conduct problems (p's&#x2009;<&#x2009;.05). Odds of an ADHD diagnosis increased with longer SOL (+&#x2009;1.92% per minute) and slower N3 decline (+&#x2009;89.4% per 0.01 units) but decreased with higher SE (-&#x2009;7.78% per 1%). Odds of an internalizing disorder increased with higher SE (+&#x2009;12.4% per 1%) and greater wake after sleep onset (+&#x2009;3.18% per minute), but decreased with more REM sleep (-&#x2009;9.62% per minute).<br><br>CONCLUSIONS: Findings highlight the clinical value of wearable sleep-EEG for detecting sleep-related risk processes during adolescence. By capturing physiological features not accessible through self-report, at-home sleep-EEG may flag youth who could benefit from sleep-focused interventions, complementing routine care in identifying risk of future health problems. Integrating such tools into pediatric settings could support more precise, developmentally informed approaches to prevention and intervention.<br><br>CURRENT STUDY/STUDY RATIONALE: Sleep disturbances are common during adolescence and increase risk for physical conditions such as obesity and hypertension, as well as behavioral health problems, yet sleep physiology is rarely adequately assessed in pediatric care. Wearable single-channel EEG offers an accessible way to capture sleep architecture and continuity that subjective reports cannot provide. This study shows that EEG-derived sleep features, including REM, N3 sleep, sleep efficiency, and sleep-onset latency, are associated with physical and behavioral health outcomes above and beyond adolescent and caregiver reports.<br><br>STUDY IMPACT: These findings highlight the potential value of integrating wearable EEG into routine care to identify sleep-related vulnerabilities and support targeted prevention efforts.},
}
@article {pmid42445293,
year = {2026},
author = {Jo, TS and Murakami, H},
title = {Variability in Fish Environmental DNA Concentration in Coastal Ecosystems at Hierarchical Levels: Focusing on the Magnitude, Structure, and Environmental Dependence.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e74002},
pmid = {42445293},
issn = {2045-7758},
abstract = {Understanding variability in environmental DNA (eDNA) concentration is essential for improving the precision of quantitative eDNA analyses. While previous laboratory and field studies suggest that technical variation arising from sampling and PCR processes is relatively small, the hierarchical structure of this variability and its environmental dependence remain poorly understood. In this study, we conducted spatiotemporally replicated seawater sampling from a coastal ecosystem, quantified Japanese jack mackerel (Trachurus japonicus) eDNA concentrations using quantitative real-time PCR (qPCR), and assessed the magnitude, structure, and environmental drivers of eDNA variability across multiple levels. Variance component analysis revealed that more than 90% of the total variance in eDNA concentration was explained by differences among sampling sites and time points, reflecting differences in organismal distribution and dynamics, whereas sampling and PCR steps together contributed less than 10%. Using Taylor's Power Law, we demonstrated that the relationship between mean eDNA concentration and variance differed across hierarchical levels, with stronger mean-variance scaling at larger spatial and temporal scales. Notably, the relative contribution of the PCR level to the total variance increased substantially under low-concentration conditions, indicating that stochastic measurement error becomes dominant when eDNA is scarce. We also demonstrated that the PCR-level variability (Coefficient of variance; CV) increased with chlorophyll-α and decreased with pH, whereas no significant environmental effects were detected at the sample level. These results suggest that different mechanisms govern variability at each hierarchical level, including ecological processes, physical heterogeneity, and biochemical constraints. Our findings highlight that optimal sampling and replication strategies should be tailored to expected eDNA concentrations and environmental conditions in the field, helping provide a framework for maximizing signal-to-noise ratios in quantitative eDNA studies.},
}
@article {pmid41933506,
year = {2026},
author = {Qiu, CW and Zhang, S and Gao, ZF and Chen, ZH and Zhang, C and Ali, MA and Wu, F},
title = {First Tetraploa Genome and Multi-Omics Analysis Reveal Key Plant-Microbe-Soil Interactions for Salt Tolerance and Yield Improvement of Wheat.},
journal = {Plant biotechnology journal},
volume = {24},
number = {8},
pages = {4748-4765},
pmid = {41933506},
issn = {1467-7652},
support = {32161143035//National Natural Science Foundation of China/ ; BP0618021//the 111 Project of China/ ; FT210100366//Australian Research Council/ ; WSU2303-001RTX//Grains Research and Development Corporation/ ; },
mesh = {*Triticum/microbiology/growth &amp; development/genetics/physiology/metabolism ; *Salt Tolerance/genetics ; Multiomics ; Rhizosphere ; Soil Microbiology ; *Genome, Fungal ; },
abstract = {Salinity is a major threat to global agricultural productivity of staple crops such as wheat. Although microbial-based solutions hold promise for alleviating salinity stress, practical implementation is hindered by insufficient mechanistic characterization of bioinoculants and their interactions with plants. Here, we assembled the first complete reference genome of a halotolerant strain within the genus Tetraploa-the endophytic fungus Tetraploa sp. E00680. This novel genomic resource serves as a foundation for exploring previously uncharacterised salt tolerance mechanisms in this potential fungal inoculant. Our research demonstrates that E00680 enhances wheat yield under both controlled and field saline conditions. We found that E00680 systematically modulates the plant-microbe-soil interactions by optimizing rhizosphere microbial communities, increasing nutrient bioavailability, and triggering coordinated transcriptional and metabolic reprogramming in wheat. Notably, E00680 expands tryptophan metabolism to synergistically boost auxin biosynthesis in wheat by supplying precursors and activating relevant metabolic pathways. This cross-kingdom metabolic coupling facilitates better growth and salt tolerance in wheat plants. Our findings offer multi-omics and rhizosphere-level insights that can guide the development of microbial inoculants to enhance climate-resilient and sustainable crop production.},
}
@article {pmid42178518,
year = {2026},
author = {Porfirio-Sousa, AL and Jones, RE and Brown, MW and Lahr, DJG and Tice, AK},
title = {CSI-SSU: phylogenetic contamination screening of genomic datasets, demonstrated on The Protist 10,000 Genomes (P10K) Project.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42178518},
issn = {1471-2164},
support = {GBMF13832//Gordon and Betty Moore Foundation/ ; 2100888//National Science Foundation/ ; 2019/22815-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {*Phylogeny ; *Genomics/methods ; *Software ; *Eukaryota/genetics/classification ; Databases, Genetic ; *DNA Contamination ; },
abstract = {BACKGROUND: Genomic data are essential for uncovering the evolutionary history, ecological roles, and diversity of life. Yet, diverse microbial eukaryotes, predominantly unicellular and traditionally referred to as protists, remain critically underrepresented in genomic repositories, limiting our ability to address fundamental questions in eukaryotic evolution. The Protist 10,000 Genomes (P10K) initiative seeks to fill this gap by generating and compiling genomic and transcriptomic data for a wide range of microbial eukaryotes. However, large-scale sequencing efforts face persistent challenges, including contamination and imprecise taxonomic identification, particularly for poorly studied taxa that require specialized taxonomic expertise. To ensure the reliability of these resources, robust and scalable approaches for taxonomic identification and contamination screening are essential.<br><br>RESULTS: We developed CSI-SSU (https://github.com/AlexTiceLab/CSI-SSU), a command-line tool for Contaminant Sequence Investigation (CSI) that uses small subunit ribosomal RNA (SSU) sequences, chimeric sequence detection, and phylogenetic placement to rapidly identify, retrieve, and classify SSU sequences from eukaryotic genomic-level assemblies. CSI-SSU incorporates a curated SSU reference dataset representing the major known eukaryotic supergroups, with sequences and taxonomic nomenclature derived from the Protist Ribosomal Reference (PR[2]) database. In addition to detecting contaminant sequences, CSI-SSU enables approximate taxonomic assignment of the target lineage in each assembly, with resolution constrained by the current diversity represented in PR[2]. To further assess potential bacterial contamination, CSI-SSU employs bacterial BUSCO searches as a proxy. We demonstrate CSI-SSU utility and performance by screening 2,960 genomic-level assemblies spanning a broad diversity of eukaryotes from P10K. CSI-SSU efficiently detected non-target eukaryotic SSU sequences, revealing cross-group contamination. Classifications also corroborated or refined the original taxonomic assignments, with resolution depending on PR[2] representation. Bacterial BUSCO searches indicated bacterial contamination. Independent SSU and COI phylogenies of Amoebozoa supported CSI-SSU classifications, highlighting its accuracy and sensitivity.<br><br>CONCLUSION: CSI-SSU provides a scalable and reproducible framework for phylogenetically informed contamination screening and taxonomic validation of genomic and transcriptomic data. Coupling phylogenetic placement with contamination detection enabled us to distinguish high-quality P10K datasets from those requiring decontamination or additional sequencing before downstream use. These findings serve as a reference for future analyses and guide further sequencing efforts to expand the taxonomic diversity of microbial eukaryotes at the genomic level. Addressing imprecise taxonomic assignments, contamination, and reproducibility in genomic-level datasets will enhance the value of these resources and facilitate studies illuminating the evolution and diversification of eukaryotic life.},
}
@article {pmid42185792,
year = {2026},
author = {Mirzaei, S and Tefagh, M},
title = {MOFA: microbial optimization without forced altruism.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {42185792},
issn = {1471-2105},
mesh = {Algorithms ; *Methanococcus/metabolism/genetics ; Desulfovibrio vulgaris/metabolism/genetics ; *Models, Biological ; *Computational Biology/methods ; },
abstract = {BACKGROUND: Microorganisms typically exist in communities, where interactions among them define the complexity of these ecosystems. Developing in silico frameworks to investigate the behavior and functionality of these communities is therefore essential for advancing our understanding of microbial ecology. In recent years, several computational modeling frameworks based on genome-scale models have been developed for the community-level analysis of microbial systems.<br><br>RESULTS: Here, we introduce microbial optimization without forced altruism (MOFA), a bilevel optimization framework that considers both species-level and community-level fitness criteria. By imposing constraints on species biomass in the outer problem, it prevents the forced altruism observed in previous algorithms. We applied MOFA to a toy model and to community models of Desulfovibrio vulgaris and Methanococcus maripaludis, which exhibit a cross-feeding relationship that causes the community objective to override individual fitness goals by prioritizing the export of metabolites for other community members. For this microbial community, a comparison with the results of NECom, OptCom, and Joint-FBA shows that MOFA yields predictions that better match the experimental results. Additionally, for pairs with a cross-feeding relationship in which exported metabolite production associated with this mutual interaction competes with species biomass, such as D. vulgaris and M. maripaludis, NECom fails to predict the community growth rate, whereas our method succeeds.<br><br>CONCLUSIONS: MOFA effectively analyzes community growth rates without relying on forced altruism. In cases where NECom fails to predict community growth, MOFA successfully predicts these growth rates. Furthermore, MOFA enhances computational efficiency by eliminating the need for the binary variables required in the NECom algorithm.},
}
@article {pmid42283633,
year = {2026},
author = {Gómez-Gallego, T and Udaondo, Z and Palacios-Ferrer, R and Díaz-Martínez, L and Ramos, JL},
title = {Development of advanced bioinformatic profiles to improve the detection and functional understanding of fungal acid phosphatases.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {7},
pages = {e0210625},
doi = {10.1128/aem.02106-25},
pmid = {42283633},
issn = {1098-5336},
support = {862695//PRIORITY 'Excellent science'/ ; PDI-2021-123469OB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PID2024-161463NA-I00//Agencia Estatal de Investigaci&#xf3;n/ ; },
mesh = {*Acid Phosphatase/genetics/metabolism ; *Computational Biology/methods ; Phylogeny ; *Fungi/enzymology/genetics/classification ; *Fungal Proteins/genetics/metabolism ; 6-Phytase/genetics ; },
abstract = {We have retrieved approximately 9,000 protein sequences annotated as fungal acid phosphatase or phytase from the UniProtKB database. Following stringent quality filtering, a curated dataset comprising 3,058 high-confidence sequences was assembled. Phylogenetic analysis resolved these enzymes into eight distinct clades, representing distinct groups of fungal acid phosphatases: purple acid phosphatases, phytases, and groups containing both phytases and acid phosphatases annotations. Based on this classification, we have developed three representative protein profiles referred to as Prf-A-Fungal_phos, Prf-B-Fungal_phos, and Prf-C-Fungal_phos, each designed to capture the phylogenetic and functional diversity of these enzyme families. Heat-map analyses confirmed the breadth and high specificity of these profiles. Application of these profiles to public protein and metagenomic databases enabled the identification of hundreds of previously uncharacterized fungal proteins, with a broad taxonomic distribution and notable prevalence in the Ascomycota and Basidiomycota phyla. Functional validation through heterologous expression of selected candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, supporting the accuracy of the in silico predictions. By integrating large-scale bioinformatics with experimental validation, this study provides robust tools for the discovery of novel fungal phosphatases and for investigation of their ecological roles in nutrient-limited environments.IMPORTANCEFungal acid phosphatases are critical enzymes in global phosphorus cycling, yet no dedicated bioinformatic tools exist to comprehensively identify and classify them across fungal diversity. Here, we present the first PROSITE generalized profiles specific to fungal acid phosphatases, derived from a curated data set of over 3,000 high-confidence sequences spanning eight phylogenetic groups. These profiles exhibit high specificity and sensitivity, enabling the detection of hundreds of previously uncharacterized proteins from public protein databases. Experimental expression of representative candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, validating our in silico predictions. By bridging large-scale bioinformatics with functional validation, this study delivers robust resources to uncover novel fungal phosphatases and to explore their ecological roles in nutrient-limited environments. The developed profiles will advance metagenomic annotation, support soil and environmental microbiology research, and foster biotechnological innovation in sustainable phosphorus management.},
}
@article {pmid42434844,
year = {2026},
author = {Chen, J and Gong, J and Wang, Z and Yang, L and Yang, Y and Xu, Q and Zhang, S and Tian, X and Yan, L and Zhou, Q},
title = {Digital Affective Resilience: A Cross-Sectional Observational Study of Anxiety-Related Chinese Social Media.},
journal = {Nursing open},
volume = {13},
number = {7},
pages = {e70691},
pmid = {42434844},
issn = {2054-1058},
mesh = {Humans ; *Social Media/statistics &amp; numerical data ; Cross-Sectional Studies ; Male ; Female ; China ; *Anxiety/psychology ; Emotions ; Adult ; *Resilience, Psychological ; Digital Media ; Phobic Disorders/psychology ; Data Mining ; Media Exposure ; },
abstract = {BACKGROUND: Anxiety disorders, including phobias, are a growing public health concern, profoundly affecting quality of life. While existing research utilizes text-based and physiological data for detection, a multimodal, ecologically valid understanding of how anxiety is expressed and regulated in natural social contexts remains limited. Social media offers a unique setting for studying spontaneous emotional disclosure and collective coping mechanisms.<br><br>METHODS: A text-mining study was conducted on 28,349 social media comments related to phobia/anxiety from three Chinese platforms (XiaoHongShu, Zhihu, and Weibo) using convenience sampling of publicly available posts up to November 1, 2025. Social media comments related to phobia discussions were collected and analysed using the Dalian University of Technology Chinese Sentiment Vocabulary Ontology lexicon-based methods. Demographic variables were analysed using Independent Samples t-test and One-way ANOVA.<br><br>RESULTS: The most frequent emotion categories were happiness (31.6%) and surprise (15.3%), followed by fear (18.4%), sadness (14.7%), anger (12.1%), and disgust (7.9%). Gender differences based on complete-case analysis (n&#x2009;=&#x2009;12,845) showed that female users expressed significantly more happiness- and sadness-related language than male users (p&#x2009;=&#x2009;0.005 and p&#x2009;=&#x2009;0.034, respectively). The sentiment classifier achieved moderate performance (F1&#x2009;=&#x2009;0.72).<br><br>CONCLUSION: The emotional discourse surrounding phobia on Chinese social media reflects co-occurring linguistic patterns of fear alongside happiness, surprise, sadness, anger, and low-frequency disgust, rather than fear amplification alone. These findings suggest that online communication may shape how anxiety-related emotions are collectively expressed and interpreted, although causal inferences cannot be drawn from cross-sectional text data.<br><br>This study addressed the limited understanding of anxiety-related emotional expression on Chinese social media. The findings showed that anxiety discourse involved not only fear, but also supportive, empathetic, and coping-oriented emotions. These results may help nurses and mental health professionals better understand digital emotional communication, improve psychosocial support, and inform AI-assisted emotional monitoring and online mental health interventions.<br><br>REPORTING GUIDELINE: This study was reported in accordance with the STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) Statement for cross-sectional observational studies.<br><br>No patients or members of the public were directly involved in the design, conduct, analysis, or manuscript preparation of this study. The research was based on secondary analysis of publicly available and anonymized social media data.},
}
@article {pmid42248261,
year = {2026},
author = {Qi, H and Ruan, C and Yuan, MM and Byeon, H and Liao, J and Zhu, L and Yu, P},
title = {Longitudinal transcriptomic insights into microbial aggregation, trophic cooperation, and genomic adaptation during algal-bacterial granular sludge formation.},
journal = {Bioresource technology},
volume = {458},
number = {},
pages = {135082},
doi = {10.1016/j.biortech.2026.135082},
pmid = {42248261},
issn = {1873-2976},
mesh = {*Sewage/microbiology ; *Transcriptome/genetics ; *Bacteria/genetics ; Quorum Sensing/genetics ; *Adaptation, Physiological/genetics ; Cyanobacteria/genetics ; Biofilms/growth &amp; development ; Genome, Bacterial ; Gene Expression Profiling ; Multiomics ; Genomics ; },
abstract = {Microbial aggregates such as algal-bacterial granular sludge (ABGS) rely on tightly coordinated microbial interactions to maintain structural stability and functional performance. Despite the significance of co-assembly of phototrophs and heterotrophs in ABGS systems, the ecological and genomic succession during their formation remains poorly understood. Here, time-series multi-omics analysis was conducted to track the dynamic shifts in microbial interactions during ABGS maturation. The granulation process entailed the establishment of extensive cross-phylum nutrient exchange networks between Cyanobacteria and core heterotrophs (e.g., Pseudomonadota and Bacteroidota). Concurrently, metatranscriptomic profiling revealed a significant upregulation of genes associated with biofilm formation (e.g., rpoS, glgC, and cysE) and quorum sensing processes (e.g., yidC and secG) in Cyanobacteria as ABGS stabilized. Furthermore, the spatial densification and metabolic stabilization were accompanied by distinct shifts in community evolutionary strategies: the enrichment of energetically costly antiviral defense systems (R[2] = 0.65, P < 0.05) but decreased frequency of horizontal gene transfer (HGT). Additionally, analyses of public datasets confirmed that these structural, metabolic, and genomic patterns were conserved across diverse structured algal-bacterial communities. Collectively, our findings demonstrate how physical aggregation, trophic cooperation, and genomic adaptation co-evolve during ABGS formation, providing new insights into the ecological principles governing engineered ecosystems.},
}
@article {pmid41940873,
year = {2026},
author = {Sharma, S and Khadka, A},
title = {Managing diabetes across borders and screens: mHealth use among older late-life South Asian migrants in the United States.},
journal = {Ethnicity &amp; health},
volume = {31},
number = {6},
pages = {558-582},
doi = {10.1080/13557858.2026.2655621},
pmid = {41940873},
issn = {1465-3419},
mesh = {Humans ; United States ; South Asian People ; Aged ; *Telemedicine/statistics &amp; numerical data ; Female ; Middle Aged ; Qualitative Research ; Male ; *Diabetes Mellitus, Type 2/therapy/ethnology ; Digital Health ; Asia, Southern/ethnology ; Interviews as Topic ; *Self-Management ; *Transients and Migrants/psychology ; Emigrants and Immigrants ; },
abstract = {OBJECTIVES: This study explores how older South Asian migrants in the United States navigate mobile health (mHealth) tools for type 2 diabetes self-management. The goal is to identify multilevel facilitators and barriers to digital engagement within culturally and structurally embedded contexts.<br><br>METHODS: We conducted a qualitative descriptive study using semi-structured interviews with 21 South Asian adults aged 55 and older who had migrated to the U.S. later in life and had recent experience using a diabetes management app. Thematic analysis was guided by the Social-Ecological Model (SEM) and the Consolidated Criteria for Reporting Qualitative Research (COREQ).<br><br>RESULTS: Participants' engagement with mHealth tools was shaped by personal confidence, emotional response, and adaptive strategies at the individual level; family and peer dynamics at the interpersonal level; lack of provider support and culturally misaligned features at the organizational level; culturally rooted norms and informal peer networks at the community level; and broader systemic exclusions related to language access, insurance coverage, and technology infrastructure at the policy level. While participants demonstrated motivation and resilience, emotional fatigue, app complexity, and cultural mismatches often limited sustained use.<br><br>CONCLUSIONS: Older South Asian migrants are not disinterested in digital health; rather, they are systemically excluded. For mHealth to meaningfully support diabetes self-management, tools and systems must be designed with linguistic access, cultural alignment, and policy-level support in mind. Findings underscore the need for culturally tailored, relationally supported, and digitally inclusive interventions that affirm the everyday realities of aging immigrant populations.},
}
@article {pmid42324754,
year = {2026},
author = {Kanamori, S and Sugimoto, K and Miyata, S and Nakatani, J and Nagata, T},
title = {Occupational health nurse involvement and Bright 500 certification among Japanese small- and medium-sized enterprises: a repeated cross-sectional analysis of 4 annual health and productivity management survey waves.},
journal = {Journal of occupational health},
volume = {68},
number = {1},
pages = {},
pmid = {42324754},
issn = {1348-9585},
support = {23JA2001//Japanese Ministry of Health, Labour and Welfare/ ; JSPS KAKENHI//JSPS KAKENHI/ ; 23&#xa0;K16526//JSPS KAKENHI/ ; },
mesh = {Humans ; *Certification/statistics &amp; numerical data ; Cross-Sectional Studies ; Efficiency ; *Health Promotion ; Japan ; *Occupational Health Nursing/statistics &amp; numerical data ; *Small Business ; Surveys and Questionnaires ; Secondary Data Analysis ; },
abstract = {OBJECTIVES: To investigate the association between occupational health nurse (OHN) involvement and Bright 500 certification, an indicator of high-performing health and productivity management (HPM), among Japanese small- and medium-sized enterprises (SMEs) using multi-year survey data.<br><br>METHODS: This observational study used secondary data from the 2021-2024 HPM Survey. Each annual response was analyzed as a corporation-year observation, and within-corporation correlation was handled with a random intercept for corporations. OHN involvement was defined as the appointment of public health nurses and/or nurses as health promotion officers. Bright 500 certification, obtained from publicly available certification records, was used as an indicator of more advanced HPM. The association was examined using a mixed-effects logistic regression model.<br><br>RESULTS: The analytical sample comprised 12&#x2009;847 (2021), 14&#x2009;401 (2022), 17&#x2009;316 (2023), and 20&#x2009;267 (2024) SMEs. OHN involvement increased from 5.1% (2021) to 5.8% (2024). Bright 500 certification was consistently higher in corporations with OHN involvement (10.8% in 2021, 8.4% in 2024) than in those without (2%-3% across years). After adjustment for survey year, region, insurer category, industry type, employee size, internal and external dissemination of HPM initiatives, and occupational physician involvement, OHN involvement was independently associated with certification (odds ratio: 2.35; 95% CI, 1.21-4.54; P&#x2009;=&#x2009;.011).<br><br>CONCLUSIONS: Across the 4 survey waves, OHN involvement was positively associated with Bright 500 certification among SMEs. These findings suggest that OHNs may be relevant to advanced HPM implementation in this setting. Future studies should capture OHN staffing arrangements, intensity and roles, and initiative timing to clarify mechanisms and potential causality.},
}
@article {pmid42427819,
year = {2026},
author = {Karapliafis, D and Neri, U and Olendraite, I and Charon, J and Sakaguchi, S and Hou, X and de Ridder, D and Zwart, MP and Kupczok, A},
title = {RdRpCATCH: a unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov models.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag076},
pmid = {42427819},
issn = {2631-9268},
mesh = {*RNA-Dependent RNA Polymerase/genetics ; *RNA Viruses/genetics/enzymology ; Hidden Markov Models ; *Software ; Genome, Viral ; Computational Biology/methods ; Viral Proteins/genetics ; Markov Chains ; },
abstract = {Recent advances in large-scale sequence mining have expanded our knowledge of RNA virus diversity. Most genome mining approaches for detecting RNA viruses rely on identifying the conserved RNA-dependent RNA polymerase (RdRp) by scanning sequencing datasets with specialized profile Hidden Markov Models (pHMMs). Recently, several new pHMM databases for RdRp detection have been released, each following distinct design principles. However, their relative performance remains unclear, and their accessibility to users without advanced computational expertise is limited. Here, we introduce the RdRp Collaborative Analysis Tool with Collections of pHMMs (RdRpCATCH: https://github.com/dimitris-karapliafis/RdRpCATCH), a platform that consolidates publicly available RdRp pHMM resources into a single, user-friendly framework. RdRpCATCH enables the scanning of (meta)transcriptomic assemblies to discover RNA viruses and provides subsequent taxonomic annotation of detected contigs. A comparative analysis of RdRp pHMM databases reveals that most are highly effective at detecting the known diversity of RNA viruses while minimizing false positives, supporting their joint use within RdRpCATCH. RdRpCATCH is distributed as both a conda package and a web server application (https://rdrpcatch.bioinformatics.nl), facilitating access for researchers with diverse levels of computational expertise. By integrating multiple pHMM resources, this unified framework addresses fragmentation in the field and reduces technical barriers, enabling comprehensive viral discovery.},
}
@article {pmid42428246,
year = {2026},
author = {Wei, J and Yangsong, Q and Hongjia, R and Bingqiang, Z and Conggao, Y},
title = {From Exposure to Biomarker: Cumulative Tobacco Burden and Integrated Multiomics Signatures of High Tumor Mutational Burden in Lung Adenocarcinoma-A Secondary Analysis of the Cancer Genome Atlas.},
journal = {Human mutation},
volume = {2026},
number = {},
pages = {1906706},
pmid = {42428246},
issn = {1098-1004},
mesh = {Humans ; *Biomarkers, Tumor/genetics ; Multiomics ; *Mutation ; *Adenocarcinoma of Lung/genetics/etiology/pathology ; *Lung Neoplasms/genetics/etiology ; Female ; Male ; Middle Aged ; Smoking/adverse effects ; Aged ; Genomics/methods ; Proteomics ; },
abstract = {Environmental exposures are upstream determinants of molecular variation, yet exposure-to-biomarker gradients remain insufficiently quantified in harmonized multiomics cancer cohorts. Using TCGA lung adenocarcinoma as a model, we evaluated cumulative tobacco exposure and smoking history as determinants of variant-derived biomarkers and tested whether integrating clinical, genomic, transcriptomic, and proteomic data improves identification of high tumor mutational burden (TMB). This secondary analysis used public cBioPortal-linked TCGA data. Among 522 patients with clinical and molecular annotations, 302 ever-smokers with nonmissing pack-years, TMB, and covariates comprised the primary adjusted logistic-regression cohort, and 250 cases had matched multiomics data for prediction modeling. Higher cumulative tobacco exposure was associated with greater odds of high TMB: Compared with pack-year tertile 1, tertile 3 had an adjusted odds ratio of 2.28 (95% CI: 1.18, 4.41; p trend = 0.013), and each 10 pack-year increment was associated with an odds ratio of 1.12 (95% CI: 1.02, 1.23). Smoking categories also showed strong gradients for TMB, total nonsynonymous mutation counts, and C > A substitution fraction. Current smoking was positively associated with TP53 mutation and inversely associated with EGFR mutation relative to never-smoking. High-TMB tumors showed 201 differentially expressed transcripts and 15 differentially abundant proteins. Driver-augmented models discriminated high TMB better than broader multiomics models, although integrated scores retained prognostic relevance. These findings support exposure-aware biomarker development in lung adenocarcinoma. High TMB was defined as a cohort-specific top-quartile analytic endpoint rather than a universal clinical threshold. The findings support biomarker interpretation and hypothesis generation, not direct immunotherapy-response prediction or a clinically deployable model.},
}
@article {pmid42429114,
year = {2026},
author = {Grafström, A and Prentius, W},
title = {Distributionally balanced sampling designs.},
journal = {Biometrics},
volume = {82},
number = {3},
pages = {},
doi = {10.1093/biomtc/ujag124},
pmid = {42429114},
issn = {1541-0420},
mesh = {Computer Simulation ; *Models, Statistical ; *Research Design ; Sampling Studies ; *Biometry/methods ; Data Interpretation, Statistical ; Ecology ; Humans ; Probability ; Sample Size ; Reproducibility of Results ; },
abstract = {We propose Distributionally Balanced Designs (DBD), a new class of probability sampling designs that target representativeness at the level of the full auxiliary distribution rather than for selected moments. In disciplines such as ecology, forestry, and environmental sciences, where field data collection is expensive, maximizing the information extracted from a limited sample is critical. More precisely, DBD can be viewed as minimum discrepancy designs that minimize the expected discrepancy between the sample and population auxiliary distributions. The key idea is to construct samples whose empirical auxiliary distribution closely matches that of the population. We present a first implementation of DBD for equal inclusion probabilities, based on an optimized circular ordering of the population and a random selection of a contiguous block of units. The ordering is chosen to minimize the design-expected energy distance, a discrepancy measure that captures differences between distributions beyond low-order moments. This criterion promotes strong spatial spread, and yields low variance for Horvitz-Thompson estimators of totals of functions that vary smoothly with respect to auxiliaries. Simulation results show that approximate DBD achieves better distributional fit than state-of-the-art methods such as the local pivotal and local cube designs. Hence, DBD can improve the reliability of estimates from costly field data, making distributional balancing effective for constructing representative surveys in resource-constrained applications.},
}
@article {pmid42429144,
year = {2026},
author = {Wei, L and Kong, X and Li, Y and Wu, H and Gan, Y and Sun, F},
title = {Gut dysbiosis‑derived butyrate loss predicts feeding intolerance: Multiomics evidence guiding nurse‑driven microbiota‑supportive interventions (Review).},
journal = {Molecular medicine reports},
volume = {34},
number = {3},
pages = {},
pmid = {42429144},
issn = {1791-3004},
mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; Multiomics ; *Gastrointestinal Microbiome ; *Butyrates/metabolism ; Critical Illness ; },
abstract = {Feeding intolerance (FI) is a common and debilitating challenge among critically ill patients that is linked to a pathway involving the collapse of the gut microbial ecology. The present review synthesizes multiomics evidence supporting a framework whereby critical illness‑associated gut dysbiosis results in a functional deficit of a microbially derived short‑chain fatty acid butyrate, a pivotal metabolite involved in maintaining intestinal barrier integrity, immuneoregulation and gastrointestinal motility. The loss of butyrate‑producing bacteria and their genetic pathways is strongly correlated with FI and may represent a contributory pathogenic mechanism. Key butyrate‑producing organisms diminished during this process include Faecalibacterium prausnitzii and Roseburia spp. Building upon this mechanistic framework, a pragmatic, nurse‑driven intervention model aimed at preserving and restoring microbial health in critically ill patients was proposed. This model is founded on four principal strategies: Minimizing iatrogenic harm (such as antibiotic/proton pump inhibitor stewardship), targeted microbiota nourishment (pre/synbiotics), cautious microbial restoration (probiotics/fecal microbiota transplantation) and innovative monitoring approaches. By integrating principles of microbial ecology with clinical nursing science, the present review provides a framework for developing nurse‑driven protocols designed to address the underlying pathophysiology of FI and improve patient outcomes.},
}
@article {pmid42430437,
year = {2026},
author = {Ansari, AF and Sambamoorthy, G and Alexander, TC and Reddy, YBS and Raut, J and Dixit, NM},
title = {Quartet: Disentangling positive and negative components of microbial interactions.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1014502},
doi = {10.1371/journal.pcbi.1014502},
pmid = {42430437},
issn = {1553-7358},
mesh = {*Microbiota/physiology ; *Microbial Interactions/physiology ; *Models, Biological ; Computational Biology/methods ; Computer Simulation ; Mouth/microbiology ; },
abstract = {Interspecies interactions are characterized conventionally by the net influence, positive or negative, a species exerts on another. Community ecology theories rely on these net interactions to describe the behaviour of multispecies communities. The net interactions in turn comprise positive and negative components, arising typically from cross-feeding metabolites and competition for resources. The components remain challenging to disentangle, compromising descriptions of community behaviour. Here, we devised a method to estimate the components when metabolic interactions predominate. We conceived a theoretical resource partitioning strategy which when applied to data on species growth rates disentangles the components. Consequently, the net influence a species has on another is decomposed into its positive and negative components. The interactions between a pair of species are thus defined by the 'quartet' of underlying components, specifically the positive and negative components of the net influence of each species on the other. We applied the method to 28 in silico species pairs from a representative oral microbiome and an experimental auxoptroph pair from the literature. We found that positive and negative components had comparable strengths on average. Interestingly, we found species pairs with similar net interactions but disparate components, highlighting the importance of the quartet. Further, weak net interactions could arise from cancellation of strong components. Estimating the quartet helped better understand the complex transitions in community behaviour observed upon varying resource supply in silico and in vitro. The quartet thus offers a more fundamental characterization of interspecies interactions and may help build more reliable community ecology theories, with implications for understanding and design of microbial communities.},
}
@article {pmid42430441,
year = {2026},
author = {Arnoux, J and Mainguy, J and Bry, L and Fernandez de Grado, Q and Hoblos, Y and Vallenet, D and Calteau, A},
title = {Panorama: A robust pangenome-based method for predicting and comparing biological systems across species.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1013856},
pmid = {42430441},
issn = {1553-7358},
mesh = {*Genome, Bacterial/genetics ; *Computational Biology/methods ; *Genomics/methods ; Pseudomonas aeruginosa/genetics ; *Software ; Genetic Variation ; Species Specificity ; Enterobacteriaceae/genetics ; Algorithms ; },
abstract = {Over the last decade, the expansion in the number of available genomes has profoundly transformed the study of genetic diversity, evolution, and ecological adaptation in prokaryotes. However, traditional bioinformatic approaches based on the analysis of individual genomes are showing their limitations when faced with the sheer scale of the data. To overcome these constraints, the concept of pangenome has emerged, offering a comprehensive framework to capture the full genetic repertoire of a species. In this study, we present PANORAMA, an innovative pangenomic tool designed to exploit pangenome graphs, enabling their annotation and comparison to explore the genomic diversity of several species. Based on the PPanGGOLiN pangenome graphs, PANORAMA integrates advanced methods for rule-based prediction of macromolecular systems and comparative analysis of conserved features between different pangenomes, such as spots of insertion. We illustrate the use of PANORAMA on a dataset of 941 Pseudomonas aeruginosa genomes, evaluating its performance against reference defense system prediction tools such as PADLOC and DefenseFinder. The analysis was then extended to a larger set, including four species of Enterobacteriaceae (>6,000 genomes), demonstrating PANORAMA's ability to annotate, compare, and explore the diversity and distribution of biological systems across multiple species. This work provides new methods for the large-scale comparative study of microbial genomes and highlights the relevance of pangenome approaches in deciphering their evolutionary dynamics. PANORAMA is freely available and accessible at: https://github.com/labgem/PANORAMA.},
}
@article {pmid42423304,
year = {2026},
author = {Rehman, M and Sajjad, W and Kang, S and Rafiq, M and Zhao, Y},
title = {Mobilization of the ancient resistome from thawing permafrost.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/1040841X.2026.2698958},
pmid = {42423304},
issn = {1549-7828},
abstract = {Permafrost, ground frozen for at least two consecutive years, covers nearly one-quarter of the Northern Hemisphere and hosts diverse microbial communities. Climate-driven thaw is releasing preserved microorganisms and genetic material into contemporary ecosystems, where ancient genetic elements may be reintroduced into modern microbes and participate in gene exchange processes. Among these, antibiotic resistance genes (ARGs), which confer resistance to antibiotics, represent a critical yet underrecognized threat. Many originate from ancient microbial ecosystems shaped by natural antibiotic production and resistance, encode mechanisms not yet observed in clinical settings, and are associated with mobile genetic elements (MGEs) that facilitate horizontal gene transfer across microbial domains. Here, we synthesize evolutionary, molecular, and ecological perspectives on the preservation, release, and mobilization of permafrost-derived ARGs. We highlight mineral-DNA interactions that enhance the long-term stability of extracellular DNA containing ARGs and review the roles of MGEs in redistributing resistance determinants following thaw. We discuss conceptual models of rare cross-domain gene transfer and consider ecological and evolutionary implications under thawing conditions. ARG release from permafrost represents a neglected environmental factor that may contribute to antimicrobial resistance (AMR) dynamics and warrants investigation. Finally, identify key knowledge gaps and propose interdisciplinary frameworks for surveillance, risk assessment, and mitigation.},
}
@article {pmid42424242,
year = {2026},
author = {Alraihan, NM and French, M and Moore, DC and Sedda, L},
title = {Public health informatics tools for dengue risk management: A systematic review.},
journal = {PLOS digital health},
volume = {5},
number = {7},
pages = {e0001495},
pmid = {42424242},
issn = {2767-3170},
abstract = {Public health informatics (PHI) tools, including Geographic Information Systems (GIS), Electronic Health Records (EHRs), and Health Information Exchange systems, are increasingly applied to dengue fever surveillance, prevention, and control. Despite their growing adoption, a synthesis of empirical evidence examining their real-world application across endemic settings has not previously been conducted. This systematic review aimed to examine how PHI tools have been applied to dengue risk management, and to evaluate the certainty of evidence supporting their use. A structured literature search was conducted across PubMed, EBSCO/MEDLINE, and Web of Science. Nineteen peer-reviewed empirical studies published between 2010 and 2024 were included following eligibility screening against pre-defined inclusion and exclusion criteria. Study quality was assessed using the Newcastle-Ottawa Scale adapted for cross-sectional studies. Certainty of evidence was evaluated using the GRADE framework across five domains: risk of bias, inconsistency, indirectness, imprecision, and publication bias. Findings were synthesised narratively and organised into three functional categories: mapping and visualisation (n = 12), epidemiological insights (n = 5), and enhanced surveillance (n = 2). GIS was the most frequently used tool, consistently identifying dengue hotspots and supporting spatial dengue risk mapping across diverse geographic settings. EHR-linked health information systems supported epidemiological profiling and, in a limited number of studies, improved outbreak detection. Certainty of evidence was rated as very low across all three categories, reflecting the low evidence associated to observational study designs, methodological heterogeneity, and the uniform reporting of positive findings across all included studies. PHI tools show consistent descriptive utility in dengue surveillance across diverse settings. However, given the very low certainty of evidence, conclusions should be interpreted with caution. Gaps remain in high-burden regions including Sub-Saharan Africa and the Middle East. Standardised evaluation frameworks, broader geographic representation, and integration with emerging digital health technologies are needed to strengthen the evidence base. Systematic review registration: PROSPERO; registration number CRD42024572021.},
}
@article {pmid42426003,
year = {2026},
author = {Lei, Z and Liu, H and Zhang, Y and Li, X and Xiao, C and Xing, G and Guo, R and Zhang, Y and Xu, J and Yang, W and Chen, H and Li, M and Lu, T and Li, S and Lu, Y and Yan, Q},
title = {The Cat Gut Microbial Genome Collection reveals global structure of the feline gut microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01088-3},
pmid = {42426003},
issn = {2055-5008},
support = {32202857//National Natural Science Foundation of China/ ; 2024BBB073//Hubei Key Research and Development Project/ ; YXYX2506//Open Research Project of Sichuan Provincial Clinical Research Center for Imaging Medicine/ ; XN202402//Open Project of Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education/ ; 2022CXRC9555//Ganzhou Science and Technology Innovation Talent Project - Youth Talent Project/ ; },
abstract = {The gut microbiome is a critical determinant of mammalian health, yet our understanding is largely derived from humans and laboratory models. The ecological principles governing the microbiome of globally important companion animals, such as cats, remain poorly defined. We generated the Cat Gut Microbial Genome Collection (CGMGC), a comprehensive resource encompassing over 40,000 microbial genomes. This collection spans 874 prokaryotic species, 6 fungal species, and 5543 viral operational taxonomic units, derived from feline gut samples across diverse geographical regions. Our analysis reveals that the cat gut microbiome is a highly host-specific ecosystem whose structure is primarily driven by geography rather than host genetics or diet. Over 50% of the identified prokaryotic species are unique to felines and contain novel taxonomic lineages. Functionally, the virome encodes a vast repertoire of auxiliary metabolic genes, indicating pervasive inter-kingdom control over bacterial hosts. Surprisingly, the feline gut shares significantly more microbial species with humans than with laboratory mice, suggesting convergent evolution in cohabiting species. The core ecological principles of the feline gut are profound host-specificity, geographic structuring, and pervasive viral modulation of bacterial function. This work redefines the feline microbiome as a unique model for host-microbe co-evolution and establishes a genomic foundation for a new era of evidence-based veterinary medicine.},
}
@article {pmid41861125,
year = {2026},
author = {Hopkins, B and Davies, P and Noble, PJ and Bunford-Davies, A and Lawson, A and Pinchbeck, G and Lloyd, I and Smith, R and Radford, AD},
title = {Reusing health records from farm animal practices at scale: A potential complementary method of surveillance.},
journal = {The Veterinary record},
volume = {199},
number = {2},
pages = {e73-e81},
doi = {10.1002/vetr.70501},
pmid = {41861125},
issn = {2042-7670},
support = {//Welsh Government/ ; //Llywodraeth Cymru/ ; //Arwain DGC/ ; },
mesh = {Animals ; Cattle ; Sheep ; *Electronic Health Records/statistics &amp; numerical data ; *Sheep Diseases/drug therapy/epidemiology ; *Cattle Diseases/drug therapy/epidemiology ; Wales/epidemiology ; Pilot Projects ; Data Mining ; Anti-Bacterial Agents/therapeutic use ; *Population Surveillance/methods ; Animals, Domestic ; Farms ; },
abstract = {BACKGROUND: Disease in primary care frequently represents a surveillance blind spot, particularly for diseases affecting farm animals.<br><br>METHODS: Electronic health records (EHRs) were collected from four farm animal veterinary practices in Wales (February 2024&#x2012;January 2025) as part of a pilot study. Information collected included species treated, date, owner postcode, products sold and clinical free text. Text mining and topic modelling were used to describe treatments and classify syndromes.<br><br>RESULTS: In total, 32,799 records were collected. Antimicrobials were prescribed in 32.6% and 63.8% of cattle and sheep records, respectively. The most frequent antibiotic classes in both species were tetracyclines, macrolides, penicillins and penicillin&#x2012;aminoglycoside combinations. There were no recorded category A antimicrobials, and category B antimicrobials were prescribed in only 0.12% and 0.04% of cattle and sheep EHRs, respectively. Text mining and topic modelling seemed efficient methods to identify key syndromes, including mastitis, joint ill, lameness and pneumonia, and how these were treated.<br><br>LIMITATIONS: Some EHRs described more than one animal with different diagnoses, obfuscating the attribution of treatment to syndrome.<br><br>CONCLUSION: The increasing availability of EHRs at scale and in real-time represents a complementary opportunity to survey disease and treatment on farms. Text mining methods, including artificial intelligence, could efficiently identify important syndromes and provide novel insight into use of antibacterials.},
}
@article {pmid42049773,
year = {2026},
author = {Wei, X and Tang, D and Peng, Y and Huang, B and Zhu, Y and Liang, Z and Hu, Y},
title = {A telomere-to-telomere reference genome for Stemona tuberosa.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42049773},
issn = {2052-4463},
mesh = {*Genome, Plant ; Haplotypes ; *Stemonaceae/genetics ; *Telomere/genetics ; Datasets as Topic ; },
abstract = {Stemona tuberosa is a medicinally important species, however, a complete telomere-to-telomere (T2T) genome assembly has remained unavailable. Here, we present the first T2T genome assembly for S. tuberosa, generated by integrating PacBio HiFi, ultra-long Oxford Nanopore, Illumina, and Hi-C sequencing technologies. The assembly produced two highly contiguous haplotype-resolved genomes, with total sizes of 803.04 Mb and 795.04 Mb, and contig N50 values of 113.29 Mb and 111.11 Mb, respectively. The proportion of fully assembled chromosomes reached 100% in both haplotypes. In addition, 14 putative centromeric regions were successfully identified across 7 pseudochromosomes, along with the annotation of 25,561 and 25,854 genes in the two haplotypes, respectively. This T2T genome assembly of S. tuberosa provides a valuable reference for elucidating the genetic architecture of the species. It significantly advances our capacity to investigate structural variations, gene function, and evolutionary processes within Stemona and related medicinal plant lineages.},
}
@article {pmid42056141,
year = {2026},
author = {Li, W and Yu, D and Que, Y and Tian, H and Dong, W and Wang, E and Xu, N and Shao, K and Zhu, B and Hu, X},
title = {The first chromosomal level genome assembly and annotation of Pareuchiloglanis anteanalis.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42056141},
issn = {2052-4463},
support = {31572593//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Catfishes/genetics ; *Chromosomes ; *Genome ; Molecular Sequence Annotation ; Datasets as Topic ; },
abstract = {Pareuchiloglanis anteanalis belonging to the genus Pareuchiloglanis, within the family Sisoridae (order Siluriformes), is a group of small benthic-dwelling freshwater fishes adapted to alpine canyon environments characterized by steep slopes, rapid currents, and marked seasonal fluctuations in water discharge between dry and flood periods. This species is primarily distributed in the Jinsha River, Dadu River, and Bailong River, all located within the upper reaches of the Yangtze River drainage. In this research, through the integration of PacBio HiFi long read sequencing and Hi-C (high-throughput chromatin capture) technology, we generated a high-quality chromosome-level genome of the P. anteanalis. The assembly yielded a genome of 873.97 Mb, with a scaffold N50 length of 50.12 Mb, covering 98.59% of the contig-level genome, were accurately mapped onto 18 chromosomes by using Hi-C data. The BUSCO analysis indicated that the completeness of the genome assembly and the annotation both reached 93.3% and 93.4%, respectively. This high-quality genomic resource provides a solid foundation for deciphering genome architecture and functional elements, thereby enabling deeper investigations into the genetic mechanisms underlying adaptation in P. anteanalis. Moreover, it offers valuable support for resource conservation, artificial propagation, and selective breeding of this native species.},
}
@article {pmid42106342,
year = {2026},
author = {Mateo, M and Briand, C and Korta, M and Beaulaton, L and Drouineau, H and Pella, H and Amilhat, E and Bardonnet, A and Antunes, C and De Miguel Rubio, R and Domingos, I and Fernández-Delgado, C and Labedan, M and Herrera, M and Sagnes, P and Zamora, L and Díaz, E},
title = {A database of eels and their freshwater habitats in southwestern Europe.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42106342},
issn = {2052-4463},
mesh = {Animals ; *Ecosystem ; Rivers ; *Anguilla ; Fresh Water ; Spain ; Portugal ; Animal Migration ; France ; Databases, Factual ; },
abstract = {The European eel stock (Anguilla anguilla) is outside safe biological limits. A range-wide stock assessment requires the creation and standardisation of databases that include information on eels and their habitats in different countries throughout their distribution range. The SUDOANG 1.0.4 database compiles standardised data on river courses in France and the Iberian Peninsula (Spain and Portugal). Using GIS tools, information on water surface and on other potential aquatic habitats surrounding each river segment has been collected. This common river network provides tools to quickly accumulate information along the river or along the natural path of migration from/to the sea. The database also compiles information on the surface of other habitats, human pressures (including 106400 obstacles), and provides eel abundance and biometric estimations derived from the Eel Density Analysis (EDA) model at the river reach scale for the reference year 2015. The river network supports ecological assessment of the eel habitats, and should also be useful for studies on other migratory species.},
}
@article {pmid42174524,
year = {2026},
author = {Yuan, M and Bi, S and Chen, Z and Fan, X and Chen, X and Shen, K},
title = {Development of an interpretable machine learning model-based online tool for risk prediction of falls and fall-related injuries in Chinese middle-aged and older adults with depressive symptoms-a longitudinal study based on the CHARLS database.},
journal = {BMC public health},
volume = {26},
number = {1},
pages = {},
pmid = {42174524},
issn = {1471-2458},
mesh = {Humans ; *Accidental Falls/statistics &amp; numerical data ; China/epidemiology ; Longitudinal Studies ; Middle Aged ; Predictive Learning Models ; *Wounds and Injuries/epidemiology ; *Depression/epidemiology ; Risk Assessment/methods ; Aged ; Female ; Male ; *Machine Learning ; Boosting Machine Learning Algorithms ; Databases, Factual ; Prediction Algorithms ; East Asian People ; },
abstract = {BACKGROUND: This study aimed to establish and validate interpretable Machine Learning (ML) models for predicting falls and fall-related injuries in middle-aged and older adults with depressive symptoms (DS) and to develop relevant online computational tools.<br><br>METHODS: Using data from the China Health and Retirement Longitudinal Study (CHARLS) survey from 2015 to 2018, 32 predictor variables related to the risk of falls and fall-related injuries in middle-aged and older adults with DS were included based on five dimensions of the health ecology model, and the important predictor variables were screened using Principal Component Analysis and LASSO regression at the same time. We further developed eight ML algorithms-Logistic Regression(LR), Support Vector Machine(SVM), Gradient Boosting Machine (GBM), Neural Network (NN), eXtreme Gradient Boosting (XGBoost), Adaptive Boosting (AdaBoost), Light Gradient Boosting Machine (LightGBM) and Categorical Boosting (CatBoost)-to construct the risk prediction model, and selected the best predictive variables based on grid search and 10-fold cross-validation. SHapley Additive exPlanations (SHAP) was used for personalised interpretation of the models. In addition, we further performed stratified analyses by dividing participants into two age groups: 45-59 years and 60 years and older.<br><br>RESULTS: Among 3,664 middle-aged and older adults with DS, the incidence rate of falls and fall-related injuries after three years of follow-up was 20.36% and 8.92%, respectively. Among all models, LightGBM had the best performance. LightGBM performed the best, with an area under the curve (AUC) of 0.821 (95% CI: 0.802-0.841) for the fall risk test set and an AUC of 0.905 (95% CI: 0.892-0.919) for the fall injury risk test set. We identified important risk factors for falls and fall-related injuries in middle-aged and older adults with DS. The optimal predictive model and risk predictors differed from those identified before stratification by age. SHAP visualises the specific contributions of these risk factors, thereby enhancing the model's value for application. Online tools to implement the model are available at https://riskpredictiontool.shinyapps.io/falls_prediction_tool/ and https://riskpredictiontool.shinyapps.io/fall_related_injuries_prediction_tool/.<br><br>DISCUSSION AND CONCLUSIONS: The results can help predict risk of falls and fall-related injuries among middle-aged and older adults with DS. These findings provide an important guide for the development of public health strategies.},
}
@article {pmid42418234,
year = {2026},
author = {Araujo Serrao de Andrade, A and Silverj, A and Josephs, T and Gregory, AC},
title = {Evolving strategies for virus discovery.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
pmid = {42418234},
issn = {2057-5858},
mesh = {*Viruses/genetics/isolation &amp; purification/classification ; Genome, Viral ; *Metagenomics/methods ; *Virome/genetics ; Artificial Intelligence ; Computational Biology/methods ; },
abstract = {Viruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack of a universal marker gene and the extensive diversity of viral genomes. Despite this, the speed of viral discovery is quickly increasing, driven by the growing number of virome studies, improved sequencing technologies and the decreased cost of sequencing. In this review, we examine the evolution of virus identification approaches from classical and molecular methods to contemporary genome-resolved and computational frameworks. By aggregating genome-resolved virome studies from 2010 to early 2026 that meet defined criteria (n=502), we synthesize the current landscape of virus identification methods, including similarity-based, sequence-based artificial intelligence (AI) and hybrid approaches. We also highlight the key limitations of the current methods, particularly biases in reference databases that contribute to persistent viral 'dark matter'. Finally, we identify emerging opportunities for the field in structure-based and AI-driven approaches that extend detection beyond sequence similarity and outline how these integrative frameworks are poised to improve virus discovery across ecosystems.},
}
@article {pmid42419831,
year = {2026},
author = {Li, JW and Wang, Y and Chaurasia, A},
title = {Microbial biomarkers for OPMD progression.},
journal = {Advances in immunology},
volume = {169},
number = {},
pages = {193-212},
doi = {10.1016/bs.ai.2026.03.001},
pmid = {42419831},
issn = {1557-8445},
mesh = {Humans ; *Microbiota ; Disease Progression ; *Mouth Neoplasms/microbiology/diagnosis ; *Dysbiosis/microbiology ; Biomarkers ; *Carcinoma, Squamous Cell/microbiology/diagnosis ; *Biomarkers, Tumor ; *Precancerous Conditions/microbiology ; Metabolomics ; Multiomics ; },
abstract = {Oral potentially malignant disorders (OPMDs) present a heterogeneous risk of progression to oral squamous cell carcinoma (OSCC), underscoring the need for reliable, non-invasive biomarkers to aid in clinical stratification. This chapter evaluates the utility of the oral microbiome as a source of predictive biomarkers for OPMD progression. Current evidence indicates that OPMDs and OSCC are frequently associated with microbial dysbiosis, characterized by a shift toward anaerobic, periodontal-associated taxa, such as Fusobacterium and Porphyromonas, and a concomitant depletion of health-associated Streptococcus. However, translating these taxonomic signatures into clinical practice is hindered by overlapping community structures across healthy, premalignant, and malignant mucosal states, alongside significant confounding from periodontal inflammation and lifestyle exposures. Furthermore, the field remains divided on whether this dysbiosis acts as an upstream driver of carcinogenesis or a downstream consequence of tumor-associated microenvironmental selection. To overcome these methodological and biological limitations, this chapter advocates for an ecology-driven, multi-omics approach. By integrating taxonomic profiling with functional readouts like metabolomics and metaproteomics, and contextualizing these signals within host microenvironmental strata (e.g., hypoxia and inflammation), researchers can achieve greater mechanistic interpretability and robustness. Ultimately, microbiome-informed tools are best positioned not as standalone diagnostic tests, but as adjunctive instruments for clinical triage and risk enrichment, provided they are rigorously validated in prospective, longitudinal converter/non-converter cohorts.},
}
@article {pmid42422686,
year = {2026},
author = {Lyu, Y and Luo, C},
title = {Digital access, digital health information engagement, and self-reported preventive behavior among rural adults in Guizhou, China: media-use ecologies and cross-sectional associations.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1794204},
pmid = {42422686},
issn = {2296-2565},
mesh = {Humans ; Cross-Sectional Studies ; Female ; Male ; China ; Adult ; *Rural Population/statistics &amp; numerical data ; Middle Aged ; Digital Health ; Digital Media ; Self Report ; *Health Behavior ; Media Exposure ; Adolescent ; Young Adult ; Aged ; },
abstract = {BACKGROUND: Digital health education may help reduce health-information inequality in underdeveloped rural areas, but evidence remains limited on how rural residents encounter health information across different media environments and how digital access, usability, engagement, and self-reported preventive behavior are interrelated. This study examined media-use ecologies and cross-sectional associations among digital access and skills, digital health information engagement, and self-reported preventive behavior among rural adults in Guizhou, China.<br><br>METHODS: A cross-sectional survey was conducted among 1,265 adult rural residents recruited from five selected counties/districts in Guizhou Province using a multistage non-probability sampling design. Latent class analysis was used to characterize health-information media-use ecologies based on nine indicators of information channels and social media platforms. Regression-based cross-sectional association models examined associations among digital access and skills, perceived ease of understanding digital health content, lower operational difficulty, digital health information engagement, attitudes and willingness toward health education, and self-reported preventive behavior, adjusting for sex, age, education, income, and media-use ecology.<br><br>RESULTS: Five media-use ecologies were identified, reflecting different combinations of offline interpersonal/professional channels, traditional media, and digital platforms. Residents in omnichannel and short-video/social-platform-centered ecologies reported higher digital health information engagement, whereas those in the offline village doctor/traditional channels ecology reported the lowest engagement. Higher digital access and skills were associated with stronger engagement, and this association was attenuated after accounting for perceived ease of understanding and lower operational difficulty. Greater engagement was associated with more frequent self-reported preventive behavior, and this association was attenuated after accounting for attitudes toward health education and willingness to adopt new forms of health education.<br><br>CONCLUSION: In this non-probability adult sample from selected rural sites in Guizhou, digital health inequality was reflected not only in unequal access to devices and networks, but also in differences in understanding, usability, engagement, and self-reported preventive behavior. The findings should be interpreted as cross-sectional associations among field-feasible indicators rather than evidence of causal mechanisms.},
}
@article {pmid41543584,
year = {2026},
author = {Gupta, S and Patil, AB and Soman, AS and Vijay, N},
title = {Master of none: GPRC6A gene loss is more widespread than previously known.},
journal = {Genetica},
volume = {154},
number = {1},
pages = {5},
pmid = {41543584},
issn = {1573-6857},
support = {B.T./11/IYBA/2018/03//Department of Biotechnology, Ministry of Science and Technology, India/ ; E.C.R./2017/001430//Science and Engineering Research Board/ ; },
mesh = {*Receptors, G-Protein-Coupled/genetics ; *Mammals/genetics ; Humans ; Animals ; *Synteny ; *Evolution, Molecular ; Genome ; Datasets as Topic ; },
abstract = {GPRC6A encodes a class C GPCR that can be activated by multiple ligands and potentially acts as a central regulator of diverse metabolic processes by modulating endocrine pathways. Experimental studies have reported numerous distinct functions for GPRC6A, suggesting it may be a key drug target for several metabolic disorders. Yet, the actual function of GPRC6A has been the focus of considerable debate due to contradictory results and the prevalence of loss-of-function mutations in human populations, leading to the perception of GPRC6A as a "Master of none". Interestingly, a genome-wide screen for gene loss events in vertebrate species identified the disruption of the GPRC6A gene in toothed whales, in contrast to widespread conservation in the closely related Bovidae family. We employ a synteny-informed comparative genomic approach to demonstrate that the loss of the GPRC6A gene among mammalian species is more widespread than previously reported, encompassing the entire Bovidae group within Artiodactyla and other fully aquatic mammals, including those belonging to Sirenia. An in-depth search of the genomes and short and long-read sequencing datasets of monotremes, hystricomorphs, rhinolophoid bats, pika, koala, and two shrews (white-toothed pygmy shrew and Asian house shrew) reveals at least nine independent GPRC6A gene loss events in vertebrates, highlighting its lineage-specific dispensability and raising questions regarding its ubiquitous functionality. The evolutionary loss of GPRC6A likely represents a lineage-specific response to specialised diets and ecological niches, reshaping metabolic regulation and taste perception and illuminating how niche specialisation influences gene retention or loss within the GPCR landscape across species.},
}
@article {pmid41921848,
year = {2026},
author = {Xu, H and Sun, J and Lu, F and Luo, Y and Bie, L and Xia, Q and Wang, Y and Lin, P and Shen, G},
title = {IMDD: A Database for Exploring Tissue-Specific Gene Expression Dynamics During Holometabolous Insects.},
journal = {Journal of molecular biology},
volume = {438},
number = {18},
pages = {169781},
doi = {10.1016/j.jmb.2026.169781},
pmid = {41921848},
issn = {1089-8638},
mesh = {Animals ; *Metamorphosis, Biological/genetics ; *Gene Expression Regulation, Developmental ; *Databases, Genetic ; Drosophila melanogaster/genetics/growth &amp; development ; *Holometabola/genetics/growth &amp; development ; Bombyx/genetics/growth &amp; development ; Transcriptome/genetics ; Biocuration ; Organ Specificity/genetics ; Gene Regulatory Networks ; Bees/genetics/growth &amp; development ; },
abstract = {The intricate process of insect metamorphosis is governed by precise tissue-specific gene expression dynamics. To facilitate the exploration of these complex regulatory programs, we have developed the Insect Metamorphic Development Database (IMDD), an interactive platform for four key holometabolous species, including Drosophila melanogaster, Bombyx mori, Aedes aegypti and Apis mellifera, which hold significant ecological, economic, and medical importance. IMDD integrates over 1200 bulk-tissue transcriptomes and more than 1.4 million single-cell profiles, providing broad coverage of developmental stages. The platform is specifically designed to empower researchers to explore dynamic gene expression changes at both tissue and single-cell resolutions, investigate cellular heterogeneity, and trace cell-type transitions. By providing a user-friendly interface for dissecting the molecular underpinnings of insect development, IMDD serves as a critical resource for exploring the spatiotemporal gene regulatory networks that drive metamorphosis. The database is freely accessible at http://www.bioimdd.com/.},
}
@article {pmid42050343,
year = {2026},
author = {Sun, H and Wang, X and Deng, H and Xie, L and Zhou, E and Tan, N and Wu, Y},
title = {The chromosome-level genome assembly and annotation of Parabotia bimaculata (Cypriniformes: Cobitidae: Botiinae).},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42050343},
issn = {2052-4463},
support = {KJZD-M202401301//Major Science and Technology Research Project of Chongqing Municipal Education Commission/ ; R2022YS08//Tower Foundation Program of Chongqing University of Arts and Sciences in China/ ; },
mesh = {Animals ; *Chromosomes ; *Cypriniformes/genetics ; *Genome ; Molecular Sequence Annotation ; Datasets as Topic ; },
abstract = {Parabotia bimaculata is a rare loach species endemic to southwestern China. A high-quality reference genome is essential for advancing research across various biological fields concerning this species. Here, we report the first chromosome-level genome assembly and annotation of P. bimaculata. The assembled genome spans 610.59 Mb with a contig N50 of 21.19 Mb. Hi-C scaffolding anchored 96.92% of the sequences into 25 pseudo-chromosomes. By integrating homology-based prediction with RNA-sequencing data, we identified 26,312 protein-coding genes, of which 23,833 (90.58%) were functionally annotated. The assembly achieved a 98.54% BUSCO completeness score. This work provides a valuable genomic resource for P. bimaculata, establishing a foundation for future studies in genomics, evolutionary biology, and conservation.},
}
@article {pmid42143165,
year = {2026},
author = {Yang, J and Liang, BY and Fang, CY and Li, JJ and Zhang, P and Xiang, P and Zhang, LW and Liu, H},
title = {Exploring dysregulation of cuproptosis-related genes molecular clusters and candidate biomarkers in pterygium.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42143165},
issn = {2045-2322},
support = {ZKF2024042//National clinical key specialty ophthalmology open foundation/ ; ZKF2024041//National clinical key specialty ophthalmology open foundation/ ; 82560205//National Natural Science Foundation of China/ ; 82460201//National Natural Science Foundation of China/ ; 202208535051//China Scholarship Council/ ; 24JCQNJC02050//Tianjin Natural Science Foundation/ ; YDYXJJ2024-0003//Yunnan University Medical Research Foundation/ ; 2024YNLCYXZX0343//Key Project of the Provincial Clinical Center of Yunnan Province/ ; },
mesh = {Humans ; *Pterygium/genetics/pathology/immunology/metabolism ; *Cuproptosis/genetics ; Biomarkers/metabolism ; Gene Expression Profiling ; Transcriptome ; Female ; Gene Expression Regulation ; Male ; Computational Biology/methods ; Machine Learning ; },
abstract = {Pterygium is a common ocular surface disorder, with its prevalence strongly correlated to ultraviolet (UV) exposure in geographic regions. Epidemiological investigations reveal significant demographic variations, with higher incidences observed in areas with intense UV radiation and within specific populations, notably rural individuals. Despite surgical interventions being the standard treatment, recurrent cases underline the necessity for understanding the underlying biological mechanisms contributing to pterygium pathogenesis. Recent advancements in cellular death mechanisms point to cuproptosis, a copper-dependent programmed cell death pathway, as a potential regulatory factor in ocular diseases, including pterygium. This study aims to systematically investigate the immunological significance of cuproptosis-related genes (CuRGs) in pterygium's pathogenesis using an integrative bioinformatics framework. We performed transcriptomic profiling on pterygium tissues and employed machine learning algorithms to identify pivotal biomarkers for pterygium risk stratification. Comprehensive immune profiling and functional enrichment analyses were conducted to elucidate the interplay between identified CuRGs and the immune microenvironment in pterygium. Our analysis highlighted 19 CuRGs, with eight genes displaying significant dysregulation in pterygium tissues (p < 0.05). We established robust associations between CuRG expression and prominent immune cell infiltrates, notably regulatory T cells and macrophages. Furthermore, three core biomarkers (SERTAD1, JMJD1C, CSRNP1) were identified through machine learning and validated by QPCR, with the support vector machine model demonstrating exceptional predictive performance (AUC = 0.84). Empirical validation corroborated significant downregulation of selected biomarkers in pterygium tissue samples compared to normal conjunctiva. Our findings underscore the vital role of CuRGs in modulating pterygium development through immune and metabolic interactions, establishing their potential as novel therapeutic targets. Nevertheless, our study has limitations, as these findings are hypothesis-generating and require validation in larger patient cohorts.},
}
@article {pmid42263834,
year = {2026},
author = {Veli-Quispe, D and Urquizo-Prado, S and Cesare-Ariza, E and Ybaseta-Medina, J and Panay-Centeno, J and Tasayco-Márquez, LM and Ubillus, M and Montoya, Y and Torres-Roman, JS},
title = {Trends and regional inequalities in cerebrovascular disease mortality in Peru: An ecological time-series analysis, 2017-2025.},
journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association},
volume = {35},
number = {8},
pages = {108675},
doi = {10.1016/j.jstrokecerebrovasdis.2026.108675},
pmid = {42263834},
issn = {1532-8511},
mesh = {Humans ; Peru/epidemiology ; *Cerebrovascular Disorders/mortality/diagnosis ; Female ; Male ; Time Factors ; Risk Factors ; *Health Status Disparities ; Aged ; Databases, Factual ; Middle Aged ; Risk Assessment ; Sex Distribution ; *Rural Health ; Cause of Death/trends ; Adult ; Age Distribution ; Socioeconomic Disparities in Health ; Urban Health ; Sex Factors ; Aged, 80 and over ; },
abstract = {BACKGROUND: Cerebrovascular disease remains a leading cause of mortality worldwide. In Peru, evidence on recent mortality trends and regional disparities is limited.<br><br>OBJECTIVE: To evaluate temporal trends and regional disparities in cerebrovascular disease mortality in Peru between 2017 and 2025.<br><br>METHODS: An ecological time-series study was conducted using national mortality data from the National Death Information System (SINADEF). Deaths with cerebrovascular disease as the underlying cause (ICD-10: I60-I69) were included. Age-standardised mortality rates (ASMRs) per 100,000 person-years were calculated using the SEGI world standard population. Temporal trends were analyzed using Joinpoint regression models to estimate annual percent change (APC) and average annual percent change (AAPC) with 95% confidence intervals (95% CI).<br><br>RESULTS: National cerebrovascular disease mortality rates remained relatively stable between 2017 and 2025 in both men and women. However, marked regional disparities were identified. The highest mortality rates were concentrated in Huancavelica, San Mart&#xed;n, and Apur&#xed;mac. Among men, a significant increase was identified in Huanuco (APC: 7.6%; 95% CI: 2.6 to 12.9), whereas significant decreasing trends were observed in Lambayeque (APC: -8.0%; 95% CI: -14.0 to -1.6), Madre de Dios (APC: -5.9%; 95% CI: -11.3 to -0.2), Tacna (APC: -5.8%; 95% CI: -9.7 to -1.7), and Tumbes (APC: -5.9%; 95% CI: -10.7 to -0.9). Among women, Huanuco also showed a significant increase (APC: 7.0%; 95% CI: 4.0 to 10.1), while significant decreasing trends were identified in Callao (APC: -5.3%; 95% CI: -8.2 to -2.3), La Libertad (APC: -5.7%; 95% CI: -11.0 to -0.02), Moquegua (APC: -8.6%; 95% CI: -14.0 to -2.9), and Tacna (APC: -6.5%; 95% CI: -11.2 to -1.5).<br><br>CONCLUSION: Cerebrovascular disease mortality in Peru remained relatively stable at the national level but showed important regional heterogeneity. These findings highlight geographic disparities in mortality patterns and underscore the need for further research and region-specific public health strategies to improve cerebrovascular disease prevention and care.},
}
@article {pmid42395566,
year = {2026},
author = {Formenti, G and Absolon, DE and Abueg, LAL and Ackerman, F and Al-Ajli, FO and Aleixo, A and Antunes, A and Arcila, D and Audet, JN and Balacco, JR and Beavan, AJS and Belov, K and Betancur-R, R and Bidwell, SL and Biegler, MT and Bista, I and Blaxter, M and Boyer, K and Braasch, I and Bradbury, IR and Brajuka, N and Bronikowski, AM and Brown, T and Butler, G and Cao, S and Charvel, E and Chen, Y and Ciofi, C and Clawson, HM and Collins, JC and Correard, S and Corrigan, S and Couture, M and Crawford, AJ and D'Alessandre, ND and da Conceicao, HB and da Fonseca, RR and Daigavane, M and Dalapicolla, J and de Bruyn, M and de Jong, E and De Panis, DN and Detrich, HW and Scott, CD and Diekhans, M and Duarte, E and Durbin, R and Escalona, M and Eschenbrenner, M and Fedrigo, O and Fenn, J and Flannery, P and Forde, N and Gable, SM and Galante, PA and Ganesan, R and Gardiner, A and Garrison, E and Gemmell, NJ and Gilbert, MTP and Giudicelli, F and Gonçalves, TM and Guardia, GDA and Guarracino, A and Gupta, A and Haase, B and Hays, D and Hickey, G and Hiller, M and Hime, PM and Hogg, CJ and Horan, KM and Howe, K and Jackson, D and Jain, N and Kang, L and Kliver, S and Ko, BJ and Koepfli, KP and Komissarov, A and Komoroske, LM and Koo, B and Koren, S and Korlach, J and Kovacic, I and Krasheninnikova, K and Kuderna, LF and Langlois, RA and Lariviere, D and Larkin, DM and Lee, C and Lee, YH and Lewin, HA and Lim, D and Lou, RN and Mak, SS and Makova, KD and Marín-Gual, L and Marques-Bonet, T and Martin, FJ and Mathers, TC and Mazzoni, CJ and McCaffrey, K and McCarthy, SA and Medico, JA and Mercuri, RLV and Meyer, A and Michalak, P and Mirarab, S and Morin, PA and Mountcastle, J and Murphy, RW and Murphy, TD and Myers, EW and Naylor, GJ and Near, T and Nekrutenko, A and Ning, Z and Novak, BJ and O'Brien, MF and O'Connell, MJ and O'Toole, BP and Paez, S and Paten, B and Paulini, M and Pelan, SE and Pennell, M and Pfenning, AR and Phillippy, AM and Pinto, B and Pippel, M and Popova, M and Prylutskyi, M and Rhie, A and Crollius, HR and Ruiz-Herrera, A and Ryder, O and Safonova, Y and Santos, CA and Schatz, MC and Secomandi, S and Shaffer, HB and Shalmiyev, L and Shapiro, B and Smith, JJ and Sollitto, M and Sotero-Caio, CG and Steiner, CC and Sudmant, PH and Sweeney, DJ and Talbot, SC and Taylor, CH and Teeling, EC and Thibaud-Nissen, F and Tilley, T and Timoshevskaya, N and Traore, P and Turakhia, Y and Uliano-Silva, M and Venditti, C and Venkatesh, B and Vernes, SC and Warren, WC and Whelan, CV and Wilson, MA and Winkler, S and Wood, JM and Zhang, G and Zhao, G and Jarvis, ED and , },
title = {The Vertebrate Genomes Project Phase I: A global reference genome resource.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42395566},
issn = {2692-8205},
abstract = {The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ~70,000 extant vertebrate species[1]. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for ~95% of vertebrate orders, along with additional lineages within those orders, totaling 816 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods[2-4], alongside the growth of associated consortium initiatives and international collaborations[5-9]. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers a reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine.},
}
@article {pmid42400857,
year = {2026},
author = {Meng, Q and Ma, M and Li, S and Han, X and Jin, T and Jiao, Y and Wang, L},
title = {Structural Variability in Bulk Soil and Rhizosphere Microbial Communities at Different Restoration Modes of Open-pit Coal Mine.},
journal = {Environmental management},
volume = {76},
number = {7},
pages = {},
pmid = {42400857},
issn = {1432-1009},
support = {HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; },
mesh = {*Soil Microbiology ; *Rhizosphere ; *Soil/chemistry ; *Coal Mining ; Nitrogen/analysis ; *Microbiota ; Bacteria ; *Environmental Restoration and Remediation/methods ; Carbon/analysis ; },
abstract = {Microbial communities serve as vital indicators of ecosystem health and play a crucial role in facilitating the restoration of degraded soil ecosystems, acting as key participants in soil nutrient cycling. However, the interaction mechanisms between microbial communities and plants in different soil zones under varying restoration approaches remain unclear. This study focused on a restoration area of a decommissioned open-pit coal mine in an alpine region, comparing the microbial community structure and nutrient characteristics of rhizosphere and bulk soils under two restoration methods: herbaceous vegetation restoration and sea-buckthorn shrub restoration. The aim is to reveal the impact of different restoration measures on the soil-microorganism interactions. The results demonstrated that soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), total potassium (TK), and available potassium (AK) contents were significantly higher in the herbaceous restoration area (O) than in the seabuckthorn area (S), by 51.7%, 88.6%, 38.2%, 13.1%, and 4.7%, respectively. Compared to bulk soil, rhizosphere soil exhibited higher microbial community diversity and richness. Furthermore, seabuckthorn rhizosphere microbial diversity surpassed that of herbaceous rhizosphere. Different restoration areas (DRE) significantly (p < 0.05) influenced the relative abundances of Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. The seabuckthorn area showed higher proportions of Proteobacteria (26.48 - 42.86%) and Actinobacteria (28.26 - 45.19%) compared to the herbaceous area. Functional gene prediction revealed that the seabuckthorn area expressed significantly higher abundances of core metabolic functional genes related to energy production and conversion (C), amino acid transport and metabolism (E), carbohydrate metabolism (G), and lipid metabolism (I) than the herbaceous area. Additionally, a symbiotic functional guild comprising animal pathogens, endophytes, lichen parasites, plant pathogens, and wood saprotrophs was formed in the seabuckthorn area. Redundancy analysis (RDA) indicated significant positive correlations (p < 0.05) between Acidobacteria, Chloroflexi, Actinobacteria, and Ascomycota and the contents of SOC, TN, and total phosphorus (TP). Bacterial networks formed with Actinobacteria as the core hub, comprising 300 edges connecting 50 nodes, while fungal networks were dominated by Ascomycota. Based on these findings, this study proposes a synergistic restoration strategy characterized by "herbaceous-induced short-term priming" coupled with "seabuckthorn-driven long-term stability." This strategy provides a theoretical foundation for the targeted microbial regulation of ecological restoration in mining areas.},
}
@article {pmid42404501,
year = {2026},
author = {Hossain, MJ and Mim, NA and Akter, N and Sony, SA and Saikat, EH and Hossain, MA and Parvin, N and Evan, MR and Juma, JJ and Roy, PP and Maruf, MFI and Islam, R and Labib, A and Shatabde, ZA and Das, M and Amanulla, M},
title = {Epidemiological Trends, Public Health Challenges, and Strategic Control Priorities of Dengue in Bangladesh (2000-2024): A Narrative Review.},
journal = {Health science reports},
volume = {9},
number = {7},
pages = {e72747},
pmid = {42404501},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Dengue has evolved into a major public health crisis in Bangladesh, transitioning from sporadic outbreaks to endemic transmission with increasing frequency and severity. The unprecedented 2023 epidemic recorded more deaths than the cumulative total of the previous two decades, highlighting the urgent need for a comprehensive synthesis of epidemiological trends and control challenges.<br><br>METHODS: This narrative review synthesizes published literature, surveillance reports, and national health data from 2000 to 2024 to examine the evolving epidemiology, clinical characteristics, transmission dynamics, and public health responses related to dengue in Bangladesh.<br><br>RESULTS: Epidemiological analysis reveals a dramatic rise in incidence and mortality, with widespread geographic expansion beyond Dhaka into southern and rural districts and a shift toward earlier seasonal peaks. Serotype transitions, particularly the dominance of DENV-3 followed by DENV-2-likely intensified disease severity through secondary infections. High case fatality rates were observed among females and older adults, with a substantial proportion of deaths occurring within 24&#x2009;h of hospitalization, suggesting critical gaps in care-seeking and clinical management. Transmission dynamics are shaped by interactions between Aedes vector ecology, climate change, rapid urbanization, human mobility, and extensive insecticide resistance to pyrethroids. Public health responses remain constrained by passive surveillance, limited vector control efficacy, healthcare system strain, and insufficient community engagement.<br><br>CONCLUSIONS: The dengue burden of Bangladesh underscores the need for integrated and adaptive control strategies. Strengthening multi-domain surveillance (epidemiological, entomological, genomic), implementing resistance-aware Integrated Vector Management incorporating novel approaches such as Wolbachia, enhancing healthcare readiness, promoting community-driven behavioral interventions, integrating climate adaptation measures, and advancing vaccine and therapeutic research within a One Health framework are critical for sustainable dengue prevention and control.},
}
@article {pmid42406780,
year = {2026},
author = {Colombo, EH and Tarnita, CE and Bonachela, JA},
title = {Zooplankton feeding behavioral signatures in the morphology of macroscale prey spatial distribution.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1014411},
pmid = {42406780},
issn = {1553-7358},
mesh = {Animals ; *Zooplankton/physiology ; *Feeding Behavior/physiology ; *Models, Biological ; *Predatory Behavior/physiology ; Ecosystem ; Food Chain ; Computational Biology ; Phytoplankton/physiology ; },
abstract = {The problem of pattern and scale remains central in ecology, bridging fundamental and applied questions. Marine microbial communities are a case in point. For instance, to understand the role of zooplankton in oceanic biogeochemistry, their response to changes in environmental conditions, and the implications for ecosystem services (e.g., fisheries), it is critical to understand zooplankton trophic interactions and how they change in a rapidly changing climate. This understanding, however, remains elusive because, unlike for phytoplankton, for which remote sensing of macroscale patterns can provide insight into their microscale dynamics and community composition, obtaining this information for zooplankton largely rests on quantifying the difficult-to-monitor microscale interactions among millions of individuals with different behaviors, and between individuals and their environment. Here, we investigate whether it is possible to obtain indirect information on zooplankton from the macroscale spatial distribution of their prey. To tackle this "problem of scale," we develop a rigorous coarse-graining methodology that connects individual-level properties with macroscale spatial patterns. We demonstrate that the shape of the prey spatial distribution can encode information about zooplankton feeding behavior and community dynamics. Specifically, we predict a change in dominant feeding behavior-from non-motile to motile feeding-as one moves from areas of high to areas of low prey density. These computational results are validated by our analysis of satellite images of oceanic blooms around the globe, which suggests novel opportunities for remote sensing approaches: the potential tracking of consumer behavioral signatures in the large-scale patterns of the resource. Importantly, the scaling-up methodology developed here to check for those signatures is general, and can be used to link scales rigorously and systematically in any system in which the complexity of individual dynamics makes connecting scales intractable.},
}
@article {pmid42407401,
year = {2026},
author = {Ibrahim, NA and Mehta, H and Sulieman, AME and Mir, RH and Fatima, SB and Adnan, M and Surti, M},
title = {Trichoderma-mediated biogenic synthesis of metal nanoparticles: Implications for soil health, plant resilience, and sustainable agroecosystems.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128614},
doi = {10.1016/j.micres.2026.128614},
pmid = {42407401},
issn = {1618-0623},
mesh = {*Trichoderma/metabolism ; *Metal Nanoparticles/chemistry ; Plant Development ; Soil Microbiology ; Agriculture/methods ; Agroecology ; Green Chemistry Technology ; Antifungal Agents/pharmacology ; Soil/chemistry ; Plants/microbiology ; Agrochemicals ; },
abstract = {The growing demand for sustainable agricultural practices has accelerated interest in eco-friendly alternatives to conventional agrochemicals. Among these, metal nanoparticles synthesized through biological routes have emerged as promising tools for crop protection and productivity enhancement. Trichoderma species, widely recognized for their biocontrol and plant growth-promoting properties, have gained considerable attention as efficient biofactories for the green synthesis of metal nanoparticles. The diverse metabolites produced by these fungi facilitate the reduction and stabilization of metal ions, resulting in nanoparticles with desirable physicochemical and biological properties. This review provides a comprehensive overview of the biosynthesis of metal nanoparticles by Trichoderma species, highlighting the underlying mechanisms, adaptation strategies to metal stress, and key physicochemical and biological factors influencing nanoparticle formation. Furthermore, the major types of Trichoderma-derived metal nanoparticles and their roles in antibacterial and antifungal activities, as well as plant growth promotion, are discussed. The potential of these nanoparticles to enhance plant health and support sustainable agricultural practices while minimizing the use of synthetic agrochemicals is also examined. Current limitations, challenges associated with field-level applications, and future research directions required for the successful translation of laboratory findings into practical agricultural systems are also discussed. Overall, Trichoderma-mediated nanoparticles represent a promising and sustainable approach for advancing next-generation agricultural technologies.},
}
@article {pmid42417989,
year = {2026},
author = {Castner, MD and Kitchen, C and Xiong, C and Bittle, MJ and Nestadt, PS and Wilcox, HC and Kharrazi, H},
title = {Assessing the utility of health access data and social determinants of health in ecological suicide prediction models.},
journal = {Social psychiatry and psychiatric epidemiology},
volume = {},
number = {},
pages = {},
pmid = {42417989},
issn = {1433-9285},
support = {R01 MH124724/MH/NIMH NIH HHS/United States ; R56 MH117560/MH/NIMH NIH HHS/United States ; R01 MH124724/MH/NIMH NIH HHS/United States ; },
abstract = {PURPOSE: Assess the utility of access to healthcare, clinical conditions, and social determinants of health (SDoH) variables in population-level suicide prediction models.<br><br>METHODS: Negative binomial regression models were constructed using data from population-level surveys, state death certificates, federal records of behavioral health services, and U.S. Census data. Outcomes of interest were suicidal ideation and suicide attempt (SISA), inpatient psychiatric hospitalization (IPH), and suicide death. The relative changes in pseudo R[2] were used to assess the impact of variable categories (i.e., clinical conditions, access to healthcare, and geo-derived SDoH) when added to a demographic-only baseline suicide prediction model.<br><br>RESULTS: Clinical data showed a significant impact, with the largest percent increase in pseudo R[2] compared to the demographic-only baseline model (321.9% for SISA; 736.9% for IPH; 18.9% for suicide death). Access to healthcare and geo-derived SDoH also improved model performances for all outcomes, but considerably lower than clinical variables. Models with all variable categories had the highest pseudo R[2], with .68, .58, and .46 for SISA, IPH, and suicide, respectively. Availability of emergency mental health services was found to be protective against IPH (IRR .90; 95% CI .84-.96) and suicide death (IRR .91; 95% CI .84-.97).<br><br>CONCLUSIONS: Clinical data proved to have the most effective variables in predicting a continuum of suicidal behaviors. While the impacts of access to healthcare and SDoH factors were comparatively limited, these variables also contributed to additional model improvements. These findings show the utility of population-level healthcare services and SDoH for ecological suicide behavior risk prediction.},
}
@article {pmid42390742,
year = {2026},
author = {Wu, S and Tatsis, EC},
title = {In Silico Identification and Comparative Synteny of Biosynthetic Gene Clusters in Plants.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3054},
number = {},
pages = {15-27},
pmid = {42390742},
issn = {1940-6029},
mesh = {*Multigene Family ; *Synteny ; *Computational Biology/methods ; *Plants/genetics/metabolism ; Software ; *Biosynthetic Pathways/genetics ; Genomics/methods ; Genome, Plant ; Computer Simulation ; Molecular Sequence Annotation ; },
abstract = {Biosynthetic gene clusters (BGCs) are often encoding specialized metabolic pathways in plants, yet effective methods for the comparison across multiple species are still evolving. In this protocol, we present a bioinformatics approach combining plantiSMASH and MCScan for the identification, annotation, and comparative analysis of BGCs in plant genomes. The methodology involves using plantiSMASH to predict and annotate potential BGCs, followed by the use of MCScan to perform syntenic analysis, enabling the exploration of the conservation and evolutionary dynamics of BGCs across different plant species. Here, we provide a step-by-step guide for installing and configuring the necessary software, preparing genomic data, and executing the analysis. This methodology, integrated with transcriptomic and metabolomic data, can be used to verify the functional relevance of the identified BGCs in specific biosynthetic pathways. It is applicable to a broad range of plant species and serves as a framework for the discovery and characterization of BGCs. The described methodology can significantly enhance research in plant genomics and metabolic engineering by offering new insights into the organization and function of BGCs.},
}
@article {pmid42391637,
year = {2026},
author = {Cui, B and van Beijnum, BJ and Tabak, M and Wang, Y},
title = {Sensor-Based Monitoring of Knee Osteoarthritis Symptoms in Free-Living Settings: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e84262},
pmid = {42391637},
issn = {1438-8871},
mesh = {Humans ; Digital Health ; Monitoring, Physiologic/instrumentation ; *Osteoarthritis, Knee/physiopathology/diagnosis ; Quality of Life ; *Wearable Electronic Devices ; },
abstract = {BACKGROUND: Knee osteoarthritis is a heterogeneous condition characterized by chronic pain, stiffness, and fatigue that fluctuate rapidly over time. Traditional clinical assessments provide only static diagnoses of disease severity, failing to capture the dynamic, day-to-day symptom variability that impacts patient quality of life. While wearable technologies offer the potential for continuous, high-frequency monitoring, previous reviews have examined general technological interventions for knee osteoarthritis management, yet they lack a specific synthesis of technologies for symptom monitoring.<br><br>OBJECTIVE: This study aims to synthesize current research on sensor technologies used for the continuous monitoring of knee osteoarthritis symptoms in free-living or simulated daily environments. Specifically, the review seeks to (1) map sensor modalities to specific symptom domains (biomechanical, physiological, and behavioral); (2) evaluate the alignment between objective sensor metrics and patient-reported outcome measures; and (3) identify gaps in current monitoring paradigms.<br><br>METHODS: A systematic literature search was conducted across PubMed, Embase, Web of Science, and IEEE Xplore. The review followed the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines. Eligibility criteria included studies involving participants with knee osteoarthritis using wearable or portable sensors capable of continuous monitoring (eg, inertial measurement units and electrocardiography) and assessing clinical symptoms (eg, pain, fatigue, and stiffness). Studies relying solely on stationary laboratory equipment (eg, force plates) without a portable component were excluded to ensure relevance to real-world applicability. Data regarding sensor types, sampling frequencies, monitored symptoms, and the statistical association between objective features and subjective symptom severity (key findings) were extracted.<br><br>RESULTS: A total of 16 studies met the inclusion criteria. The summary constructed from the results revealed a distinct technological saturation: the majority of studies (n=6) used inertial measurement units to quantify biomechanical deficits (eg, gait asymmetry and range of motion), which showed robust correlations with functional limitations. In contrast, there was a notable scarcity of research using physiological sensors (eg, electrocardiography and bioimpedance) to monitor systemic symptoms. Crucially, findings highlighted a significant discrepancy between subjective and objective data, particularly in sleep monitoring, where poor self-reported sleep quality predicted pain exacerbations despite stable objective actigraphy metrics. Furthermore, most systems operated as passive data loggers, with a lack of integration into active feedback loops.<br><br>CONCLUSIONS: Unlike previous reviews focused solely on biomechanics, this study innovatively maps the use of sensors across a multidimensional symptom spectrum, revealing a critical gap in the monitoring of fatigue and physiological stress. The findings suggest that current sensor applications are limited by a lack of integration with subjective patient experiences. Real-world implementation requires a hybrid monitoring paradigm that combines the ecological validity of wearable sensors with the clinical relevance of patient-reported outcomes. This approach paves the way for digital phenotyping and active feedback systems, offering a personalized strategy for managing the complex symptom burden of knee osteoarthritis.},
}
@article {pmid42391685,
year = {2026},
author = {Hirose, K and Inomata, Y and Povinec, PP and Tsumune, D and Yamada, M and Zheng, J},
title = {Temporal trends and tracing capabilities of plutonium in the western North Pacific Ocean.},
journal = {Journal of environmental radioactivity},
volume = {298},
number = {},
pages = {108086},
doi = {10.1016/j.jenvrad.2026.108086},
pmid = {42391685},
issn = {1879-1700},
abstract = {Plutonium is a valuable temporal and spatial tracer in biogeochemical research due to its strong chemical reactivity, serving as a significant resource for tracking water mass movement. Because two major sources of plutonium exist in the North Pacific Ocean - global fallout (GF-Pu) from nuclear weapons tests and close-in fallout from the US Pacific Proving Ground (PPG-Pu), investigating its distribution and cycling is highly viable. Here, we examine temporal and spatial changes in [239,240]Pu activity concentrations and [240]Pu/[239]Pu atom ratios in surface and deep waters by analyzing Pu data from 1960 to 2020. Surface [239,240]Pu in the subarctic North Pacific has showed a declining trend after 2000, with a rate of decrease comparable to that in the subtropical region (apparent half-life of 6.4 y). Deep [239,240]Pu levels in the North Pacific also declined on a decadal timescale, likely reflecting the northward flow of deep water with low [239,240]Pu concentrations near 20°N. The [240]Pu/[239]Pu atom ratio in surface waters of the subtropical North Pacific indicates that GF-derived Pu ([240]Pu/[239]Pu atom ratio of 0.18) dominated surface Pu levels until 1980, after which PPG-derived Pu ([240]Pu/[239]Pu atom ratio of 0.33) became the dominant component. In the deep waters of the North Pacific, PPG-Pu signals were detected in the subarctic region during 1981 and 1988. Consequently, the [240]Pu/[239]Pu atom ratio serves as a powerful tool for unraveling the complexities of Pu cycling. These observations are important for better understanding of surface and deep-water flows, vertical motion, and biogeochemical processes in the western North Pacific Ocean.},
}
@article {pmid42392792,
year = {2026},
author = {Abbà, S and Vallino, M and Cicerone, A and Cirrincione, S and Aiuto, B and Galetto, L and Rossi, M},
title = {Multi-Omics Profiling of the Scaphoideus titanus Yeast-Like Symbiont Guides the Bioinformatic Discovery of Related Fungal Symbioses in Insects.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70361},
pmid = {42392792},
issn = {1462-2920},
support = {CUP B17G23000320005//Ministero dell'Agricoltura, della Sovranit&#xe0; Alimentare e delle Foreste; Project MICOTI/ ; },
mesh = {Animals ; *Symbiosis ; *Hemiptera/microbiology ; Phylogeny ; Computational Biology ; Multiomics ; Proteomics ; *Hypocreales/genetics/classification ; Genomics ; },
abstract = {Symbiotic partnerships have opened new ecological niches and contributed to the remarkable diversification of insects. The leafhopper Scaphoideus titanus, a phloem-feeding insect known to be the primary vector of Flavescence dorée phytoplasma, harbours two primary endosymbionts: the bacterium 'Candidatus Karelsulcia muelleri' and a yeast-like symbiont (YLS). While most studies on insect-associated microorganisms have focused on obligate bacterial symbionts, fungal endosymbionts, although documented for almost a century, are only now gaining renewed attention for their evolutionary and ecological significance. In this study, we integrated genomic and proteomic data with phylogenetic analyses to elucidate the functional and evolutionary features of the YLS associated with S. titanus. Using a data-independent proteomic approach supported by a newly sequenced symbiont genome, we defined the proteins expressed by the YLS that may contribute to host physiology. Comparative analyses across the five currently available YLS genomes enabled a proteome-wide phylogenetic reconstruction within the genus Ophiocordyceps, refining the evolutionary placement of these symbioses. Finally, large-scale mining of NCBI transcriptomic Sequence Read Archive datasets using a novel computational workflow, combined with an extensive literature survey, identified several new candidate insect hosts and provided a comprehensive inventory of species harbouring these fungal partners.},
}
@article {pmid41604136,
year = {2026},
author = {Qian, Z and Tian, J and Chen, Q and Zhang, Y and Zhang, C and Yin, S and Zhang, K},
title = {Multi-Omics Analysis Uncovers Acute Hypoxia-Induced Gut Damage and the Underlying Protective Mechanisms of Probiotic Clostridium butyricum B3 in Yellow Catfish (Pelteobagrus fulvidraco).},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {5},
pages = {6945-6964},
pmid = {41604136},
issn = {1867-1314},
support = {JBGS[2021]034//The "JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; 32102760//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Catfishes/microbiology/metabolism ; *Probiotics/administration &amp; dosage/pharmacology ; *Clostridium butyricum/physiology ; Multiomics ; *Hypoxia/metabolism ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Acute hypoxia stress poses a significant challenge in aquaculture, not only compromising gut health but also resulting in substantial economic losses. Using an integrated multi-omics approach, this study demonstrates that hypoxia severely disrupts the intestinal function of yellow catfish (Pelteobagrus fulvidraco), specifically manifesting as phospholipid metabolism disorders, inhibited fatty acid β-oxidation, reduced short-chain fatty acid (SCFA) synthesis, imbalanced gut microbiota (e.g., decreased levels of beneficial lactic acid bacteria Lactococcus and Clostridium sensu stricto 1), and downregulation of detoxification pathways mediated by cytochrome P450. Building upon the previously isolated and identified high-yield SCFA-producing probiotic Clostridium butyricum B3 from yellow catfish in early work, this research further investigated the efficacy and mechanisms of B3 supplementation in mitigating hypoxia-induced intestinal barrier damage in yellow catfish. The results indicated that the supplementation of C. butyricum B3, particularly at a dose of 3.0 × 10[7] CFU/g, significantly reduced histological damage, enhanced the expression of key tight junction proteins (such as ZO-1 and Claudin), and modulated hypoxia-inducible factor signaling pathways (including HIF-1α, FIH, and PHD). Furthermore, the application of C. butyricum B3 restored microbial ecological balance by promoting the growth of beneficial bacteria like Cetobacterium and inhibiting potential pathogens such as Acinetobacter. In conclusion, these findings underscore the potential of C. butyricum B3 as a novel probiotic strategy for enhancing fish hypoxia tolerance and maintaining intestinal integrity, offering valuable insights for sustainable aquaculture practices.},
}
@article {pmid42283564,
year = {2026},
author = {Ardizzone, CM and Lammons, JW and Lan, RS and Elnaggar, JH and Lillis, RA and Toh, E and Pack, LM and Mott, PD and Jacobs, CD and Yeruva, L and Taylor, CM and Quayle, AJ},
title = {Integrated multi-omics analysis uncovers cervicovaginal ecological networks and their association with Chlamydia trachomatis load.},
journal = {Infection and immunity},
volume = {94},
number = {7},
pages = {e0068125},
doi = {10.1128/iai.00681-25},
pmid = {42283564},
issn = {1098-5522},
support = {T32 AI060519/NH/NIH HHS/United States ; R01 AI118860/NH/NIH HHS/United States ; },
mesh = {Female ; Humans ; Multiomics ; *Chlamydia trachomatis/physiology ; *Vagina/microbiology ; *Chlamydia Infections/microbiology ; Cytokines/metabolism ; Microbiota ; Vaginosis, Bacterial/microbiology ; Tryptophan/metabolism ; *Cervix Uteri/microbiology ; Metabolome ; RNA, Ribosomal, 16S/genetics ; *Bacterial Load ; Tandem Mass Spectrometry ; },
abstract = {Chlamydia trachomatis (Ct) is a causal agent of upper reproductive tract pathology. There is a broad spectrum of cervical Ct load in infected women, and upper tract infection is associated with higher cervical Ct load. Recent studies indicate that bacterial vaginosis (BV) can modulate host-Ct outcomes. To identify features associated with BV status and Ct load, we performed an integrated multi-omics analysis of the cervicovaginal microbiome, tryptophan metabolome, and cytokines. Samples were analyzed using 16S rRNA gene sequencing, targeted UPLC-MS/MS quantification of tryptophan metabolites, and multiplex cytokine profiling. Ordination analyses showed that BV status was separated by the microbiome, metabolome, and cytokines, whereas Ct load was separated only by cytokines. K-means clustering of tryptophan metabolites defined three metabolome state types (MSTs). MST I, associated primarily with Lactobacillus crispatus-dominated community state type (CST) I, exhibited high tryptophan availability, indole-3-lactic acid, and complete kynurenine-pathway activity. Both MST II and MST III were associated with BV-associated CST IV and showed marked tryptophan depletion. MST II was broadly depleted of most tryptophan metabolites, while MST III was enriched in downstream microbially derived indole pathway metabolites and kynurenic acid. Hierarchical all-against-all association testing revealed coordinated relationships linking clusters of bacterial taxa, metabolites, and cytokines. Importantly, multi-omics network analyses identified integrated microbial-metabolic-immune modules that predicted high versus low Ct load, highlighting CXCL9, CXCL10, IL-17, BV-associated taxa, and indole pathway metabolites as key discriminative features. Results demonstrate that cervical Ct load reflects coordinated microbial-metabolic-immune ecological states rather than microbiome composition alone and refine current models of Ct-BV interactions.},
}
@article {pmid42374709,
year = {2026},
author = {Yuan, R and Shu, P and Salam, M and Wu, S and Liu, Y and Li, H and Li, W},
title = {Cadmium(II) Loading Exacerbates the Negative Effects of Nanobiochar on Daphnia magna: Evidence from Toxicity Test and Multiomics Analysis.},
journal = {Environmental science &amp; technology},
volume = {60},
number = {27},
pages = {19090-19105},
doi = {10.1021/acs.est.6c01162},
pmid = {42374709},
issn = {1520-5851},
mesh = {Animals ; *Daphnia magna/drug effects ; *Cadmium ; Multiomics ; Water Pollutants, Chemical ; Toxicity Tests ; Daphnia ; Charcoal ; },
abstract = {Micro- (M-BC) and nanobiochar (N-BC) particles exhibit strong environmental mobility and superior adsorption capacity for heavy metals. This raises concerns regarding their ecological risks to aquatic ecosystems. However, systematic studies on the toxicity of contaminant-laden M-BC and N-BC to aquatic biota remain scarce. Here, we prepared the cadmium (Cd(II))-loaded complexes (M-BC-Cd and N-BC-Cd), identified the acute toxicity of M-BC-Cd and N-BC-Cd on zooplankton Daphnia magna, and emphasized the response in D. magna induced by N-BC and N-BC-Cd. The results indicated that N-BC alone induced minimal adverse effects on D. magna. N-BC demonstrated a higher Cd(II) adsorption capacity than M-BC, leading to a lower LC50 level for N-BC-Cd. In chronic toxicity tests, exposure to N-BC-Cd resulted in a 30% reduction in the survival of D. magna compared to that of N-BC. The particles of N-BC-Cd caused more severe impairment in growth, reproduction, and oxidative stress responses. While N-BC primarily affected predation efficiency and disrupted metabolic pathways, the amplified toxicity of N-BC-Cd was attributed to a synergistic effect of prey limitation, metabolic dysregulation, oxidative stress, inhibition of signal transduction, and down-regulation of lysosomal proteins. This finding provides novel insights into assessing the environmental risks of biochar particles in aquatic ecosystems.},
}
@article {pmid42390619,
year = {2026},
author = {Ahlendorf, A and Aharoni, A and Vahabi, K and Fischer, TG and Allard, PM and Augustin, M and Bathe, U and Broadhurst, DI and Broeckling, C and Buescher, J and Covaci, A and da Silva, KM and de Vos, RCH and Devi, MG and Döll, S and Frey, M and Frolov, A and Gaquerel, E and Gautam, V and Charria-Girón, E and Goossens, A and Grosjean, J and Halabalaki, M and Iturrospe, E and Kultima, K and Herman, S and Kutchan, TM and Larbat, R and Meier, R and Mikropoulou, EV and Mouille, G and Nicolotti, L and Shahaf, N and Perreau, F and Pétriacq, P and Reichelt, M and Reinke, SN and Robeyns, R and Soboleva, A and Spring, O and Sreenivasan, AP and Tissier, A and Totozafy, JC and Tsugawa, H and Valls-Fonayet, J and van de Lavoir, M and van der Hooft, JJJ and Vergara, F and Wishart, D and Wessjohann, LA and Wolfender, JL and Ziegler, J and Balcke, GU and Neumann, S},
title = {The MassBank contributions of the mFam collaboration.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {4},
pages = {},
pmid = {42390619},
issn = {1573-3890},
mesh = {*Metabolomics/methods ; *Tandem Mass Spectrometry/methods ; Animals ; *Metabolome ; Databases, Factual ; Mass Spectrometry/methods ; },
abstract = {INTRODUCTION: The analysis of metabolic profiles using high resolution mass spectrometry (MS) data provides deep insights into biological processes. In metabolomics, MS analysis generates a large number of features that represent metabolites. However, identifying specific metabolites from these features can be challenging. One of the major bottlenecks in the metabolomics field is the identification of MS features, which is a prerequisite for any biochemical interpretation. By identifying similarities and differences within a metabolite family (mFam), evaluating MS features at the metabolite family level can help assigning functional roles to individual MS features. These data can help interpreting metabolic pathways and processes within a biological system. For the assignment of metabolite families to MS features, it is important to have good quality, reliable, and comprehensive spectral libraries.<br><br>OBJECTIVE: We initiated a global effort to collect high-resolution MS/MS spectra of metabolites from labs working in different fields, including metabolomics of animals, microorganisms, and plants. The mFam-MS/MS collection delivers valuable training data to assign machine-readable classified information on the unknown metabolites.<br><br>RESULTS: The mFam collaboration used a standardized metadata template and has developed a globally curated MS/MS spectral library of 7,872 spectra with 2,126 unique metabolites. This library was compiled from 47 datasets contributed by 25 laboratories measured on 12 instrument types, including QTOF, Orbitrap, and Ion Mobility-QTOF systems. It comprises 4,646 spectra in positive mode and 3,226 in negative mode. This standardized resource significantly enhances metabolite identification capabilities, supports the development of machine learning-based annotation tools, and accelerates the discovery of novel metabolites. All spectra are available under the collective contributor label mFam in the MassBank system, including the web interface and the 2025.10 data release available at GitHub and Zenodo.},
}
@article {pmid42390741,
year = {2026},
author = {Konkel, Z and Slot, J},
title = {Generalized Gene Cluster Detection Using CLOCI.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3054},
number = {},
pages = {1-14},
pmid = {42390741},
issn = {1940-6029},
mesh = {*Multigene Family ; Algorithms ; *Genomics/methods ; *Software ; *Computational Biology/methods ; Evolution, Molecular ; Clustering Algorithms ; Synteny ; },
abstract = {Metabolic gene clusters (MGCs) are genomic loci that contain multiple genes that are functionally and genetically linked. MGCs collectively encode a spectrum of metabolic functions, including small molecule biosynthesis, nutrient assimilation, metabolite degradation, and production of proteins essential for growth and development. Due to their diverse ecological functions, identifying gene clusters is a powerful tool for small molecule discovery and provides insight into the ecology and evolution of organisms. Gene cluster detection algorithms have historically been specialized for detecting biosynthetic gene clusters that contain canonical "core" biosynthetic functions, while overlooking uncommon or unknown cluster classes. These overlooked clusters are a potential source of novel natural products and comprise an untold portion of overall gene cluster repertoires. Unbiased, function-agnostic detection algorithms therefore provide an opportunity to reveal novel classes of gene clusters and more precisely define genome organization.We developed CLOCI (Co-occurrence Locus and Orthologous Cluster Identifier) as a generalized, unbiased gene cluster detection algorithm. CLOCI generalizes gene cluster detection by identifying signatures of coordinated gene evolution that underlie all classes of MGCs. CLOCI first detects selection on gene colocalization by identifying and circumscribing shared synteny loci across a dataset of genomes into homologous locus groups. Gene clusters comprise a subset of these homologous locus groups, and CLOCI implements orthogonal proxies of coordinated gene evolution, such as quantifying loss and horizontal transfer of a locus, to enrich MGCs from homologous loci. Here, we describe the conceptual framework of the CLOCI algorithm and present a description of its implementation (see Note 1).},
}
@article {pmid42330077,
year = {2026},
author = {Creus-Martí, I and Moya, A and Santonja, FJ},
title = {CoDaLoMic: An R package for modeling microbiome compositional and longitudinal data.},
journal = {PLoS computational biology},
volume = {22},
number = {6},
pages = {e1014328},
doi = {10.1371/journal.pcbi.1014328},
pmid = {42330077},
issn = {1553-7358},
mesh = {*Microbiota/genetics/physiology ; *Software ; *Computational Biology/methods ; Bacteria/genetics/classification ; Animals ; Longitudinal Studies ; Humans ; Models, Biological ; },
abstract = {In this paper we present CoDaLoMic, an R package for analyzing longitudinal and compositional microbiome datasets. The CoDaLoMic package implements three models specifically designed for the analysis of microbiome data that are both compositional and longitudinal. Unlike many existing methods that focus solely on pairwise interactions, CoDaLoMic also captures interactions among groups of bacteria, providing a more robust methodological framework for studying microbial relationships at the community level. In addition, the package facilitates the analysis of microbiome variability in relation to host health status and allows for the identification of groups of taxa that exhibit similar temporal dynamics. Working with time series data makes it possible to understand not only the current state of a microbial community but also its dynamics over time, which is essential for identifying patterns of ecological succession, detecting events of dysbiosis or recovery, and inferring potential causal relationships between taxa. On the other hand, focusing on interactions among groups of bacteria, rather than analyzing only pairwise relationships, enables a more integrated and functionally meaningful view of the microbiome. Many key ecological functions are the result of the collective behavior of functionally related groups of taxa. Two datasets have been considered in CoDaLoMic, one real and one simulated. The real dataset contains the information of the genera present in the microbiome of the Blatella germanica cockroach at 105 time points. The simulated dataset is defined taking Lotka-Volterra structure into account. CoDaLoMic is available at CRAN.},
}
@article {pmid42387942,
year = {2026},
author = {Saudreau, C and Tarazona, V and De Bandt, D},
title = {French Consumption of Methylphenidate in Primary Care From 2016 to 2023, Impact of Prescribing Policy Changes-A Time-Series Analysis.},
journal = {Pharmacoepidemiology and drug safety},
volume = {35},
number = {7},
pages = {e70424},
pmid = {42387942},
issn = {1099-1557},
mesh = {*Methylphenidate/therapeutic use/economics/administration &amp; dosage ; France ; Humans ; *Central Nervous System Stimulants/therapeutic use/economics/administration &amp; dosage ; *Attention Deficit Disorder with Hyperactivity/drug therapy ; *Practice Patterns, Physicians'/trends/statistics &amp; numerical data/economics ; *Primary Health Care/trends/statistics &amp; numerical data/economics ; Drug Prescriptions/statistics &amp; numerical data ; Health Policy ; Databases, Factual ; Drug Utilization/trends ; },
abstract = {PURPOSE: In France, methylphenidate, mainly used in the treatment of ADHD, has been subject to prescription restrictions that were relaxed at the end of 2021. This study analyses trends in methylphenidate consumption in France and examines changes following the modification to prescribing rules in 2021.<br><br>METHODS: This ecological study was based on data from the Medic'AM database, which records reimbursed outpatient drug dispensation in France from January 2016 to December 2023. Methylphenidate sales were expressed as defined daily dose per thousand inhabitants per day (DDD/TID) and expenditure as euros per thousand inhabitants. Time-series analyses were conducted to assess changes in methylphenidate sales and associated expenditure following modifications to prescribing arrangements in September and November 2021.<br><br>RESULTS: Methylphenidate consumption rose from 0.607 DDD/TID per month in 2016 to 1.457 DDD/TID in 2023, an increase of 84%. Associated expenditure followed a similar upward trend. A more pronounced increase in methylphenidate sales was observed after the end of 2021.<br><br>CONCLUSION: The study shows a clear increase in methylphenidate sales after 2021, coinciding with changes in prescribing regulations. Given the ecological design, this temporal association cannot be interpreted as causal. The observed trends likely reflect multiple factors, including regulatory changes, increased recognition of ADHD, and evolving clinical practices. These findings highlight how changes in prescribing policies may be associated with variation in healthcare utilization and expenditure.},
}
@article {pmid42389374,
year = {2026},
author = {Perea García, JO and Kano, F and Sibierska, M and Fiala, V and Skrok, MK and Danel, DP and Ratajczak, EK and Zywiczynski, P and Wacewicz, S},
title = {Gaze in context: non-human eyes can be more salient under ecologically relevant conditions.},
journal = {Evolutionary human sciences},
volume = {8},
number = {},
pages = {e25},
pmid = {42389374},
issn = {2513-843X},
abstract = {Primate eyes vary strikingly in pigmentation, yet the drivers of said variation are strongly debated. Recent revisions of the cooperative eye hypothesis propose that the human eye's sclera evolved to enhance gaze communication specifically under challenging conditions of visibility. We tested this idea under ecologically realistic conditions by presenting observers with a live model wearing contact lenses that simulated either a human-like or a chimpanzee-like eye. At a university lab, observers judged gaze direction at different viewing distances and lighting levels. We found no overall difference in efficacy of different eye types. Contrary to expectations, chimpanzee-like eyes outperformed human-like eyes in dim lighting and close-viewing conditions. Human-like eyes yielded the highest accuracy under bright, far-viewing conditions, consistent with a long-distance signalling advantage. Our results demonstrate that ecological visual constraints shape the potential informativeness of distinct ocular configurations. We hypothesize that species-typical eye appearances may be tuned to their species-typical visual ecology.},
}
@article {pmid42091894,
year = {2026},
author = {Solano, I and Bro-Jørgensen, J and Lazagabaster, IA and Thomas, CD and Manzano, S},
title = {NAMPHORA: a fossil and modern pollen database from Northern Africa and adjacent Mediterranean and Arabian regions.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42091894},
issn = {2052-4463},
support = {Grant: NE/S00713X/1//Adapting to the Challenges of a Changing Environment (ACCE) Doctoral Training Partnership, funded by the Natural Environment Research Council (NERC)/ ; Grant: RPG-2021-104//Biodiversity in Ancient Egypt during Societal Transitions (BEAST) project, funded by Leverhulme Trust/ ; Grant: RYC2021-034991-I//Ministerio de Ciencia e Innovaci&#xf3;n de Espa&#xf1;a MCIN/AEI/10.13039/501100011033 and European Union NextGenerationEU/PRTR./ ; Grant: PID2024-161027NA-I00 DivAS-Cape//MICIU/AEI/ 10.13039/501100011033 and by the ERDF/EU/ ; },
mesh = {*Pollen ; *Fossils ; Africa, Northern ; Mediterranean Region ; Climate ; *Databases, Factual ; Plants ; },
abstract = {Northern Africa's climate and vegetation underwent significant changes throughout the Holocene, particularly in connection with the termination of the African Humid Period ca. 5500 years ago. Fossil pollen records are key to reconstructing past environments, yet current databases for this region are limited by the omission of significant unpublished data, taxonomic inconsistencies, and the lack of standardised plant trait information. To address these issues, we introduce the Northern African, Arabian, and Mediterranean Pollen Holocene Records Archive (NAMPHORA)- a comprehensive, machine-readable and taxonomically-harmonised database compiling fossil and modern pollen records alongside plant functional traits, and ecological and phytogeographical information. This database includes all of Africa to the north of 7.52° N and constitutes the most complete and comprehensive resource (836 pollen records; 853 harmonised pollen types, and 13 key standardised plant traits) to improve palaeoecological reconstructions, enhance biogeographical analyses, and refine climate models for northern Africa during the Holocene. It enables direct data retrieval via programming languages such as R, and all datasets and code are openly available via Zenodo.},
}
@article {pmid42387317,
year = {2026},
author = {Chen, Z and Wang, S and Sun, Z and Liao, H and Longji, Y and Zhang, Q and Wang, J},
title = {An AI-Driven Multi-Omics Framework Identifies CASP8 as a Clinically Actionable Pyroptosis Biomarker in Bladder Cancer.},
journal = {BioFactors (Oxford, England)},
volume = {52},
number = {4},
pages = {e70130},
doi = {10.1002/biof.70130},
pmid = {42387317},
issn = {1872-8081},
mesh = {*Urinary Bladder Neoplasms/genetics/pathology/metabolism ; Humans ; *Biomarkers, Tumor/genetics/metabolism ; *Caspase 8/genetics/metabolism ; *Pyroptosis/genetics ; Machine Learning ; Multiomics ; Gene Expression Regulation, Neoplastic ; Cell Line, Tumor ; Tumor Microenvironment/genetics ; Genomic Instability ; Artificial Intelligence ; },
abstract = {Despite rapid advances in multi-omics technologies, translating candidate biomarkers into clinical practice for bladder cancer remains challenging due to the difficulty of linking complex genomic instability to interpretable biological processes. To address this, we developed an AI-driven multi-omics discovery framework integrating single-cell RNA sequencing, multi-cohort transcriptomics, and machine learning-based genomic inference. By analyzing chromosomal aneuploidy and copy number variations at single-cell resolution, we identified malignant cell populations and constructed a consensus pyroptosis scoring system, followed by machine learning-assisted biomarker screening and experimental validation. Our results reveal that while global pyroptosis activity is elevated in the bladder cancer microenvironment, malignant cells with high genomic instability exhibit significant pyroptosis suppression. Through this pipeline, CASP8 was identified as a key clinically relevant biomarker; its low expression correlates strongly with increased tumor mutation burden, frequent driver gene alterations (including TP53 and RB1), and poor survival outcomes. Functional assays further confirmed that CASP8 loss promotes malignant phenotypes and alters cell death programs. Ultimately, this study establishes a next-generation framework for biomarker translation, highlighting CASP8 as a clinically actionable link between genomic instability and pyroptosis dysregulation, and demonstrating the power of AI-integrated strategies in accelerating bladder cancer research from bench to bedside.},
}
@article {pmid42275736,
year = {2026},
author = {Barcan, RA and Carradori, S and Samsing, F and Nguyen, NL and He, L and Wang, Y and Barcan, AS},
title = {Machine learning in applied microbiology, from data quality to model validation and implementation.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128588},
doi = {10.1016/j.micres.2026.128588},
pmid = {42275736},
issn = {1618-0623},
mesh = {*Machine Learning ; *Microbiology ; Reproducibility of Results ; Microbiota ; Classification Algorithms ; Predictive Learning Models ; Humans ; Databases, Factual ; },
abstract = {Machine learning (ML) is now widely applied in microbiology, but its reliability varies markedly across domains. In this review, we analysed data from 254 scientific articles that evaluates ML through three linked dimensions including data readiness, model suitability, and deployment readiness across diagnostics and pathogen identification, virology, microbiome research, industrial and environmental microbial biotechnology. This framework helps distinguish robust progress from performance inflated by methodological limitations. Our review shows that pathogen identification and antimicrobial resistance prediction consistently achieve strong performance when supported by curated datasets, reliable labels, and comprehensive reference databases. However, their practical value remains limited by internal validation, lineage confounding, and uneven transfer across strains, institutions, and regions. In virological studies, predictive stability is further challenged by incomplete reference databases, changing taxonomy, and temporal drift during outbreaks. In microbiome research, ML classifiers can detect disease and environmental signals, but their generalization across cohorts remains weak because of compositional data structure, technical bias, and incomplete metadata. Industrial bioprocessing and environmental applications show promise when process data are rich and controlled, but deployment beyond laboratory or site-specific settings remains limited. Across structured microbiological datasets, classical supervised models often remain competitive with deep learning while being easier to interpret and validate. Detailed quantitative benchmarks supporting these comparisons are synthesized in the main text and summary tables. Overall, progress will depend less on algorithmic novelty than on interoperable and well-annotated datasets, representative sampling, standardized benchmarking, reproducible workflows, and prospective multi-site validation.},
}
@article {pmid42321367,
year = {2026},
author = {Wang, X and Zhang, C and Wang, H and Reid, K and Merilä, J},
title = {How precise are mutation rate estimates? Comparison of different approaches to estimate de novo mutation rates.},
journal = {Heredity},
volume = {135},
number = {6},
pages = {445-452},
pmid = {42321367},
issn = {1365-2540},
support = {202111159018//University Grants Committee (UGC)/ ; },
mesh = {Animals ; *Mutation Rate ; *Computational Biology/methods ; Sequence Analysis, DNA ; Mutation ; High-Throughput Nucleotide Sequencing ; },
abstract = {Availability of de novo mutation rate (µ) estimates based on approaches that rely on bioinformatic validations has increased tremendously during the past few years, but the accuracy and precision of these estimates often remain unclear as Sanger sequencing validation of the mutations is often lacking. We used both long- and short-read sequencing data and different bioinformatic pipelines to estimate µ, as well as false positive (FPR) and negative (FNR) rates, for family trios of flat-headed loaches (Oreonectes platycephalus). By comparing estimates against PCR-verified mutations, we observed that the top-performing approach (as ranked by the F1 score of seven approaches at the same depth) still exhibited a 4% false positive rate (FPR) alongside a 12% false-negative rate (FNR). Across the remaining methods, FPR values ranged from 4-12%, and FNRs from 8-19%. Irrespective of the bioinformatic approach used, long-read data yielded consistently lower µ estimates than short-read data because of the larger callable genome sizes. In addition, a higher mapping depth resulted in a lower FNR. These results call for caution regarding de novo mutations without Sanger sequencing validation in non-model organisms and raise the possibility that many published µ-estimates, especially those based on low mapping depths, might be biased.},
}
@article {pmid42386298,
year = {2026},
author = {McGuinn, LA and Ngirwe, P and Walton, S and Wei, K and Tung, I and Tare, I and Mbayiwa, K and Keenan, KE and Burrows, K},
title = {Using mobile sensing and wearable technologies to assess the impact of ambient temperature on mental health among low-income black women in Chicago: a study protocol.},
journal = {BMJ open},
volume = {16},
number = {7},
pages = {e109062},
pmid = {42386298},
issn = {2044-6055},
mesh = {Adult ; Female ; Humans ; *Black or African American/psychology ; Chicago ; Digital Health ; Ecological Momentary Assessment ; Longitudinal Studies ; *Mental Health ; *Poverty ; Research Design ; Sleep ; Temperature ; },
abstract = {INTRODUCTION: Growing evidence suggests that higher ambient temperatures may increase the risk of mental health disorders and exacerbate existing conditions. Despite this, most studies evaluating the association between temperature and mental health rely on hospitalisation records or insurance claims data, which only capture the most severe outcomes. To effectively intervene to prevent mental health crises associated with ambient temperature, it is necessary to identify and develop novel ways to reach patients before they require care. Digital health tools offer a promising way to address these gaps, particularly in communities most affected by climate inequities.<br><br>METHODS AND ANALYSIS: This study aims to recruit 70 low-income black women from Chicago who are already enrolled in the Nutrition and Pregnancy Study for a 4-week longitudinal observational study. The primary objective is to examine how ambient temperature affects positive and negative affect (primary outcome), as well as sleep and physiologic markers. Over a 4-week summer period, participants will wear a smartwatch and complete ecological momentary assessment surveys three times daily. We will monitor indoor temperature and humidity using home-based sensors and link these data with wearable and self-reported mental health measures. Daily outdoor ambient temperature will also be linked. Statistical analyses will use mixed-effects longitudinal models with distributed lags to assess delayed and cumulative temperature effects.<br><br>ETHICS AND DISSEMINATION: This study has been reviewed and approved by the Institutional Review Board at the University of Chicago (IRB24-026). At the completion of the study, participants will have the option to receive a summary of their own data, with a plain-language summary of the study findings. Findings will be disseminated through peer-reviewed publications and presentations at national and international conferences. Dissemination efforts will also include engagement with local community stakeholders and public health partners to inform future climate and health efforts.},
}
@article {pmid42386781,
year = {2026},
author = {Wu, M and Sonnentag, O and Lara, MJ and Ran, Y and Chen, HW and Zhang, W and Ciais, P and Elberling, B and Li, X and Chen, A and Wang, S and Yi, Y and Peng, C and Chen, D},
title = {Vegetation browning patterns under compound soil and atmospheric dryness in northern permafrost ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-75131-4},
pmid = {42386781},
issn = {2041-1723},
support = {42525105//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Significant changes in vegetation greenness and browning have been observed across the northern permafrost zone, with important implications for ecosystem functioning and carbon uptake. While recent research has improved our understanding of the drivers of greening, the processes behind browning - especially the low-stature shrubs and herbaceous vegetation, which is more directly exposed to soil and atmospheric moisture deficits - remain less clear. To characterize browning patterns, we integrate multiple remote sensing datasets - including normalized difference vegetation index (NDVI), solar-induced chlorophyll fluorescence (SIF), and foliar chlorophyll concentration (FCC) - with gross primary productivity (GPP) simulations from CMIP6 Earth system models (ESM). We identify significant browning trends (-0.033 to - 0.025 decade-1, from MODIS NDVI) from 2001 to 2018, affecting approximately 20 % (~600,000 km[2]) of the study region. Browning is primarily modulated by compound soil and atmospheric dryness, reflected by declining soil moisture concurrent with increasing vapor pressure deficit. We further show that regional warming and changes in precipitation, together with permafrost-related constraints on infiltration and storage, modulate the spatial heterogeneity of compound dryness. CMIP6 projections suggest that compound dryness is likely to persist or intensify in permafrost ecosystems, implying continued risk of productivity loss, especially when combined with pulse disturbances such as wildfires.},
}
@article {pmid42371860,
year = {2026},
author = {Saini, P and Iquebal, MA and Jaiswal, S and Angadi, UB},
title = {Development of CypriSSR: a genome-wide, chromosome-level microsatellite database for multiple cyprinidae species.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {42371860},
issn = {1758-0463},
support = {BT/PR40161/BTIS/137/32/2021//Indian Council of Agricultural Research/ ; //Department of Biotechnology/ ; },
mesh = {Animals ; *Microsatellite Repeats/genetics ; *Cyprinidae/genetics ; *Genome/genetics ; *Chromosomes/genetics ; *Databases, Genetic ; *Databases, Nucleic Acid ; Genomics ; },
abstract = {The family Cyprinidae represents the most taxonomically diverse group of freshwater fishes, encompassing over 3 000 species of ecological and economic importance in aquaculture, conservation, and ecological monitoring. Simple sequence repeats (SSRs), also known as microsatellites, are highly informative molecular markers widely used for genetic diversity analysis, population structure assessment, and marker-assisted breeding. However, comprehensive genome-wide SSR resources for cyprinids remain limited. Existing databases, such as FishMicrosat, provide restricted taxonomic coverage and lack standardized chromosome-level datasets suitable for comparative genomic analyses. To address this gap, we developed CypriSSR, a genome-wide SSR database encompassing 11 representative cyprinid species. Chromosome-level genome assemblies were retrieved from NCBI. SSR loci were identified using MISA, and primer pairs were designed using Primer3. In total, over 7.8 million SSR loci were identified. Mononucleotide repeats were the most abundant class (39-53%), followed by dinucleotide and trinucleotide motifs. SSRs were predominantly distributed in genic regions (54%-71% across species), suggesting potential functional roles. Each database entry includes repeat type, genomic coordinates, primer sequences, melting temperatures, and predicted PCR product sizes. The CypriSSR web interface enables flexible querying of SSR markers based on species, chromosome, motif class, and genomic location, and supports sequence similarity searches through an integrated BLAST module along with data export options. CypriSSR provides a comprehensive and standardized multi-species microsatellite resource for cyprinid genomes and supports applications in population genetics, molecular breeding, and conservation genomics. Database URL: http://46.202.167.198/fishssr/.},
}
@article {pmid42383019,
year = {2026},
author = {Oh, Y and Campbell, K and Shults, J and Saby, J and Marsh, ED},
title = {Minimum data requirements and automated preprocessing for reliable EEG biomarkers in Rett syndrome.},
journal = {Frontiers in neurology},
volume = {17},
number = {},
pages = {1791834},
pmid = {42383019},
issn = {1664-2295},
abstract = {BACKGROUND: Electroencephalography (EEG) is a promising biomarker for Rett syndrome (RTT), but excessive artifact and variable tolerance for longer recording sessions pose challenges for reliable biomarker development. Establishing an automated preprocessing pipeline that matches human review and defining the minimum data needed for stable quantitative EEG (qEEG) features can support more patient-friendly protocols and provide consistent multisite analysis results.<br><br>METHODS: A mean of 10 min of resting-state EEG from 117 participants (1-18 year old; 236 sessions) in the multisite R61 RTT study was processed using a fully automated, correction-based preprocessing pipeline incorporating artifact handling, adaptive channel rejection, ASR, and ICA-based cleaning. Spectral power was extracted from artifact-free 4-s epochs. The proposed pipeline is validated using an established rejection-based pipeline. Feature stability as a function of cumulative data length was then assessed using two complementary frameworks: a Statistical Convergence approach and a Model-Based Inflection approach, and potential systemic dependencies were evaluated using permutation analyses. The relationship between clinical measures was also assessed.<br><br>RESULTS: The correction-based pipeline retained substantially more data than the rejection-based workflow (mean retention = 95.0% vs. 28.4%; p < 0.001) while preserving strong feature correspondence across frequency bands. Stable power estimates were achieved after 19-34 epochs (= 76-136 s). Based on permutation analysis, there was no statistically significant difference in minimum stabilization threshold between RTT and TD. However, the RTT group exhibited higher rates of intrinsic signal instability than typically developing (TD) controls. Age-stratified analysis revealed that the minimum epochs did not significantly differ between age groups. Spectral associations with clinical severity were preserved when using only the minimum data required for stability, as well as in an ecologically valid scenario of truncating the raw EEG up to minimum epoch recommendation and reprocessing it.<br><br>CONCLUSIONS: With the proposed correction-based pipeline, approximately 3 min of raw resting-state EEG are sufficient to obtain stable and clinically meaningful spectral features in children with Rett syndrome. These findings support shorter, more feasible EEG acquisitions and provide a reproducible framework for data sufficiency in multisite neurodevelopmental studies.},
}
@article {pmid42384029,
year = {2026},
author = {Martinho, DV and Costa, R and VAN DEN Hoek, D and Clemente, FM and Gonzalo-Skok, O and Gouveia, &#xc9;R and Campos, P and Ribeiro, AS and Field, A and Sarmento, H},
title = {A critical commentary on CrossFit Research® with coach insights on training monitoring and physical assessment.},
journal = {The Journal of sports medicine and physical fitness},
volume = {},
number = {},
pages = {},
doi = {10.23736/S0022-4707.26.17836-0},
pmid = {42384029},
issn = {1827-1928},
abstract = {BACKGROUND: CrossFit[®] has experienced rapid global growth, yet scientific research often fails to reflect the realities of training and competition in this sport. Studies frequently rely on inconsistent terminology, non-specific testing protocols, and heterogeneous samples, limiting the ecological validity and practical application of findings. This critical commentary aims to evaluate the methodological challenges in CrossFit[®] research and to highlight the importance of contextualizing scientific inquiry through the perspectives of coaches actively working within the sport.<br><br>METHODS: A targeted review of the CrossFit[&#xae;] literature was conducted, with a focus on sampling descriptions, testing protocols, and training monitoring approaches. In addition, semi-structured interviews were conducted with five national and international-level CrossFit[&#xae;] coaches. Analysis of coach responses was used to contextualize gaps in the literature.<br><br>RESULTS: Coaches reported relying primarily on competition results, training observations, and subjective feedback to guide programming, rather than standardized physical testing or technology-based monitoring. The remote nature of many coach-athlete relationships further complicates data collection and training analysis.<br><br>CONCLUSIONS: CrossFit[&#xae;] research must improve its methodological rigor by adopting sport-specific assessments, clearly defining participant characteristics, and embracing the realities of coaching practice. Integrating qualitative insights and prioritizing ecological validity will help bridge the gap between science and the sport's unique demands.},
}
@article {pmid42386290,
year = {2026},
author = {Sahana, KS and Madhu, B and Manjunatha, MC and Chaithra, M and Mounika Sree, M and Suraj, BM and Yashashwini, A and Snehalatha, B},
title = {Spatial autocorrelation and regression approach for delineating maternal mortality and its associated factors in Karnataka, India.},
journal = {BMJ open},
volume = {16},
number = {7},
pages = {e094191},
doi = {10.1136/bmjopen-2024-094191},
pmid = {42386290},
issn = {2044-6055},
mesh = {Humans ; Female ; *Maternal Mortality/trends ; Retrospective Studies ; India/epidemiology ; Pregnancy ; Geographic Information Systems ; Spatial Analysis ; Spatial Regression ; Risk Factors ; },
abstract = {OBJECTIVES: The main objective of this study is to assess the temporal distribution of taluk (sub-district)-level maternal mortality trends within Karnataka and identify the hotspots and medical and non-medical factors that were significantly contributing to maternal deaths.<br><br>DESIGN: Spatial patterns and determinants of maternal mortality were investigated using a retrospective ecological study design.<br><br>DATA SOURCE: Maternal mortality data were collected from the Directorate of Health and Family Welfare Services, Government of Karnataka, while political boundaries of state, districts and taluks were downloaded from the Karnataka Geographic Information System Portal.<br><br>METHODOLOGY: Taluk-wise (sub-district level) maternal mortality ratio was mapped using GeoPandas software. Global and local Moran's I along with spatial regression was performed using GeoDa software in evaluating the spatial dependence and identifying significant predictors of maternal mortality.<br><br>RESULTS: Maternal mortality varied geographically, according to thematic maps, and local indicators of spatial autocorrelation map showed high-high clustering (nine taluks (5.1%)) with positive Moran's I (0.114). Descriptive analysis of time of death revealed that the majority of maternal deaths (39.82%) occurred within 48 h postpartum, followed by 2-7&#x2009;(20.95%) and 8-30&#x2009;(16.23%) days. The spatial error model showed negative associations for antenatal care at the sub-centre, SDHs, deliveries conducted by doctors and private hospital (&#x3b2;=-0.047&#x2009;to -0.184, p<0.05), and a positive association was found for below poverty line, stillbirths, parity 1 and deliveries at medical colleges (&#x3b2;=0.112-0.758, p<0.05) with a &#x3bb; value of 0.286. Primary postpartum haemorrhage, sepsis, hypertensive disorder of pregnancy, cardiorespiratory disorders and other direct and indirect causes were identified as major contributors to maternal mortality in the spatial lag model (&#x3b2;=0.273&#x2009;to 1.926, p<0.05, &#x3c1;=-0.077).<br><br>CONCLUSION: Spatial analysis revealed geographic hotspots, temporal risk windows and socio-economic and medical determinants of maternal mortality in Karnataka. These findings provide actionable evidence for spatially targeted, temporally focused and socio-clinically comprehensive maternal health interventions.},
}
@article {pmid42139758,
year = {2026},
author = {van Lill, M and Steenkamp, ET and Palmer, M and Beukes, CW and Venter, SN},
title = {Using the SeqCode to validate the names of reclassified lineages of rhizobia and agrobacteria.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {4},
pages = {126720},
doi = {10.1016/j.syapm.2026.126720},
pmid = {42139758},
issn = {1618-0984},
mesh = {*Rhizobiaceae/classification/genetics ; *Bartonellaceae/classification/genetics ; Phylogeny ; *Genome, Bacterial ; Datasets as Topic ; Sequence Analysis, DNA ; Terminology as Topic ; Conserved Sequence ; },
abstract = {Genome-based taxonomy offers a powerful means to resolve long-standing ambiguities in the classifications of agrobacteria and rhizobia, two bacterial groups with major ecological and agricultural significance. We applied a robust phylogenomic framework to genomes of the families Bartonellaceae and Rhizobiaceae to comprehensively reassess evolutionary relationships. Species trees were constructed using nucleotide sequences of 92 conserved genes and amino acid sequences of 120 ubiquitous proteins, clarifying relationships that were previously obscured by marker-limited historical classifications. These analyses demonstrated several instances of taxonomic inconsistencies across genera, most notably within Mesorhizobium, which forms a paraphyletic assemblage spanning multiple divergent lineages. These findings were further reinforced by the genome-wide similarity metric, average amino acid identity (AAI), which supported reclassifications at both genus and species levels, reflecting natural discontinuities between lineages. We propose the reclassification of eight species and five new genera and the validation of their names primarily under the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). As genome-based resources expand, and with the availability of new nomenclatural frameworks such as the SeqCode, genome-informed taxonomy offers a powerful approach to delineate taxa into biologically meaningful groups that can be formally recognised. The revised taxonomy presented here brings greater coherence to the systematics of agrobacteria and rhizobia and provides a framework for future evolutionary investigations into these agriculturally and ecologically significant bacterial groups.},
}
@article {pmid42212967,
year = {2026},
author = {Albudoor, N and Anaya, JB},
title = {Extracting Word Frequencies From Child Language Corpora: A New Tool for Developmental Psycholinguistic Research.},
journal = {Journal of speech, language, and hearing research : JSLHR},
volume = {69},
number = {7},
pages = {3341-3350},
doi = {10.1044/2026_JSLHR-25-00280},
pmid = {42212967},
issn = {1558-9102},
mesh = {Humans ; *Child Language ; *Psycholinguistics/methods ; *Vocabulary ; Language Tests ; Child, Preschool ; *Language Development ; Databases, Factual ; Child ; },
abstract = {PURPOSE: We introduce childeswordfreq, an R-based tool for extracting frequency data from the CHILDES (Child Language Data Exchange System) database. This tool provides researchers with the ability to efficiently analyze word and phrase frequencies across multiple languages and speaker roles within the CHILDES database. The resulting frequency measures can be used for stimulus selection in experimental studies and for analyzing patterns in child language development. To illustrate the tool's utility, we conducted a case study using items from the Expressive One-Word Picture Vocabulary Test-Fourth Edition (EOWPVT-4), comparing their frequencies in CHILDES with adult-based Subtitle-based Word Frequency Database for American English estimates to assess how input frequency differs between child and adult linguistic environments.<br><br>CONCLUSIONS: The childeswordfreq package provides an accessible route for incorporating information on how frequently words are used in child-directed speech into research workflows. The results of our case study highlight why such access is critical. The CHILDES and SUBTLEX-US frequencies diverged in patterned ways tied to developmental progression, with earlier items on the EOWPVT-4 being overrepresented in child-directed speech and later items being more prominent in an adult corpus. These findings demonstrate how adult norms can diverge from frequency distributions relevant for acquisition. By grounding analyses in child-based input patterns, childeswordfreq strengthens developmental interpretations and supports more ecologically aligned research.<br><br>SUPPLEMENTAL MATERIAL: https://doi.org/10.23641/asha.32273607.},
}
@article {pmid42284942,
year = {2026},
author = {Yang, X and Peng, AD and Huang, YH and Cheng, JH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG},
title = {Ecological risk assessment of 1,4-thioxane and its remediation by a synthetic microbiome based on a sulfur transformation system: From multi-omics to water application.},
journal = {Water research},
volume = {303},
number = {},
pages = {126258},
doi = {10.1016/j.watres.2026.126258},
pmid = {42284942},
issn = {1879-2448},
mesh = {*Microbiota ; Risk Assessment ; Biodegradation, Environmental ; Multiomics ; Sulfur/metabolism ; },
abstract = {Among the chemicals in weapons abandoned by Japan in China during World War II, 1,4-thioxane, a typical degradation product of mustard gas, has environmental persistence and potential ecological risks. However, its toxicity mechanism and efficient remediation strategy remain unclear. This study first employed multi-omics technologies (16S sequencing, metagenomics, and metabolomics) to analyze the toxic effects of 1,4-thioxane (0-100 mg·L[-1], 120 days) on water microecology. Subsequently, an efficient degrader, Pseudomonas sp. M1, was screened, and transcriptome analysis revealed significant upregulation of Fe-S cluster assembly-related genes (sufB, sufU, sufS), which are key components of the SUF sulfur conversion system. These three genes were heterologously expressed in Escherichia coli to construct three engineered strains, each capable of degrading 1,4-thioxane via the SUF system. When mixed in equal proportions to form a synthetic microbiome, they completely degraded 100 mg·L[-1] 1,4-thioxane in culture medium within 16 h and achieved 100% removal in simulated polluted water within 15 days. Integrated multi-omics analysis demonstrated that 1,4-thioxane is highly persistent (residual rate > 98%) but significantly inhibits nitrogen cycling, manifested by NH4[+] accumulation (1.5-3.1-fold increase) and NO3[-] depletion (24.9-87.6% decrease), along with reduced ammonia monooxygenase, nitrite oxidoreductase, and nitrate reductase activities (67.8-91.0%, 53.2-90.1%, and 42.8-80.9% reductions, respectively). Ionome analysis showed K and P accumulation and Mo depletion; 16S sequencing revealed reduced microbial diversity, suppression of nitrogen-cycling genera, and enrichment of Pseudomonas; metagenomics uncovered widespread suppression of nitrogen metabolism pathways, dysregulation of antibiotic resistance genes, and decreased viral abundance; and metabolomics confirmed global inhibition of the alanine-aspartate-glutamate pathway. This is the first study to combine multi-omics toxicity analysis with synthetic microbiome remediation based on the SUF sulfur conversion system. The findings provide a theoretical basis and technical support for ecological risk assessment and bioremediation of sites contaminated by relic Japanese chemical weapons.},
}
@article {pmid42368544,
year = {2026},
author = {Liu, J and Yu, K and Song, H and Ma, J and Bijani, M and Wu, L and Xu, L and Ahmad, MN and Xu, P and Zhao, J},
title = {ZDAM: a new deep learning model for bean leaf disease diagnosis.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1842022},
pmid = {42368544},
issn = {1664-462X},
abstract = {INTRODUCTION: Accurate disease diagnosis is crucial for enhancing agricultural productivity and reducing postharvest losses, directly impacting food quality and safety. Traditional detection methods often rely on extensive feature modeling and perform poorly in complex field environments.<br><br>METHODS: This study proposes a deep learning model called ZDAM, based on an improved ZFNet integrated with a dual attention mechanism. The classical ZFNet is first optimized to improve feature extraction efficiency. A combined channel and spatial attention mechanism is then incorporated to refine feature representation for disease identification in key crops. Finally, a residual module is added to boost accuracy.<br><br>RESULTS: Evaluated on a dataset of 11,903 bean leaf images covering healthy leaves and four disease types, including leaf mould, rust, mosaic, and white spot, the model achieves an average recognition accuracy of 99.02%, outperforming MobileMamba, Vision Transformer, and Chest- OMD.<br><br>DISCUSSION: This approach offers a scalable solution for automated disease monitoring, supporting postharvest quality preservation and sustainable crop production.},
}
@article {pmid42370032,
year = {2026},
author = {Zheng, H and Wang, S and Li, X and Li, Q and Wu, D and Klimont, Z and Zhao, D and Huang, L and Dong, Z and Wu, Q and Jiang, J and Jin, LN and He, H and He, K and Zhao, J and Liu, Q and Weichenthal, S and Cohen, AJ and Hao, J},
title = {Toxicity-informed control of global PM2.5 emissions.},
journal = {National science review},
volume = {13},
number = {11},
pages = {nwag301},
pmid = {42370032},
issn = {2053-714X},
abstract = {Fine particulate matter (PM2.5) remains a leading environmental health risk, yet air pollution control policies typically assume equal toxicity across emission sources. Unravelling the unequal toxicities in global PM2.5 emissions can support more effective air pollution control. Here, we integrate cell-based toxicological profiles with global emission inventories to develop the first global dataset of toxicity-adjusted PM2.5 emissions. We show that global toxicity-adjusted emissions are dominated by residential solid-fuel combustion, and that hotspots of PM2.5 mass and toxicity diverge substantially, with the highest toxicities occurring largely in regions reliant on traditional biomass. Low-income countries exhibit disproportionately high toxicity-adjusted emissions relative to their energy use, revealing a strong global environmental inequity. Incorporating unequal toxicities reshapes emission-control priorities, shifting many countries from mass-dominated industrial or power sectors towards residential combustion. We propose a toxicity-informed framework for air pollution control, which is adaptable to diverse socioeconomic contexts and can enhance global health and sustainability.},
}
@article {pmid42370731,
year = {2026},
author = {Bresette, N and Ericsson, AC and Woods, C and Lin, A-L},
title = {MeLSI: Metric Learning for Statistical Inference in microbiome community composition analysis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0040726},
doi = {10.1128/msystems.00407-26},
pmid = {42370731},
issn = {2379-5077},
abstract = {Microbiome beta diversity analysis relies on distance-based methods, including permutational multivariate analysis of variance (PERMANOVA) combined with fixed ecological distance metrics (Bray-Curtis, Euclidean, Jaccard, and UniFrac), which treat all microbial taxa uniformly, regardless of their biological relevance to community differences. This "one-size-fits-all" approach may miss subtle but biologically meaningful patterns in complex microbiome data. We present Metric Learning for Statistical Inference (MeLSI), a novel machine learning framework that learns data-adaptive distance metrics optimized for detecting community composition differences in multivariate microbiome analyses. MeLSI employs an ensemble of weak learners using bootstrap sampling, feature subsampling, and gradient-based optimization to learn optimal feature weights, combined with rigorous permutation testing for statistical inference. The learned metrics can be used with PERMANOVA for hypothesis testing and with principal coordinates analysis for ordination visualization. Comprehensive validation on synthetic benchmarks and real data sets shows that MeLSI maintains proper type I error control while delivering competitive or superior statistical power for detecting subtle community shifts and, crucially, supplies interpretable feature-weight profiles that clarify which taxa drive group separation. On the DietSwap data set, MeLSI was the only method to achieve significance at α = 0.05, demonstrating that adaptive weighting can detect diet-induced community shifts that fixed metrics miss. Across all data sets, the learned feature weights identified biologically relevant taxa while providing actionable insight that no fixed distance metric can supply. MeLSI therefore offers a statistically rigorous tool that augments beta diversity analysis with transparent, data-driven interpretability.IMPORTANCEUnderstanding which microbes differ between groups of interest could reveal therapeutic targets and diagnostic biomarkers. However, current analysis methods treat all microbes equally (similar to using the same ruler to measure everything, regardless of what matters most). This means subtle but biologically important differences may go undetected, especially when only a few key species drive disease states while hundreds of "bystander" species add noise. Metric Learning for Statistical Inference (MeLSI) solves this by learning which microbes matter most for each specific comparison. In comparing male and female gut microbiomes, MeLSI identified specific bacterial families driving the differences, providing actionable biological insights that standard methods miss. This capability is particularly crucial for detecting early disease biomarkers, where differences are subtle and masked by biological variability. By telling researchers not just whether groups differ, but which specific microbes drive those differences, MeLSI accelerates the path from microbiome data to testable biological hypotheses and clinical applications.},
}
@article {pmid42371175,
year = {2026},
author = {Iqbal, MS and Alahmari, AK and Khan, MF and Farooqui, S and Iqbal, MZ and Khan, SU and Khan, N and Seshadri, VD and Abdelgawwad El-Sehrawy, AAM},
title = {Clonal Metamorphosis: Deconstructing MPN Evolution with Single-Cell and Spatial Multi-Omics.},
journal = {Clinical and experimental medicine},
volume = {26},
number = {1},
pages = {},
pmid = {42371175},
issn = {1591-9528},
mesh = {Humans ; Multiomics ; *Single-Cell Analysis/methods ; *Clonal Evolution/genetics ; *Myeloproliferative Disorders/genetics/pathology ; Single-Cell Gene Expression Analysis ; Mutation ; Tumor Microenvironment ; Spatial Transcriptomics ; },
abstract = {Myeloproliferative neoplasms (MPNs) present a fundamental paradox: despite sharing a small set of canonical driver mutations in JAK2, CALR, or MPL, patients exhibit striking heterogeneity in disease latency, clinical presentation, and evolutionary trajectories to myelofibrosis or secondary acute myeloid leukemia. This review synthesizes recent advances in single-cell and spatial multi-omic technologies that are resolving this paradox by moving analysis from bulk averages to individual cells and their microenvironmental ecosystems. We examine how targeted single-cell DNA sequencing reconstructs clonal architectures and phylogenies, revealing that driver mutations arise within complex mosaics where mutation order, co-mutation context, and cellular ancestry determine phenotypic outcomes. Integrated single-cell transcriptomic and epigenomic profiling exposes within-clone heterogeneity, lineage biases, and functional states that explain variable penetrance and therapy responses. Spatial transcriptomics, especially when integrated with single-cell transcriptomics, histopathology, and multiplex proteomics, further demonstrates that malignant hematopoietic stem and progenitor cells actively remodel bone marrow niches, creating localized inflammatory and fibrotic microenvironments that select for aggressive subclones. Together, these approaches support a new ecological model of MPN pathogenesis in which early epigenetic hits create permissive stem cell reservoirs, clonal competition and cooperation shape disease progression, and non-cell-autonomous niche and immune signals drive malignant metamorphosis. We discuss how this framework refines prognostication, informs rational combination therapies targeting both malignant cells and their ecosystem, and enables real-time monitoring of clonal dynamics, ultimately charting a course from descriptive atlases to actionable clinical strategies.},
}
@article {pmid41507362,
year = {2026},
author = {Elettrico, L and Piacenti, G and Levra Levron, C and Ansai, O and Croce, A and Duval, C and Proserpio, V and Donati, G},
title = {Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem.},
journal = {Cell death and differentiation},
volume = {33},
number = {7},
pages = {1312-1332},
pmid = {41507362},
issn = {1476-5403},
support = {IG2023 - Id.21640//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; postdoc fellowship//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; MFAG 2023 - Id.29203//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; postdoc fellowship//Fondazione Umberto Veronesi (Umberto Veronesi&#xa0;Foundation)/ ; },
mesh = {Humans ; Animals ; *Skin/metabolism/microbiology ; Skin Microbiome ; Multiomics ; Microbiota ; Epithelial Cells/metabolism ; },
abstract = {Skin homeostasis depends on interactions between epithelial cells and the microbiome mediated by molecular and biochemical factors. Perturbations of this interplay are linked to inflammatory disorders, including wound healing and cancer. While research has mainly illuminated shifts in microbial community composition, novel computational approaches are starting to reveal the host-microbe functional interactome in the cutaneous ecosystem. In this review, we specifically focus on known molecular and metabolic mechanisms linking skin epithelial cells and microorganisms in health and disease. Additionally, we summarise computational tools available to investigate these interactions integrating omics data. Furthermore, we present potential applications of this functional crosstalk to advance therapies targeting skin pathologies. Finally, we propose a comparative interactomics approach to envision the existence of ecological memories in the skin ecosystem, in parallel with the one described in the gut, hypothesising a link between epithelial and microbial memories in barrier tissues.},
}
@article {pmid41944781,
year = {2026},
author = {Cedden, D},
title = {Emerging experimental and bioinformatic approaches in RNA interference-based pest control research.},
journal = {Insect molecular biology},
volume = {35},
number = {4},
pages = {364-375},
pmid = {41944781},
issn = {1365-2583},
mesh = {*RNA Interference ; Animals ; *Computational Biology/methods ; *Insect Control/methods ; *Insecta/genetics ; RNA, Double-Stranded ; RNA, Small Interfering ; },
abstract = {RNA interference (RNAi) has emerged as a promising strategy for species-specific and environmentally friendly pest control, offering an alternative to conventional chemical insecticides that are increasingly constrained by resistance development and ecological concerns. RNAi-based approaches involve oral delivery of double-stranded RNA (dsRNA), which is processed into RNA-induced silencing complex (RISC)-bound small interfering RNA (siRNA) to silence essential genes of pests. This review synthesizes recent advances in experimental and bioinformatic methodologies that are facilitating and enhancing RNAi research in insect pest management. Particular emphasis is placed on molecular validation techniques that move beyond phenotype-based bioassays, including RISC-bound small RNA sequencing to resolve dsRNA processing and guide strand selection, RNA degradomics to map siRNA-mediated transcript cleavage events and transcriptomic and proteomic profiling to characterize genome-wide responses and compensatory effects. In parallel, dsRNA visualization methods provide mechanistic insight into uptake, intracellular trafficking and degradation dynamics, clarifying barriers that distinguish responsive from recalcitrant species. Complementing these experimental developments, emerging computational platforms enable insect-optimized target selection, dsRNA design and environmentally informed off-target prediction. Together, these innovations support a transition toward more predictive and mechanistically grounded RNAi-based pest control applications. The integration of high-resolution molecular tools with specialized bioinformatic pipelines is expected to enhance efficacy, safety and reproducibility, advancing RNAi-based pest control toward practical and scalable agricultural deployment.},
}
@article {pmid42010402,
year = {2026},
author = {Gabella, JL and Gualda, IAP and Beltrame, MHA and Costa, WF and Hachmann, TF and Massago, M and de Paulo, LG and Grizzo, FMF and Gurgel, SJT and de Andrade, L},
title = {Spatiotemporal patterns of femoral fractures in older adults: healthcare access and regional inequalities in southern Brazil.},
journal = {BMC geriatrics},
volume = {26},
number = {1},
pages = {},
pmid = {42010402},
issn = {1471-2318},
mesh = {Retrospective Studies ; Secondary Data Analysis ; Humans ; Male ; Female ; Middle Aged ; Aged ; Aged, 80 and over ; Brazil/epidemiology ; Spatio-Temporal Analysis ; *Femoral Fractures/mortality/therapy ; *Health Services Accessibility/statistics &amp; numerical data/trends ; Incidence ; *Healthcare Disparities/trends ; Hospitalization/statistics &amp; numerical data ; Resource-Limited Settings/statistics &amp; numerical data ; },
abstract = {BACKGROUND: Femoral fractures in older adults are associated with lethality rates of up to 30% within the first year and significantly compromised quality of life, leading to high levels of disability, institutionalization, and burden on health systems. By 2050, the global population of older adults is projected to exceed 2 billion, leading to an exponential increase in these events. In Brazil, the incidence of fractures is high and often linked to inequalities in access to diagnosis and prevention, particularly in regions with limited infrastructure. This study aimed to analyze the spatiotemporal distribution of femoral fractures in older adults and identify contextual factors associated with their occurrence. METHODS: This is an ecological and retrospective study using secondary data from 2010 to 2021 on hospitalizations for femoral fractures in older adults (≥ 60 years) in the 399 municipalities of Paraná State, Brazil. Descriptive analyses and nonparametric tests were performed to compare mortality rates according to population size. Spatiotemporal distribution was examined using space–time cubes. Spatial autocorrelation was assessed using global Moran’s I and local indicators of spatial autocorrelation (LISA). Geographically weighted regression (GWR) was applied to explore local associations with contextual variables. RESULTS: A total of 39,226 femoral fractures were recorded during the study period, with a predominance among women (66.8%). Overall lethality was 6%, being significantly higher in men. Space–time cube analysis indicated a persistent increasing trend in fractures (Z = 2.8115, p = 0.0049). Spatial analysis revealed significant positive spatial autocorrelation (I = 0.705, p < 0.001) and identified significant clusters and groupings (p < 0.05). GWR demonstrated a negative association between fracture incidence and access to specialists and osteoporosis medication, and a positive association with falls and densitometry availability in some regions. CONCLUSION: The findings indicate that the distribution of fractures is not random but rather influenced by factors such as access to diagnosis, medication, and specialized care. This evidence underscores the value of geospatial tools in the planning of health actions, enabling more targeted and equitable interventions in response to population aging.},
}
@article {pmid42103911,
year = {2026},
author = {Sun, H and Hua, Y},
title = {Study on GIS-based suitability evaluation of the landscape environment of celebrity former residences in Huanggang.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42103911},
issn = {2045-2322},
mesh = {*Geographic Information Systems ; Humans ; China ; *Conservation of Natural Resources ; *Environment ; Geography ; Ecosystem ; },
abstract = {Celebrity former residences, as cultural carriers shaped by historical evolution, embody profound cultural significance and hold immeasurable historical, social, political, and economic value. Grounded in the theories of human settlement science, settlement geography, and landscape ecology, this study takes the preserved celebrity former residences in Huanggang City as its research objects. Using the Analytic Hierarchy Process (AHP) and adopting a geographical perspective, eight geographical evaluation factors were selected in ArcGIS to represent topography, hydrology, ecology, and geomorphological stability as assessment indicators. By analyzing the relationship between these geographical factors and the spatial distribution of the residences, a suitability evaluation system for the landscape environment of celebrity former residences in Huanggang was established. The results indicate that, among the 136 officially protected celebrity residences in the city, 66 are located in highly suitable areas, accounting for 48.53%; 49 are located in suitable areas, accounting for 36.03%; 18 are located in less suitable areas, accounting for 13.24%; and 3 are located in unsuitable areas, accounting for 2.20%. In addition, a case study of the former residence of Li Siguang in Tuanfeng County demonstrates that its siting highly corresponds to the established evaluation framework. These findings suggest that geographical environmental factors are not only closely linked to the site selection of celebrity residences in Huanggang but also provide valuable references and guidance for future architectural siting and landscape environmental planning.},
}
@article {pmid42108422,
year = {2026},
author = {Shetty, P and Vuong, T and Li, C and Wagner, V and Myrzakhmetova, D and Peng, CC and Li, W and Ching, J and Zander, A and Weiser, S and Rosenbaum, MA and Allen, RJ and Lakemeyer, M and Mittag, M},
title = {Multiomics studies reveal how ambient temperature changes govern cellular responses of Chlamydomonas.},
journal = {The Plant cell},
volume = {38},
number = {7},
pages = {},
doi = {10.1093/plcell/koag136},
pmid = {42108422},
issn = {1532-298X},
support = {//Deutsche Forschungsgemeinschaft/ ; //DFG under Collaborative Research Centre/ ; //China Scholarship Council/ ; //Bio Pilot Plant of the Leibniz-HKI/ ; },
mesh = {*Temperature ; Multiomics ; *Chlamydomonas reinhardtii/genetics/physiology/metabolism ; *Chlamydomonas/genetics/physiology/metabolism ; Proteomics/methods ; Carbon Dioxide/metabolism ; Cilia/metabolism ; Gene Expression Profiling ; Photosynthesis ; Proteome ; Transcriptome ; },
abstract = {Photosynthetic protists, known as microalgae, face increasing temperatures due to climate change. The green biflagellate alga Chlamydomonas reinhardtii (Chlamydomonas) serves as a model for thermoregulation. While responses to thermal stress are well characterized, much less is known about the impact of ambient temperature shifts. Understanding microalgal responses to environmental temperature changes is critical, as these primary producers drive ecosystem productivity and food web dynamics. Here, Chlamydomonas grew mixotrophically at ambient temperatures from 18 °C to 33 °C. Transcriptomic profiling revealed extensive reorganization, with over 5,000 transcripts significantly affected, including those involved in algal-bacterial interactions, photoreception, lipid metabolism, photosynthesis, cilia formation, and the secretome. CO2 transfer rates and acetate levels measured at 18 °C and 28 °C suggest decreased photoautotrophic algal growth at 28 °C at first. Antagonistic bacterial activity was sustained longer at lower temperatures. Proteomic analyses of isolated cilia and secreted proteins corroborate major abundance changes within these sub-proteomes, particularly in ciliary intraflagellar transport complexes and mating-related proteins in the secretome. Together, these molecular alterations resulted in pronounced changes in growth, the lengths of cells and cilia swimming behavior, mating ability, and bacterial antagonism. These data reveal major cellular responses caused by ambient, even short-term temperature shifts.},
}
@article {pmid42148581,
year = {2026},
author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S},
title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0377525},
pmid = {42148581},
issn = {2165-0497},
support = {//Guizhou Province 2020 Science and Technology Support Plan Project/ ; },
mesh = {Fermentation ; Multiomics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Alcoholic Beverages/microbiology/analysis ; *Flavoring Agents/metabolism/analysis ; Metagenomics ; China ; Microbiota ; Metagenome ; Metabolomics ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; },
abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.},
}
@article {pmid42262077,
year = {2026},
author = {Ran, S and Fu, S and Dai, T and Wei, H and Peng, J and Zhou, Y},
title = {Multi-omics profiling of gut-serum axis dynamics in gestational sows with different reproductive performance.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0113225},
pmid = {42262077},
issn = {2165-0497},
mesh = {Animals ; Female ; Swine/blood/microbiology ; Pregnancy ; Multiomics ; *Reproduction/physiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Feces/microbiology ; Litter Size ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; *Serum/chemistry ; },
abstract = {UNLABELLED: Sustainable swine production hinges on optimizing sow reproductive efficiency, yet mechanisms driving healthy litter size and weak piglet rates remain unclear. This study categorized sows into high (group H) and low (group L) healthy litter size groups based on median performance. Multi-omics analyses (16S rRNA sequencing, metagenomics, and serum metabolomics) revealed distinct fecal microbiota and metabolic profiles between groups. The results showed significant differences in microbiota composition between groups L and H. Group H exhibited a marked increase in Bacteroidetes abundance (particularly Prevotella sp. CAG1092), concurrent with reduced Firmicutes populations. Metabolomic analysis identified 197 differentially abundant metabolites, with 85 metabolites significantly enriched in group H. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the differentially abundant metabolites were mainly involved in amino acid synthesis and metabolism, and multiple amino acid metabolic pathways were associated with polyamine synthesis. The correlation results showed a significant correlation (P < 0.05) between these metabolites and litter size as well as litter weight. For instance, Prevotellaceae NK3B31 abundance positively correlated with L-alanine, urea, and securinine, while Prevotella sp. CAG1092 exhibited direct associations with reproductive performance. These findings suggest that gut microbiota dysbiosis may disrupt amino acid homeostasis and polyamine regulation, potentially serving as mechanistic links to reproductive efficiency. Reproductive performance dynamically shapes gut microbiota and systemic metabolism in gestating sows, with litter size influencing fecal metabolite diversity and microbial structure. This integrative analysis establishes a framework for improving both sow productivity and economic viability in pig farming.<br><br>IMPORTANCE: Optimizing sow reproductive efficiency is vital for sustainable swine production. This study identifies gut microbiota dysbiosis and metabolic imbalances as key drivers of litter size variability. Sows with lower productivity displayed marked reductions in Bacteroidetes (notably Prevotella spp.) and disrupted amino acid/polyamine metabolism, directly linking microbial shifts to poorer litter outcomes. Integrated multi-omics approaches revealed strong correlations between specific taxa (Prevotella sp. CAG1092), metabolites (L-alanine and urea), and reproductive metrics, underscoring the gut-reproductive axis. These findings elucidate mechanistic connections between microbial ecosystems and host physiology, providing a foundation for targeted strategies like microbiota modulation or dietary interventions to enhance metabolic homeostasis and farrowing success. By bridging microbial ecology with livestock productivity, this work advances practical solutions to improve both animal health and agricultural profitability within precision farming frameworks.},
}
@article {pmid42294705,
year = {2026},
author = {Wang, J and Jiang, P and Yan, J and Shen, H and Wu, L and Wei, F and Lin, X and Xu, L},
title = {Spatial ecology meets quality control: a GIS-integrated strategy for visualizing and managing microbial contamination in sterile pharmaceutical cleanrooms.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0026826},
pmid = {42294705},
issn = {2165-0497},
support = {202423110050060//Anhui Provincial Department of Science and Technology/ ; },
mesh = {*Geographic Information Systems ; *Drug Contamination/prevention &amp; control ; *Bacteria/classification/isolation &amp; purification/genetics ; Quality Control ; *Environmental Monitoring/methods ; *Environmental Microbiology ; RNA, Ribosomal, 16S/genetics ; Drug Industry/standards ; Environment, Controlled ; },
abstract = {To enhance contamination source identification in sterile drug manufacturing, this study innovatively developed an integrated strategy combining geographic information system (GIS) spatial visualization with microbial contamination control. Between 2022 and 2025, researchers collected 1,117 environmental microbial isolates from sterile preparation workshops, analyzing their population structure, distribution patterns, and potential risks through 16S rRNA/ITS sequencing. GIS technology was employed to associate strain data with workshop spatial information, thereby providing a visual representation of microbial quantity, species composition, and distribution patterns. Results showed that Staphylococcus and Micrococcus dominated in clean areas, with microbial diversity highest in Controlled Not Classified (CNC) environments and lowest in A-grade areas. The microbial community structure in A-grade areas significantly differed from that in CNC/C/B-grade areas, while CNC/C/B-grade areas exhibited relative similarity. In the case study, the environmental microbial distribution maps clearly demonstrated regional variations and aggregation patterns. By identifying critical control areas and transmission pathways through contamination risk analysis, targeted interventions were designed and implemented, reducing the microbial contamination rate in target C-grade areas from 4.3% to 2.2%, thereby validating the strategy's effectiveness. This study targets the deficiency of "spatial visualization analysis" in clean area environmental monitoring. The proposed comprehensive strategy effectively fills the methodology gap in spatial analysis and contamination control for current clean area microbial monitoring. It provides a feasible framework for transforming environmental monitoring in the pharmaceutical industry from a passive surveillance system to an active early-warning system, assisting in enhancing the sterility assurance level of pharmaceutical production.IMPORTANCEAnalyzing the spatial distribution characteristics of microorganisms is crucial for developing effective pollution control strategies. However, existing environmental monitoring methods have limitations in revealing these spatial distribution patterns. This paper proposes an innovative strategy that integrates geographic information system (GIS) spatial analysis with microbial ecology research to enhance the accuracy and scientific rigor of pollution source identification and risk control. This approach enables the visualization of environmental microbial quantities, types, and spatial distribution, providing a quantitative tool for analyzing microbial contamination patterns and tracing transmission pathways. The developed "GIS-integrated strategy" methodology promotes a paradigm shift from merely confirming "microbial presence" to systematically analyzing the multidimensional relationships among "microorganism-environment-control." This study not only provides a scientific basis for formulating pollution control protocols in the pharmaceutical industry, contributing to improved sterility assurance, but also serves as a practical example of interdisciplinary integration between microbial ecology and spatial information science, demonstrating significant theoretical value and industry application prospects.},
}
@article {pmid42360987,
year = {2026},
author = {Abuzaid, AS and Abbas, HH and El Ghonamy, YK and Mostafa, MA and Rebouh, NY and Shokr, MS},
title = {A GIS-based multi-criteria framework for mapping potential irrigated agricultural zones in newly reclaimed arid agroecosystem.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0351546},
pmid = {42360987},
issn = {1932-6203},
mesh = {*Geographic Information Systems ; *Agricultural Irrigation/methods ; Soil/chemistry ; Groundwater ; *Agriculture/methods ; Fuzzy Logic ; Egypt ; *Agroecology ; Ecosystem ; Conservation of Natural Resources ; },
abstract = {Geographic assessment of natural resources is a pillar for sustainable agriculture in newly developed agroecosystems. The current work provides a new framework to discriminate agricultural potential zones by integrating the analytical hierarchy process (AHP) with fuzzy logic under the geographic information system (GIS) platform. The study was conducted on 303.54 km2 (30354 ha) in the western Nile Delta fringes, Egypt. Topographic maps, field surveys, and laboratory analyses were employed to specify parameters characterizing terrain, soil, and groundwater qualities. The main criteria and their respective sub-criteria were ranked and weighted using the AHP. The GIS tools were employed to generate raster layers using ordinary kriging geostatistical models, normalize the thematic layers using fuzzy membership functions, and integrate the fuzzified layers with their AHP-derived weights using the weighted sum algorithm. Results revealed that the consistency ratio of all the developed pairwise comparison models did not exceed 10%, indicating the efficacy of AHP in allocating the specific contribution of each criterion. Salinity, sodicity, and depth were key parameters controlling soil performance; meanwhile, potential salinity and infiltration problems primarily determined the feasibility of groundwater irrigation. Among four major criteria, the greatest impact was due to groundwater quality (50%), followed by chemical soil quality (24%) and physical soil quality (21%), while slope had the least contribution (5%). The potentiality analysis indicated that the studied soils are promising since good-quality soils occupied more than 60% of the studied area. Groundwaters with good, marginal, and poor quality occupied 40, 23, and 37% of the total area, respectively. The overall potentiality map showed that 36, 26, and 38% of the studied area displayed high, moderate, and low potential for agricultural expansion, respectively. The integration of AHP with GIS tools (geostatistical analysis and fuzzy set) can enhance insight into sustainable land-use planning and suggest also timely cropping practices. Further investigations are advocated to quantify the suitable cropping patterns in the studied region.},
}
@article {pmid42361963,
year = {2026},
author = {Loc, DH and Sulesco, T and Tóth, GE and Lühken, R and Schmidt-Chanasit, J and Velavan, TP},
title = {First Mosquito-Based Molecular Evidence of Tembusu Virus in Vietnam.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108927},
doi = {10.1016/j.ijid.2026.108927},
pmid = {42361963},
issn = {1878-3511},
abstract = {BACKGROUND: Mosquito borne flavivirus diversity in Vietnam remains incompletely characterized. Tembusu virus (TMUV), an emerging flavivirus associated with ducks and other avian hosts, has been reported in poultry in Vietnam, but molecular evidence from field-caught mosquitoes has been lacking.<br><br>METHODS: We screened 10,658 mosquitoes representing four major arbovirus vector species including Aedes aegypti, Ae. albopictus, Culex quinquefaciatus, Cx. tritarniorhynchus, collected across multiple ecological settings in Vietnam. Mosquitoes were grouped into 586 pools and tested using broad range RT-PCR assays targeting flaviviruses and alphaviruses. Positive flavivirus amplicons were subjected to sequencing, and one TMUV positive pool underwent deeper sequencing and phylogenetic analysis.<br><br>RESULTS: The Cx. tritaeniorhynchus pool (25 specimens) collected in rural southern Vietnam yielded a TMUV draft genome. In the complete genome phylogeny, the Vietnamese mosquito derived sequence clustered within a distinct monophyletic clade comprising strains from China, Thailand, Taiwan, and Vietnam.<br><br>CONCLUSIONS: These findings provide the first mosquito-based molecular evidence of a TMUV related virus in Vietnam and suggest that mosquito surveillance can reveal previously unrecognized viral diversity and transmission patterns.},
}
@article {pmid42364147,
year = {2026},
author = {Villhauer, H and Hellwig, T and Labarosa, SJ and Metzger, S and Moore, J and Wysocki, A and Straube, H and Blume, DVM and Straube, J and Durka, W and Brankov, M and Konowalik, K and Lexa, M and Kheloufi, A and Mansouri, LM and Blanco Moreno, JM and Neira, P and Torra, J and Royo-Esnal, A and da Silva, LP and Santi, F and Zarantonello, AE and Rodríguez-García, E and Romeralo, C and Hampe, A and Manzanares-Vázquez, V and Myśliwy, M and Bomanowska, A and Kaczmarek, K and Kolanowska, M and Rewicz, A and Nikolić, N and Mudrák, O and Nobis, M and Nobis, A and Radak, B and Ilić, M and Baranow, P and Nowak, S and Nosalewicz, A and Krzemińska, I and Backhaus, AE and Szitár, K and Einspanier, S and Pincebourde, S and Leclerc, M and Wagner, M and Mitschunas, N and Bignon, A and Sahri, A and Saatkamp, A and Drouzas, AD and Kopriva, S and von Korff, M and Bucharova, A},
title = {Climate-driven in-situ trait variation in an annual ruderal grass across Europe.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcag164},
pmid = {42364147},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: Plant functional traits link environmental conditions to plant performance and adaptation. Growing evidence suggests that intraspecific trait variation can be as important as differences between species, yet large intraspecific studies of in-situ variation remain rare. While most studies have focused on plant morphological traits, the concentrations of elemental nutrients in seeds have received much less attention so far.<br><br>METHODS: We conducted a large-scale in-situ study of the widespread annual ruderal grass Hordeum murinum. We sampled 2070 individuals from 207 populations across a large part of its native range in Europe and North Africa. We measured seed ripening phenology and growth-related traits in-situ and analyzed concentrations of elemental nutrients in the seeds.<br><br>KEY RESULTS: We found that Hordeum murinum grew larger, produced seeds later, and had heavier seeds in colder and wetter regions. Plants growing in denser vegetation were taller and produced heavier seeds but formed fewer spikes. Concentrations of elemental nutrients in the seed generally declined with seed weight and were primarily driven by climatic variables, whereas soil conditions had only minor effects on plant traits and seed nutrients. Population identity explained a substantial proportion of trait variation, indicating a possible genetic component.<br><br>CONCLUSIONS: Our findings provide a comprehensive view of how Hordeum murinum responds to environmental gradients across its European distribution. Climatic variables, particularly temperature, are key drivers of reproductive timing and concentrations of elemental nutrients in the seed, whereas local environmental conditions, such as biotic pressures, are more critical for growth-related traits. Together, these patterns indicate that Hordeum murinum modulates its growth and reproductive investment along environmental gradients, balancing phenology, stress tolerance, and limited competitive capacity.},
}
@article {pmid41914406,
year = {2026},
author = {Lu, ZN and Ren, S and Hao, Y and Yuan, C},
title = {Digital Determinants of Health: Evaluating the Impact of Information and Communication Technology on Chinese Health Outcomes.},
journal = {The International journal of health planning and management},
volume = {41},
number = {4},
pages = {593-606},
doi = {10.1002/hpm.70074},
pmid = {41914406},
issn = {1099-1751},
support = {72321002//National Natural Science Foundation of China/ ; 2022WCXTD022//Guangdong Provincial Ordinary University Innovation Team Project/ ; 2022CX01013//Technology Innovation Program of Beijing Institute of Technology/ ; 2023CX13028//Technology Innovation Program of Beijing Institute of Technology/ ; },
mesh = {China ; Humans ; Female ; Male ; Digital Health ; Adult ; Middle Aged ; Surveys and Questionnaires ; *Health Status ; *Information Technology ; },
abstract = {BACKGROUND: The new generation of network information technology has become a significant tool to promote public health. The application of information and communication technology (ICT) in the traditional medical industry has changed the medical service model, improved the public medical service system, and provided diversified medical services to the public.<br><br>OBJECTIVE: This paper discusses the impact of ICT on residents' health, and analyzes the possible heterogeneity impact in different groups and its impact mechanism using the China Family Panel Studies (CFPS) data and a fixed-effects model.<br><br>METHODS: The ordinary least squares estimation method was adopted to quantitatively identify the impact mechanism of ICT applications on residents' health. Multisource big data were collected, including the CFPS questionnaire (gender, age, marriage status, work status, income level, smoking, sports, and insurance participation), regional economic development, as well as service industry development. The quantitative phase involved conducting in-depth investigation across 25&#xa0;Chinese provinces. Then, a quantitative analyse-based study empirically tested the effects of internet applications on residents' health by matching macro data and micro survey data. After controlling for these identified factors, the data were tested using ordinary least squares and fixed effect models, with the assistance of STATA version 14 to measure and validate the proposed model.<br><br>RESULTS: The regression results support the conclusion that ICT can significantly improve residents' health (p&#xa0;<&#xa0;0.001). After a series of robustness tests through replacing explanatory variables and choosing appropriate exogenous policy shocks, the results still hold. We analyse the possible heterogeneous effects and conclude that the health-promoting effect of ICT is stronger among middle-aged individuals, high-income groups, women, urban residents, unmarried individual, those who engage in sports and non-smokers.<br><br>CONCLUSIONS: Our study confirms a significant association between ICT applications and residents' health and reveals substantial heterogeneity in this effect. It also provides insights into how to apply internet information to better realise disease surveillance and prevention goals.},
}
@article {pmid42360102,
year = {2026},
author = {Chen, J and Li, Z and Wu, J and Xing, Y and He, S and Sheng, Y and Zhu, L},
title = {Elucidating the Adverse Outcome Pathway for Grain-Quality Deterioration Induced by Brominated Flame Retardants in Rice: A Multiomics and Lifecycle Analysis.},
journal = {Environmental science &amp; technology},
volume = {60},
number = {26},
pages = {18519-18533},
doi = {10.1021/acs.est.6c04723},
pmid = {42360102},
issn = {1520-5851},
mesh = {*Flame Retardants ; *Oryza ; Multiomics ; Halogenated Diphenyl Ethers ; Edible Grain ; },
abstract = {Brominated flame retardants (BFRs) pose a growing threat to agricultural safety, yet their dynamic transfer mechanisms and interference with crop metabolism remain poorly understood. This study systematically unravels the lifecycle translocation of BFRs in rice and deciphers the signaling-mediated cascade leading to grain-quality deterioration. BFR accumulation did not follow a simple xylem-mediated transport pattern; instead, secondary enrichment occurred during grain filling, inversely correlated with their logKow and molecular weight. In particular, the concentration of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) in the panicles increased sharply from ∼1 ng/g at the heading stage to 16.5 ng/g at the filling stage, reaching 42.0 ng/g at maturity, representing an order-of-magnitude increase. This accumulation critically coincided with a marked depletion of nutritional components: amylopectin and total protein decreased by 10.3-17.7%, accompanied by a 12.5% reduction in 1000-grain weight. Through integrated transcriptomic, proteomic, and metabolomic analyses, along with a novel motif-based unbiased screening method, we deciphered the core adverse outcome pathway (AOP). BFRs advanced the abscisic acid (ABA) peak by 5 days and increasing its concentration ∼20% compared to the control. This intensified ABA signaling pathway upregulated tricarboxylic acid cycle enzymes by 2-5-fold, and redirected carbon flux from starch synthesis toward energy production. This metabolic shift accelerates the cotransport of selected BFRs (e.g., BDE-47) into the developing grain, driving premature maturation and nutritional loss. By establishing a complete "signal activation → metabolic reprogramming → pollutant co-transport → quality deterioration" AOP framework, this study provides a mechanistic foundation for understanding the potential dietary implications of BFRs in rice, offering crucial insights for safeguarding food safety and controlling agricultural contamination.},
}
@article {pmid41540071,
year = {2026},
author = {Sun, T and Hughes, AC and He, K and Yu, L},
title = {Ecological Integrity Index, timely annual tracking of biodiversity change.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {174},
pmid = {41540071},
issn = {2052-4463},
mesh = {Humans ; *Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; Datasets as Topic ; },
abstract = {Despite numerous global initiatives and policy framework to mitigate ongoing biodiversity decline, progress remains limited due to lack of biodiversity indicators that are timely, scientifically rigorous, and representative. Furthermore, databases underlying previous indicators are spatially, temporally, geographically and taxonomically biased, making it difficult to track biodiversity change dynamics and set proper biodiversity targets. Here, we constructed a new version of the global human footprint, and used it to infer temporally explicit annual shifting patterns of biodiversity across all scales by incorporating remote sensing and mapping out human pressures. This indicator (the Ecological Integrity Index- EII) successfully differentiates high- and low- biodiversity biomes, especially for deserts and tundra. Moreover, shifting annual patterns can identify global hotspots (e.g., major rainforests and regional hotspots), and shows biodiversity change dynamics at regional level based on estimating biodiversity change over time. Changes of evolving human footprint were further analyzed with relationships to biodiversity patterns. At more a local level, the patterns perfectly reflect biodiversity and intactness. Compared to other indicators (e.g., BII, BHI) in the Kunming-Montreal Global Biodiversity Framework (GBF) and biodiversity models (e.g., GLOBIO), the EII can better reflect biodiversity. EII shows a good performance, with the potential to inform biodiversity conservation efforts, and support the implementation of the post-2020 global biodiversity framework.},
}
@article {pmid42360682,
year = {2026},
author = {Rg, C and Ott-Conn, CN and Euclide, PT and Blanchong, JA and Schmoldt, A and DeYoung, RW and Walsh, DP and Larson, WA and Latch, EK},
title = {A Practical Framework for GT-Seq Panel Optimization.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70169},
pmid = {42360682},
issn = {1755-0998},
support = {F22AP00694-00//Multistate Conservation Grant Program/ ; 107048 MSU//the Michigan Department of Natural Resources/Michigan State University Joint Wildlife Disease Initiative/ ; //UW-Milwaukee Graduate School/ ; },
mesh = {Animals ; Polymorphism, Single Nucleotide ; *Genotyping Techniques/methods ; *Deer/genetics/classification ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; DNA Primers/genetics ; },
abstract = {Genotyping-in-thousands by sequencing (GT-seq) panels are powerful tools in ecological, evolutionary and conservation genomics, yet the optimization process critical for robust and reproducible genotyping remains poorly formalized. Here, we present an iterative workflow for GT-seq panel optimization that emphasizes systematic refinement, quality control and structured decision-making to improve panel performance across diverse populations and study contexts. We illustrate this framework through the development and optimization of a GT-seq panel for white-tailed deer, a widely distributed and ecologically important North American species. From an initial set of 1200 candidate SNPs selected from a commercial microarray (OVSNP60, containing 72,728 SNPs) and prioritized for high heterozygosity, primers were designed for 646 loci. The final optimized panel contains 508 high-performing markers retained after iterative removal of overamplifying primer pairs, adjustment of primer concentrations, PCR conditions and bioinformatic filtering. The overall proportion of SNPs with more than 70% genotype rate increased from 25.5% in the first optimization round to 87.8% in the final round. Consequently, the overall genotype rate increased from 39.4% to 84%. We also identify key quality-control checkpoints and practical criteria to guide panel refinement and ensure consistent performance. By prioritizing optimization as an integral component of GT-seq panel development, this work provides a reproducible framework for generating robust, high-throughput genotyping tools in non-model species and underscores the importance of iterative refinement to maximize data quality and utility.},
}
@article {pmid42359335,
year = {2026},
author = {Fraser, B and Gasparini, C and Santi, F and Böhne, A and Monteiro, R and Marcussen, T and Oomen, RA and Struck, TH and , and , and , and Denton, A and Howard, C and Howe, K and Blaxter, M and McCarthy, S and Wood, JMD and Martin, F and Sinha, S and Haggerty, L and Bortoluzzi, C},
title = {ERGA-BGE reference genome of Gambusia holbrooki, a globally invasive freshwater fish.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {48},
doi = {10.12688/openreseurope.22693.2},
pmid = {42359335},
issn = {2732-5121},
abstract = {The Gambusia holbrooki (eastern mosquitofish) reference genome will offer a crucial resource for understanding the evolution and adaptation of invasive freshwater fish species. The genome of G. holbrooki was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the genome sequence was assembled into 24 contiguous chromosomal pseudomolecules and 1 mitochondrial genome. This chromosome-level assembly encompasses 0.67 Gb, composed of 421 contigs and 318 scaffolds, with contig and scaffold N50 values of 15.9 Mb and 29.6 Mb, respectively.},
}
@article {pmid42049755,
year = {2026},
author = {Zhou, K and Kosmopoulos, JC and Colón, ED and Badciong, PJ and Anantharaman, K},
title = {V- and VL-scores unveil viral signatures and origins of protein families.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42049755},
issn = {2041-1723},
support = {DBI2047598//National Science Foundation (NSF)/ ; 42576129//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Viral Proteins/genetics/metabolism ; *Genome, Viral/genetics ; *Viruses/genetics ; Databases, Protein ; *Computational Biology/methods ; },
abstract = {Viruses are key drivers of microbial ecology and evolution, yet their study is hindered due to challenges in culturing. Traditional gene-centric methods, which focus on a few hallmark genes like for capsids, miss much of the viral genome, leaving key viral proteins and functions undiscovered. Here, we introduce two powerful annotation-free metrics, V-score and VL-score, designed to quantify the "virus-likeness" of protein families and genomes and create an open-access searchable database, 'V-Score-Search'. By applying V- and VL-scores to public protein databases, we link 19 - 59% of protein families with viruses representing a 5 - 8x increase over current estimates. These metrics outperform existing approaches, enabling high efficiency in detection of viral genomes, prophages, and host-derived auxiliary viral genes (AVGs) from fragmented sequences. Remarkably, we identify up to 17 times more AVGs dominated by non-metabolic proteins of unknown function. This innovation unlocks new insights into virus signatures and host interactions, with wide-ranging implications from genomics to biotechnology.},
}
@article {pmid42097135,
year = {2026},
author = {Ausman, LM and Namirembe, G and Mezzano, J and Lauer, JM and Shrestha, R and Agaba, E and Bashaasha, B and Griffiths, JK and Marino-Costello, E and Wang, JS and Erhardt, JG and Gewirtz, AT and Duggan, CP and Webb, P and Ghosh, S},
title = {Maternal Aflatoxin Exposure, Birth Outcomes, and Infant Growth in Uganda.},
journal = {The American journal of tropical medicine and hygiene},
volume = {115},
number = {1},
pages = {167-175},
pmid = {42097135},
issn = {1476-1645},
mesh = {Humans ; Female ; Uganda/epidemiology ; Pregnancy ; Infant ; *Maternal Exposure/adverse effects ; *Aflatoxin B1/blood ; Adult ; Infant, Newborn ; Birth Weight ; *Child Development ; Male ; *Aflatoxins/blood ; Young Adult ; },
abstract = {The association between maternal aflatoxin exposure and infant anthropometric birth and growth outcomes was investigated in the present study, controlling for possible confounders. Pregnant women (N = 1,210) from 16 Ugandan subcounties were enrolled in a birth cohort study to track birth outcomes and subsequent growth of infants. Serum concentrations of aflatoxin B1 (AFB1)-lysine adduct, environmental enteric dysfunction markers of anti-lipopolysaccharide and anti-flagellin IgG and IgA, and markers of systemic inflammation, alpha-1 acid glycoprotein, and C-reactive protein were measured in mothers at birth and infants at 6 months of age. A generalized estimating equations model with an exchangeable correlation matrix was used to assess associations between maternal AFB1 blood concentration and weight, length, weight-for-age (WAZ), length-for-age (LAZ), and weight-for-length (WLZ) Z scores. Multivariable linear and logistic regressions were used to assess the association between infant aflatoxin concentrations and growth outcomes at 3 to 6 months of age. Serum aflatoxin concentrations in women at parturition were associated with reduced birth weight (P = 0.037) and WAZ (P = 0.034), but not with other birth outcomes. Aflatoxin concentrations in infants 6 months of age were not associated with changes in weight, height, WAZ, LAZ, or WLZ between 3 and 6 months of age. The present study confirmed an association between maternal aflatoxin and specific birth outcomes, but not between infant serum aflatoxin and infant early growth, which may be due to low exposure to aflatoxin-contaminated foods in early life. This finding highlights the importance of promoting national policy actions that minimize aflatoxin contamination of local food supplies, both on farms and in markets.},
}
@article {pmid42069816,
year = {2026},
author = {Anitha, M and Prasad, CR and Awotunde, JB and Adeniyi, AE and Aroba, OJ},
title = {Breast ultrasound images for segmentation and classification using multi-task U-Net.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42069816},
issn = {2045-2322},
mesh = {Humans ; Female ; *Breast Neoplasms/diagnostic imaging/classification ; *Ultrasonography, Mammary/methods ; Deep Learning ; Classification Algorithms ; *Image Interpretation, Computer-Assisted/methods ; *Image Processing, Computer-Assisted/methods ; Algorithms ; *Breast/diagnostic imaging ; },
abstract = {Breast ultrasound imaging is widely used for the early detection of breast cancer due to its accessibility and effectiveness, particularly in dense breast tissues. However, its diagnostic performance is often affected by operator dependency, speckle noise, low contrast, and variability in data quality. Although deep learning methods have shown promise in automated tumor segmentation and classification, their clinical applicability remains limited due to challenges such as small and imbalanced datasets, inconsistent annotations, and the lack of integrated learning strategies. In this work, we propose a Multi-Task U-Net framework that jointly performs lesion segmentation and tumor classification by leveraging shared feature representations. The proposed method incorporates a deterministic oversampling strategy for handling class imbalance, a prediction-refinement module to ensure consistency between segmentation and classification outputs, and an attention-guided feature learning mechanism to enhance lesion localization. Additionally, a curated version of the BUSI dataset is constructed by removing duplicate and inconsistent samples to ensure reliable evaluation. The proposed model achieves a Dice score of up to 0.81 in comparative evaluation, along with classification accuracy of up to 0.96-0.98, demonstrating improved performance over baseline methods. The consistent performance across both segmentation and classification tasks indicates good generalization capability despite dataset limitations. Finally, the proposed multi-task framework provides an effective and reliable solution for automated breast cancer detection in ultrasound images and shows strong potential for clinical application.},
}
@article {pmid42136370,
year = {2026},
author = {Wu, C and Liu, H and Carvalhais, LC and Guo, J and Cai, P and Zhong, J and Zhang, H and Jin, B and Li, G and Yang, J and Chen, J and Ge, T},
title = {Root exudate-associated microbiome assembly contributes to viral disease resistance in wheat.},
journal = {The New phytologist},
volume = {251},
number = {3},
pages = {1397-1414},
doi = {10.1111/nph.71254},
pmid = {42136370},
issn = {1469-8137},
support = {CARS-08-G09//China Agriculture Research System from the Ministry of Agriculture of P.R. China/ ; U24A20404//National Science Foundation of China/ ; 42477341//National Science Foundation of China/ ; 2022YFD1400700//National Key Research and Development Program of China/ ; 2022YFA1304401//National Key Research and Development Program of China/ ; 2024YFC3406003//National Key Research and Development Program of China/ ; //K.C. Wong Magna Fund of Ningbo University/ ; YLS-2025-ZY01012//Yuelushan Laboratory Breeding Program/ ; },
mesh = {*Triticum/microbiology/virology/immunology ; *Disease Resistance ; *Microbiota/genetics ; *Plant Diseases/virology/microbiology/immunology ; *Plant Roots/microbiology/virology ; Rhizosphere ; *Plant Exudates/metabolism ; Multiomics ; },
abstract = {Early mutualistic interactions between host plants and their rhizosphere microbes have the potential to provide soil-borne disease resistance. However, it remains unclear how the early rhizosphere microbiome protects against viral diseases such as wheat yellow mosaic virus, which is a major threat to global wheat production. We combined field trials with microbiome transplantation experiments to investigate the role of early rhizosphere microbiomes in suppressing wheat yellow mosaic disease. To uncover the underlying mechanisms, we further performed integrated multi-omics analyses of microbial communities, functional genes, and metabolic profiles. Disease-resistant wheat cultivars were consistently associated with distinct seedling rhizosphere microbiome assembly, including a lower Polymyxa graminis abundance, lower community compositional variation, and enrichment of beneficial taxa such as Bacillus, Pseudomonas, and Trichoderma. Resistant cultivars also exhibited distinct rhizosphere metabolite profiles, including higher levels of glyceraldehyde and N-acetyltryptophan, which were positively associated with keystone microbial taxa and stimulated representative isolates in vitro. Isolate-based and synthetic community validation further supported the functional relevance of these taxa, while microbial inoculation was associated with reduced vector abundance, lower virus accumulation, and activation of host defense-related pathways. Our findings showed that early cultivar-dependent rhizosphere microbiome assembly was closely linked to resistance against soil-borne viral disease in wheat.},
}
@article {pmid42144817,
year = {2026},
author = {Oliveira, DN and Ordóñez-Parra, CA and Chen, SC and Arnold, AE and Davis, AS and González, AMT and Morales-Pérez, AL and Díaz-Castellanos, AR and Pérez-Enriquez, A and Fidelis, A and Carvalho, ASR and Santos, AS and Sandoval, AC and Crestani, ACV and Mairinck, ALA and Neto, ADA and Coetzee, A and Traveset, A and Andrade, ACS and Datta, A and Teles, AM and Nerlekar, AN and Sengupta, A and Munje, A and Negret, BS and Basu, B and Rocha, CS and De Melo E Silva-Neto, C and Santos, CHB and Sarmiento, C and da Cruz Vasconcelos, C and Offord, CA and López, CL and Mayta, C and Ordoñez-Salanueva, CA and Seal, CE and Cruz, CRP and Seymour, CL and Almeida, DS and Pifano, DS and Vieira, DLM and Dias, DP and Ramos-Chuquimia, D and Vieira, DCM and Sánchez, DA and Cruz-Tejada, DM and Cunha, DDS and Escobar, DFE and Santos, DL and Silva, DA and Gonçalves, EP and Damasceno, ES and Duarte, EF and Mendes, ETB and Peña-Miranda, ET and do Carmo, EM and Tarazona-Tubens, FL and Silva, FFS and Piña-Rodrigues, FCM and Souza, FC and Faria, FS and Nascimento, FA and Torres-Romero, FJ and Motta, GST and Oda, GA and Liyanage, GS and Calvi, GP and Costa, GFL and Errington, G and Joseph, GS and Da Costa, GM and Canassa, GG and Gama, G and Liang, H and Wang, HY and Yadav, H and Consolaro, HN and Ferreira, HD and Miranda, HS and Zirondi, HL and Botey, HM and Fontenele, HGV and Pritchard, HW and Pinto, &#xcd;M and Araujo-Santos, I and Ferraz, IDK and Da Gama, IG and Zambrano, IAN and Dalling, JW and Santos, JAD and Viana, JS and Castellanos-Barliza, JJ and Rodríguez, JVD and Hoyos, JLL and Powers, JS and Corredor-Prado, JP and Vázquez-Ramírez, J and Sansevero, JBB and Vargas-Figueroa, JA and Magalhães, JGS and Borges, JPGDS and Flores, J and Ribeiro, JWF and Barlow, J and Rojas, JM and Fonseca-Altahon, JD and Morante-Filho, JC and Santos, JHSD and Silva, JN and Hurtado, JS and Ley-López, JM and Villalba-Malaver, JC and Lage, JMM and Benítez-Malvido, J and Lim, JY and Jayasuriya, KMGG and Sommerville, KD and Pradhan, K and Chong, KGJ and Mcconkey, KR and Garcia, LA and Brito, L&#xc9; and Marín, LER and Morellato, LPC and Aona, LYS and de Oliveira, LS and Macias-Sposito, L and Martinez-Martinez, LA and Navarro, L and Daibes, LF and Coelho, LFM and Pinheiro, LFS and Melgarejo, LM and Benchimol, M and Wijayasinghe, MM and Meiado, MV and Amador-Cubides, MC and Braz, MIG and Dairel, M and Villegas, M and Guedes, MR and Conde, MMS and Magalhães, MLL and Shibata, M and Côrtes, MC and Ooi, MKJ and Prates, MB and Chua, MSE and Figueiredo, MA and Galetti, M and Ferreira, MC and Arthur, M and Soto-Avendaño, MV and Cházaro-Basañez, M and Koutouan-Kontchoi, MN and Da Silva, MAD and Alves, M and Bullón, NR and Borawake, N and Santos, NSCD and Razafindratsima, OH and Dávila-Aranda, P and Zalamea, PC and Laumann, PD and León-Lobos, P and Poschlod, P and Souza-Perera, R and Cavalcante, RAS and Gasparini, R and Rodrigues, RG and Frigeri, RBC and Alvarez-Espino, RX and Portela, RCQ and Timmers, R and Naniwadekar, R and Staneke, R and Kolb, RM and Contreras, RD and Heleno, RH and Swart, RC and Tangney, R and Madriñán, S and McInnes, SJ and Amoêdo, SC and Kim, S and Phartyal, SS and Escalante-Rebolledo, SE and Gallegos, SC and Le Stradic, S and Hernandez-Ortiz, SM and Sidhu, S and Zupo, TM and Vilas-Boas, T and Ulian, T and Shukla, U and Pivello, VR and Klein, VLG and Da Silva, VMF and De Lima, VF and Londoño-Lemos, V and Simioni, WB and Barranco-Pérez, WA and Varela, YCDS and Athugala, YS and Newby, ZJ and Silveira, FAO},
title = {Tropical Seed Trait Database: advancing seed functional ecology in the world's most biodiverse region.},
journal = {The New phytologist},
volume = {251},
number = {3},
pages = {945-958},
doi = {10.1111/nph.71268},
pmid = {42144817},
issn = {1469-8137},
support = {//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; //Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {*Seeds/physiology ; *Tropical Climate ; *Databases, Factual ; *Ecology ; *Quantitative Trait, Heritable ; Biodiversity ; Ecosystem ; Phenotype ; Biocuration ; },
abstract = {Plant functional traits connect biodiversity to ecosystem processes, serving as key metrics for assessing how biota responds to environmental conditions. Functional seed traits are critical because they underpin recruitment and colonization, shaping biodiversity patterns and influencing ecosystem resilience. Yet, seed traits remain underrepresented in major data repositories, with severe gaps in the tropics. Climatic, geological, and historical differences between tropical and temperate regions drive distinct regeneration dynamics, suggesting that the paucity of tropical seed trait data limits our ability to predict regeneration niches and weakens global models largely based on temperate ecosystems. To address this gap, we introduce the Tropical Seed Trait Database (TSTD), an open-access repository spanning the full ecological spectrum of tropical seeds. The TSTD is conceived as a community-driven repository of primary data contributed directly by data owners, rather than as a secondary aggregation of global databases. It was built through contributions from ecologists working across all tropical regions, reached through direct contact, and its first version compiles 78 datasets, totaling 137 583 records across 44 functional traits. Covering 5115 species in 33 countries, with the Neotropics overrepresented, the TSTD marks a crucial step toward more inclusive, globally representative trait databases that can open multiple research avenues.},
}
@article {pmid42341031,
year = {2026},
author = {Volpatto, D and Contaldo, SG and Pernice, S and Beccuti, M and Cordero, F and Sirovich, R},
title = {A new cancer progression model: From synthetic tumors to real data and back.},
journal = {PLoS computational biology},
volume = {22},
number = {6},
pages = {e1013991},
doi = {10.1371/journal.pcbi.1013991},
pmid = {42341031},
issn = {1553-7358},
mesh = {*Neoplasms/genetics/pathology ; Humans ; Disease Progression ; *Models, Biological ; Stochastic Processes ; Computer Simulation ; Computational Biology ; Mutation ; Algorithms ; Phenotype ; },
abstract = {Intratumor heterogeneity (ITH) arises from the combined effects of genetic alterations, clonal interactions, and environmental constraints, and plays a central role in therapeutic resistance and disease progression. While ITH has been extensively documented in empirical tumor data, the scientific debate regarding the biological mechanisms underlying this heterogeneity remains complex, highlighting the need for cancer evolution models that are sufficiently flexible and sophisticated to reproduce the observed behaviors and to give insights on the unobserved ones. Here, we present a stochastic modelling framework for tumor evolution that integrates genotypic inheritance with phenotype driven functional traits and resource mediated competition. Mutational events are associated with functional capabilities such as altered proliferation, increased mutation rates, limit evasion potential or enhanced control over shared resources, allowing multiple genotypes to converge on similar phenotypes. The model explicitly tracks subclonal lineages while incorporating environmental constraints that modulate growth and competition. The framework is defined through a mathematically rigorous construction and is accompanied by an efficient simulation algorithm. To facilitate exploration and reproducibility, we provide an open-source graphical user interface that allows users to configure model parameters, run simulations, and inspect clonal genealogies and population dynamics without requiring direct interaction with the underlying code. Using this model, we illustrate how ecological feedbacks can shape clonal dynamics over time, supporting an interpretation in which early tumor growth is dominated by stochastic expansion, while later evolution increasingly reflects selection for traits that alleviate environmental constraints. Rather than constituting a new evolutionary paradigm, this behaviour demonstrates how well-documented biological patterns can emerge naturally from a unified stochastic and ecological description. Overall, our approach offers a flexible and extensible platform for investigating how chance, functional traits, and environmental interactions jointly govern tumor heterogeneity.},
}
@article {pmid42341845,
year = {2026},
author = {Mancuso, M and Suranse, V and Seneci, L and Senoner, T and Koludarov, I and Sunagar, K and Fry, BG},
title = {CAPtivating toxins: Molecular evolution of CAP proteins (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1) in the chemical arsenals of diverse venomous animals.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {},
number = {},
pages = {109199},
doi = {10.1016/j.toxicon.2026.109199},
pmid = {42341845},
issn = {1879-3150},
abstract = {The cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 (CAP) superfamily represents one of the most widely recruited molecular scaffolds in animal venoms. Despite their ubiquity, the evolutionary forces shaping their diversification are still mostly unknown. Here, we integrate Bayesian and maximum-likelihood phylogenetics with site- and branch-level selection analyses (FUBAR, MEME, CodeML, and BUSTED) to investigate CAP evolution across 12 venomous metazoan lineages, spanning insects, arachnids, centipedes, lizards, and snakes. Our results reveal a spectrum of evolutionary regimes, with purifying selection dominating across arthropods, whereas episodic and pervasive positive selection strongly shape CAP diversification in toxicoferan reptiles. Exceptional diversification was also detected in triatomine bugs and Ixodes ticks, suggesting host-driven lineage-specific adaptive pressures. Three-dimensional representations show that diversification frequently targets exposed and functionally relevant residues, supporting coevolutionary arms race scenarios. Altogether, our findings demonstrate that CAP proteins have undergone multiple recurrent trajectories of molecular innovation, reflecting the convergent interplay between ecology, structure, and lineage-specific pressures. This study establishes a comprehensive framework for understanding how a single ancestral protein scaffold has been repeatedly co-opted and diversified across the animal kingdom's chemical arsenals. Additionally, we describe a hybrid loop-β-sheet extension of the CAP1 motif based on sequence and structural conservation evidence across CAP proteins.},
}
@article {pmid42342705,
year = {2026},
author = {Liu, G and Su, D and Liu, Y and Shi, Z and Gao, S and He, X and Zhang, S and Deng, H and Xiao, J and Yao, Y and Shu, P},
title = {A chromosome-level genome assembly of SAGS Anisodus tanguticus (Maxim.) Pascher (Solanaceae) from the Tibetan region of Sichuan, China.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07697-z},
pmid = {42342705},
issn = {2052-4463},
support = {CARS-34//China Forage and Grass Research System/ ; },
abstract = {Anisodus tanguticus (Maxim.) Pascher (A. tanguticus), a cold-tolerant perennial herb in the Solanaceae family, is distributed across China's Qinghai-Tibet Plateau and extends to Nepal, Bhutan, Sikkim, and India. As a Tibetan medicinal plant, it is used to treat pain, ulcers, etc.; its roots yield antispasmodic and anesthetic compounds, and other parts are used as a feed additive for yaks to enhance cold resistance in northwest Sichuan. In this study, samples were collected from Seda County (northwestern Sichuan, China) for sequencing. Using PacBio HiFi sequencing and Hi-C scaffolding, a high-quality chromosome-scale genome assembly was generated, with a genome size of 1599.64 Mb, a scaffold N50 of 62.01 Mb, and a contig N50 of 38.51 Mb. A total of 24 superscaffolds (93.65% of the genome) were anchored to 24 chromosomes. Compared with previously reported assemblies of A. tanguticus and A. acutangulus, this assembly shows improved scaffold length and completeness. Genome annotation identified 64.95% repetitive elements and 45,930 protein-coding genes, and comparative analysis of four Anisodus genomes revealed conserved patterns of gene density, GC content, LTR, and LINE elements. This study provides the first high-quality chromosome-scale genome resource of A. tanguticus from the Qinghai-Tibet Plateau, supporting studies on phylogeny, genetic diversity, and breeding, as well as further exploration of its genomic basis of high-altitude adaptation.},
}
@article {pmid42347528,
year = {2026},
author = {Tedjou, AN and Keumeni, CR and Yougang, AP and Njiokou, F and Lines, J and Clarke, SE and Wondji, CS and Kamgang, B},
title = {Anthropophagy and Ecological Bridges: Blood-Meal Patterns of Invasive Aedes albopictus (Skuse, 1894) and Native Aedes aegypti Linnaeus, 1762 and Their Implications for Arbovirus Emergence in Central Africa.},
journal = {Tropical medicine and infectious disease},
volume = {11},
number = {6},
pages = {},
pmid = {42347528},
issn = {2414-6366},
support = {204862/WT_/Wellcome Trust/United Kingdom ; 204862/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Aedes (Ae.) aegypti and Ae. albopictus are important vectors of arboviruses. Yet their blood-feeding pattern remains poorly characterised in Africa, including Cameroon. In this study, we characterised the blood-meal sources in both species collected from vegetation, household surroundings, and animal cages across four urban sites, one rural site, and a zoo-botanical garden where humans and animals in captivity are the main hosts. Overall, Aedes mosquitoes represented about half of 10,054 female mosquitoes collected, with Ae. albopictus strongly dominating Ae. aegypti among 5001 Aedes females, and only 5.95% of females visibly blood-fed. Sequencing a 748 base pairs (bp) fragment of the cytochrome oxidase I gene from 156 blood-fed abdomens yielded 126 high-confidence host assignments, of which 98.25% were humans, indicating a strong anthropophagic pattern in both species. Unpredictably, two Ae. albopictus individuals had fed on a baboon (Papio anubis) and a frugivorous bat (Pteropodidae), as confirmed by bio informatic analyses, highlighting the species' opportunistic blood-feeding nature and providing preliminary molecular evidence consistent with a potential bridge-vector role in this setting. Despite the extreme anthropophagy of both species observed, results indicate that Ae. albopictus could also serve as a bridge vector enabling spillover of enzootic viruses to humans, including urbanised settings where wild animals are present. These findings emphasise the urgent need for enhanced arbovirus surveillance in Central Africa using a One Health approach.},
}
@article {pmid42348219,
year = {2026},
author = {Mederer, M and Gautam, A and Kohlbacher, O and Lupas, A and Elhabashy, H},
title = {Interacting Species Database (ISDB): Comprehensive Resource for Interspecies Interactions at the Molecular Level.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag419},
pmid = {42348219},
issn = {1367-4811},
abstract = {MOTIVATION: Organisms within ecological systems often engage in molecular interactions that mediate key biological processes, such as protein-protein interactions involved in host-pathogen recognition and symbiosis. Characterization of these interactions at a molecular level is essential for understanding the mechanistic, evolutionary, and functional basis of interspecies interactions, as well as for informing potential therapeutic interventions. However, progress in this field is significantly impeded by the lack of a comprehensive database of interacting species at molecular resolution and the limited availability of experimental data.<br><br>RESULTS: We introduce the Interacting Species Database (ISDB), a comprehensive resource that catalogs interspecies interactions, annotated with NCBI taxonomic identifiers, interaction types and known molecular interactions. The ISDB encompasses 858,229 interacting species pairs and 171,713 interspecies protein-protein interactions within 261,287 organisms. ISDB is designed to support researchers in searching for, downloading, and depositing interspecies interaction data, which facilitates the study of ecological dynamics across diverse research domains.<br><br>AVAILABILITY: The ISDB is available via a web interface (https://www.elhabashylab.org/isdb), open-source code on GitHub (https://github.com/ElhabashyLab/ISDB) under the MIT license and is archived on Zenodo (Version v1.0.1, DOI: 10.5281/zenodo.20162385).},
}
@article {pmid42350135,
year = {2026},
author = {Liu, YT and Liu, MH and Chen, NN and Mi, N and Yu, WY and Wu, JW and Feng, R},
title = {Variation characteristics of high-temperature and drought compound disasters in Liaoning Province based on Copula function and random forest.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {37},
number = {5},
pages = {1595-1604},
doi = {10.13287/j.1001-9332.202605.028},
pmid = {42350135},
issn = {1001-9332},
mesh = {*Droughts ; *Disasters ; China ; *Hot Temperature ; Random Forest ; *Climate Change ; Geographic Information Systems ; Models, Theoretical ; Ecosystem ; },
abstract = {Under the backdrop of global climate change, the frequent occurrence of combined disasters of high temperature and drought poses severe challenges to food security, ecological environment, and sustainable socio-economic development. Based on the meteorological observation data from 1971 to 2024, we constructed an intensity index by combining the nested Copula model with the random forest algorithm, and analyzed the spatiotemporal variations, recurrence interval characteristics and intensity evolution law of compound high-temperature and drought disasters in Liaoning Province by coupling GIS technology. The results showed that the occurrence frequency of compound high-temperature and drought disasters presented a pattern of being high in the west and low in the east. The western region was a continuously expanding and intensifying high-frequency agglomeration area, while the eastern and coastal areas remained a stable low-frequency area for a long time. Compound high-temperature and drought disasters in Liaoning Province were dominated by short recurrence interval (0-2 years) events, which featured with high occurrence frequency and strong spatial agglomeration. The western region as the core high-incidence area. With the extension of the return period, the occurrence scope of disasters shrank sharply and the frequency decreased, and long recurrence interval events were only sporadically distributed in the western region. The intensity of single events experienced a phased evolution of weak occurrence-initial increase-rapid increase-maintenance-attenuation, peaking in the 1990s. The cumulative intensity gradually evolved from a pattern of single low-value agglomeration in the western region in the 1970s to a dual high-intensity agglomeration pattern in the western and central regions in the 2010s. The intensity of the core western region reached its peak at the end of the study period. In summary, the western region of Liaoning Province was the core affected area of compound high-temperature and drought disasters, and the disaster intensity showed an increasing trend. This study could provide a scientific basis for the formulation of disaster prevention and mitigation strategies and risk management in Liaoning Province.},
}
@article {pmid42352964,
year = {2026},
author = {Ding, Y and Liu, T and Guo, S and Zhu, J and Zhu, J and Tang, Q and Jia, Q and Li, J and Zhang, Z and Liu, X},
title = {Integrative Multi-Omics Reveals Microbiome and Genome Streamlining Underlie Ecological Divergence in Chinese and Xinjiang Cordyceps: A Preliminary Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {12},
pages = {},
pmid = {42352964},
issn = {1422-0067},
support = {xjnkywdzc-2026002-7//Xinjiang academy of agricultural sciences/ ; xjnkywdzc-2026003-9//Xinjiang Academy of Agricultural sciences/ ; },
mesh = {*Cordyceps/genetics/classification/metabolism ; Multiomics ; *Microbiota/genetics ; Metabolomics/methods ; Genomics/methods ; *Genome, Fungal ; Phylogeny ; },
abstract = {Chinese Cordyceps (Ophiocordyceps sinensis) and Xinjiang Cordyceps (Paraisaria gracilis) are related entomopathogenic fungi that occupy different elevations and habitats. Whether their holobiont architectures have diverged accordingly is unknown. In this hypothesis-generating study based on samples from single locations (Altai Mountains for Xinjiang Cordyceps and Nagqu, Tibet for Chinese Cordyceps), we compared the two species using amplicon sequencing, untargeted metabolomics, and comparative genomics. Chinese Cordyceps from the sampled site comprises a specialized parasitic fungus and host-adapted bacteria for nutrient acquisition. Xinjiang Cordyceps from the Altai site contains diverse saprotrophic fungi and a rhizosphere-like bacterial consortium enriched in oxidative defense and biofilm genes, a finding that may explain why its sclerotia remain intact for 3-5 years in this population. Metabolomic profiles distinguish the two species at these sites. Xinjiang Cordyceps shows upregulation of tyrosine and porphyrin pathways, and its bacterial community shows functional enrichment in the same pathways, suggesting cross-kingdom coordination. P. gracilis has lost many gene families, and the retained species-specific genes are linked to cell adhesion and acyltransferase activity. Xinjiang Cordyceps is not a simple substitute for Chinese Cordyceps but appears to represent a different ecological strategy shaped by genome streamlining and host-microbe coadaptation. Our findings generate testable hypotheses for future large-scale, multi-population investigations.},
}
@article {pmid42353171,
year = {2026},
author = {Miao, J and Han, S and Dang, X and Chen, Q and Diao, J and Zhu, W},
title = {Benzovindiflupyr Is Associated with Metabolic Homeostasis Disturbance and Gut-Liver Axis Alterations in Zebrafish: Insights from a Multi-Omics Approach.},
journal = {International journal of molecular sciences},
volume = {27},
number = {12},
pages = {},
pmid = {42353171},
issn = {1422-0067},
support = {2016YFD0200202//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Zebrafish/metabolism ; *Liver/metabolism/drug effects/pathology ; *Homeostasis/drug effects ; Gastrointestinal Microbiome/drug effects ; Multiomics ; Metabolomics/methods ; Oxidative Stress/drug effects ; Metabolome/drug effects ; Intestines/drug effects ; *Fungicides, Industrial/toxicity ; },
abstract = {Benzovindiflupyr (BZF) is a newly developed succinate dehydrogenase inhibitor (SDHI) fungicide that is widely used in crop protection, but its potential effects on non-target aquatic organisms remain a concern. In this study, we exposed adult zebrafish (Danio rerio) to 5.0 and 50 μg/L BZF for 28 days. We investigated its impact on the gut-liver axis using a combination of microbiome, biochemical, histological, and metabolomic analyses. BZF exposure damaged intestinal structure, downregulated barrier-related genes, and altered the composition of the gut microbiota. At the same time, serum lipopolysaccharide (LPS) levels increased, which indicates impaired intestinal barrier integrity and microbial dysbiosis. In the liver, BZF caused histopathological alterations, increased serum ALT, AST, and ALP activities, enhanced oxidative stress, and upregulated inflammation-related genes. Liver metabolomic profiling further showed marked disturbances in redox balance and metabolic homeostasis. Correlation analysis also revealed significant associations between altered microbial taxa and differential liver metabolites. Taken together, these results suggest that BZF exposure disrupted intestinal homeostasis and was associated with hepatic metabolic disturbance in zebrafish, potentially through gut-liver axis perturbation. This study expands current understanding of the toxic effects of SDHI fungicides and provides useful evidence for the ecological risk assessment of BZF in aquatic environments.},
}
@article {pmid42353853,
year = {2026},
author = {Zhang, Y and Jiang, Y and Qian, S and Jing, S and Liu, Z and Zhao, Z},
title = {Co-Analysis of Transcriptome and Metabolome Reveals Anthocyanin Accumulation in the Female Flower Tissues of Fig Cultivar 'Silu Hongyu'.},
journal = {Genes},
volume = {17},
number = {6},
pages = {},
pmid = {42353853},
issn = {2073-4425},
support = {2023-JC-QN-0194//Shaanxi Science and Technology Department/ ; ZK22-57//Shaanxi A&amp;F Technology University/ ; LZJB2024KY008//the Modern Forestry Vocational Education Group in Northern China/ ; },
mesh = {*Anthocyanins/genetics/metabolism/biosynthesis ; *Flowers/genetics/metabolism ; *Metabolome/genetics ; *Transcriptome/genetics ; *Ficus/genetics/metabolism ; Gene Expression Regulation, Plant/genetics ; Gene Expression Profiling ; Plant Proteins/genetics/metabolism ; Multiomics ; Metabolomics ; },
abstract = {BACKGROUND/OBJECTIVES: Fig (Ficus carica L.) is considered a valuable fruit owing to its rich health-promoting ingredients, including anthocyanins. However, little information is available on the regulatory networks that reveal anthocyanin biosynthesis in figs, especially the new fig cultivar "Silu Hongyu" (HY).<br><br>METHODS: In this study, multi-omics analysis was performed to dissect the regulatory networks responsible for anthocyanin accumulation in the female flower tissues of HY.<br><br>RESULTS: we found that the anthocyanin content in the female flower tissues of HY is higher than that of "Chinese Ziguo" (ZG). Metabolomic profiling identified 350 differentially accumulated metabolites (DAMs), among which 108 were flavonoids. The contents of multiple metabolites responsible for anthocyanin accumulation, such as naringenin chalcones, cyanidin 3-glucoside, and pelargonidin 3,5-diglucoside, were significantly increased in the HY female flower tissues. Transcriptomic analysis revealed that 3696 differentially expressed genes (DEGs) were screened from the female flower tissues of ZG and HY, with 1730 upregulated DEGs and 1966 downregulated DEGs in HY compared to ZG. The key structural genes involved in anthocyanin biosynthesis, including FcPAL, Fc4CL, FcCHS, FcF3'H, and FcBZ1, were significantly upregulated in the female flower tissues of HY compared with ZG. KEGG analysis also demonstrated that five flavonoid biosynthesis pathways were co-enriched by DAMs and DEGs.<br><br>CONCLUSION: These findings provide a multi-omics framework that governs anthocyanin biosynthesis in the female flower tissues of HY, which will facilitate the genetic breeding and improvement of high-anthocyanin fig cultivars.},
}
@article {pmid42357690,
year = {2026},
author = {Deng, T and Liu, D and Zhu, X and Zhang, H and Zhang, Z},
title = {VIP-DB: A Comprehensive Database of Virus-Insect-Plant Relationships.},
journal = {Viruses},
volume = {18},
number = {6},
pages = {},
pmid = {42357690},
issn = {1999-4915},
support = {YLS-2025-ZY03018//Yuelushan Laboratory Special Program for Seed Industry/ ; },
mesh = {Animals ; *Plant Viruses/physiology/classification ; *Plant Diseases/virology ; *Insect Vectors/virology ; *Plants/virology ; *Insecta/virology ; *Databases, Factual ; Biocuration ; Host-Pathogen Interactions ; },
abstract = {Insect-mediated transmission is central to the epidemiology of plant viruses and has major implications for global food security and agricultural production. Although several resources have compiled information on plant virus transmission, evidence-traceable integration of virus-insect vector-host plant relationships remains limited. Here, we developed the Virus-Insect-Plant Database (VIP-DB), an evidence-guided database that links literature-derived virus-insect transmission records, host plant information, transmission mode annotations, taxonomic information, and traceable literature evidence. VIP-DB compiles 583 virus-insect transmission relationships, 855 virus-plant relationships with non-missing host plant information, and 1375 integrated virus-insect-plant records. Among these records, 120 lack host plant information and 51 lack transmission mode annotation. VIP-DB provides a curated and searchable resource for querying documented plant virus, insect vector, host plant, and transmission mode information. This database offers an evidence-traceable framework for comparative analyses of plant virus transmission relationships and supports future studies in plant virology, vector ecology, and disease management.},
}
@article {pmid42331683,
year = {2026},
author = {Visser, ME and Hengeveld, GM and de Kraker, J and Athanasiadis, IN and Bakker, ES and Kissling, WD and Nmor, S and Philippart, CJM and Soetaert, K and Vriend, SJG and Woutersen, A and Zhao, Z and Zhan, Q and Hof, AF},
title = {Digital twins as a tool for ecosystem research.},
journal = {Trends in ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2026.04.016},
pmid = {42331683},
issn = {1872-8383},
abstract = {To understand the functioning of ecosystems and to carry out scenario studies to forecast functional change, we need to integrate different fields of research. An emerging approach to do so is digital twins: innovative tools for integrated ecosystem analysis, capturing species interactions, biodiversity dynamics, and ecosystem carrying capacity. Digital twins can be characterised as (i) being tailored to and behave like a specific ecosystem, and as such accepted by empiricists as representing a description of a real ecosystem, (ii) having a dynamic interaction between the digital twin and the physical ecosystem, (iii) integrating diverse information and data sources, (iv) combining complementary models, and (v) enabling scenario studies. Development of digital twins of ecosystems is instrumental to bend the curve of biodiversity loss and enhance climate resilience, and is timely because of breakthroughs in digital technologies.},
}
@article {pmid42331863,
year = {2026},
author = {Litavský, J and Majzlan, O and Langraf, V and Iracký, S and Šerá, B},
title = {Effects of roadside habitat management on epigeic arthropod diversity: a case study from the Nitra-Selenec expressway junction.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-54425-z},
pmid = {42331863},
issn = {2045-2322},
support = {VV-MVP-24-0207//Agent&#xfa;ra na Podporu V&#xfd;skumu a V&#xfd;voja/ ; 1/0211/25//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; 1/0255/23//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; },
abstract = {Linear transport infrastructure fragments habitats, but its edges can serve as significant refuges for invertebrates. Management of these verges is crucial to realise this conservation potential, but the impact of specific habitat measures on epigeic arthropods remains poorly understood. This study assessed the impact of roadside habitat management on the diversity and composition of epigeic arthropods, using ground beetles (Carabidae) and harvestmen (Opiliones) as bioindicators at the Nitra-Selenec expressway junction, Slovakia. Over two years, we used pitfall traps to sample epigeic arthropods at ten sites managed under three different regimes: passive management (no intervention), active management with renewal/seeding (commercial grass-herb mixture), and active management with mulching only. We analysed the influence of management, vegetation structure, and landscape variables on species assemblages using redundancy analysis and predicted population trends using machine learning. We recorded 1,416 carabids (50 species) and 1,409 harvestmen (6 species). The renewal/seeding intervention had a significant negative effect on the community composition. The structure of the vegetation, specifically the cover of the herb layer and species richness of the shrub layer, were the most significant positive drivers of community assembly. Furthermore, distance from the road significantly influenced species distribution. Analysis of population trends revealed a gradual increase in carabid abundance over time, but an alarming decline in harvestmen. Active revegetation with commercial seed mixtures creates a homogeneous habitat that is less suitable for diverse epigeic communities than passive management. The structural complexity provided by various native vegetation is a key factor in supporting invertebrates. Implications for insect conservation: We recommend that roadside managers prioritise passive management or regionally appropriate native seed mixtures over commercial revegetation, maintain structural complexity of vegetation through a reduced frequency of mowing (1-2 times annually at ≥ 10 cm height), and adopt mosaic approaches that combine intensive mowing only in safety-critical zones with extensive management elsewhere.},
}
@article {pmid42333934,
year = {2026},
author = {Simčič, G and Skrbinšek, T},
title = {Wild Pedigree exploreR (wpeR): Streamlined Analysis and Visualization of Wild Pedigrees in Time and Space.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70171},
pmid = {42333934},
issn = {1755-0998},
support = {//European Commission/ ; P1-0184//Slovenian Research and Innovation Agency/ ; },
mesh = {*Pedigree ; Animals ; *Software ; *Genetics, Population/methods ; *Computational Biology/methods ; *Animals, Wild/genetics/classification ; Genotype ; },
abstract = {Advances in non-invasive genetic sampling and long-term genetic monitoring programmes have enabled collection of large individual genotype datasets for many wildlife populations, often accompanied by rich field metadata that place the genotyped individuals in time and space. These datasets allow reconstruction of multigenerational pedigrees and have the potential to provide valuable insights into population demography, reproduction, dispersal, social structure and genetic processes. But while the tools for construction of pedigrees keep improving, their interpretation remains challenging. Integrating multigenerational pedigree data with field metadata creates significant complexity, yet specialized tools to facilitate the interpretation of such datasets remain scarce. Here we introduce wild pedigree exploreR (wpeR), an R package designed to simplify exploration, organization and interpretation of complex pedigrees. The package enables users to link reconstructed pedigrees with genetic sample metadata, enabling evaluation of biological plausibility of inferred relationships, but also allowing exploration of other characteristics of individuals and populations in spatial and temporal contexts. wpeR implements a linear workflow through which the pedigree data is imported, formatted, organized into families and integrated with field metadata. The resulting dataset can be visualized through temporal plots that track individuals and families over time, as well as with spatial outputs representing parent-offspring relationships and individual movement patterns as geographic features that can be either directly visualized on maps within R, or exported to be further explored with common GIS tools. wpeR allows exploration of lineage relationships within their ecological context, bridging the gap between statistically reconstructed pedigrees and their biological interpretation. It provides a scalable and flexible framework for analyzing these complex data, providing a practical tool for researchers and managers working with genetic monitoring datasets.},
}
@article {pmid42336424,
year = {2026},
author = {Yu, XY and Gao, YX and Wei, GP and Zhou, T},
title = {[Characterization and Prediction of Spatial and Temporal Evolution of Vegetation Coverage and Vegetation Resilience: A Case Study of the Ecological Restoration Project in Inner Mongolia].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {6},
pages = {3795-3803},
doi = {10.13227/j.hjkx.202504012},
pmid = {42336424},
issn = {0250-3301},
mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; Environmental Monitoring ; *Environmental Restoration and Remediation ; Spatio-Temporal Analysis ; *Plant Development ; },
abstract = {The aim of this study was to analyze the spatial and temporal characteristics of vegetation coverage and resilience in Inner Mongolia， to explore the correlation between the two time series， and to predict the evolutionary trend of vegetation resilience from 2024 to 2026. Based on the kernel normalized vegetation index （kNDVI） dataset constructed by satellite （MOD13Q1V6.1） and early warning indicators， the spatial and temporal changes of vegetation coverage and vegetation resilience are assessed from 2004 to 2023 in Inner Mongolia. The correlation between the spatial changes of the vegetation coverage and vegetation resilience is analyzed using Pearson's correlation analysis， and the evolutionary trend of vegetation resilience in the next three years is predicted by the BP neural network. The results show that： ① From 2004 to 2023， approximately 85.63% of the vegetation coverage in Inner Mongolia showed an increasing trend， and the changes in vegetation resilience showed a spatial distribution pattern of increasing in the east and central part of Inner Mongolia and decreasing in the western part. ② The trends of vegetation coverage and vegetation resilience in spatial and temporal changes were not completely consistent. In the ecological restoration project， only pursuing the increase of cover may not be able to enhance the stability of the system， and more attention should be paid to the dynamic response mechanism of vegetation resilience. ③ In the next three years， the overall trend of vegetation resilience in Inner Mongolia will be upward， mainly focusing on the ecological restoration projects in the Yinshan Mountains， Horqin Sands， and Daxing'anling Mountains， but the problem of declining vegetation resilience in the ecological restoration projects in the western parts of the country and other local areas still requires further attention.},
}
@article {pmid42337211,
year = {2026},
author = {Fenta, AA and Tsunekawa, A and Haregeweyn, N and Zegarek, M and Kabała, C and Stavi, I and Sulwiński, M and Mętrak, M and Orazov, A and Suska-Malawska, M},
title = {Unveiling fine-scale distribution of endemic shrub Prunus ledebouriana through integrating multi-source remote sensing with deep learning.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {7},
pages = {},
pmid = {42337211},
issn = {1573-2959},
support = {BOB-661-846/2023 and WNE II.2.1/03/2024//Excellence Initiative - Research University at the University of Warsaw/ ; },
mesh = {*Remote Sensing Technology ; *Prunus/growth &amp; development ; *Deep Learning ; *Environmental Monitoring/methods ; Kazakhstan ; Convolutional Neural Networks ; Geographic Information Systems ; },
abstract = {This study aims to unveil a fine-scale spatial distribution of endemic shrub Prunus ledebouriana (Schltdl.) Y.Y.Yao in Kazakhstan's Tarbagatay National Park by integrating multi-source remote sensing with deep learning. Accurate characterization of plant species distribution requires spatially precise ground-truth data; however, conventional GPS-based methods often introduce positional uncertainties that compromise alignment with very high-resolution imagery. To overcome this limitation, we employed a hybrid ground-truthing strategy that combines very high-resolution (5 × 5 cm) drone imagery with field-based onscreen digitization, enabling the generation of spatially accurate reference data. This data was used to extract training and validation data points from 18 predictor variables, encompassing spectral bands, vegetation indices, and texture features derived from Pléiades Neo imagery (30 × 30 cm), along with ancillary topographic and climatic variables. Based on these inputs, a deep one-dimensional convolutional neural network (1D CNN) model was developed to characterize the spatial distribution of P. ledebouriana. The model achieved an overall mapping accuracy of about 80%, with feature importance analysis highlighting texture metrics as the most influential predictors. Results revealed that P. ledebouriana covers about 7.5% of the study area; with distribution strongly linked to specific topographic settings. Nearly 70% of occurrences were found between 700 and 1200 m elevation, peaking at 900-1000 m.a.s.l., and about 75% were located on moderately slopped terrains (5-30%). Aspect also influenced distribution, with 83% of occurrences on southeast- to west-facing hillslopes. The limited occurrence of P. ledebouriana in lowland agricultural areas and on steep slope terrains suggests a combined influence of anthropogenic land-use pressures and ecological preferences. This study demonstrates the potential of integrating spatially precise ground-truthing, multi-source remote sensing, and deep learning for accurately mapping plant species distribution in mountainous drylands, supporting biodiversity monitoring and conservation planning in these fragile ecosystems.},
}
@article {pmid41513706,
year = {2026},
author = {Cui, J and Xu, Y and Liu, J and Zhang, X and Chen, Z and Yang, W and Ge, J and Sun, C and Zhai, Y and Chang, Z and Tian, L and Duan, Y and Song, F and Cai, W and Li, H and Tian, L},
title = {Chromosome-level genome assembly and annotation of two Asian bumble bees.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {248},
pmid = {41513706},
issn = {2052-4463},
support = {32370487//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2115 Talent Development Program//China Agricultural University (CAU)/ ; },
mesh = {Animals ; *Bees/genetics ; *Chromosomes, Insect ; *Genome, Insect ; Molecular Sequence Annotation ; Male ; Datasets as Topic ; },
abstract = {The bumblebee Bombus patagiatus Nylander, 1848 and Bombus lantschouensis Vogt, 1908 (Hymenoptera: Apidae) are ecologically important bumble bee species native to East Asia, with considerable value for agricultural pollination and domestication. Despite their ecological and economic relevance, the lack of high-quality genomic resources has hindered in-depth investigations into their genetic architecture and evolutionary adaptations. Here, we present chromosome-level genome assemblies for both species, generated using a combination of PacBio HiFi long-read sequencing, Illumina short-read resequencing, and Hi-C scaffolding. The assembled genomes span 240.28 Mb (B. patagiatus) and 241.30 Mb (B. lantschouensis), with 94.38% and 94.00% of sequences anchored to 18 chromosomes, respectively. Genome annotation identified 17,351 and 16,023 protein-coding genes in B. patagiatus and B. lantschouensis, along with comprehensive repetitive element characterization. Both assemblies exhibit exceptional completeness, with BUSCO scores exceeding 99%, confirming their high quality and reliability. These genomic resources provide a critical foundation for future research on bumble bee evolution, population genetics, and the molecular basis of domestication traits.},
}
@article {pmid41974979,
year = {2026},
author = {Martín-Vélez, V and Navarro, J and Afán, I and Montalvo, T and Green, AJ},
title = {Conflicts hinder research into animal movements.},
journal = {Ambio},
volume = {55},
number = {8},
pages = {2018-2021},
pmid = {41974979},
issn = {1654-7209},
support = {10.13039/501100011033//Agencia Estatal de Investigaci&#xf3;n/ ; },
mesh = {Animals ; *Geographic Information Systems ; *Animal Migration ; *Charadriiformes/physiology ; Europe, Eastern ; *Warfare ; Influenza in Birds/transmission ; Influenza A Virus, H5N1 Subtype ; },
abstract = {Satellite tracking has revolutionized our understanding of animal migration, yet its reliability increasingly depends on the geopolitical stability of the regions frequented by wildlife. Here, we show that military-induced interference with global navigation satellite systems (GNSS) during ongoing conflicts in Eastern Europe has severely compromised the accuracy of global positioning systems (GPS)-based tracking data for black-headed gulls (Chroicocephalus ridibundus). In 2024-2025, GPS trajectories revealed erratic, low-quality, and geographically implausible positions coinciding with known zones of electronic warfare. These inaccuracies hinder efforts to locate breeding colonies, identify key stopover habitats, and assess disease transmission risks posed by migratory birds, particularly for zoonoses such as highly pathogenic avian influenza (HPAI) H5N1. Our findings illustrate how modern conflicts now extend their impact into ecological research infrastructures, calling for systematic correction methods and international coordination to safeguard the robustness of movement ecology studies and One Health models in a geopolitically unstable world.},
}
@article {pmid42329868,
year = {2026},
author = {Grimm, V and Berger, U and Mammola, S},
title = {Ten simple rules for making the supplement increase your paper's impact.},
journal = {PLoS computational biology},
volume = {22},
number = {6},
pages = {e1014419},
pmid = {42329868},
issn = {1553-7358},
mesh = {Humans ; *Periodicals as Topic/standards ; *Publishing/standards ; Computational Biology ; },
abstract = {Have you ever lost hours navigating supplementary materials-clicking between the main text and dozens of auxiliary files only to encounter broken links, illegible figures, and undefined variables and acronyms? If so, you're not alone. What should support scientific communication has instead become an obstacle: supplementary information (SI) increasingly suffers from inconsistent formatting, poor accessibility, and fragmented organization that impedes rather than advances understanding. This is disheartening since the SI, if used effectively, has the power to enhance transparency, credibility, and reproducibility of research. Therefore, we propose 10 simple rules to help authors design SI that genuinely increase the impact of their research. The rules emphasize treating SI with the same care as the main text, using it strategically to support the scientific narrative while preserving clarity and focus. Key recommendations include creating a single, well-structured, self-contained SI master document; ensuring explicit cross-referencing between the main text and SI; making SI machine-readable; and avoiding the misuse of SI as a substitute for proper data repositories. We also highlight the importance of creativity in choosing appropriate formats and strict adherence to journal-specific guidelines. Finally, when available, we advocate the use of standardized templates to improve consistency, readability, and reuse across studies. By following these rules, authors can substantially increase the scientific impact of their work while at the same time contributing to more sustainable research practices.},
}
@article {pmid42312893,
year = {2026},
author = {Zhang, X and Lu, B and Jin, LN and Yang, S and Ji, Y and Cao, K and Fan, C and Li, D and Chen, J},
title = {Crowded Public Spaces as Hotspots of Airborne Microbial Risk: A Population-Weighted Risk Assessment in Urban Environments.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c04000},
pmid = {42312893},
issn = {1520-5851},
abstract = {Airborne pathogens and antimicrobial resistance (AMR) pose growing health risks in cities, where enclosed spaces, inadequate ventilation, and high population density enhance their persistence and dissemination. However, the microbial burden and risk associated with high-occupancy public spaces remain poorly quantified. Here, we compared bioaerosol characteristics across university cafeterias and a subway station, dry- and mixed-waste collection facilities (WCFs), and an urban air monitoring site by using culture-based, molecular, source-tracking, and risk-assessment approaches. The results showed that Crowded Public Spaces (CPSs) harbored culturable bacterial and AMR burdens comparable to those in WCFs, both far exceeding levels at the urban air monitoring site. Human-associated sources contributed to ∼50% of airborne bacteria, and multidrug-resistant isolates (∼60%), high-risk β-lactam ARGs, and clinically relevant pathogens were further enriched in CPSs. We further applied a population-weighted infection burden (PWIB) metric that integrates infection risk with pedestrian volume and dwell time. Although contamination levels in CPSs were similar to those in conventional microbial hotspots, CPSs contributed more to the city-scale infection burden once population exposure was taken into account. These findings reveal that urban airborne microbial risk is shaped not only by contamination intensity but also by human occupancy and exposure patterns. This study highlights the value of incorporating human activity into microbial risk assessment in high-density urban environments.},
}
@article {pmid42315803,
year = {2026},
author = {Guo, J and Frederick, J and Cunningham, L and Jacobson, NC and Fisher, AJ and Pettit, JW and McMakin, DL and Ng, MY},
title = {Feasibility and Acceptability of a Smartphone and Wearable Assessment Protocol for Adolescents with Depression.},
journal = {Research on child and adolescent psychopathology},
volume = {54},
number = {4},
pages = {},
pmid = {42315803},
issn = {2730-7174},
support = {R21MH126394/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; Female ; Adolescent ; *Smartphone ; Feasibility Studies ; *Actigraphy/instrumentation ; Child ; *Wearable Electronic Devices ; *Depression/diagnosis ; Male ; *Mobile Applications ; *Ecological Momentary Assessment ; Sleep ; Digital Health ; *Patient Acceptance of Health Care ; },
abstract = {Smartphones and wearables are low-burden tools for assessing real-time mood and behavior. Although these methods have been used with adolescents for behavioral tracking (e.g., activity, sleep), less is known about longer-term use (beyond one week) with adolescents with depression and about mobile sensing for monitoring mood for any adolescent population. This study examined acceptability and feasibility of a one-month EMA, actigraphy, and mobile sensing protocol for adolescents with elevated depressive symptoms. Adolescents aged 12 to 18 (N = 69; Mage = 15.46; 67% assigned female at birth; 42% White; 71% Hispanic or Latine; 38% sexual minority) completed EMA surveys on depressive symptoms, processes, and affect multiple times daily via a smartphone app that also collected passive sensor data (e.g., motion, geolocation). An actigraph measured physical activity and sleep. A feedback interview assessed protocol acceptability. Most participants (91%) completed all components, were willing to participate again (91%), and would recommend participation to peers (93%). EMA response rates improved (mean completion 57% to 66%) after shifting to a semi-personalized schedule with extended response windows. Actigraph wear time was high (> 70%) despite device-related issues. Sensor data availability varied by operating system, and privacy concerns influenced participation. Adherence was correlated within and between modalities, suggesting that individual compliance played a central role in consistent engagement. Findings support the feasibility and acceptability of smartphone and wearable methods for capturing real-world mood and behavior in adolescents, however careful attention to design, engagement, and ethical considerations remains essential.},
}
@article {pmid42318582,
year = {2026},
author = {Dodampegama, H and Sridharan, M},
title = {Collaborate and explain on-the-fly: knowledge-based reasoning and learning in ad hoc teamwork.},
journal = {Frontiers in artificial intelligence},
volume = {9},
number = {},
pages = {1765191},
pmid = {42318582},
issn = {2624-8212},
abstract = {This paper focuses on ad hoc teamwork, the problem of enabling an AI agent to collaborate with other agents without prior coordination. Methods considered state of the art for ad hoc teamwork formulate it primarily as a learning problem, using a large labeled dataset of different situations to model the action choices of other agents (or agent types) and determine the actions of the ad hoc agent. Such datasets are not readily available in practical domains, and these methods lack transparency and make it difficult to rapidly revise existing knowledge (or models) in response to changes in the domain, team composition, or agents' capabilities. Our architecture for ad hoc teamwork embeds the principles of refinement, ecological rationality, interactive learning, and explainable agency, leveraging the complementary strengths of knowledge-based and data-driven methods for reasoning and learning. Specifically, for any given goal, our architecture enables an ad hoc AI agent to determine its actions through non-monotonic logical reasoning with: (a) prior domain-specific commonsense knowledge; (b) models learned and revised rapidly to predict the behavior of other agents; and (c) anticipated abstract future goals based on generic knowledge of similar situations in a pretrained Large Language Model. In addition, the ad hoc agent processes natural language descriptions and observations of other agents' behavior, using a combination of a pretrained Large Language Model and decision-tree induction to incrementally acquire and revise knowledge in the form of objects, actions, and axioms that govern domain dynamics. Furthermore, the ad hoc agent generates relational descriptions as on-demand explanations of its decisions and beliefs, and those of other agents, in response to various types of questions. We ground and experimentally evaluate the capabilities of our architecture in VirtualHome, a realistic, physics-based 3D simulation environment. We demonstrate reliable, efficient, transparent, and scalable performance, providing a substantial improvement in performance compared with a purely knowledge-based baseline, and comparable or better performance than a purely data-driven baseline while using orders of magnitude fewer resources.},
}
@article {pmid42328538,
year = {2026},
author = {Lu, Q and Luo, J and Wang, J and Zhao, B and Wang, X and You, L},
title = {QeITH: Quantifies Tumor Ecosystem Heterogeneity to Predict Cancer Progression and Treatment Benefit.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0061},
pmid = {42328538},
issn = {2001-0370},
abstract = {Intratumor heterogeneity (ITH) is a fundamental driver of therapeutic failure and disease progression. However, the complexity of the tumor ecosystem is a critical yet underexplored aspect, making its precise quantification essential for fully deciphering ITH and its clinical implications. To address this, we developed Quantifying Ecosystem Intratumor Heterogeneity (QeITH), a computational framework that applies Shannon entropy to quantify ecosystem heterogeneity by measuring the diversity and distributional entropy of cellular compositions and functional states across single-cell, bulk, and spatial transcriptomics. At the single-cell resolution, QeITH identifies elevated ITH as intrinsic markers of malignant transformation, yet enhanced sensitivity to therapy. Pan-cancer bulk analyses further link elevated QeITH scores to increased neoantigen burden, PD-L1 expression, and unfavorable prognosis. Notably, spatial transcriptomics reveals that ecological complexity is nonuniformly distributed, peaking at invasive fronts and within tertiary lymphoid structures (TLS), where enhanced diversity within TLS modulates therapeutic vulnerability. Thus, QeITH reveals a dual role for ITH: While high scores associated with tumor aggressiveness, they also predict favorable treatment responses by capturing an immunologically active tumor ecosystem state. By integrating single-cell precision with spatial context, this framework elucidates the biological drivers of cancer progression and serves as a robust tool for optimizing personalized therapeutic strategies in precision oncology.},
}
@article {pmid41765879,
year = {2026},
author = {Yu, X and Ramli, SHB and Hamid, HA and Norowi, NM and Surip, SS and Yu, G and Zhang, C and Liu, Z},
title = {Defining "critical" maternal health information for healthy lifestyle self-management in pregnancy: perspectives of pregnant women and obstetricians in China and Malaysia.},
journal = {BMC pregnancy and childbirth},
volume = {26},
number = {1},
pages = {},
pmid = {41765879},
issn = {1471-2393},
mesh = {Humans ; Female ; Pregnancy ; Obstetricians/psychology ; Malaysia ; China ; *Healthy Lifestyle ; Adult ; Qualitative Research ; *Self-Management/psychology ; *Pregnant People/psychology ; *Maternal Health ; Social Support ; *Prenatal Care/methods ; Digital Health ; Attitude of Health Personnel ; },
abstract = {BACKGROUND: Pregnancy is a critical window for adopting and sustaining healthy lifestyle behaviors. This study explored perspectives of pregnant women and obstetricians on key lifestyle domains, barriers, and support needs during pregnancy in China and Malaysia. METHODS: A qualitative in-depth interview study was conducted from October 2023 to February 2024. Pregnant women were recruited from two antenatal clinics in China and one general hospital in Malaysia. Obstetricians involved in routine antenatal care were also interviewed. Interviews were audio-recorded, transcribed verbatim, and analyzed thematically. RESULTS: Twenty pregnant/postpartum women and six obstetricians participated. Four integrated themes from pregnant women described “critical” maternal health information as: (1) bonding-oriented interpretability that motivates health behaviors, (2) lifestyle self-management under uncertainty requiring safety boundaries and red-flag clarity, (3) social support as psychosocial coping infrastructure, and (4) digital information appraisal in partnership with clinicians. Three complementary themes from obstetricians emphasized time-pressured clinical encounters shaping communication and trust, ethically/institutionally mediated disclosure practices, and a contested digital information ecology in which digital tools may support continuity while raising credibility concerns. CONCLUSIONS: Pregnant women and obstetricians highlighted multi-domain lifestyle support needs that extend beyond clinical check-ups. Strengthening credible information access and tailored professional guidance may facilitate healthier lifestyle practices during pregnancy across contexts.},
}
@article {pmid41832485,
year = {2026},
author = {Anjana, RM and Nitika, S and Kuriakose, S and Gibson, AA and Kamotho, C and Heine, M and Brant, LC and Tromp, J and Jose, AP and Ranjani, H},
title = {Digital divide in diabetes care: qualitative insights from the DIG-EQUITY study, India.},
journal = {BMC public health},
volume = {26},
number = {1},
pages = {},
pmid = {41832485},
issn = {1471-2458},
mesh = {Humans ; India ; Female ; Qualitative Research ; Male ; Focus Groups ; Adult ; *Telemedicine/statistics &amp; numerical data ; Digital Health ; *Digital Divide ; Middle Aged ; Interviews as Topic ; *Diabetes Mellitus/therapy ; *Healthcare Disparities ; Diabetes Mellitus, Type 2/therapy ; Pregnancy ; },
abstract = {BACKGROUND: Digital health technologies have the potential to improve health outcomes in underserved settings. However, in low and middle-income countries with weak public health systems, unequal access to digital tools can worsen existing healthcare disparities. The DIG-EQUITY study explored the facilitators and barriers to equitable use of mobile and telehealth solutions for diabetes care in India, incorporating perspectives from people with diabetes, their family members (caregivers), healthcare providers, policymakers, and community organisations. METHODS: A qualitative design was employed across urban (Chennai) and rural (Chunampet) settings in Tamil Nadu, following the 32-item COREQ checklist. A total of 54 participants (including type 1 diabetes (T1DM), type 2 diabetes (T2DM), and gestational diabetes mellitus (GDM)) were included in four focus group discussions (FGDs) and 12 key informant interviews (KIIs). Participants were purposively sampled to ensure diversity in demographics and healthcare exposure. The analysis was guided by the Social Ecological Model (SEM), which informed the structuring and interpretation of themes across domains. RESULTS: The different domains of the SEM influenced the utilisation of digital health. Individual factors such as age, digital literacy, and diabetes type shaped preferences. Interpersonal support from caregivers enabled access, particularly for older adults and children. Organisational and community influences included urban–rural infrastructure gaps, socioeconomic constraints, and shared device ownership. Policy-level concerns regarding data privacy, security, and app reliability affected trust and continued engagement. CONCLUSION: Socioeconomic status, sex, and geographic location influenced access and adoption of digital solutions. Bridging the divide through targeted digital literacy initiatives and inclusive strategies is essential to ensure equitable and effective use of digital health solutions for diabetes care in India. TRIAL REGISTRATION: The trial was registered with Central Trials Registry of India (CTRI/2022/04/041941).},
}
@article {pmid41910822,
year = {2026},
author = {Kumar, V and Nautiyal, CS},
title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41910822},
issn = {1573-0972},
mesh = {*Endophytes/genetics/physiology/classification ; *Symbiosis ; *Agroecology ; Genomics ; *Plants/microbiology ; Multiomics ; Agriculture ; Ecosystem ; Microbiota ; Metagenomics ; Bacteria/genetics/classification ; },
abstract = {Plants, together with their resident endophytes, constitute a functional holobiont whose integrated traits enable plant growth, stress resilience, disease resistance, and ecosystem remediation. This review discusses advances across ten converging domains that are reshaping research and applications of endophytes, including the following: genomics and metagenomics that identify core genes for colonization, nitrogen fixation, hormone modulation, and stress adaptation; functional genomics and systems biology deciphering host-microbe signaling networks; synthetic biology and CRISPR-based tools for the rational improvement of beneficial traits; microbiome engineering aimed at designing and stabilizing endophytic consortia; multi-omics integration connecting genomic, transcriptomic, proteomic, and metabolomic layers during colonization and under stress; environmental and climatic factors shaping endosphere diversity; bioinformatic platforms predicting biosynthetic gene clusters, secretomes, and metabolic potential; and agricultural and environmental applications in biocontrol and bioremediation. Remaining challenges are the uncultured majority of endophytes, context-dependent transitions between mutualism and pathogenicity, limited field validation, and evolving biosafety frameworks. Thus, the forward framework developed here emphasizes the importance of standard strain benchmarking, causal multi-omics workflows, synthetic community design, and multisite agronomic trials. For their part, endophytes form a scalable, climate-resilient platform for the dual purposes of sustainable agriculture and environmental restoration. In the process, endophytes are emerging as a tractable and scalable foundation for climate-resilient biotechnology, wherein molecular innovation connects with field-level sustainability.},
}
@article {pmid42171373,
year = {2026},
author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE},
title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0030526},
pmid = {42171373},
issn = {2379-5077},
support = {K08AI159619//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/genetics/immunology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; *Bacterial Toxins/genetics ; *Metagenome ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Machine Learning ; Computational Biology/methods ; },
abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.},
}
@article {pmid42275032,
year = {2026},
author = {Yuan, S and Tan, D and Zhu, D and Balcazar, JL and Wang, H and Friman, VP and Sun, M and Hu, F},
title = {Global transmission and distribution of phage-encoded cholera toxin genes constrained by toxin-repression genes and anti-phage defense systems.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42275032},
issn = {1751-7370},
mesh = {*Cholera Toxin/genetics ; *Bacteriophages/genetics ; *Vibrio cholerae/genetics/virology ; *Gene Transfer, Horizontal ; Cholera/microbiology ; Humans ; Animals ; CRISPR-Cas Systems ; Computational Biology ; },
abstract = {Cholera is a severe diarrheal disease caused by toxigenic Vibrio cholerae, whose virulence depends on lysogenic infection by CTXφ bacteriophages encoding the cholera toxin genes (ctxA and ctxB) and associated accessory genes (ace and zot). However, the global distribution and transmission dynamics of phage-encoded cholera toxin genes across environments remain poorly understood. To address this, we performed a large-scale bioinformatic analysis of publicly available whole genomes. We show that both phages and bacteria carrying toxin genes are globally distributed across human-associated, freshwater, fish, and mammalian habitats, with Vibrio and Aeromonas being the dominant bacterial taxa and Inoviridae is the most prevalent phage family. Phage-mediated horizontal gene transfer (HGT) of toxin genes occurred in both Vibrio and non-Vibrio species, with the highest transfer between Inoviridae and V. cholerae occuring predominantly among bacteria from the same habitat. Temporal analysis revealed an increase in candidate HGT events after 2000, peaking at 377845 events during 2010-2019. HGT events negatively correlated with the presence of CRISPR-Cas system and toxin-repression genes (hns, hapR, and tsrA) in host bacteria. Experimental validation indicated that H-NS and HapR inhibit phage infection by repressing phage release. Together, our results suggest that CRISPR-Cas phage defense system and toxin-repression mechanisms could constrain the spread of toxin-carrying phages, with potential implications for the occurrence and severity of cholera outbreaks worldwide.},
}
@article {pmid41345617,
year = {2025},
author = {Franco-Duarte, R and Saati-Santamaría, Z and Choowong, P and Dharmarathne, G and Menéndez, E and Soares, P and Rito, T and Cheung, W and Spahr, A and Eberhard, J and Jayasinghe, TN},
title = {Oral-associated bacteria in the gut microbiome of individuals with type 2 diabetes: a secondary analysis of metagenomic data.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {1915},
pmid = {41345617},
issn = {1472-6831},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; *Mouth/microbiology ; Secondary Data Analysis ; *Microbiota ; },
abstract = {With an astounding global prevalence, both diabetes mellitus and gum disease pose significant health concerns. Gum disease has been identified as a risk factor for diabetes mellitus, and its treatment has shown improvements in markers of glucose management. We hypothesised that bacteria commonly associated with the oral microbiome could be disproportionately present in the gut of individuals with type 2 diabetes mellitus (T2DM) compared to healthy controls, suggesting a possible association between oral-associated bacteria and metabolic dysregulation. This hypothesis is supported by known interactions between the oral microbiome and systemic health, particularly the role of inflammation in both conditions. Therefore, we aimed to conduct a secondary analysis of whole-genomic sequencing data of studies published over the last twenty years (2004–2024) related to the gut microbiome of patients with T2DM to identify oral-associated bacteria in their gut compared to healthy individuals. We searched for studies related to the gut microbiome, whole metagenomics, and T2DM in Ovid Medline, EMBASE, and Web of Science databases. Studies that included whole metagenomic data from adult populations of all genders with T2DM were selected, resulting in the reanalysis of metagenomic sequencing data from a total of 9 studies (n = 1,224 metagenomes) for bacterial species data. From the 41,689 gut microbial species identified across the selected studies, 497 were classified as of oral-associated bacteria, corresponding with entries in the Human Oral Microbiome Database (HOMD). These oral bacteria comprised 1.19% of the gut microbiome. Notably, twenty oral-associated bacterial species were statistically significant in their presence among patients with diabetes compared to healthy individuals, irrespective of their abundance. Key oral pathogens included Corynebacterium striatum, Staphylococcus capitis, Kingella kingae, Corynebacterium propinquum, Prevotella sp. oral taxon 820, Prevotella scopos, Selenomonas artemidis, Bordetella pertussis, Selenomonas sp. oral taxon 137, and Staphylococcus hominis. Specifically, periodontal pathogens such as, Porphyromonas gingivalis, Tannerella forsythia, and Capnocytophaga sp. oral taxon 332 were found to be significantly higher in patients with T2DM. These bacteria are associated with conditions like endocarditis, bacteremia, and inflammatory responses, which are prevalent in both diabetes and periodontitis. Although causal relationships cannot be directly established, our findings suggest that bacteria typically originating from the oral cavity may be more prevalent in the gut microbiome of patients with T2DM, supporting the potential role of oral-gut microbial interactions in metabolic dysregulation.},
}
@article {pmid41582220,
year = {2026},
author = {Cai, J and Chen, X and Li, X and Zhang, M and Lin, X and Hu, Y and Feng, H and Li, X and Hu, J and Yang, S and Wang, L and Niu, X and Wang, G and Tang, B and Wang, S and Qin, Y and Cheng, Y},
title = {IGD: a multi-omics database for Ipomoea pes-caprae genomic and biological research.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {342},
pmid = {41582220},
issn = {1471-2229},
support = {2023J01442//Natural Science Foundation of Fujian Province/ ; 32170380//National Natural Science Foundation of China/ ; },
mesh = {*Ipomoea/genetics ; *Genome, Plant ; Genomics ; *Databases, Genetic ; Multiomics ; Salt-Tolerant Plants/genetics ; },
abstract = {Ipomoea pes-caprae (IPC) is a perennial halophytic vine with remarkable salt and drought tolerance, playing a critical ecological and medicinal role in tropical and subtropical coastal ecosystems. Despite the availability of a high-quality chromosome-level reference genome and abundant transcriptome data, the absence of an integrated data platform has hindered in-depth functional gene discovery and genomic research in IPC. To address this gap, we developed the IPC Genome Database (IGD), the first comprehensive multi-omics database dedicated to IPC. IGD provides high-quality genomic sequences, gene structure annotations, and functional annotations, along with transcriptomic expression profiles under salt stress across different tissues. It also includes time-course expression data of roots and leaves under salt stress treatment, as well as leaf expression profiles under cold and heat stress conditions. The platform also integrates a suite of user-friendly, interactive bioinformatics analysis and visualization tools to facilitate efficient data exploration and functional mining. In particular, we established a specialized subset of stress-responsive genes to support rapid candidate gene screening and evolutionary analysis related to IPC’s salt and stress tolerance traits. By implementing automated data integration and quality control pipelines tailored for non-model species, IGD overcomes technical challenges such as fragmented data and delayed updates. As a centralized and scalable resource, IGD significantly lowers the barrier to functional genomics research in IPC and other halophytes, promoting their application in genetic improvement and ecological sustainability. In the future, IGD will continue to incorporate more omics data from halophytic species, further enhancing its value in salt tolerance research and molecular breeding efforts.},
}
@article {pmid41619051,
year = {2026},
author = {Paulino, A and Fernandes, I and Pires, RC and Usié, A and Faustino, A and Santos, J and Brás, T and Rosa, D and Paulo, OS and Duarte, MF and Marum, L},
title = {Unravelling the molecular mechanisms of vegetative-to-reproductive transition in Cynara cardunculus by RNA-Seq analysis.},
journal = {Plant molecular biology},
volume = {116},
number = {1},
pages = {15},
pmid = {41619051},
issn = {1573-5028},
mesh = {*Cynara/genetics/growth &amp; development/metabolism/physiology ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Flowers/genetics/growth &amp; development ; RNA-Seq ; Reproduction/genetics ; Transcriptome ; Plant Proteins/genetics/metabolism ; Gene Ontology ; Flavonoids ; Transcription Factors/metabolism/genetics ; },
abstract = {Cynara cardunculus inflorescence plays a significant role in cheese manufacturing and human consumption due to the milk-clotting capacity and the production of edible immature capitula. Consequently, it is crucial to understand the complex cellular and molecular processes involved in the development of cardoon flowers. The current study used western wild cardoon in two developmental stages, vegetative and reproductive, to understand the molecular mechanisms mediating cardoon`s vegetative-to-reproductive transition. Transcriptome profiling identified 552 differentially expressed genes (DEGs) between vegetative and reproductive stages, with 321 upregulated in stage 4 (vegetative state) and 231 in stages 5/6 (reproductive state). Gene Ontology (GO) analysis revealed DEGs involved in biological processes such as oxidation-reduction, lipid metabolism, and defense responses. Metabolic pathways, including phenylpropanoid biosynthesis and anther/pollen development, were significantly enriched. Genes associated with lignin formation, flavonoid synthesis, and acetyltransferase activity were upregulated in the vegetative stage. At the same time, those related to flower development and sesquiterpene lactone biosynthesis were prominent in the reproductive stage. Transcription factors, including MADS-box and ethylene-responsive families, were critical in regulating developmental transitions. This study provides comprehensive insights into the morphological, chemical, and molecular dynamics of C. cardunculus across its phenological stages, underscoring the plant’s adaptability and potential for pharmaceutical and industrial applications. The findings highlight the importance of seasonal and developmental timing in optimizing the production of valuable secondary metabolites, such as cynaropicrin.},
}
@article {pmid41629809,
year = {2026},
author = {Wang, R and Liu, C and Ma, ZC and Qin, T and Zhang, W and Guo, H},
title = {Integrated physiology and multi-omics elucidate photosynthetic adaptation and osmolyte accumulation mechanisms in buffalograss under osmotic stress.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {41629809},
issn = {1471-2229},
mesh = {*Photosynthesis/physiology ; *Osmotic Pressure ; *Poaceae/physiology/genetics/metabolism ; Drought Resistance ; Multiomics ; Adaptation, Physiological ; Plant Leaves/metabolism/physiology ; Chlorophyll/metabolism ; },
abstract = {Water deficit threatens global agriculture and ecological construction. Buffalograss (Buchloe dactyloides (Nutt.) Engelm.), a C4 perennial grass native to arid regions, is an ideal model for dissecting drought tolerance mechanisms. In this study, we investigated the physiological responses of buffalograss to PEG-induced osmotic stresses through integrated transcriptomic and metabolomic analyses. The results showed that buffalograss could maintain plant dry weight, chlorophyll content and leaf water use efficiency, simultaneously increase leaf K+ and NO3− accumulation under osmotic stress. After 20% PEG treatment, key metabolites, including amino acids (e.g., aspartate, glutamate and leucine) and other organic acids (e.g., salicylic acid and citrate) were enriched. At the transcriptional level, genes related to chlorophyll biosynthesis (e.g., GluTR, MgCH, POR and DVR) and carbon fixation (e.g., rbcL and PPDK) were coordinately upregulated, implying a proactive reinforcement of photosynthetic capacity to sustain energy supply under water deficit. Several transcripts related to uptake and transport of K+ (e.g., HAK4, KUP6, HAK16 and NHX1) and NO3− (e.g., NPF6;3, NPF2;9, NRT2;1 and NPF8;5) were significantly altered, implying accumulation of K+ and NO3− in leaves may be a strategy for buffalograss to resist drought. In the root, organic acids appear to be the main osmotic regulators. The genes involved in biosynthetic pathways of aspartate (e.g., GOT), glutamate (e.g., ALT), leucine (e.g., BCAT), salicylic acid (e.g., PTAL), citrate (e.g., CS) were significantly induced. This study provides new insights into the drought adaptation mechanisms of buffalograss, emphasizing the roles of sustained photosynthesis, inorganic ion homeostasis and organic acid accumulation.},
}
@article {pmid41639730,
year = {2026},
author = {Hirsch, S and Ip, YCA and Brandão-Dias, PFP and Allan, EA and Kelly, R},
title = {Understanding practical barriers to the global adoption of environmental DNA (eDNA) methods, tools, and standards.},
journal = {BMC research notes},
volume = {19},
number = {1},
pages = {},
pmid = {41639730},
issn = {1756-0500},
mesh = {*DNA, Environmental/analysis/genetics ; *Environmental Monitoring/methods/standards ; Biodiversity ; Computational Biology/methods ; Conservation of Natural Resources/methods ; },
abstract = {OBJECTIVE: Environmental DNA (eDNA) is a rapidly emerging data source with the potential to support environmental monitoring and biodiversity conservation around the world. Current efforts to standardize eDNA methods and reporting are aimed at strengthening credibility and supporting adoption. In doing this, however, researchers must be mindful of diverse capacities and ecological contexts both regionally and around the world. The objective of our research is to understand how international standards for eDNA may support or hinder the uptake of eDNA methods and tools for conservation and biodiversity work. This was accomplished through two interactive workshops that brought together eDNA researchers and practitioners from around the world to surface broad and specific barriers to uptake of eDNA methods and tools. RESULTS: The most prevalent concern across all stages of the workflow was affordability. Workshop participants found the sampling and bioinformatics workflow stages to be the largest barriers. Participants also identified substantial hurdles: (1) the need for more clarity around eDNA methods and appropriate applications and protocols, (2) lack of access to suitable laboratories, (3) the need for different standards for diverse systems, species, and locations, and (4) the lack of trained experts in bioinformatics.},
}
@article {pmid41656241,
year = {2026},
author = {Liu, X and Qiao, Y and He, W and Chen, X and Zhou, Q and Xu, Y and Yang, Y and Li, C and Yu, J and Luo, P},
title = {Integrated multi-omics profiling reveals effects of exogenous plant growth regulators on tobacco rhizosphere under Vulpia myuros rotation.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {41656241},
issn = {1471-2229},
support = {110202101009 (XJ-01)//Key Science and Technology Project of China National Tobacco Corporation/ ; 110202201040 (XJ-11)//Key Science and Technology Project of China National Tobacco Corporation/ ; },
mesh = {*Rhizosphere ; *Nicotiana/microbiology/metabolism/drug effects ; Multiomics ; Soil Microbiology ; *Plant Growth Regulators/pharmacology/metabolism ; Microbiota/drug effects ; },
abstract = {BACKGROUND: Soil degradation poses a significant threat to agricultural sustainability. The integration of plant growth regulators (PGRs) with cover cropping systems represents a promising strategy for enhancing soil health and plant resilience. However, the synergistic effects of PGRs and cover crops on soil microbial communities and plant metabolism remain poorly understood. RESULTS: Exogenous PGRs under Vulpia myuros rotation were linked to distinct restructuring of tobacco rhizosphere microbiomes and metabolic networks. High-throughput sequencing of 16 S rRNA and ITS regions revealed that NaHS was associated with enhanced fungal diversity, promotion of beneficial saprotrophic taxa, and activation of phenylpropanoid and lignin metabolism. VB1-based treatments modulated bacterial communities, enriched cooperative Firmicutes–Proteobacteria clusters, and drove sphingolipid, coenzyme, and amino acid pathways, while multivitamins promoted synergistic microbial clusters and stimulated phenolic antioxidant and secondary metabolite production. Glutamate maintained overall microbial diversity but induced rare taxa, reshaping lipid and ceramide metabolism and activating neurotransmitter and amino acid pathways. Integrated metabolomics–microbiome analysis revealed treatment-specific microbial–metabolite interactions, including lipid remodeling, pollutant degradation, and phenolic activation, linking microbial shifts with metabolic reprogramming. Network analyses demonstrated that PGRs differentially modulate microbial co-occurrence, enhancing cooperation, centrality, or competitive partitioning, collectively optimizing rhizosphere ecological functions and plant stress adaptation. CONCLUSIONS: Our findings demonstrate that exogenous PGRs differentially reshape rhizosphere microbial communities and metabolic networks, enhancing plant stress adaptation in a cover crop system. These results provide a mechanistic basis for optimizing PGR-cover crop synergies to improve soil health and crop resilience.},
}
@article {pmid41721912,
year = {2026},
author = {Mertens, ECA and Asscher, JJ and Sergiou, CS and van Gelder, JL},
title = {Bringing Technology to Justice-Involved Youth.},
journal = {Research on child and adolescent psychopathology},
volume = {54},
number = {2},
pages = {},
pmid = {41721912},
issn = {2730-7174},
mesh = {Humans ; Adolescent ; *Juvenile Delinquency/rehabilitation ; Digital Health ; *Virtual Reality ; },
abstract = {Conventional assessment and treatment approaches targeting justice-involved youth have typically yielded low engagement and modest long-term impact on recidivism and psychosocial functioning. Technologies such as virtual reality, smartphone applications, and wearable devices, offer promising opportunities to address such limitations by providing scalable, engaging and ecologically valid approaches that align well with the often complex needs of this population. The contributions in the special issue aim to showcase some of the potential of these technologies. The special issue originated from a 5-day international Lorentz workshop that brought together researchers and professionals working in clinical practice to explore opportunities, needs, and barriers related to technology implementation in this context. The included contributions comprise empirical case studies illustrating efficiency gains through technological support of existing practices; papers detailing innovative methods that leverage unique capabilities of specific technologies, such as enhanced accessibility and immersive experiences; state-of-the-art reviews; and a viewpoint paper addressing ethical considerations. Collectively, the contributions highlight the promise of technology as well as the need for methodologically robust research to ensure effective and ethical implementation.},
}
@article {pmid41742154,
year = {2026},
author = {Ullah, H and Selvarajan, R and Lau Vetter, MCY},
title = {Genome-mining revealed biosurfactant production capacity and gene co-occurrence patterns in diverse ecosystems.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {41742154},
issn = {1475-2859},
support = {Scholarship//Alliance of International Science Organizations/ ; IDSSE-SJBS-202501//Institute of Deep-sea Science and Engineering/ ; Y970011001//Knowledge Innovation Program of Chinese Academy of Sciences/ ; E2500001//Hainan Provincial Talent Development Bureau/ ; },
mesh = {*Biosurfactants/metabolism ; *Ecosystem ; Data Mining ; *Genome, Bacterial ; *Bacteria/genetics/metabolism/classification ; Glycolipids/biosynthesis ; Fungi/genetics/metabolism ; Genomics ; *Surface-Active Agents/metabolism ; },
abstract = {Biosurfactants produced by microorganisms play essential roles in ecosystem function and hold significance promise for biotechnological applications. However, their diversity and distribution remain poorly depicted due to the limitations of culture-based approaches. In this study, we conducted a large-scale genomic data mining of 142,135 microbial genomes of putative biosurfactant-producing taxa, spanning 21 distinct ecosystems, to systematically profile gene association with 10 major biosurfactant classes. Using a list of 18 key functional genes, we mapped their taxonomic and ecological distribution and analyzed patterns of gene co-occurrence. We found that rhamnolipid biosynthesis genes are nearly ubiquitous across microbial lineages, reflecting their fundamental role in microbial adaptation. In contrast, emulsan and serrawettin pathways are more restricted to plant-associated and fungal ecosystems. The highest diversity of biosurfactant-related genes was found in genomes recovered from nutrient-rich habitats, including plant-associated, algal, and wastewater ecosystems. Co-occurrence network analysis revealed two distinct organizational strategies: a rare, conserved core cluster of genes associated with fengycin, surfactin, iturin lichenysin and plipastatin production, and a widespread, modular periphery linked to rhamnolipid, emulsan, and serrawettin W1 pathways, that are likely driven by the need to adapt to environmental complexity. Notably, we identified previously unreported genomes with biosurfactant production potential, significantly expanding the known biodiversity and ecological range of potential producers. Our findings establish biosurfactant production as a key microbial trait shaped by habitat, with broad implications for microbial ecology, ecosystem monitoring and sustainable biotechnology. This work provides comprehensive genomic resource for biosurfactant research, laying the foundation for targeted bioprospecting and integrative functional studies.},
}
@article {pmid41866514,
year = {2026},
author = {Mieres-Castro, D and Maldonado, C and Mora-Poblete, F},
title = {Multi-omics prediction of terpene constituents and phenolic traits in Eucalyptus globulus using Bayesian models and tree-based machine learning.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {41866514},
issn = {1471-2229},
support = {3220576//ANID FONDECYT postdoctoral/ ; 11240273//ANID FONDECYT/ ; 1231681//ANID FONDECYT/ ; },
mesh = {*Eucalyptus/genetics/chemistry/metabolism ; Bayes Theorem ; *Terpenes/metabolism/chemistry ; *Machine Learning ; *Phenols/metabolism/chemistry ; Multiomics ; Polymorphism, Single Nucleotide ; Oils, Volatile ; },
abstract = {BACKGROUND: Terpenes and phenolic compounds are multifunctional plant metabolites that contribute to defense, signaling, and ecological interactions, while supporting industrial applications. Here, we implemented an integrative multi-omics framework to dissect the genetic and metabolic architecture of biobased compound production in a Eucalyptus globulus breeding population, a tree species of global economic importance. The dataset comprised 14,442 high-confidence SNPs genotyped using the EUChip60K array and 3,279 haplotype blocks, complemented by phenomic datasets derived from near-infrared (NIR) spectral absorbance (~ 900–2,500 nm) and pigment-related indices (chlorophyll, anthocyanins, flavonols, and nitrogen balance index). RESULTS: Gas chromatography-mass spectrometry (GC–MS) and ultra-high-performance liquid chromatography-quadrupole-time-of-flight tandem MS (UHPLC–QqTOF–MS2) revealed substantial inter-individual variation: essential oils were dominated by 1,8-cineole (42.70% ± 7.19%) and α-pinene (38.02% ± 5.20%), while phenolic extracts were enriched in phloroglucinol derivatives (92.67% ± 1.59%), notably the macrocarpal C isomer (12.98% ± 1.48%). Total additive heritability integrating SNP- and pedigree-based effects was high for MeOH extract yield (h2 = 0.721), total phenolics (h2 = 0.646), α-terpineol (h2 = 0.718), and 1,8-cineole (h2 = 0.658), indicating strong genetic control. Predictive modeling revealed that haplotype-based Bayesian approaches outperformed SNP- and phenomic-based models, with the highest accuracies for α-terpineol (prediction accuracy = 0.717), α-pinene (prediction accuracy = 0.554), and methanolic extract yield (prediction accuracy = 0.624). Feature selection identified pleiotropic markers (e.g., SNP12778, HAP205, HAP272, NIR2429) co-localized with genes involved in photosynthesis, signaling, and metabolic regulation. CONCLUSION: These findings lay the foundation for omics-assisted E. globulus breeding aimed at generating elite genotypes for large-scale production of high-value bioactive compounds with practical applications in health, agriculture, and bioenergy.},
}
@article {pmid41896359,
year = {2026},
author = {Placide, A and Kelly, M and Tartarotti, B},
title = {The de novo transcriptome of the freshwater copepod Cyclops abyssorum tatricus reveals high-elevation adaptation.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41896359},
issn = {2045-2322},
support = {10.55776/P35886//Austrian Science Fund/ ; },
mesh = {Animals ; *Copepoda/genetics/physiology ; *Transcriptome ; Gene Expression Profiling ; *Adaptation, Physiological/genetics ; Fresh Water ; Molecular Sequence Annotation ; Lakes ; Gene Ontology ; *Acclimatization/genetics ; Ecosystem ; },
abstract = {Copepods, small aquatic crustaceans, are one of the most abundant zooplankton in the world. These animals play a critical ecological role in aquatic ecosystems such as oceans, streams, or, as in this study, alpine lakes. In these ecosystems, copepods have adapted to stressful and dynamic environments, a process which can be investigated via comparative transcriptomics. An assembled transcriptome is a pre-requisite to applying transcriptomic tools in physiological research, but there are few transcriptome assemblies available for copepods. To address this gap, we assembled a de novo transcriptome of Cyclops abyssorum tatricus by merging Pacific Bioscience long reads from copepods collected in two lakes at two different time points. The final assembly consisted of 52,521 contigs with a BUSCO score of 80.7%. We annotated a total of 26,255 (49.99%) protein sequences using the eggNOG database. Gene ontology analyses revealed that most gene annotations were involved in cellular processes and signaling (34.61%). Comparisons with two other copepod species showed that the transcriptome assembly of C. abyssorum tatricus is enriched for cold acclimation genes, consistent with its long-term adaptation to cold water environments. This de novo transcriptome will enable comparative transcriptomic studies in this species, allowing us to investigate physiological adaptations to alpine environments.},
}
@article {pmid41913152,
year = {2026},
author = {Lysaker, DT and Struckhoff, ED and Chakravarti, I and Bognanni, OJ and Machtinger, ET},
title = {Development of the vector education, communication, and training online resource (VECTOR) library: a vector-borne disease education database.},
journal = {BMC public health},
volume = {26},
number = {1},
pages = {},
pmid = {41913152},
issn = {1471-2458},
support = {NU50CK000637/CC/CDC HHS/United States ; },
mesh = {Humans ; United States ; Animals ; *Vector Borne Diseases/prevention &amp; control ; *Internet ; *Databases, Factual ; *Health Education ; Information Dissemination ; *Disease Vectors ; },
abstract = {BACKGROUND: The emergence of invasive arthropod vectors and the rising prevalence of vector-borne diseases (VBDs) affecting humans and domestic animals have spurred a rapid increase in educational materials. In the United States, the Cooperative Extension System (Extension) can play a role in developing and sharing these resources. MAIN TEXT: Extension has historically served rural and agricultural audiences but has expanded to provide information to a variety of other communities throughout the states it serves. One topic that Extension has begun to expand its focus on in certain areas of the U.S. is VBDs. Due to the way each Extension service may focus on and address its own set of issues and topics, regional gaps in material and a lack of information sharing between institutions may arise. We created the Vector Education, Communication, and Training Online Resource (VECTOR) Library as a repository of educational materials related to vectors and VBDs, developed by Extension offices from across the United States, to address issues of knowledge sharing and access. We hope to continue curating VBD content from Extension offices, as well as to add educational materials created by other non-Extension university departments and each state’s state public health department. CONCLUSION: This database offers a single platform for accessing educational VBD materials from Extension offices nationwide.},
}
@article {pmid41922959,
year = {2026},
author = {Sun, Y and Zhang, F and Yan, S and Kong, X and Wang, H and Shang, J and Liu, JX},
title = {DHGCMDA: a dual-view heterogeneous graph contrastive learning framework for miRNA-disease association type prediction.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {41922959},
issn = {1471-2105},
support = {62472250//National Natural Science Foundation of China/ ; },
mesh = {*MicroRNAs/genetics ; Humans ; *Computational Biology/methods ; Graph Neural Networks ; Algorithms ; },
abstract = {BACKGROUND: Accumulating evidence demonstrates that microRNA (miRNA) dysregulation drives the pathogenesis of diverse human diseases via intricate, context-dependent molecular mechanisms. Hence, prediction of miRNA-disease association types is a critical prerequisite for dissecting functional roles of miRNAs in disease initiation and progression. Although computational methods offer cost-effective, time-efficient alternatives to wet-lab experiments for miRNA-disease association type prediction, most of them are hampered by three key limitations: excessive reliance on association-derived similarity metrics gives rise to quantification bias, traditional pairwise graph architectures inadequately capture high-order biological interactions, and existing representation learning strategies fail to generate consistent embeddings across heterogeneous views and modalities. RESULTS: To address these issues, this study presents DHGCMDA, a dual-view heterogeneous graph contrastive learning framework for miRNA-disease association type prediction. Specifically, dual-view hypergraphs are first constructed based on heterogeneous similarity data to avoid excessive reliance on association-derived similarity metrics. A hypergraph convolutional network is then employed to capture high-order topological relationships between miRNAs and diseases, with its convolution cooperatively integrated with contrastive learning, intra-modality for cross-view consistency and cross-modality for embedding space alignment, to enhance feature representation quality. Finally, an attention-guided adaptive view fusion strategy dynamically weights and integrates distinct view representations, and type-aware message passing via heterogeneous graph Transformer simultaneously enables prediction of association presence and functional types. 5-fold cross-validation on HMDD v2.0 and v3.2 datasets demonstrates that DHGCMDA outperforms several state-of-the-art methods. Furthermore, case studies on breast neoplasms and hepatocellular carcinoma reveal that most predicted association types are corroborated by published literature, thereby validating the efficacy of DHGCMDA in miRNA-disease association type prediction. CONCLUSIONS: DHGCMDA exhibits robust discriminative power and generalization capability, providing a reliable computational alternative for miRNA-disease association type prediction. The source code is publicly available at https://github.com/CDMBlab/DHGCMDA .},
}
@article {pmid41942920,
year = {2026},
author = {Barjij, I and Lamsyah, O and Kdadri, S and Lkhoyaali, S and Najem, S and Naciri, S and Inrhaouen, H and Elghissassi, I and Boutayeb, S and Mrabti, H and Errihani, H},
title = {Spatial and temporal intratumoral heterogeneity in breast cancer: a systematic and conceptual review of single-cell and spatial omics studies.},
journal = {BMC cancer},
volume = {26},
number = {1},
pages = {},
pmid = {41942920},
issn = {1471-2407},
mesh = {Humans ; Female ; *Breast Neoplasms/genetics/pathology ; *Single-Cell Analysis/methods ; Multiomics ; Tumor Microenvironment/genetics ; Spatial Transcriptomics ; Single-Cell Gene Expression Analysis ; Genetic Heterogeneity ; },
abstract = {BACKGROUND: Spatial and temporal intratumoral heterogeneity (ITH) remains a major challenge in the diagnosis, prognosis, and treatment of breast cancer. Recent advances in single-cell and spatial omics technologies have enabled unprecedented resolution of subclonal architectures, evolutionary trajectories, and microenvironmental interactions. This systematic and conceptual review aimed to synthesize and integrate current evidence on spatiotemporal ITH in human breast cancer, bridging empirical data with mechanistic interpretation through high-resolution profiling platforms. METHODS: We conducted a systematic review following PRISMA 2020 guidelines, searching three databases (PubMed, Scopus, and Web of Science) and screening 1037 records published between January 2018 and May 2025. 19 original studies were included based on predefined eligibility criteria targeting single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, or multi-omics approaches applied to human breast tumor samples. Data extraction focused on study design, technologies used, subclonal dynamics, spatial/temporal resolution, tumor–immune interactions, and risk of bias. RESULTS: The included studies analyzed over 400,000 single cells from diverse breast cancer subtypes, with a predominance of triple-negative breast cancer. Subclonal plasticity was a recurrent feature, often characterized by EMT (epithelial-to-mesenchymal transition) signatures, cell-cycle heterogeneity, and immune evasion. Spatial analyses revealed discrete ecological niches shaped by immune exclusion and stromal patterning, while temporal assessments uncovered therapy-driven clonal selection, metabolic reprogramming, and enhancer remodeling. Interclonal and tumor–immune communication were consistently associated with poor prognosis or therapeutic resistance. Most studies were judged to have low or moderate risk of bias, with transparent reporting and accessible data pipelines. CONCLUSIONS: Single-cell and spatial omics studies provide critical insights into the evolutionary ecology of breast cancer. By conceptually integrating spatial, temporal, and microenvironmental dimensions, this review highlights convergent evolutionary programs underlying tumor aggressiveness and resistance. Spatiotemporal ITH is a key driver of disease progression, and its systematic characterization could inform biomarker development, personalized therapies, and future multi-modal diagnostics. Continued integration of spatial, temporal, and functional data is essential to move from descriptive maps to clinically actionable frameworks.},
}
@article {pmid41945111,
year = {2026},
author = {Lai, Z and Zhang, B and Fu, Z and Li, R and Qian, Y and Zhang, Y and Xu, P and Du, Y},
title = {Research advances on Cordyceps sinensis and its components in relation to omics biomarkers for the neurological disorders.},
journal = {Die Naturwissenschaften},
volume = {113},
number = {3},
pages = {},
pmid = {41945111},
issn = {1432-1904},
support = {2026ZL0010//Zhejiang Traditional Chinese Medicine Science and Technology Program of China/ ; 82202605//National Natural Science Foundation of China/ ; 2023, DU YAOQIANG//Zhejiang Provincial Special Support Program for Cultivation of High-Level Innovative Health Talents of China/ ; },
mesh = {*Cordyceps/chemistry ; Animals ; *Nervous System Diseases/drug therapy ; Humans ; Biomarkers/analysis ; Multiomics ; Neuroprotective Agents/pharmacology ; },
abstract = {Cordyceps is a traditional medicinal fungus belonging to the species Ophiocordyceps sinensis. It grows in the alpine ecological zone of the Tibetan Plateau and exhibits dual characteristics of both insects and fungi. The primary species include Cordyceps sinensis and Cordyceps militaris. Rich in bioactive components such as cordycepin, polysaccharides, adenosine, and peptides, cordyceps demonstrates broad applications in immune regulation, anti-tumor activity, anti-inflammatory, and neuroprotection. Cordyceps sinensis and its components show great therapeutic potential in neurological diseases such as epilepsy, Alzheimer’s disease and Parkinson’s disease through multi-level and multi-target actions However, current research faces challenges including unclear mechanisms of action and insufficient clinical translation. In this review, we analyze the molecular mechanisms underlying cordyceps’ neuroprotective effects, including the regulating of apoptosis, improvement of mitochondrial function, and promoting of nerve repair. Utilizing network pharmacology, we explore the multi-targeted actions of cordyceps and predict the key pathways. Further we summarize the research progress in the integrated multi-omics analyses (genomics, transcriptomics, proteomics and metabolomics), to reveal the synergistic roles of cordyceps components in treating neurological disorders and identify potential molecular biomarkers. Additionally, we highlight the findings from preclinical experiments and animal models on cordyceps-based drugs, discussing their advantages and challenges for clinical application. Future studies should prioritize systematic exploration of standardized drug development, advanced multi-omics integration, and rigorous clinical trials. This will provide a more robust scientific foundation and practical guidance for the treatment of neurological diseases with cordyceps.},
}
@article {pmid41951704,
year = {2026},
author = {Rocchi, L and Mattioli, S and Collin, A and Bonnefous, C and Warin, L and Tuyttens, F and Thobe, P and Re, M and Castellini, C},
title = {First evaluation framework based on the one welfare concept in extensive broiler rearing systems.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41951704},
issn = {2045-2322},
support = {N&#x2da;816172//European Commission/ ; },
mesh = {Animals ; *Animal Welfare ; *Chickens/growth &amp; development ; *Animal Husbandry/methods ; Humans ; Decision Support Techniques ; Environment ; },
abstract = {The One Welfare concept has emerged to counter the traditional separation of human well-being, environmental sustainability, and animal welfare, emphasizing their interdependence within specific ecological and socio-technical contexts. Despite its promise, the practical operationalization of One Welfare as an evaluation framework remains limited. This study proposes and tests an operational One Welfare approach (OWA) for extensive broiler rearing systems (ERS), explicitly promoting direct and indirect links between animal and human welfare and situating them within the environmental performance. Although ERS constitute a minor share of EU broiler output (≈ 5%), interest in and adoption of ERS have grown markedly over the past two decades, underscoring the need for assessment tools that capture their broader contributions. Conventional evaluation methodologies, designed around intensive systems, tend to prioritize yield, short-term efficiency, and market indicators, and may therefore underrepresent the ecological, social, and welfare advantages achievable in diversified, outdoor systems. We implemented a multicriteria decision analysis (MCDA) using the One Welfare Approach to synthesize indicators across the animal welfare, environmental, economic, and social pillars in a broiler case study. The framework proved feasible despite data constraints (limited availability and some invariant parameters typical of ERS, and its outputs aligned with published evidence on slow-growing genotypes in outdoor systems, supporting construct validity. The Key results showed that: (1) Environmental enrichment with olive trees improved OWA performance: all enriched options outperformed their non-enriched counterparts, showing that tree/shrub cover increases outdoor use, reduces predation and fear, and improves integument condition in free-range birds. (2) Under enrichment, RJ_E ranked first overall. Flow decomposition indicated that CB_E exhibited higher positive flow (Phi+), but RJ_E had a lower negative flow (Phi[-]); given the non-compensatory OWA stance, suppressing negatives proved more decisive than marginal gains in positives. A weight-sensitivity check showed ranking stability across pillars, with limited shifts confined to the Economic pillar, where criterion values were tightly clustered. Taken together, these findings indicate that One Welfare assessment can capture trade-offs and synergies that conventional metrics overlook, offering actionable guidance for extensive organic broiler systems. The approach is compatible with prevailing outcome-based welfare assessment practice. It can be simplified into a transparent index for on-farm self-assessment and external communication, provided that its governance and evidence base meet current best practice expectations.},
}
@article {pmid41954832,
year = {2026},
author = {Kong, X and Sun, Y and Shang, J and Zhang, X and Tang, X and Wang, H and Qiu, D and Zhang, Y and Liu, JX},
title = {MsDGCN: multi-scale diffusion graph convolutional network for the prediction of drug-disease association.},
journal = {Journal of computer-aided molecular design},
volume = {40},
number = {1},
pages = {},
pmid = {41954832},
issn = {1573-4951},
support = {62472250//National Natural Science Foundation of China/ ; },
mesh = {Graph Neural Networks ; Humans ; *Drug Repositioning/methods ; *Computational Biology/methods ; Boosting Machine Learning Algorithms ; },
abstract = {Drug-disease association prediction is crucial for accelerating drug repurposing, yet existing computational models largely focus on integrating biological attributes while neglecting topological regulatory patterns within heterogeneous biological networks. To address this, we propose MsDGCN, a novel multi-scale diffusion graph convolutional network. The model is built upon two key innovations: a multi-scale architecture that captures complex topological signals through meta-path guided diffusion and cross-path attention mechanisms, and a dedicated hard negative mining strategy that selects biologically plausible confounders to sharpen the decision boundary. To handle severe data imbalance, an XGBoost classifier with dynamic class weighting is integrated to model nonlinear feature interactions. Extensive ten-fold cross-validation demonstrates that MsDGCN significantly outperforms state-of-the-art baselines across key metrics, confirming its capability to effectively leverage network topology for improved drug-disease association prediction. MsDGCN provides a robust and generalizable framework for predicting drug-disease associations. Code and data are available at: https://github.com/CDMBlab/MsDGCN.},
}
@article {pmid41992084,
year = {2026},
author = {Lu, W and Dong, Y and Dong, Z and Xie, Y and Zhang, H and Han, Y and Zhang, D and Liu, Y and Weng, Q},
title = {Multi-omics analysis reveals seasonal variation in ovarian lipid metabolism associated with vitamin D3 in the muskrats.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41992084},
issn = {1471-2164},
support = {202410022032//National Undergraduate Training Programs for Innovation and Entrepreneurship/ ; NO. BLX202219//Fundamental Research Funds for the Central Universities/ ; No. BLRC 2023C02//5&#xb7;5 Engineering Research &amp; Innovation Team Project of Beijing Forestry University/ ; 7232240//Beijing Municipal Natural Science Foundation/ ; },
mesh = {Animals ; Female ; *Lipid Metabolism ; *Seasons ; *Arvicolinae/metabolism/genetics ; *Cholecalciferol/metabolism/blood ; *Ovary/metabolism ; Multiomics ; Receptors, Calcitriol/metabolism/genetics ; Metabolomics ; Gene Expression Profiling ; Transcriptome ; },
abstract = {BACKGROUND: Seasonal reproduction is critical for animals adapting to environmental changes, yet the mechanisms driving these shifts remain incompletely understood. Gut microbiota are increasingly recognized as important modulators of reproductive health, but their roles in seasonal breeding species remain unclear. RESULTS: In the muskrat (Ondatra zibethicus), a well-established seasonal breeder, morphological and histological analyses revealed enhanced follicular development during the breeding season (BS). Subsequent integrated ovarian transcriptomics and metabolomics identified that lipid metabolic processes were significantly enriched during the BS. This was validated by the increased expression of key lipid metabolic enzymes (e.g., DGAT1, CPT1A) and elevated triglyceride content in BS ovaries. Systemically, we found that serum vitamin D3 (VD3) and ovarian vitamin D receptor (VDR) expression were significantly elevated during BS. In contrast, analysis of upstream factors during the non-breeding season (NBS) showed a significant enrichment of gut Lactobacillus and a concurrent elevation of plasma lithocholic acid (LCA), a known VDR agonist. Correlation analyses confirmed that both Lactobacillus and LCA were inversely associated with serum VD3 levels. Critically, in vitro experiments demonstrated that VD3 treatment enhanced the expression of key lipid metabolism genes in muskrat granulosa cells. CONCLUSIONS: Collectively, our findings provide evidence for a gut microbiota-VD3-ovary axis that modulates seasonal ovarian lipid metabolism and function. This axis represents a new layer of host-microbiota interaction in reproductive physiology.},
}
@article {pmid41997985,
year = {2026},
author = {Orozco, LR and Weaver, AE and Klee, DJ and Pauli, CS and Grassa, CJ and Vergara, D and Baptista, A and White, K and Emery, BF and Castro, NRM and Garuda, S and Guerrero, RF and Keegan, BC and Kane, NC},
title = {Network ontology transcript annotation identifies genetic signals underlying sex determination.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41997985},
issn = {2045-2322},
mesh = {*Gene Regulatory Networks ; *Sex Determination Processes/genetics ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Flowers/genetics ; Transcriptome ; Gene Ontology ; Molecular Sequence Annotation ; Signal Transduction ; },
abstract = {Cannabis sativa L. (marijuana, hemp, cannabis) is an angiosperm species currently evolving sex chromosomes. Genetic mechanisms, primarily an XY chromosome system, dictate cannabis sex expression in dioecious populations. However, sexual expression is also governed by the interplay of hormone regulatory gene networks, influenced by both genetic and environmental factors. Within the species, some populations exhibit dioecy, monoecy, or a gradient of both. Dioecious individuals produce exclusively male or female flowers, while monoecious plants bear both male and female flowers. Remarkably, through interruption of phytohormone signal transduction via abiotic stressors, genetically male or female cannabis are able to produce flowers of the opposite sex. Previous transcriptomic analysis have identified genes associated with masculinization through the application of phytohormone signal disruption using silver thiosulfate treatment. We analyzed transcriptomic data from cannabis treated with colloidal silver to similarly induce masculinization. Using Nota (Network ontology transcript annotation), a multilayer network analysis (Random-Walk-with-Restart) tool, we identified candidate genes involved in sex-determination. Nota and a companion program Jack facilitate multi-layer network analyses, enabling discovery and annotation of gene-trait associations. Our findings highlight Nota’s robust application to enrich the genetic architecture of complex traits, particularly in non-model systems like cannabis, and complex traits such as sex determination. Our analyses identified genes associated with cell wall morphogenesis and embryogenic tissue homeostasis, indicating that silver ion treatment perturbs phytohormone signal transduction through metal ion imbalance. In this reproductive strategy, cannabis is able to make use of its widely investigated sex-determining genetic architecture to navigate transient changes in co-expression and cross-cellular signaling driving embryogenic cell wall re-patterning.},
}
@article {pmid41998442,
year = {2026},
author = {Paveen, P and Ryota, K and Kumar, V},
title = {Omics-informed insights into biochar-Trichoderma interactions in plant-soil systems: mechanisms of defense and context-dependent responses.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41998442},
issn = {1573-0972},
mesh = {*Trichoderma/physiology/metabolism ; *Plants/microbiology/metabolism/immunology ; Multiomics ; Proteomics ; Soil Microbiology ; *Charcoal ; Metabolomics ; Signal Transduction ; Soil/chemistry ; Cyclopentanes/metabolism ; Oxylipins/metabolism ; Salicylic Acid/metabolism ; },
abstract = {The combined application of biochar and Trichoderma spp. represents a promising strategy for enhancing plant resilience and soil health; however, the molecular mechanisms underlying their synergistic interactions remain poorly understood and inadequately integrated. This review critically synthesizes evidence from transcriptomic, proteomic, metabolomic, and microbiome analyses to elucidate how biochar-Trichoderma interactions modulate plant defense signaling pathways and stress adaptation responses. Transcriptomic analyses reveal context-dependent activation of the jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) signaling pathways. Correspondingly, proteomic and metabolomic datasets demonstrate variable yet recurrent upregulation of pathogenesis-related (PR) proteins, reactive oxygen species (ROS)-scavenging enzymes, and phenylpropanoid-derived metabolites. Notably, accumulating evidence suggests that these molecular responses are highly context-dependent, varying substantially with soil type, biochar physicochemical characteristics, and Trichoderma strain specificity. We critically examine major methodological limitations in existing omics investigations, including inadequate reproducibility under field conditions and insufficient integration of molecular and ecological datasets. Finally, we propose a systems biology framework for designing functionally optimized biochar–microbe formulations and identify research priorities for translating insights into agronomically robust and field-deployable technologies.},
}
@article {pmid42310879,
year = {2026},
author = {Wu, B and Pan, Y and Harefa, AMS and Zhou, H and Li, J and Wang, Y and Hansen, PJ and Lundholm, N and Altenburger, A and Li, Q},
title = {Decoding a Multigenomic Symphony: Divergent Evolutionary Tempos Across the Four Genomic Compartments of Teleaulax Cryptophytes.},
journal = {Molecular ecology},
volume = {35},
number = {12},
pages = {e70441},
doi = {10.1111/mec.70441},
pmid = {42310879},
issn = {1365-294X},
support = {SKJC-2024-01-002//Sanya Yazhou Bay Science and Technology City/ ; 32370666//National Natural Science Foundation of China/ ; 4181-00484//Danmarks Frie Forskningsfond/ ; SYSPG20241211173844007//Shenzhen Science and Technology Program/ ; },
mesh = {*Cryptophyta/genetics ; *Evolution, Molecular ; Cell Nucleus/genetics ; *Symbiosis/genetics ; Genome, Plastid/genetics ; *Genome, Plant ; Genome, Mitochondrial ; Phylogeny ; Plastids/genetics ; Biological Evolution ; },
abstract = {Secondary endosymbiosis drives eukaryotic diversification by integrating genetic compartments from disparate lineages, yet how the host and endosymbiont genomes co-evolve over deep time remains poorly understood. Cryptophytes provide a compelling model to dissect this integration, as they uniquely retain four distinct genomes within a single cell: the host nucleus and mitochondrion, alongside a red algal-derived plastid and its relict nucleus (nucleomorph). Here, we investigate the evolutionary and regulatory dynamics of these four coexisting genomes in two ecologically important cryptophytes, Teleaulax amphioxeia and Teleaulax acuta. We reveal a striking decoupling of evolutionary tempos across these genomic compartments. Plastid genomes exhibit structural and functional stasis, while mitochondrial genomes, despite also maintaining high synteny, show faster sequence evolution and mobile element invasion. Nucleomorph genomes evolves even more rapidly, but their gene expression is rigid, with regulatory flexibility limited to a small, conserved set of plastid-supporting genes. Intriguingly, Teleaulax host nuclear genomes have undergone massive expansion, likely driven by ancient whole-genome duplication that might explain their greatest divergence among the four genomic compartments. This divergence is further characterised by differential expansion of gene families (e.g., PHYB-like photoreceptors and motor-related proteins) potentially linked to ecological adaptation. Diel transcriptomic analyses highlight conserved core metabolic responses across both species, but also unveil lineage-specific adaptations, such as enhanced circadian regulation in T. acuta associated with PHYB-like gene expansion. Overall, our findings uncover a constraint gradient from plastid stasis to high evolutionary flexibility toward nucleus, highlighting how secondary plastid-bearing cells achieve a balance between long-term stability and adaptive innovation.},
}
@article {pmid42311787,
year = {2026},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Regal Piercer, Pammene regiana (Zeller, 1849) (Lepidoptera: Tortricidae).},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {232},
pmid = {42311787},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Pammene regiana (Regal Piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 863.59 megabases. Most of the assembly (99.44%) is scaffolded into 29 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.5 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genome assemblies for eukaryotic species found in Britain and Ireland.},
}
@article {pmid40646445,
year = {2025},
author = {Duan, G and Liang, C and Su, J and Liang, Y and Li, W and Zhang, J and Zhang, Y},
title = {Integrative transcriptomic and metabolomic analysis elucidates the vital pathways underlying the differences in salt stress responses between two chickpea (Cicer arietinum L.) varieties.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {903},
pmid = {40646445},
issn = {1471-2229},
support = {ZYYD2022C02//Central Guidance on Local Science and Technology Development Fund/ ; 32360095//National Natural Science Foundation of China/ ; },
mesh = {*Cicer/genetics/metabolism/physiology ; *Salt Stress/genetics ; *Transcriptome ; Metabolomics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Metabolome ; Salt Tolerance/genetics ; Multiomics ; Stress, Physiological ; },
abstract = {BACKGROUND: Salinity, a major abiotic stress, significantly impairs crop productivity by inducing osmotic, ionic, and secondary stresses that disrupt metabolic processes. Chickpea (Cicer arietinum L.), a diploid annual legume of the Fabaceae family, is one of the major pulse crops cultivated by farmers with limited resources. While previous studies have explored salt tolerance in chickpeas, this study provides a comprehensive multi-omics perspective. Exploring the mechanism of chickpea adaptation to the saline environment can effectively supplement the problem of single source of plant protein. RESULTS: The present study analyzed the transcriptomic and metabolomic profiles of two distinct chickpea varieties, DY3 and DY1, with contrasting salinity tolerance capacities. The salinity tolerance of DY3 was associated with greater biomass, higher antioxidant enzyme activity, and higher photosynthetic efficiency. Transcriptomic analysis revealed that the genes induced in DY3 under salinity stress were associated with ion homeostasis, antioxidant defense system, and plant hormone signaling. Metabolomics analysis revealed significant enrichment of components of diverse secondary metabolites pathways, as well as carbohydrate metabolism. Integrated multi-omics analysis highlighted the anthocyanin biosynthesis pathway, functioning within the broader flavonoid metabolic network, as a key regulator of salt tolerance in the chickpea. Subsequent, RT-qPCR confirmed the upregulation of key genes associated with anthocyanin metabolism. CONCLUSIONS: These findings reveal the key regulatory role of the flavonoid pathway in salt tolerance of chickpeas, offering insights for breeding improved varieties.},
}
@article {pmid40830831,
year = {2025},
author = {Jiang, W and Liu, X and Li, W and Yang, J and Li, P and Xie, M and Zhou, G},
title = {Dual-omics analysis reveals B vitamin regulation and metabolism in Areca Catechu inflorescence.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {757},
pmid = {40830831},
issn = {1471-2164},
support = {Hnky2024-23//the Education Department of Hainan Province/ ; HSZK-KYQD-202421//the Hainan Normal University Talent Research Start-up Fund Project Funding/ ; },
mesh = {*Metabolomics ; *Vitamin B Complex/metabolism ; *Areca/metabolism/genetics ; Gene Expression Regulation, Plant ; *Inflorescence/metabolism/genetics ; Gene Expression Profiling ; Multiomics ; Transcriptome ; Metabolome ; Plant Proteins/genetics/metabolism ; },
abstract = {Areca catechu flowers are an important component of traditional Chinese medicine for the treatment of various diseases. Studies on its secondary metabolites have largely focused on pyridine alkaloids yet a high-resolution metabolic profile of another important nutrient and coenzyme, the B vitamins, remains lacking. Here, we analyzed the levels of eight B vitamins in the inflorescence of A. catechu by targeted metabolomics. Our results showed that pantothenic acid and riboflavin were the predominant B vitamins, and that different B vitamins exhibited tissue-specific expression patterns within the various parts of the inflorescence. Furthermore, panoramic expression profiles of genes related to B vitamin biosynthesis in the inflorescence were mapped. Notably, we characterized a key rate-limiting enzyme in the thiamine biosynthesis pathway, the thiazole synthase (AcTHI1), that plays a crucial role in regulating thiamine biosynthesis. Additionally, integrated transcriptomic and targeted metabolomic analyses revealed hub transcription factors, including AcNAC73, AcMYB61, and AcARF9, that are associated with the regulation of pantothenic acid and thiamine metabolism. Taken together, our results lay a foundation for understanding the regulation of B vitamin metabolism during the development of A. catechu inflorescence and provide a theoretical basis for the development of the medicinal and nutritional potential of the plant.},
}
@article {pmid40836216,
year = {2025},
author = {Wang, T and Tang, C and De, K and Qi, J and Li, Y and Li, X},
title = {Integrated transcriptomic and metabolomic analysis reveals stage-associated molecular profiles in Ophiocordyceps sinensis.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {763},
pmid = {40836216},
issn = {1471-2164},
support = {K9922050//Qinghai Province Science and Technology Department project/ ; QHCY-2023-057//Protective Harvesting and Utilization Project for Ophiocordyceps sinensis in Qinghai Province/ ; LHZX-2022-01//Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; 2021-SF-A4//The major science and technology projects of Qinghai Province/ ; },
mesh = {*Metabolomics/methods ; *Gene Expression Profiling ; Multiomics ; *Transcriptome ; *Hypocreales/genetics/metabolism ; *Metabolome ; Amino Acids/metabolism ; },
abstract = {Ophiocordyceps sinensis is globally recognized for its exceptional nutritional and medicinal properties. Variations in the edible qualities and tonic values of O. sinensis at different harvesting stages remain poorly understood in terms of compositional changes and regulatory mechanisms. Utilizing UPLC-MS/MS and transcriptome sequencing (RNA-seq), this study unveiled discrepancies in metabolite accumulation and gene expression of O. sinensis across various harvesting stages. Metabolomics analysis identified 596 differentially accumulated metabolites (DAMs), primarily enriched in amino acid-related metabolic pathways such as tyrosine, tryptophan, cysteine, and methionine metabolism. The up accumulation of organic acids and derivatives with delayed harvesting led to distinct abundances and compositions of amino acids, peptides, analogs, and fatty acids and conjugates, ultimately influencing the quality of O. sinensis. Transcriptomic analysis revealed 2550 differentially expressed genes (DEGs) at different harvesting stages, with KEGG-based enrichment analysis highlighting their involvement in amino acid-related activities like tyrosine metabolism and fatty acid degradation. The upregulation of these DEGs in amino acid-related pathways presents a promising target for studying O. sinensis quality. Integrative metabolomic and transcriptomic analyses indicated potential roles for DDC (G6O67_000335), TYR (G6O67_005660), AOC (G6O67_005457), and fahA (G6O67_004634) in the synthesis pathways of amino acids, peptides, and their analogs, suggesting a possible indirect association with O. sinensis quality. These findings offer novel insights into the molecular mechanisms underlying the quality formation and metabolic evolution of O. sinensis.},
}
@article {pmid41085836,
year = {2025},
author = {Vidal-Silva, IM and Loza, A and Gutierrez-Rios, RM},
title = {Unlocking microbial potential: advances in omics and bioinformatics for aromatic hydrocarbon degradation.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {10},
pages = {384},
pmid = {41085836},
issn = {1573-0972},
support = {IN202524//PAPIIT-DGAPA/ ; 319234//Ciencia B&#xe1;sica y/o Ciencia de Frontera. Modalidad: Paradigmas y Controversias de la Ciencia 2022/ ; },
mesh = {Biodegradation, Environmental ; *Computational Biology/methods ; *Bacteria/metabolism/genetics/classification ; *Hydrocarbons, Aromatic/metabolism ; Environmental Pollutants/metabolism ; Multiomics ; Genomics ; Metagenomics ; Polycyclic Aromatic Hydrocarbons/metabolism ; Metabolic Networks and Pathways ; Anaerobiosis ; },
abstract = {Aromatic hydrocarbons (AHs) are persistent environmental pollutants with high toxicity. Bacterial degradation of AHs provides a sustainable and cost-effective approach for the remediation of sites contaminated with both mono- and polycyclic aromatic hydrocarbons. Aerobic degradation of AHs typically involves oxygenases-mediated hydroxylation followed by aromatic ring cleavage. In contrast, anaerobic degradation relies on diverse activation mechanisms that ultimately converge on the central intermediate benzoyl-CoA. Over the past decades, research on bacterial degradation of AHs has grown steadily, supported by advances in omics and bioinformatics. In this review, we summarize the current knowledge on the pathways, enzymes, and microbial diversity involved in AH degradation, highlighting how omics and bioinformatic approaches are advancing our understanding of this process. However, to improve our knowledge of microbial AHs catabolism, it is crucial to prioritize the characterization of novel enzymes and pathways, especially those mediating anaerobic and hybrid degradation strategies. Addressing this gap requires the development of specialized resources that incorporate a broader taxonomic diversity and an expanded inventory of anaerobic genes and enzymes supported by experimental evidence. Equally important is the integration of multi-omics technologies, artificial intelligence, and ecological modeling into unified analytical pipelines. These efforts will be key to fully unlocking microbial metabolic potential and guiding more effective bioremediation and monitoring strategies for AHs.},
}
@article {pmid41372785,
year = {2025},
author = {Zhou, Y and Pan, J and Cheng, H and Xiao, L and Zhang, W and Huang, H and Liu, K and Fang, L and Ma, W and Xia, Y and Li, J and Lv, D and Hu, Y and Chang, Y and Wang, Z and Tao, H and Zhang, C and Li, C and Peng, Y and Zhao, Q and Zhang, Y and Mei, J and Wang, X and Wei, T and Zhou, M and Zhang, Y and Chen, Q and Chan, NY and Zhang, B and Wing, YK and Lei, B and Zhang, J},
title = {Digital multi-modal approaches to subtyping insomnia disorder (DIMOSI): study design, rationale, digital platform, and preliminary baseline characteristics of a national prospective cohort study.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {74},
pmid = {41372785},
issn = {1471-244X},
mesh = {Humans ; *Sleep Initiation and Maintenance Disorders/classification/diagnosis/psychology ; Prospective Studies ; Female ; Adult ; Male ; Digital Health ; Middle Aged ; Wearable Electronic Devices ; Research Design ; Surveys and Questionnaires ; Young Adult ; Sleep ; },
abstract = {BACKGROUND: Insomnia disorder exhibits complex manifestations and heterogeneous clinical trajectories. Accurate subtyping of insomnia might enhance understanding of its clinical presentations and facilitate precision management. The Digital Multi-modal approaches to Subtyping Insomnia disorder (DIMOSI) study is a national prospective cohort study utilizing multi-modal assessments to explore the subtypes of insomnia disorder, their natural trajectories, and related mental health outcomes. METHODS: A total of 4,000 adult participants meeting International Classification of Sleep Disorders, 3rd Edition (ICSD-3) criteria for insomnia disorder will be recruited from community or clinical settings. Eligible participants will be invited to complete the multi-dimensional assessments via a digital platform, including a structured interview, questionnaires, cognitive tasks, sleep-activity diary, physiological characteristics, and ecology momentary assessments, as well as 7-day physical activity and sleep tracking using wearable devices. All participants will be followed up at 6 and 12 months. The primary outcome is the identification of multi-modal subtypes of insomnia disorder and their correlates. Secondary outcomes include the longitudinal trajectories of these subtypes, associated risk factors, and mental health outcomes. RESULTS: As of June 30, 2025, a total of 2937 patients with insomnia disorder have been recruited, with a mean age of 37.3 years (SD = 12.6), 59.3% from outpatient clinics, and 66.5% female. Among the participants, 2850(97.1%) were suffering from current insomnia disorder, while the mean score of the ISI was 15.5 ± 5.8. A total of 2134 participants (72.7%) wore accelerometers, while 2429 (82.7%) wore wearable EEG monitors for continuous assessments. DISCUSSION: The DIMOSI study is a large-scale national prospective cohort investigating insomnia disorder utilizing a self-developed digital multi-modal platform. It integrates comprehensive subjective and objective assessments from 33 centers in China. The current study offers a unique opportunity to explore subtypes of insomnia disorder and their natural course and their correlates through the digital multi-modal platform that provides enriched and comprehensive assessments. It may provide the potential to inform the development of personalized prevention and intervention strategies, ultimately improving patient outcomes. TRIAL REGISTRATION: Clinical Trial Registry Name: Digital Multi-modal approaches to deep phenotyping insomnia disorder. Registration Number: ChiCTR2200056425. Date of Registration: 2022-02-05.},
}
@article {pmid41430187,
year = {2025},
author = {Lee, E and Hwang, J and Kim, DW and Choi, BY and Bae, HJ and Won, SH and Park, YH and Kim, S},
title = {Association between high carbohydrate to dietary fiber ratio and risk of dementia in older adults: analysis from the UK biobank.},
journal = {BMC neurology},
volume = {26},
number = {1},
pages = {33},
pmid = {41430187},
issn = {1471-2377},
mesh = {Humans ; *Dementia/epidemiology ; United Kingdom/epidemiology ; Female ; *Dietary Fiber/administration &amp; dosage ; *Dietary Carbohydrates/administration &amp; dosage ; Aged ; Male ; Middle Aged ; Biological Specimen Banks ; Prospective Studies ; UK Biobank ; Risk Factors ; Magnetic Resonance Imaging ; Cohort Studies ; },
abstract = {BACKGROUND: The dietary carbohydrate-to-fiber ratio (CFR) provides a comprehensive measure of carbohydrate quality; however, its association with cognitive outcomes remains unexplored. Given the distinct health effects of different types of carbohydrates, understanding the impact of CFR on dementia risk and brain structure is valuable. METHODS: This prospective cohort study analyzed 107,785 UK Biobank participants aged ≥ 55 years who completed at least one 24-hour dietary recall between 2011 and 2012, with follow-up until April 2024. CFR was calculated as the ratio of daily carbohydrate intake to fiber intake. Total carbohydrate and dietary fiber intake were included as secondary exposures. CFR outliers were excluded using Tukey’s method (3.0 × interquartile range). The primary outcome was all-cause dementia incidence identified through linked hospital and death registry data. Secondary outcomes were hippocampal volume, entorhinal cortical thickness and frontal cortical thickness. Cox proportional hazards models estimated dementia risk, and multiple linear regression analyzed MRI markers. Models were adjusted for age, sex, education, BMI, physical activity, smoking, alcohol intake, hypertension, diabetes, and total energy intake. Interactions between dietary factors and polygenic risk score (PRS) were examined. RESULTS: During a median follow-up of 11.8 years, 2,000 dementia cases occurred, corresponding to incidence rates of 1.44 and 1.82 per 1,000 person-years in the lowest and highest CFR quartiles, respectively. A higher CFR was significantly associated with increased dementia risk (HR per 1 SD = 1.07, 95% CI: 1.02–1.12, p = 0.003). The association was slightly attenuated in individuals with increased genetic susceptibility (p for interaction = 0.02). Total carbohydrate intake was associated with dementia risk (HR per 1 SD = 1.15, 95% CI: 1.05–1.25, p = 0.001), whereas fiber intake was not (p = 0.99). An elevated CFR was also associated with reduced entorhinal cortical thickness (FDR p = 0.03) and with thinner frontal pole, medial orbitofrontal cortex, and rostral middle frontal cortex (all FDR p = 0.01) among 14,388 participants with MRI data. CONCLUSIONS: A higher CFR was associated with increased dementia risk, reduced entorhinal thickness, and thinner frontal cortical regions, suggesting that CFR may serve as a practical indicator of carbohydrate quality with potential implications for dietary and public health approaches to cognitive aging.},
}
@article {pmid41634580,
year = {2026},
author = {Gong, X and Chen, B and Yang, L and Zhang, Y and Chang, S and Yang, T and Chen, Y and Zhu, Y and Wang, Z and He, X and Xue, L},
title = {Location and growth period influence the bioactive compounds of Angelica sinensis (Oliv.) diels: multi-omics insights.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {41634580},
issn = {1471-2229},
support = {24JRRA1134; 2024YQ-04//the Natural Science Foundation of Gansu Province of China; the Outstanding Youth Fund of the Gansu Academy of Sciences/ ; 22ZSCQ037//Intellectual Property Plan Project Gansu Province of China/ ; 24JRRA1137; 2024QN-13//the Science and Technology Program of Gansu Province of China; the Young Scientists Fund Project of Gansu Academy of Sciences/ ; },
mesh = {*Angelica sinensis/growth &amp; development/metabolism/genetics/microbiology/chemistry ; Multiomics ; Rhizosphere ; Soil Microbiology ; Bacteria/genetics ; Fungi/genetics ; Gene Expression Profiling ; Microbiota ; Plant Roots/microbiology ; Transcriptome ; },
abstract = {Angelica sinensis, a traditional medicinal herb, exhibits significant variations in efficacy quality linked to geographical origin and rhizosphere microbiome composition. However, the microbial factors driving the synthesis of its bioactive compounds in authentic (historically recognized for superior quality geoherbs, Min County) and adjacent regions remain poorly understood. This study integrated transcriptomic profiling of plant tissues with 16 S rRNA (bacteria) and ITS (fungi) sequencing of rhizosphere soils over multiple growth stages in authentic and near-authentic regions (the latter characterized by a similar climate but differing soil ecology). By combining these data with targeted metabolomics and soil property analysis, substantial regional and temporal variations in bioactive compound levels and soil properties were identified. Specifically, 2,367 differentially expressed genes (DEGs), 417 bacterial amplicon sequence variants (ASVs), and 295 fungal ASVs were detected with significant abundance shifts. Key genera, including Vicinamibacter and Bacillus (bacteria), and Bisifusarium and Longitudinalis (fungi), were linked to secondary metabolite production. Functional differences, such as those related to chitinolysis and fermentation pathways, were also observed. Co-occurrence networks revealed correlations between plant genes and microbial communities. Notably, soil parameters, including organic matter, total nitrogen, and soil alkaline phosphatase, were identified as key factors influencing microbial community structure. The rhizosphere microbiome was further associated with nutrient absorption, potentially impacting bioactive compound accumulation. This multi-omics analysis highlights the role of regional and growth-period variations in A. sinensis quality, offering valuable insights for optimizing its cultivation and efficacy across diverse regions.},
}
@article {pmid42153259,
year = {2026},
author = {Katchborian-Neto, A and de Jesus Nicácio, K and Bueno, PCP and Ferreira, MS and Fernandes Alves, M and de Oliveira Silva, D and Dos Santos, WT and de Monroe Gonçalves, M and de Paula, ACC and Dias, DF and Soares, MG and Edrada-Ebel, R and Lago, JHG and Chagas-Paula, DA},
title = {The Metabolome of the Ocotea spp.: From Biosynthetic Aspects to Bioactive Chemical Scaffolds by Integrating the Genus Chemical Database (OcoteaDB).},
journal = {Journal of natural products},
volume = {89},
number = {6},
pages = {1631-1654},
doi = {10.1021/acs.jnatprod.5c01567},
pmid = {42153259},
issn = {1520-6025},
mesh = {*Metabolome ; *Databases, Chemical ; Molecular Structure ; Alkaloids/chemistry ; Terpenes/chemistry/metabolism ; },
abstract = {The genus Ocotea is a significant source of bioactive agents within the Lauraceae, yet it remains underexplored. Despite its ethnomedicinal relevance and chemical diversity, Ocotea species remain taxonomically challenging as they belong to the multifaceted "Ocotea complex", a phylogenetically unresolved group. Moving beyond previous literature Ocotea surveys, this review provides the first curated, genus-specific data set of both volatile and nonvolatile specialized metabolites. Covering research articles from 1830 to 2025, this review provides the most comprehensive synthesis to date, documenting 984 unique chemical compounds across 115 species. This effort culminated in the construction of the Ocotea Chemical Database (OcoteaDB), a novel digital resource created to streamline the genus's chemical diversity for the global scientific community. Furthermore, it presents current knowledge of biosynthetic routes leading to key bioactive scaffolds, including aporphinoid and benzylisoquinoline alkaloids, lignoids, glycosylated flavonoids, and a diverse array of terpenoids, while addressing the stereochemical and structural intricacies unique to the genus. This review lays a robust foundation to drive future Ocotea-focused bioprospecting studies and guides research in the fields of natural products, chemophenetics, metabolomics, and medicinal chemistry regarding the Ocotea species, its chemical scaffolds, and specialized metabolites.},
}
@article {pmid42166742,
year = {2026},
author = {Bowman, GI and Seymour, N and Reynolds, C and Evans, LM},
title = {Development and validation of an electronic health record-based frailty index in the UK Biobank.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {81},
number = {7},
pages = {},
doi = {10.1093/gerona/glag131},
pmid = {42166742},
issn = {1758-535X},
support = {//PetaLibrary and computational analysis was supported by the Blanca and Alpine high performance computing resources at the University of Colorado Boulder/ ; //University of Colorado Boulder, the University of Colorado Anschutz, and Colorado State University/ ; },
mesh = {Humans ; *Electronic Health Records ; Female ; Male ; United Kingdom/epidemiology ; *Frailty/diagnosis/mortality ; Aged ; UK Biobank ; *Geriatric Assessment/methods ; Proportional Hazards Models ; Biological Specimen Banks ; },
abstract = {BACKGROUND: Frailty, an age-related loss of the ability to withstand stressors, is commonly measured using health deficit indices, often using survey or questionnaire data. We aimed to develop an electronic frailty index (eFI) using electronic health record (EHR) data linkages in the UK Biobank and assess its association with mortality.<br><br>METHODS: We calculated an eFI using 43 deficits, each corresponding to phecodes mapped to the United Kingdom (UK) and international classification coding systems. We compared this eFI to a validated 49-item survey-based FI for the UK Biobank (UKB) and assessed associations of the eFI with risk of all-cause mortality (follow-up&#x2009;&#x2264;&#x2009;10.2&#x2009;years) and mortality following a stressor (heart attack or stroke) using Cox proportional hazard models.<br><br>RESULTS: Mean eFI in this cohort (N&#x2009;=&#x2009;208,982) was 0.058 (SD&#x2009;=&#x2009;0.06) and was higher in females than males. A 10% higher baseline frailty was associated with higher risk of all-cause mortality (HR (95% CI)=2.00 (1.93-2.07)), although the magnitude of this association decreased when adjusting for socioeconomic-related covariates (HR (95% CI)=1.44 (1.38-1.51)). Associations were stronger in men than women. Electronic frailty index predicted mortality following both heart attack and stroke (HR (95% CI) = 1.59 (1.25-2.04) and HR&#x2009;=&#x2009;1.33 (1.13-1.57), respectively).<br><br>CONCLUSIONS: This EHR-based eFI has robust associations with mortality, suggesting that it can be used as a valid measure of frailty in the UKB and can potentially be applied to other datasets with EHR data.},
}
@article {pmid42169502,
year = {2026},
author = {Isaacs, KK and Williams, AJ and Phillips, K and Jahne, M and Thimons, S},
title = {A curated geospatial dataset of chemicals used in hydraulic fracturing and their functions.},
journal = {Journal of environmental quality},
volume = {55},
number = {3},
pages = {e70185},
doi = {10.1002/jeq2.70185},
pmid = {42169502},
issn = {1537-2537},
support = {//Oak Ridge Institute for Science and Education/ ; },
mesh = {*Hydraulic Fracking ; *Water Pollutants, Chemical/analysis ; Databases, Factual ; },
abstract = {Produced water (PW) is generated by the oil and gas industry as a byproduct of conventional extraction and hydraulic fracturing (HF) activities. Chemicals used in HF must be evaluated for risk to humans and ecological species when considering the conditions of PW reuse. FracFocus (FF) is a public database of chemicals used in HF where operators of wells report information either voluntarily or as mandated under specific state statutes. However, data reported to FF is standardized in terms of neither chemical identifier nor chemical function. Here, using cheminformatic methods, we develop a curated database of chemicals reported to FF, harmonized to chemical identifiers and function categories used by the US Environmental Protection Agency, facilitating linkage to toxicity and other data in its CompTox Chemicals Dashboard. The resulting dataset of over 5.7 million records reflects 1567 unique chemical substances and 45 unique functions. This dataset provides a resource to risk assessors and environmental programs when evaluating the potential impact of HF chemicals in PW reuse.},
}
@article {pmid42213775,
year = {2026},
author = {Yuan, K and Lian, Y and Huang, P and Cao, F and Yang, X and Lu, Y and Ding, X and Wang, L and Yang, H and Ye, Z and Chen, Q and Fu, J and Yuan, S and Fan, Y and Cai, S and Du, D and Ren, J and Zhang, X and Xu, H},
title = {Integrative analysis reveals intra-tumoral microbial enterotypes shape host transcriptomes in colorectal cancer.},
journal = {Cell reports},
volume = {45},
number = {6},
pages = {117413},
doi = {10.1016/j.celrep.2026.117413},
pmid = {42213775},
issn = {2211-1247},
mesh = {*Colorectal Neoplasms/microbiology/genetics/immunology/pathology ; Humans ; Animals ; *Transcriptome/genetics ; Bacteroides fragilis ; Mice ; *Microbiota/genetics ; Tumor Microenvironment/immunology/genetics ; Multiomics ; Mice, Inbred C57BL ; },
abstract = {The intratumor microbiome and host gene regulation are key contributors to colorectal cancer (CRC), yet their interactions remain unclear. To investigate the interplay between intra-tumoral microbe and host gene, we analyzed paired tumor and normal tissues from 31 patients. Integrated multi-omics analysis identified 4,197 significant bacteria-gene correlation pairs involving 30 bacterial taxa. Patient stratification based on these associations reveals two distinct molecular subgroups characterized by unique microbial signatures and immune profiles. In a mouse model, Bacteroides fragilis alters the tumor immune microenvironment, promoting myeloid-derived suppressor cell (MDSC)-mediated CXCL signaling that impaired CD8[+] T cell activation and promotes exhaustion. B. fragilis directly promotes CXCL2 expression and ROS production in MDSCs, which subsequently drives CD8[+] T cell exhaustion and immune evasion. These findings reveal that intra-tumoral microbiota influence host transcriptomes and immune modulation in CRC, supporting microbiome-based molecular stratification and offering insights into potential microbiota-targeted therapies.},
}
@article {pmid42227660,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Zhang, SR and Lai, JL and Zhang, Y and Luo, XG},
title = {Synergistic Remediation of Organic Arsenicals via an Integrated Plant-Microbe Remediation Platform: A Multiomics Interrogation of Degradation and Detoxification Mechanisms.},
journal = {Environmental science &amp; technology},
volume = {60},
number = {24},
pages = {17366-17381},
doi = {10.1021/acs.est.6c02129},
pmid = {42227660},
issn = {1520-5851},
mesh = {Multiomics ; Biodegradation, Environmental ; *Arsenicals ; Soil Pollutants ; },
abstract = {The organic arsenic compounds diphenylarsonic acid (DPAA) and phenylarsonic acid (PAA) are pervasive and hazardous soil pollutants. To address this, we constructed a remediation system by first screening and combining two functional bacteria: Bacillus subtilis and Bacillus cereus. This synthetic consortium rapidly degraded DPAA and PAA within 24 h, primarily through the cleavage of arsenic-carbon bonds and aromatic rings, facilitated by specific enzymes (ArsI and ring-opening dioxygenase). Concurrently, we employed alfalfa, a plant capable of efficiently absorbing inorganic arsenic released during microbial degradation. This plant-microbe system, tested over 60 days in contaminated soil, successfully removed both organic pollutants and the derived inorganic arsenic. Multiomics analyses confirmed that the remediation process beneficially restructured the soil environment, stimulating microbial activity and key metabolic functions and reducing potential risks like antibiotic resistance genes. This integrated strategy, verified through multiomics to drive beneficial soil ecosystem restructuring, provides a novel and mechanistically informed approach for the sustainable cleanup of complex organoarsenical contamination.},
}
@article {pmid42287835,
year = {2026},
author = {Yu, H and Gao, C and Xu, J and Wu, X and Zhang, J},
title = {Hepatic lipid metabolic dysregulation mediates fluxapyroxad-induced hepatotoxicity: Insights from multi-omics profiling.},
journal = {Ecotoxicology and environmental safety},
volume = {320},
number = {},
pages = {120352},
doi = {10.1016/j.ecoenv.2026.120352},
pmid = {42287835},
issn = {1090-2414},
mesh = {Animals ; Zebrafish/metabolism ; *Lipid Metabolism/drug effects/genetics ; *Liver/drug effects/metabolism/pathology ; Multiomics ; *Fungicides, Industrial/toxicity ; *Water Pollutants, Chemical/toxicity ; *Chemical and Drug Induced Liver Injury/metabolism ; Lipidomics ; Gene Expression Profiling ; },
abstract = {Fluxapyroxad (FLU), a widely used succinate dehydrogenase inhibitor (SDHI) fungicide, can enter aquatic environments and pose potential risks to aquatic organisms. This study investigated the hepatotoxic effects of long-term FLU exposure in adult zebrafish exposed to 0, 30, 60, and 90 μg/L FLU for 28 days. High-dose (90 μg/L) exposure significantly reduced body weight, increased liver weight, and induced hepatic vacuolization and reduced glycogen storage in histological analysis. Transcriptomic analysis of the high-dose group revealed significant upregulation of lipid metabolism-related genes (ldlr, lpin1, apoc2), enriched in PPAR signaling and non-alcoholic fatty liver disease pathways; lipidomic profiling showed widespread lipid alterations (especially phosphatidylcholine species), with glycerophospholipid metabolism as the most affected pathway, and 11 differential lipid species including PC(18:0/16:0) and TG(20:0/14:0/14:0) were identified as candidates. Integrated multi-omics analysis demonstrated that high-dose FLU exposure triggered hepatic lipid metabolic disorders via dysregulated expression of genes involved in lipid synthesis, transport and degradation. These findings reveal the mechanism of FLU-induced hepatotoxicity, and provide reference for identifying FLU-responsive hepatic differential lipids, as well as ecological risk assessment of FLU and related SDHI fungicides in aquatic systems.},
}
@article {pmid42303245,
year = {2026},
author = {Tiao, PH and Chan, HY and Huang, YM},
title = {Navigating Diabetes Management in the Digital Era: Scoping Review of Online Health Information-Seeking Behavior.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e82081},
doi = {10.2196/82081},
pmid = {42303245},
issn = {1438-8871},
mesh = {Humans ; Digital Health ; *Information Seeking Behavior ; *Diabetes Mellitus/therapy ; Digital Media ; *Internet ; },
abstract = {BACKGROUND: Online health information seeking (OHIS) has become a central component of chronic disease management within an increasingly interactive, algorithm-mediated digital ecosystem. For individuals with diabetes, ongoing self-management demands create sustained needs for accessible, actionable health information. Although prior reviews have described general information-seeking behaviors, few have integrated technological evolution, multilevel determinants, and equity considerations specific to diabetes.<br><br>OBJECTIVE: This scoping review maps patterns of OHIS among individuals with diabetes, identifies the types of information sought, synthesizes the multilevel determinants of OHIS, and explores temporal shifts across major phases of digital health development.<br><br>METHODS: This scoping review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) and Preferred Reporting Items for Systematic Reviews and Meta-Analyses literature search extension (PRISMA-S) reporting guidelines and was guided by the Sample, Phenomenon of Interest, Design, Evaluation, Research type framework. Five electronic databases (PubMed, Scopus, Web of Science, CINAHL, and Embase) were systematically searched for English-language empirical studies from inception to May 4, 2026. Eligible studies included empirical research investigating OHIS behaviors among individuals with type 1 diabetes, type 2 diabetes, or gestational diabetes. Data were extracted using a standardized charting form and synthesized descriptively. Determinants were organized according to the Social Ecological Model, and qualitative findings were analyzed using content analysis. Studies were stratified into 3 periods reflecting shifts in digital infrastructure: early web environments (2002-2010), expansion of social media and mobile technologies (2011-2018), and integrated digital and artificial intelligence (AI)-enabled ecosystems (2019-2025).<br><br>RESULTS: Eighty-one studies from 32 countries met the inclusion criteria. The use of digital sources diversified over time. Early studies emphasized search engines and institutional websites, whereas later studies increasingly reported engagement with social media platforms and online communities. Mobile health apps and generative AI chatbots appeared in recent publications, although evidence on AI use remained limited. The most frequently sought content included self-management and lifestyle guidance, general diabetes knowledge, and treatment-related information. Determinants of OHIS operated across multiple levels. At the individual level, younger age, greater educational attainment, higher income, and better eHealth literacy were associated with increased engagement, while psychological factors such as perceived knowledge gaps and a desire for autonomy motivated searching. Interpersonal influences included peer support and clinician communication. Organizational and environmental factors encompassed health care access, digital infrastructure, information quality, and platform characteristics. Persistent disparities were observed among older adults and socioeconomically disadvantaged groups.<br><br>CONCLUSIONS: This review synthesizes OHIS among individuals with diabetes through the lenses of technological evolution, multilevel determinants, and digital health equity. Unlike previous reviews that focused on specific platforms or general information-seeking behaviors, it maps the transition from web-based resources to social media and emerging AI-enabled ecosystems. This temporally informed synthesis advances understanding of digital engagement in diabetes self-management, identifies key evidence gaps, and informs clinical, organizational, and policy strategies to promote equitable access to trustworthy online health information.},
}
@article {pmid42303641,
year = {2026},
author = {Yang, J and Han, S and Li, L and Peng, J and Liu, J and Liu, J and Han, Z},
title = {Study on the mechanical characteristics of the stress relaxation in the carbonate rock after high-temperature acidification.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42303641},
issn = {2045-2322},
support = {52404020//National Natural Science Foundation of China/ ; U1762216//The National Natural Science Foundations of China/ ; 2023ZZ14YJ07//Tarim Oilfield Co., LTD. Phase IV Project/ ; 2025ZD1402405//The National Key Special Project in China/ ; },
abstract = {To elucidate the mechanism by which acidification influences wellbore stability in deep reservoir formations, this study investigates the rheological and mechanical behaviors of the carbonate rock subjected to high-temperature acid etching. A novel experimental system was developed to characterize the stress relaxation behavior of the acid-etched carbonate rock, and the characteristics of the stress relaxation curves under various acid etching conditions and strain levels were systematically analyzed. Combined with Burgers model and the Levenberg-Marquardt algorithm, the evolution of rheological parameters of the carbonate rock under different acid etching regimes was quantitatively evaluated. The results indicate that the acid-etched carbonate rock exhibit significant rheological mechanical properties due to the presence of developed microcracks and complex pore structures. Under the identical acid etching duration and temperature, the initial stress, residual stress, and time required for stress relaxation stabilization all increase with increasing the strain level. Overall, the stress relaxation magnitude prior to the core fracture ranges from 15 to 25 MPa, and the stabilization time for the core stress relaxation falls between 5 and 7 h. The stress relaxation behavior of the acid-etched carbonate core is well described by the Burgers model. At fixed strain levels and temperatures, the instantaneous shear modulus [Formula: see text] decreases linearly with extended acid etching time, whereas the instantaneous shear modulus [Formula: see text] and the viscosity coefficients [Formula: see text] and [Formula: see text] exhibit exponential degradation. The final variation ranges of the key rheological parameters are determined as follows: instantaneous shear modulus [Formula: see text] ranges from 5 × 10[3] to 2 × 10[4] MPa, instantaneous shear modulus [Formula: see text] ranges from 6 × 10[5] to 2 × 10[6] MPa, viscosity coefficient [Formula: see text] ranges from 2 × 10[7] to 8 × 10[7] MPa h, and viscosity coefficient [Formula: see text] ranges from 1 × 10[5] to 1.2 × 10[6] MPa h. Furthermore, the evolutionary equations correlating the global model fitting parameters with the porosity of acid-etched samples are established, using acid etching time as an intermediate variable. The results of this study provide a theoretical basis for the analysis of wellbore stability after acidification and the selection of acid fracturing completion methods of deep reservoirs.},
}
@article {pmid42304410,
year = {2026},
author = {Schmelkin, L and Chung, S and Haldane, A and Townsend, JP and Carnevale, V and Levy, RM and Kumar, S},
title = {Epistasis plays a limited role in driving entrenchment during neutral protein evolution.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-04157-0},
pmid = {42304410},
issn = {1474-760X},
support = {GM132090-04/GM/NIGMS NIH HHS/United States ; GM139540-05/GM/NIGMS NIH HHS/United States ; AI178849//National Institute of Allergy and Infectious Diseases/ ; 1934848//National Science Foundation/ ; },
abstract = {BACKGROUND: Substitutional entrenchment arising from epistatic interactions renders previously acceptable amino-acid states unfavorable over evolutionary time and has often been attributed to novel adaptive processes. However, recent simulations based on Potts-Hamiltonian models have suggested that entrenchment may also emerge during protein evolution governed by the neutral theory of molecular evolution (NTME).<br><br>RESULTS: Here, we re-examine this conclusion by assessing whether substitutions permitted in such simulations are consistent with empirical expectations of NTME. Since Potts models are inferred from a large collection of homologous rather than orthologous sequences, they may allow substitutions that are incompatible with NTME. Our analysis revealed that Potts-based simulations permit amino-acid substitutions whose Hamiltonian energies (PHE, &#x3c6;) often fall outside empirically derived NTME &#x3c6; neighborhoods, thus allowing non-neutral evolution of domain sequences. To prevent such transgressions, we implement simulations that impose purifying selection whenever Potts-acceptable substitutions depart from the NTME &#x3c6; neighborhood. When these substitutions are eliminated, we observed limited substitutional entrenchment, with site-specific amino-acid preferences remaining stable over biologically relevant timescales in neutral protein evolution. We further find that overdispersion of the molecular clock is modest and scales directly with the proportion of evolutionary lineages displaying epistasis-driven among-site rate heterogeneity, independent of entrenchment.<br><br>CONCLUSIONS: These results demonstrate that significant&#xa0;entrenchment is not an inherent property of epistasis during protein evolution consistent with NTME. Our findings establish baseline expectations for neutral evolution with epistasis and suggest that pronounced entrenchment observed in natural protein evolution likely reflects non-neutral evolutionary histories, including adaptation.},
}
@article {pmid42306263,
year = {2026},
author = {Brook, JBH and Salo, T and Luo, AC and Bagautdinova, J and Rush, S and Alexander-Bloch, AF and Baller, EB and Calkins, ME and Cieslak, M and Cooper, EC and Detre, JA and Elliott, MA and Fair, DA and Freedman, P and Gehrman, PR and Gur, RC and Gur, RE and Klein, A and Laney, N and Laumann, TO and Mehta, K and Merikangas, K and Milham, MP and Mitchell, JA and Moore, TM and Nelson, SM and Ruparel, K and Sevchik, BL and Shanmugan, S and Shou, H and Taso, M and White, LK and Wolf, DH and Tisdall, MD and Roalf, DR and Satterthwaite, TD},
title = {An open, fully-processed data resource for studying mood and sleep variability in the developing brain.},
journal = {Aperture neuro},
volume = {6},
number = {SI 1},
pages = {},
pmid = {42306263},
issn = {2957-3963},
abstract = {Brain development during adolescence and early adulthood coincides with shifts in emotion regulation and sleep. Despite this, few existing datasets simultaneously characterize affective dynamics, sleep variation, and multimodal measures of brain development. Here, we describe the study protocol and initial release (n = 10) of an open data resource of neuroimaging paired with densely sampled behavioral measures in adolescents and young adults. All participants complete multi-echo functional MRI, compressed-sensing diffusion MRI, and advanced arterial spin-labeled MRI. Behavioral measures include ecological momentary assessment, actigraphy, extensive cognitive assessments, and detailed clinical phenotyping focused on emotion regulation. Raw and processed data are openly available without a data use agreement and will be regularly updated as accrual continues. Together, this resource will accelerate research on the links between mood, sleep, and brain development.},
}
@article {pmid42306785,
year = {2026},
author = {Broeckhoven, C and Minne, B and Hui, C},
title = {ArmourTraits: A comparative dataset on the ecological and evolutionary correlates of dermal armour in squamates.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {112904},
pmid = {42306785},
issn = {2352-3409},
abstract = {The evolution of defensive traits is a central topic in evolutionary biology, yet quantitative data linking variation in defensive morphology to ecological and environmental factors remain limited. ArmourTraits is a comprehensive dataset that quantifies variation in body armour across 131 species from two distantly related squamate lineages, Cordyliformes and Anguimorpha, which convergently evolved armour in the form of osteoderms. The dataset integrates morphological measurements of osteoderm expression and hindlimb skeletal traits derived from micro-computed tomography scans, species-level ecological, life-history, and environmental data, as well as estimated predation risk and a time-calibrated phylogeny. By providing standardised, quantitative metrics of defensive morphology alongside locomotor traits and associated ecological variables, ArmourTraits enables phylogenetic comparative analyses of ecological correlates, functional trade-offs, convergent evolution, and the diversification of defensive traits across squamates.},
}
@article {pmid42118191,
year = {2026},
author = {Mansingh, A and Pradhan, A and Gopinath, JS and Rout, M and Panda, BP and Ekka, NJ},
title = {Assessing the climatic effects of landscape transformation through long-term temperature trends in an industrial region of eastern India.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {6},
pages = {},
pmid = {42118191},
issn = {1573-2959},
mesh = {India ; *Environmental Monitoring ; *Climate Change ; *Temperature ; Industry ; Forests ; Urbanization ; Geographic Information Systems ; Conservation of Natural Resources ; },
abstract = {Rapid industrial expansion in emerging urban districts is increasingly transforming land systems and modifying local thermal regimes, yet long-term assessments from secondary industrial hubs remain limited. This study evaluates three decades (1993-2023) of land use/land cover (LULC) change and associated land surface temperature (LST) dynamics in Jharsuguda district, eastern India, using multi-temporal Landsat imagery integrated with GIS-based analysis. Six LULC classes were delineated using maximum likelihood supervised classification and validated with ground control points and normalized difference vegetation index (NDVI), yielding overall classification accuracies exceeding 91% (kappa > 0.90). Substantial forest decline was observed, with very dense forest decreasing by 65.47%, moderately dense forest by 26.37%, and open forest by 64.54%. In contrast, built-up area expanded by 317.87%, while non-forest land increased by 21.01%, reflecting accelerated industrialization and urban growth. Concurrently, the pre-monsoon LST range widened from 7-37 °C in 1993 to 16-52 °C in 2023. The proportion of land exceeding 40°C in April increased dramatically from 0 to 59%, indicating intensification of the urban heat island effect. Correlation and random forest analyses demonstrate that forested landscapes exert a significant cooling influence, whereas built-up and non-forest surfaces consistently elevate LST, with seasonal variability in their relative importance. The findings highlight a strong spatial-temporal linkage between industrial expansion, forest degradation, and surface warming. This study provides critical evidence to inform climate-responsive land-use planning, emphasizing urban greening, forest conservation, and nature-based solutions to mitigate heat stress and strengthen regional climate adaptation strategies.},
}
@article {pmid42141314,
year = {2026},
author = {Yang, J and Liao, Z and Li, J and Liu, M and Mao, Y and Yang, G and Liu, L},
title = {Integrative metabolomic and transcriptomic analyses reveal coordinated variation in phenolic acid metabolism and redox-related traits in Ocimum basilicum accessions.},
journal = {Planta},
volume = {263},
number = {6},
pages = {},
pmid = {42141314},
issn = {1432-2048},
support = {2025ZNSFSC0184//Sichuan Provincial Natural Science Foundation General Project/ ; 2023ZYDF076//Mianyang Science and Technology Program/ ; CXTD2023LX01//Innovation Team Project of Mianyang Normal University/ ; QD2023A01//Scientific research initiation project of Mianyang Normal University/ ; },
mesh = {*Ocimum basilicum/genetics/metabolism ; Oxidation-Reduction ; *Hydroxybenzoates/metabolism ; Gene Expression Profiling ; Metabolomics/methods ; Antioxidants/metabolism ; Gene Expression Regulation, Plant ; Transcriptome ; Multiomics ; },
abstract = {This study describes the enzymatic and transcriptional correlates of phenolic acid biosynthesis in Ocimum basilicum, suggesting an association between accession-specific metabolic diversity and differences in redox homeostasis under common‑garden conditions. The metabolic diversity of phenolic acids in Ocimum basilicum contributes to its distinct chemical profiles and potential nutraceutical value, but the transcriptional correlates underlying accession-specific variation remain unclear. This study employed an integrated multi-omics approach combining LC-MS/MS metabolomics, antioxidant enzyme assays, and transcriptome sequencing to profile four O. basilicum accessions (G002, G083, G082, and G122). We identified 292 phenolic acids, with 267 showing differential accumulation based on our screening criteria (VIP > 1 and fold change ≥ 2 or ≤ 0.5, used for metabolite prioritization rather than formal statistical inference). Accessions G002 and G122 exhibited distinct antioxidant profiles, characterized by lower lipid peroxidation (MDA), distinct SOD/POD activities, and elevated levels of specific metabolites including rosmarinic acid methyl ester and 5-O-caffeoylshikimic acid. Transcriptomic analysis revealed that the differential expression of key phenylpropanoid pathway genes (e.g., HCT, C3'H, RAS) is correlated with these distinct metabolic profiles. Correlation and network analyses further suggest an association between variation in phenolic acid accumulation to variations in antioxidant enzyme activities. Additionally, computational prediction suggested that the key differential metabolites are predicted to possess multi-target interactions with proteins relevant to human health, providing a basis for hypothesis generation. Our integrative analysis provides insights into the metabolic plasticity of O. basilicum under basal conditions and highlights specific genetic and metabolic signatures associated with O. basilicum redox homeostasis and phenolic acid diversity. These findings provide a basis for further investigation of metabolic variation among accessions.},
}
@article {pmid42150167,
year = {2026},
author = {Kunas, B and Jung, O and Schranz, C and Schmoigl-Tonis, M and Mehlis, J and Laireiter, AR},
title = {Multimodal Personalized Mobile Health Just-in-Time Adaptive Intervention for Occupational Stress Management: Pilot Study.},
journal = {JMIR mHealth and uHealth},
volume = {14},
number = {},
pages = {e79642},
pmid = {42150167},
issn = {2291-5222},
mesh = {Humans ; Pilot Projects ; *Occupational Stress/psychology/therapy ; Male ; Adult ; Female ; Surveys and Questionnaires ; Mobile Applications/standards/statistics &amp; numerical data ; Telemedicine/standards ; Middle Aged ; Digital Health ; },
abstract = {BACKGROUND: As digital health solutions gain traction, there is an urgent need for effective, person-centered stress management tools for employees. Advances in wearable stress monitoring and machine learning now enable the collection of high-resolution, real-time data and the delivery of personalized interventions with respect to both timing and content. Despite this technological progress, there remains a notable paucity of mobile health (mHealth) interventions that capitalize on these capabilities to implement just-in-time adaptive interventions (JITAIs).<br><br>OBJECTIVE: This pilot study aimed to examine the preliminary effects of the RELAX mHealth app, which uses a JITAI framework to reduce occupational stress, with a particular focus on initial indications of stress reduction, the influence of the app's degree of personalization on these effects, and overall user experience.<br><br>METHODS: A 2-arm randomized trial was conducted with 46 employees across two phases of 3 weeks each. Participants used the RELAX mHealth app, which adapts intervention timing based on real-time stress data and tailors content according to users' preferences. Stress was assessed via multiple heart rate variability (HRV) parameters measured with wearable sensors, alongside subjective questionnaires and ecological momentary assessment (EMA) questionnaires. Usability and user satisfaction were also evaluated. In the second phase, a group randomization was implemented, with two groups of different degrees of in-app personalization.<br><br>RESULTS: The findings were mixed. While selected subjective stress indicators decreased from baseline to the end of the study, one physiological measure increased. Retrospective chronic stress (P=.048) and arousal related to the most recent stress event prior to EMA entry (P=.02) were reduced; however, the low frequency (LF)-to-high frequency (HF) ratio of HRV increased (P=.03). Other stress variables, such as work-related stress, valence of daily experiences, and momentary arousal, showed no change over the course of the study. No between-group differences were observed with respect to the assigned degree of personalization. Additionally, usability increased (P<.001), whereas satisfaction decreased at a trend level (P=.05).<br><br>CONCLUSIONS: Although the results provide selective preliminary indications of stress reduction with app use, the variability of outcomes raises concerns about its current practical utility. The effects are also discussed with regard to the specific design of the prototype and the study setup. Technical issues and user discomfort were noted despite increasing usability over the study period, indicating areas for improvement in the developed prototype. Given the absence of a control group and the use of interventional arms only, no definitive conclusions about effects can be drawn. Nevertheless, this study highlights both the potential and the challenges of a personalized mHealth approach to occupational stress management. Further refinement of the app and more comprehensive evaluations are needed to fully understand the impact and functional usability of this JITAI-based approach in real-world settings.},
}
@article {pmid41980997,
year = {2026},
author = {Liu, M and Huang, Q and Tang, H and Wang, Z and Zheng, W and Wang, Z and Huang, X and Zhang, Y and Wang, Y and Huang, L},
title = {A chromosome-scale nuclear genome and complete mitogenome of the bio-control fungus Cordyceps cateniannulata.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41980997},
issn = {2052-4463},
mesh = {*Cordyceps/genetics ; *Genome, Fungal ; *Genome, Mitochondrial ; Datasets as Topic ; },
abstract = {Cordyceps cateniannulata, a recently characterized entomopathogenic fungus, has been employed in biological control, plant disease management, and growth promotion. In this study, the complete genomic sequences of C. cateniannulata were generated using BGI, PacBio, and Hi-C sequencing platforms. The nuclear genome spans 32.71 Mb, comprising seven pseudochromosomes (chromosome-scale scaffolds) with an N50 length of 4,790,175 bp and a guanine-cytosine content of 53.82%. For the first time, a fully assembled mitochondrial genome of 24,712 bp and a ribosomal DNA tandem repeat sequence of 7,974 bp were obtained. Furthermore, after meticulous annotation and manual refinement of structural features, 10,744 protein-coding genes and 156 non-coding RNAs were identified. This study has produced the high-quality whole-genome map of the C. cateniannulata, offering substantial theoretical significance and application potential for the innovative exploitation of Cordyceps fungal germplasm resources. Additionally, it provides novel perspectives on the evolutionary trajectory, infection strategies, and ecological adaptability of entomopathogenic fungi.},
}
@article {pmid42037368,
year = {2026},
author = {Arango, C and Vieta, E and Fañañás, L and Courtet, P and De Picker, L and Kas, MJH and Kéri, P and Mohr, P and Myin-Germeys, I and Penninx, BWJH and Reif, A and Kuzman, MR and Leboyer, M and Fiorillo, A and Cataln, A},
title = {Precision medicine in mental health: applications, challenges, and recommendations.},
journal = {European psychiatry : the journal of the Association of European Psychiatrists},
volume = {69},
number = {1},
pages = {e53},
pmid = {42037368},
issn = {1778-3585},
mesh = {Humans ; *Precision Medicine/methods ; *Mental Disorders/therapy/diagnosis ; Europe ; Digital Health ; *Psychiatry/methods ; *Mental Health ; },
abstract = {Mental disorders represent a major and growing public health challenge in Europe and worldwide, characterised by marked clinical, biological, and functional heterogeneity, that limits the effectiveness of current diagnostic and therapeutic approaches. In recent years, advances in precision medicine have initiated a paradigm shift in psychiatry, offering new opportunities to improve prevention, prediction, diagnosis, treatment selection, and long-term management by integrating biological, psychological, social, and environmental information.This EPA Guidance Paper provides an overview of the current state of precision medicine in mental health and outlines its potential clinical, scientific, and policy implications. We review key advances in genomics, epigenetics, neuroimaging, transcriptomics, digital technologies, and artificial intelligence, highlighting their relevance across the full clinical pathway, from risk prediction and early detection to treatment personalisation and monitoring. We also examine major barriers to implementation, including limited biomarker validation, insufficient representativeness of research populations, ethical and regulatory challenges, data protection concerns, and inequalities in access across healthcare systems.Based on the available evidence, we propose strategic recommendations to support the responsible and equitable integration of precision approaches into mental health care in Europe. These include strengthening translational research, promoting multidisciplinary collaboration, updating regulatory and ethical frameworks, enhancing professional training, and prioritising mental health within national and European research and health agendas. By addressing these challenges, precision psychiatry has the potential to contribute to more effective, person-centred, and sustainable mental health care, while supporting innovation, reducing stigma, and improving outcomes for patients and society.},
}
@article {pmid42060133,
year = {2026},
author = {Chow, PI and Slipetz, L and Daniel, KE and Sun, S and Henry, T},
title = {Identifying person-level factors to guide digital mental health treatments for cancer survivors: an ecological momentary assessment study.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {34},
number = {5},
pages = {},
pmid = {42060133},
issn = {1433-7339},
mesh = {Humans ; Female ; Ecological Momentary Assessment ; *Cancer Survivors/psychology ; Middle Aged ; Male ; Digital Health ; Adult ; Sleep Duration ; *Neoplasms/psychology ; Aged ; Emotional Regulation ; Interpersonal Relations ; Affect ; Mental Health ; Smartphone ; Pain/epidemiology ; },
abstract = {PURPOSE: The growing population of cancer survivors in the US highlights the need for adaptive digital mental health treatments that can help address a large gap in mental health treatment. Although just-in-time adaptive interventions (JITAIs) hold promise for improving mental health outcomes, none have been developed specifically for cancer survivors, in part due to their complexity. The purpose of this study was to identify survivor-level factors that could inform the development and optimization of adaptive treatments aimed at improving affective outcomes in this population.<br><br>METHODS: A total of 426 adults diagnosed with cancer within the past five years participated in a 5-week observational study. Participants completed smartphone-based surveys three times per day assessing momentary affect, affective forecasting, emotion regulation attempts, social interaction quality, pain, and sleep duration from the previous night. Linear mixed-effects models were conducted at the momentary level to examine associations with positive affect (PA) and negative affect (NA).<br><br>RESULTS: Higher momentary PA was associated with longer sleep duration the previous night, lower pain, fewer emotion regulation attempts, higher-quality social interactions, and forecasting one's future affect as more positive. In contrast, higher momentary NA was associated with shorter sleep duration the previous night, greater pain, more frequent emotion regulation attempts, poorer-quality social interactions, and forecasting one's future affect as more negative.<br><br>CONCLUSION: These findings identify several modifiable meta-emotion and psychosocial factors that may serve as promising targets for future JITAIs designed to improve affective well-being among cancer survivors.},
}
@article {pmid42069381,
year = {2026},
author = {Kuhn, E and Hallenbeck, HW and Owen, JE},
title = {Assessment and Treatment of Posttraumatic Stress Disorder via Digital Mental Health Technology.},
journal = {The Psychiatric clinics of North America},
volume = {49},
number = {2},
pages = {359-375},
doi = {10.1016/j.psc.2025.08.025},
pmid = {42069381},
issn = {1558-3147},
mesh = {Humans ; *Stress Disorders, Post-Traumatic/therapy/diagnosis ; Digital Health ; Mobile Applications ; Telemedicine ; Digital Media ; Virtual Reality Exposure Therapy/methods ; Ecological Momentary Assessment ; },
abstract = {This article presents a review of examples of digital mental health technology (DMHT) for assessing and treating posttraumatic stress disorder (PTSD), including research supporting these innovative solutions. Tools for assessing PTSD are reviewed, including digital administration of self-report measures, ecological momentary assessment methods, personal sensing, electronic medical record and other naturalistic data sources, and emerging digital assessment tools. Next, DMHTs for PTSD treatment are reviewed, including Internet-based interventions, mobile mental health apps, virtual reality therapy, and several emerging digital interventions. DMHT applications for PTSD have demonstrated promise in research and are beginning to be used in clinical practice.},
}
@article {pmid42075636,
year = {2026},
author = {Marano, G and Acanfora, M and Mandracchia, G and Traversi, G and Mazza, O and Pallotti, A and Veneziani, G and Lai, C and Caroppo, E and Mazza, M},
title = {Digital and Immersive Technologies for Rehabilitation in Complex Psychosis: State of the Art and Future Directions.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {4},
pages = {},
pmid = {42075636},
issn = {1648-9144},
mesh = {Humans ; *Psychotic Disorders/rehabilitation/psychology ; Digital Health ; Telemedicine ; Virtual Reality ; },
abstract = {Complex psychosis (CP) remains one of the most challenging conditions in mental health, characterized by persistent symptoms, cognitive impairment, functional disability, and reduced autonomy. Traditional rehabilitation approaches, although essential, are often insufficient to address the multidimensional needs of these individuals. Over the past decade, rapid advances in digital health have opened new opportunities to enhance psychosocial rehabilitation, improve engagement, and personalize treatment pathways. This narrative review synthesizes current evidence on the use of digital and immersive technologies in the rehabilitation of people with CP, including virtual reality (VR), augmented reality (AR), telerehabilitation platforms, mobile health (m-Health) applications, digital phenotyping, and AI-assisted cognitive remediation. We examine clinical trials, feasibility studies, and real-world implementations published between 2015 and 2025, highlighting the efficacy of VR-based social cognition training, remote cognitive remediation, ecological momentary interventions, and hybrid digital-in-person rehabilitation models. Mechanisms of action, transfer to real-world functioning, and predictors of engagement are described. Barriers such as digital literacy, access disparities, privacy concerns, and clinical integration are critically discussed. We also outline future directions, including adaptive algorithms, biosensor integration, and the development of multimodal digital ecosystems tailored to individual recovery trajectories. By integrating technological innovation with recovery-oriented care, digital rehabilitation tools have the potential to transform the treatment landscape for people with CP. This review offers a roadmap for clinicians, researchers, and policymakers seeking to incorporate evidence-based digital solutions into modern psychiatric rehabilitation.},
}
@article {pmid42102286,
year = {2026},
author = {Petit, P and Vuillerme, N},
title = {The Digital Exposome: A Life Course Framework for Health in the Digital Age.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e90153},
pmid = {42102286},
issn = {1438-8871},
mesh = {Humans ; *Exposome ; Digital Health ; *Digital Technology ; Digital Media ; },
abstract = {Digital technologies are reshaping human behavior, health care delivery, and population health; however, their cumulative effects across the lifespan remain underexplored. This viewpoint argues that exposures arising from interactions with digital technologies should be formally integrated into exposome science as a distinct, measurable component of the human environment. Our aims are to (1) redefine the digital component of the exposome (the digital exposome) within the broader exposome framework, (2) examine its life course implications for health and equity, and (3) outline a research and policy agenda to enable its systematic measurement and integration into clinical and public health practice. Digital technology-related exposures can confer benefits such as enhanced health monitoring, personalized interventions, improved access to care, and the promotion of healthy behaviors. However, they may also introduce potential risks, including mental health challenges, cognitive and circadian disruptions, sedentary lifestyles, exposure to misinformation, and widening inequities among vulnerable populations. Despite their ubiquity, digital technology-related exposures remain poorly integrated into clinical medicine, epidemiology, or public and global health policies. Drawing on interdisciplinary evidence from exposure science, epidemiology, and digital phenotyping research, we propose a refined conceptual definition of the digital exposome grounded in the classical exposome domains. We propose redefining the digital exposome as the full spectrum of exposures resulting from interactions or proximities with digital technologies and their combined influence on health across the lifespan. This framework conceptualizes digital technology-related exposures as a dynamic set of environmental influences operating through sociotechnical, behavioral, and biological pathways over the life course. To operationalize this framework, we discuss practical approaches using validated behavioral instruments, objective device use logs, ecological momentary assessments, smartphone-based digital phenotyping, and wearable sensing technologies. Systematic measurement, large-scale longitudinal studies, and harmonized exposure metrics are needed to characterize the cumulative health impacts of digital environments more accurately. Emerging tools such as digital markers or biomarkers and digital phenotypes offer promising opportunities to link real-world technology use with physiological and biological outcomes, thereby supporting precision medicine and population health strategies. Ethical governance, privacy safeguards, and equity considerations must be embedded from the start, drawing on emerging exposomethics frameworks. Recognizing the digital exposome as a modifiable determinant of health offers a foundation for evidence-based guidance, prevention strategies, and policy interventions suited to increasingly digital societies. By integrating digital technology-related exposures into exposome science, clinical practice, and public health research, this viewpoint seeks to foster interdisciplinary dialogue, guide future empirical work, and support the development of safer and more equitable digital environments across the lifespan.},
}
@article {pmid42108299,
year = {2026},
author = {Wang, F and Zhang, H},
title = {Microbial Omics Analysis for Multispecies Symbioses in Staple and Traditional Fermented Foods.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {217-240},
pmid = {42108299},
issn = {1940-6029},
mesh = {*Fermented Foods/microbiology ; *Symbiosis ; Fermentation ; *Food Microbiology/methods ; *Microbiota ; Multiomics ; Vegetables/microbiology ; Humans ; },
abstract = {Fermented foods represent a cornerstone of global culinary traditions, underpinned by intricate microbial communities that drive flavor development and preservation. This chapter examines the microbial ecology and functional interactions across representative staple and traditional fermented foods, including fermented vegetables (sauerkraut, kimchi), fermented condiments (soy sauce, vinegar, miso, doubanjiang), and fermented alcoholic beverages (Chinese baijiu, wine, sake, Huangjiu). Recent meta-omics advances have revealed dynamic community succession, cross-feeding networks, quorum-sensing mechanisms, and key microorganisms contributing to flavor metabolites and health-promoting compounds. Furthermore, synthetic microbial communities and starter engineering are discussed as strategies to standardize fermentation, enhance quality, and develop novel functional products.},
}
@article {pmid41956654,
year = {2026},
author = {Xian, S and Wang, X and Wang, Y and Zhang, W and Liu, X and Shen, G and Zhang, Z and Hou, X and Xu, F and Chen, A},
title = {Flavor remodeling in Paocai during round spontaneous fermentation: an integrative analysis of active microbial succession and metabolic processes.},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 2},
pages = {118973},
doi = {10.1016/j.foodres.2026.118973},
pmid = {41956654},
issn = {1873-7145},
mesh = {*Fermentation ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis ; *Food Microbiology ; *Fermented Foods/microbiology/analysis ; *Taste ; Microbiota ; Multiomics ; Lactiplantibacillus plantarum/metabolism ; },
abstract = {Traditional paocai is a representative Chinese fermented vegetable that is typically produced through successive fermentation cycles. However, the mechanisms underlying flavor differences between paocai fermented in fresh and aged brine during continuous fermentation remain unclear, particularly the dynamic coupling among environmental variation, active microbial communities, and flavor development across fermentation rounds. Here, comprehensive two-dimensional gas chromatography-mass spectrometry and metatranscriptomic analyses were integrated with nonlinear modeling, machine learning, and time-decay relationship analysis to investigate physicochemical evolution, microbial succession, and flavor formation during continuous fermentation of traditional paocai. The results showed that pH, organic acids, and microbial diversity exhibited pronounced nonlinear dynamics across 11 successive fermentation rounds. Random forest analysis identified Phenylethyl alcohol, Hexadecanoic acid, ethyl ester, and Tetradecanoic acid, ethyl ester as key volatile compounds discriminating fermentation rounds. Lactiplantibacillus plantarum and Lactobacillus japonicus were identified as core microorganisms throughout continuous fermentation, while microbial community structures progressively diverged from their initial states, consistent with a significant time-decay relationship. Multi-omics integration using O2PLS further revealed tight and complex cross-omics associations between active microbial taxa and volatile flavor compounds, enabling reconstruction of key flavor-related metabolic pathways during successive fermentation rounds of Sichuan paocai. Comparative metatranscriptomic analyses between fresh and aged paocai clarified the metabolic basis underlying flavor differentiation at later fermentation stages. Overall, this study elucidates flavor evolution in paocai under continuous round fermentation from microbial ecological and metabolic perspectives, providing a theoretical basis for flavor regulation and quality stabilization in traditional fermented foods.},
}
@article {pmid41960380,
year = {2026},
author = {Chen, L and Yao, W},
title = {Fall detection and pre-impact prediction technologies in older adults: a scoping review of translational maturity and public health integration.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1737644},
pmid = {41960380},
issn = {2296-2565},
mesh = {Humans ; *Accidental Falls/prevention &amp; control ; *Wearable Electronic Devices ; *Public Health ; Aged ; Digital Health ; Prediction Algorithms ; },
abstract = {OBJECTIVE: To map the current landscape of wearable and sensor-based fall detection and pre-impact prediction technologies relevant to older adults and to evaluate their translational maturity within public health contexts.<br><br>METHODS: A scoping review was conducted following PRISMA-ScR guidelines. Four electronic databases (PubMed, Web of Science, Scopus, and IEEE Xplore) were systematically searched for studies published between January 2005 and September 2025. Eligible studies reported the development or validation of fall detection or pre-impact prediction systems incorporating wearable, vision-based, environmental, or multimodal sensing modalities. In total, 243 studies were included in the overall synthesis, with a predefined subgroup of 21 studies involving real-world or mixed real-world validation in older adult populations (&#x2265;65&#x202f;years).<br><br>RESULTS: Across the 243 included studies, wearable inertial measurement unit (IMU)-based systems constituted the dominant technological stream, and post-fall detection remained the most frequently investigated functional objective. However, more than half of studies relied primarily on laboratory-based simulated fall protocols. Within the real-world validated older adult subgroup (n&#x202f;=&#x202f;21), 71.4% focused on post-fall detection, 19.0% investigated pre-impact prediction, and 9.5% addressed fall risk modeling. While technical performance metrics such as sensitivity and specificity were frequently reported under controlled conditions, evidence regarding long-term adherence, workflow integration, and health economic impact was limited. A maturity gradient emerged across modalities, with wearable detection systems demonstrating stronger ecological grounding than predictive, multimodal, and ecosystem-level approaches.<br><br>CONCLUSION: Although technological innovation in fall-related sensing systems has expanded rapidly, translational maturity remains uneven. Bridging the gap between algorithmic performance and scalable public health implementation will require robust real-world validation, longitudinal adherence evaluation, implementation science frameworks, and economic assessment. Advancing along a continuum from reactive detection toward predictive and personalized prevention represents a critical pathway for supporting safe and independent aging.},
}
@article {pmid41988563,
year = {2026},
author = {Guo, RL and Sun, Y},
title = {Digital art as a novel medium for health communication: enabling interactive interventions and reconstructing health experiences in public health.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1786916},
pmid = {41988563},
issn = {2296-2565},
mesh = {Humans ; Digital Media ; *Health Communication/methods ; *Public Health ; *Art ; *Health Promotion/methods ; Digital Health ; },
abstract = {This perspective article explores digital art as an innovative medium for health communication. It argues that traditional health communication-often unidirectional and emotionally detached-frequently fails to support lasting behavioral change. In contrast, digital art introduces interactivity, immersive environments, and emotionally resonant narratives, enabling more engaging forms of health messaging and fostering deeper public involvement and awareness. Drawing on social cognitive theory, experiential learning, and media ecology, the article develops a conceptual framework and examines practical strategies such as narrative reconstruction, data visualization, and community-based co-creation. It also addresses key challenges, including issues of access, content accuracy, and ethical use of personal data in artistic health interventions. Looking forward, this perspective calls for stronger interdisciplinary collaboration, supportive policies, and evidence-based research to further integrate digital art into public health practice. By doing so, digital art could contribute meaningfully to more inclusive, participatory, and sustainable approaches to health promotion.},
}
@article {pmid41990036,
year = {2026},
author = {Conejero, I and de Granda-Beltrán, AM and Albarracín-García, L and Porras-Segovia, A and Barrigón, ML and Lopez-Castroman, J and Courtet, P and Artés-Rodriguez, A and Baca-Garcia, E and , },
title = {Impact of age and clinical factors on the feasibility of mobile digital monitoring in people at risk of suicide.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0346772},
pmid = {41990036},
issn = {1932-6203},
mesh = {Humans ; Female ; *Suicide/psychology/statistics &amp; numerical data ; Aged ; *Mobile Applications ; Male ; Middle Aged ; Feasibility Studies ; Age Factors ; *Suicide Prevention ; *Ecological Momentary Assessment ; Smartphone ; Adult ; Risk Factors ; Digital Health ; },
abstract = {OBJECTIVE: Assessing the risk of suicidal outcomes is challenging, particularly in older people. Smartphone-based digital phenotyping may help to monitor suicide risk through ecological momentary assessment (EMA) applications. In this real-world study, we investigated if age and other clinical factors were associated with participation in EMA at baseline, and with retention in EMA monitoring among patients at risk of suicide.<br><br>METHODS: Participation in EMA was determined by quantifying the installation of the MEmind mobile application in individuals involved in the SmartCrisis 1.0 and 2.0 studies. The patients were followed-up over a 6-month period.<br><br>RESULTS: N&#x2009;=&#x2009;512 patients met inclusion criteria, of which 387 installed the MEmind application on their smartphone. While age as a continuous variable was not associated with using EMA at baseline, being aged older than 50 and being engaged in an intimate relationship were independently associated with longer participation in EMA (OR 2.070, 95%CI [1.054-4.066], and OR 2.103, 95%CI [1.076-4.110], respectively). In an exploratory survival analysis, we found that EMA retention increased with age (p&#x2009;<&#x2009;0.001).<br><br>CONCLUSION: Feasibility of EMA seems warranted in older people at risk of suicide. Clinicians should be encouraged to offer EMA monitoring to older adults, as they commonly face limitations in their access to healthcare facilities.},
}
@article {pmid41991939,
year = {2026},
author = {Tang, W and Yin, C and Gao, H and Lu, Z and Lu, Y and Xu, H},
title = {Chromosome level genome assembly of the American sloughgrass (Beckmannia syzigachne).},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41991939},
issn = {2052-4463},
support = {31300873//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Chromosomes, Plant ; *Genome, Plant ; *Poaceae/genetics ; Datasets as Topic ; },
abstract = {American sloughgrass [Beckmannia syzigachne (Steud.) Fernald] is a problematic annual grass weed in winter wheat fields of China, which causes great loss of wheat yield. A lack of high-quality genome resources has hindered understanding of the Herbicide resistance characteristics and ecological adaptations. Here, we combined Illumina short read, PacBio long-read, and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to generate a high-quality, chromosome-scale genome assembly of B. syzigachne. The genome assembly was 3.19 Gb in size, consisting of seven pseudo-chromosomes. The contig and scaffold N50 values were 62.2 Mb and 431.7 Mb, respectively. The genome assembly completeness was estimated at 97.1% by BUSCO assessment. Annotation revealed 36,944 protein-coding genes and 88.83% repeat sequences. This high-quality genome assembly is a valuable resource for future fundamental research and agricultural management of B. syzigachne, and provides significant new insights into the herbicide resistance as well as the adaptive evolution of B. syzigachne.},
}
@article {pmid42008585,
year = {2026},
author = {Kaveladze, BT and Schueller, SM and Mohr, DC},
title = {Popular Online Content as a Treatment-as-Usual Control in Digital Mental Health Intervention Trials: Secondary Analysis of Two Online Randomized Controlled Trials With Repeated Measures.},
journal = {JMIR mental health},
volume = {13},
number = {},
pages = {e83707},
pmid = {42008585},
issn = {2368-7959},
mesh = {Humans ; Digital Media ; Adult ; Secondary Data Analysis ; Female ; Internet ; Randomized Controlled Trials as Topic ; *Depression/therapy ; *Anxiety/therapy ; Mental Health Teletherapy ; Digital Health ; Feasibility Studies ; },
abstract = {BACKGROUND: Treatment-as-usual (TAU) conditions are intended to reflect the support typically received in routine treatment settings. For digital mental health interventions (DMHIs) delivered online, TAU conditions should reflect the usual patterns of online help-seeking. The lack of ecologically valid TAU control conditions has been a gap in effectiveness trials of online DMHIs. In this study, mental health-related popular online content (eg, advice TikToks, lived experience vlogs, and self-care infographics) was examined as a valuable TAU control condition.<br><br>OBJECTIVE: This study examined the feasibility of popular online content as a TAU control condition in DMHI trials.<br><br>METHODS: This study was a secondary analysis of two randomized controlled trials. Both trials recruited participants online, primarily via an online study recruitment platform. In study 1 (N=916), US adults with elevated depression or anxiety were randomized to either (1) complete a single-session DHMI for depression and anxiety (n=291), (2) search the web for popular online content relevant to their struggles (n=312), or (3) search a curated library of mental health-related popular online content (n=313). In study 2 (N=431), US adults with elevated loneliness were randomized to (1) complete a single-session DHMI for loneliness (n=136), (2) search a curated library of popular online content related to loneliness (n=145), or (3) complete an attention-matched control condition (n=150). All 6 programs took approximately 10 to 20 minutes to complete and were entirely self-guided. Participants rated each program's credibility and expected benefit, as well as their feelings of distress (study 1) and loneliness (study 2). The studies did not involve interaction between participants and the research team.<br><br>RESULTS: In study 1, dropout during the treatment was 4.8% (14/291) for the single-session intervention, 25.9% (81/312) for online help-seeking, and 9.6% (30/313) for the curated library. The curated library's credibility and expected benefit score did not differ from that of the single-session intervention (Cohen d=0.08; P=.88) and was higher than that of unguided help-seeking (Cohen d=0.23; P=.01). In study 2, dropout was higher in the curated library condition (7/145, 4.8%) than in the single-session intervention and the attention-matched control condition (0/136, 0.0% and 0/150, 0.0%). The mean credibility and expected benefit score for the curated library was comparable to that of the attention-matched control condition (Cohen d=0.00; P>.99) but lower than that of the single-session intervention (Cohen d=0.32; P=.02). Changes in distress and loneliness from baseline to 8-week follow-up did not differ across the conditions in study 1. All effect sizes were small in study 1 (Cohen d<0.15), and no comparisons were statistically significant (P>.06). Similarly, in study 2, all effect sizes were small (Cohen d<0.12), and no comparisons were statistically significant (P>.25).<br><br>CONCLUSIONS: Curated libraries of popular online content are a feasible, ecologically valid TAU benchmark for effectiveness trials of online DMHIs. Future research on TAU conditions in online help-seeking contexts should better align with observed DMHI attrition rates and account for the increasingly central role of conversational artificial intelligence in online mental health support.},
}
@article {pmid42015346,
year = {2026},
author = {Li, Z and Samui, S and Liu, J and Yang, Y and Liu, X and Chen, Q and Li, J and Gopinath, D and Luo, P and Shan, D},
title = {Gut microbiome and metabolic health: mechanisms and precision interventions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644677},
pmid = {42015346},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Fecal Microbiota Transplantation ; *Metabolic Diseases/microbiology/therapy/metabolism ; Precision Medicine ; Obesity/microbiology/metabolism ; Probiotics/administration &amp; dosage ; Fatty Acids, Volatile/metabolism ; Diabetes Mellitus, Type 2/microbiology/metabolism ; Multiomics ; Prebiotics ; Metabolic Syndrome/microbiology/metabolism ; },
abstract = {The gut microbiome is increasingly recognized as a fundamental regulator of metabolic health, shaping energy balance, insulin sensitivity, inflammatory tone, and inter-organ communication through a broad spectrum of microbial metabolites that engage host signaling pathways. In this review, we synthesize current mechanistic insights into how gut microbial communities shape metabolic function, with particular emphasis on short-chain fatty acids, secondary bile acid signaling, gut barrier integrity, immune modulation, and the microbiota-gut-brain-pancreas axis. We further summarize disease-associated alterations in microbial composition and function across obesity, type 2 diabetes, metabolic dysfunction-associated steatotic liver disease, and metabolic syndrome, highlighting key microbial and metabolic features that contribute to metabolic dysfunction. Evidence from germ-free models, fecal microbiota transplantation studies, and strain-level interventions suggests that shifts in microbial ecology may causally shape metabolic outcomes. We also critically evaluate emerging microbiome-centered therapeutic strategies, including targeted probiotics, prebiotics, dietary modulation, and fecal microbiota transplantation, while addressing factors that underlie inter-individual variability in treatment responses. In addition, we discuss the growing influence of multi-omics technologies, microbial metabolic modeling, and machine learning approaches in advancing precision microbiome medicine. To integrate these advances within a coherent framework, we outline a precision microbiome intervention pipeline linking multidimensional profiling to functional stratification and targeted therapeutic design. We also introduce a conceptual Precision Microbiome Intervention Triangle to mechanistically explain heterogeneity in responses to microbiome-targeted therapies. Collectively, these insights establish and position the gut microbiome as both a mechanistic driver and a modifiable therapeutic target in metabolic disease, and highlight key challenges and future directions for the development of personalized microbiome-based metabolic interventions.},
}
@article {pmid42025075,
year = {2026},
author = {Liang, Y and Shi, J and Cheng, X and Feng, M and Jiao, D and Du, X and Ji, K and Hu, S and Dong, Q and Yang, G},
title = {Integrative transcriptomics and metabolomics analyses reveal changes in meat quality and muscle lipid metabolism in sheep supplemented with rumen-protected glucose.},
journal = {Meat science},
volume = {238},
number = {},
pages = {110110},
doi = {10.1016/j.meatsci.2026.110110},
pmid = {42025075},
issn = {1873-4138},
mesh = {Animals ; *Lipid Metabolism/drug effects ; *Glucose/administration &amp; dosage ; Muscle, Skeletal/metabolism ; Dietary Supplements ; Sheep, Domestic/growth &amp; development/metabolism ; Diet/veterinary ; Animal Feed/analysis ; Metabolomics ; Transcriptome ; Rumen ; *Red Meat/analysis ; Gene Expression Profiling ; Multiomics ; Sheep ; Male ; Oxidative Stress ; Malondialdehyde/blood ; },
abstract = {The effects of dietary rumen-protected glucose (RPG) supplementation on Dumengsa sheep growth performance, meat quality, and transcriptomic and metabolomic profiling are reported. Twelve sheep were randomly assigned to a control (basal diet, n = 6) or RPG (basal diet +1.0% RPG, n = 6) group for 100 d. RPG increased serum malondialdehyde (P = 0.015) and cholesterol (P = 0.046) concentrations, enhanced intramuscular fat content (P = 0.016), and tended to produce lower meat lightness (P = 0.072), redness (P = 0.053), and hue angle (P = 0.072) values. In total, 319 differentially expressed genes and 30 differentially abundant metabolites were identified. Transcriptomic analysis revealed RPG to alter the expression of genes related to oxidative phosphorylation, β-oxidation, and fat deposition. Metabolomic analysis revealed that RPG supplementation primarily increases the abundance of short-chain fatty acids. Integrated analysis using a Data Integration Analysis for Biomarker discovery using Latent Components (DIABLO) model revealed a strong and significant correlation (r = 0.93) between omics profiles. We report dietary supplementation with 1% RPG to modulate muscle lipid metabolism and potentially stimulate intramuscular fat deposition, but also to possibly induce a state of potential oxidative stress.},
}
@article {pmid42034665,
year = {2026},
author = {Sato, Y},
title = {RuSpacer: a CRISPR spacer database derived from ruminant-associated prokaryotes for virome analysis.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42034665},
issn = {2045-2322},
support = {25K18347//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Ruminants/virology/microbiology ; Rumen/microbiology/virology ; *Virome/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; *Prokaryotic Cells/virology ; *Databases, Genetic ; },
abstract = {Microorganisms in the ruminant gastrointestinal tract play key roles in lignocellulose degradation and energy conversion. Prokaryote-infecting viruses play a pivotal role in shaping host abundance and metabolism. Despite their importance, host-virus prediction in this environment remains limited, partly due to the lack of specialized clustered regularly interspaced short palindromic repeat spacer datasets. Here, RuSpacer, a database of 181,023 clustered regularly interspaced short palindromic repeat spacers extracted primarily from publicly available rumen-associated prokaryotic genomes, was established. Each spacer is annotated with the taxonomic identity of the genome from which it was derived. RuSpacer enables host-virus prediction via spacer-protospacer matching, particularly in the rumen ecosystem. It can also be integrated with existing publicly available spacer datasets and used for host-virus prediction in environments other than the rumen. Overall, this resource supports research on host-virus interactions, microbial ecology, and virus-based biocontrol strategies in livestock and other complex microbiomes.},
}
@article {pmid42036564,
year = {2026},
author = {Shin, D and Kim, YK},
title = {Ecological Momentary Assessment and Voice-Informed Forecast and Detection for the Diagnosis of Major Depression.},
journal = {Advances in experimental medicine and biology},
volume = {1502},
number = {},
pages = {95-109},
pmid = {42036564},
issn = {0065-2598},
mesh = {Humans ; *Major Depressive Disorder/diagnosis/psychology/physiopathology ; *Ecological Momentary Assessment ; Digital Health ; *Voice/physiology ; Predictive Value of Tests ; },
abstract = {Major depressive disorder (MDD) is a prevalent and disabling mental health condition traditionally diagnosed through subjective clinical interviews and retrospective self-reports, methods that are limited by recall biases and diagnostic heterogeneity. To address these limitations, ecological momentary assessment (EMA) and voice-based analysis have emerged as innovative diagnostic and monitoring tools. EMA captures real-time, context-rich data in naturalistic settings, providing nuanced insights into the dynamics of depressive symptoms, daily stressors, and coping strategies. Voice analysis leverages quantitative acoustic and linguistic biomarkers, reflecting underlying neurophysiological and psychomotor changes characteristic of depressive episodes. Integrating these technologies offers objective, scalable, and real-time approaches to enhance diagnostic accuracy, personalize interventions, and facilitate continuous patient monitoring. Nevertheless, practical challenges, including technological accessibility, participant adherence, data interpretation complexities, ethical concerns, and the necessity for robust validation, remain critical barriers. Future research directions highlight the need for digital phenotyping strategies using big data analytics to redefine depressive disorders beyond conventional DSM frameworks, ultimately paving the way for precision psychiatry.},
}
@article {pmid42041254,
year = {2026},
author = {Wang, M and Yang, J and Hu, T and Lin, Z and Wang, T and Liu, Z and Chen, X and Fan, X},
title = {Probing the genomic and proteomic basis of encystment in Oxytricha granulifera.},
journal = {mSystems},
volume = {11},
number = {5},
pages = {e0175725},
pmid = {42041254},
issn = {2379-5077},
support = {32570525, 32170446, 32270512//National Natural Science Foundation of China/ ; },
mesh = {*Proteomics/methods ; Multiomics ; *Protozoan Proteins/genetics/metabolism ; *Genomics/methods ; Transcriptome ; *Proteome ; *Genome, Protozoan ; },
abstract = {Protozoan encystment constitutes a pivotal survival strategy against environmental stressors; however, the molecular architecture governing this transition remains enigmatic, owing to limited genomic resources and a scarcity of integrated multi-omics investigations. Here, we elucidate the mechanisms underlying encystment in Oxytricha granulifera by reporting the first macronuclear genome assembly and conducting a comprehensive integration of transcriptomic, proteomic, and morphological analyses across vegetative and cyst stages. Morphological restructuring, typified by ciliary dedifferentiation and cyst wall formation, is molecularly supported by the downregulation of microtubule dynamics-associated genes and the concurrent upregulation of vesicle transport machinery. Furthermore, expanded gene families linked to carbohydrate metabolism and cellular acidification coincide with observed autophagic clearance and mucocyst activity, highlighting a coordinated metabolic shift essential for cyst formation. Elevated expression of the ubiquitin-proteasome system and autophagy pathways, which mediate protein turnover, along with upregulation of antioxidant enzyme genes, contributes to alleviating oxidative damage. Notably, we identified rewired post-transcriptional regulation that increases spliceosome activity and alternative splicing frequency, with each trend validated at the protein level. Concurrently, we observed a distinct epigenetic signature characterized by the significant downregulation of DNA N[6]-adenine methylation (6mA) methyltransferases (homologs of AMT1 and AMT6/7), suggesting a potential repressive role of methylation during the cyst stage. Collectively, these findings provide a multidimensional atlas of the encystment process, revealing that O. granulifera accomplishes cellular structural remodeling through a multilayered regulatory network spanning morphological, genetic, transcriptomic, and proteomic levels.IMPORTANCEOxytricha species are widely distributed in freshwater and terrestrial ecosystems, playing significant ecological roles in microbial communities. Their ability to undergo encystment provides a powerful model for studying cellular differentiation and stress adaptation in microbial eukaryotes. This study presents the first multi-omics analysis of encystment in Oxytricha granulifera, revealing microbial survival strategies through enhanced protein turnover, autophagy, alternative splicing, and DNA methylation reprogramming. These findings offer fundamental insights into dormancy mechanisms and environmental adaptation in protists, advancing our understanding of microbial resilience, evolutionary innovation, and ecological success in fluctuating environments.},
}
@article {pmid42044372,
year = {2026},
author = {Lin, YP and Lu, SH and Lee, KC and Ma, WF and Ho, YF and Liao, WC and Yang, HT and Hong, O},
title = {Short-Term Effects of an mHealth Intervention on Healthy Behaviors and Cardiometabolic Health in Sedentary Employees: Quasi-Experimental Study.},
journal = {JMIR mHealth and uHealth},
volume = {14},
number = {},
pages = {e70074},
pmid = {42044372},
issn = {2291-5222},
mesh = {Humans ; Female ; Male ; Middle Aged ; *Sedentary Behavior ; Taiwan ; Adult ; *Health Behavior ; Digital Health ; Telemedicine/standards/statistics &amp; numerical data ; Health Promotion/methods/standards/statistics &amp; numerical data ; Surveys and Questionnaires ; Exercise/psychology ; },
abstract = {BACKGROUND: Sedentary employees face increased chronic health risks due to physical inactivity, immobility, and unhealthy eating behavior. Although mobile health (mHealth) interventions show promise in improving lifestyle behaviors, their effectiveness in occupational settings remains underexplored. Building on previous workplace interventions, this study developed and evaluated a mobile-enabled web app, SIMPLE HEALTH, developed with Din-J Design Co, Ltd, integrating activity tracking, healthy eating, and behavioral support for sedentary employees.<br><br>OBJECTIVE: This study evaluated the short-term effects of a 12-week mHealth intervention on physical activity, sedentary behavior, dietary habits, and cardiometabolic health indicators among sedentary employees in Taiwan.<br><br>METHODS: A 2-arm quasi-experimental study was conducted at 2 aerospace industrial workplaces. A total of 101 sedentary employees (mean age 46.9, SD 12.2 years; 52/101, 51.5% female) were enrolled from 2 worksites that were assigned by coin toss to either the intervention condition (n=50) or the control condition (n=51). The intervention group participated in the SIMPLE HEALTH program, an mHealth intervention grounded in Social Cognitive Theory and the Ecological Model, consisting of 8 components: activity tracking, goal setting, behavior logging, reminders, personalized advice, educational and motivational electronic booklets, and individual and team challenges. The control group received 6 print educational booklets. Cardiometabolic biomarkers, objectively measured physical activity (Fitbit Charge 3; Fitbit Inc), occupational sitting (occupational sitting and physical activity questionnaire), and dietary behavior (3-day photographic food records and the healthy eating behavior inventory) were assessed at baseline and 12 weeks. Data were analyzed using generalized estimating equations following the intention-to-treat principle.<br><br>RESULTS: At 12 weeks, the intervention group showed a significant increase in step counts (adjusted mean difference, MD 1227.13, 95% CI 2.90-2451.36; P=.049), a more favorable between-group change in moderate physical activity (adjusted MD 0.17, 95% CI 0.01-0.33; P=.04), and favorable dietary behaviors, including reduced intake of calories (adjusted MD -144.59, 95% CI -276.57 to -12.60; P=.03), carbohydrates (adjusted MD -19.88, 95% CI -37.99 to -1.78; P=.03), fats (adjusted MD -6.99, 95% CI -13.69 to -0.29; P=.04), and grains (adjusted MD -1.46, 95% CI -2.43 to -0.50; P=.003), and increased vegetable intake (adjusted MD 0.47, 95% CI 0.06-0.88; P=.02), compared to the control group. Favorable trends were noted in diastolic blood pressure (adjusted MD -2.38, 95% CI -4.99 to 0.22; P=.07) and soft lean mass (adjusted MD 0.34, 95% CI -0.06 to 0.75; P=.10). Both groups showed significant within-group improvements in low-density lipoprotein cholesterol (intervention: P=.01; control: P=.03), body fat percentage (intervention: P<.001; control: P=.01), waist circumference (intervention: P=.001; control: P=.002), and occupational sitting (intervention: P<.001; control: P=.03), and occupational walking (intervention: P=.01; control: P=.046), but between-group differences were nonsignificant.<br><br>CONCLUSIONS: The 12-week mHealth intervention improved physical activity and dietary behaviors and showed favorable trends in cardiometabolic indicators among sedentary employees. These findings support integrating mHealth programs into employee wellness initiatives to promote healthy behaviors, mitigate productivity loss, and reduce chronic disease burden. Further research should assess long-term sustainability, scalability, and cost-effectiveness in diverse occupational settings.},
}
@article {pmid42047208,
year = {2026},
author = {Xu, L and Zhu, H and Jiang, S and Zheng, Q and Yu, C},
title = {Effects of IT-enabled entrepreneurship on gender equality in a digital economy: Evidence from Qualitative Studies.},
journal = {African journal of reproductive health},
volume = {30},
number = {8},
pages = {85-101},
doi = {10.29063/ajrh2026/v30i8.9},
pmid = {42047208},
issn = {1118-4841},
mesh = {Humans ; *Entrepreneurship ; Female ; *Gender Equity ; Qualitative Research ; China ; *Women's Health ; Empowerment ; Grounded Theory ; Interviews as Topic ; Digital Health ; },
abstract = {Persistent digital divides and gendered health inequalities constrain women's participation in the digital economy, even in highly connected contexts like China. This study develops an explanatory framework for how information-technology-enabled entrepreneurship (ITEE) affects women's economic security, health, and capabilities. Using a constructivist grounded theory approach based on 80 interviews in China, the analysis reveals four themes. Capability formation shows how increased income and flexibility allow women to invest in health. Algorithmic exposure highlights the dual nature of platform visibility, boosting sales but also enabling harassment and anxiety. Care negotiation examines how unpaid care duties and infrastructure impact sustainability, showcasing adaptive strategies. Trajectory configuration integrates these into differentiated pathways, from vulnerable to healthenhancing, depending on aligned support. The findings position health centrally in digital capability and link platform governance and care ecologies to sustainable empowerment, suggesting safe platforms, caring support, and integrated policies are essential for women's wellbeing.},
}
@article {pmid42048645,
year = {2026},
author = {Hou, J and Zhang, Z and Cheng, X and Wang, W},
title = {Patient Concerns Regarding Artificial Intelligence Applications in Health Care: Systematic Review and Meta-Synthesis Based on Social Ecological Theory.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e85663},
pmid = {42048645},
issn = {1438-8871},
mesh = {Humans ; *Artificial Intelligence ; *Delivery of Health Care ; Digital Health ; },
abstract = {BACKGROUND: The use of artificial intelligence (AI) in health care is growing quickly, but there is not enough research that looks at patient concerns from a multilevel perspective. Existing reviews predominantly summarize patient attitudes descriptively, lacking theoretical frameworks to explain the underlying mechanisms of these concerns.<br><br>OBJECTIVE: This systematic review and meta-synthesis aimed to identify and analyze patient concerns regarding health care AI applications, using social ecological theory to reveal the multilevel interactive mechanisms of concern at the individual, interpersonal, organizational, and societal levels.<br><br>METHODS: Following the PRISMA-S (Preferred Reporting Items for Systematic Reviews and Meta-Analyses literature search extension) guidelines, databases including PubMed, Embase, Web of Science, CINAHL, and Scopus were searched on March 1, 2026. Qualitative studies exploring patient perceptions of clinical AI applications were included, excluding those involving only healthy populations, technical performance, or nonclinical settings. Two researchers independently screened the literature and assessed methodological quality using the JBI-QARI (Joanna Briggs Institute Qualitative Assessment and Review Instrument) checklist. Confidence in synthesized findings was assessed using the GRADE-CERQual (Confidence in the Evidence from Reviews of Qualitative Research) approach.<br><br>RESULTS: A total of 25 qualitative studies involving 528 participants from diverse patient groups across multiple countries were included. Six themes emerged: (1) microlevel worries about privacy and data security, including data breaches and loss of control over personal health information; (2) worries about the limits and reliability of technology, especially AI diagnostic accuracy and "black box" decision-making; (3) mesolevel effects on physician-patient relationships, including reduced face-to-face interaction and empathy; (4) trust and accountability issues, including unclear responsibility attribution and institutional oversight problems; (5) macrolevel ethical and equity issues, including algorithmic bias and health care access inequalities; and (6) worries about technology diffusion and possible replacement of health care workers.<br><br>CONCLUSIONS: This review represents the first meta-synthesis applying social ecological theory to construct patient concerns regarding medical AI. Unlike previous descriptive reviews, it reveals the interconnected "ecological imbalance" mechanisms at micro-, meso-, and macrolevels when AI is embedded in health care systems. The findings suggest that many patient concerns are based on facts rather than just misunderstandings, indicating that systemic rather than isolated interventions are needed. Practical implications include explainable algorithm design at the microlevel, improved physician-patient communication, and institutional accountability at the mesolevel, and coordinated global ethical norms and equity-promoting policies at the macrolevel. Limitations include the inclusion of studies primarily from developed regions, significant heterogeneity in AI application scenarios, and constraints inherent to secondary research. Nevertheless, addressing these multilevel concerns remains crucial for balancing technological advancement with patient-centered care and enabling sustainable AI integration.},
}
@article {pmid42143584,
year = {2026},
author = {Lv, Y and Li, A and Gu, X and Hu, J and Wen, S and Xu, S and Deng, Y and Chen, D and He, X},
title = {Integrative omics analyses of ectomycorrhizal fungi modulate root growth and defense for mitigating aluminum toxicity in Pinus massoniana.},
journal = {Tree physiology},
volume = {46},
number = {6},
pages = {},
doi = {10.1093/treephys/tpag065},
pmid = {42143584},
issn = {1758-4469},
support = {NSFC 32171753//National Natural Science Foundation of China/ ; },
mesh = {*Mycorrhizae/physiology ; *Aluminum/toxicity ; *Pinus/microbiology/growth &amp; development/drug effects/metabolism/physiology ; *Plant Roots/growth &amp; development/microbiology/drug effects ; Stress, Physiological ; Multiomics ; *Basidiomycota/physiology ; Transcriptome ; },
abstract = {Aluminum (Al) toxicity is a critical environmental factor limiting plant productivity in acidic soils. Some ectomycorrhizal fungi (ECMF) can mitigate Al-induced stress and promote root growth in Pinus massoniana Lamb., however the underlying molecular and metabolic mechanisms have not yet been fully elucidated. In this study, P. massoniana seedlings inoculated with Lactarius deliciosus (L.) Gray (Ld) were subjected to acidic Al stress (pH 3.8) at Al3+ concentrations of 0.0 and 1.0 mM. Root growth, transcriptomic, metabolic and hormonal characteristics of the mycorrhizal symbionts were determined and analyzed. The study aimed to identify the key metabolites and metabolic pathways involved in ECMF-enhanced Al stress tolerance of P. massoniana, and to further elucidate on the underlying mechanism of ECMF in improving the Al resistance of P. massoniana from molecular and metabolic-physiological perspectives. Results showed that Ld inoculation significantly enhanced Al tolerance and promoted root growth and branching in P. massoniana. Specifically, it activated the phenylpropanoid-lignin biosynthesis pathway in mycorrhizal symbionts, downregulated carbon metabolism pathways and reduced intracellular accumulation of citric acid and specific amino acids (L-proline, L-threonine, serine). Furthermore, Ld elevated salicylic acid and gibberellin levels, decreased jasmonic acid content, upregulated growth-promoting genes (MYC2, GH3, TCH4) and downregulated inhibitory genes (ARF9/19, DELLA). This study further refines and clarifies the mechanism underlying ECMF-enhanced Al resistance in P. massoniana, and provides a theoretical basis for the application of ECMF in the ecological restoration of P. massoniana forest areas affected by Al toxicity.},
}
@article {pmid42284363,
year = {2026},
author = {Utkarsh, K and Shah, NR and Banerjee, T and Abrams, DM},
title = {A new method for augmenting short time series, with application to pain events in sickle cell disease.},
journal = {PLoS computational biology},
volume = {22},
number = {6},
pages = {e1014389},
doi = {10.1371/journal.pcbi.1014389},
pmid = {42284363},
issn = {1553-7358},
mesh = {*Anemia, Sickle Cell/physiopathology/complications ; Humans ; *Pain/physiopathology/etiology ; Computational Biology/methods ; Reproducibility of Results ; Algorithms ; Pain Measurement/methods ; },
abstract = {Researchers across different fields, including but not limited to ecology, biology, and healthcare, often face the challenge of sparse data. Such sparsity can lead to uncertainties, estimation difficulties, and potential biases in modeling. Here we introduce a novel data augmentation method that combines multiple sparse time series datasets when they share similar statistical properties, thereby improving parameter estimation and model selection reliability. We demonstrate the effectiveness of this approach through validation studies comparing Hawkes and Poisson processes, followed by application to subjective pain dynamics in patients with sickle cell disease (SCD), a condition affecting millions worldwide, particularly those of African, Mediterranean, Middle Eastern, and Indian descent.},
}
@article {pmid42302574,
year = {2026},
author = {Castro Avila, A and Cookson, R and Kontopantelis, E and Doran, T},
title = {Socioeconomic inequalities in causes of death related to behavioural risk-taking in England and Wales: A longitudinal small-area ecological study.},
journal = {Public health},
volume = {257},
number = {},
pages = {106382},
doi = {10.1016/j.puhe.2026.106382},
pmid = {42302574},
issn = {1476-5616},
abstract = {OBJECTIVES: We examined socioeconomic trends in behavioural risk-taking deaths (BRDs) before and after the 2008-09 recession at the small area level.<br><br>STUDY DESIGN: Longitudinal ecological study METHODS: We analysed death registration data for behavioural risk-taking causes (suicide, drug-related, alcohol-related, accidental, and tobacco-related) in England and Wales from 2001 to 2021&#xa0;at the small areas (population 5,000-8,000) level, aggregated into area deprivation quintiles. Age and sex standardised mortality rates were calculated using annual population estimates. We used a multilevel random-slopes negative binomial segmented regression with interruptions in 2009 and 2011 to estimate the association between mortality rates and the recession.<br><br>RESULTS: There were over 6.5 million BRDs between 2001 and 2021 (92.4% tobacco-related). Mortality rates were higher among men, in more deprived areas, and in northern regions. The pre-recession declines in tobacco-related mortality slowed after 2011, especially outside London and in more deprived areas. For non-tobacco-related BRDs, mortality rates increased in the post-recession period, but patterns varied by cause and place, with the greatest increases for accidental and drug-related deaths and in deprived areas outside London. Had pre-recession trends continued, there would have been 247,093 (95% CI: 239,942-254,243) fewer tobacco-related deaths and 12,585 (95% CI: 10,510-14,661) fewer non-tobacco-related BRDs between 2011 and 2021.<br><br>CONCLUSIONS: Socioeconomic inequalities in behavioural risk-taking deaths in England and Wales were stable prior to the 2008-09 recession but widened after 2011 for specific causes, especially outside London.},
}
@article {pmid41874421,
year = {2026},
author = {Wang, J and Lu, L and Sun, Y and Messer, LF and Wu, M and Duan, Z and Shi, J and Yang, Y and Li, C and Mao, Y and Zhu, D and Rillig, MC and Wang, X},
title = {AHL-mediated quorum sensing drives plastisphere formation and elevates pathogenic potential.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {41874421},
issn = {1751-7370},
support = {2024YFD1700702//National Key Research and Development Program of China/ ; U24A20634//National Natural Science Foundation of China/ ; 42377381//National Natural Science Foundation of China/ ; U21A2038//National Natural Science Foundation of China/ ; //2115 Talent Development Program of China Agricultural University/ ; //Alexander von Humboldt Foundation/ ; },
mesh = {*Quorum Sensing/genetics ; *Acyl-Butyrolactones/metabolism/pharmacology ; *Biofilms/growth &amp; development ; Gene Expression Regulation, Bacterial ; *Plastics ; Multiomics ; Virulence ; },
abstract = {The biofilm colonizing plastic debris, termed "the plastisphere," is of growing global concern due to escalating plastic pollution. However, the biological mechanisms underpinning plastisphere formation remain poorly understood. Here, we analyzed public global metagenomes, revealing a significant enrichment of genes associated with quorum sensing (QS) and biofilm formation, with a pronounced signal for acyl-homoserine lactone (AHL) QS. Using controlled microfluidic and tubular column experiments, we further demonstrate that exogenous AHL actively promotes plastisphere formation, biomass accumulation, and extracellular polymeric substance production on microplastics, whereas a quorum-quenching agent (AHL acylase) effectively inhibits these processes. Multi-omics analyses revealed that AHLs can transcriptionally activate genes involved in adhesion, motility, chemotaxis, and matrix production, fundamentally reshaping community structure, restructuring inferred microbial interaction networks, and driving community assembly toward stronger deterministic selection. AHL stimulation also increased the relative abundance and expression of pathogen-associated and virulence-related functions, suggesting an elevated virulence potential within the plastisphere under QS-promoting conditions. Together, our findings establish AHL-mediated QS as a central driver of plastisphere assembly and a key determinant of risk profile, highlighting its critical role in understanding and potentially mitigating the growing environmental and health hazards associated with microplastic pollution.},
}
@article {pmid41877492,
year = {2026},
author = {Dumas, A and Hokayem, J and Goodman, G and Venkatasubramanian, K and Chai, P},
title = {Smartphone-Based Digital Phenotyping Across Health Conditions: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e84146},
pmid = {41877492},
issn = {1438-8871},
mesh = {*Smartphone ; Humans ; Digital Health ; *Phenotype ; Mental Health ; },
abstract = {BACKGROUND: Smartphone-based digital phenotyping uses built-in sensors and usage patterns to passively capture behavioral and environmental data relevant to health and has been applied extensively in mental health and chronic disease contexts.<br><br>OBJECTIVE: This review synthesizes studies that use smartphone-based digital phenotyping, defined as approaches that rely exclusively on onboard smartphone sensors to characterize specific health conditions. To our knowledge, this work provides the most comprehensive cross-condition synthesis of smartphone-based digital phenotyping to date, spanning mental health, physical health, and substance use disorders (SUDs), and highlighting common practices, gaps, and opportunities for future research.<br><br>METHODS: We conducted a scoping review of English-language, peer-reviewed papers published between 2012 and 2025 in Google Scholar, IEEE Xplore, ACM Digital Library, and PubMed using terms such as "mobile sensing" and "digital phenotyping." Eligible papers used onboard smartphone sensors to assess health and went beyond self-report. Studies that did not rely on smartphone auxiliary sensing modalities or digital phenotyping were excluded.<br><br>RESULTS: We performed a descriptive synthesis of study characteristics, sensors, and health domains. Of 111 papers identified, 65 met inclusion criteria. Most studies were observational and relied on passive sensing. Sample sizes ranged from fewer than 10 to over 18,000 participants, with a median of 52 (IQR=26-126). Mental health conditions were most frequently examined, including depression (n=16), bipolar disorder (n=11), stress or anxiety (n=10), and schizophrenia (n=8). Less commonly studied conditions included SUDs (n=7), Parkinson disease (n=4), and sleep apnea (n=2). Sensor streams varied widely and included diverse passive smartphone data sources capturing mobility, communication, device usage, environmental context, and user interaction patterns. Ground-truth measurements most commonly relied on validated clinical scales (eg, Patient Health Questionnaire-9, Young Mania Rating Scale [YMRS], and Pittsburgh Sleep Quality Index; n=41), followed by ecological momentary assessments (n=18), clinician-confirmed diagnoses (n=9), and physiological measures such as polysomnography (n=3). Across studies, recurring methodological limitations included incomplete or inconsistent sensor descriptions, limited reporting of data quality (eg, sampling rates and missingness), and heterogeneous validation practices. These issues limit comparability and reproducibility and underscore the need for clearer reporting standards and greater data availability.<br><br>CONCLUSIONS: This scoping review provides the first comprehensive synthesis of smartphone-only digital phenotyping studies spanning mental health, physical health, and SUDs. Unlike prior reviews, this work maps behavioral associations derived exclusively from smartphone sensors across a broad range of health domains. The primary contribution of this review lies in its consolidation of behavioral associations observed across studies, enabling researchers to correlate new findings to the existing evidence base and identify opportunities for replication, extension, or clinical translation. Collectively, these findings highlight both the promise of smartphone-based digital phenotyping in real-world settings and the need for improved standardization to support translation into clinical and public health applications.},
}
@article {pmid41904758,
year = {2026},
author = {Gopakumar, L and Parambil, JN and Joseph, A},
title = {Biomonitoring and GIS-based spatial modelling for soil ecosystem health in rural home garden agroecosystems in Chengamanad, Kerala, India.},
journal = {Environmental science and pollution research international},
volume = {33},
number = {13},
pages = {6068-6083},
pmid = {41904758},
issn = {1614-7499},
support = {Grant No. F.15-6(DEC 2013)/2014(NET)//University Grants Commission, India/ ; },
mesh = {*Soil/chemistry ; *Ecosystem ; India ; Geographic Information Systems ; *Environmental Monitoring ; Animals ; Gardens ; Agroecology ; *Biological Monitoring ; Seasons ; Arthropods ; },
abstract = {This study addresses the microarthropod-based estimation of biological soil quality in rural home gardens using the Qualitative Biological Soil-arthropods (QBS-ar) index. Soil microarthropods, soil properties, soil nutrients, and trace elements were systematically estimated from soil samples collected from 25 home gardens during summer and northeast monsoon seasons over 5 years (2014-2018). The relationships among QBS-ar, microarthropod abundance, soil properties, and soil nutrients were assessed. The microarthropods reported from the study area included Protura, Collembola, Coleoptera, Hymenoptera, Diplopoda, Araneae, Acari, Diptera, and Hemiptera showing statistically significant variations in Summer and monsoon abundance from 2014 to 2018. The QBS-ar index values ranging from 25.28 ± 9.77 to 48 ± 13.12 in summer and from 29.48 ± 18.63 to 56.12 ± 12.55 in monsoon indicated that the home gardens were ranked medium to good in soil quality, with index values ranging from 2 to 4 throughout the study period. Discriminant analysis of soil nutrients with soil properties and microarthropod abundance showed that the 2018 dataset was distinctly separated from the other years. A notable finding was the absence of trace elements (Pb, Cd, Cr) above permissible limits. Hazard estimation through Geographic Information System (GIS), integrating soil properties, nutrients and QBS-ar, indicated that the home gardens functioned as ecosystems with reduced biological soil quality post-flood. This study is among the first to utilize combined QBS-ar scores, soil properties, soil nutrients, and trace elements for long-term soil quality estimation in rural home garden agroecosystems. The study provides a simple, scalable methodological approach for soil ecosystem monitoring and management.},
}
@article {pmid41910342,
year = {2026},
author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D},
title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.},
journal = {mSphere},
volume = {11},
number = {4},
pages = {e0085625},
pmid = {41910342},
issn = {2379-5042},
mesh = {Humans ; Multiomics ; Metagenomics ; *Glutens/metabolism/adverse effects ; Irritable Bowel Syndrome/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metabolomics ; Metabolome ; Archaea/classification/genetics ; Bacteria/classification/genetics ; },
abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.<br><br>IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.},
}
@article {pmid41911042,
year = {2026},
author = {Zhang, Y and Wang, S and Wu, Q and Shi, Z and Ouyang, D and Li, S and Qian, Z and Shen, X and Yang, Y and Wang, L and Su, J and Wang, H and Tian, J and Tan, Q and Zhu, Y and Zhao, B},
title = {City-Level Decision Model and Technology Pathways for Benefit-Oriented Synergistic Control of Air Pollutants and Carbon Dioxide.},
journal = {Environmental science &amp; technology},
volume = {60},
number = {14},
pages = {10717-10727},
doi = {10.1021/acs.est.5c13715},
pmid = {41911042},
issn = {1520-5851},
mesh = {*Carbon Dioxide ; *Air Pollutants ; Air Pollution ; Cities ; China ; Decision Support Techniques ; Models, Theoretical ; },
abstract = {Climate change and air pollution control are two urgent global challenges that demand effective solutions. Cities are the fundamental units for implementing control policies of air pollutants and carbon dioxide emissions. However, research on optimized city-level pathways that maximize integrated benefits and synergies of air pollution and carbon reduction remains limited. Here, we develop a decision-making model for coordinated control of air pollutants and carbon dioxide at the city level. The model systematically evaluates the air quality-related benefits, carbon reduction benefits, and their synergies across various emission reduction measures, and uses these evaluations to construct optimized emission reduction scenario under joint air quality and carbon targets. The model is applied to Beijing, Shanghai, and Chengdu: three megacities with populations above 10 million but distinct differences in city functions, industrial structure, and resource endowments. Results show that under enhanced policy regulation, all three cities can achieve national strategy-compliant air quality improvement and carbon reduction. Structural adjustments in energy, industry, and transportation are central to all cities, but priorities vary. Beijing relies on electric vehicles and imported green power; Shanghai focuses on local green power and transportation electrification; Chengdu emphasizes dust control and promoting clean power. Across all cases, monetized benefits exceed costs, though the benefit-to-cost ratio decreases with tightened environmental targets. This research provides methodological tools for improving environmental quality and promoting low-carbon development at the city level, and offers practical references for formulating region-specific policies tailored to local conditions.},
}
@article {pmid41923171,
year = {2026},
author = {Delgadillo-Ordoñez, N and Schwarzenberg, A and Zhang, H and Beenham, L and Bensaddek, D and Raimundo, I and Terraneo, T and Benzoni, F and Peixoto, RS},
title = {Coral color morphs exhibit distinct microbial and proteomic profiles linked to stress and immune mechanisms in a changing ocean.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41923171},
issn = {2049-2618},
mesh = {*Anthozoa/microbiology/immunology/metabolism/physiology ; Animals ; Proteomics/methods ; Multiomics ; *Bacteria/classification/isolation &amp; purification/genetics ; *Microbiota ; Oceans and Seas ; Pigmentation ; Stress, Physiological ; Metabolome ; *Proteome ; Metabolomics ; Lipidomics ; },
abstract = {BACKGROUND: Coral phenotypic plasticity facilitates acclimation and adaptation to environmental variability. Coral species often display a variety of color morphs, yet key biological and ecological implications of such phenotypic variation remain underexplored. Here, we present the first proteomic and untargeted lipidomic and metabolomic survey to explore the biological characteristics and potential ecological significance of different color morphs (pink and brown) of healthy Pocillopora verrucosa sampled along a latitudinal gradient.<br><br>RESULTS: Our multi-omic approach elucidated distinct mechanisms associated with these dominant color morphs. We discovered bacterial indicators specific to each morph: putative pathogens such as Salmonella, Escherichia-Shigella, and carotenoid-producing Gemmatimonas were notably associated with the pink morph, whereas the brown morph was associated with potentially beneficial bacteria, such as Lysobacter, Acinetobacter, and Endozoicomonas. Despite these microbiome differences, the lipidome and metabolome of P. verrucosa were surprisingly homogeneous across colors and locations, suggesting similar metabolic performances during summer conditions. Key polar and apolar lipid classes, such as fatty acids, glycerophosphocholines, and retinoids, were prevalent. Notably, our proteomic analysis revealed morph-specific expressions, with pink morphs exhibiting enhanced levels of GFP-like proteins, Ankyrin, and the enzyme pullulanase, suggesting novel putative&#xa0;protective roles. In contrast, the brown morphs showed a higher abundance of heat shock proteins, indicating putative differential stress response capabilities.<br><br>CONCLUSION: This comprehensive study provides the first proteomic survey of P. verrucosa and identifies key physiological pathways and trade-offs linked to color morphs, which can further contribute to enhancing our understanding of coral resilience in the face of climate change.<br><br>SIGNIFICANCE STATEMENT: Understanding the phenotypic plasticity of corals is crucial for uncovering mechanisms of resilience in warming oceans, yet the biological significance of coral color morphs still needs to be explored. Using an innovative multi-omic approach (proteomics, lipidomics, and metabolomics), we provide the first comprehensive analysis of differences between pink and brown morphs of Pocillopora verrucosa. Our data reveal key taxa, potentially pathogenic or beneficial, associated with each morph, and suggest different strategies for each color morph to cope with heat stress, either expressing proteins involved in UV protection and heterotrophic activity or enhanced levels of heat stress resilience and DNA repair. These findings offer insights into the phenotypic plasticity of coral color morphs and their differential responses to climate change. Video Abstract.},
}
@article {pmid41823308,
year = {2026},
author = {Gramaje, D and Eichmeier, A},
title = {Beyond Koch's postulates: the pathobiome paradigm in grapevine esca disease.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {4},
pages = {},
pmid = {41823308},
issn = {1574-6941},
support = {//European Regional Development Fund/ ; PID2023-147360OR-C32//Ministry of Science, Innovation and Universities/ ; },
mesh = {*Vitis/microbiology ; *Plant Diseases/microbiology ; *Ascomycota/physiology/genetics ; Host-Pathogen Interactions ; Multiomics ; Stress, Physiological ; },
abstract = {Esca is one of the most damaging fungal diseases of grapevine and continues to defy Koch's postulates. Although Phaeomoniella chlamydospora, Phaeoacremonium minimum, and Fomitiporia mediterranea are consistently associated with wood necrosis in esca-symptomatic vines, they also occur in asymptomatic vines and even in apparently healthy wood tissues without visible necrosis, and single-species but also mixed-species inoculations rarely reproduce the characteristic foliar symptoms. We hypothesize that esca is best understood as a stress-mediated pathobiome disorder of the grapevine holobiont rather than a predictable outcome of specific fungal combinations, shifting focus from pathogen identity to holobiont functional state and environmental context. In this Review, we integrate evidence from community ecology, vascular biology, and multi-omics studies to link microbial community structure and activity with host hydraulics, defence, and environmental drivers. Metabarcoding and metatranscriptomics indicate that symptom expression correlates with functional reprogramming of trunk-inhabiting fungi more than their mere presence, while metabolomics and epigenomics reveal localized physiological disruption combined with systemic regulatory responses. Climatic and edaphic stresses, particularly drought, are strongly associated with holobiont destabilization and dysbiosis, altering symptom expression without necessarily modifying pathogen occurrence. We propose a temporal, multi-phase model integrating colonization history, microbiome restructuring, and host stress physiology through long-term feedbacks. This framework emerges through convergent multi-omics evidence and generates testable predictions for early detection, microbiome-informed biocontrol, and resilience-oriented vineyard management strategies.},
}
@article {pmid41827056,
year = {2026},
author = {Chen, X and Xu, X and Lin, Y and Shi, X and Wang, D and Zhang, T},
title = {Pilea: profiling bacterial growth dynamics from metagenomes with sketching.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41827056},
issn = {2049-2618},
support = {T21-705/20-N//University Grants Committee/ ; },
mesh = {*Bacteria/growth &amp; development/genetics/classification ; *Metagenome ; Software ; *Metagenomics/methods ; *Computational Biology/methods ; Microbiota ; },
abstract = {BACKGROUND: Quantifying bacteria's growth rates is essential for understanding their ecological roles and for building predictive models in environmental and clinical settings. Peak-to-trough ratios (PTRs) derived from shotgun metagenomes offer a culture-independent proxy for in situ growth rates of bacterial species, yet their reliable computation remains challenging.<br><br>RESULTS: We introduce Pilea&#xa0;(https://github.com/xinehc/pilea), an alignment-free, sketching-based method that incorporates statistical models for robust PTR estimation. Pilea achieves speed improvements over existing methods while also enhancing accuracy, as demonstrated on both simulated and real datasets.<br><br>CONCLUSIONS: By scaling efficiently to comprehensive reference collections such as the Genome Taxonomy Database (GTDB), Pilea enables large-scale analyses of bacterial growth dynamics across biomes, unlocking new insights for ecological research. Video Abstract.},
}
@article {pmid41840746,
year = {2026},
author = {Zoch-Lesniak, B and Steiger, E and Kroll, LE and von Stillfried, DG},
title = {Evaluating the impact of a medical telephone helpline and the use of a structured initial assessment on demand for acute and emergency care in Germany: an ecological study using secondary data.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e107343},
pmid = {41840746},
issn = {2044-6055},
mesh = {Humans ; Germany/epidemiology ; *Triage/methods ; *Hotlines/statistics &amp; numerical data ; *Emergency Service, Hospital/statistics &amp; numerical data ; Emergency Room Visits ; *COVID-19/epidemiology ; *Emergency Medical Services/statistics &amp; numerical data ; SARS-CoV-2 ; After-Hours Care/statistics &amp; numerical data ; Secondary Data Analysis ; Telephone ; },
abstract = {OBJECTIVES: To assess whether a medical telephone helpline and the use of a computer-assisted structured triage tool led to a reduction in demand for acute and emergency care in hospital emergency departments (EDs) or other ambulatory out-of-hour (OOH) services.<br><br>DESIGN: We conducted an ecological study using secondary data on outpatient care.<br><br>SETTING: The study was conducted in 10 out of 16 federal states of Germany.<br><br>PARTICIPANTS: The analysis was based on ambulatory claims data for the years 2016-2020&#x2009;by 11 Associations of Statutory Health Insurance Physicians (ASHIPs) covering more than 64% of the total German population.<br><br>INTERVENTIONS: The evaluated intervention comprised two components. The first was the introduction of a 24/7 medical helpline (116117), established to assist individuals with medical concerns in accessing appropriate care. The second component was the introduction of the computer-assisted triage tool SmED (Strukturierte medizinische Ersteinsch&#xe4;tzung in Deutschland, Structured medical initial assessment in Germany) to support call-takers by suggesting medically relevant questions to identify red flags and determine the urgency of treatment and a possible treatment facility. For the analysis, approximately 3 years before and 1 &#xbd; years during the intervention were considered.<br><br>OUTCOME MEASURES: Main outcome was the effect on acute and emergency care which was measured as the number of personal doctor-patient contacts (1) in EDs (ED cases, data of 10 ASHIPs could be considered) and (2) in EDs or other OOH services (ED and OOH cases, data of 11 ASHIPs could be considered).<br><br>RESULTS: The analysis was limited by legal changes mandating intervention components across all study sites-leading to a loss of control groups and delayed implementation-and the onset of the COVID-19 pandemic. Across all ASHIPs and counties, the number of calls to 116117 and the number of SmED assessments showed a negative association with the number of ED cases (total change: 295.0 cases to 224.5 cases per 100&#x2009;000 inhabitants, 116117 calls: r=-0.04; 95%&#x2009;CI -0.04 to -0.035; p&#x2264;0.001, SmED: r=-0.15; 95%&#x2009;CI -0.35 to 0.05; p=0.138) as well as with the combined number of ED and OOH cases (total change: 516.4 cases to 400.3 cases per 100&#x2009;000 inhabitants, 116117 calls: r=-0.02; 95%&#x2009;CI -0.03 to -0.001; p&#x2264;0.01, SmED: r=-0.58; 95%&#x2009;CI -0.98 to -0.19; p&#x2264;0.01). However, the association between the number of SmED assessments and ED cases was not statistically significant. Moreover, the magnitude and direction of effects varied across ASHIPs. Sensitivity analyses restricted to time periods preceding the onset of the COVID-19 pandemic showed a non-significant negative association for 116117 calls and a significant positive association for SmED assessments with both ED cases and combined ED and OOH cases (ED cases: 116117 calls: r=-0.001; 95%&#x2009;CI -0.019 to -0.018; p=0.928; SmED: r=0.37; 95%&#x2009;CI 0.29 to 0.45; p&#x2264;0.001; ED and OOH services cases: 116117 calls: r=-0.03; 95%&#x2009;CI -0.06 to 0.003; p=0.077; SmED: r=0.34; 95%&#x2009;CI 0.20 to 0.48; p&#x2264;0.001).<br><br>CONCLUSIONS: Our findings indicate a trend suggesting that implementation of a 24/7 medical helpline may reduce the demand for acute and emergency care at EDs and OOH services, although clear evidence is lacking. The impact of SmED use remains inconclusive. Further research should ideally incorporate data linkage and controls and assess the effectiveness and efficiency of the triage process, as well as the quality of subsequent care at the individual level.},
}
@article {pmid41805265,
year = {2026},
author = {Kim, KW and Byun, AJS and Castillo, J and Youn, YC and Torous, J},
title = {Metadata in Smartphone-Based Cognitive Assessments: Current State and Emerging Evidence in Psychiatric Disorders.},
journal = {Harvard review of psychiatry},
volume = {34},
number = {2},
pages = {85-94},
doi = {10.1097/HRP.0000000000000453},
pmid = {41805265},
issn = {1465-7309},
mesh = {Humans ; *Smartphone ; *Mental Disorders/diagnosis ; *Ecological Momentary Assessment ; *Metadata ; Digital Health ; *Cognitive Dysfunction/diagnosis ; },
abstract = {Smartphone-based cognitive assessments have emerged as promising tools for frequent and ecologically valid monitoring of cognitive function in real-world settings. These tools enable continuous capture of cognitive and behavioral patterns, including intra-individual variability, practice-related improvement, and contextual influences. Repeated assessments offer a unique opportunity to detect subtle cognitive changes over time. The interpretability and clinical utility of the metadata generated by such assessments, however, remain underexplored. In this review, we consider the current landscape of smartphone-derived cognitive metadata in the context of cognitive and affective disorders. We focus on emerging evidence linking metadata features to functional outcomes and symptom fluctuations across conditions such as schizophrenia, bipolar disorder, and depression. Additionally, we discuss methodological considerations for optimizing metadata analysis, including test design, sampling frequency, and analytical strategies. We propose that cognitive metadata may serve as sensitive indicators of early cognitive change and support personalized mental health monitoring and targeted intervention.},
}
@article {pmid41813102,
year = {2026},
author = {Shi, Y and Kim, J and Mizushima, R and Mizuno, S and Yanagisawa, T and Nakata, Y},
title = {Understanding User Perspectives to Inform Personalized Physical Activity Promotion in a Health Care App: Qualitative Focus Group Interview Study.},
journal = {JMIR formative research},
volume = {10},
number = {},
pages = {e85390},
pmid = {41813102},
issn = {2561-326X},
mesh = {Humans ; Female ; Focus Groups/methods ; *Exercise/psychology ; Male ; Adult ; Qualitative Research ; Middle Aged ; *Health Promotion/methods/standards ; *Mobile Applications/standards/statistics &amp; numerical data ; Motivation ; *Perception ; Aged ; Digital Health ; },
abstract = {BACKGROUND: Health care apps are widely used to support weight loss and lifestyle modification. Many of these apps offer tailored feedback on dietary intake and nutritional behavior. However, most lack personalized features that promote physical activity (PA), which is important for weight management, metabolic health, and chronic disease prevention. To develop future personalized PA promotion functions, it is essential to understand users' perceptions of PA.<br><br>OBJECTIVE: This study aimed to explore health care app users' perception of PA, including perceived motivators and barriers.<br><br>METHODS: A qualitative study was conducted using focus group interviews with health care app users. Participants were recruited regardless of age, sex, or body mass index. A thematic analysis was conducted using a combination of inductive and deductive approaches. Question 1 ("How do you perceive the importance of physical activity?") was analyzed inductively, whereas questions 2 ("What are the motivating factors for engaging in physical activity?") and 3 ("What are the barriers to engaging in physical activity?") were analyzed deductively based on the social ecological model.<br><br>RESULTS: Eleven participants were interviewed and were unfamiliar with the term "physical activity" but recognized the importance of movement and reducing sedentary behavior. The identified motivators included improvements in mood; changes in physical appearance; support from family; alignment with personal routines and conditions (eg, goal setting, feedback, reminders, and praise); and tailoring to physical condition, daily schedules, and weather. The reported barriers included time restrictions due to work, fatigue, weather, remote work, and social pressure in workplace settings.<br><br>CONCLUSIONS: This study provides user-informed insights that can inform the design of personalized approaches better aligned with daily routines, competing demands, and situational barriers. Future work should evaluate how incorporating such user perspectives into personalized support strategies affects engagement and PA.},
}
@article {pmid41813445,
year = {2026},
author = {Hayes, G and Buck, C and Cardon, G and Cimler, R and Elavsky, S and Fezeu K, L and Harrington, JM and Kühnová, J and Oppert, JM and Sigcha, L and Van de Ven, P and Vetrovsky, T and Woods, CB and Hebestreit, A and Donnelly, AE},
title = {Standardized Methods for Evaluating Physical and Eating Behaviors: The WEALTH Cross-Sectional Study Protocol.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e70186},
pmid = {41813445},
issn = {1929-0748},
mesh = {Humans ; Cross-Sectional Studies ; *Feeding Behavior/physiology ; Female ; Adult ; *Wearable Electronic Devices/standards ; Male ; *Exercise/physiology ; Surveys and Questionnaires ; Germany ; Czech Republic ; Anthropometry/methods ; Ireland ; Digital Health ; Middle Aged ; },
abstract = {BACKGROUND: The accurate measurement of physical behaviors (PBs) and eating behaviors (EBs) is critical for designing, monitoring, and implementing public health guidelines and intervention strategies. The objective of the Wearable Sensor Assessment of Physical and Eating Behaviours (WEALTH) project was to develop standardized methods to identify daily PBs and EBs from wearable research- and consumer-grade sensors and evaluate the interaction and contexts of these behaviors.<br><br>OBJECTIVE: The aim of this paper is to describe the study design and methods and report on the descriptive characteristics of the participants.<br><br>METHODS: Within the framework of the WEALTH project, a cross-sectional study (spring 2023 to spring 2024) was completed in 5 European research centers in the Czech Republic, France, Germany, and Ireland. In each center, participants attended a research lab, completed an online questionnaire, and provided measures of anthropometry and handgrip strength. The participants were then fitted with 2 research-grade and 2 consumer-grade devices and participated in a standardized semistructured lab-based activity protocol. The latter was specifically designed to collect labeled data that simulated common PBs and EBs typical for a daily routine. Participants were then followed during a 9-day free-living data collection period, which combined the assessment of PB and EB via wearable devices and time-based, event-based, and self-initiated ecological momentary assessments (EMAs). The EMA surveys were complemented by three 24-hour dietary recalls, using validated web-based programs. Upon the completion of the survey protocol, participants completed a questionnaire that assessed the feasibility of the procedures.<br><br>RESULTS: The final sample includes 627 participants, of whom 44% (n=275) were male. The mean age was 32.7 (SD 13.3) years, and the mean body mass index was 24.5 (SD 4.0) kg/m&#xb2;. The WEALTH study data will be used to develop machine learning (ML) models for classifying daily activities from wrist and hip-worn accelerometer data, evaluate EMA methods for studying interactions between PB and EB, and evaluate the feasibility and compliance of the methods. Data processing and ML model development are currently underway, with primary results expected to be published in 2026.<br><br>CONCLUSIONS: The output of the WEALTH project will be provided via a repository and a comprised toolbox of publicly available labeled data, ML models for behavior classification from accelerometer data, and a methodology to simultaneously capture EB and PB, thereby producing an integrated data collection system to support future research.},
}
@article {pmid41813489,
year = {2026},
author = {Takano, A and Okuda, K and Sese, J and Ono, K and Matsumoto, T},
title = {Individual Variability in Physiological Responses and Psychological Conditions Associated With Methamphetamine Use: Pilot Ecological Momentary Assessment Study Using a Wearable Device and Self-Monitoring Mobile App.},
journal = {JMIR formative research},
volume = {10},
number = {},
pages = {e73790},
pmid = {41813489},
issn = {2561-326X},
mesh = {Humans ; Pilot Projects ; *Methamphetamine/adverse effects ; Female ; Male ; Ecological Momentary Assessment ; Adult ; *Mobile Applications/standards/statistics &amp; numerical data ; *Wearable Electronic Devices/statistics &amp; numerical data/standards ; Heart Rate/physiology ; Middle Aged ; Japan ; Digital Health ; *Amphetamine-Related Disorders/psychology/physiopathology ; Craving ; },
abstract = {BACKGROUND: Digital mental health approaches offer a novel means to monitor and reduce harms associated with substance use in daily life. However, limited evidence exists on their application for methamphetamine (MAMP) use, particularly regarding individual variability in physiological responses and psychological conditions.<br><br>OBJECTIVE: This pilot study aimed to explore inter- and intraindividual differences in craving, emotion, and heart rate associated with MAMP use, using data collected from a wearable device (Fitbit) and a mobile-based self-monitoring app.<br><br>METHODS: Participants were individuals with MAMP use disorder receiving outpatient treatment in Japan. The analysis included 7 participants who used MAMP during an 8-week observation period. Physiological data, including heart rate and sleep patterns, were collected using Fitbit devices, while daily self-reported MAMP use, craving intensity, and emotional status were recorded via a mobile app. After syncing the data, we visualized and summarized individual MAMP use patterns in detail. Correlations between physiological and psychological indicators and the frequency of MAMP use per day were analyzed. In addition, heart rate trends before and after MAMP use events were evaluated using a linear mixed effects model, and both interindividual variability and intraindividual variability were assessed.<br><br>RESULTS: Patterns of MAMP use varied widely across participants, with it most commonly occurring in the morning or at night, regardless of the day of the week. Craving and negative emotions were frequently reported on MAMP use days and were positively correlated with the number of MAMP use episodes per day. Participants who used MAMP more frequently exhibited relatively higher resting heart rates. Following MAMP use, heart rate increased significantly and remained elevated for up to 9 hours. Sleep duration and frequency were reduced or absent on MAMP use days. Approximately 64% of the variance in heart rate was attributable to interindividual differences, while 12% reflected variability across events within the same individual.<br><br>CONCLUSIONS: This pilot study demonstrates the feasibility and value of using digital tools to examine physiological responses and psychological conditions associated with MAMP use in real-world settings. Persistent cardiovascular activation and disrupted sleep highlight the potential risks of long-term MAMP use. Individual differences in heart rate responses, craving, and emotional states underscore the importance of personalized intervention strategies. Integrating real-time self-monitoring, notifications for elevated heart rate, and online cognitive behavioral therapy into digital therapeutic interventions may improve health outcomes for individuals with MAMP use disorder.},
}
@article {pmid41813698,
year = {2026},
author = {Winter, M and Vogel, C and Schobel, J and Schlüter, M and Baumeister, H and Terhorst, Y and Schlee, W and Langguth, B and Heuschmann, P and Cohrdes, C and Pryss, R},
title = {Longitudinal mental health data collected via the Corona Health smartphone app during COVID-19.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41813698},
issn = {2052-4463},
support = {01KX2021//German Federal Ministry of Education and Research/ ; },
mesh = {Humans ; *COVID-19/psychology ; *Mental Health ; *Mobile Applications ; Adult ; Pandemics ; *Smartphone ; Longitudinal Studies ; Germany ; Quality of Life ; Ecological Momentary Assessment ; Surveys and Questionnaires ; SARS-CoV-2 ; Adaptation, Psychological ; Adolescent ; Female ; Telemedicine ; Young Adult ; Middle Aged ; Male ; Digital Health ; },
abstract = {Mental health impacts during the COVID-19 pandemic underscored the importance of real-time assessment methods to capture population-level changes (e.g., longitudinal changes in quality of life). This dataset contains questionnaire responses collected with the Corona Health app, a multilingual mHealth app available on Android and iOS platforms. The dataset includes baseline from 2,704 participants (i.e., adults aged 18 years and older, living in Germany) and 11,541 repeated ecological momentary assessment (EMA) responses, providing longitudinal mental health data throughout various phases during the pandemic period (i.e., data collected between July, 2020 and January, 2025). The questionnaires assessed domains such as quality of life, psychological well-being, coping mechanisms, and pandemic-related concerns. In addition to questionnaire responses, the dataset includes sensor data such as GPS location information and app usage statistics collected with participant consent. The described dataset enables researchers to examine mental health trajectories during and after COVID-19, analyze relationships between psychological factors and pandemic experiences, and investigate patterns in longitudinal mental health data.},
}
@article {pmid41814663,
year = {2026},
author = {Wang, T and Hu, W and Song, W and Liao, X and Zheng, H and Zhang, X and Xin, X and Singh, PK and Chen, Y and Xu, Y},
title = {From triangle to pyramid: Understanding host-pathogen-microniome-environment interplay for sustainable, enviromics-empowered management of plant diseases.},
journal = {Plant communications},
volume = {7},
number = {5},
pages = {101815},
pmid = {41814663},
issn = {2590-3462},
mesh = {*Plant Diseases/microbiology/prevention &amp; control ; *Host-Pathogen Interactions ; Multiomics ; *Microbiota ; *Plants/microbiology/genetics ; Environment ; },
abstract = {Understanding plant disease development requires moving beyond the classic disease triangle, which considers the host, pathogen, and environment. Recent advances in multi-omics have highlighted the importance of a disease pyramid that integrates the host, pathogen, microbiome, and environment to capture the complex interactions among these core biological/ecological components. This pyramid framework emphasizes how host genetic architecture, pathogen traits, microbiome dynamics, and environmental conditions collectively and interactively shape disease outcomes, plant phenotypes, and adaptive potential. The conceptual expansion from the disease triangle to a pyramid model reflects this shift, providing a more holistic and dynamic view of plant disease ecology. Environmental factors regulate host susceptibility and restructure both pathogenic and non-pathogenic microbial communities, thereby influencing infection severity and disease progression. Multi-omics approaches-encompassing hostomics, pathomics, microbiomics, and enviromics-hold strong promise for dissecting these interactions, enabling predictive disease modeling and the development of sustainable management strategies. Moreover, integrating enviromics data into resistance breeding enables the identification of key environmental variables and their interactions with host genotypes and pathogenic and non-pathogenic microbes, thereby supporting the deployment of durable resistance across diverse agroecosystems. Together, these perspectives advance a systems-level understanding of plant health and open new avenues for disease management through omics-driven breeding, microbiome-informed strategies, and environmentally responsive interventions.},
}
@article {pmid42059404,
year = {2026},
author = {Wang, C and Liu, Y and Lin, G and Deng, X and Lin, S and Jiao, N},
title = {Molecular mechanisms, metabolic remodeling, and energy reallocation underlying calcification in the coccolithophore Gephyrocapsa huxleyi.},
journal = {Journal of phycology},
volume = {62},
number = {3},
pages = {943-958},
doi = {10.1111/jpy.70170},
pmid = {42059404},
issn = {1529-8817},
support = {42476128//National Natural Science Foundation of China/ ; 42188102//National Natural Science Foundation of China/ ; 2025029//Scientific Research Foundation of the Third Institute of Oceanography/ ; //Ocean Negative Carbon Emissions (ONCE) program/ ; },
mesh = {*Haptophyta/metabolism/physiology/genetics ; *Energy Metabolism ; *Calcification, Physiologic ; Photosynthesis ; Multiomics ; },
abstract = {Coccolithophores play a dual role in the marine carbon cycle, serving as CO2 sinks through photosynthesis while simultaneously emitting CO2 via calcification, resulting in uncertainty regarding their net carbon sequestration potential. In addition, their calcite coccoliths (CaCO3) can increase the carbon export efficiency by functioning as ballasts for organic matter. Although biogeochemically significant, the molecular mechanisms governing calcification and associated metabolic adaptations in coccolithophores remain poorly characterized, impeding accurate predictions of their responses to climate change. Through comparative multiomics analyses of calcified (RCC1266) and noncalcified (PML B92/11) Gephyrocapsa huxleyi strains, as well as chemically induced decalcified and recalcified states, we screened several ion transport genes, which potentially facilitate Ca[2+] and HCO3 [-] uptake/transport coupled with H[+] extrusion during calcification in the calcified strain, along with their associated proteins, including signal molecules and chaperones. Furthermore, an energy-intensive process was observed in calcifying cells, and this process was principally sustained by enhanced photosynthetic efficiency, supplemented by glucose accumulation as an energy reserve and COX6B translational upregulation, providing nocturnal energy. Notably, calcifying cells employed an energy conservation strategy characterized by transcriptional downregulation yet translational maintenance of photosynthesis and carbon metabolism genes while simultaneously upregulating protein biosynthesis and trafficking pathways to probably meet calcification demands, a process potentially facilitated by increased glutamine biosynthesis. Through multiomic technology, our findings provide insights into the molecular adaptations in the calcified coccolithophorid cells, revealing critical physiological trade-offs, carbon metabolism, and energy allocation that can inform predictions of their acclimation capacity under changing oceanic conditions.},
}
@article {pmid42172829,
year = {2026},
author = {Yang, H and Xie, Y and Wang, H and Sun, H and Li, X and Yao, X and Ding, J and Wang, Q and Lv, H and Turner, BL and Sun, S and Wang, J},
title = {Multi-omics association analysis of the toxicity mechanism differences of typical veterinary antibiotics on tomatoes: From physiological inhibition to metabolic reprogramming.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142457},
doi = {10.1016/j.jhazmat.2026.142457},
pmid = {42172829},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/toxicity ; *Solanum lycopersicum/drug effects/metabolism/growth &amp; development ; Chlortetracycline/toxicity ; Tylosin/toxicity ; Enrofloxacin/toxicity ; Oxidative Stress/drug effects ; Photosynthesis/drug effects ; Multiomics ; *Veterinary Drugs/toxicity ; *Soil Pollutants/toxicity ; Seedlings/drug effects/growth &amp; development/metabolism ; },
abstract = {Widespread application of veterinary antibiotics is contaminating soil via animal feces, leading to uptake by plants and environmental damage. Currently, research on the toxicological mechanisms associated with various classes of antibiotics remains inadequate. Therefore, this study utilized tomato as the test species and selected three representative antibiotics-chlortetracycline (CTC), enrofloxacin (ENR), and tylosin (TYL)-to systematically evaluate their differential toxicity and associated metabolic mechanisms through 14 and 28 days exposure experiments. At the individual level, antibiotics significantly suppressed biomass accumulation and photosynthesis in tomato seedlings, the ENR exhibited maximum inhibition rates of 37.4% for fresh weight and 26.7% for plant height. In contrast, the CTC recorded peak values of 28% for leaf area and 25.1% for SPAD measurements. Furthermore, exposure to antibiotics induced oxidative stress in tomato seedlings, with SOD demonstrating its highest activation rate of 18.3% in the TYL. Within the rhizosphere microenvironment, there was a notable decrease in the abundance of the dominant phylum Bryobacter, which was accompanied by alterations in bacterial community structure, an increase in network complexity, and a reduction in modularity. Under antibiotic stress, microbial communities demonstrated distinct metabolic responses: enhanced lipid metabolism in CTC, elevated carbohydrate metabolism with ENR, and activated nucleotide metabolism associated with TYL. In summary, antibiotics present global ecological risks by inhibiting plant growth and disrupting the rhizosphere microbiome. The class-specific toxicity of these substances necessitates the implementation of targeted risk management strategies.},
}
@article {pmid42298119,
year = {2026},
author = {Sorboni, SG and Pourebrahim, S and Chen, JE and Hadipour, M},
title = {Anthropogenic accessibility and observer inequality dictate spatial biodiversity patterns in Malaysia.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-58296-2},
pmid = {42298119},
issn = {2045-2322},
support = {SUR-JSC-SSERV-2024-13//Sunway University/ ; },
abstract = {Global biodiversity monitoring increasingly relies on open-access community science data, but these opportunistic records harbor complex biases that can severely distort macroecological inference. Here, we disentangle how human behavior, infrastructure, and taxonomy interact to shape perceived biodiversity patterns across the two distinct biogeographic regions of Malaysia. Analyzing 336,042 research-grade iNaturalist records, we quantified observer inequality and taxonomic disproportionality. We estimated true species richness (Chao2) to map spatial inventory completeness (median = 33.3%) and employed Zero-Inflated Negative Binomial GLMMs and effort-corrected Generalized Additive Models (GAMs) to test the effects of topography, accessibility, and observer classification. We demonstrate extreme observer inequality (Gini = 0.854), with data collection heavily anchored to urban centers. Crucially, a significant three-way interaction revealed that dedicated "Power Users" successfully penetrate roadless interiors in Peninsular Malaysia, whereas casual observers remain strictly road-bound. Taxonomically, the data exhibits a severe charismatic skew, massively over-representing Aves and Reptilia while under-sampling foundational hyper-diverse clades like Insecta and Fungi. Furthermore, explicitly modeling non-linear sampling effort (user-days) rendered the effects of elevation and terrain ruggedness statistically non-significant. This demonstrates that perceived biodiversity deficits in rugged, high-elevation terrains are anthropogenic artifacts of human inaccessibility rather than true ecological absences. To meet global conservation targets, state funding and structured monitoring should complement opportunistic data by actively targeting these remote, under-sampled geographic and taxonomic shortfalls.},
}
@article {pmid41789991,
year = {2026},
author = {Shi, J and Fantke, P and Jolliet, O},
title = {A harmonized ecotoxicity dataset for honeybee based on the ECOTOX database.},
journal = {Environmental toxicology and chemistry},
volume = {45},
number = {6},
pages = {1470-1482},
doi = {10.1093/etojnl/vgag054},
pmid = {41789991},
issn = {1552-8618},
support = {//Bayer AG Crop Science Division/ ; },
mesh = {Animals ; Bees/drug effects ; *Pesticides/toxicity ; Ecotoxicology ; Databases, Factual ; *Environmental Pollutants/toxicity ; },
abstract = {Among the most crucial pollinators, managed honeybee (Apis mellifera) colonies frequently experience colony losses, which impose significant economic burdens on beekeeping and threaten the reliability of pollination services. Pesticide exposure is recognized as one stressor among others contributing to these losses. However, the curated harmonized dataset to characterize the impacts of multiple pesticides on different stages of honeybees is missing. To address this data gap, we generated an extensive and consistent honeybee ecotoxicity dataset of top (dermal)-acute 10% effective dose (ED10) and oral-chronic ED10 from the U. S. Environmental Protection Agency Ecotoxicology Knowledgebase (ECOTOX databases) for life cycle impact assessment (LCIA) and other comparative assessments. Primary harmonization and standardization were conducted to resolve inherent inconsistencies in life stages, exposure types, effect types, units, endpoints, and test types. Subsequently, weighted linear regressions were applied to extrapolate various endpoints to a harmonized ED10-equivalent (ED10eq), with R2 ranging from 0.38-0.99. The resulting integrated datasets comprise 540 chemicals across oral-chronic, oral-acute, and acute-topical exposure scenarios, consistently spanning approximately eight orders of magnitude for the adult groups and six orders of magnitude for the larval groups. Additionally, the relationship between adult and larva ecotoxicity data was analyzed, along with an uncertainty assessment for the oral-chronic and top-acute datasets, further enhancing the reliability and applicability of the harmonized data. These harmonized ecotoxicity datasets significantly enhance the LCIA framework by replacing the median effective dose (ED50) acute data with oral-chronic top-acute ED10 data, thus facilitating a more environmentally realistic assessment of pesticide impacts on honeybees.},
}
@article {pmid41896705,
year = {2026},
author = {Jan, S and Jan, F and Rathore, M and Singh, Y and Kapoor, P and Chaturvedi, P and Ghatak, A and Ramesh, P and Kumar, U and Prasad, M and Kumar, S and Rustgi, S and Weckwerth, W and Kalia, S and Varshney, RK and Mir, RR},
title = {Deciphering Cold Stress Resilience: Multiomics Insights in Contrasting Wheat Genotypes From the Western Himalayas.},
journal = {Plant biotechnology journal},
volume = {24},
number = {7},
pages = {4577-4598},
doi = {10.1111/pbi.70594},
pmid = {41896705},
issn = {1467-7652},
support = {BT/Ag/Network/Wheat/2019-20//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Triticum/genetics/metabolism/physiology ; Multiomics ; Genotype ; *Cold-Shock Response/genetics/physiology ; Proteomics ; Metabolomics ; Cold Temperature ; Transcriptome ; Gene Expression Regulation, Plant ; Lipidomics ; Gene Expression Profiling ; Plant Proteins/metabolism/genetics ; Metabolome ; },
abstract = {Cold stress threatens wheat productivity, particularly in regions with extreme climatic conditions. To elucidate the molecular mechanisms underlying wheat's response to cold stress, we performed a multiomics analysis integrating lipidomics, transcriptomics, proteomics and metabolomics. Our study focused on two wheat genotypes with contrasting cold tolerance levels, SKAU_52 (tolerant) and SKAU_4301 (susceptible) to capture genotype-specific responses under cold stress. Lipidomic analysis revealed significant changes in lipid composition, with unsaturated lipids such as digalactosyldiacyl glycerols (DGDGs) and monogalactosyldiacylglycerols (MGDGs) upregulated in response to cold stress. These lipids are associated with maintaining membrane fluidity, whereas saturated lipids were downregulated in the cold-tolerant genotype. Transcriptomics analysis provides a strong evidence that cold tolerance in wheat is governed by coordinated activation of the ICE-CBF-COR regulatory cascade, with the cold-tolerant genotype 'SKAU_52' showing stronger and more sustained induction across pathway tiers than the cold susceptible wheat genotype 'SKAU_4301'. Similarly, proteomic data highlighted differential abundance of proteins involved in antioxidative defence, osmotic adjustment and signal transduction, including late embryogenesis abundant (LEA) proteins. Metabolome assessment revealed substantial alterations in carbohydrate and amino acid metabolism, with sucrose and amino acids such as hydroxyproline identified as key contributors to cold tolerance. Additionally, defence hormones such as salicylic acid (SA), jasmonic acid (JA) and abscisic acid (ABA) exhibited genotype-specific regulation with higher accumulation in cold-tolerant genotype. Overall, this integrated multi-omics approach provides novel insights into the complex molecular mechanisms underlying cold stress adaptation in wheat, supporting the development of resilient wheat varieties capable of thriving in challenging cold environments.},
}
@article {pmid41949699,
year = {2026},
author = {Shen, H and Zhang, L and Ma, X and Yin, Y and Wang, J and Tan, B},
title = {Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.},
journal = {Science China. Life sciences},
volume = {69},
number = {7},
pages = {2230-2248},
pmid = {41949699},
issn = {1869-1889},
mesh = {Multiomics/methods ; *Machine Learning ; Humans ; *Microbiota/genetics ; Computational Biology/methods ; *Host Microbial Interactions ; Benchmarking ; Algorithms ; Data Analytics ; Translational Research, Biomedical ; },
abstract = {The human microbiome is a dynamic ecosystem that profoundly influences host physiology through complex molecular interactions. Advances in high-throughput profiling now enable multi-omics measurements at scale, yet integration remains difficult due to biological complexity, technical variability, sparsity, and small cohorts. This review targets bioinformatics practitioners and clinical microbiology researchers applying machine learning to host-microbiome studies. Here, we survey state-of-the-art methods for integrating heterogeneous data types and highlight algorithmic innovations for high dimensionality and small cohorts. We also examine approaches for interpretability that translate mechanistic insight into clinically actionable models. Finally, we outline a standardized benchmarking framework emphasizing open data, rigorous evaluation, and biologically informed architectures. By synthesizing multi-omics measurements with advanced analytics, we chart a pathway toward personalized, microbiome-based therapies while deepening our understanding of host-microbiome crosstalk.},
}
@article {pmid42030616,
year = {2026},
author = {Rosić, I and Sokić, M and Ranković, T and Medić, O and Berić, T and Stanković, S and Dillon, MM and Nikolić, I},
title = {Filling in the blanks: In silico prediction of novel type III secreted effectors in the Pseudomonas syringae species complex.},
journal = {Computational biology and chemistry},
volume = {124},
number = {Pt 1},
pages = {109083},
doi = {10.1016/j.compbiolchem.2026.109083},
pmid = {42030616},
issn = {1476-928X},
mesh = {*Pseudomonas syringae/genetics/metabolism ; *Computational Biology ; Genome, Bacterial ; *Computer Simulation ; *Bacterial Proteins/genetics/metabolism ; },
abstract = {Predicting novel type III secreted effectors (T3SEs) in bacteria remains challenging because of their extensive sequence diversity and our heavy reliance on features derived from previously annotated genes. The available tools for predicting T3SS effectors produce a high number of false positives, which complicates their reliable identification. To address this gap, we developed a new bioinformatics workflow and meta-analysis designed to improve confidence in novel T3SE prediction by integrating multiple complementary approaches, including Effectidor2, Bastion3, EffectiveT3, curated effector databases, all-vs-all BLAST comparisons, comparative genomics, and localization-based features. We applied this approach to 57 complete P. syringae genomes, a diverse species complex whose pathogenicity is closely tied to its type III secreted effector (T3SE) content, allowing us to reduce an initial collection of 283 candidate T3SEs to 15 high-confidence predictions. By applying our newly customized EffRank scoring pipeline, three candidates emerged as high-confidence novel T3SEs in P. syringae strains: PsaNZ45_RS26420 (P. syringae pv. actinidiae ICMP20586), ACOZ4J_RS28825 (P. syringae pv. actinidiae FX219), and RRP28_RS13015 (P. syringae pv. actinidiae Yunnan2.4). Furthermore, our scoring pipeline successfully detected and removed likely false positive T3SEs, such as YenB-like toxins, among the high-confidence candidates that persisted through earlier curation steps, highlighting the challenges and biases of current publicly available prediction tools. Finally, we also characterized the final T3SE repertoires of each strain, which were consistent with phylogroup clustering based on the core-genome. As expected, PG1 strains carried larger and more conserved T3SE repertoires and contributed the majority of the promising novel T3SE candidates, while the likely false-positive YenB-like toxin was detected in PG2.},
}
@article {pmid42293552,
year = {2026},
author = {Aldriwesh, MG and Bin Shuraym, H and Asiri, NY and Asiri, WY and Abukhalid, NF and Alasiri, A and Alghoribi, MF},
title = {Microbiome and One Health in GCC countries: current status, research gaps, and future directions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1821688},
pmid = {42293552},
issn = {1664-302X},
abstract = {BACKGROUND: Microbiome science has emerged as a central component of the One Health framework, linking human, animal, and environmental health. Although global microbiome research has expanded rapidly, a comprehensive evaluation of microbiome research development and integration across the Gulf Cooperation Council (GCC) countries remains lacking. This systematic review aimed to characterize microbiome research in the GCC countries, identify major research gaps, and evaluate alignment with One Health principles while proposing a strategic framework to support coordinated regional development.<br><br>METHODS: This systematic review followed PRISMA 2020 guidelines. A structured search of PubMed, ScienceDirect, Google Scholar, and EBSCO databases identified microbiome-related studies published up to January 31, 2025. Eligible studies included original research conducted in the GCC countries (Saudi Arabia, Qatar, Kuwait, United Arab Emirates, Oman, and Bahrain) investigating human, animal, or environmental microbiomes. Findings were synthesized descriptively to assess study distribution, research design, analytical methodologies, and thematic focus.<br><br>RESULTS: A total of 110 studies met the inclusion criteria. Human microbiome studies accounted for 49% of publications, followed by environmental microbiome studies (40%) and animal microbiome studies (11%). Research output increased substantially after 2020 but remained uneven among the GCC countries, with Saudi Arabia contributing 44% of publications, whereas Bahrain and Oman together accounted for fewer than 7%. Most studies were observational and primarily used 16S rRNA gene sequencing on Illumina platforms. Human studies focused mainly on gut and oral microbiomes and frequently investigated metabolic disorders such as obesity and diabetes. Animal microbiome research was limited and largely centered on camels, with minimal investigation of livestock relevant to food security. Environmental studies predominantly examined soil and desert environments. No included study simultaneously investigated human, animal, and environmental microbiomes within an integrated One Health study design.<br><br>CONCLUSION: Microbiome research in the GCC countries is growing but remains uneven and largely disconnected across human, animal, and environmental studies, with limited adoption of One Health approaches. A coordinated regional strategy integrating governance, infrastructure, funding, and workforce development is needed to advance translational microbiome research and strengthen the GCC's contribution to global health, food security, and environmental sustainability.},
}
@article {pmid42294911,
year = {2026},
author = {Duque-Jaramillo, A and Symeonidi, E and Neumann, M and Ashkenazy, H and Allen, M and Weigel, D and Karasov, TL},
title = {Biosynthetic gene clusters in Pseudomonas viridiflava have a fitness cost during Arabidopsis thaliana infection.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0021226},
doi = {10.1128/msystems.00212-26},
pmid = {42294911},
issn = {2379-5077},
abstract = {UNLABELLED: Specialized or secondary metabolites mediate biotic interactions, including virulence and defense. In plant-pathogenic Pseudomonas, certain specialized metabolites can enhance colonization of plant hosts, yet their broader contribution to plant-microbe interactions and the relative importance of different metabolites remain unclear. Specialized metabolites are products of enzymes encoded in biosynthetic gene clusters (BGCs), whose prediction from genome sequences has become routine but whose functional roles are rarely tested experimentally. Here, we characterize the BGC repertoire of 225 P. viridiflava isolates from Arabidopsis thaliana and assess BGC contributions to fitness and disease severity in planta. The BGC landscape of P. viridiflava was dominated by non-ribosomal peptide synthetase (NRPS) and NRPS-like BGCs, which accounted for 50% of the predicted BGCs. One-third of the BGC families were restricted to a single isolate. Transposon mutagenesis coupled with random barcode transposon sequencing (RB-TnSeq) revealed that the majority of BGCs reduce rather than increase fitness during A. thaliana infection, with the magnitude of the fitness cost varying across host genotypes. This cost could be due to exploitation of public goods by cheater mutant strains. In single-isolate plant infections, where public goods are not available, we found 11/34 BGC families correlated with disease severity. Yet, only two of these (an N-acetylglutaminylglutamine amide [NAGGN] and an NRPS) were negatively associated with disease severity, which is positively correlated with bacterial growth in this pathosystem, further indicating that BGCs are generally not beneficial in planta. Our findings reveal extensive and largely uncharacterized biosynthetic potential in populations of P. viridiflava and indicate that candidate metabolites are likely not adaptive for direct interactions with the plant, but perhaps for microbe-microbe interactions either in planta or in other ecological niches.<br><br>IMPORTANCE: Bacteria, including plant-associated bacteria such as Pseudomonas viridiflava, produce a vast array of chemical compounds, called secondary or specialized metabolites, that can mediate their interaction with the plant host or other microorganisms. Some of these compounds are known to directly influence how bacteria interact with plants, but it has been unclear whether this is a general rule. We studied a large collection of closely related leaf-dwelling P. viridiflava-a plant pathogen-that varied in their ability to cause disease. We found that very few of the gene clusters responsible for making specialized metabolites improved the ability of the bacteria to colonize its natural host Arabidopsis thaliana. On the contrary, carrying these gene clusters often reduced bacterial growth and disease severity in plants. Specialized metabolites may instead primarily be important for interacting with other microbes, different host species, or under environmental conditions we did not test. These are questions that remain for future research.},
}
@article {pmid42296150,
year = {2026},
author = {Shirani, F and Freeman, BG},
title = {Environmental "knees" and "wiggles" as strong stabilizers of species' range limits set by interspecific competition.},
journal = {PLoS computational biology},
volume = {22},
number = {6},
pages = {e1014336},
doi = {10.1371/journal.pcbi.1014336},
pmid = {42296150},
issn = {1553-7358},
mesh = {Animals ; *Ecosystem ; *Models, Biological ; *Competitive Behavior/physiology ; Gene Flow ; *Biological Evolution ; Species Specificity ; Computational Biology ; },
abstract = {Whether interspecific competition is a major contributing factor to setting species' range limits has been debated for a long time. Theoretical studies have proposed that the interactions between interspecific competition and disruptive gene flow along an environmental gradient can halt range expansion of ecologically similar species where they meet. However, the stability of such range limits has not been well addressed. We use a deterministic mathematical model of adaptive range evolution over a continuous habitat to show that the range limits set by interspecific competition are unlikely to be evolutionarily stable if the environmental optima for fitness-related traits vary (almost) linearly in space. That is, in a linear environment without a dispersal barrier or a third (or more) species, the range borders formed between two competing species constantly move towards the weaker species. We demonstrate that environmental nonlinearities such as "knees" and "wiggles"-wherein an isolated sharp change or a step-like change occurs in the steepness of a trait optimum-can strongly stabilize competitively formed range limits. The stabilization mechanism relies on the contrast that such nonlinearities create in the level of disruptive gene flow to the peripheral population of each species, and succeeds when an additional process, such as Allee effects, prevents the establishment of an infinitesimal population in the presence of an abundant competitor. We show that the stability of the range limits at these nonlinearities is robust against moderate environmental disturbances. Whether strong disturbances such as rapid high-amplitude climate changes can destabilize such range limits depends on how the competitive dominance of the species changes across the nonlinearity. Therefore, our findings underscore the importance of assessing species' competitive ability when predicting responses to climate change, and identify geographic regions where established range limits are likely to persist as well as regions where shifting limits may eventually stabilize.},
}
@article {pmid42296265,
year = {2026},
author = {Chen, L and Chen, L and Jin, LN and Qiu, A and Jia, Y and Zhang, P and Ji, Y and Xu, C and Zhang, Y and Li, D and Chen, J},
title = {Nasal Instillation of Complex Metal Oxide Particles Induces Brain Metal Accumulation and Neurobehavioral Toxicity in Mice.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16262},
pmid = {42296265},
issn = {1520-5851},
abstract = {The rapid expansion of complex metal oxide particles (CMOPs) in energy technologies raises emerging health concerns, yet their neuropsychiatric impacts remain unclear. Using intranasal exposure to lithium iron phosphate (LFP) and nickel-cobalt-manganese oxide (NCM) at dose levels selected with reference to reported ambient and occupational monitoring scenarios (0.8 and 8 mg/kg/day, n = 8 per group), we show that short-term CMOP exposure induces distinct neurobehavioral alterations in mice, characterized by changes in cognitive performance, risk assessment, and stress-related coping behavior. These changes co-occurred with dose-dependent brain accumulation of Li, Ni, Mn, and Co. Unexpectedly, low-dose exposure yielded 5-17-fold higher brain bioaccumulation factors than high-dose exposure, indicating disproportionate brain retention at lower exposure levels. Neurotransmitter profiling showed alterations consistent with perturbation of catecholamine metabolism, the tryptophan-kynurenine pathway, and the glutamate-glutamine cycle. At the molecular level, brain metal burden was associated with changes in barrier-related, neuroimmune, and synaptic signaling markers prioritized in relation to behavioral outcomes. Collectively, the findings indicate that short-term CMOP exposure can co-occur with brain metal bioaccumulation and neurobehavioral dysfunction, supporting the need for future inhalation-based and chronic studies to better define toxicokinetics, exposure relevance, and long-term health implications.},
}
@article {pmid42298048,
year = {2026},
author = {Bell, AR and Rakotonarivo, S and Manzoor, T and Moreira, R and Schaafsma, M and Fiwa, L and Zhang, W},
title = {US funding cuts offer a rare chance to remodel Global North-Global South research collaboration.},
journal = {Nature human behaviour},
volume = {},
number = {},
pages = {},
pmid = {42298048},
issn = {2397-3374},
}
@article {pmid41795303,
year = {2026},
author = {Zeng, Y and Zhang, J and Wang, Q and Han, X and Liu, L and Yang, K and Zhang, R and Luo, K and Ren, L and Liu, S},
title = {Dual-layered epigenetic regulation links water body size constraints to somatic growth in an allotetraploid fish.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {59},
number = {},
pages = {101787},
doi = {10.1016/j.cbd.2026.101787},
pmid = {41795303},
issn = {1878-0407},
mesh = {*Tetraploidy ; *Goldfish/genetics/growth &amp; development ; *Carps/genetics/growth &amp; development ; *Epigenesis, Genetic ; Multiomics ; Hybridization, Genetic ; *Adaptation, Biological ; Muscle Development ; Eye/growth &amp; development ; Male ; Female ; Animals ; *Body Size/genetics ; Promoter Regions, Genetic ; Enhancer Elements, Genetic ; },
abstract = {Polyploidy endows fish with genomic plasticity to colonize restricted environments, yet the molecular mechanisms linking ecological constraints to somatic growth remain elusive. Here, we investigated the adaptive response of an allotetraploid lineage (Carassius auratus × Cyprinus carpio) to contrasting water body sizes using multi-omics approaches. We found that spatial constraints triggered targeted transcriptional remodeling specifically in the eye and muscle. This response effectively links sensory perception to growth regulation. Meanwhile, we identified a dual-layered epigenetic strategy. Environmental stress forced a reduction in the active gene pool via promoter silencing, while concurrently depressing the expression levels of growth-related structural genes through enhancer inhibition. Interestingly, this plasticity exhibited striking subgenome asymmetry. The Cyprinus subgenome displayed higher epigenetic responsiveness and acted as the primary adaptive buffer, exemplified by the targeted repression of a Cyprinus-derived enhancer regulating the mTOR gene rps6kb1a. Our findings demonstrate how subgenome-biased epigenetic remodeling aligns growth phenotypes with ecological constraints, offering molecular insights into the evolutionary success of polyploids in fragmented habitats.},
}
@article {pmid41795790,
year = {2026},
author = {Özkan Vardar, D and Ekmen, B and Çalı, A},
title = {Interactions between polystyrene-derived micro- and nanoplastics and the microbiota: a systematic review of multi-omics mouse studies.},
journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis},
volume = {44},
number = {2},
pages = {141-159},
doi = {10.1080/26896583.2026.2636868},
pmid = {41795790},
issn = {2689-6591},
mesh = {Animals ; *Polystyrenes/toxicity ; *Microplastics/toxicity ; Mice ; Multiomics ; *Gastrointestinal Microbiome/drug effects ; *Nanoparticles/toxicity ; },
abstract = {Micro- and nanoplastics (MNPs), especially polystyrene-derived particles (PS-MPs/PS-NPs), have become a growing concern due to their increasing presence in the environment and their proven biological toxicity. Although PS particles have been identified in various human tissues, including feces, placenta, and blood, their impact on the gut microbiota and microbiota-driven metabolic pathways remains insufficiently synthesized. This systematic review aims to compile current in vivo evidence from mouse studies to assess how PS-MP/NP exposure influences gut microbial diversity, taxonomic composition, microbial metabolites, and subsequent physiological outcomes. A PRISMA-guided literature search identified 15 controlled mouse studies published between 2010 and 2024. Across these studies, PS exposure consistently induced gut dysbiosis, characterized by reductions or shifts in alpha-diversity, distinct beta-diversity clustering, loss of beneficial commensals such as Lactobacillus, Bifidobacterium, and members of Ruminococcaceae, and enrichment of opportunistic or pro-inflammatory taxa including Proteobacteria, Helicobacter, and Staphylococcus. Notably, MNPs particles induced more pronounced microbial disruption than micro-sized forms. Overall, current experimental evidence indicates that PS-MPs/PS-NPs induce multidimensional toxicity by simultaneously disrupting gut microbial ecology and host metabolic pathways. These findings emphasize the need for standardized methodologies in microplastic research and highlight the importance of clarifying the long-term health effects of human exposure to micro- and nanoplastics.},
}
@article {pmid42263638,
year = {2026},
author = {Lucas, ER and Ellis, E and Paustian, K and Dorsey, S and Toor, GS},
title = {Modeling soil organic carbon stocks and changes in agricultural cropping systems using a decision support tool and process-based model.},
journal = {Journal of environmental management},
volume = {411},
number = {},
pages = {130171},
doi = {10.1016/j.jenvman.2026.130171},
pmid = {42263638},
issn = {1095-8630},
mesh = {*Agriculture/methods ; *Soil/chemistry ; *Carbon/analysis ; *Decision Support Techniques ; Models, Theoretical ; },
abstract = {Soil organic carbon (SOC) is a key indicator of soil health, yet changes in SOC often take decades to detect. Assessment tools, accessible to non-expert users, are needed to accurately and cost-effectively quantify SOC stocks. Soil sampling and analysis are ideal for quantification but are also resource- and time-intensive. A decision-support tool, COMET-Farm, could improve the transition to low-C agricultural supply chains; however, it was designed to estimate ΔSOC rather than SOC stocks directly, and its accuracy across diverse agricultural settings remains uncertain. We investigated whether the COMET-Farm tool could accurately estimate SOC stocks on 15 working farms in Maryland with variable management practices, including tillage, cover cropping, manure application, and irrigation. Field-measured SOC stocks (0-20 cm soil depth) of 17.1 to 73.6 Mg ha[-1] were compared with model-predicted values using farmer-reported data in (i) COMET-Farm with default inputs supplied to DayCent, versus (ii) expert-applied DayCent. We found COMET-Farm predictions were lower than measured SOC stocks (R[2] = 0.101; RMSE = 18.80 Mg ha[-1]), while expert-applied DayCent predictions more closely matched field measurements (R[2] = 0.73; RMSE = 7.89 Mg ha[-1]). Poorly drained soils and long-term manure applications caused greater discrepancies between measured and predicted SOC. These findings suggest that COMET-Farm estimates could improve with better model initialization, more accurate site-specific soil data, such as measured soil texture and drainage conditions, and more regionally representative land-use histories. With these improvements and further testing, COMET-Farm could be expanded beyond its original purpose of estimating ΔSOC to directly estimate SOC stocks for non-expert users.},
}
@article {pmid42263641,
year = {2026},
author = {Hendler, R and Tischew, S and Hensen, H and Metze, K and Schütz, L and Bade, K and Fischer, C},
title = {Successful restoration of heathlands and grasslands associated with long-term habitat preferences of cattle and horses: Insights from GPS tracking.},
journal = {Journal of environmental management},
volume = {411},
number = {},
pages = {130113},
doi = {10.1016/j.jenvman.2026.130113},
pmid = {42263641},
issn = {1095-8630},
mesh = {Animals ; Cattle ; *Grassland ; *Ecosystem ; Horses ; Germany ; Geographic Information Systems ; Seasons ; *Conservation of Natural Resources ; Herbivory ; },
abstract = {Long-term, year-round grazing by large herbivores is increasingly used to restore degraded temperate heathlands and grasslands, yet the behavioral mechanisms of grazers underlying restoration remain insufficiently understood. We combined over 13 years of high-resolution GPS-tracking data of free-ranging Heck cattle and Konik horses with repeated vegetation surveys across various habitat types (encroachment-derived Calamagrostis epigejos stands, dry sandy grasslands, dry heaths, and pioneer forests) in Central Germany. We quantified how habitat preference and vegetation structure co-develop under low-intensity, year-round grazing following abandonment. Habitat preference differed among habitat types and showed clear seasonal patterns. Preference values were consistently higher in summer than in winter for both grazer species, reflecting selective use of productive regrowth. Winter preferences were weak, indicating low selectivity and homogeneous space use that facilitated grazing in habitats otherwise avoided during the growing season, including dry heaths and pioneer forests. Across the study period, we detected long-term shifts in habitat preference that corresponded with vegetation changes associated with the restoration of dry heaths and sandy grasslands. As standing biomass declined, C. epigejos and grass litter decreased, open soil increased, and Calluna vulgaris advanced into the optimal phase. These structural improvements reduced forage-quality contrasts among habitats, resulting in progressively weaker preference patterns and a more even distribution of habitat use across the landscape. Our results provide rare long-term empirical evidence linking grazer behavior and vegetation dynamics in conservation grazing systems and highlight that year-round extensive grazing, rather than summer-only grazing, is required to achieve stable long-term restoration outcomes.},
}
@article {pmid42269263,
year = {2026},
author = {Li, M and Zhou, S and Jiang, M and Geng, J and Ni, H and Li, G and Zhao, Y and Dong, Y},
title = {ABA-cytokinin crosstalk regulate drought tolerance in Ziziphus jujuba var. spinosa through the phenylpropanoid pathway: insights from physiological and multi-omics integration.},
journal = {Plant physiology and biochemistry : PPB},
volume = {236},
number = {},
pages = {111466},
doi = {10.1016/j.plaphy.2026.111466},
pmid = {42269263},
issn = {1873-2690},
mesh = {*Abscisic Acid/pharmacology/metabolism ; Drought Resistance ; *Cytokinins/metabolism/pharmacology ; *Ziziphus/metabolism/physiology/genetics/drug effects ; Gene Expression Regulation, Plant/drug effects ; Multiomics ; *Propanols/metabolism ; Droughts ; Plant Proteins/metabolism/genetics ; Seedlings/metabolism ; Plant Growth Regulators ; Stress, Physiological ; Cytochrome P-450 Enzyme System/metabolism ; },
abstract = {Drought stress is a major constraint in jujube production. Although abscisic acid (ABA) and cytokinin exert opposing effects on plant growth, recent findings revealed that their combined application enhanced drought tolerance in jujube; however, the underlying mechanism remains elusive. In this study, three exogenous treatments were applied to sour jujube seedlings under drought stress: 5 mg L[-1] ABA, a cytokinin mixture of 50 mg L[-1] 6-benzylaminopurine (6-BA) and 100 mg L[-1] kinetin (KT), and a combined ABA and cytokinins solution. Transcriptomic and metabolomic analyses were integrated to elucidate how ABA and cytokinins jointly modulate drought responses. The results showed that ABA induced stem thickening, enhanced osmotic regulation and antioxidant capacity, upregulated the expression of cytochrome P450 84A1-like (CYP84A1) involved in lignin biosynthesis, and downregulated cinnamyl alcohol dehydrogenase (CAD). In contrast, cytokinins promoted stem elongation by upregulating elongation factor 2 and L-lactate dehydrogenase B, downregulating anthocyanin synthase (ANS) and peroxidase, and altering galactose/starch metabolism, thereby prioritizing growth at the expense of stress tolerance. The combined treatment reconciled these opposing effects, enhancing stress defense without compromising cytokinin-mediated growth advantage, inducing 3018 differential genes and 285 metabolites. The phenylpropanoid biosynthesis pathway was identified as central to ABA-cytokinin crosstalk, with upregulation of two CADs contributing to drought resistance and four genes encoding CAD, peroxidase, and cinnamate 4-hydroxylase (C4H) playing a critical role in this crosstalk. Additionally, beta-glucosidase 18 (BGLU18) was identified as a candidate gene correlated with 13 phenylpropanoids. Our findings reveal the molecular link between the phenylpropanoid pathway and ABA-cytokinin crosstalk in jujube drought tolerance.},
}
@article {pmid42284784,
year = {2026},
author = {Luo, P and Liu, X and Mao, Y and Yang, J and Wang, X and Cai, L and Filatova, I and Liu, Y},
title = {Enhanced PFHxS degradation by DBD combined with microbubbles and sulfite: Synergistic effects and mechanisms.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142684},
doi = {10.1016/j.jhazmat.2026.142684},
pmid = {42284784},
issn = {1873-3336},
abstract = {Perfluorohexane sulfonate (PFHxS), a persistent member of the PFAS family, remains challenging to degrade, and its transformation mechanisms are not yet fully understood. Here, a dielectric barrier discharge coupled with microbubbles and sulfite (DBD/MBs/sulfite) system was developed for PFHxS degradation. Among all tested systems, the ternary process achieved the best performance, reaching 96.7% degradation and 26.3% defluorination within 60 min, with rate constant of 0.049 min[-1]. The enhancement mainly arose from the coupling of MB-enhanced gas-liquid interfacial transport and sulfite-mediated reactive-species conversion under DBD conditions. Higher discharge power and sulfite concentration enhanced PFHxS degradation, whereas higher initial PFHxS concentration reduced removal efficiency but increased energy yield. Reactive-species identification by optical emission spectroscopy (OES), electron spin resonance (ESR), and scavenging experiments showed that PFHxS degradation proceeded through a complex oxidative-reductive network involving SO4[-]•, •OH, eaq[-], [1]O2, •O2[-], and nitrogen-related oxidizing species, among which SO4[-]• and •OH were the dominant radicals. Electronic-structure analysis indicated that PFHxS reactivity was highly localized at the sulfonate end, especially around O14, O16, and S15. Combined with LC-MS identification of intermediates, the pathways involved desulfonation, H/F exchange, hydroxylation, sequential -CF2 elimination, and C-C bond cleavage, leading to shorter-chain and structurally simplified products. Acidic conditions favored PFHxS degradation, whereas coexisting anions exerted inhibition. Nevertheless, the system still achieved 77.8% degradation in the most inhibitory realistic water matrix, demonstrating good matrix tolerance. Overall, the DBD/MBs/sulfite system provided an efficient and adaptable strategy for PFHxS removal and offered mechanistic insight into plasma-assisted degradation of perfluorinated sulfonates.},
}
@article {pmid42290710,
year = {2026},
author = {Pereira, CA and Nascimento, JM and Grellert da Silva, M and Carvalho, JT and Kaster, MP},
title = {Analysis of health infrastructure and suicide rates in Brazil: a nationwide ecological spatial-temporal study, 2009-2023.},
journal = {Lancet regional health. Americas},
volume = {60},
number = {},
pages = {101519},
pmid = {42290710},
issn = {2667-193X},
abstract = {BACKGROUND: Suicide remains a major global health concern and disproportionately affects low- and middle-income countries (LMICs), where socio-economic stressors and limited healthcare resources contribute to higher burdens. This study characterizes annual patterns of suicide rates in Brazil from January 2009 until December 2023, across its five geographic regions (North, Northeast, Southeast, South, and Central-West). Additionally, we constructed a harmonized dataset integrating sociodemographic and healthcare infrastructure indicators, and identified which municipal-level infrastructure components are most informative for classifying suicide rate categories.<br><br>METHODS: We integrated nationwide data from the Mortality Information System (SIM/SUS), the National Registry of Healthcare Establishments (CNES), and demographic estimates from the Brazilian Institute of Geography and Statistics (IBGE). Primary analyses were conducted using municipality-level annual observations across all Brazilian cities covering more than 170,000 suicide deaths nationally. Suicide was expressed annually as rates per 100,000 inhabitants and categorized as low, moderate, or high. Using a data-mining workflow with XGBoost classifier models, we identified healthcare infrastructure features most relevant for distinguishing suicide rate categories. Secondary analyses focused on the sociodemographic characterization of suicide deaths and on the distribution of Psychosocial Care Centers (CAPS), as well as their correlation with suicide rates.<br><br>FINDINGS: Across the descriptive analyses, suicide rates increased in all Brazilian regions (2009: 4&#xb7;5, 95% CI 4&#xb7;4-4&#xb7;6; 2023: 7&#xb7;6, 95% CI 7&#xb7;5-7&#xb7;7). Machine learning models identified healthcare infrastructure components (e.g., healthcare establishments, registered professionals, primary care units, diagnostic services, and mental health facilities) as the most informative features for distinguishing municipalities by suicide rate categories (low, moderate, or high), with accuracy across regions ranging from 72% (95% CI 69-75%) to 79% (95% CI 76-81%). CAPS availability was correlated with lower suicide rates across all regions (&#x3c1; = -0&#xb7;71 to -0&#xb7;81, p < 0&#xb7;01).<br><br>INTERPRETATION: In this exploratory analysis, general healthcare infrastructure features are associated with variations in suicide mortality, suggesting that access to basic and mental health services is an informative predictor for distinguishing suicide rate patterns across regions. Findings at the aggregate level cannot be assumed to be consistent at the individual level.<br><br>FUNDING: Santa Catarina State Research and Innovation Support Foundation (FAPESC) and the Research Program for the Unified Health System (PPSUS); Brazilian National Council for Scientific and Technological Development (CNPq); Department of Science and Technology of the Secretariat of Science, Technology, Innovation and the Health Economic-Industrial Complex of the Ministry of Health of Brazil (Decit/SECTICS); and Coordination for the Improvement of Higher Education Personnel (CAPES).},
}
@article {pmid42292476,
year = {2026},
author = {Zhou, Y and Li, Z and Chu, Y and Zhou, Z and Zhang, T and Yi, N and Sun, W and Yan, J and Yan, Z and Zhu, A},
title = {Reframing precision nutrition in irritable bowel syndrome: a mechanism-informed conceptual framework for responder prediction and clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1809221},
pmid = {42292476},
issn = {1664-3224},
mesh = {Humans ; *Irritable Bowel Syndrome/diet therapy/microbiology/metabolism ; *Gastrointestinal Microbiome ; FODMAP Diet ; *Precision Medicine/methods ; Multiomics ; Translational Research, Biomedical ; },
abstract = {BACKGROUND: The low-Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols (FODMAP) diet is widely used for irritable bowel syndrome (IBS), but response varies markedly across patients. This heterogeneity has shifted the field from testing average efficacy toward forecasting individual benefit and translating microbiome science into practical precision-nutrition tools.<br><br>METHODS: We present a conceptual analysis grounded in evidence mapping from human IBS studies that paired dietary interventions (primarily low-FODMAP pathways) with baseline microbiome and/or multi-omics measurements. Findings are organized within a "microbiome-to-model" roadmap that specifies responder endpoints, candidate data layers (taxa, functions, metabolites and volatile signatures), modeling choices, and the validation and implementation requirements needed for clinical decision support.<br><br>RESULTS: Three recurring signals emerge across cohorts. Baseline microbial ecology can stratify response, but taxonomic features alone often fail to transport across studies. Functional readouts, including metabolites and volatile signatures, are closer to symptom mechanisms and can improve interpretability; however, clinical deployment is still limited by endpoint heterogeneity, imperfect exposure and adherence measurement, batch effects, and insufficient external validation and calibration.<br><br>CONCLUSION: IBS is well suited for microbiome-informed responder prediction, provided that models are developed with deployment in mind. Progress will depend on validation-first study designs, harmonized responder endpoints and adherence capture, robust multi-omics pipelines, and biologically interpretable decision rules that can be prospectively tested and monitored for temporal instability in real-world care.},
}
@article {pmid42270437,
year = {2026},
author = {De Keyzer, ELR and Herder, F and Böhne, A and Jiménez, FC and Burskaia, V and Kukowka, S and Tracey, A and Denton, AL and Oatley, G and , and , and , and Mokodongan, DF and Wowor, D and Svardal, H},
title = {Ancient and Recent Riverine Gene Flow Contributed to the Adaptive Radiation of Sailfin Silversides in Wallace's Dreampond.},
journal = {Molecular ecology},
volume = {35},
number = {11},
pages = {e70414},
pmid = {42270437},
issn = {1365-294X},
support = {G0A9B24N//Fonds Wetenschappelijk Onderzoek/ ; V408023N//Fonds Wetenschappelijk Onderzoek/ ; 12A8423N//Fonds Wetenschappelijk Onderzoek/ ; 11A2P26N//Fonds Wetenschappelijk Onderzoek/ ; ID2022SIN349A102//VLIRUOS/ ; 54084//VLIRUOS/ ; ID2025SIN4SEL104//VLIRUOS/ ; 48620//Universiteit Antwerpen/ ; },
mesh = {Animals ; Indonesia ; *Gene Flow ; *Phylogeny ; *Genetic Speciation ; Hybridization, Genetic ; Lakes ; Sequence Analysis, DNA ; Rivers ; *Killifishes/genetics ; },
abstract = {While adaptive radiations significantly contribute to the world's biodiversity, much is unknown about the genetic and ecological factors underlying these rapid successions of speciation. It has been suggested that hybridisation can facilitate the speciation process by generating genetic diversity on which diversifying selection can act. Sailfin silverside fishes (Telmatherinidae) in the Malili Lakes system in Sulawesi have diversified within the last 2 million years. To establish a phylogenetic framework and investigate the presence of hybridisation in this radiation, we assembled and annotated a chromosome-scale reference genome of the riverine sailfin silverside Telmatherina bonti and generated whole genome sequences of all species of Telmatherina in Lake Matano, South Sulawesi, Indonesia, one of the world's oldest and deepest lakes. We reconstructed the phylogenetic relationships and inferred past and ongoing introgression patterns. Genome-wide tests confirmed two monophyletic clades, sharpfins and roundfins. However, within clades, we found mismatches between morphology-based taxonomic assignments and genome-wide genetic relationships. We found signs of both old and ongoing introgression between river-dwelling T. bonti and the lacustrine sharpfin group, as shown in elevated D-statistic, f4-ratio and f-branch statistic. Levels of excess allele sharing between riverine species and the three most common lacustrine species declined with increasing distance from the river-inlet, indicating ongoing introgression at the lake-river interface. This combination of past and ongoing hybridisation in a radiating species flock makes Lake Matano Telmatherina a particularly valuable system to study fundamental mechanisms driving rapid speciation under genomic exchange. The phylogenomic framework elaborated in this study provides the foundation for studies of the processes shaping this charismatic radiation.},
}
@article {pmid42275639,
year = {2026},
author = {Rueda, A and Martin, J and Parkington, K and Perivolaris, A and Teferra, BG and Lee, GH and Tassone, VK and Lin, Q and Ivanov, M and Darnell, B and Beavers, L and Campbell, DM and Torres, A and Lou, W and Nazarov, A and Ashbaugh, A and Kapralos, B and Litz, B and Jetly, R and Dubrowski, A and Strudwick, G and Krishnan, S and Bhat, V},
title = {Digital Health Monitoring and Intervention Suite for Stress in Frontline Nurses: Prospective Cohort Trial.},
journal = {JMIR formative research},
volume = {10},
number = {},
pages = {e77818},
pmid = {42275639},
issn = {2561-326X},
mesh = {Humans ; Female ; Prospective Studies ; Adult ; Digital Health ; *Nurses/psychology/statistics &amp; numerical data ; Male ; Frontline Workers/psychology ; *Stress, Psychological/psychology ; Middle Aged ; Cohort Studies ; Monitoring, Physiologic/methods/instrumentation ; },
abstract = {BACKGROUND: Stress among health care workers (HCWs) contributes to burnout, workforce attrition, and adverse patient outcomes. Although virtual reality (VR), psychoeducation, ecological momentary assessments (EMAs), and wearables have independently shown promise in stress research, no integrated digital suite has combined controlled stress induction, intervention delivery, and longitudinal real-world monitoring in HCWs.<br><br>OBJECTIVE: This study aimed to evaluate the feasibility, engagement, and preliminary effectiveness of a multimodal Digital Health Monitoring and Intervention suite for Stress framework integrating VR simulation, psychoeducation, EMAs, and wearable biometrics. We examined (1) the impact of VR simulation and psychoeducation on stress outcomes and (2) associations between physiological and self-reported mental health outcomes.<br><br>METHODS: Ninety-nine nurses (mean age 33.7, SD 8.9 yr, 87% female) were enrolled in 2023. We conducted a single-arm prospective cohort study (NCT05923398). Using convenience sampling, participants were recruited from social media advertisements, flyers, and email notices distributed through professional listservs. Participants completed &#x2265;2-week baseline monitoring, a single VR session (2 runs separated by a brief psychoeducation intervention), and 12-week follow-up. In-VR stress was assessed using the Subjective Units of Distress Scale (SUDS) and 4-item Moral Injury Outcome Scale (MIOS-4), with synchronous heart rate variability. Longitudinal outcomes included weekly and biweekly EMAs alongside 70 wearable-derived features. Paired t tests, aligned rank transform ANOVA, and Pearson correlations informed study objectives, with P values adjusted for multiple comparisons. Qualitative content analysis classified emotional responses during and after VR.<br><br>RESULTS: VR significantly increased subjective stress across checkpoints in both runs, with attenuation in Run B relative to Run A (all P<.001). No significant heart rate variability differences were observed between runs (P=.15). During VR, 92% (91/99) of participants felt stressed, 36% (36/99) reported anxiety or nervousness, and 51% (50/99)-78% (77/99) endorsed anger, guilt, shame, and/or betrayal. Most (59/99, 60%) HCWs returned to an emotional baseline post-VR, although 12% (12/99) reported lingering distress. Immediate reliable improvements in anger, guilt, shame, and/or betrayal occurred for 50% (50/99)-75% (74/99) of participants post intervention. Anxiety (mean -0.53, SD 2.34; P=.03) and stress (mean -3.05, SD 11.35; P=.01) decreased 2 weeks post intervention, but were not sustained at 12 weeks. Increased sleep restlessness was the only wearable feature showing significant changes (mean 2.46%, SD 5.43; Padj<.001). In-VR stress correlated with 12-week real-world stress (SUDS: r=0.57-0.58; MIOS-4: r=0.58-0.61; all P<.01). Data completion exceeded 90%, with 71% achieving full compliance.<br><br>CONCLUSIONS: This study moves beyond single-tool interventions to demonstrate the feasibility and preliminary effectiveness of an integrated, multimodal stress platform within a single coordinated framework. This trial demonstrates high engagement, short-term symptom responsiveness, ecological validity, and emotional safety. The framework provides a scalable model for proactive stress identification, skills training, and implementation in high-risk occupational settings. Randomized controlled trials are needed to establish sustained efficacy and optimize deployment for real-world implementation.},
}
@article {pmid42281079,
year = {2026},
author = {Mapinduzi, J and Daniels, K and Kossi, O and Verbrugghe, J and Bonnechère, B},
title = {Wearable Sensors and Artificial Intelligence for Ecological Knee Osteoarthritis Assessment: Development and Feasibility of a Hybrid Digital Phenotyping Framework.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {11},
pages = {},
pmid = {42281079},
issn = {1424-8220},
mesh = {Aged ; Female ; Humans ; Middle Aged ; Digital Health ; Feasibility Studies ; *Intelligent Systems ; *Monitoring, Physiologic/instrumentation/methods ; *Osteoarthritis, Knee/diagnosis/physiopathology ; Phenotype ; *Wearable Electronic Devices ; },
abstract = {Osteoarthritis (OA) is a highly prevalent musculoskeletal disorder and a major cause of disability, posing growing challenges for healthcare systems worldwide. Conventional supervised clinical assessments provide valuable insights but are largely limited to cross-sectional snapshots and often fail to reflect the variability of real-world functioning, physical activity patterns, and symptom fluctuations experienced by individuals with OA, especially those with knee OA. This perspective introduces a multisensor digital phenotyping framework for smart knee OA assessment, integrating supervised laboratory evaluations with unsupervised continuous monitoring in daily living environments using wearable sensors, smart insoles, activity trackers, and mobile devices. Feasibility was tested in 40 participants (20 knee OA patients, 20 controls). Raw data from questionnaires, electronic goniometry, dynamometry, force plate, connected insoles, and seven-day home monitoring were harmonized via a standardized pipeline aligned with the ICF framework. The pipeline employed anomaly detection, missing data imputation, z-score normalization, and cloud-based storage. This framework is envisioned to facilitate advanced data integration and machine-learning-ready analytics, enabling longitudinal monitoring, pattern recognition, and individualized health profiling. By conceptually bridging cross-sectional and continuous sensing modalities, this approach has the potential to enhance ecological validity, support earlier identification of functional decline, and inform data-driven clinical decision-making. Key methodological, technological, and ethical challenges-including data quality, interpretability, privacy, digital literacy, and clinical adoption-are also highlighted. Overall, this paper underscores the promise of AI-enabled multisensor digital phenotyping to advance smart, personalized, and precision healthcare for individuals with knee OA.},
}
@article {pmid41722541,
year = {2026},
author = {Ashaolu, TJ and Suttikhana, I},
title = {Probiotic therapeutics: A critical review of mechanisms, clinical efficacy, and the frontier of precision microbiome modulation.},
journal = {International immunopharmacology},
volume = {175},
number = {},
pages = {116412},
doi = {10.1016/j.intimp.2026.116412},
pmid = {41722541},
issn = {1878-1705},
mesh = {*Probiotics/therapeutic use ; Humans ; Animals ; Precision Medicine ; *Gastrointestinal Microbiome ; Multiomics ; Irritable Bowel Syndrome/therapy/microbiology ; },
abstract = {Probiotic therapeutics are evolving from generalized wellness supplements to precision Live Biotherapeutic Products aimed at specific disease targets. This review elucidates the multi-layered mechanistic framework of probiotic action, which spans ecological niche modulation, epithelial barrier reinforcement, and systemic signaling via the gut-brain axis. While clinical efficacy is established for conditions like antibiotic-associated diarrhea, trial outcomes remain highly heterogeneous for complex disorders such as irritable bowel syndrome and metabolic syndrome. We deconstruct this variability, attributing it to critical factors often overlooked in study design: stringent strain-specificity, host-specific colonization resistance, and the lack of standardized core outcome sets. The field is now advancing toward precision microbiome modulation through next-generation biotics like Akkermansia muciniphila, synbiotics, and engineered microbial therapeutics. We conclude that integrating multi-omics technologies with artificial intelligence is essential to transition from empirical supplementation to personalized, evidence-based clinical practice.},
}
@article {pmid42025964,
year = {2026},
author = {Liao, Z and Chen, Y and Wang, L and Chen, A and Gu, X and Li, X and Guo, Y and Du, Z and Li, W and Zhu, B and Zhao, W and Niu, J},
title = {Gut-Liver Axis Disruption Induced by Total Fish Oil Substitution with Black Soldier Fly Oil Impairs Growth and Health in Rainbow Trout (Oncorhynchus mykiss): Insights from Multiomics Analysis.},
journal = {The Journal of nutrition},
volume = {156},
number = {6},
pages = {101545},
doi = {10.1016/j.tjnut.2026.101545},
pmid = {42025964},
issn = {1541-6100},
mesh = {Animals ; *Liver/drug effects/metabolism ; *Fish Oils/pharmacology/administration &amp; dosage ; *Oncorhynchus mykiss/growth &amp; development ; Multiomics ; Animal Feed/analysis ; Gastrointestinal Microbiome/drug effects ; *Gastrointestinal Tract/drug effects ; Diet/veterinary ; },
abstract = {BACKGROUND: Black soldier fly oil (BSFLO) is a sustainable alternative to fish oil (FO), but its dose-dependent effects on fish health remain unclear.<br><br>OBJECTIVES: This study evaluated the effects of dietary BSFLO on growth, liver health, fillet quality, and gut-liver metabolism in rainbow trout.<br><br>METHODS: In a feeding trial, 480 rainbow trout (initial body weight: 215.16 &#xb1; 2.30 g; 12 mo old) were allocated to 6 dietary treatments (4 replicate tanks per treatment, 20 fish per tank): FO control or BSFLO replacing FO at 20% (BSFLO20), 40% (BSFLO40), 60% (BSFLO60), 80% (BSFLO80), or 100% (BSFLO100). After 8 wk of feeding trail, growth performance, plasma biochemistry, tissue histology, gut microbiota (16S rRNA), and multiomics (transcriptomics, proteomics, and metabolomics) were analyzed.<br><br>RESULTS: The BSFLO60 and BSFLO80 groups had significantly higher growth rate compared with FO (P < 0.05). The hepatosomatic index increased in BSFLO40, BSFLO60, BSFLO80, and BSFLO100 groups (P < 0.05). The BSFLO100 group exhibited a lower aspartate aminotransferase-to-alanine transaminase ratio in plasma, and hepatic tissue showed more lipid vacuolation. In muscles, hardness, springiness, and chewiness decreased in the BSFLO100 group, while adhesiveness and cohesiveness increased (P < 0.05). Gut microbiota analysis showed higher abundance of Firmicutes and Staphylococcus species in the BSFLO100 group. Transcriptomics and qRT-PCR revealed upregulation of srebp1, ppar&#x3b1;, ppar&#x3b3;, fasn, acc1, and atgl, with downregulation of cpt1. Proteomics and Western blotting indicated that BSFLO100 led to the upregulation of peroxisome proliferator-activated receptor &#x3b3; expression and acetyl-CoA carboxylase phosphorylation, along with inhibited phosphorylation of AMP-activated protein kinase &#x3b1; and carnitine palmitoyltransferase 1. Metabolomics showed reductions in SFAs and MUFAs, increases in omega-3 PUFAs, elevated glycolytic intermediates and amino acids, and declines in tricarboxylic acid cycle- and glutamate-related metabolites.<br><br>CONCLUSIONS: A moderate BSFLO inclusion (60%) improves growth, whereas complete replacement (100%) reshapes the gut microbiota, activates the peroxisome proliferator-activated receptor &#x3b3; lipogenic axis, and suppresses AMP-activated protein kinase/oxidative pathways, jointly inducing hepatic steatosis and inferior muscle texture.},
}
@article {pmid42098572,
year = {2026},
author = {Wang, WL and Yang, CH and Nordgren, R and Li, J and Intille, S and Dunton, GF and Hedeker, D},
title = {Modeling intraindividual means and variances from ecological momentary assessment data: comparing standard computational formulas to mixed-effects location-scale model estimates.},
journal = {Journal of behavioral medicine},
volume = {49},
number = {2},
pages = {254-274},
pmid = {42098572},
issn = {1573-3521},
support = {R01 CA240713/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Ecological Momentary Assessment/statistics &amp; numerical data ; *Models, Statistical ; Computer Simulation ; Data Interpretation, Statistical ; },
abstract = {Traditionally, intraindividual means and variances derived from ecological momentary assessment (EMA) data have been calculated using standard computational formulas (SCF), such as subject-level means and standard deviations. However, these SCF methods assume uniform precision across subjects, disregarding variation in the number of observations, missing data issues, and the non-continuous nature of data scales. This study evaluated the predictive accuracy of the coefficients of intraindividual means and variances computed via SCF against those estimated using random effects from a Mixed-Effects Location Scale (MELS) model. A five-scenario simulation study was conducted: (1) varying numbers of observations per subject, (2) varying mean-to-variance ratios, (3) varying proportions of missing data under a missing completely at random (MCAR) assumption, (4) varying proportions of missing data under a missing at random (MAR) assumption, and (5) varying categories of ordinal scale responses. Bias and coverage of the mean levels and variability coefficients were compared across methods. In addition, a real-life dataset was used to compare the difference of means and variances between SCF and MELS approaches. Results consistently showed that the MELS model approach outperformed SCF method, yielding lower bias and higher coverage of the coefficients across all scenarios. These findings support the use of MELS for more accurate and reliable estimation of intraindividual means and variances in EMA data, highlighting its advantages for subsequent predictive modeling.},
}
@article {pmid42172788,
year = {2026},
author = {Ge, H and Wang, J and Wu, DY and Zhou, H},
title = {Investigating the relationship between psychological stress and physical activity through individual-based geographic ecological momentary assessment.},
journal = {Social science &amp; medicine (1982)},
volume = {403},
number = {},
pages = {119411},
doi = {10.1016/j.socscimed.2026.119411},
pmid = {42172788},
issn = {1873-5347},
mesh = {Humans ; *Stress, Psychological/psychology/epidemiology ; Female ; *Ecological Momentary Assessment ; Ontario ; Male ; Adult ; *Exercise/psychology ; Accelerometry ; Geographic Information Systems ; Young Adult ; Middle Aged ; Self Report ; },
abstract = {Physical Activity (PA) is known to buffer stress, yet evidence remains limited when examining real-time stress responses alongside objective measures of activity and environmental exposures in daily life. To address the gap, this study employs a Geographic Ecological Momentary Assessment (GEMA) framework that integrates accelerometer, GPS tracking, and survey data. The primary objective of this study is to assess the association between self-reported psychological stress and moderate-to-vigorous physical activity (MVPA) during the hours preceding GEMA prompts. Additionally, the study examines whether engaging in MVPA later in the day is associated with greater reductions in stress relative to morning baseline levels. Data were collected from 130 participants in the City of Mississauga, Ontario, over 7 days. Results revealed that higher levels of MVPA in the 5-h window preceding GEMA prompts were associated with significantly lower odds of reporting higher stress. On weekends, the stress-reduction effect was stronger after completing PA later in the day than on weekdays. Lower-income participants engaged in outdoor MVPA in environments perceived as safer, more beautiful, and greener compared to those of higher-income participants. Yet, no significant association was found between stress and environmental exposures, possibly because aggregated exposure measures were not sensitive enough to capture short-term changes in the daily context. The findings demonstrate the value of GEMA in capturing interactions among behaviour, environment, and health, and suggest that future research should apply more dynamic GEMA approaches to better assess short-term environmental exposures and stress.},
}
@article {pmid42256231,
year = {2026},
author = {Gomez-Ramirez, U and De La Torre-González, C and Villamor, P and Huante Guido, M and Contreras-Rodríguez, A and Velázquez-Guadarrama, N},
title = {Recolonization dynamics of the middle ear microbiota following MESNA-assisted dissection in pediatric cholesteatomatous chronic otitis media.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1830192},
pmid = {42256231},
issn = {2235-2988},
mesh = {Humans ; *Microbiota/drug effects ; *Otitis Media/microbiology/surgery ; RNA, Ribosomal, 16S/genetics ; *Ear, Middle/microbiology/surgery ; *Mesna/therapeutic use ; Chronic Disease ; Child ; Female ; Male ; Bacteria/classification/genetics/isolation &amp; purification ; *Cholesteatoma, Middle Ear/surgery/microbiology ; Child, Preschool ; DNA, Bacterial/genetics ; Computational Biology ; Sequence Analysis, DNA ; },
abstract = {INTRODUCTION: Cholesteatomatous chronic otitis media (CCOM) remains a clinical challenge due to its high recurrence rates despite surgical intervention. Sodium 2-mercaptoethanesulphonate (MESNA) is used to assist dissection, yet its impact on the middle ear microbiome and ecological recovery remains poorly understood. The aim of this study is to characterize the microbiota of paediatric CCOM and evaluate the ecological shifts induced by MESNA-assisted surgery.<br><br>METHODS: We analyzed 16S rRNA gene sequences (V3-V4) from middle ear tissue of paediatric patients with CCOM (CCOM Before MESNA, n = 13; CCOM After MESNA, n = 13) and healthy controls (n = 11). Bioinformatic processing was performed via QIIME2 and DADA2. We employed a Compositional Data Analysis (CoDA) framework, centering on Aitchison distances, ALDEx2 for differential abundance, and consensus co-occurrence networks (SparCC, SPIEC-EASI, and CLR-Pearson). Functional potential was inferred using PICRUSt2.<br><br>RESULTS: CCOM was associated with a marked reduction in microbial network connectivity, decreasing from 185 edges in healthy controls to only two total edges in the CCOM Before MESNA stage. Cutibacterium emerged as a candidate keystone pathobiont, exhibiting profound ecological isolation and predicted metabolic shifts toward lipid catabolism and biofilm formation in dysbiotic states. MESNA application disrupted the disease-associated community equilibrium, initiating secondary succession. However, post-treatment recovery was marked by taxonomic homogenization and the expansion of Pseudomonas in several patients.<br><br>DISCUSSION: Our findings identify network fragmentation and functional dysbiosis as the ecological signatures of pediatric CCOM. While MESNA disrupts the dysbiotic equilibrium, it does not fully restore a healthy stable climax community within the studied timeframe, as defined in ecological succession theory. These results support a paradigm shift from simple pathogen eradication toward ecological restoration as a strategy to prevent disease recurrence in CCOM patients.},
}
@article {pmid42258566,
year = {2026},
author = {Tran-Nam, H and Che-Ngoc, H},
title = {A black-winged kite improved fuzzy clustering handling imbalanced uncertain data.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0349753},
pmid = {42258566},
issn = {1932-6203},
mesh = {Clustering Algorithms ; *Fuzzy Logic ; Algorithms ; *Data Mining/methods ; Cluster Analysis ; Soft Computing ; Uncertainty ; },
abstract = {Clustering uncertain data is a fundamental problem in data mining. Imbalance among uncertain objects significantly degrades clustering performance, as minority clusters are repeatedly overshadowed by dominant ones. Consequently, existing clustering techniques often fail due to initialisation biases and inadequate similarity modelling. This paper proposes a novel algorithm, the Black-winged Kite Improved Fuzzy clustering for probability density Functions (BKIFF), which combines an optimisation-based initialisation strategy with an enhanced fuzzy clustering framework. Specifically, BKIFF incorporates the Hellinger distance into the clustering objective to more reliably capture similarities between probability density functions (pdfs), and introduces improved membership updating and prototype estimation mechanisms tailored for uncertain and imbalanced data formulated as Improved Fuzzy clustering for probability density Functions (IFF) while theoretical convergence is established. In addition, the algorithm employs Black-winged Kite Optimisation (BKO) to enhance prototype selection, improving clustering stability and convergence. As a result, comprehensive experiments with synthetic Gaussian probability distributions, skewed pdfs, and real-world image datasets demonstrate that BKIFF consistently outperforms baseline methods such as FCF, FCF-[Formula: see text], KMEANS, and Self-Updating. Across all three examples, BKIFF achieves near-perfect ARI, improving from near-zero values in highly imbalanced cases {20,50,80,100}
by approximately 30-35% in moderate settings, while increasing NMI by about 25-95%. Additionally, it reduces computational time by approximately 95-99% compared to baseline methods. In conclusion, BKIFF demonstrates superior performance and opens up new possibilities for applications in medical diagnostics, ecological analysis, and high-dimensional uncertain data mining, particularly in imbalanced environments.},
}
@article {pmid42263378,
year = {2026},
author = {Zeng, Y and Makuková, J and Báčová, J and Roušar, T and Ševčovičová, A and Roch, T and Qin, P and Jelínková, &#x160; and Vlček, A and Wu, Y and Monfort, O and Motola, M},
title = {When TiO2 meets pharmaceuticals: Photocatalytic degradation and environmental safety unveiled.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120353},
doi = {10.1016/j.ecoenv.2026.120353},
pmid = {42263378},
issn = {1090-2414},
abstract = {Building on our previous work on electrochemically synthesized anatase TiO2 nanoparticles (NPs), this study evaluates their environmental relevance by linking pharmaceutical photocatalytic degradation with transformation product identification and toxicity-oriented assessment. The incomplete removal of pharmaceuticals in wastewater treatment plants raises concerns about both parent compounds and transformation products formed during advanced treatments. Here, the synthesized TiO2 NPs were applied to the photocatalytic degradation of ibuprofen (IBU) and paracetamol (PCT) under ultraviolet A (UVA) irradiation. The TiO2 NPs showed higher degradation efficiency than commercial P25, with Kobs of 10.82 × 10[-3] min[-1] for IBU and 10.75 × 10[-3] min[-1] for PCT, and approximately 95% removal for both pollutants after 4 h of UVA irradiation. Liquid chromatography tandem mass spectrometry (LC-MS/MS) identified 8 transformation products for IBU and 9 for PCT, suggesting degradation pathways involving hydroxylation, decarboxylation, bond cleavage, and formation of smaller oxygenated products. In-vitro assays were performed using A549 lung cells and HepG2 liver cells. In A549 cells, TiO2 NPs caused no significant decrease in dehydrogenase activity at 1-100 µg/mL after 24 and 48 h. In HepG2 cells, TiO2 NPs showed lower cytotoxicity than P25, with viability remaining at approximately 68% after 48 h at 250 µg/mL, compared with about 60% for P25. IBU and PCT solutions before and after 4 h of photocatalytic treatment maintained HepG2 viability above 90%. The toxicity-oriented assessment, supplemented by Ecological Structure Activity Relationships (ECOSAR) software predictions, suggested that further transformation could reduce predicted ecological concern.},
}
@article {pmid42269581,
year = {2026},
author = {Jimenez, MF and Khalighifar, A and Horton, KG},
title = {Within-Night Variation in Predictor Importance Highlights Dynamic Nature of Bird Migration.},
journal = {Ecology letters},
volume = {29},
number = {6},
pages = {e70422},
pmid = {42269581},
issn = {1461-0248},
support = {/NASA/NASA/United States ; },
mesh = {Animals ; *Animal Migration ; *Birds/physiology ; Seasons ; Radar ; },
abstract = {Ecological forecasting is increasingly important for conservation. Predicting nocturnal bird migration events is a promising vehicle for forecasts but isn't often explored at fine temporal scales. We use weather surveillance radar to examine dynamic drivers of migration in 2-h periods throughout a night. We assess the relative importance of terrestrial, atmospheric and sampling predictors (which relate to radar position and scan timing) across spring and fall. Atmospheric conditions were consistently strong predictors. In contrast, terrestrial predictors contributed relatively little to explaining variation in activity. Sampling variables, such as time after sunset, varied in importance, with the highest influence shortly after sunset. We highlight the temporal variability in predictors of migration, emphasising it as a dynamic process, involving continuous decisions and adjustments rather than following fixed routes. We underscore the value of radar for capturing transitions between habitats while revealing key limitations and opportunities for understanding fine-scale migratory behaviour.},
}
@article {pmid42269612,
year = {2026},
author = {Balakrishnan, CN and Toda, Y and Ko, MC and Wirthlin, ME and Driver, RJ and Bolton, PE and Miller, ET and Mendez-Aranda, D and Dikow, RB and Frandsen, PB and Shogren, EH and Bennett, KFP and Anderson, HL and Bursell, MG and Cramer, JF and Sadanandan, KR and Nakagita, T and Pizo, MA and Caetano, DS and Anciães, M and Ferreira, CF and Berv, JS and Long, KM and Lim, HC and Moncrieff, AE and Kingston, SE and White Carreiro, ND and Friedrich, SR and Cuta, CA and Pease, JB and Nevue, AA and Tomlinson, C and Zimin, A and Louder, MIM and Brewer, MS and Bay, RA and Ruegg, K and Smith, TB and Ishimaru, Y and Pfenning, AR and Frankl-Vilches, C and Gahr, M and Mello, CV and Kimball, RT and Braun, EL and Blake, JG and Day, LB and Ryder, TB and Moore, IT and Horton, BM and Schlinger, BA and Fuxjager, MJ and Warren, WC and DuVal, EH and Boyle, WA and Loiselle, BA and Braun, MJ and Baldwin, MW},
title = {Genomic and physiological changes in a sexually selected and frugivorous bird radiation.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.05.021},
pmid = {42269612},
issn = {1879-0445},
abstract = {Across diverse organisms, the strength and ecological drivers of sexual selection vary enormously. In birds, some of the families with the most elaborate plumage and display-such as birds of paradise, manakins, and cotingas-are also specialist frugivores, yet links between shifts in diet, changes in breeding system, and the evolution of elaborate traits are poorly understood. We focus on manakins, a radiation of frugivorous Neotropical birds well known for spectacular courtship rituals and colorful plumage, and present an integrative analysis of the transition in both diet and mating systems in this clade to examine the causes and consequences of strong sexual selection. In manakins, we find reduced genetic diversity on the Z sex chromosome relative to autosomes, a predicted signature of sexual selection. We also identify targets of positive selection across the manakin radiation, including genes related to muscle function, visual perception, and the transition to frugivory. Among these, we observe selection on sugar-sensing taste receptors, as well as on lactase-phlorizin hydrolase, implicated in the consumption of chemically defended fruits. For both, we confirm that selection signatures correspond to functional changes and infer the relative time of these changes, as well as of shifts in diet, breeding systems, and plumage coloration: elaborated traits evolved subsequent to changes in mating systems and after key physiological changes facilitating fruit-eating. Altogether, these results suggest that intensified frugivory set the stage for the radiation of one of the planet's most colorful and acrobatic avian lineages.},
}
@article {pmid41725240,
year = {2026},
author = {Anum, H and Ishfaq, S and Yu, K and Krutovsky, KV and Cheng, R and Tong, Y},
title = {Integrated Physiological and Omics Responses of Red Lettuce (Lactuca sativa) Driven by Varying Light Spectrum: Insights Into Anthocyanin Synthesis.},
journal = {Physiologia plantarum},
volume = {178},
number = {1},
pages = {e70791},
doi = {10.1111/ppl.70791},
pmid = {41725240},
issn = {1399-3054},
support = {2022YFDZ0086//Key Research and Development Program, Department of Science and Technology, Inner Mongolia Autonomous Region, China/ ; //Innovation Project of the Institute of Evironment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China/ ; },
mesh = {*Lactuca/radiation effects/physiology/genetics/metabolism ; *Anthocyanins/biosynthesis/metabolism ; *Light ; Gene Expression Regulation, Plant/radiation effects ; Plant Leaves/radiation effects/metabolism/physiology ; Multiomics ; Chlorophyll/metabolism ; Gene Expression Profiling ; Flavonoids/metabolism ; Transcriptome ; Plant Proteins/metabolism/genetics ; },
abstract = {The health benefits of anthocyanins for humans are well established. However, the influence of spectral light composition in plant factories on plant growth and anthocyanin biosynthesis remains poorly understood. This study selected red lettuce as a model plant due to its high anthocyanin content. Using a plant factory with artificial lighting, we applied three light treatments: control (R:B = 160:40), T1 (R:B:G = 130:20:50) and T2 (R:B:G = 75:75:50) to examine their effects on plant physiology and anthocyanin production. A multi-omics analysis further identified potential pathways and genes regulating anthocyanin synthesis under different light conditions. Plants under T2 had higher levels of anthocyanins, flavonoids, phenolics, and carotenoids. Conversely, fresh and dry biomass, total leaf area, chlorophyll content, and sugar levels were higher in red lettuce leaves grown under T1. In total, 110 anthocyanidin metabolites and 573 genes showed differential expression under different light combinations. Transcriptomic analysis revealed a substantial increase in the activity of genes related to anthocyanin precursors, such as PAL and 4-CL, as well as structural genes involved in anthocyanin synthesis, including F3H, DFR, ANS, and UDP-glucosyltransferase, specifically under T2. Furthermore, our findings identified 14 transcription factors, comprising 4 bHLH, 3 MYB, 3 bZIP, and 4 WRKY genes, which could play crucial roles in regulating anthocyanin biosynthesis. These findings lay the groundwork for investigating the molecular mechanisms underlying anthocyanin biosynthesis in lettuce leaves. Moreover, they provide valuable insights that could contribute to advancements in leaf color genetics for lettuce production in plant factories.},
}
@article {pmid41752312,
year = {2026},
author = {Alhassan, GN and Ozturkcan, A and Cavdar, SC},
title = {Global Disparities in Teletherapy Adoption: A Cross-Income Analysis of Mental Health Access.},
journal = {International journal of environmental research and public health},
volume = {23},
number = {2},
pages = {},
pmid = {41752312},
issn = {1660-4601},
mesh = {Humans ; Mental Health Teletherapy ; *Health Services Accessibility/statistics &amp; numerical data ; Developing Countries ; *Healthcare Disparities/statistics &amp; numerical data ; *Mental Disorders/therapy ; Digital Health ; Socioeconomic Disparities in Health ; *Telemedicine ; },
abstract = {Mental health disorders affect nearly one billion people worldwide, yet treatment gaps exceed 75% in low- and middle-income countries. Teletherapy has emerged as a scalable solution, but its adoption differs sharply by economic context. This comparative ecological policy analysis used secondary aggregate data from WHO, World Bank, ITU, and national reports to examine teletherapy adoption in low-income (Nigeria, Kenya), middle-income (South Africa, India), and high-income countries (Norway, Canada). Descriptive statistics and simple linear regression were applied, with findings interpreted through the Consolidated Framework for Implementation Research (CFIR), Technology Acceptance Model (TAM), and Diffusion of Innovations theory. High-income countries achieved widespread adoption (>70%), enabled by universal broadband, comprehensive regulation, and strong reimbursement. Middle-income countries showed moderate uptake (15-30%), constrained by rural-urban digital divides and inconsistent policies. Low-income countries reported minimal integration (<5%), limited by unreliable internet, severe workforce shortages, high data costs, and sociocultural barriers. Digital infrastructure, regulatory maturity, and mental health workforce density explained 78% of the cross-country variance in adoption rates (R[2] = 0.78). Equitable scale-up of teletherapy directly supports SDGs 3, 9, 10, and 17. Targeted investment and cross-income collaboration are essential to prevent digital mental health solutions from exacerbating existing inequities.},
}
@article {pmid41761014,
year = {2026},
author = {Karmakar, D and Saha, P},
title = {In silico structural and dynamic stability analysis of an endo-1,4-β-xylanase from Agrobacterium sp. strain DKPNP3, isolated from the gut of Gonocephalum sp.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {3},
pages = {},
pmid = {41761014},
issn = {1572-9699},
mesh = {*Coleoptera/microbiology ; Animals ; Molecular Dynamics Simulation ; Enzyme Stability ; *Agrobacterium/enzymology/isolation &amp; purification/genetics/classification ; *Endo-1,4-beta Xylanases/chemistry/metabolism/genetics ; Molecular Docking Simulation ; Protein Conformation ; Phylogeny ; Amino Acid Sequence ; Computational Biology ; Computer Simulation ; Models, Molecular ; Molecular Weight ; },
abstract = {Xylanases are one of the most important hydrolytic enzymes involved in plant hemicellulose degradation with potential industrial as well as ecological significance. This study presents a comprehensive characterization of an endo-1,4-β-xylanase enzyme from Agrobacterium sp. Strain DKPNP3 isolated from the beetle gut of Gonocephalum sp. (Coleoptera: Tenebrionidae). Bioinformatics analyses were performed, including physicochemical characterization, phylogenetic assessment, conserved domain identification, secondary and tertiary structure prediction, subcellular localization prediction, homology modeling, structural validation, molecular docking and molecular dynamics simulation to assess the stability of this protein. The enzyme belongs to the glycoside hydrolase family 10 (GH10) with 339 amino acids, molecular weight of 37.8 kDa, and acidic in nature (pi 5.8). The homology model demonstrated high structural reliability, with an ERRAT score of 96.364% and a QMEAN Z-score of 0.59. Molecular dynamics simulations demonstrated that the enzyme is structurally stable in both its apo and ligand-bound forms. The apo form showed stability comparable to a well-characterized synthetic construct xylanase from Bacillus halodurans (GenBank accession number: MW311490), which was used as a positive control. Furthermore, simulations performed at multiple temperatures indicated retention of conformational integrity under different thermal conditions, suggesting potential thermostability. The intracellular nature of the enzyme, as predicted by in silico analysis, was confirmed by experimental validation using Congo Red-xylan agar assay and quantification with di nitro salicylic acid (DNSA).},
}
@article {pmid41762157,
year = {2026},
author = {Ryan, SJ and Huxley, PJ and Lippi, CA and Pawar, S and Cator, L and Rund, SSC and Johnson, LR},
title = {MIReVTD, a minimum information standard for reporting vector trait data.},
journal = {GigaScience},
volume = {15},
number = {},
pages = {},
pmid = {41762157},
issn = {2047-217X},
support = {2016265//NSF/ ; 2016264//NSF/ ; 2016282//NSF/ ; },
mesh = {Animals ; *Aedes/genetics ; Humans ; *Mosquito Vectors/genetics ; *Computational Biology/methods ; *Software ; Vector Borne Diseases/transmission ; },
abstract = {Vector-borne diseases pose a persistent and increasing challenge to human, animal, and agricultural systems globally. Mathematical modeling frameworks incorporating vector trait responses are powerful tools for assessing risk and predicting vector-borne disease impacts. Developing these frameworks and the reliability of their predictions hinge on the availability of experimentally derived vector trait data for model parameterization and inference of the biological mechanisms underpinning transmission. Trait experiments have generated data for many known and potential vector species, but the terminology used across studies is inconsistent, and accompanying publications may share data with insufficient detail for reuse or synthesis. The lack of data standardization can lead to information loss and prohibit analytical comprehensiveness. Here, we present MIReVTD, a Minimum Information standard for Reporting Vector Trait Data. Our reporting checklist balances completeness and labor intensity to make these important experimental data easier to find and reuse, without onerous effort for scientists generating the data. To illustrate the standard, we provide an example reproducing results from an Aedes aegypti mosquito study.},
}
@article {pmid41771790,
year = {2026},
author = {Wang, S and Zhou, T and Wang, X and Zhao, J and Wang, X},
title = {Bridging the gap: Prevotella/Segatella's impact on gut barrier function and advanced cultivation strategies to realize the uses in gut health.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638001},
pmid = {41771790},
issn = {1949-0984},
mesh = {Humans ; Intestinal Barrier Function ; *Prevotella/growth &amp; development/physiology/isolation &amp; purification/genetics ; *Gastrointestinal Microbiome ; Probiotics ; Animals ; Multiomics ; },
abstract = {Prevotella and Segatella are important, keystone genera in the gut microbiota, renowned for their exceptional fiber-degrading capacity. These genera critically modulate gut microbial composition, influence host metabolic pathways and gut barrier function, and exhibit formidable ecological niche competitiveness, underscoring their pivotal role in gut ecosystem dynamics. While they dominate healthy gut microbiomes, their probiotic potential on epithelial barrier function has been disproportionately overlooked. This review comprehensively elucidates their microbial eco-profiling and the underlying molecular mechanisms in sustaining intestinal barrier function, considering physical, chemical, biological, and microbiological dimensions, thereby providing insights relevant to the prevention and treatment of intestinal diseases such as inflammatory bowel disease, irritable bowel syndrome, and metabolic disorders. Most importantly, we have summarized 23 current commercial and research-based isolation and cultivation approaches for Prevotella/Segatella, integrating the emerging high-throughput methodologies to expand the available strain repertoire. We also emphasize the critical need for subsequent research to characterize strain-specific functional profiles through multi-omics approaches, which will be essential for developing targeted and personalized microbial therapeutics.},
}
@article {pmid41772970,
year = {2026},
author = {Javal, M and Lehmann, P and Bierman, A and Koštál, V and Moos, M and Smit, C and Vogel, H and Conlong, DE and Terblanche, JS},
title = {Integrative -omics approaches reveal mechanisms of combined heat stress and extreme hypoxia tolerance in a Cerambycid beetle larva.},
journal = {The Journal of experimental biology},
volume = {229},
number = {6},
pages = {},
doi = {10.1242/jeb.251552},
pmid = {41772970},
issn = {1477-9145},
support = {//Stellenbosch University/ ; //South African Sugarcane Research Institute/ ; },
mesh = {Animals ; *Coleoptera/physiology/growth &amp; development/genetics ; Larva/physiology/growth &amp; development/genetics ; *Heat-Shock Response ; Transcriptome ; Metabolomics ; *Metabolome ; Multiomics ; *Oxygen/metabolism ; *Thermotolerance ; Hot Temperature ; },
abstract = {Atmospheric oxygen, which is essential for energy metabolism, can directly influence an animal's heat tolerance by affecting oxygen transport processes, especially in those living in oxygen-poor environments such as plant tissues, underground or aquatic environments. Yet, oxygen availability and heat tolerance are rarely studied together, limiting our ability to predict their combined effects on insect performance. This study examines the larval tolerance of a large xylophagous cerambycid beetle Cacosceles newmannii to combined hypoxic and thermal stress using performance assays (duration of righting response) coupled with metabolomic and transcriptomic analyses. Metabolomic profiling showed that most metabolites were downregulated in the body but upregulated in the haemolymph as stress increased. Transcriptomic profiles clustered primarily by temperature (25°C vs 35°C), independent of oxygen level. Cacosceles newmannii appeared capable of modulating its performance to reduce the energy costs and physiological damage induced by hypoxia. This suggested a high baseline hypoxia tolerance rather than a rapid plastic (induced) physiological hypoxia response, probably due to the species' endophytic lifestyle. Conversely, thermal stress led to a predictable increase in metabolic activity but did not markedly affect performance, triggering adjustments to maintain cellular functions while limiting the impact of stresses expected under conditions of high temperature, such as desiccation. In short, our study highlights the distinct metabolic pathways mobilised to cope with hypoxic versus thermal stress, emphasizing the importance of integrated approaches in understanding insect responses to environmental challenges. These findings have significant implications for understanding the ecology of the species, with applications for pest management and sustainable agriculture in the context of climate change.},
}
@article {pmid41777690,
year = {2026},
author = {Ivanova, NV and Watson, LC and Comte, J and Bessonov, K and Abrahamyan, A and Crevecoeur, S and Watson, SB},
title = {Rapid assessment of phytoplankton assemblages using Next Generation Sequencing and Barcode of Life Data System: a widely applicable HAB-ID toolkit for detecting and monitoring biodiversity loss and harmful algal blooms.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20747},
pmid = {41777690},
issn = {2167-8359},
mesh = {*Phytoplankton/genetics/classification ; *High-Throughput Nucleotide Sequencing/methods ; *Harmful Algal Bloom ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Cyanobacteria/genetics/classification ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Harmful algal blooms have important implications for the health, functioning, and services of aquatic ecosystems. Our ability to detect and monitor these events is often challenged by the lack of rapid and cost-effective methods to identify bloom-forming organisms and their potential for toxin production. Here, we developed and applied a combination of DNA barcoding and Next Generation Sequencing (NGS) for the rapid assessment of phytoplankton community composition with a focus on two important indicators of ecosystem health: toxigenic bloom-forming cyanobacteria and impaired planktonic biodiversity. To develop this molecular toolset for identification of cyanobacterial and algal species present in HABs (harmful algal blooms), hereafter called HAB-ID, we achieved three goals: creating a validated reference database, optimizing molecular protocols, and developing original bioinformatics pipeline tailored to uncertainty of algal taxonomy. The BOLD (Barcode of Life Data System) 16S reference database from cultures of 211 cyanobacterial and algal strains representing 102 species with particular focus on bloom and toxin producing taxa was constructed with Sanger sequencing and further refined using Single Molecule Real Time Sequencing (SMRT-sequencing). Using the new reference database of 16S rDNA sequences and constructed mock communities of mixed strains for protocol validation, we developed new NGS primer sets which can recover 16S from both cyanobacteria and eukaryotic algal chloroplasts. We also developed DNA extraction protocols for cultured algal strains and environmental samples, which match commercial kit performance and offer a cost-efficient solution for large scale ecological assessments of harmful blooms while giving benefits of reproducibility and increased accessibility. Our innovative bioinformatics pipeline was designed to handle low taxonomic resolution for problematic genera of cyanobacteria such as the Anabaena-Aphanizomenon-Dolichospermum complex, two clusters of Anabaena (I and II), Planktothrix and Microcystis. This newly developed HAB-ID toolset was further validated by applying it to assess cyanobacterial and algal composition in field samples from waterbodies with recurrent HABs events.},
}
@article {pmid41790862,
year = {2026},
author = {Acs, R and Ibrahim, A and Zhuang, H and Chérubin, LM},
title = {Contrastive learning for passive acoustic monitoring: A framework for sound source discovery and cross-site comparison in marine soundscapes.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1014005},
pmid = {41790862},
issn = {1553-7358},
mesh = {*Acoustics ; Animals ; Clustering Algorithms ; *Sound ; Computational Biology ; *Environmental Monitoring/methods ; Cluster Analysis ; Sound Spectrography/methods ; Fishes/physiology ; Autoencoder ; Marine Biology/methods ; Biodiversity ; *Machine Learning ; Reproducibility of Results ; Signal Processing, Computer-Assisted ; Aquatic Organisms/physiology ; },
abstract = {Passive acoustic monitoring (PAM) is a powerful tool for studying marine biodiversity, but large-scale analysis of underwater recordings is constrained by noise, overlapping signals, and limited labeled data. Here, we present a scalable, unsupervised contrastive learning framework for marine soundscapes. Using a large PAM dataset spanning multiple biogeographies, we show that the proposed approach organizes recordings into clusters with well-defined internal structure, as assessed using intrinsic clustering metrics and within-cluster similarity. The resulting clusters reveal recurring acoustic patterns that correspond to broad sound-source categories, including biological sounds such as fish calls and choruses, and anthropogenic sounds such as vessel noise, without explicitly enforcing these distinctions during training. Compared with established approaches, including cepstral features, variational autoencoders, and supervised pipelines, the proposed framework produces embeddings that support more compact and stable unsupervised clustering while preserving fine-scale acoustic variation beyond predefined species labels. By learning a shared representation across recordings from multiple sites and years, we examine the reproducibility of acoustic patterns across locations and identify both site-shared and site-specific sound signatures. Although the method is not designed to recover coarse species labels, it enables label-efficient analysis by reducing reliance on manual annotation and supporting exploratory characterization of complex marine soundscapes. Together, these results highlight multi-positive contrastive learning with a teacher network and acoustically informed augmentations as an effective strategy for scalable, discovery-driven analysis of passive acoustic monitoring data.},
}
@article {pmid41794632,
year = {2026},
author = {Salamat, NA and Zulkifli, NW and Wong, YY and Karuppannan, M and Wahab, MSA},
title = {Multifaceted interventions to enhance patient's adherence to self-monitoring blood glucose: A systematic review.},
journal = {Primary care diabetes},
volume = {20},
number = {3},
pages = {283-291},
doi = {10.1016/j.pcd.2026.03.001},
pmid = {41794632},
issn = {1878-0210},
mesh = {Humans ; *Blood Glucose Self-Monitoring ; Adherence Interventions ; *Blood Glucose/metabolism/drug effects ; Health Knowledge, Attitudes, Practice ; *Patient Compliance ; *Diabetes Mellitus/blood/diagnosis/psychology ; Biomarkers/blood ; *Glycemic Control ; Patient Education as Topic ; Digital Health ; Treatment Outcome ; },
abstract = {PURPOSE: Routine Self-Monitoring of Blood Glucose (SMBG) is essential for achieving glycemic targets and hence reducing diabetes-related complications. However, patient's adherence to SMBG remains suboptimal worldwide. This systematic review aims to identify interventions that enhance SMBG adherence among patients with diabetes mellitus.<br><br>METHODS: An extensive search of relevant literature was conducted using two databases (Scopus and Web of Science (WoS)) to identify the significant studies. Only English-language articles published between 2015 and 2024 were included in this review. Quality assessment was performed using the Critical Appraisal Skills Program (CASP) and Joanna Briggs Institute (JBI) Critical Appraisal Checklist. A narrative analysis approach was employed, utilizing the Social-Ecological Model (SEM) as the analytical framework for data interpretation.<br><br>FINDINGS: A total of 24 articles resulted in a total of 38 interventions were included in the review. The interventions addressed four levels of SEM: intrapersonal (i.e., education and digital health tools to enhance knowledge and skills), interpersonal (i.e., family involvement and guidance by healthcare workers), community (i.e., involvement of community health workers and support group) and policy (i.e., reward or incentives for SMBG). Among the 38 interventions, 27 were implemented at multiple levels and exhibited improvement in SMBG frequency among the patients.<br><br>CONCLUSION: A suitable approach is needed to strengthen SMBG empowerment among patients with diabetes. These findings highlighted that interventions that targeted multiple levels of SEM are more likely to promote SMBG adherence among patients with diabetes and ultimately lead to better health outcomes.},
}
@article {pmid41794860,
year = {2026},
author = {Noori, S and Hughes, AC and Vasconcelos, TNC and Ascher, JS and Miller, JT and Gaugel, SM and Ostwald, MM and Dorey, JB and Gonzalez, VH and Martins, AC and Orr, MC and Seltmann, KC},
title = {A curated and integrated dataset for exploring global bee-plant interactions.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41794860},
issn = {2052-4463},
support = {DBI-2101851//National Science Foundation (NSF)/ ; DBI-2102006//National Science Foundation (NSF)/ ; },
mesh = {Bees/physiology/classification ; Animals ; *Pollination ; *Plants/classification ; Biodiversity ; Biocuration ; },
abstract = {Bees are one of the most important pollinators in terrestrial ecosystems, supporting biodiversity and food production. However, global knowledge of their interactions with host plants remains limited. To address this, we describe and refine a subset of the Global Biotic Interactions (GloBI) database focused on bee-plant interactions. We updated taxonomy using current checklists and enhanced the dataset with metadata on geography, endemism, and human uses of plants. The resulting dataset includes 981,982 unique interaction records between 5,537 bee species and 12,699 plant taxa. Despite its scale, the dataset is affected by strong taxonomic and geographic biases. It covers only 26% of described bee species and 4% of flowering plant taxa-primarily those used by humans-and is heavily skewed toward North America and Western Europe. Nevertheless, GloBI represents a valuable resource for incorporating bee-plant interactions into biodiversity and conservation-oriented research and represents a considerable advance in our current knowledge.},
}
@article {pmid41986376,
year = {2026},
author = {Khan, A and Breselge, S and O'Mahony, AK and O'Sullivan, O and Cotter, PD and McCarthy, SN and Mahony, J and Kenny, JG},
title = {Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41986376},
issn = {2055-5008},
support = {101060218//European Union's Horizon Europe research and innovation program/ ; },
mesh = {*Kefir/microbiology ; Multiomics ; Fermentation ; *Food Microbiology ; *Fermented Foods/microbiology ; Genomics ; Models, Biological ; },
abstract = {Water Kefir is a plant-based fermented beverage, traditionally produced on a small scale by fermenting a sucrose solution with fresh or dried fruits, using water kefir grains as inoculum. The grains are relatively simple communities that consist of both eukaryotes and prokaryotes, rendering them a paradigm for studying microbial ecology and interspecies interactions. Recently, water kefir has attracted growing research and industrial interest due to its potential and perceived health benefits. Owing to its increasing popularity, there is a growing demand for controlled and standardised production on an industrial scale. However, industrial-scale production remains a challenge due to the limited knowledge of the biological interactions of the microbial consortia and the lack of defined starter cultures. This review examines the current understanding of microbial and metabolic complexity of water kefir obtained from various omics studies. It further investigates the potential of an integrated multi-omics approach to elucidate mechanisms of microbial interactions and provides a roadmap for conducting multi-omics studies on fermented foods using water kefir as an example. This review also explores the potential application of genome-scale metabolic modelling in the development of functional and defined microbial communities for food fermentation. It identifies key challenges associated with such modelling and provides perspectives to address them. Finally, this review briefly discusses the regulatory challenges associated with the use of defined communities in food systems.},
}
@article {pmid42104964,
year = {2026},
author = {Lawson, TN and Jones, MR and Chetwynd, AJ and Sostare, E and Weidt, S and Mistrik, R and Dunn, WB and Weber, RJM and Viant, MR},
title = {Experimental and computational approaches for deep metabolome annotation with application to the ecotoxicological model organism Daphnia magna.},
journal = {GigaScience},
volume = {15},
number = {},
pages = {},
pmid = {42104964},
issn = {2047-217X},
support = {NE/J017442/1//NERC/ ; NE/L002493/1//NERC/ ; 965406//European Union/ ; },
mesh = {Animals ; *Daphnia magna/metabolism/genetics ; *Metabolome ; *Metabolomics/methods ; *Computational Biology/methods ; *Ecotoxicology/methods ; *Daphnia/metabolism ; },
abstract = {BACKGROUND: Comprehensively characterizing the metabolomes of model organisms with high coverage and confidence is a critical step towards interpreting the metabolic basis of human and environmental health, yet there are formidable challenges involved in annotating metabolomes. A wide range of genotypes and phenotypes should be sampled with multiple complementary analytical approaches to cover the large and dynamic biochemical space they exhibit. In addition, multiple computational tools and approaches are required to annotate the metabolites from raw analytical data.<br><br>RESULTS: To address this, we developed the deep metabolome annotation (DMA) workflow. Applied to the ecological sentinel species, Daphnia magna, a pooled sample comprising 10 distinct strains exposed to both normal and stressed environmental conditions was extracted and systematically physicochemically separated via solid-phase extraction and liquid- and gas-chromatography prior to extensive multiple-stage mass spectrometric fragmentation, generating >8,000 raw data files, and supplemented by nuclear magnetic resonance spectroscopy. An extensive Galaxy-based computational approach was built to analyse these data, comprising >30 tools. The overall DMA efforts resulted in 8,181 annotated polar metabolites and lipids in D. magna, with the raw and processed data, tools, and annotations disseminated freely via public data repositories and a custom web-based interface to maximize reusability.<br><br>CONCLUSIONS: The DMA workflow has generated one of the largest metabolome annotation datasets for any non-human model organism and provides the first in-depth characterization of the D. magna metabolome, serving as both a resource and a valuable catalyst for future DMA studies of other model organisms.},
}
@article {pmid42252228,
year = {2026},
author = {Yu, LR and Zhou, LH and Zhang, CC and Lu, Y and Gong, Q and Duan, OW and Yuan, Q},
title = {[Prevalence and causes of blindness and visual impairment in China from 1990 to 2021: an analysis based on the Global Burden of Disease 2021 Database].},
journal = {[Zhonghua yan ke za zhi] Chinese journal of ophthalmology},
volume = {62},
number = {6},
pages = {425-433},
doi = {10.3760/cma.j.cn112142-20260330-00128},
pmid = {42252228},
issn = {0412-4081},
support = {2022BCA044//Hubei Provincial Key Research and Development Program/ ; WJ2023Z006//Scientific Research Project of Hubei Provincial Health Commission/ ; },
mesh = {China/epidemiology ; *Blindness/epidemiology/etiology ; Humans ; Prevalence ; Female ; Male ; Global Burden of Disease ; Middle Aged ; Adult ; Aged ; Adolescent ; Child ; Databases, Factual ; Young Adult ; Child, Preschool ; Infant ; Aged, 80 and over ; },
abstract = {Objective: To investigate the prevalence and etiologies of blindness and visual impairment in China from 1990 to 2021, and to provide references for formulating prevention and treatment strategies for blindness and visual impairment. Methods: This study was an ecological trend study based on the Global Burden of Disease (GBD) 2021 database. Data on the number of cases, prevalence, age-standardized prevalence and etiologies of blindness and visual impairment in China from 1990 to 2021 were extracted. The prevalence and changes in etiological composition in different genders and age groups were analyzed. Joinpoint regression model was used to calculate the Average Annual Percentage Change (AAPC). Decomposition analysis was performed to quantify the contributions of population aging, population growth and epidemiological change to the changes in the number of cases. Results: In 2021, the number of cases of blindness, severe visual impairment and moderate visual impairment in China was 8.768 2 million, 4.178 9 million and 47.757 2 million, respectively, which increased by 64.90%, 129.47% and 139.80% compared with 1990, with AAPCs of 1.70%, 2.87% and 2.89%, respectively (all P<0.05). The age-standardized prevalence rates were 465.14 per 100 000 population, 214.09 per 100 000 population and 2 501.72 per 100 000 population, respectively, which showed changes of -28.63%, -8.73% and+7.74% compared with 1990, with AAPCs of -1.03% (P<0.05), -0.15% (P=0.281) and 0.28% (P<0.05), respectively. The prevalence of visual impairment was higher in females than in males. In 2021, the highest number of cases of blindness and severe visual impairment was in the 70-74-year age group; the highest number of cases of moderate visual impairment was in the 65-69-year age group. Population aging contributed 133.40%, 87.49% and 68.54% to the changes in the number of cases of blindness, severe visual impairment and moderate visual impairment, respectively; population growth contributed 39.82%, 23.78% and 22.18%, respectively; epidemiological change contributed -73.22%, -10.56% and 9.28%, respectively. Refractive error and cataract were the top two etiologies of blindness and visual impairment. Conclusion: The number of cases of blindness and visual impairment in China showed an upward trend from 1990 to 2021. With population growth and aging, the disease burden will further increase. Focusing on cataract in the elderly and refractive error in children and adolescents is an important strategy to reduce the burden of blindness and visual impairment in China.},
}
@article {pmid42254647,
year = {2026},
author = {Tucker, I and Bertotti, M and Hanafiah, A and Hossain, S and Watts, P and Ahad, MAR},
title = {Developing a digital ecological momentary assessment tool for 'real time' evaluation in implementation science: testing through evaluation of a novel digital social prescribing intervention.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1718302},
pmid = {42254647},
issn = {2296-2565},
mesh = {Humans ; *Social Prescribing ; Female ; Male ; *Ecological Momentary Assessment ; Adult ; Feasibility Studies ; London ; Middle Aged ; Digital Health ; *Yoga ; Self Report ; Wearable Electronic Devices ; },
abstract = {INTRODUCTION: Social prescribing is increasingly adopted as a strategy to address psychosocial determinants of health, yet evaluating complex community-based interventions remains methodologically challenging. Digital ecological momentary assessment (EMA) offers potential for capturing real-time, multi-modal data in naturalistic settings. This study aimed to develop and assess the feasibility of a novel digital EMA approach integrating wearable-derived physiological data with repeated self-report wellbeing measures within a digital social prescribing (DSP) context. Despite increasing interest in EMA and wearable technologies, their integration within social prescribing evaluations remains underexplored.<br><br>METHODS: A mixed-methods feasibility study was conducted alongside a four-week online chair-based yoga programme delivered through a social prescribing service in East London, UK. Participants wore smartwatches to collect physiological indicators (stress, sleep, heart rate) and completed twice-daily wellbeing assessments using an adapted Short Warwick-Edinburgh Mental Wellbeing Scale. Quantitative data were analysed using exploratory linear mixed-effects models to examine data behaviour and integration within the intensive longitudinal dataset. Participant workshops explored feasibility and acceptability.<br><br>RESULTS: Thirteen participants were recruited, with eleven included in quantitative analyses. The study indicated that integrating wearable and self-report EMA data within routine-style DSP delivery is feasible, although challenges were identified regarding device synchronisation, questionnaire adherence, and missing data. Exploratory modelling illustrated substantial within- and between-person variability in wellbeing trajectories and provided an indication of the feasibility of analysing intensive longitudinal EMA data, with no consistent associations between same-day yoga participation and physiological stress markers. Qualitative findings suggested that participants found the approach acceptable and highlighted factors influencing engagement, including flexibility, motivation, and perceived burden.<br><br>CONCLUSION: Integrated wearable and self-report EMA methodologies can be deployed in DSP contexts, but their implementation is associated with important methodological and technical challenges. Findings highlight the need for validated EMA measures, improved data infrastructure, and careful management of participant burden. While not designed to assess intervention effectiveness, this study provides one of the first applied demonstrations of integrating wearable-derived physiological data with EMA self-report measures in a DSP context, offering a methodological foundation for real-time evaluation of complex community-based health interventions.},
}
@article {pmid40811268,
year = {2026},
author = {Chen, N and Schram, M and Bucur, D},
title = {gFlora: A Topology-Aware Method to Discover Functional Co-Response Groups in Soil Microbial Communities.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {23},
number = {3},
pages = {919-930},
doi = {10.1109/TCBBIO.2025.3560853},
pmid = {40811268},
issn = {2998-4165},
mesh = {*Soil Microbiology ; *Microbiota/genetics/physiology ; Bacteria/genetics/classification ; *Computational Biology/methods ; Algorithms ; Ecosystem ; },
abstract = {Microorganisms such as bacteria perform critical functions in the soil ecosystem: they mediate essential carbon, nitrogen, and nutrient cycling processes in soils. To manage the health and functions of soils, it is important to understand which soil functions are related the most to which microbial taxa-but this taxon-to-function link is difficult to discover because of the size and complexity of the soil ecosystem. A feasible solution is to discover functional links at the level of groups instead of individuals, using observational data of both taxa abundance and soil function indicators. We thus aim to learn the functional co-response group: a group of taxa whose co-response effect (the representative characteristic of the whole functional group) co-responds (associates well statistically) to a functional variable. Unlike the existing method, we model the soil microbial community as an ecological co-occurrence network with the taxa as nodes (weighted by their abundance) and their relationships (a combination from both spatial and functional ecological aspects) as edges (weighted by the strength of the relationships). Then, we design a method called gFlora which notably uses graph convolution over this co-occurrence network to compute the co-response effect of the group, such that the network topology is also considered in the discovery process. We evaluate gFlora on four real-world soil microbiome datasets (bacteria and nematodes combined with two soil functions: nitrogen mineralization and crop yield). gFlora outperforms the competing method on all evaluation metrics, and it discovers new functional evidence for taxa which were so far under-studied. We show that the graph convolution is crucial to taxa with relatively low abundance (thus removing the bias towards taxa with higher abundance), and the discovered bacteria of different genera are distributed in the co-occurrence network but remain tightly connected among themselves, demonstrating that topologically they fill different but collaborative functional roles in the ecological community.},
}
@article {pmid41717717,
year = {2026},
author = {Adil, M and Tiwari, P and Kanwal, S},
title = {Nanoinformatics-Based, Predictive Toxicological Screening of Nanomaterials.},
journal = {Journal of applied toxicology : JAT},
volume = {46},
number = {5},
pages = {1476-1486},
doi = {10.1002/jat.70112},
pmid = {41717717},
issn = {1099-1263},
mesh = {Animals ; *Nanostructures/toxicity/chemistry ; Humans ; *Toxicity Tests/methods ; Databases, Factual ; *Nanotechnology/methods ; },
abstract = {Nanoparticles have gained substantial attention in view of their distinctive physicochemical attributes and widespread applications in several fields. However, the prompt development and extensive consumption of nanotechnology may provoke inexorable diffusion of nanoparticles into the environment, associated with potential toxic effects. Hence, the preliminary toxicological screening of nanomaterials becomes indispensable for their harmless utilization and ecological safety. Nanotoxicology deals with the study of undesirable effects attributed to nanoparticles. It includes the nature, intensity, and characteristics of toxic insult caused by individual or combined use of nanoparticles. Nanoinformatics represents a systematic approach for collecting, organizing, validating, storing, sharing, visualizing, modeling, and analyzing data from nanotechnology processes and materials. The conventional nanotoxicity assessment methods using in vitro assays or animal models are time-consuming and relatively expensive, whereas computational modeling of physicochemical properties and existing toxicity data can be effectively used to determine the safety of nanomaterials. Nanoinformatics involves the integration of nanospecific databases (e.g., NanoDatabank, eNanoMapper, Data and Knowledge on Nanomaterials, Online Chemical Modeling Environment, and Nanoparticle Information Library) with modeling frameworks such as quantitative nanostructure-activity/toxicity relationship, molecular docking, physiologically based toxicokinetic models, and molecular dynamics simulation for predictive nanotoxicity assessment. Moreover, the process of computer-aided nanotoxicity prediction can be further expedited using the latest data mining techniques. Challenges in collecting sufficient, high-quality, nanotoxicity data, as well as in standardizing the training data sets require careful consideration to further expand the applications of nanoinformatics techniques in predictive nanotoxicology. This article highlights the current status and future perspective of nanoinformatics-based predictive toxicological screening of nanomaterials.},
}
@article {pmid41719536,
year = {2026},
author = {Crosley-Lyons, R and Hatzinger, L and Hewus, M and Wang, WL and Van Dyck, D and Huh, J and Hekler, E and Dunton, GF},
title = {An Early-Stage Digital Therapeutic Intervention to Enhance Affective Response During Physical Activity Among Adults With Overweight or Obesity: Benchmark-Driven Formative Testing Study.},
journal = {JMIR human factors},
volume = {13},
number = {},
pages = {e71472},
pmid = {41719536},
issn = {2292-9495},
support = {F31 HL176165/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; *Exercise/psychology/physiology ; Adult ; Middle Aged ; *Obesity/therapy/psychology ; Benchmarking ; *Overweight/therapy/psychology ; Digital Health ; *Affect ; },
abstract = {BACKGROUND: Mobile device-enabled interventions known as digital therapeutics (DTx) are increasingly used to prevent chronic disease by targeting psychological and behavioral processes. Individuals' unique experiences while receiving DTx comprise real-world evidence (RWE) for evaluating DTx performance. An emerging strategy for early-stage DTx formative work uses small sample sizes, which facilitate efficient iteration and agile learning, while evaluating performance against descriptive benchmarks defined a priori, therefore minimizing the risk for confirmation bias. This study test benchmarks from the DTx RWE framework to formatively evaluate a novel DTx (the eMOTION study) to enhance affective response (ie, how people feel) during physical activity (PA).<br><br>OBJECTIVE: This study aimed to determine whether the eMOTION DTx met a priori benchmarks for safety (<1% of participants report an adverse event), plausibility (&#x2265;51% of participants experience increased enjoyment in PA), usability (eg, &#x2265;51% of participants report adequate usability), sustainability, feasibility (eg, <70% of participants report dissatisfaction), and equity (equity and accessibility are approximately equal across subgroups).<br><br>METHODS: Participants (N=36; mean age 46, SD 14 years; 20/37, 54% female) underwent stratified random assignment to test one of four DTx versions for 14 days (n=9 each): (1) intensity PA goals, (2) affect PA goals with type and context recommendations, (3) affect PA goals with savoring exercises, and (4) affect PA goals with type, context, and savoring. Participants completed daily intervention sessions, asking them to focus on achieving a target heart rate (intensity) or feeling good (affect) during PA. Smartwatches were used to track PA and answer ecological momentary assessment (EMA) questions about how they felt during PA. Performance toward benchmarks was primarily assessed via official Institutional Review Board reporting channels (safety), interviews (plausibility, accessibility, and usability), and questionnaires (System Usability Scale [usability], Delighted-Terrible Scale [sustainability and feasibility], and equity).<br><br>RESULTS: The eMOTION DTx versions exceeded all a priori safety, plausibility, accessibility, usability, sustainability, feasibility, and equity thresholds. For safety, no adverse events were reported. Regarding plausibility, more than half of the participants who received affect goals reported increased PA enjoyment at the end of the study. Moreover, 64%-72% (23-26 out of 36) of participants rated the DTx at or above the standard System Usability Scale cutoff point for acceptable usability. More than 60% (22/36) of participants reported satisfaction with all DTx components, supporting DTx sustainability and feasibility. Finally, there was evidence for equity, with plausibility and accessibility comparable across sex, race, ethnicity, income, age, BMI, mobility, and physical constraint subgroups.<br><br>CONCLUSIONS: Since DTx RWE Framework benchmarks for safety, plausibility, accessibility, usability, sustainability, feasibility, and equity were largely met, the eMOTION Study DTx is ready for a full-scale efficacy trial to refine the DTx and optimize efficiency and feasibility. Our approach incorporated transparent decision-making to generate results that are more readily translatable, easily replicable, and reflect current best practices in the field of DTx.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT06125964; https://clinicaltrials.gov/study/NCT06125964.},
}
@article {pmid41724800,
year = {2026},
author = {Bhuyan, B and Chutia, B and Singh, LS},
title = {Emerging strategies for heavy metal removal in soils: plant-microbe interactions and omics perspectives.},
journal = {Archives of microbiology},
volume = {208},
number = {5},
pages = {},
pmid = {41724800},
issn = {1432-072X},
mesh = {*Metals, Heavy/metabolism ; Biodegradation, Environmental ; *Plants/microbiology/metabolism ; *Soil Pollutants/metabolism ; Soil Microbiology ; Bacteria/metabolism/genetics ; Soil/chemistry ; Proteomics ; Multiomics ; Metabolomics ; },
abstract = {Rapid industrial expansion, intensive agricultural practices, and widespread petroleum extraction have led to the significant buildup of heavy metals (HMs) in soils and related ecosystems, posing serious environmental and public health risks. Hence, this review highlights the major sources, ecological impacts, and toxicity of HMs in the environment. However, physical and chemical remediation methods can reduce HMs concentrations, but issues such as high operational costs, prolonged treatment durations, and poor sustainability limit their suitability for large-scale application. Thus, bioremediation methods, especially those that utilize plants and microbes, have gained increasing attention as eco-friendly and cost-effective options. Plant-microbe-based interactions play an important role, as they act synergistically to facilitate metal uptake, stabilization, transformation, and detoxification of HMs in contaminated soils. Though, it is important to understand the plant-microbe interactions, especially since most current research is about how plants and microbes can work together to clean up contaminants in their natural environments. However, achieving higher remediation performance under stress conditions depends on the selection of plant and microbial species. Therefore, this review explores the mechanisms of plant-microbe interactions along with omics technologies employed to analyze samples for understanding this interaction in HMs-contaminated soils at the metagenomics, metatranscriptomics, proteomics, and metabolomics levels in enhancing the effectiveness of remediation. This review article also highlights key factors affecting remediation efficiency and discusses limitations, challenges, and future prospects of plant-microbe interactions in HMs-contaminated soils.},
}
@article {pmid41872333,
year = {2026},
author = {Fayad, ZA and Hirten, RP and Nadkarni, GN and Kim, YS},
title = {Wearable technologies in clinical trials for drug development: trends and emerging opportunities.},
journal = {Nature reviews. Drug discovery},
volume = {25},
number = {6},
pages = {448-468},
pmid = {41872333},
issn = {1474-1784},
mesh = {Humans ; *Wearable Electronic Devices/trends ; *Drug Development/methods/trends ; *Clinical Trials as Topic/methods ; Digital Health ; },
abstract = {Wearable technologies are increasingly being integrated into clinical trials, offering new tools to capture physiological and behavioural endpoints in real-world settings. By enabling continuous, remote, participant-friendly monitoring, wearables address key limitations of traditional trials, such as frequent site visits, sparse sampling and limited ecological validity, while supporting the development of digital biomarkers. To characterize how wearables are used in drug development, we curated 1,021 interventional trials registered between 2001 and 2025 that incorporated wearable-derived data into study protocols. We identified five application archetypes - drug effects, dosing optimization, adherence, delivery medium and delivery technique optimization - through which wearables are deployed in trials, underscoring a broadening role across study objectives. Adhesive patches, largely driven by continuous glucose monitoring, now dominate trial deployments, with expanding coverage of physiological domains including sleep, cardiovascular function, motor activity and brain signals. Despite this progress, formal regulatory qualification of wearable-derived measures remains rare, with SV95C in Duchenne muscular dystrophy the only such example to date. Looking ahead, we highlight emerging biochemical sensing modalities beyond glucose, as well as transdermal spectroscopy and wearable ultrasound. This Review provides a structured, forward-looking overview of wearables in trials and supports their responsible, effective integration into clinical development.},
}
@article {pmid41879886,
year = {2026},
author = {Chen, W and Li, X and Zhao, X and Zuo, Z and Wang, D and Zhao, F},
title = {GMW: a hybrid graph-based approach for post-assembly metagenome analysis and decontamination.},
journal = {Science China. Life sciences},
volume = {69},
number = {6},
pages = {1910-1917},
pmid = {41879886},
issn = {1869-1889},
mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Algorithms ; Genome, Viral/genetics ; Influenza A virus/genetics ; *Computational Biology/methods ; *Software ; Decontamination/methods ; },
abstract = {Accurate genome assembly from metagenomic sequencing data remains challenging, particularly in mixed infections involving multiple pathogens, due to data complexity and contaminant sequences. Here, we present GMW (Genomic Microbe-Wise), a novel computational tool that improves pathogen genome assembly accuracy and enhances contaminant removal capabilities by simplifying the post-assembly graph. GMW leverages community detection algorithms, sequence similarity analysis, and coverage patterns to resolve strain mixtures and improve assembly accuracy. Using datasets of influenza A virus subtypes, we demonstrate GMW's ability to disentangle mixed infections and reconstruct complete viral genomes with high precision. Additionally, GMW outperforms traditional sequence similarity methods in classifying target contigs from contaminants. This tool also provides interactive visualization modules to streamline the inspection of assembly outputs, including simplified representations of complex assembly graphs. By enhancing assembly quality and contamination filtering, GMW emerges as a versatile solution for applications in clinical diagnostics, microbial ecology, and pathogen surveillance.},
}
@article {pmid42084394,
year = {2026},
author = {Liu, C and Ribeiro, MM and Yang, J and Li, L and Li, J and Chen, X and Wang, Y and Wang, L-L and Wang, B and Zhou, Y and Zhang, J and Jiang, J and Lin, J and Delbaje, E and Xu, J-F and Goldman, GH and Liang, S},
title = {Multi-omics profiling of fungal balls in chronic pulmonary aspergillosis patients reveals microbiome dynamics and metabolic adaptations.},
journal = {mBio},
volume = {17},
number = {6},
pages = {e0034826},
pmid = {42084394},
issn = {2150-7511},
support = {//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; No. 82170051//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Pulmonary Aspergillosis/microbiology/immunology ; Multiomics ; Aspergillus fumigatus/metabolism/genetics ; *Microbiota ; Metabolomics ; Chronic Disease ; Pseudomonas aeruginosa ; Gene Expression Profiling ; Biofilms/growth &amp; development ; Haemophilus influenzae ; },
abstract = {Fungal balls (aspergillomas) are a debilitating complication of chronic pulmonary aspergillosis, but their functional biology as multi-kingdom ecosystems is poorly understood. Through integrated multi-omics analysis of 61 patient-derived fungal balls, we reveal their complex ecology. While Aspergillus fumigatus dominates the fungal niche (59% of patients), bacterial co-colonization is ubiquitous, primarily by Pseudomonas aeruginosa and Haemophilus influenzae. Metabolomics and metatranscriptomics unveil a structured division of labor and active warfare, including metabolic cross-feeding, competition for iron, and reciprocal antagonism via secondary metabolites, such as fumagillin and fumigaclavine C produced by A. fumigatus. Host metabolomics and transcriptomics revealed a potent but dysregulated human immune response, characterized by neutrophil activation and failed resolution. Our findings redefine aspergilloma not as a mere fungal aggregate, but as a resilient polymicrobial biofilm across kingdoms, in which synergistic and antagonistic inter-kingdom interactions drive pathogenesis and chronicity, suggesting new therapeutic strategies targeting the pathogenic consortium.IMPORTANCEChronic pulmonary aspergillosis (CPA) and its hallmark fungal balls (aspergillomas) represent a debilitating and difficult-to-treat respiratory disease, affecting millions worldwide. Here, we provide the first integrated multi-omics profile of surgically resected fungal balls from 61 CPA patients, revealing these structures not as mere fungal colonies, but as resilient, cross-kingdom biofilms teeming with bacterial co-colonizers, particularly Pseudomonas aeruginosa and Haemophilus influenzae. Our findings uncover a dynamic battlefield where fungi and bacteria engage in metabolic cross-feeding, chemical warfare, and competition for nutrients such as iron. We demonstrate that the host mounts a potent but dysregulated immune response characterized by chronic neutrophilic inflammation and failed resolution, driving tissue damage and disease persistence. Our data provide a foundation for novel therapeutic strategies aimed at disrupting microbial synergy, modulating host inflammation, and breaking the cycle of chronic infection, an approach that could significantly improve outcomes for patients with this refractory disease.},
}
@article {pmid42144115,
year = {2026},
author = {Wang, Y and Wu, W and Liang, F and Zhao, T and Li, S and Yang, M and Leng, F and Zhu, X and Wang, X},
title = {Integrated multi-omics reveals divergent salt stress response mechanisms in three alfalfa (Medicago sativa L.) cultivars.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {370},
number = {},
pages = {113216},
doi = {10.1016/j.plantsci.2026.113216},
pmid = {42144115},
issn = {1873-2259},
mesh = {*Medicago sativa/physiology/genetics/metabolism/growth &amp; development ; *Salt Stress ; *Salt Tolerance/genetics ; Multiomics ; Germination ; Sodium Chloride ; Photosynthesis ; Transcriptome ; },
abstract = {Soil salinization is a major environmental constraint limiting plant growth and agricultural productivity worldwide. Alfalfa (Medicago sativa L.), a high-quality leguminous forage crop with high nutritional and ecological value, serves as an important model for investigating salt tolerance mechanisms in forage species. This study aimed to elucidate the physiological and molecular mechanisms underlying varietal differences in salt tolerance among independently bred alfalfa cultivars. Three alfalfa varieties-Zhongtian No.1 (A.ZT1), Zangmu No.1 (A.ZM1), and Zhonglan No.1 (A.ZL1)-were exposed to two salinity levels (100 and 200 mM NaCl). Germination traits, growth performance, physiological parameters, and photosynthetic characteristics were evaluated, and integrated transcriptomic and metabolomic analyses were conducted to compare their responses to salt stress. Salt stress significantly inhibited seed germination and plant growth in all varieties, with stronger inhibitory effects observed under 200 mM NaCl. Under 100 mM NaCl, the vigor index decreased by 34.69% in A.ZM1 and up to 51.27% in A.ZL1 compared with the control. Under 200 mM NaCl, the vigor index declined dramatically by 92.13% in A.ZT1 and 93.66% in A.ZL1, indicating severely restricted seedling development. Physiological analyses showed that salt stress increased malondialdehyde and osmolyte accumulation, while disturbing ionic homeostasis. At 200 mM NaCl, A.ZL1 exhibited the highest Na[+]/K[+] ratio and oxidative damage, whereas A.ZM1 maintained relatively lower MDA levels and stronger antioxidant enzyme activities. Photosynthetic performance also declined with increasing salinity; however, A.ZM1 maintained a net photosynthetic rate of 27.72 μmol m[-2] s[-1] under 200 mM NaCl, indicating superior physiological tolerance. Integrated transcriptomic and metabolomic analyses revealed coordinated regulation of phenylpropanoid, flavonoid, and diterpenoid biosynthesis pathways under salt stress. Key flavonoid biosynthesis genes, such as CHS, were up-regulated in A.ZT1 and A.ZM1 but down-regulated in A.ZL1. In addition, several gibberellin-related metabolites, including GA20, GA3, and GA8, showed differential accumulation. Notably, A.ZM1 exhibited the largest number of differentially expressed genes and metabolites, indicating a broader molecular response to salinity. Overall, A.ZT1 and A.ZM1 displayed stronger salt tolerance than A.ZL1, which may be associated with more effective antioxidant regulation and metabolic pathway activation. These findings provide new insights into the physiological and molecular basis of salt tolerance variation among independently bred alfalfa varieties and offer valuable references for breeding salt-tolerant cultivars and improving the utilization of saline soils.},
}
@article {pmid42172845,
year = {2026},
author = {Zhang, S and Zhang, C and Zhou, Y and Gu, W and Wang, R and Zhang, C and Shih, K and Bai, J},
title = {A multi-omics study of polystyrene degradation.},
journal = {Journal of environmental management},
volume = {409},
number = {},
pages = {129988},
doi = {10.1016/j.jenvman.2026.129988},
pmid = {42172845},
issn = {1095-8630},
mesh = {*Polystyrenes/metabolism ; Multiomics ; Biodegradation, Environmental ; *Stenotrophomonas/metabolism ; Proteomics ; },
abstract = {Polystyrene (PS) is highly persistent in the environment, presenting a significant ecological challenge, while microbial degradation offers a potential green solution. However, the molecular mechanisms of microbial responses to such inert substrates remain unclear. This study focuses on Stenotrophomonas sp. (SM313), a strain capable of degrading PS, and investigates its adaptive reprogramming through multi-omics analysis. Characterization of the material shows a 4.53% reduction in PS mass over 60 days, with surface erosion, reduced molecular weight, introduction of oxygen-containing groups, and increased hydrophilicity. Whole-genome analysis highlights its genetic potential in xenobiotic degradation, energy conversion, and membrane transport. Transcriptomic, proteomic, and metabolomic data reveal a synergistic molecular response: significant upregulation of ribosomal and translation machinery ensures the rapid synthesis of degradation-related enzymes, while energy metabolism pathways like oxidative phosphorylation are activated to provide energy for the degradation process. Additionally, peroxisomal-pathway-equivalent oxidative stress defence and DNA repair mechanisms are upregulated to counteract oxidative stress. Pathway enrichment analysis indicates that PS degradation follows bifurcated metabolic pathways: the aromatic ring undergoes ring-opening via benzoate pathways, and the aliphatic side chains are degraded via β-oxidation, with metabolites entering central carbon metabolism. This study provides a systems biology perspective, emphasizing the complex, multi-enzyme collaboration involved in PS biodegradation.},
}
@article {pmid42189851,
year = {2026},
author = {Kwon, J and Li, K and Warren, JL and Pandya, S and Hahn, AM and , and Pitzer, VE and Weinberger, DM and Grubaugh, ND},
title = {Utilizing virus genomic surveillance to predict vaccine effectiveness.},
journal = {PLoS computational biology},
volume = {22},
number = {5},
pages = {e1014329},
doi = {10.1371/journal.pcbi.1014329},
pmid = {42189851},
issn = {1553-7358},
mesh = {*SARS-CoV-2/genetics/immunology ; *COVID-19 Vaccines/immunology ; *Vaccine Efficacy/statistics &amp; numerical data ; *Genome, Viral/genetics ; Humans ; *COVID-19/prevention &amp; control/virology/immunology/epidemiology ; Spike Glycoprotein, Coronavirus/genetics ; Bayes Theorem ; Amino Acid Substitution ; Genomics ; Computational Biology ; },
abstract = {BACKGROUND: Since the development of the first vaccines targeting the original SARS-CoV-2 virus sequence in 2020, mRNA-based vaccines have been updated three times: targeting Omicron BA.4/BA.5 in 2022, the XBB lineage in 2023, and the KP.2 variant in 2024. While genomic surveillance has advanced our understanding of pathogen diversity, gaps remain in incorporating genomic information to evaluate vaccine effectiveness (VE) against emerging variants. This study aims to characterize the relationship between VE and sequence-based genetic distance, to establish a framework for predicting near real-time changes in the level of vaccine protection from virus surveillance data.<br><br>METHODS: We analyzed 10,156 whole genome sequences of SARS-CoV-2 cases from Connecticut, USA, between April 2021 to July 2024. We first assessed how genetic distance, specifically the number of amino acid substitutions in the spike gene between COVID-19 case sequences and the mRNA vaccine formulation sequence(s), correlates with vaccine protection levels. Incorporating data from over 1 million test-negative controls, we developed a Bayesian time-varying model with autoregressive terms to assess VE at a weekly level. The analysis was adjusted for ZIP-code-level income, age, sex, and prior vaccine doses received. We then employed a random effects meta-regression to explore the relationship between VE and amino acid distance over time. Finally, we used the meta-regression model to estimate potential vaccine protection against emerging variants.<br><br>FINDINGS: We found that spike gene amino acid distance showed a negative correlation with VE over time. Stepwise increases in amino acid distance aligned with sharp VE declines during variant emergence, while accumulation of within-variant changes was also associated with gradual VE decline. Each 10 amino acid increase in distance in the spike gene corresponds to a predicted 15.4% (95% credible intervals (CrI): -2.0%, 34.6%) reduction in VE. For the 2023/24 updated vaccine, spike distance rose from 12.25 to 30.23, predicting a 43.4% (95% CrI: -5.7%, 90.1%) drop in VE using sequence information alone.<br><br>CONCLUSION: Our framework quantifies how the emergence of new variants is expected to affect VE for SARS-CoV-2. By quantifying the relationship between amino acid substitutions and time-varying VE, we leverage intrinsic pathogen features, such as spike amino acid distance, to inform future vaccine updates using genomic sequences. As genomic surveillance data becomes more widely available across pathogens, this framework can serve as a near-real time surveillance tool to infer population-level protection and offers valuable insights for vaccine update decisions.},
}
@article {pmid42210596,
year = {2026},
author = {Li, X and Wang, F and Shi, F and Wei, Y and Zhou, M and Wu, F and Su, H and Liu, X},
title = {Multiomics Reveals the Mechanisms of Rhizosphere Symbiotic Fungi in Mitigating Micro(nano)plastics Transfer and Toxicity in Food Chains.},
journal = {Environmental science &amp; technology},
volume = {60},
number = {22},
pages = {16099-16110},
doi = {10.1021/acs.est.5c16131},
pmid = {42210596},
issn = {1520-5851},
mesh = {*Rhizosphere ; *Food Chain ; Multiomics ; Mycorrhizae ; Soil Microbiology ; Animals ; Symbiosis ; },
abstract = {Soil micro(nano)plastics (MNPs) pollution is becoming increasingly prominent, posing a serious threat to ecological security. However, few studies have examined the remediation of soil MNPs pollution. This study constructed a multidimensional coupled system of soil-microbe interface plants-animals, in order to investigate the pathways and key mechanisms underlying rhizosphere microbiome-mediated inhibition of trophic transfer and toxicity of MNPs. The findings demonstrated that the common root-associated soil microorganisms, arbuscular mycorrhizal fungi (AMF), exhibit a mitigation effect on the food chain ecological stress of various MNPs in the environment. The mitigation was primarily manifested as a 45.57-56.52% reduction of MNPs concentration in animals and plants (due to changes in the rhizosphere environment and MNPs aging, which inhibit MNPs migration) and a decrease in MNPs binding ability to organisms. Additionally, analysis of molecular regulatory mechanisms showed that AMF mediation improved the substance synthesis and defensive pathways of plants under MNPs stress, and their palatability as food, leading to increased immune regulation and energy metabolism functions in snails consuming AMF-mediated leaves. These findings provide a theoretical basis and technical support for the development of green and efficient biological control technologies for soil MNPs pollution.},
}
@article {pmid42244264,
year = {2026},
author = {Cooke, A and Brickley, MB},
title = {Ecology of Malaria Mortality: A Spatiotemporal Mapping Approach.},
journal = {American journal of biological anthropology},
volume = {190},
number = {2},
pages = {e70272},
pmid = {42244264},
issn = {2692-7691},
support = {752-2024-2545//Social Sciences and Humanities Research Council of Canada/ ; },
mesh = {Ontario/epidemiology ; *Malaria/mortality/history ; Humans ; Geographic Information Systems ; Spatio-Temporal Analysis ; History, 19th Century ; },
abstract = {OBJECTIVES: This study examines the spatiotemporal ecology of probable malaria mortality in 19th-century southern Ontario to evaluate how settlement expansion, landscape transformation, and infrastructure development structured transmission risk in a temperate, settler-colonial context.<br><br>MATERIALS AND METHODS: Probable malaria-attributed deaths recorded in Ontario death certificates (1869-1900; n&#x2009;=&#x2009;2683) were geocoded and analyzed using Geographic Information Systems (GIS). Mortality locations were examined in relation to historical settlements, railways, and wetlands derived from 19th-century spatial datasets. Spatial clustering was assessed using Average Nearest Neighbor analysis and kernel density estimation. Temporal changes in proximity to landscape features were tested using nonparametric statistics, while malaria mortality density was modeled using negative binomial regression and generalized additive models.<br><br>RESULTS: Malaria mortality was significantly clustered across all decades but became progressively less spatially concentrated through time. Mortality locations shifted farther from mapped wetlands as drainage intensified, while proximity to settlements consistently decreased. Regression models identified settlement proximity as the strongest and only significant predictor of malaria mortality density, whereas distances to wetlands were not independently associated once settlement effects were accounted for.<br><br>DISCUSSION: These results indicate a reorganization of malaria risk from environmentally constrained ecologies toward anthropogenic landscapes shaped by settlement, agriculture, and infrastructure. Malaria transmission in southern Ontario was embedded within everyday settlement practices rather than static environmental features, demonstrating how colonial landscape transformation structured disease risk in a temperate region. This study highlights the value of spatiotemporal GIS approaches for interpreting past disease ecologies within biological anthropology and paleopathology.},
}
@article {pmid42259880,
year = {2026},
author = {Prieto-González, P and Yagin, FH and Martín, V and Marcelino, R and Alghannam, AF and Yagin, B and Sal-de-Rellán, A},
title = {A data-driven performance index for center forwards in the English Premier League.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-55681-9},
pmid = {42259880},
issn = {2045-2322},
abstract = {Despite the growing availability of performance data in professional soccer, existing player rating systems lack positional specificity and fail to capture the multidimensional demands of center forwards. Building on composite index and regularized regression approaches in sports analytics, this study develops a Soccer Performance Index (SPI) tailored to center forwards in the English Premier League (EPL) across the 2021-2024 seasons. Data from 194 player-season observations were analysed using 109 Wyscout performance metrics as predictors. Three SPI versions were constructed using Lasso and Ridge regression: one based on market value, one on the InStat Index, and a hybrid combining both. The hybrid model, weighting market value at 70% and the InStat Index at 30%, achieved the strongest explanatory fit (R[2] = 0.676, RMSE = 0.669), accounting for approximately 68% of variance in player valuation - a result consistent with the complexity inherent in behavioural and performance modelling contexts. xG per 90, shots, and key passes per 90 emerged as the strongest predictors. Methodological considerations include the use of a minimum participation threshold (≥ 20 matches), which may introduce survivorship bias; the treatment of player-season observations as independent units, which does not account for repeated-measures dependence; and the reliance on internal validation only. The SPI demonstrates ecological relevance by integrating both financial and on-field performance indicators, offering a structured framework for talent identification and recruitment support in applied professional contexts.},
}
@article {pmid42263105,
year = {2026},
author = {Cope, AL and Pak, D and Gilchrist, MA},
title = {The importance of nonsense errors: Estimating the rates and implications of ribosome drop-off during protein synthesis.},
journal = {PLoS genetics},
volume = {22},
number = {6},
pages = {e1012162},
doi = {10.1371/journal.pgen.1012162},
pmid = {42263105},
issn = {1553-7404},
abstract = {The process of translation is both energetically costly and relatively error-prone compared to transcription and replication. Nonsense errors during translation occur when a ribosome drops off a transcript before reaching a stop codon, resulting in energetic investment in an incomplete and likely non-functional protein. Nonsense errors impose a potentially significant energy burden on the cell, making it critical to quantify their frequency and energetic cost. Here, we present a model of ribosome movement for estimating protein production, elongation, and nonsense error rates from high-throughput ribosome profiling data. Applying this model to an exemplary ribosome profiling dataset in S. cerevisiae, we find that nonsense error rates vary substantially between codons and that these types of errors place an energetic burden on cells comparable to ribosome pausing. Overall, we present multiple lines of evidence that selection against nonsense errors is a prominent force shaping protein-coding sequence evolution and codon usage bias, in particular.},
}
@article {pmid42182272,
year = {2026},
author = {Liu, Y and Harris, RE and Clauw, D and Bayman, E and Leroux, A and Lindquist, MA and , },
title = {A Beta-Binomial Model for Estimating Zero- or One-inflated Pain Trajectories.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42182272},
issn = {2692-8205},
abstract = {Chronic pain is a widespread public health issue that imposes substantial health, emotional, and economic burdens on individuals and communities. Because pain is subjective and lacks objective biomarkers, it is typically measured using patient-reported scores, often on a numerical scale from zero to ten. Increasingly, pain studies use ecological momentary assessment, with multiple daily assessments over days and across study phases (e.g., a series of baseline and post-intervention assessments). These data frequently show many ratings at the extremes (i.e., at minimum or maximum pain scores), commonly referred to as zero- and one-inflation in the statistical literature, along with considerable within-person variability both within and across days. These phenomena present challenges for statistical analyses, as they violate assumptions of most commonly used statistical techniques (e.g., the normality assumption of linear mixed models). We propose a Bayesian beta-binomial mixed-effects model for modeling potential zero- or one-inflated pain scores while accounting for variability using random effects on the mean and variance parameters across subjects. A simulation study demonstrates that the method accurately estimates model parameters across realistic sample sizes, time points, and zero- and one-inflation levels. An application to data from two longitudinal pain studies demonstrates that the model fits the data better and, when correctly specified, yields accurate uncertainty intervals for longitudinal changes in pain compared to existing models, especially for zero- and one-inflated outcomes. Additionally, the model directly estimates the probability of clinically meaningful pain events. The proposed method provides a powerful statistical framework for studying the patient-reported pain trajectories.},
}
@article {pmid42190532,
year = {2026},
author = {Ding, X and Li, W and Sun, X and Peng, Y},
title = {Assessing the potential of urban agriculture at the community scale: Spatial heterogeneity, influencing factors, and planning implications.},
journal = {Journal of environmental management},
volume = {409},
number = {},
pages = {130046},
doi = {10.1016/j.jenvman.2026.130046},
pmid = {42190532},
issn = {1095-8630},
mesh = {*Agriculture ; Geographic Information Systems ; Cluster Analysis ; Conservation of Natural Resources ; Urbanization ; City Planning ; Decision Making ; },
abstract = {Urban development faces challenges like food shortages, farmland loss, ecological degradation, and weakened community ties. Urban agriculture can help alleviate food pressure, enhance ecology, and strengthen social interactions. Communities are ideal sites for its implementation. However, existing research lacks methods for assessing urban agriculture potential at the community level, particularly when considering the full range of spatial elements, multi-scale benefits, and the spatial heterogeneity of different types of communities. Thus, our study comprehensively employs cluster analysis, three-dimensional image reconstruction, multi-criteria decision-making (MCDM) and GIS methods to evaluate urban agriculture potential across community types. The research consists of four phases: (1) Classifying community types and identifying their spatial characteristics; (2) Constructing 3D community models and extracting spatial data; (3) Developing an MCDM model to rank urban agriculture potential; (4) Analyzing the spatial heterogeneity of the potential of communities and identifying the influencing factors. Results indicate that low-density high-rise communities exhibit the strongest spatial suitability, while high-density low-rise communities score highest in sustainable potential. Overall potential is ranked in the order: low-density high-rise > high-density low-rise > large-footprint pitched-roof > old communities. Construction year is identified as a key factor leading to the superior urban agriculture potential of newly built communities compared to older ones. Building density, gross floor area, and roof slope also shape potential by affecting sunlight exposure, planting area, and accessibility. Our study further proposes planning strategies for community-based urban agriculture and differentiated urban agriculture development suggestions. We also explore the applicability of the research conclusions and the generalizability of the potential assessment method. The research offers scientific decision-making basis for urban planners, and a novel approach to potential assessment in urban agriculture.},
}
@article {pmid42239005,
year = {2026},
author = {Zhang, S and Chen, X},
title = {Public perceptions and engagement with Traditional Chinese Medicine on Japanese social media (2010-2025): a text mining approach.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1826864},
pmid = {42239005},
issn = {2296-2565},
mesh = {*Medicine, Chinese Traditional ; Humans ; *Data Mining ; *Social Media/statistics &amp; numerical data ; Japan ; *Public Opinion ; Media Exposure ; Digital Media ; East Asian People ; },
abstract = {Traditional Chinese Medicine (TCM) is a holistic medical system whose global visibility has increased markedly, yet large-scale studies on public perceptions and engagement remain limited. Using Japanese Twitter data from 2010 to 2025, this study employs text mining techniques including BERTopic modeling, sentiment analysis, and co-occurrence network analysis to examine public discourse on TCM. Building on the Cognition-Affect-Behavior (CAB) framework, this study employs multilevel relational analyzes to examine the interplay between topics, sentiment, and behavioral engagement. The results show that public discussions mainly focus on clinical efficacy and daily wellness, traditional knowledge and scientific innovation, business and cultural promotion of TCM. Despite the dominance of neutral and positive sentiment, negative sentiment shows an increasing trend. Concerns are related to scientific rigor, ecological ethics, and adverse experiences. Japanese users are most engaged with tweets about TCM wellness, ingredients, and therapies. These behaviors reflect patterns of active learning, cultural identity, and experiential exploration. This study provides empirical support for the CAB pathway in social media environments and elucidates both the diffusion patterns of TCM-related discourse and the mechanisms underlying public responses on Japanese social media. It offers theoretical and empirical implications for cross-cultural health communication and the analysis of TCM discourse in digital contexts.},
}
@article {pmid41673365,
year = {2026},
author = {Jena, R and Ramakrishnan, S and Sarma, A and Sinha, VSP and Jayaraman, A},
title = {Estimation of surface water susceptibility to pollution index of natural wetlands of North-East India using multi-criteria decision model.},
journal = {Environmental science and pollution research international},
volume = {33},
number = {8},
pages = {3360-3378},
pmid = {41673365},
issn = {1614-7499},
mesh = {*Wetlands ; India ; Water Quality ; *Environmental Monitoring/methods ; *Water Pollution/analysis ; Models, Theoretical ; Decision Support Techniques ; },
abstract = {This study aims to develop a comprehensive and spatially explicit Surface Water Susceptibility to Pollution (SWSP) index using a Multi-Criteria Decision-Making (MCDM) framework, integrated with spatial environmental considerations. The proposed SWSP model employs a data-driven modelling approach, incorporating eight independent watershed characteristics and 55 sub-factors into the index to assess the health and quality of the wetland landscape. Unlike conventional single-parameter or empirical assessments, it includes a holistic evaluation of determinants contributing to surface water pollution within a catchment. The study was conducted in the wetland-dominated area of northeast India to demonstrate the scalability and replicability of the model for larger applications. Meanwhile, the Water Quality Index (WQI) is scientifically important because it consolidates multiple water quality parameters into a single, standardised score that reflects the overall health of a wetland, which depends on watershed characteristics. Therefore, the WQI can be used to cross-validate the SWSP index by comparing predicted pollution vulnerability with actual water quality measurements. In the present study, the WQI was measured through in situ and laboratory tests of the physicochemical parameters of surface water in three natural wetlands: Deepor Beel, Chandubi Lake, and Digholi Bil. This measurement was used to validate the SWSP index. The water quality analysis reveals that 96% of the total geographical area (TGA) of Deepor Beel has a WQI above 200, characterised by high turbidity (73.6 NTU), rendering the water unsuitable for any use. High and very high SWSP index areas within the catchment of Deepor Beel (72% TGA), Digholi Bil (63% TGA), and Chandubi Lake (62% TGA) are encompassed by built-up areas, agricultural land, and hilly forested regions. Linear regression shows a significant correlation between the SWSP Index and the WQI in all three wetlands: Deepor Beel (R[2] = 0.72), Chandubi Lake (R[2] = 0.85), and Digholi Bil (R[2] = 0.68), with p < 0.05. A strong correlation between the two confirms the model's reliability, while discrepancies suggest the need for refinement. This cross-validation enhances the scientific credibility of the SWSP index, supporting policymakers in sustainable watershed management, public health protection, and ecological conservation.},
}
@article {pmid42254981,
year = {2026},
author = {Nwinyi, OC and Siyanbola, KF},
title = {Spatial Heterogeneity of CYP9K1 Gene Overexpression Driving Cross-Resistance to Insecticide in Anopheles Mosquitoes Across Sub-Saharan Africa: A Systematic Review and Meta-Analysis.},
journal = {Journal of parasitology research},
volume = {2026},
number = {},
pages = {7708566},
pmid = {42254981},
issn = {2090-0023},
abstract = {Insecticide resistance in Anopheles mosquitoes poses a growing challenge to malaria elimination efforts across sub-Saharan Africa, threatening the continued effectiveness of frontline interventions. Among the metabolic mechanisms driving resistance, the cytochrome P450 monooxygenase gene CYP9K1 has been increasingly associated with detoxification and cross-resistance to multiple insecticide classes, particularly pyrethroids. This review assessed spatial heterogeneity in CYP9K1 overexpression (log2 fold change) in cross-resistant Anopheles mosquito populations across sub-Saharan Africa. This systematic review was conducted in accordance with PRISMA guidelines, drawing data from PubMed, Scopus, Web of Science, ScienceDirect, BioMed Central, and Google Scholar (2015-2025). Random-effects models using restricted maximum likelihood (REML) estimation were applied in JASP, alongside subgroup, sensitivity, and publication bias analyses. Out of 17,163 retrieved records, 11 studies met the inclusion criteria, representing data from six sub-Saharan African countries. The pooled log2 fold change for CYP9K1 expression was 1.910 (95% CI: 1.274-2.545; p < 0.001), confirming significant upregulation in resistant mosquito populations. Subgroup analyses further revealed that CYP9K1 overexpression followed a similar trend across countries, with no statistically significant differences observed between the countries (p > 0.05). This consistency suggests that the same CYP9K1-linked resistance mechanism may be spreading across different ecological and geographic regions, possibly through gene flow or shared selection pressure from insecticide use. These findings highlight CYP9K1 as a key metabolic marker conferring cross-resistance among Anopheles mosquitoes. The integration of CYP9K1 molecular surveillance into national vector control programs will strengthen early detection of resistance hotspots, inform insecticide rotation policies, and support the development of next-generation long-lasting insecticidal nets (LLINs) incorporating synergists or nonpyrethroid active ingredients. This evidence-based approach could guide tailored resistance management strategies essential for sustaining malaria control gains across sub-Saharan Africa.},
}
@article {pmid42255360,
year = {2026},
author = {Falk, S and Grzywacz, A and , and , and , and , and , and , and , },
title = {The genome sequence of a muscid fly, Phaonia angelicae (Scopoli, 1763) (Diptera: Muscidae).},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {236},
pmid = {42255360},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Phaonia angelicae (muscid fly; Arthropoda; Insecta; Diptera; Muscidae). The assembly contains two haplotypes with total lengths of 1 593.88 megabases and 1 575.57 megabases. Most of haplotype 1 (97.48%) is scaffolded into 5 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.82 kilobases. Gene annotation of this assembly on Ensembl identified 13 923 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 {pmid42258804,
year = {2026},
author = {Yeung, SK and Tong, ACY and Zhao, H and Mak, WWS},
title = {Using Ultra-Abridged Individual Difference Scales for Personalization in Digital Mental Health to Improve Uptake, Engagement, and Experiences: Three-Tiered Decision Framework for Scale Shortening.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e80662},
doi = {10.2196/80662},
pmid = {42258804},
issn = {1438-8871},
mesh = {Humans ; Digital Health ; *Mental Health ; *Individuality ; Digital Media ; },
abstract = {Given the diversity of human characteristics and experiences, personalization in nudges, messages, choice presentations, interventions, and overall product design has been increasingly adopted in digital health to promote engagement. Past studies on moderators and personalization in digital health and mental health services generally focused on demographic and symptom variables, with generally inconsistent findings or null findings. Cognitive, motivational, and decisional psychological attributes are largely overlooked. Psychology often uses long self-report scales to measure various psychological attributes. Although they are useful in tapping into individuals' psychological profiles, when applied in real-life, everyday settings to assess individual differences, people are most likely unwilling to complete them. With the pressing need to personalize digital health platforms to enhance uptake, retention, and engagement, ultrashort versions of these psychological scales may be considered to allow assessment of multiple attributes at the same time. Scale shortening can be achieved through regression analyses of each item, factor analyses, item response theory, ant colony optimization, and machine learning methods, with each method having advantages, disadvantages, and conditions required to make it suitable. To illustrate, we provided examples of regression analyses of each item and factor analyses, with potential implications for personalizing narrative versus research-based messages in digital mental health contexts. We present a 3-tiered decision framework for scale shortening method selection depending on goals and possible constraints, with guidelines on validation methods for ultrashort scales. Moving forward, more validation studies and field studies in digital health platforms are needed to evaluate the ecological validity, reliability, and generalizability of these methods, bearing in mind the limitations and conditions where such shortening methods may not work well. Researchers may compare the effectiveness and limitations of personalization using ultrashort scales with other commonly adopted personalization methods (eg, based on longer scales, behavioral data, and large language models). Ethical concerns need to be considered and mitigated carefully, respecting diverse preferences, informed choices, and the privacy of service users. Our viewpoint piece is primarily intended for digital mental health researchers and practitioners, but may also be informative for the fields of digital health and medicine as well as personalization (eg, personalized health care, personalized nudging, and message matching) more broadly, given the common goal of boosting uptake and engagement as well as improving service users' experiences.},
}
@article {pmid41654280,
year = {2026},
author = {Zhao, L and Liu, W},
title = {Metabolomics applications in lactic acid bacteria: Identification, classification, and functional analysis.},
journal = {Biotechnology advances},
volume = {88},
number = {},
pages = {108838},
doi = {10.1016/j.biotechadv.2026.108838},
pmid = {41654280},
issn = {1873-1899},
mesh = {*Metabolomics/methods ; *Lactobacillales/metabolism/classification/genetics ; Multiomics ; },
abstract = {BACKGROUND: Lactic acid bacteria (LAB) exhibit a limited correlation between genomic attributes and expressed metabolic traits, with their metabolic profiles being strongly influenced by ecological and environmental conditions. Recent advances in metabolomics have enabled high-resolution profiling of LAB-specific metabolic fingerprints and bioactive compounds. Nevertheless, challenges such as metabolite instability, incomplete annotation of LAB-derived metabolites, and environmental interference within complex fermentation matrices continue to hinder data standardization, reproducibility, and mechanistic interpretation.<br><br>SCOPE AND APPROACH: This review synthesizes recent advances in LAB metabolomics, highlighting how state-of-the-art analytical platforms, in combination with single-cell and metabolic flux-based approaches, improve strain identification, metabolic phenotyping, and functional metabolite discovery. It further addresses LAB-specific methodological challenges and observed discordance between phylogenetic relationships and metabolomic phenotypes, and discusses how the integration of metabolomics with genome-scale metabolic models (GSMMs) and multi-omics frameworks can improve functional prediction and provide deeper mechanistic insights.<br><br>KEY FINDINGS AND CONCLUSIONS: Overall, the integration of metabolomics is transforming functional studies in LAB by enabling strain-specific functional differentiation and the direct inference of adaptive traits from metabolic phenotypes. As metabolomics increasingly integrates with multi-omics datasets, GSMMs, and experimental validation approaches, a more unified framework for LAB functional analysis is emerging. This integrated approach provides a robust foundation for mechanistic elucidation, functional strain selection, and targeted applications in fermented food systems.},
}
@article {pmid41662579,
year = {2026},
author = {Monasterio, G and Fernández-López, MJ and Valero, E and Martin, U and Ayala-García, A},
title = {Digital Inequalities in the Use of eHealth Services in European Public Health Care Systems: Systematic Review of Observational Studies.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e81841},
pmid = {41662579},
issn = {1438-8871},
mesh = {Humans ; *Telemedicine/statistics &amp; numerical data ; Europe ; Digital Health ; Socioeconomic Disparities in Health ; Observational Studies as Topic ; *Healthcare Disparities ; *Public Health ; Health Services Accessibility ; Socioeconomic Factors ; Social Determinants of Health ; },
abstract = {BACKGROUND: European public health care systems are expanding eHealth tools such as teleconsultations, online appointment bookings, and electronic health records to improve efficiency and access to health care. However, their use depends on factors such as digital skills and internet access, which are unequally distributed across socioeconomic and demographic determinants. Most existing evidence on these inequalities is qualitative or outside universal health care systems.<br><br>OBJECTIVE: This systematic review aims to synthesize quantitative evidence on social inequalities in access to and use of eHealth services within European public health care systems. Specifically, we sought to identify which social determinants were most consistently associated with unequal use of online appointment booking, teleconsultations, electronic health records, and eHealth portals, across major social determinants of health.<br><br>METHODS: A systematic search was conducted across PubMed, Scopus, Web of Science, and PsycINFO for studies published in English or Spanish between 2015 and October 2025. Eligible quantitative studies included adults (&#x2265;18 years) using public health care systems in European countries. The primary outcome was differential access to or use of eHealth tools by social determinants in any level of care. Screening and data extraction were independently performed by 3 reviewers using Rayyan, resolving disagreements through consensus. Data extracted covered study design, population, eHealth tools, social determinants, and outcomes. Risk of bias was evaluated using Joanna Briggs Institute tools. Due to study heterogeneity in digital tools and inequality dimensions, results were synthesized narratively by tool type and social inequality factors. Point estimates and 95% CIs were extracted when available.<br><br>RESULTS: Of the 2366 records retrieved, 18 observational studies met the inclusion criteria: 13 cross-sectional, 3 prevalence, 1 retrospective cohort, and 1 ecological cohort. Publication output increased from 2020 onward, mostly driven by cross-sectional studies from northern and western Europe. Findings revealed consistent social gradients in eHealth use: older adults, individuals with lower educational or socioeconomic level, ethnic minorities, and those with limited digital skills or poorer health were less likely to use eHealth tools. Most studies were rated as high quality (78%), and the remainder as moderate, heterogeneity in designs, outcomes, and populations may limit generalizability.<br><br>CONCLUSIONS: Digital transformation in European public health systems has not benefited all groups equally. This review highlights persistent social inequalities in the use of key digital health tools. While many included studies were of high quality, heterogeneity in study designs, populations, and outcomes, as well as risk of bias, limits causal inference and the direct translation of findings into policy and practice. The findings nonetheless reveal systematic patterns of exclusion that are highly relevant for policy. Emphasizing an intersectional approach and standardizing measures of digital access will be essential to develop effective, equity-focused policies that ensure inclusive digital health services for all.},
}
@article {pmid41959181,
year = {2026},
author = {Yuan, H and Mandava, A and Samart, K and Ganz, J and Krishnan, A},
title = {Linking Genetic Risk to Disease-Relevant Cellular States via Metacell-Informed Modeling with ICePop.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.01.715877},
pmid = {41959181},
issn = {2692-8205},
abstract = {Genome-wide association studies (GWAS) have implicated thousands of loci in complex diseases, but translating these population-level signals into specific cellular contexts remains a central challenge. Integrating GWAS with single-cell transcriptomics data has enabled systematic identification of disease-relevant cell types, yet existing methods face a fundamental tradeoff: approaches like seismic that optimized for statistical power operate at the annotated cell-type level and miss heterogeneous disease signals concentrated in specific cellular states, while single-cell-resolution approaches like scDRS that capture such heterogeneity often lack sufficient power to detect subtle associations. Here we present ICePop (Informative Cell Populations), a framework that resolves this tradeoff by performing disease-cell type association at metacell resolution, thus achieving statistical power comparable to cell-type-level methods while detecting heterogeneous disease signals within cell types. In simulations against seismic and scDRS, ICePop maintains appropriate false positive rates and demonstrates superior power when disease effects are concentrated in cellular subpopulations. Applied to Tabula Muris across 81 traits and 120 cell types, ICePop identifies 1,684 disease-cell type associations, including the preferential vulnerability of differentiated gut epithelial cells in ulcerative colitis and loss of cell identity in immune-stressed lung capillary endothelial cells underlying their association with lung function. Clustering diseases by metacell association profiles reveals groupings that diverge from genetic risk-based clustering, including separation of blood cell count traits from immune diseases despite shared genetic architecture, reflecting differences in cellular rather than genetic etiology. In autism spectrum disorder, ICePop identifies preferential enrichment of genetic risk in specific enteric neuron subtypes, implicating dysfunction of the enteric nervous system in gastrointestinal comorbidities. ICePop's resolution of disease-relevant cell states within annotated cell types enables generation of testable, cell-state-specific hypotheses about disease mechanisms and therapeutic targets.},
}
@article {pmid42146430,
year = {2026},
author = {Ramola, R and De Paolis Kaluza, MC and Piovesan, D and Peng, Y and Joshi, P and Mehdiabadi, M and Quaglia, F and Pancsa, R and Chemes, LB and Ahmadi, M and Ahn, H and Altenhoff, AM and Asgari, E and Aspromonte, MC and Atalay, V and Babbi, G and Baldazzi, D and Barot, MM and Ben-Hur, A and Benso, A and Berenberg, D and Björne, J and Boecker, F and Boldi, P and Bonello, J and Bordin, N and Borole, P and Boroojeny, AE and Cao, R and Di Carlo, S and Casadio, R and Casiraghi, E and Chang, JM and Chen, C and Chen, TM and Cheng, J and Chiu, S and Dalkıran, A and Davidović, RS and Dessimoz, C and Diao, R and Djeddi, WE and Dogan, T and Flannery, ST and Fontana, P and Frasca, M and Freddolino, L and Gemović, B and Gillis, J and Ginter, F and Gligorijevic, V and Grossi, G and Heinzinger, M and Hippe, K and Hoehndorf, R and Holm, L and Hou, J and Hover, JR and Huang, YT and Ispano, E and Jabin, S and Jain, A and Jones, DT and Kaewphan, S and Kagaya, Y and Kanerva, J and Kihara, D and Kulmanov, M and Kumar, S and Kurgan, L and Lavezzo, E and Lees, J and Liao, WH and Lin, H and Linial, M and Littmann, M and Liu, L and Liu, T and Liu, YW and Makrodimitris, S and Manuto, L and Martelli, PL and Mchardy, AC and Merino, GA and Milone, DH and Mishra, S and Mofrad, MRK and Moi, D and Nakamura, T and Narsapuram, VK and Nugnes, MV and Obayashi, T and Ofer, D and Paccanaro, A and Perovic, VR and Petrini, A and Politano, G and Raimondi, D and Rappoport, N and Rehman, HU and Reijnders, MJMF and Reinders, MJT and Renfrew, PD and Rifaioglu, AS and Romero, AE and Saraswathi, A and Savojardo, C and Scholes, HM and Schoof, H and Shen, Y and Sillitoe, I and Stegmayer, G and Stern, A and Tiittanen, H and Toonsi, S and Toppo, S and Toronen, P and Torres, M and Trucco, G and Valentini, G and Veljkovic, N and Vesztrocy, AW and Vidulin, V and Villegas-Morcillo, A and Virtanen, A and Vranken, W and Vucetic, S and Wan, C and Wang, Z and Wass, MN and Waterhouse, RM and Ben Yahia, S and Yang, H and Yao, S and You, R and Yunes, J and Zhang, C and Zhang, Y and Zhao, C and Zhou, X and Zhu, YH and Zhu, S and Zhu, H and Özsari, G and Rost, B and Orengo, C and Robinson-Rechavi, M and Durand, D and Brenner, SE and Greene, CS and Mooney, SD and Tosatto, SCE and Friedberg, I and Radivojac, P},
title = {On the state of protein function prediction: a report on the fourth CAFA challenge.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42146430},
issn = {2692-8205},
abstract = {BACKGROUND: The Critical Assessment of Functional Annotation (CAFA) is a community effort held to understand the field of computational protein function prediction. Every three years, since 2010, the organizers initiate an experiment to collect function predictions on a large set of proteins and then evaluate the performance of predicting methods on a subset of proteins that have accumulated experimental annotations between the submission deadline and the evaluation time. CAFA provides an independent and rigorous assessment of the current state of the art, thus leveling the playing field, highlighting successes, revealing bottlenecks, and offering a forum for the exchange of ideas in protein science. Here, we report the results of the fourth CAFA experiment (CAFA4).<br><br>RESULTS: CAFA4 featured the participation of 148 methods from 70 research groups on a total of 46,205 unique proteins over a 5-year annotation accumulation phase, the longest in any CAFA. In a comparison across CAFA2-CAFA4 methods, the prediction of Gene Ontology (GO) terms has clearly improved across all three GO aspects and traditional evaluation settings. While not achieving the first rank, several CAFA2 and CAFA3 methods featured in the top ten methods in many evaluations, suggesting that earlier methods still hold relevance. The performance is weaker in the newly introduced "partial knowledge" evaluation category (proteins with experimental annotations before submission deadline that gained additional annotations in the same GO aspect during the annotation accumulation phase), highlighting the need for a new class of methods. The rankings of the methods were stable over the years in traditional evaluation settings, but less so in the new partial knowledge evaluation. Overall, the field continues to progress with some influx of new participants. Sustained efforts will be necessary to substantially advance it.},
}
@article {pmid42189907,
year = {2026},
author = {Wang, YJ and Schaal, KA and Nauta, J and Liaghat, A and De Domenico, M and Hall, JPJ and Pilosof, S},
title = {The interplay between ecological networks drives host-plasmid community dynamics.},
journal = {PLoS computational biology},
volume = {22},
number = {5},
pages = {e1014339},
pmid = {42189907},
issn = {1553-7358},
mesh = {*Plasmids/genetics/physiology ; *Models, Biological ; Computational Biology ; *Host-Pathogen Interactions/genetics ; },
abstract = {Plasmids drive evolution by transferring traits across microbial hosts. Transmission depends on both host-plasmid (infection) and plasmid-plasmid (compatibility) interactions, yet how the structure of these networks shapes transmission remains poorly understood. We hypothesized that these two ecological networks interact in non-additive ways to influence community outcomes. To test this, we developed a stochastic agent-based model that embeds both network structures and simulates coupled host-plasmid dynamics. We systematically varied the structure of each network, both individually and in combination, to isolate the effect of structure on host-plasmid dynamics. A modular (interactions organized into clusters) and hub (interactions concentrated on the highly connected) plasmid-plasmid compatibility network promoted transient host coexistence, while a modular host-plasmid infection network promoted plasmid diversity and stable host coexistence. Importantly, structured networks interacted non-additively, and their impact was most apparent when plasmid carriage imposed a moderate fitness cost on hosts. For example, combining a modular infection network with a hub compatibility network reversed the expected plasmid prevalence patterns, demonstrating that the structure of one network can counteract the effects of the other. We further re-parameterized our model to recapitulate empirical host-plasmid community dynamics, showing that infection network structure can strongly shape plasmid prevalence even in the presence of substantial biological heterogeneity. Our results highlight the necessity of jointly considering host-plasmid infection and plasmid-plasmid compatibility networks to understand host-plasmid community dynamics and their eco-evolutionary potential. More broadly, this work provides an initial mechanistic framework for generating testable hypotheses and underscores that systems involving multiple hosts and infectious agents require explicit consideration of how different ecological networks interact to shape community dynamics.},
}
@article {pmid42251245,
year = {2026},
author = {Kupika, OL and Zlotnikova, I},
title = {Biodiversity conservation informatics under anthropogenic climate change: an open and FAIR bibliometric review.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {42251245},
issn = {2676-8607},
abstract = {Informatics technologies are transforming biodiversity conservation by enabling large-scale data analysis, predictive modelling, and real-time monitoring in the face of anthropogenic climate change. This study presents a bibliometric analysis of global research on the application of informatics tools - such as machine learning, remote sensing, geographic information systems, and big data analytics - to biodiversity conservation and anthropogenic climate change. Using the Scopus database, we analysed 643 publications from 1993 to 2024 to identify research trends, collaboration networks, and emerging thematic areas. The results reveal a rapid increase in publications over the last decade, with developed countries and China leading research output, while contributions from Africa remain limited. Keyword co-occurrence analysis highlights key research themes, including species distribution modelling, climate change impacts, conservation technology, and ecological informatics. Co-authorship network mapping underscores the interdisciplinary and collaborative nature of biodiversity informatics and anthropogenic climate change research. This bibliometric review provides a quantitative synthesis of knowledge production in this field, offering insights into dominant research trajectories and identifying gaps in geographic representation and thematic coverage. Overall, the review reveals a large but geographically skewed scientific footprint whose future value depends on closing gaps in data-poor, biodiversity-rich regions and explicitly linking biodiversity informatics outputs to climate-resilient policy and practice. The findings inform future research and policy efforts aimed at leveraging informatics technologies for effective and inclusive biodiversity conservation strategies in a changing climate. This study is FAIR-aligned and accompanied by openly shared data and materials with ISO-aligned, machine-readable metadata.},
}
@article {pmid42252446,
year = {2026},
author = {Kim, Y and Lee, H and Lee, E and Kim, YH and Oh, CK},
title = {Oxidative aging facilitates biological barrier penetration of polyethylene microplastics, amplifying systemic lipotoxicity in aquatic species.},
journal = {Particle and fibre toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12989-026-00689-2},
pmid = {42252446},
issn = {1743-8977},
support = {RS-2025-02303107//National Research Foundation of Korea/ ; RS-2025-02214034//Korea Institute for Advancement of Technology/ ; },
abstract = {BACKGROUND: Environmental aging processes, such as oxidation, can substantially modify the physicochemical properties and toxicity of microplastics (MPs). Nevertheless, most studies have focused on pristine MPs, overlooking aged forms that more accurately represent environmental exposure conditions. Understanding the toxicological consequences of oxidative aging is essential for realistic ecological risk assessment.<br><br>RESULTS: We investigated the toxicological effects of pristine polyethylene (PE) and oxidized polyethylene (OPE) microplastics using a dual-species aquatic model comprising Daphnia magna and zebrafish (Danio rerio) embryos. Physicochemical characterization revealed that OPE particles exhibited increased surface roughness, a more negative surface charge, and a higher proportion of oxygen-containing functional groups on the particle surface compared with PE. Exposure to OPE induced pronounced lipid accumulation and significantly reduced heart rate in both models. Transcriptomic analysis indicated that OPE downregulated key genes related to lipid transport and metabolism, including mttp, apoea, and apobb. These findings were further validated by quantitative PCR and Oil Red O staining. Notably, zebrafish embryos exposed to OPE displayed developmental impairment even with intact chorions, implying enhanced bioavailability and barrier penetration of oxidized particles.<br><br>CONCLUSIONS: Our findings demonstrate that oxidative aging amplifies the biological toxicity of polyethylene microplastics by disrupting lipid metabolism and developmental processes. This study underscores the importance of considering environmentally aged MPs in ecological risk evaluations, as pristine particles may underestimate their actual hazard potential in aquatic ecosystems.},
}
@article {pmid41609929,
year = {2026},
author = {Mo, Y and Ahlgren, N and Fuhrman, JA and Sun, F and Hou, S},
title = {A Beginner's Guide to Using DeepVirFinder for Viral Sequence Identification From Metagenomic Datasets.},
journal = {Current protocols},
volume = {6},
number = {2},
pages = {e70310},
doi = {10.1002/cpz1.70310},
pmid = {41609929},
issn = {2691-1299},
support = {549943//Simons Foundation/ ; 42476109//National Natural Science Foundation of China/ ; 42276163//National Natural Science Foundation of China/ ; EF-2125142//National Science Foundation/ ; 3779//Gordon and Betty Moore Foundation/ ; },
mesh = {*Metagenomics/methods ; *Software ; *Deep Learning ; *Viruses/genetics ; Genome, Viral ; *Computational Biology/methods ; },
abstract = {Identifying viral sequences from metagenomic datasets is critical for investigating their origins, evolutionary patterns, and ecological functions. Previously, we developed a novel deep learning software, DeepVirFinder, to predict viral sequences from shotgun metagenomic assemblies. This method employs a twin convolutional neural network model to extract features from known viral and prokaryotic host genomic sequences for binary classification of input query sequences. With the rapid accumulation of environmental metagenomic data, this approach has accelerated the discovery of novel viruses from diverse environments through an alignment-free and reference-free deep learning strategy. To facilitate the rapid adoption of this software for beginning users, here we have further improved DeepVirFinder by optimizing its runtime performance, while maintaining the essential user interface of the original version. This comprehensive guide provides basic workflows for the most common use cases of DeepVirFinder. Additionally, to assist users in downstream analyses, supplementary scripts were provided in the software for extracting viral sequences and inspecting the results, thereby helping researchers more effectively mine viral information from metagenomic datasets. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Predicting viral sequences in metagenomic assemblies Basic Protocol 2: An integrated pipeline for viral sequence analysis: Prediction, extraction, and visualization Basic Protocol 3: Retraining the DeepVirFinder model using a customized dataset.},
}
@article {pmid41617485,
year = {2026},
author = {Chang, YH and Hong, TC and Lin, KT and Hsiao, YJ and Hsu, HE and Waniwan, JT and Silva, RE and Lai, IR and Lee, PC and Lin, MT and Shun, CT and Hsieh, MS and Chen, YJ and Wang, SW and Hsu, WH and Wu, IC and Wang, YK and Li, CC and Wang, JY and Hsu, YC and Fang, H and Lin, ZS and Chang, WH and Lin, JH and Chen, YS and Ko, YC and Shen, CY and Chen, YM and Wang, CY and Jheng, YT and Liu, WY and Wang, YT and Yeh, CW and Huang, PR and Liou, JM and Chen, LT and Han, CL and Wu, DC and Chen, HY and Yu, SL and Wu, MS and Chen, YJ and , },
title = {Integrative proteogenomics maps multifactorial aetiology, progression and therapeutic vulnerabilities in gastric cancer.},
journal = {Gut},
volume = {75},
number = {5},
pages = {886-904},
doi = {10.1136/gutjnl-2025-337247},
pmid = {41617485},
issn = {1468-3288},
mesh = {Humans ; *Stomach Neoplasms/microbiology/genetics/etiology/pathology/therapy ; *Proteogenomics/methods ; Male ; Female ; Disease Progression ; Multiomics ; Helicobacter pylori ; Helicobacter Infections/complications/microbiology ; Middle Aged ; Taiwan ; Gastrointestinal Microbiome ; Aged ; Microbiota ; },
abstract = {BACKGROUND: Gastric cancer, with disproportionately higher incidence in East Asia, arises from complex host-microbiome-environment interactions beyond Helicobacter pylori (HP) infection. However, the molecular architecture linking environmental carcinogens, microbial succession and host response remains unclear.<br><br>OBJECTIVE: To delineate multifactorial aetiologies and clinically actionable subtypes/biomarkers of gastric cancer through integrative proteogenomic, microbial and environmental exposure profiling.<br><br>DESIGN: We established a multiomics atlas of paired tumour, adjacent mucosa tissues and blood from 154 treatment-na&#xef;ve Taiwanese patients, integrating whole-exome sequencing, RNA-seq, proteome and phosphoproteome profiling with carcinogen signatures, HP status, microbiome composition and refined anatomical mapping. Cell-based functional assays tested carcinogen effects. Microbial subtype was assessed in an independent cohort.<br><br>RESULTS: A polycyclic-aromatic-hydrocarbon signature, dibenz[a,h]acridine, emerged as a high-risk exposure promoting invasion, immune suppression and poor survival, significantly exceeding nitrosamine-linked risk in this cohort. Multilayer integration defined three initiation ecologies: HP-driven inflammatory, non-HP microbiome-enriched immune-silent and HP-free microbially depleted states. Among HP-negative tumours, a Streptococcus-enriched subtype associated with tight-junction (CLDN18.2/ZO-1/OCLN) disruption and epithelial-mesenchymal transition, whereas a subset of clinically aggressive cases retained CLDN18.2-high epithelial-stable subtype for therapeutic accessibility. An independent cohort revealed gastric juice-derived Streptococcus anginosus abundance inversely correlated with tight-junction proteins. Anatomical mapping reveals location-specific, sex-specific, subtype-specific oncogenic networks and kinase activity, including CDK4 activation in clinical biomarker-negative tumours. Decision-tree models combining exposure and proteome-immune states refined recurrence and survival prediction beyond stage.<br><br>CONCLUSION: This proteogenomic framework defines exposure-informed and microbiome-informed gastric cancer subtypes, providing a molecular schema for patient stratification, prevention and actionable therapeutic vulnerabilities.},
}
@article {pmid41649858,
year = {2026},
author = {Lane, R and Millard, LAC and Salway, R and Stone, CJ and Skinner, AL and Brady, SM and Mariapun, J and Rajakumar, S and Ramadas, A and Rizal, H and Johnson, L and Su, TT and Armstrong, MEG},
title = {The Feasibility of Smartwatch Micro-Ecological Momentary Assessment for Tracking Eating Patterns of Malaysian Children and Adolescents in the South-East Asian Community Observatory Child Health Update 2020: Cross-Sectional Study.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e73435},
pmid = {41649858},
issn = {1438-8871},
mesh = {Humans ; Child ; Adolescent ; Male ; Malaysia ; *Ecological Momentary Assessment ; Female ; Cross-Sectional Studies ; Feasibility Studies ; *Feeding Behavior ; Cell Phone ; Digital Health ; },
abstract = {BACKGROUND: Mobile phone ecological momentary assessment (EMA) methods are a well-established measure of eating and drinking behaviors, but compliance can be poor. Micro-EMA (μEMA), which collects information with a single tap response to brief questions on smartwatches, offers a novel application that may improve response rates. To our knowledge, there is no data evaluating μEMA to measure eating habits in children or in low-to-middle-income countries.<br><br>OBJECTIVE: In this study, we investigated the feasibility of micro-EMA to measure eating patterns in Malaysian children and adolescents.<br><br>METHODS: We invited 100 children and adolescents aged 7-18 years in Segamat, Malaysia, to participate in 2021-2022. Smartwatches were distributed to 83 children and adolescents who agreed to participate. Participants were asked to wear the smartwatch for 8 days and respond to 12&#xa0;prompts per day, hourly, from 9AM to 8PM, asking for information on their meals, snacks, and drinks consumed. A questionnaire captured their experiences using the smartwatch and &#x3bc;EMA interface. Response rate (proportion of prompts responded to) assessed participants' adherence. We explored associations between response rate with time of day, across days, age, and sex using multilevel binomial logistic regression modeling.<br><br>RESULTS: Eighty-two participants provided usable smartwatch data. The median number (IQR) of meals, drinks, and snacks per day was 2 (2-4), 3 (1-5), and 1 (0-2), respectively, on the first day of the study. The median response rate across the study was 68% (IQR 50-83). The response rate decreased across study days from 74% (68-78) on Day 1 to 40% (30-50) on Day 7 (odds ratio [OR] per study day 0.73, 95% CI 0.64-0.83). Response rate was lowest at the start of the day and highest between the hours of 12 PM and 2 PM. Female participants responded to more prompts than male participants (OR 1.72, 95% CI 1.03-2.86). There was no evidence of differential response by age (OR 0.73, 95% CI 0.41-1.28). Most participants (65%) rated their experience using the smartwatch positively, with 33% saying they were happy to participate in future studies using the smartwatch. For children that did not wear the smartwatch for the full study duration (n=22), discomfort was the most common complaint (41%).<br><br>CONCLUSIONS: In this study of the feasibility of &#x3bc;EMA on smartwatches to measure eating in Malaysian children, we found the method was acceptable. However, response rates declined across study days, resulting in substantial missingness. Future studies (eg, through focus groups) should explore approaches to improving response to event prompts, trial alternative devices to increase children's comfort, and evaluate revised protocols for reporting of intake events.},
}
@article {pmid41596418,
year = {2026},
author = {Wang, J and Zeng, NK and Zhang, X},
title = {Tuber Inoculation Drives Rhizosphere Microbiome Assembly and Metabolic Reprogramming in Corylus.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
pmid = {41596418},
issn = {1422-0067},
support = {2019RC185 and 320RC597//Natural Science Foundation of HainanProvince/ ; (2024)171//Project of Science and Technology Programs of Guizhou Province/ ; Gui(2024)TG12//Project of Central Government Financial Fund for Forest Reform and Development/ ; },
mesh = {*Rhizosphere ; *Microbiota ; *Corylus/microbiology/metabolism ; Symbiosis ; Multiomics ; Plant Roots/microbiology/metabolism ; Metabolic Reprogramming ; Mycorrhizae/physiology ; *Plant Tubers/microbiology/metabolism ; Metabolomics/methods ; Soil Microbiology ; },
abstract = {To elucidate the potential of integrated multi-omics approaches for studying systemic mechanisms of mycorrhizal fungi in mediating plant-microbe interactions, this study employed the Tuber-inoculated Corylus system as a model to demonstrate how high-throughput profiling can investigate how fungal inoculation reshapes the rhizosphere microbial community and correlates with host metabolism. A pot experiment was conducted comparing inoculated (CTG) and non-inoculated (CK) plants, followed by integrated multi-omics analysis involving high-throughput sequencing (16S/ITS), functional prediction (PICRUSt2/FUNGuild), and metabolomics (UPLC-MS/MS). The results demonstrated that inoculation significantly restructured the fungal community, establishing Tuber as a dominant symbiotic guild and effectively suppressing pathogenic fungi. Although bacterial alpha diversity remained stable, the functional profile shifted markedly toward symbiotic support, including antibiotic biosynthesis and environmental adaptation. Concurrently, root metabolic reprogramming occurred, characterized by upregulation of strigolactones and downregulation of gibberellin A5, suggesting a potential "symbiosis-priority" strategy wherein carbon allocation shifted from structural growth to energy storage, and plant defense transitioned from broad-spectrum resistance to targeted regulation. Multi-omics correlation analysis further revealed notable associations between microbial communities and root metabolites, proposing a model in which Tuber acts as a core regulator that collaborates with the host to assemble a complementary micro-ecosystem. In summary, the integrated approach successfully captured multi-level changes, suggesting that Tuber-Corylus symbiosis constitutes a fungus-driven process that transforms the rhizosphere from a competitive state into a mutualistic state, thereby illustrating the role of mycorrhizal fungi as "ecosystem engineers" and providing a methodological framework for green agriculture research.},
}
@article {pmid41603972,
year = {2026},
author = {Rossmann, C and Karnowski, V and Metag, J and Raupp, J and Reifegerste, D and Riesmeyer, C and Sawalha, N and Lux, A and Esser, AL and Kammerer, R and Singh, F and Rödel, N and Brill, J and Gerling, E and Wiedicke, A},
title = {The Role of Digital Media in Chronic Disease Self-Management: Protocol for a Multimethod Study of the DISELMA Research Consortium.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e77811},
pmid = {41603972},
issn = {1929-0748},
mesh = {Humans ; *Digital Media ; Chronic Disease/therapy/psychology ; *Self-Management/methods/psychology ; Focus Groups ; Surveys and Questionnaires ; Digital Health ; },
abstract = {BACKGROUND: Chronic diseases, such as type 1 and type 2 diabetes, asthma, and chronic obstructive pulmonary disease , demand long-term treatment and permanent adaptation. One important pillar in coping with these diseases is individuals' self-management, including support from digital media. Research on their effects confirms their potential. However, it is flawed by theoretical underdevelopment and methodological weaknesses, such as a focus on short-term effects, single digital features, and microlevel studies.<br><br>OBJECTIVE: The research unit (RU) DISELMA ("Digital Media in Chronic Disease Self-Management") aims to examine the continued use patterns and effects of the digital self-management of chronic diseases, as well as the role of the interpersonal, organizational, and societal levels to gain a comprehensive picture of the individual processes, their contextual embeddedness, and cross-level interactions.<br><br>METHODS: To fully capture the manifold multilevel influences, the RU comprises 6 individual projects (IPs), each of which conducts several studies. Two projects at the individual level analyze determinants of use, usage patterns, and effects of digital media, combining systematic reviews, experience sampling method studies, focus groups, panel surveys, and content analysis of apps used. Two projects examine the interpersonal context by analyzing the role of health care providers and the diffusion of digital media in informal networks, conducting a scoping review, online surveys with physicians, semistructured interviews, and participant observations of physician-patient dyads, patient focus groups, and interviews with peers. One project aims to analyze the role of organizations within the mobile health market by conducting a content analysis of organizational messages and a survey. Finally, one project analyzes journalistic and social media to gain insight into the discourses about digital chronic disease self-management on the societal level.<br><br>RESULTS: The RU received funding approval from the Deutsche Forschungsgemeinschaft (German Research Foundation; grant 456132969) in July 2023, and the 4-year funding period ranges from December 2023 to November 2027. IP1 is currently conducting its systematic reviews and experience sampling method studies, both to be finalized in 2026. IP2 is conducting its systematic review and meta-analysis alongside panel surveys until June 2026. IP3 has completed its online survey with physicians and is currently conducting observations until August 2026. IP4 is conducting its scoping review and peer interviews through 2026, while IP5 is working on its content analysis and survey, and IP6 on its manual content analysis. First publications of the results are expected in 2026.<br><br>CONCLUSIONS: The results will contribute to the existing research through a theoretically and methodologically comprehensive approach that improves our understanding of the processes within and between all levels. These insights will inform providers of digital health solutions and health care practitioners about users' needs, advance evidence-based disease self-management programs, and contribute to better coping with chronic diseases, improved well-being of affected individuals, and reduced health care costs.},
}
@article {pmid41617725,
year = {2026},
author = {Xu, X and Lin, J and Zhu, LT and Long, L and Duan, Y and Hayatov, J and Lin, L and Chen, H and Huang, Q},
title = {Extracellular vesicles as structured vectors of quorum sensing signals influence aquatic microbial communities.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41617725},
issn = {2055-5008},
support = {32161143016//National Natural Science Foundation of China/ ; NO. NBSDC-DB-21//National Basic Science Data Center "Environment Health DataBase"/ ; },
mesh = {*Quorum Sensing ; *Extracellular Vesicles/metabolism ; Acyl-Butyrolactones/metabolism ; *Microbiota ; *Bacteria/classification/metabolism/genetics ; Multiomics ; Signal Transduction ; *Water Microbiology ; Proteomics ; },
abstract = {Quorum sensing (QS) orchestrates collective microbial behaviors and functional acclimatization through chemical communication. However, QS in natural waters is challenged by dilution, alkaline hydrolysis, and enzymatic degradation of freely dissolved autoinducers. Here, we demonstrate that extracellular vesicles (EVs) act as selective, durable, and protective vectors for QS signal molecules under environmental stresses. Specifically, EVs preferentially package hydrophobic acyl‑homoserine lactones, concentrate them locally, and shield them from alkaline hydrolysis, and exhibiting long-distance transport. In addition, EVs possess specific affinity to recipients, thus influencing microbial community. Field investigation via multi-omics showed that EV abundance covaried with salinity, nutrients, chlorophyll a, and biomass, which were validated by culture experiments. Our statistical framework demonstrated that organisms producing moderate EV levels contributed significantly to maintaining community stability and ecosystem functions. Distinctively within this group, QS-active species (including Burkholderiaceae, Pseudomonadaceae, Rhodobacteraceae, Roseobacteraceae, Flavobacteriaceae etc.) emerge as key drivers facilitating these crucial ecological roles. Furthermore, metaproteomics of field EVs reveal QS receptor and synthesis proteins, suggesting coordinated transport of signals and proteins, which indicate new routes for QS crosstalk, particularly for taxa bearing luxR/I solos. Our results show that moderately generated EVs are the potentially important QS signal carriers and ecological regulation hubs in natural waters.},
}
@article {pmid41634036,
year = {2026},
author = {Huang, L and Pu, YT and Zhao, YH and Sun, XY and Zhu, Y and Lu, YP and Leng, HX and Feng, J and Jin, LR and Sun, KP},
title = {Diet and environmental factors jointly drive the gut microbiome, resistome, and virulome of urban bats.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41634036},
issn = {2055-5008},
support = {32430066//National Natural Science Foundation of China/ ; 32171525//National Natural Science Foundation of China,China/ ; },
mesh = {Animals ; *Chiroptera/microbiology ; *Diet ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Environment ; Gene Transfer, Horizontal ; Female ; Genes, Bacterial ; Multiomics ; Drug Resistance, Bacterial ; },
abstract = {The coexistence and horizontal transfer of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) carried by urban wildlife represent an emerging form of biological pollution, constituting a significant threat to public health. We employed meta-omic approaches to evaluate the effects of host traits (sex, age, etc.), environmental factors (including geographical location and time), and diet (including food composition and antibiotic residues) on the bacterial, ARG, and VFG profiles of Vespertilio sinensis, an urban-dwelling bat. Our results demonstrate that the feces of V. sinensis harbor diverse ARGs and VFGs, but their genomic evidence for horizontal mobility in bacterial communities is limited. Notably, environmental changes over time and across geographical locations are associated with the ARG and VFG profiles, potentially due to the influence of pollutants in specific habitats. Dietary factors are associated with their dynamics through the microbiome, with antibiotic residues exerting selective pressure on ARG profiles. No significant impacts of sex, age, body size, and reproductive status on the gut microbiota, resistome, or virulome were observed. This study provides valuable insights into the ecological drivers of the gut microbiome, resistome, and virulome in bats, thereby contributing to our understanding of the public health risks associated with urban wildlife.},
}
@article {pmid41637624,
year = {2026},
author = {Kadirvelu, B and Bellido Bel, T and Freccero, A and Di Simplico, M and Nicholls, D and Faisal, AA},
title = {Digital Phenotyping for Adolescent Mental Health: Feasibility Study Using Machine Learning to Predict Mental Health Risk From Active and Passive Smartphone Data.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e72501},
pmid = {41637624},
issn = {1438-8871},
mesh = {Humans ; Adolescent ; Feasibility Studies ; *Smartphone ; Female ; *Machine Learning ; Male ; *Mental Health ; *Mental Disorders/diagnosis ; Digital Health ; *Phenotype ; Predictive Learning Models ; *Mobile Applications ; },
abstract = {BACKGROUND: Adolescents are particularly vulnerable to mental disorders, with over 75% of lifetime cases emerging before the age of 25 years. Yet most young people with significant symptoms do not seek support. Digital phenotyping, leveraging active (self-reported) and passive (sensor-based) data from smartphones, offers a scalable, low-burden approach for early risk detection. Despite this potential, its application in school-going adolescents from general (nonclinical) populations remains limited, leaving a critical gap in community-based prevention efforts.<br><br>OBJECTIVE: This study evaluated the feasibility of using a smartphone app to predict mental health risks in nonclinical adolescents by integrating active and passive data streams within a machine learning (ML) framework. We examined the utility of this approach for identifying risks related to internalizing and externalizing difficulties, eating disorders, insomnia, and suicidal ideation.<br><br>METHODS: Participants (n=103; mean age 16.1 years, SD 1.0) from 3 UK secondary schools used the Mindcraft app (Brain and Behaviour Lab) for 14 days, providing daily self-reports (eg, mood, sleep, and loneliness) and continuous passive sensor data (eg, location, step count, and app usage). We developed a deep learning model incorporating contrastive pretraining with triplet margin loss to stabilize user-specific behavioral patterns, followed by supervised fine-tuning for binary classification of 4 mental health outcomes, namely, the Strengths and Difficulties Questionnaire (SDQ)-high risk, insomnia, suicidal ideation, and eating disorder. Performance was assessed using leave-one-subject-out cross-validation (LOSO-CV), with balanced accuracy as the primary metric. Comparative analyses were conducted using CatBoost (Yandex) and multilayer perceptron (MLP) models without pretraining. Feature importance was assessed using Shapley Additive Explanations (SHAP) values, and associations between key digital features and clinical scales were analyzed.<br><br>RESULTS: Integration of active and passive data outperformed single-modality models, achieving mean balanced accuracies of 0.71 (0.03) for SDQ-high risk, 0.67 (0.04) for insomnia, 0.77 (0.03) for suicidal ideation, and 0.70 (0.03) for eating disorder. The contrastive learning approach improved representation stability and predictive robustness. SHAP analysis highlighted clinically relevant features, such as negative thinking and location entropy, underscoring the complementary value of combining subjective and objective data. Correlation analyses confirmed meaningful associations between key digital features and mental health outcomes. Performance in an independent external validation cohort (n=45) achieved balanced accuracies of 0.63-0.72 across outcomes, suggesting generalizability to new settings.<br><br>CONCLUSIONS: This study demonstrates the feasibility and utility of smartphone-based digital phenotyping for predicting mental health risks in nonclinical, school-going adolescents. By integrating active and passive data with advanced machine modeling techniques, this approach shows promise for early detection and scalable intervention strategies in community settings.},
}
@article {pmid41882511,
year = {2026},
author = {Yu, X and Hunt, BJ and Wang, S and Troczka, BJ and Shangguan, C and Zhu, W and Kuang, Y and Bass, C},
title = {A chromosome-level genome assembly and multi-omics analysis reveal fenpropathrin resistance mechanisms in the turnip aphid, Lipaphis erysimi.},
journal = {Pest management science},
volume = {82},
number = {7},
pages = {6564-6574},
doi = {10.1002/ps.70744},
pmid = {41882511},
issn = {1526-4998},
support = {20212ACB215001//Natural Science Foundation for Distinguished Young Scholars of Jiangxi Province/ ; 32160634//National Natural Science Foundation of China/ ; JXSQ2019101058//Double Thousand Plan of Jiangxi Province/ ; },
mesh = {Animals ; *Pyrethrins/pharmacology ; *Insecticide Resistance/genetics ; *Insecticides/pharmacology ; *Aphids/genetics/drug effects/metabolism ; Multiomics ; *Genome, Insect ; Insect Proteins/genetics/metabolism ; Cytochrome P-450 Enzyme System/genetics/metabolism ; },
abstract = {BACKGROUND: The turnip aphid Lipaphis erysimi is a cruciferous crop pest with the potential to reduce yields by up to 90%. Treatment of L. erysimi infestations using insecticides has resulted in numerous cases of resistance in field populations yet genomic resources are lacking for this species, limiting the ability of researchers to investigate the molecular basis of resistance and develop management strategies.<br><br>RESULTS: Here we describe the creation of a chromosome scale genome assembly for L. erysimi and the characterization of fenpropathrin resistance in this species using multi-omics analysis. A 409&#x2009;Mb genome was assembled for L. erysimi, with an N50 of 95.2&#x2009;Mb and 90% of assembled content contained within four chromosome-scale scaffolds. We identified a key M903L mutation in a voltage-gated sodium channel gene that is targeted by fenpropathrin and the accompanying up-regulation of cytochrome P450 and UDP-glycosyltransferase detoxification genes. Using transgenic flies, we further confirmed the ability of L. erysimi CYP4CJ1 to confer fenpropathrin resistance in vivo.<br><br>CONCLUSION: Mechanisms for fenpropathrin resistance in L. erysimi were identified through multi-omics analysis and functional characterization. Collectively, this study provides valuable genomic resources for molecular investigations of L. erysimi and establishes a foundation for developing novel strategies to enhance pyrethroid efficacy in this species. &#xa9; 2026 Society of Chemical Industry.},
}
@article {pmid41926903,
year = {2026},
author = {Lin, C and Gao, M and Chen, H and Guo, J and Zhang, B and Lin, J and Zhao, C},
title = {Multi-omics analysis reveals polyethylene microplastics-induced gill damage, metabolic disruption and immune dysregulation in Lateolabrax maculatus.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {59},
number = {},
pages = {101815},
doi = {10.1016/j.cbd.2026.101815},
pmid = {41926903},
issn = {1878-0407},
mesh = {Animals ; *Microplastics/toxicity ; *Gills/drug effects/metabolism/pathology ; *Polyethylene/toxicity ; *Water Pollutants, Chemical/toxicity ; Multiomics ; Oxidative Stress/drug effects ; Transcriptome/drug effects ; },
abstract = {Microplastics (MPs) are emerging environmental pollutants that can induce physiological toxicity in aquatic organisms. This study investigated the toxicological effects of dietary exposure to polyethylene microplastics (PE-MPs) on gill tissues of Lateolabrax maculatus, using diets containing 0%, 4%, and 8% (w/w) PE-MPs. Histological, transcriptomic, and biochemical analyses were performed to assess structural damage, alterations in gene expression, and changes in antioxidant and immune parameters. Histological examination revealed structural abnormalities, including bending of gill lamellae and epithelial cell swelling, suggesting that gills may be sensitive to MP exposure. Transcriptomic analysis indicated that differentially expressed genes were enriched in pathways related to energy metabolism and immune response, including glycolysis/gluconeogenesis, oxidative phosphorylation, and phagosome. Key glycolytic enzymes (HK, PFK, PK) were upregulated, and the PPAR signaling pathway was activated, suggesting enhanced energy demands under stress conditions. Biochemical assays showed dynamic changes in antioxidant enzyme activities, with increased malondialdehyde (MDA) content in the high-concentration group, indicating oxidative stress. Immune-related genes associated with the NF-κB pathway (e.g., IL-1β, TNF-α) were upregulated, while TGF-β expression showed no significant changes. Following a 14-day depuration period without MP exposure, most antioxidant and immune parameters showed a trend toward recovery, indicating that the observed effects may be partially reversible. These findings suggest that MP exposure can contribute to gill structural impairment and perturbations in energy metabolism, redox homeostasis, and immune regulation in Lateolabrax maculatus, providing insights into the potential ecological risks of microplastic pollution in aquaculture environments.},
}
@article {pmid42118777,
year = {2026},
author = {Wang, Z and Fu, Y and Goyal, A and Maslov, S},
title = {Fitness advantage of sequential metabolic strategies emerges from community interactions in strongly fluctuating environments.},
journal = {PLoS computational biology},
volume = {22},
number = {5},
pages = {e1014277},
pmid = {42118777},
issn = {1553-7358},
mesh = {*Models, Biological ; Proteome/metabolism ; Biomass ; Ecosystem ; Computational Biology ; *Microbial Interactions/physiology ; },
abstract = {Microbes growing in fluctuating environments employ two key metabolic strategies: sequential (diauxic) utilization and co-utilization of nutrients. Most work has focused on understanding and comparing these strategies physiologically for the growth of single species, rather than ecologically for the assembly of complex natural communities. This is in part because of the lack of a framework for directly comparing the fitness of these strategies in an ecological context. Here, we present a new consumer-resource framework that incorporates dynamic proteome reallocation, and use it to compare the fitness of metabolic strategies during community assembly. We introduce two notions of fitness of a strategy in fluctuating environments: the time-averaged growth rate and the biomass-weighted prevalence of microbes using a given strategy. We find that sequential utilizers, although disadvantaged in pairwise competitions, gain a significant edge during community assembly - an advantage that becomes more pronounced with increasing community diversity and the size of the species pool from which they are assembled. Low diversity communities resemble pairwise competitions and are dominated by co-utilizers, whereas high diversity, mature communities (i.e., those assembled from a larger species pool) are dominated by the sequential utilizers. This shift is driven by two factors: the difference in lag times and the increased structural stability conferred by sequential strategies. Overall, our work provides several testable predictions about the co-occurrence patterns of microbes using different metabolic strategies.},
}
@article {pmid42250063,
year = {2026},
author = {Boxrud, B and Siegle, E and Shankman, SA and Reddy, M and Griffith, JW and Ashaie, SA},
title = {Measuring affective symptoms of depression in aphasia: development of an accessible ecological momentary assessment tool.},
journal = {Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation},
volume = {35},
number = {7},
pages = {},
pmid = {42250063},
issn = {1573-2649},
support = {K23DC020757/DC/NIDCD NIH HHS/United States ; },
abstract = {PURPOSE: Post-stroke depression is highly prevalent in aphasia, yet existing depression measures rely heavily on language and lack sufficient validity for this population. The aim of this study was to develop an aphasia-accessible Ecological Momentary Assessment (EMA) of depression based on the input of people with aphasia, their care partners, and speech-language pathologists (SLPs).<br><br>METHODS: Nine focus groups were conducted with people with aphasia (n&#x2009;=&#x2009;15), care partners (n&#x2009;=&#x2009;13), and SLPs (n&#x2009;=&#x2009;13) to identify relevant depression symptoms. Items were selected based on factors such as endorsement ratings and qualitative feedback across stakeholder groups. Participants with aphasia also took part in individual cognitive interviews to ensure comprehensibility and accessibility of the final items, corresponding pictures, and pictorial rating scale.<br><br>RESULTS: The final set of items to be included in the EMA consisted of three positive affect items (determined, proud, interested) and three negative affect items (sad, like a failure, angry). Cognitive interviews confirmed comprehensibility and accessibility of the items, though the picture for interested required revision. Additionally, participants found 3-4 daily assessments feasible.<br><br>CONCLUSION: Stakeholder engagement revealed that positive affect dysregulation (e.g., reduced interest in previously rewarding activities) may be particularly salient for depression in aphasia in addition to negative affect dysregulation (e.g., increased feelings of failure and anger). The resulting six-item EMA uses multimodal supports (e.g., text, pictures, pictorial rating scale, audio recordings) to capture both valence systems.},
}
@article {pmid41586531,
year = {2026},
author = {Han, J-R and Li, S and Lian, W-H and Xu, L and Duan, L and Li, J-L and Shi, G-Y and Wei, Q-C and Ali, M and Li, W-J and Dong, L},
title = {Fermentation conditions outweigh phylogeny in shaping the metabolome of novel Micromonospora strains: an integrated genomics-metabolomics analysis.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {2},
pages = {e0223525},
pmid = {41586531},
issn = {1098-5336},
support = {2024CXTD04//Guangdong Province Modern Agricultural Industry Technology System Innovation Team Construction Project Focused on Agricultural Products (Agricultural Microorganisms)/ ; 2025A04J3495//Guangzhou Basic and Applied Basic Research Foundation, China/ ; 32270076//National Natural Science Foundation of China/ ; },
mesh = {*Micromonospora/genetics/metabolism/classification/isolation &amp; purification ; Phylogeny ; *Metabolome ; Genomics ; Metabolomics ; Fermentation ; Multiomics ; Genome, Bacterial ; Geologic Sediments/microbiology ; Soil Microbiology ; Terpenes/metabolism ; Polyketides/metabolism ; },
abstract = {The genus Micromonospora, a key member of the actinomycetes, has demonstrated considerable potential for natural product biosynthesis. In this study, we isolated 15 Micromonospora spp. strains from desert soil and marine sediment samples, eight of which represent four novel species. To explore the biosynthetic capacity of this genus, we performed an integrated analysis of Micromonospora reference genomes. Pan-genomic analysis further unveiled the core biosynthetic characteristics of the genus responsible for producing terpenes and polyketides. Further multi-omics investigation, combining genomic and metabolomic data, uncovered a positive correlation between phylogenetic relationships and biosynthetic potential, alongside a decoupling of metabolic profiles. Notably, metabolomic findings emphasized the dominant influence of culture conditions on the expression of biosynthetic capabilities. Overall, our study provides a comprehensive elucidation of the biosynthetic potential of the genus Micromonospora and highlights the value of investigating novel strains and applying diverse cultivation strategies in natural product discovery.IMPORTANCEOur study provides a comprehensive genomic and metabolomic elucidation of the significant biosynthetic potential within the genus Micromonospora. It reveals a core biosynthetic capacity for terpenes and polyketides that is phylogenetically linked, whereas the resulting natural product repertoire is subject to strong modulation by cultivation conditions. These findings underscore the critical importance of exploring novel species and employing diverse cultivation strategies to unlock the full potential of microbial resources for natural product discovery.},
}
@article {pmid42146349,
year = {2026},
author = {Wagner, J and Keskus, AG and Oshima, KK and Ranallo-Benavidez, TR and McDaniel, J and Sikic, M and Lin, D and Paulin, LF and English, AC and Sedlazeck, FJ and Munding, EM and Sanborn, JZ and Carroll, A and Chang, PC and Cook, DE and Shafin, K and de Ligt, J and Hassaine, R and Cameron, D and Catreux, S and Lee, Y and Murray, L and Truong, S and Brueffer, C and Zimin, AV and Cross, E and McGowan, M and Vernich, M and Liss, AS and Kocher, JP and Stephens, Z and Ahmad, T and Bryant, A and Dwarshuis, N and He, HJ and He, Z and Olson, ND and Thibaud-Nissen, F and Antipov, D and Koren, S and Phillippy, A and Musunuri, RL and Narzisi, G and Jain, M and Wenger, AM and Eacker, S and Sahraeian, SME and Boutros, PC and Patel, Y and Yamaguchi, TN and McConnell, J and Borchers, M and Gerton, JL and Kostos, P and Guarracino, A and Jehangir, M and Benjamin, H and Mootor, MFE and Xu, Y and Asri, M and Miga, KH and Park, J and Paten, B and Luo, R and Zheng, Z and Choi, JY and Nguyen, L and Vats, P and Robinson, DR and Vo, JN and Gao, S and Murtaza, G and Mason, CE and Cheng, H and Barthel, FP and Xiao, C and Logsdon, GA and Kolmogorov, M and Zook, JM},
title = {A complete human pancreatic cancer genome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42146349},
issn = {2692-8205},
support = {U54 CA302435/CA/NCI NIH HHS/United States ; },
abstract = {Cancer genome sequencing is essential for understanding tumor evolution and advancing precision medicine.[1] However, reference gaps and germline variants obscure detection of small and large somatic variants and methylation in repetitive regions.[1-3] It is common for tumor cells to gain or lose chromosome arms due to somatic structural changes that occur inside highly repetitive satellite DNA sequences in the centromeres.[4] To identify the full spectrum of somatic variants, including complex rearrangements, we construct and curate near-complete, haplotype-resolved assemblies of the most recent common ancestor of an early-passage broadly-consented hypodiploid pancreatic cancer cell line and matched normal tissues. The tumor assembly completely recapitulates all 35 tumor chromosomes observed with karyotyping, with multiple translocation-induced hybrid chromosomes. The hybrid chromosomes contain putative functional dicentric and fused centromeres, nested foldback inversions causing 14 breakpoints with a haplotype switch in a single event, and centromeric satellite tandem duplications up to 136 kbp. Direct comparison of tumor and normal assembly haplotypes uncovers >7,000 variants altering >1 Mbp of sequence in repetitive regions that have been hidden by reference gaps and germline variants. 44 % of somatic small variants change representation because they alter germline variants on GRCh38, impacting mutational signatures and kataegis/omikli clusters. Most somatic LINE insertions originate from two hypomethylated non-reference germline LINE insertions, highlighting their impact on insertion mutation burden. These assemblies demonstrate that centromeric, acrocentric, and telomeric regions conventionally excluded from analysis harbor extensive somatic and epigenetic changes. Resolving complete tumor genomes enables a deeper understanding of cancer structural plasticity and the endpoints of breakage-fusion-bridge cycles. These assembled, curated paired normal-tumor benchmarks will serve as a critical foundation for developing future algorithms to characterize the most intractable regions of cancer genomes.},
}
@article {pmid42233158,
year = {2026},
author = {Zhong, S and Xing, L and Li, H and Wang, L and Zhu, X and Wang, C},
title = {Genomic characterization and niche adaptive analysis of Pseudomonas promysalinigenes W2469: the first clinical isolate from a human bile specimen.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1825480},
pmid = {42233158},
issn = {2235-2988},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Pseudomonas/genetics/isolation &amp; purification/classification/drug effects/physiology ; *Genome, Bacterial ; *Bile/microbiology ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; *Pseudomonas Infections/microbiology ; Phylogeny ; Genomics ; Microbial Sensitivity Tests ; DNA, Bacterial/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Computational Biology ; Lipopeptides ; },
abstract = {BACKGROUND: Pseudomonas promysalinigenes is a newly described bacterial species renowned for producing promysalin, a species-selective lipopeptide antibiotic. All previously reported strains of this species are derived from environmental niches such as plant rhizospheres, and no clinical infection cases associated with this bacterium have been documented to date. Thus, the clinical microbiology relevance, genomic features, and adaptive potential of P. promysalinigenes remain largely unexplored, and current reference databases have limited coverage of this rare species.<br><br>METHODS: A bacterial strain designated W2469 was isolated from the bile specimen of a patient with acute suppurative cholecystitis and cholecystolithiasis. Conventional phenotypic and molecular identification [matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), VITEK 2 biochemical assay, 16S ribosomal RNA (rRNA), and whole-genome sequencing (WGS)] was performed. Bioinformatics analyses, including average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), core genome single-nucleotide polymorphism (cgSNP), pan-genome analysis, and functional annotation against COG, KEGG, CAZy, VFDB, and CARD databases, were conducted to characterize the strain.<br><br>RESULTS: Conventional methods yielded consistent misidentification of the strain, while WGS definitively assigned it to P. promysalinigenes (ANI&#xa0;=&#xa0;98.8%, dDDH = 91.1% against the type strain RW10S1). The strain exhibited a narrow-spectrum resistance phenotype, with resistance to aztreonam and ticarcillin/clavulanic acid, intermediate susceptibility to meropenem, and susceptibility to most clinically used antibiotics. Genomic annotation identified 25 antimicrobial resistance genes and 139 niche adaptation-related factors, most of which are low-identity homologs (<80%) of canonical reference sequences. Pan-genome analysis identified 571 clinical-specific genes associated with host adaptation, with complete loss of the environmental promysalin biosynthetic gene cluster.<br><br>CONCLUSION: This study provides the first documentation of P. promysalinigenes as a clinical isolate from human bile, expanding the known ecological niche of this species to the clinical setting. Conventional methods are prone to misidentifying this rare species, and WGS is critical for accurate taxonomic identification. Importantly, the strain exhibits clear adaptive phenotypes despite low sequence identity to known functional elements, highlighting profound knowledge gaps in the genomic diversity and uncharacterized adaptive mechanisms of this rare Pseudomonas species. This work provides a foundational genomic resource for future investigations into this emerging opportunistic pathogen.},
}
@article {pmid42246990,
year = {2026},
author = {Rajan, DK and Rajan, DK and Li, H and Yang, W and Wu, J and Zhang, S and Jiang, H and Zhang, S},
title = {One-pot fabrication and characterization of ZnO nanoflowers using Zanthoxylum simulans and evaluating their biomedical claims.},
journal = {Mikrochimica acta},
volume = {193},
number = {7},
pages = {},
pmid = {42246990},
issn = {1436-5073},
support = {(2025M782323)//China Postdoctoral Science Foundation/ ; (2025JJ80166)//Natural Science Foundation of Hunan Province of China/ ; },
abstract = {Novel zinc oxide nanoflowers (ZnO NFs) were synthesized using the aqueous extract of Zanthoxylum simulans. The green synthesized Zs-ZnO NFs were characterized using FT-IR, XPS, XRD, HR-TEM, EDAX, DLS, and zeta potential (ZP) analysis to confirm the physicochemical properties. HR-TEM analysis exposed the flower-like morphology with uniform size. The XPS analysis exposed the elements present in the Zs-ZnO NFs. Further, the Zn element exhibited two binding energy peaks at 1021.41 and 1044.50 eV. The purity of Zs-ZnO NFs was confirmed using EDAX analysis. The Zs-ZnO NFs displayed bactericidal properties against the tested pathogens. To evaluate the effectiveness of Zs-ZnO NFs against dental pathogens via MIC, antibacterial, biofilm ring formation, and TTC assays were performed. A concentration-dependent biofilm inhibition was also observed against Staphylococcus aureus and Streptococcus mutans upon treatment with Zs-ZnO NFs, and it was confirmed using a 2.5D fluorescence imaging technique. A 100 µg/mL of Zs-ZnO NFs treatment displayed bacterial cell death, which was confirmed via dual staining. Furthermore, Zs-ZnO NFs induced protein leakage was observed upon treatment with 100 µg/mL concentration against the pathogens. Cytotoxicity of Zs-ZnO NFs was confirmed using HUVECs cells. Overall, the synthesized Zs-ZnO NFs exhibits efficient bactericidal, antibiofilm and biocompatible properties.},
}
@article {pmid42247603,
year = {2026},
author = {Haberkorn, C and Gettle, N and Elsen, J and Medina Chavez, NO and Sivigny, J and Baselga-Cervera, B and Greig, D and Travisano, M and Saxer, G and Stelkens, R},
title = {Adaptive Benefits of Hybridization in Saccharomyces Yeast are Constrained by Genomic Background and Depend on Temperature.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpag108},
pmid = {42247603},
issn = {1558-5646},
abstract = {Climate change urges us to better understand and predict evolutionary responses to temperature shifts. Hybridization, by increasing genetic variation, can widen the range of adaptive responses and genetic mechanisms available to survive temperature changes. However, genomic data on the long-term effect of hybridization on adaptation is rare, and the molecular mechanisms usually remain unclear. Here, we hybridized two divergent species of Saccharomyces yeast. We experimentally evolved both hybrid and parental populations for 200 generations under hot (30°C), cold (16°C), and fluctuating (16-30°C) temperature regimes. Most hybrids showed intermediate growth but the large variance produced by hybridization also led to thermally transgressive hybrids with high performance. Across regimes, response to selection scaled negatively with ancestral growth, consistent with diminishing-returns epistasis. Analysis of genes with identified mutations revealed enrichment in multiple shared annotation terms between populations evolved in cold and fluctuating environments, such as cell wall functions. Evolved hybrid populations, across all evolution regimes, accumulated significantly more de novo copy number variants (CNVs) than both parental species, indicating extensive genome restructuring in hybrids. This increased structural variation may provide a substrate for selection and adaptive divergence among hybrid lineages. Our results suggest that hybridization can lead to increased growth, especially in hot and thermally unstable environments, by capitalizing on the genomic content inherited from one or the other parental species.},
}
@article {pmid41538705,
year = {2026},
author = {Li, R and Xu, X and Li, Q and Liu, H and Zhou, TT and Amhare, AF and Liu, P and Tang, J and Wang, W and Zheng, F and Han, J},
title = {Internet Health Care Service Use Behavioral Pattern Among Older Adults and the Role of the Technology Acceptance and Social Ecological Theory Model: Cross-Sectional Survey.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e78037},
pmid = {41538705},
issn = {1438-8871},
mesh = {Humans ; Cross-Sectional Studies ; Male ; Aged ; Middle Aged ; Digital Health ; *Internet ; Female ; China ; Surveys and Questionnaires ; *Telemedicine/statistics &amp; numerical data ; *Patient Acceptance of Health Care ; Models, Theoretical ; Digital Media ; },
abstract = {BACKGROUND: The rapid growth of internet health care (IH) offers older adults convenient medical services like remote consultations and health monitoring. However, its adoption among this group remains low, highlighting a significant digital divide. Understanding the behavioral patterns and determinants of IH use in the older population is crucial for optimizing digital health design and improving service accessibility.<br><br>OBJECTIVE: This study aimed to analyze the multidimensional influencing factors of Chinese older adults' use of IH services based on the integrated framework of the technology acceptance model and social ecological model, and explore their behavioral patterns and key driving factors.<br><br>METHODS: A cross-sectional study design was adopted to conduct a multistage stratified cluster random sampling survey in 3 cities in Shandong Province from May 2024 to July 2024, with a total of 1828 older adults aged 60 to 75 years included. The study uses latent category analysis to classify the use of IH service behaviors and employs multiple logistic regression, decision tree models, and structural equation modeling to analyze influencing factors and mediating pathways.<br><br>RESULTS: Five distinct user groups were identified: nonusers (n=911), registration-dominant users (n=286), low-activity users (n=320), moderate comprehensive users (n=288), and full-service users (n=23). Multinomial logistic regression with nonusers as the reference group identified key determinants: individuals with below primary education had 96% lower odds of membership (odds ratios [OR] 0.039, 95% CI 0.012-0.084) compared to the reference group with junior college education or above in moderate comprehensive users, while male participants had higher odds of being full-service (OR 1.980, 95% CI 1.126-3.514) or moderate comprehensive (OR 1.310, 95% CI 1.012-1.705) users. Older age was consistently associated with lower adoption across all classes. Full-service users exhibited exceptionally high social support (OR 4.502, 95% CI 3.601-5.627), while moderate comprehensive users showed the highest technology acceptance (OR 2.803, 95% CI 2.355-3.342). The decision tree model (area under the curve of 0.94) found the optimal path: sufficient social support (&#x2265;2), good health status (>5), and high technical acceptance (&#x2265;30) yield the highest use probability (92%&#x2192;96%). Mediation analysis indicated that social support influences usage willingness through both direct and indirect pathways. The direct effect was 0.712 (95% CI 0.552-0.972; P<.001). Among indirect pathways, technology availability and practicality accounted for the largest proportion of mediation (19.7%, 95% CI 16.8%-22.6%), followed by technology acceptance (13.7%, 95% CI 11.1%-16.3%) and social influence (8.9%, 95% CI 6.9%-10.9%).<br><br>CONCLUSIONS: Optimizing age-friendly design, strengthening social support networks, and improving technological usability are keys to increasing the adoption of IH services among the older population. Future policies should develop targeted intervention strategies for different user groups to narrow the digital health divide.},
}
@article {pmid41649265,
year = {2026},
author = {Gu, C and Han, M and Chen, X and Liu, Y and Jian, G and Qin, Q and Yin, H and Zhou, L and Cai, D and Zhang, L and Wang, D and Li, P},
title = {Gut microbiota and metabolomic changes across preterm stages: potential associations with bronchopulmonary dysplasia.},
journal = {Microbiology spectrum},
volume = {14},
number = {3},
pages = {e0274025},
pmid = {41649265},
issn = {2165-0497},
support = {823RC606//Hainan Provincial Natural Science Foundation of China/ ; },
mesh = {Humans ; *Bronchopulmonary Dysplasia/microbiology/metabolism ; *Infant, Premature/metabolism ; Infant, Newborn ; *Metabolome ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Female ; Male ; Streptococcus/isolation &amp; purification/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Metabolomics ; Biomarkers ; Oxidative Stress ; },
abstract = {UNLABELLED: The coordinated post-natal development of the gut microbiome and metabolome is essential for preterm infant health, yet its disruption is increasingly linked to adverse outcomes such as bronchopulmonary dysplasia (BPD). In this study, we performed an integrated multiomics analysis of fecal samples collected from preterm infants to characterize temporal changes in gut microbial and metabolic profiles and explore their potential associations with BPD development. This study observed a distinct trajectory of the phylum Bacteroidota as a hallmark of normal gut maturation, with its abundance progressively declining across non-BPD infants. In contrast, infants who later developed BPD exhibited early depletion followed by irregular enrichment of Bacteroidota. Correlation analysis revealed that Streptococcus abundance was positively associated with elevated cysteic acid, a metabolite linked to oxidative stress. Together, these findings suggest that altered Bacteroidota succession and Streptococcus-associated oxidative imbalance may reflect early microbial-metabolic perturbations in infants at risk of BPD. This work provides preliminary, hypothesis-generating insights into gut-associated signatures potentially relevant to BPD pathogenesis.<br><br>IMPORTANCE: Bronchopulmonary dysplasia (BPD) remains a leading cause of morbidity in preterm infants, yet early biomarkers and targeted preventive strategies are limited. By integrating microbiome and metabolome data from a pilot cohort, this study identified patterns of disrupted Bacteroidota succession and Streptococcus-associated oxidative stress that are associated with BPD risk. These findings highlight the gut as a potential extrapulmonary contributor to disease susceptibility and support early risk assessment and guide future microbiome-targeted interventions in preterm infants.},
}
@article {pmid42105545,
year = {2026},
author = {Shan, X and Wang, H and Liu, X and Li, P and Zhang, F and Wang, R and Xue, M and Li, F},
title = {Remodeling distinct rhizosphere interactions of plant-microbiome by legacy and alternative PFASs: A multi-omics insight and biphasic role of iron plaque.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142313},
doi = {10.1016/j.jhazmat.2026.142313},
pmid = {42105545},
issn = {1873-3336},
mesh = {*Rhizosphere ; Plant Roots/microbiology/metabolism ; *Microbiota/drug effects ; *Iron ; Multiomics ; Soil Microbiology ; *Soil Pollutants/toxicity/metabolism ; Photosynthesis/drug effects ; Molecular Docking Simulation ; Oxidative Stress ; },
abstract = {Rhizosphere microhabitat as a dominant sink for per(poly)fluoroalkyl substances (PFASs) and hotspot for redox reactions and root iron plaque (IP) forming is largely affected by the interactions between plants and bacteria. However, whether PFOA and its substitute (HFPO-DA) modulated distinct rhizosphere symbiotic patterns and what roles IP played remain unclear. This study integrated plant physiology, metabolism and rhizosphere microbiome to systematically elucidate their differences in remodulating plant-microbiome interactions and IP roles. Results showed that PFOA preferred to accumulate in roots and induced serious oxidative stress, while HFPO-DA was more easily transported to shoots directly affecting photosynthesis. Molecular docking suggested higher proteinic affinity of HFPO-DA, inhibiting superoxide dismutase activity. PFOA and HFPO-DA increased organic acids and sugars in root exudates recruiting differential beneficial bacteria. However, HFPO-DA downregulated the glycerophospholipid metabolism, shaped a more vulnerable and simpler bacterial network. Remarkably, PFASs concentration determined the double-edged roles of IP. At environmental levels, IP promoted glycerophospholipids and small peptides release facilitating azotobacter recruitment and photosynthesis. But under high-dose stress, it induced accelerated pollutant migration especially HFPO-DA, thereby exacerbating phytotoxicity. Partial least squares path modeling revealed that PFOA indirectly influenced plant phenotypes via shaping bacterial community, while HFPO-DA not only modified that but also altered root exudates. This work unveils distinct rhizosphere symbiotic patterns and IP biphasic role remodulated by legacy and alternative PFASs, and provides a reference for their risk assessment and control through nature-based solutions.},
}
@article {pmid42150507,
year = {2026},
author = {Xu, L and Cheng, C and Xie, S and Pu, E and Zeng, Y and Pu, R and Xie, H and Liu, Y and He, Y and Chen, X and Zhang, Z and Liu, Q},
title = {Advancing safe and value-added Hydrilla verticillata silage: multi-omics deciphering of Lactiplantibacillus plantarum mediated pesticide detoxification and antibiotic resistance genes attenuation based on AI-autonomous learning.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142265},
doi = {10.1016/j.jhazmat.2026.142265},
pmid = {42150507},
issn = {1873-3336},
mesh = {*Lactiplantibacillus plantarum/metabolism/genetics ; *Drug Resistance, Microbial/genetics ; *Hydrocharitaceae/metabolism ; *Silage/microbiology ; Multiomics ; Genes, Bacterial ; Pyrethrins/metabolism ; *Pesticide Residues/metabolism ; *Pesticides/metabolism ; Animals ; },
abstract = {Water-purifying Hydrilla verticillata (SXY) in crab ponds paradoxically poses pollution risks. It accumulates pesticide residues (PRs) and antibiotic resistance genes (ARGs), which leach back into water after fished out and left on pond ridges to deteriorate, triggering cyclic pollution. Objectives of this study were to address this pollution: PRs and ARGs in SXY were first characterized. Correspondingly, two anti-pesticide Lactiplantibacillus plantarum strains (L1 and L3) were screened. Traditional mixture of SXY and wheat bran (HXY) was inoculated without (the control, WCON) or with L1 (WL1), L3 (WL3), and L. pentosus h (WLh) for ensiling 60 days to pesticide detoxification and ARGs attenuation. SXY ensiled alone as the negative control (CON). Results showed that 35 kinds of PRs and 11 types of ARGs were identified. SXY ensiling alone increased abundances of coumafuryl, mepanipyrim, and dinoterb, and ARGs of multidrug, fluoroquinolone, and beta-lactam, but they were lowered in the WCON and inoculation groups. Furthermore, WL1 enhanced averaged degradation rates of organochlorine, fenvalerate, and deltamethrin, reduced abundances of hazardous etoxazole and benomyl, and improved fermentation quality and levels of value-added antioxidants and peptides. WL3 increased bioavailable phosphorus content compared with WCON. L. plantarum acted as leader and keystone species, interacting with 2 outstanding contributing and 4 keystone species through 3 critical KEGG pathways and 3 metabolites to construct a pesticide-degradation causal network, according to AI autonomously learned from authors' inspiration. This study offered an effective approach to turn SXY into safe and value-added feed for eliminating cyclic pollution in crab farming.},
}
@article {pmid42228842,
year = {2026},
author = {Astill Wright, L and Rawsthorne, M and Nixon, N and Guo, B and Morriss, R},
title = {Recommendations for Research and Clinical Implementation of Ambulatory Assessment, Mood Monitoring, Digital Phenotyping, and Remote Measurement Technology in Mood Disorders: Synthesis of Systematic Review Findings.},
journal = {JMIR mental health},
volume = {13},
number = {},
pages = {e79501},
pmid = {42228842},
issn = {2368-7959},
abstract = {BACKGROUND: Ambulatory assessment and active and passive monitoring all offer a real-time, flexible approach to assessing mood and behavior in mood disorders. Despite their potential, concerns remain regarding the performance, usability, adherence, and potential safety of these tools.<br><br>OBJECTIVE: This study synthesizes the findings from 7 systematic reviews, integrating quantitative and qualitative data from randomized trials, observational studies, and user experience research to evaluate the performance, feasibility, acceptability, and clinical impact of ambulatory assessment and mood monitoring in people with depression and bipolar disorder. We assessed studies over the medium or long term (3 months or more).<br><br>METHODS: A summary of a series of systematic reviews was carried out by the authors-including meta-analyses (for quantitative data) and meta-syntheses (for qualitative data). Eight electronic databases were searched, and mixed methods studies were included. Studies were assessed for risk of bias. The results were checked for coherence, and recommendations were made by individuals with lived experience, methodologists, and psychiatrists. GRADE (Grading of Recommendations Assessment, Development, and Evaluation) was used to assess the quality and strength of the evidence.<br><br>RESULTS: The 111 included studies included 19,945 participants and used 69 different ambulatory assessment protocols or mood-monitoring interventions. Key barriers to implementation were identified, including performance inconsistency, adverse effects, and user disengagement. Evidence-based recommendations are provided to guide future clinical and research applications.<br><br>CONCLUSIONS: Ambulatory assessment and mood monitoring hold promise in research and clinical practice, yet their implementation requires more rigorous evaluation, greater personalization, and responsible, user-centered design. Crucially, these measures can add granularity and confirmation, but additional context is often required, and none of these measures are robust enough yet to replace current outcomes.},
}
@article {pmid42237540,
year = {2026},
author = {Banik, P and Zimmann, F and Thakur, PK and Dudakova, L and Večerková, K and Kostov, O and Caruthers, MH and Kolář, M and Krejčířová, I and Vajter, M and Liskova, P and Bárta, T and Staněk, D},
title = {Targeted antisense oligonucleotide therapy rescues PRPF31 expression in retinitis pigmentosa caused by a splicing mutation.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymthe.2026.05.033},
pmid = {42237540},
issn = {1525-0024},
abstract = {Pathogenic variants in splicing factors are the second most common cause of autosomal dominant retinitis pigmentosa (RP), with mutations in PRPF31 being the most prevalent. Here, we characterize a novel intronic variant in PRPF31 (c.1074-11C>G) that creates a cryptic 3' splice site, resulting in an aberrantly spliced transcript predicted to encode a protein with an altered C-terminus. However, the pathogenic protein is unstable and undetectable in patient-derived induced pluripotent stem cells (iPSCs). In addition, expression of the full-length PRPF31 protein was reduced in patient-derived retinal pigment epithelium (RPE). To correct the splicing defect, we designed a panel of antisense oligonucleotides (ASOs) targeting putative RNA-binding sites in exon 10 and intron 10 and identified a candidate that corrects PRPF31 splicing in a minigene reporter system as well as in patient-derived iPSCs and RPE. We further showed that ASO treatment enhances PRPF31 protein expression in patient-derived iPSC and RPE carrying the intronic mutation, supporting the potential of the ASO-based approach to restore PRPF31 expression in patients with the same or similar splicing defects.},
}
@article {pmid42241802,
year = {2026},
author = {Ye, JF and Lai, YK and Kim, N and Liu, PL},
title = {Discussing diseases in everyday talk: Examining the roles of medical and phatic patient-provider communication in promoting Chinese patients' healthy lifestyle behaviors.},
journal = {Patient education and counseling},
volume = {150},
number = {},
pages = {109727},
doi = {10.1016/j.pec.2026.109727},
pmid = {42241802},
issn = {1873-5134},
abstract = {OBJECTIVE: Previous patient-provider communication (PPC) research has focused on treatment or illness-centered medical PPC but has overlooked phatic PPC. Based on the ecological model of communication in medical encounters, this study examines how medical PPC and phatic PPC relate to patients' healthy lifestyle behaviors through perceived patient-centeredness and patient activation.<br><br>METHODS: Cross-sectional data from one representative sample of Chinese patients (N&#x202f;=&#x202f;5000) were analyzed.<br><br>RESULTS: Medical PPC was positively associated with perceived patient-centeredness (&#x3b2; =.204, p&#x202f;<&#x202f;.001), which in turn was positively associated with patient activation (&#x3b2; =.405, p&#x202f;<&#x202f;.001) and healthier lifestyle behaviors. Phatic PPC showed a small negative direct association with patient-centeredness (&#x3b2; = -.056, p&#x202f;<&#x202f;.05), but it positively moderated the relationship between medical PPC and patient-centeredness (b =.030, p&#x202f;<&#x202f;.01).<br><br>CONCLUSION: By testing a moderated mediation model, the study demonstrates the complementary role of phatic PPC for medical PPC and elucidates how these two functionally distinct forms of PPC jointly promote healthy lifestyle behaviors.<br><br>PRACTICAL IMPLICATIONS: Healthcare providers should be trained to strategically integrate medical and phatic PPC, using brief relational cues to build supportive patient-centered care without compromising the efficiency of medical communication.},
}
@article {pmid42242207,
year = {2026},
author = {Yasuma-Mitobe, K and Liao, C and Németh, T and Byrne, K and Billips, A and Faustino Ramos, RJJ and Salinas, CN and Chan, E and Perissinoto, M and Adami-Sampson, S and Salman, A and Sidebottom, AM and Plitas, G and Butler, G and Cross, JR and Pamer, EG and Gácser, A and Xavier, JB and Hohl, TM},
title = {Intracellular acidification by microbiota-derived valeric acid facilitates trans-kingdom ecology limiting Candida parapsilosis colonization.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.008},
pmid = {42242207},
issn = {1934-6069},
abstract = {In hematopoietic cell transplant (HCT) patients, intestinal Candida parapsilosis expansion and translocation can cause life-threatening candidemia, yet whether commensal intestinal bacteria prevent Candida expansion remains incompletely defined. Here, we trained a machine learning model on supernatant metabolomic profiles of Lachnospiraceae to identify bacteria-derived inhibitors of fungal growth, identifying valeric and butyric acids as top hits. Fecal samples from HCT patients supported this association, with valeric and butyric acid levels inversely correlating with C. parapsilosis growth. In cell culture and mice, valeric acid inhibited C. parapsilosis growth by increasing intracellular acidification. Administration of glycerol valerate, or free or microencapsulated valeric acid, to release valeric acid along the entire intestinal tract blunted C. parapsilosis growth at murine intestinal sites where valeric acid was detected. Thus, machine learning identified a mechanistic driver of trans-kingdom ecology limiting C. parapsilosis intestinal expansion and may inform strategies to reduce patient risk of candidiasis.},
}
@article {pmid41538056,
year = {2026},
author = {Rehman, U and Sarfraz, M and Bibi, F and Noor, A and Ullah, M and Tarafder, E and Shinwari, ZK},
title = {DNA barcoding and phylogenomics in mushrooms: current progress, challenges, and future prospects.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {2},
pages = {40},
pmid = {41538056},
issn = {1572-9699},
mesh = {*DNA Barcoding, Taxonomic/methods/trends ; *Agaricales/genetics/classification ; Multiomics ; *Phylogeny ; Genomics/methods ; Genome, Fungal ; High-Throughput Nucleotide Sequencing ; },
abstract = {Mushrooms represent a taxonomically and ecologically diverse group of fungi with profound significance for ecosystems, biotechnology, and human welfare. However, their accurate identification and classification have long been hindered by morphological convergence, cryptic speciation, and limited diagnostic traits. This review synthesizes recent progress in DNA barcoding, phylogenomics, and multi-omics approaches that are reshaping the molecular systematics of mushrooms. The internal transcribed spacer (ITS) region remains the universal fungal barcode, yet its limitations have driven the adoption of multilocus and genome-scale datasets for deeper evolutionary resolution. Advances in high-throughput sequencing (HTS), whole-genome phylogenies, and core-gene frameworks have refined species boundaries and clarified evolutionary trajectories across major fungal lineages. The integration of multi-omics platforms including genomics, transcriptomics, proteomics, and metabolomics has enabled holistic insights into fungal metabolism, adaptation, and ecological functions. Despite these advances, challenges persist, including database inconsistencies, incomplete sampling, and analytical complexities. Addressing these issues through standardized molecular protocols, AI-driven data analytics, and global open-data collaboration will be essential for achieving reproducible and evolutionarily coherent fungal systematics. Ultimately, the convergence of barcoding, phylogenomics, and omics technologies represents a transformative step toward an integrative, data-driven framework for understanding and utilizing fungal diversity in science, sustainability, and innovation.},
}
@article {pmid41538613,
year = {2025},
author = {Soares Filho, AM and Vasconcelos, CH and Vasconcelos, NM and Lima, CM and Souza, MFM and Pinto, IV and Cardoso, LO and Malta, DC},
title = {Mapping of underreporting of interpersonal violence based on the occurrence of homicides in Brazilian municipalities, 2016-2018.},
journal = {Ciencia &amp; saude coletiva},
volume = {30},
number = {12},
pages = {e08432024},
doi = {10.1590/1413-812320253012.08432024},
pmid = {41538613},
issn = {1678-4561},
mesh = {Brazil/epidemiology ; Humans ; *Homicide/statistics &amp; numerical data ; Female ; *Violence/statistics &amp; numerical data ; Adult ; Cities ; Middle Aged ; Young Adult ; *Information Systems/statistics &amp; numerical data ; },
abstract = {Identify municipalities with underreporting of interpersonal violence based on homicide in Brazil, 2016 to 2018. Ecological study with rate on violence from the Notifiable Diseases Information System and homicide estimates from the Global Burden of Disease concerning < 20 years, women of 20 to 59 years, ≥ 60 years and the total of these subgroups. Bivariate Local Moran identified clusters of critical areas of low reporting rates and high homicide rates (p < 0.05). Municipalities in the North, Northeast, and Midwest of Brazil represented 29% of all reports of violence and 58% of homicides. The majority of these municipalities were concentrated in low reporting rates (≤ 0.8/10,000) and high homicide rates (≥ 13.7/100,000); and 31.4% of municipalities with high homicide rate reported zero cases. Reports of violence and homicide rates showed a negative spatial correlation (I<20 = -0.083; Iwomen20-59 = -0.023; I≥60 = -0.086; Itotal = -0.085), showing that nearby places have inverse values. Critical municipalities for underreporting of violence reach 16% of < 20 years, 12% of women, 23% of the elderly, and 18% in total. The low reporting in seriously violent areas provides evidence of underreporting. The findings can provide management with tools for initiatives to improve violence surveillance and access to the protection network.},
}
@article {pmid42166940,
year = {2026},
author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM},
title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.},
journal = {Pathology, research and practice},
volume = {285},
number = {},
pages = {156543},
doi = {10.1016/j.prp.2026.156543},
pmid = {42166940},
issn = {1618-0631},
mesh = {Humans ; *Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; *Tumor Microenvironment/genetics ; Multiomics ; Animals ; },
abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.},
}
@article {pmid42235263,
year = {2026},
author = {Kim, J and Müller, F and Ribeiro, CC and Dietz, C and Hero, D and Witayakran, S and Gallei, M},
title = {Cyclodextrin-modified core-shell particle synthesis and photonic crystal film formation for redox-mediated surface interaction.},
journal = {Journal of colloid and interface science},
volume = {722},
number = {},
pages = {140824},
doi = {10.1016/j.jcis.2026.140824},
pmid = {42235263},
issn = {1095-7103},
abstract = {In recent years, extensive efforts have been made to develop and utilize smart optical materials. Carbohydrate-based materials are abundant, readily accessible, and essential for advancing sustainable science and ecological cycles. Carbohydrates containing α-glycosidic linkages are naturally generated, and cyclodextrin represents a typical oligosaccharide with such a structure. The ring-shaped architecture of cyclodextrin has been widely studied because, unlike conventional chemical bonds, it enables host-guest interactions based on noncovalent binding. Incorporating cyclodextrin into nanosized, highly uniform core-shell particles could enable the production of photonic crystal films. A synthesis route for the preparation of β-cyclodextrin-modified core-shell particles with host functionality has been reported and characterized at the molecular and material levels. The molecular structures and particle-based optical film formation were validated by spectroscopic and microscopic analysis. The resulting photonic crystal films displayed vivid structural colors. Their capture property was demonstrated by a decrease in the electrochemical redox signal arising from host-guest interactions with ferrocene, while maintaining structural coloration after capture. These findings highlight the potential of the developed system for applications involving selective particle-surface interactions that can be triggered by an electrochemical response. This method will pave the way to new capturing and separation strategies and optical anti-counterfeiting technologies.},
}
@article {pmid40764303,
year = {2025},
author = {Xu, Y and Gkoutos, GV},
title = {A computational framework for inferring species dynamics and interactions with applications in microbiota ecology.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {87},
pmid = {40764303},
issn = {2056-7189},
support = {101095480//HYPERMARKER/ ; 101095480//HYPERMARKER/ ; 731032//Nanocommons H2020-EU/ ; 965286//MAESTRIA/ ; 101057014//PARC/ ; HDRUK/CFC/01//MRC Heath Data Research UK/ ; },
mesh = {Animals ; *Computational Biology/methods ; Mice ; Humans ; *Microbiota ; Computer Simulation ; Machine Learning ; Gastrointestinal Microbiome ; *Ecology/methods ; Ecosystem ; Clostridioides difficile ; Clostridium Infections/microbiology ; Models, Biological ; Microbial Interactions ; },
abstract = {We present MBPert, a generic computational framework for inferring species interactions and predicting dynamics in time-evolving ecosystems from perturbation and time-series data. In this work, we contextualize the framework in microbial ecosystem modeling by coupling a modified generalized Lotka-Volterra formulation with machine learning optimization. Unlike traditional methods that rely on gradient matching, MBPert leverages numerical solutions of differential equations and iterative parameter estimation to robustly capture microbial dynamics. The framework is assessed within the context of two experimental scenarios: (i) paired before-and-after measurements under targeted perturbations, and (ii) longitudinal time-series data with time-dependent perturbations. Extensive simulation studies, benchmarking on standardized MTIST datasets, and application to Clostridium difficile infection in mice and repeated antibiotic perturbations of human gut micribiota, demonstrate that MBPert accurately recapitulates species interactions and predicts system dynamics. Our results highlight MBPert as a powerful and flexible tool for mechanistic insight into microbiota ecology, with broad potential applicability to other complex dynamical systems.},
}
@article {pmid40770074,
year = {2025},
author = {Myers, T and Song, SJ and Chen, Y and De Pessemier, B and Khatib, L and McDonald, D and Huang, S and Gallo, R and Callewaert, C and Havulinna, AS and Lahti, L and Roeselers, G and Laiola, M and Shetty, SA and Kelley, ST and Knight, R and Bartko, A},
title = {Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1159},
pmid = {40770074},
issn = {2399-3642},
mesh = {Humans ; *Aging ; *Biometry/methods ; *Deep Learning ; *Gastrointestinal Microbiome ; *Principal Component Analysis/methods ; *Skin Microbiome ; Software Validation ; },
abstract = {Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of transformer architectures and interpretability of Robust Principal Component Analysis. To investigate benefits of TRPCA over conventional machine learning models, we benchmarked performance on age prediction from three body sites(skin, oral, gut), with 16S rRNA gene amplicon(16S) and whole-genome sequencing(WGS) data. We demonstrated prediction of age from longitudinal samples and combined classification and regression tasks via multi-task learning(MTL). TRPCA improves age prediction accuracy from human microbiome samples, achieving the largest reduction in Mean Absolute Error for WGS skin (MAE: 8.03, 28% reduction) and 16S skin (MAE: 5.09, 14% reduction) samples, compared to conventional approaches. Additionally, TRPCA's MTL approach achieves an accuracy of 89% for birth country prediction across 5 countries, while improving age prediction from WGS stool samples. Notably, TRPCA uncovers a link between subject and error prediction through residual analysis for paired samples across sequencing method (16S/WGS) and body site(oral/gut). These findings highlight TRPCA's utility in improving age prediction while maintaining feature-level interpretability, and elucidating connections between individuals and microbiomes.},
}
@article {pmid40770961,
year = {2026},
author = {Lopes-Araujo, HF and Guimarães, RL and Carvalho-Silva, WHV},
title = {Correlations between new HIV infections and hospital admissions for non-Hodgkin lymphoma in Brazil.},
journal = {International journal of cancer},
volume = {158},
number = {1},
pages = {84-93},
doi = {10.1002/ijc.70076},
pmid = {40770961},
issn = {1097-0215},
mesh = {Humans ; Brazil/epidemiology ; Male ; *HIV Infections/epidemiology/complications ; Female ; *Lymphoma, Non-Hodgkin/epidemiology/virology ; Adult ; Middle Aged ; *Hospitalization/statistics &amp; numerical data ; Adolescent ; Incidence ; Young Adult ; Aged ; Child ; },
abstract = {Despite advancements in antiretroviral therapy, human immunodeficiency virus (HIV) infections remain a significant global health challenge. With increasing life expectancy among people living with HIV, the emergence of HIV-related malignancies, notably non-Hodgkin lymphoma (NHL), has become a prominent concern. This study aims to investigate the correlation between new HIV infections and NHL hospitalizations in Brazil from 2010 to 2022. Using an ecological time series design, data from authoritative sources, including the Notifiable Diseases Information System and the Department of Unified Health System Informatics, were analyzed. The study cohort comprised individuals admitted to the Brazilian Unified Health System, categorized by geographical region, sex, and age cohorts. Pearson's and Spearman's correlation coefficients were utilized to examine the correlation between new HIV infections and NHL hospitalizations. Our analysis revealed a strong positive and statistically significant correlation between the incidence of new HIV cases and NHL hospitalizations in Brazil (r = 0.8901; p = .0001) and in most regions (r > 0.80; p < .001). Moreover, our findings indicate that this correlation becomes evident from the age of 15 onward, with a discernible tendency to escalate with advancing age from moderate to very strong (r > 0.62; p < .02). Regarding sex, the observed correlations were strong positive for male (r = 0.8681; p = .0003) and female (r = 0.7912; p = .0020). These results underscore the importance of vigilant monitoring for individuals living with HIV. Furthermore, we emphasize the importance of rigorous screening practices and adherence to antiretroviral therapy, which may hold promising implications for managing neoplastic conditions.},
}
@article {pmid40772542,
year = {2025},
author = {Reddy, S and Wacker, K and Fahmy, M and Hekkala, E and Bates, JM and Goodman, SM and Hackett, SJ and Raherilalao, MJ and Maddox, JD},
title = {VoronaGasyCodes: A Public Database of Mitochondrial Barcodes for Malagasy Birds.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70027},
pmid = {40772542},
issn = {1755-0998},
mesh = {Animals ; Madagascar ; *Birds/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *DNA, Mitochondrial/genetics/chemistry ; Biodiversity ; *Databases, Genetic ; },
abstract = {Molecular tools are increasingly being used to survey the presence of biodiversity and their interactions within ecosystems. Indirect methods, like environmental DNA (eDNA) and invertebrate-derived DNA (iDNA), are dependent on sequence databases with accurate and sufficient taxonomic representation. These methods are increasingly being used in regions and habitats where direct detection or observations can be difficult for a variety of reasons. Madagascar is a biodiversity hotspot with a high proportion of endemic species, many of which are threatened or endangered. Here we describe a new resource, VoronaGasyCodes, a curated database of newly published genetic sequences from Malagasy birds. Our database is currently populated with six mitochondrial genes or DNA barcodes for 142 species including 70% of the birds endemic to the island and will be periodically updated as new data become available. We demonstrate the utility of our database with an iDNA study of leech blood meals where we successfully identified 77% of the hosts to species. These types of resources for characterising biodiversity are critical for insights into species distribution, discovery of new taxa, novel ecological connections and advancing conservation and restoration measures.},
}
@article {pmid40772610,
year = {2025},
author = {Tsuji, S and Kunimatsu, S and Watanabe, K},
title = {Environmental DNA Comparative Phylogeography: Simultaneous Estimation of Population Structures Within a Species-Rich Group of Freshwater Gobies.},
journal = {Molecular ecology},
volume = {34},
number = {18},
pages = {e70059},
doi = {10.1111/mec.70059},
pmid = {40772610},
issn = {1365-294X},
support = {23K13967//Japan Society for the Promotion of Science/ ; //ESPEC Foundation for Global Environment Research and Technology/ ; },
mesh = {Phylogeography ; Animals ; *DNA, Environmental/genetics ; Fresh Water ; Japan ; *Genetics, Population ; Haplotypes ; *Perciformes/genetics/classification ; Cytochromes b/genetics ; Phylogeny ; Biodiversity ; DNA, Mitochondrial/genetics ; Genetic Variation ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; },
abstract = {Comparative phylogeography provides crucial insights into evolutionary processes shaping biodiversity patterns by analysing spatial genetic variations across multiple species. However, conventional capture-based methods are often labour-intensive, particularly for multi-species analyses. Environmental DNA (eDNA) analysis has significant advantages in comparative phylogeography, including simplified field surveys requiring only water collection and the potential to simultaneously analyse multiple species from a single sample. To further expand the eDNA application and demonstrate its utility in comparative phylogeographic studies, this study employed eDNA analysis to simultaneously analyse the phylogeographic patterns in a species-rich freshwater goby group (Rhinogobius) in the Japanese Archipelago. DNA amplification was performed on eDNA samples collected from 573 sites across the archipelago using newly designed group-specific primers targeting the mitochondrial cytochrome b region of Rhinogobius. High-throughput sequencing detected haplotypes of all nine known species (or species groups) occurring in this region, followed by phylogenetic and network analyses. The eDNA analysis successfully revealed the genetic population structures across multiple species. A landlocked species, R. flumineus, exhibited fine-scale population differentiation shaped by geomorphological barriers, while amphidromous species showed broader genetic patterns likely influenced by ocean currents and their ecological traits. The phylogenetic and phylogeographic patterns reconstructed by the eDNA analysis were almost completely concordant with previously identified patterns of limited groups based on conventional methods, demonstrating the reliability of eDNA-based comparative phylogeography. This study highlights the potential of eDNA to complement and partially replace conventional methods, facilitating large-scale comparative phylogeographic research to gain new insights into spatial patterns and evolutionary processes of biodiversity.},
}
@article {pmid40774342,
year = {2025},
author = {Cao, W and Cao, X and Sutherland, AD},
title = {Planning for the Unexpected and Unintended Effects of mHealth Interventions: Systematic Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e68909},
pmid = {40774342},
issn = {1438-8871},
mesh = {*Telemedicine ; Humans ; },
abstract = {BACKGROUND: Mobile health (mHealth) interventions can produce both intended and unintended effects. Examining these unintended effects helps create a more complete and objective understanding of mHealth interventions and can reduce potential harm to participants. Existing studies on the unintended effects, which were published several years ago, tend to have either a general focus on health IT or a specific focus on health care providers, thereby excluding other key stakeholders (eg, patients and community health workers). Additionally, these studies did not systematically outline the causes of the unintended effects or strategies for their prevention.<br><br>OBJECTIVE: To address this gap, this systematic review, guided by the ecological framework, aims to systematically identify the unintended effects of mHealth interventions, create a typology for them, investigate the reasons for their occurrence, describe how they were detected, and propose ways to prevent or lessen them.<br><br>METHODS: Following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, a systematic review was performed to examine the unintended effects of health interventions that use mobile technology.<br><br>RESULTS: A total of 15 papers were included in the review. An ecological typology of mHealth intervention unintended effects (mHUE) was developed, which includes 26 distinct effects (eg, silencing and boomerang). The majority of these unintended effects (n=20) occur at the individual level and span physical or behavioral (n=7), psychological (n=8), cognitive (n=4), and financial (n=1) domains. Three effects occur at the interpersonal level and another 3 at the community or institutional level. Most of the identified effects (n=22) were negative. Potential causes for these effects include the improper use of mHealth technology, poorly designed interventions, the application of unsuitable intervention mechanisms, or a misalignment between the intended outcomes and the sociocultural context. Strategies and recommendations (eg, considering the context such as cultural norms) were suggested to help prevent or reduce the unintended effects.<br><br>CONCLUSIONS: The unintended effects detailed in the mHUE typology were heterogenous and context-dependent. These effects can influence individuals across different domains and also affect unintended people within the ecological system. As most of the unintended effects are negative, if they are not monitored, mHealth interventions designed to empower participants could paradoxically disempower them (eg, decreasing self-efficacy for disease management, undermining patient control, and engagement). The mHUE typology, together with the proposed recommendations and strategies, can be used as a guide to enhance the planning, design, implementation, and postimplementation evaluation on mHealth interventions. Future research should concentrate on understanding the specific mechanisms behind these unintended effects.},
}
@article {pmid40774411,
year = {2025},
author = {Zhang, L and Liu, Y and Chen, K and Yue, Q and Wang, C and Xie, L and Molnár, I and Xu, Y},
title = {Genome mining of tailoring enzymes from biosynthetic gene clusters for synthetic biology: A case study with fungal methyltransferases.},
journal = {Metabolic engineering},
volume = {92},
number = {},
pages = {125-135},
doi = {10.1016/j.ymben.2025.08.001},
pmid = {40774411},
issn = {1096-7184},
mesh = {*Methyltransferases/genetics/metabolism ; *Multigene Family ; *Genome, Fungal ; *Fungal Proteins/genetics/metabolism ; *Synthetic Biology/methods ; *Fungi/genetics/enzymology ; *Data Mining/methods ; Biosynthetic Pathways/genetics ; Biological Products/metabolism ; },
abstract = {Harnessing the potential of tailoring enzymes within fungal natural product (NP) biosynthetic gene clusters (BGCs) can significantly enhance NP diversity and production efficiency via artificially constructed microbial cell factories. To achieve this, an efficient genome mining method is crucial, especially since the functions of many putative enzymes in databases are unknown. As a test case, we aimed to identify methyltransferases (MTs) that modify a polyketide substrate without a known cognate MT. 16,748 putative MTs were annotated in 101,321 fungal BGCs and grouped into orthologous families. Three methods were explored to prioritize suitable enzymes. Among these, the machine learning method proved superior, with 11 out of 15 tested MTs successfully methylating the test substrate. This demonstrates the effectiveness of machine learning to mine tailoring enzymes that modify selected compounds, aiding synthetic biology in optimizing NP biosynthesis and facilitating the production of "unnatural products" for pharmaceutical or other bioindustrial applications.},
}
@article {pmid40774560,
year = {2025},
author = {Guo, J and Lei, W and Liang, X and Wang, H and Qi, W and Huang, S and Chen, X and He, S},
title = {Three-dimensional distribution and key drivers of neonicotinoid residues in hilly agricultural areas.},
journal = {Environmental research},
volume = {285},
number = {Pt 3},
pages = {122524},
doi = {10.1016/j.envres.2025.122524},
pmid = {40774560},
issn = {1096-0953},
mesh = {*Neonicotinoids/analysis ; *Soil Pollutants/analysis ; *Insecticides/analysis ; *Environmental Monitoring ; Agriculture ; *Pesticide Residues/analysis ; Soil/chemistry ; China ; Nitro Compounds/analysis ; Guanidines/analysis ; Thiazoles ; },
abstract = {Neonicotinoids (NNIs) raise global concern due to their substantial soil residues and potential health risks to animal and human health. High water solubility and low soil adsorption enhanced vertical and horizontal migration of NNIs. However, understanding of NNIs' three-dimensional distribution in soils and influencing factors remains limited, limiting accurate risk assessment and remediation strategies for agriculture ecosystems. This study selected typical mountainous farmland soil to investigate the three-dimensional distribution of NNIs contents and composition. The findings indicated that the average detection rate of imidacloprid (IMI) in the 0-20 cm layer was 33 % higher than that in the 30-40 cm layer, whereas clothianidin (CLO) detection rates remained consistent across 0-40 cm layer. The contents of eight NNIs (∑8NNIs) in the study area ranged from 0.09 to 37.08 ng/g, with the 6.58 ± 8.65 ng/g in the 0-10 cm and 2.60 ± 7.78 ng/g in the 30-40 cm layer. The contents of ∑8NNIs, IMI, and CLO decreased by 60 %, 62 %, and 75 %, respectively, with increasing depth. The proportion of IMI and CLO to ∑8NNIs decreased and increased by 35 % and 12 %, respectively, in the 0-40 cm soil, leading to IMI predominance in the topsoil (60 %) and CLO in the deeper soil (29 %). Correlation analysis revealed that soil particle size, slope, and elevation were significantly associated with both the ∑8NNIs and the proportions of IMI and CLO. These results highlighted the substantial influence of topography and soil structure on the vertical distribution of NNIs. Additionally, the ∑8NNIs content in stem mustard soil was higher than in sweet potato, rice, corn, and forest. Overall, the study found very low health risks to humans (hazard index, HI < 1) and no overall potential ecological risk in the study area, though localized sublethal risks to non-target organisms were identified. Furthermore, the spatial correlation between IMI and CLO health risk regions identified overlapping high-risk areas.},
}
@article {pmid40774918,
year = {2025},
author = {Hung, CC and Hsieh, HH and Chou, WC and Liu, EC and Chow, CH and Chang, Y and Lee, TM and Santsch, PH and Ranatunga, RRMKP and Bacosa, HP and Shih, YY},
title = {Corrigendum to "Assessing CO2 sources and sinks in and around Taiwan: Implication for achieving regional carbon neutrality by 2050" [Mar. Pollut. Bull. 206 (2024) 116664].},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118543},
doi = {10.1016/j.marpolbul.2025.118543},
pmid = {40774918},
issn = {1879-3363},
}
@article {pmid40776104,
year = {2025},
author = {Bauberg, H and Tachnai, N and Hanan, G and Nehama, D and Tamburis, O and Darmoni, S and Grosjean, J and Benis, A},
title = {Automated Elicitation of Human and Ecological Health Indicators: An LLM-Based Practical Implementation for One Digital Health.},
journal = {Studies in health technology and informatics},
volume = {329},
number = {},
pages = {1488-1492},
doi = {10.3233/SHTI251086},
pmid = {40776104},
issn = {1879-8365},
mesh = {Humans ; *One Health ; *Health Status Indicators ; *Environmental Health/methods ; Digital Health ; },
abstract = {This paper presents a new method for automating the identification of human and ecological health indicators using the One Digital Health framework, which combines One Health and Digital Health principles. By applying mainly Large Language Models, we conduct a systematic literature review on urban freshwater environments. This automation streamlines the process of finding and analyzing relevant research, allowing us to extract vital health indicators related to urban aquatic ecosystems and human wellness. The findings support the OneAquaHealth project's goals, enhancing environmental monitoring and linking human, animal, and environmental health in a digital context.},
}
@article {pmid40777262,
year = {2025},
author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R},
title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40777262},
issn = {2692-8205},
support = {R01 AI143638/AI/NIAID NIH HHS/United States ; R01 AI188648/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; },
abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes including colony morphology, cell elongation, and cell chaining in C. difficile. Here we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state leading to chaining and a rough colony morphology. This phenomenon preferentially occurs with E. faecalis among the enterococci, as other enterococcal species do not show a similar effect, suggesting that the composition of the polymicrobial environment in the gut is likely critical to shaping C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.},
}
@article {pmid40778113,
year = {2025},
author = {Sprint, G and Schmitter-Edgecombe, M and Weaver, R and Wiese, L and Cook, DJ},
title = {CogProg: Utilizing Large Language Models to Forecast In-the-moment Health Assessment.},
journal = {ACM transactions on computing for healthcare},
volume = {6},
number = {2},
pages = {},
pmid = {40778113},
issn = {2637-8051},
support = {R01 AG066748/AG/NIA NIH HHS/United States ; R01 AG083925/AG/NIA NIH HHS/United States ; R25 AG046114/AG/NIA NIH HHS/United States ; R01 AG065218/AG/NIA NIH HHS/United States ; R35 AG071451/AG/NIA NIH HHS/United States ; R01 EB009675/EB/NIBIB NIH HHS/United States ; },
abstract = {Forecasting future health status is beneficial for understanding health patterns and providing anticipatory support for cognitive and physical health difficulties. In recent years, generative large language models (LLMs) have shown promise as forecasters. Though not traditionally considered strong candidates for numeric tasks, LLMs demonstrate emerging abilities to address various forecasting problems. They also provide the ability to incorporate unstructured information and explain their reasoning process. In this paper, we explore whether LLMs can effectively forecast future self-reported health state. To do this, we utilized in-the-moment assessments of mental sharpness, fatigue, and stress from multiple studies, utilizing daily responses (N=106 participants) and responses that are accompanied by text descriptions of activities (N=32 participants). With these data, we constructed prompt/response pairs to predict a participant's next answer. We fine-tuned several LLMs and applied chain-of-thought prompting evaluating forecasting accuracy and prediction explainability. Notably, we found that LLMs achieved the lowest mean absolute error (MAE) overall (0.851), while gradient boosting achieved the lowest overall root mean squared error (RMSE) (1.356). When additional text context was provided, LLM forecasts achieved the lowest MAE for predicting mental sharpness (0.862), fatigue (1.000), and stress (0.414). These multimodal LLMs further outperformed the numeric baselines in terms of RMSE when predicting stress (0.947), although numeric algorithms achieved the best RMSE results for mental sharpness (1.246) and fatigue (1.587). This study offers valuable insights for future applications of LLMs in health-based forecasting. The findings suggest that LLMs, when supplemented with additional text information, can be effective tools for improving health forecasting accuracy.},
}
@article {pmid40779849,
year = {2025},
author = {Zhu, J and Ding, X and Xu, Q and Fan, Y and Zhu, P and Li, X and Zhang, X and Zhang, Q and Du, X and Zhou, W and Jiao, J and Lu, B and Lu, C},
title = {Insights into the disinfection byproduct bromochloroacetamide-induced cardiotoxicity of zebrafish embryo-larvae: A multiomics approach and comparison of biomarker responsiveness.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118805},
doi = {10.1016/j.ecoenv.2025.118805},
pmid = {40779849},
issn = {1090-2414},
mesh = {Animals ; *Zebrafish/embryology ; Biomarkers/metabolism ; *Water Pollutants, Chemical/toxicity ; *Cardiotoxicity/etiology ; *Acetamides/toxicity ; Embryo, Nonmammalian/drug effects ; Larva/drug effects ; *Disinfectants/toxicity ; Heart/drug effects ; Metabolomics ; Disinfection ; Multiomics ; },
abstract = {Bromochloroacetamide (BCAcAm), an inevitable byproduct of the water treatment disinfection process, is widely detected in drinking water. Previous toxicological and in silico results suggested that developmental effects are associated with analogous chemical exposure; however, the key molecular events and underlying mechanisms remain unclear, especially in the early stages of aquatic organisms. In the present study, a zebrafish larval model was used to comprehensively assess the developmental toxicity of BCAcAm via transcriptional, metabolic, biochemical and morphological tests. Integration analyses of RNA sequencing and untargeted metabolomic data revealed crucial biological processes related to drug metabolism, cardiac muscle contraction and oxidative phosphorylation, which started from the initial stage, and ferroptosis progressed to the advanced stage in validated cardiac defects. Biochemical assays further verified ATP depletion, ROS and MDA accumulation, and hyperactivation of detoxification (increased GST activity) and the antioxidative system (increased GSH and GSSG levels). Transcriptionally, BCAcAm led to gpx4 downregulation, iron homeostasis perturbation (upregulated tfr and tf and downregulated fth) and lipid peroxidation (elevated alox12 and lpcat3), suggesting the involvement of ferroptosis. Moreover, the application of Fer-1 (a ferroptosis inhibitor) reversed BCAcAm-induced mitochondrial dysfunction and subsequent cardiotoxicity. In addition, the BMD and IBRv2 indices were derived from molecules across various biological levels. The general ranking of the different biomarkers in terms of better responsiveness and sensitivity performance is as follows: transcriptomics > metabolomics > biochemical assays. In the present study, an approach to detecting chemical-induced adverse outcomes and deciphering the underlying mechanisms through high-throughput data analysis is applied. This study provides valuable insights into the responsiveness and sensitivity of biomarkers, which may be instrumental for evaluating the ecological and health risks associated with newly emerged contaminants.},
}
@article {pmid40781089,
year = {2025},
author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Gooden, AA and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Behera, S and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Salas-González, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Baybayan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, GL and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Krieger, G and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, AG and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Bhakta, MS and Sanborn, JZ and Munding, EM and Wagner, J and Xiao, C and Liss, AS and Zook, JM},
title = {Correction: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1385},
doi = {10.1038/s41597-025-05752-9},
pmid = {40781089},
issn = {2052-4463},
support = {R44 CA278140/CA/NCI NIH HHS/United States ; R44 HD104323/HD/NICHD NIH HHS/United States ; },
}
@article {pmid40781446,
year = {2025},
author = {Rauniyar, S and Samanta, D and Thakur, P and Saxena, P and Singh, RN and Bazin, A and Bomgni, A and Fotseu, E and Etienne, GZ and Gadhamshetty, V and Peyton, BM and Fields, M and Subramaniam, M and Sani, RK},
title = {Mapping the pangenome of sulfate reducing bacteria: core genes, plasticity, and novel functions in Desulfovibrio spp.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {8},
pages = {305},
pmid = {40781446},
issn = {1573-0972},
support = {5P20GM103443-20/NH/NIH HHS/United States ; 1736255//National Science Foundation/ ; },
mesh = {*Desulfovibrio/genetics/metabolism/classification ; *Genome, Bacterial ; *Sulfates/metabolism ; Phylogeny ; Multigene Family ; Gene Regulatory Networks ; Genes, Bacterial ; Gene Ontology ; },
abstract = {The pangenome of sulfate reducing bacteria represents a genetic reservoir that deciphers the intricate interplay of conserved and variable elements driving their ecological dominance, evolutionary adaptability, and industrial relevance. This study introduces the most comprehensive pangenome analysis of the genus Desulfovibrio till date, incorporating 63 complete and high-quality genomes using the Partitioned Pangenome Graph of Linked Neighbors (PPanGGOLiN) pipeline. The structure and dynamics of core gene families were investigated through gene ontology, KEGG pathway mapping, and gene network analyses, shedding light on the functional organization of the Desulfovibrio genomes. The analysis categorized 799, 4053, and 43,581 gene families into persistent, shell, and cloud groups, respectively. A core set of 326 gene families, conserved across Desulfovibrio genomes, highlights their essential role in community functionality. Genome plasticity analysis identified 4,576 regions of genome plasticity, with 1,322 hotspots enriched in horizontally acquired genes (89% in the cloud partition). Key gene families in these regions included glpE, fdhD, petC, and cooF, linked to sulfur metabolism. Out of 29 hypothetical genes, one was linked to actin nucleation, another contained a TRASH domain, while the other regulates filopodium assembly. Other predicted functions included lnrL, folE, RNA binding, and pyrG/pyrH involvement in CTP biosynthesis. Additionally, genomic islands revealed evolutionary events, such as cheY acquisition in Oleidesulfovibrio alaskensis G20. This study provides a genus-wide view of Desulfovibrio, emphasizing genome plasticity, hypothetical gene functions, and adaptation mechanisms.},
}
@article {pmid40782603,
year = {2025},
author = {Benvenuti, MC and Merkle, EC and McCarthy, DM},
title = {Physical context of alcohol use and craving: An EMA exploratory study.},
journal = {Addictive behaviors},
volume = {170},
number = {},
pages = {108450},
pmid = {40782603},
issn = {1873-6327},
support = {R01 AA019546/AA/NIAAA NIH HHS/United States ; T32 AA013526/AA/NIAAA NIH HHS/United States ; },
mesh = {Humans ; *Craving ; Male ; Female ; *Ecological Momentary Assessment ; *Alcohol Drinking/psychology/epidemiology ; Adult ; Young Adult ; Adolescent ; Geographic Information Systems ; Self Report ; },
abstract = {While environmental and physical contextual factors play an important role in alcohol use and motivation for use, assessment of the physical context of use, even when using ecological momentary assessments (EMA), has been limited. While EMA research has examined drinking locations at the event level using categories of drinking locations, there is considerable within-category variability in the attributes of drinking locations. Using data from a 6-week EMA study (N = 207), this exploratory study sought to determine drinking locations through the combination of EMA self-report and GPS coordinates. Through multilevel modeling, we also tested whether specific locations were associated with variability in drinking (self-reported drinking and breathalyzer readings) and craving for alcohol. Results indicated significant differences in both alcohol consumption and craving between home, friend's houses, and on-premises drinking locations. Our results offer proof of concept for using mobile and geospatial data to passively identify on-premise drinking locations. This approach has the potential to aid in the development of targeted intervention strategies that identify and mitigate risks associated with specific drinking environments.},
}
@article {pmid40786600,
year = {2025},
author = {Boyes, D and Gardiner, A and , and , and , and , and , and , and , and , },
title = {The genome sequence of the V-Pug moth, Chloroclystis v-ata (Haworth, 1809).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {197},
pmid = {40786600},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Chloroclystis v-ata (V-Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 275.35 megabases. Most of the assembly (99.95%) is scaffolded into 17 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.49 kilobases.},
}
@article {pmid40788461,
year = {2025},
author = {Torres, MC and Breyer, GM and da Silva, MERJ and de Itapema Cardoso, MR and Siqueira, FM},
title = {Metagenomic approaches for the quantification of antibiotic resistance genes in swine wastewater treatment system: a systematic review.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {816},
pmid = {40788461},
issn = {1573-4978},
support = {408693/2022-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico,Brazil/ ; },
mesh = {Swine ; *Wastewater/microbiology ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; },
abstract = {This systematic review aims to identify the metagenomic methodological approaches employed for the detection of antimicrobial resistance genes (ARGs) in swine wastewater treatment systems. The search terms used were metagenome AND bacteria AND ("antimicrobial resistance gene" OR resistome OR ARG) AND wastewater AND (swine OR pig), and the search was conducted across the following electronic databases: PubMed, Scopus, ScienceDirect, Web of Science, Embase, and Cochrane Library. The search was limited to studies published between 2020 and 2024. Of the 220 studies retrieved, eight met the eligibility criteria for full-text analysis. The number of publications in this research area has increased in recent years, with China contributing the highest number of studies. ARGs are typically identified using bioinformatics pipelines that include steps such as quality trimming, assembly, metagenome-assembled genome (MAG) reconstruction, open reading frame (ORF) prediction, and ARG annotation. However, comparing ARGs quantification across studies remains challenging due to methodological differences and variability in quantification approaches. Therefore, this systematic review highlights the need for methodological standardization to facilitate comparison and enhance our understanding of antimicrobial resistance in swine wastewater treatment systems through metagenomic approaches.},
}
@article {pmid40789383,
year = {2025},
author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK},
title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.},
journal = {Gene},
volume = {967},
number = {},
pages = {149720},
doi = {10.1016/j.gene.2025.149720},
pmid = {40789383},
issn = {1879-0038},
mesh = {*Metagenomics/methods ; *Ecosystem ; Microbiota/genetics ; *Water Microbiology ; Environmental Monitoring/methods ; Computational Biology/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples such as soil, water, air, and the human body. Metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the broad applications of metagenomics in environmental monitoring, encompassing sample collection, high-throughput sequencing, data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will become crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.},
}
@article {pmid40794746,
year = {2025},
author = {Alkhatib, SA and Arya, S and Islayem, D and Nyadzayo, RM and Mohamed, S and Yousef, AF and Hernandez, HH and Pappa, AM},
title = {Revealing bioremediation potential of novel indigenous bacteria from oil-contaminated sites in the UAE: A combined bioinformatics and experimental validation.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0329515},
pmid = {40794746},
issn = {1932-6203},
mesh = {*Biodegradation, Environmental ; *Computational Biology/methods ; United Arab Emirates ; Polycyclic Aromatic Hydrocarbons/metabolism ; *Bacteria/metabolism/genetics/isolation &amp; purification ; Phenols/metabolism ; *Soil Pollutants/metabolism ; },
abstract = {Microbial biodegradation of recalcitrant aromatic hydrocarbon pollutants represents an environmentally sustainable strategy for remediating contaminated sites. However, elucidating the metabolic capabilities and genetic determinants of biodegrading strains is crucial for optimizing bioremediation strategies. In this study, we comprehensively characterize the aromatic catabolic potential of two indigenous bacterial isolates, A. xylosoxidans C2 (A. x. C2) and A. xylosoxidans KW38 (A. x. KW38), obtained from hydrocarbon-impacted environments in the United Arab Emirates (UAE). Experimental validation through aromatic hydrocarbons supplemented growth studies confirmed the capability of the isolated bacteria to mineralize bisphenol A, 4-hydroxybenzoic acid, 1-naphthalenemethanol, and the high molecular weight polycyclic aromatic hydrocarbon (PAH), pyrene, in the presence of glucose. Their degradation efficiencies were comparable to or greater than those of Pseudomonas paraeruginosa, a well-characterized model organism for aromatic compound degradation. Integrated bioinformatic analyses uncovered fundamental aromatic catabolic pathways conserved across Achromobacter species, along with strain-specific genes that potentially confer specialized degradative capacities, highlighting the genomic basis of the observed metabolic versatility. Further, protein modeling based on the curated sequences revealed unique features of individual catabolic enzymes and their interaction networks. Notably, a dehydrogenase enzyme involved in aromatic ring cleavage was identified exclusively in these UAE isolates. These findings establish A. x. C2 and A. x. KW38 as promising bioremediators of diverse aromatic pollutants. Overall, the study exemplifies a powerful and comprehensive methodological framework that bridges bioinformatic analysis and experimental research to further optimize the effectiveness of experimental design. We achieved a substantial reduction in the number of unknown genetic and metabolic determinants of aromatic hydrocarbon degradation in the strains, reducing uncertainty by 99.3%, thereby enhancing the overall process and outcomes for systematic biodiscovery of pollutant-degrading environmental microbes to address ecological challenges.},
}
@article {pmid40796553,
year = {2025},
author = {Arehart, CH and Lin, M and Gibson, RA and , and Raghavan, S and Gignoux, CR and Stanislawski, MA and Grotzinger, AD and Evans, LM},
title = {Modeling the genomic architecture of adiposity and anthropometrics across the lifespan.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7494},
pmid = {40796553},
issn = {2041-1723},
support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; R01 AG046938/AG/NIA NIH HHS/United States ; T32 MH016880/MH/NIMH NIH HHS/United States ; RF1 AG073593/AG/NIA NIH HHS/United States ; K01 HL157658/HL/NHLBI NIH HHS/United States ; R01 MH120219/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Adiposity/genetics ; Male ; Female ; Genome-Wide Association Study ; *Obesity/genetics ; Multifactorial Inheritance ; Adult ; Middle Aged ; Anthropometry ; *Longevity/genetics ; Genomics ; Polymorphism, Single Nucleotide ; Aged ; Body Size/genetics ; },
abstract = {Obesity-related conditions are among the leading causes of preventable death and are increasing in prevalence worldwide. Body size and composition are complex traits that are challenging to characterize due to environmental and genetic influences, longitudinal variation, heterogeneity between sexes, and differing health risks based on adipose distribution. Here, we construct a 4-factor genomic structural equation model using 18 measures, unveiling shared and distinct genetic architectures underlying birth size, abdominal size, adipose distribution, and adiposity. Multivariate genome-wide associations reveal the adiposity factor is enriched specifically in neural tissues and pathways, while adipose distribution is enriched more broadly across physiological systems. In addition, polygenic scores for the adiposity factor predict many adverse health outcomes, while those for body size and composition predict a more limited subset. Finally, we characterize the factors' genetic correlations with obesity-related traits and examine the druggable genome by constructing a bipartite drug-gene network to identify potential therapeutic targets.},
}
@article {pmid40796641,
year = {2025},
author = {Sanad, H and Moussadek, R and Mouhir, L and Lhaj, MO and Dakak, H and Manhou, K and Zouahri, A},
title = {Monte carlo simulation for evaluating spatial dynamics of toxic metals and potential health hazards in sebou basin surface water.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {29471},
pmid = {40796641},
issn = {2045-2322},
mesh = {Monte Carlo Method ; Humans ; *Metals, Heavy/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; Risk Assessment ; *Environmental Monitoring/methods ; Morocco ; Geographic Information Systems ; Principal Component Analysis ; },
abstract = {Surface water is vital for environmental sustainability and agricultural productivity but is highly vulnerable to heavy metals (HMs) pollution from human activities. The focus of this research is to provide an analysis of ecological and human exposure to HMs in the Sebou Basin, an agriculturally significant region within Morocco's Gharb Plain. Using a multi-index integration approach, encompassing HM pollution indices, Human Health Risk Assessment (HHRA), Monte Carlo Simulation (MCS), multivariate statistical analysis (MSA), and Geographic Information Systems (GIS), twenty samples of surface water were taken and subjected to analysis. The results demonstrated notable spatial variability, with the northwestern, southwestern, and western parts of the Sebou Basin showing higher contamination levels. Cu exhibited the highest hazard quotient for ingestion, while Cr exceeded the hazard index (HI) threshold in both age categories. Statistical analysis uncovered strong associations, particularly between As and Cr, while principal component analysis (PCA) detected two key factors explaining 74.44% of the overall variability. Pollution indices classified all samples as highly contaminated (HPI > 30), with 65% categorized as "seriously affected" (MI > 6). The HHRA results indicated a heightened non-carcinogenic risk for children and carcinogenic risks exceeding acceptable thresholds (TCR > 10[-4]), with Ni presenting the highest risk (TCR = 2.32 × 10[-3] for children). MCS results revealed that Cu and Cr pose potential risks, with Cu exceeding the safety threshold for ingestion in both adults and children. These results emphasize the urgent necessity for tailored strategies to reduce contamination and foster sustainable agricultural and environmental management practices.},
}
@article {pmid40797121,
year = {2025},
author = {Kaplan, DM and Alvarez, SJA and Palitsky, R and Choi, H and Clifford, GD and Crozier, M and Dunlop, BW and Grant, GH and Greenleaf, MN and Johnson, LM and Maples-Keller, J and Levin-Aspenson, HF and Mascaro, JS and McDowall, A and Pozzo, NS and Raison, CL and Zarrabi, AJ and Rothbaum, BO and Lam, WA},
title = {Fabla: A voice-based ecological assessment method for securely collecting spoken responses to researcher questions.},
journal = {Behavior research methods},
volume = {57},
number = {9},
pages = {257},
pmid = {40797121},
issn = {1554-3528},
support = {UL1 TR002378/TR/NCATS NIH HHS/United States ; UL1TR002378/NH/NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; Adult ; *Voice ; Young Adult ; *Mobile Applications ; *Speech ; Middle Aged ; Adolescent ; },
abstract = {This article reports on the validation of Fabla, a researcher-developed and university-hosted smartphone app that facilitates naturalistic and secure collection of participants' spoken responses to researcher questions. Fabla was developed to meet the need for tools that (a) collect longitudinal qualitative data and (b) capture speech biomarkers from participants' natural environments. This study put Fabla to its first empirical test using a repeated-measures experimental design in which participants (n = 87) completed a 1-week voice daily diary via the Fabla app, and an identical 1-week text-entry daily diary administered via Qualtrics, with diary method order counterbalanced and randomized. A preregistered analysis plan investigated (1) adherence, usability, and acceptability of Fabla, (2) concurrent validity of voice diaries (vs. text-entry diaries) by comparing linguistic features obtained via each diary method, and (3) differences in the strength of the association between linguistic features and their known psychological correlates when assessed by voice versus text-entry diary. Voice diaries yielded more than double the mean daily language volume (word count) compared to text-entry diaries and received high usability and acceptability ratings. Linguistic markers consistently associated with depression in prior research were significantly associated with depression symptoms when assessed via voice but not text-entry diaries, and the difference in correlation magnitude was significant. Word-count-adjusted linguistic patterns were highly correlated between diary methods, with statistically significant mean differences observed for some linguistic dimensions in the presence of these associations. Fabla is a promising tool for collecting high-quality speech data from participants' naturalistic environments, overcoming multiple limitations of text-entry responding.},
}
@article {pmid40798830,
year = {2025},
author = {Abraham, AJ and Clauss, M and Bailey, MA and Duvall, ES},
title = {Body Mass Scaling of Sodium Regulation in Mammals.},
journal = {Acta physiologica (Oxford, England)},
volume = {241},
number = {9},
pages = {e70090},
doi = {10.1111/apha.70090},
pmid = {40798830},
issn = {1748-1716},
}
@article {pmid40800427,
year = {2024},
author = {Merritt, H and Faskowitz, J and Gonzalez, MZ and Betzel, RF},
title = {Stability and variation of brain-behavior correlation patterns across measures of social support.},
journal = {Imaging neuroscience (Cambridge, Mass.)},
volume = {2},
number = {},
pages = {},
pmid = {40800427},
issn = {2837-6056},
abstract = {The social environment has a critical influence on human development, cognition, and health. Research in health psychology and social neuroscience indicate an urgent need to understand how social relationships are associated with brain function and organization. To address this, we apply multilayer modeling and modularity maximization-both established tools in network neuroscience-to jointly cluster patterns of brain-behavior associations for seven social support measures. By using network approaches to map and analyze the connectivity between all pairs of brain regions simultaneously, we can clarify how relationships between brain regions (e.g. connectivity) change as a function of social relationships. This multilayer approach enables direct comparison of brain-behavior associations across social contexts for all brain regions and builds on both ecological and developmental neuroscientific findings and network neuroscientific approaches. In particular, we find that subcortical and control systems are especially sensitive to different constructs of perceived social support. Network nodes in these systems are highly flexible; their community affiliations, which reflect groups of nodes with similar patterns of brain-behavior associations, differ across social support measures. Additionally, our application of multilayer modeling to patterns of brain-behavior correlations, as opposed to just functional connectivity, represents an innovation in how multilayer models are used in human neuroscience. More than that, it offers a generalizable technique for studying the stability and variation of brain-behavior associations.},
}
@article {pmid40801436,
year = {2025},
author = {Karaman, MZ and Yetiman, AE and Zhan, J and Fidan, O},
title = {Biochemical Characterization and Genome Analysis of Pseudomonas loganensis sp. nov., a Novel Endophytic Bacterium.},
journal = {MicrobiologyOpen},
volume = {14},
number = {4},
pages = {e70051},
pmid = {40801436},
issn = {2045-8827},
support = {//This study was financially supported by The Scientific and Technological Research Council of Turkiye (TUBITAK) (Grant No: 221Z280)./ ; },
mesh = {*Pseudomonas/genetics/classification/isolation &amp; purification/drug effects/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/genetics/chemistry ; *Endophytes/genetics/classification/isolation &amp; purification ; Multigene Family ; Microbial Sensitivity Tests ; Carotenoids/metabolism ; Sequence Analysis, DNA ; Computational Biology ; },
abstract = {Pseudomonas species are highly adaptable, thriving in diverse environments and exhibiting remarkable genetic and metabolic diversity. While some strains are pathogenic, others have significant ecological and industrial applications. Bioinformatics and biochemical analyses, including antibiotic sensitivity testing, revealed that Pseudomonas loganensis sp. nov. can tolerate NaCl concentrations up to 5% and pH ranges between 5 and 9. Antibiogram results corroborated genome data, demonstrating resistance to vancomycin, ampicillin, methicillin, oxacillin, and penicillin G. Phylogenetic analysis based on 16S rRNA, rpoB, rpoD, and gyrB genes, combined with average nucleotide identity (ANI) comparisons, confirmed P. loganensis sp. nov. as a novel species within the Pseudomonas genus. Genome analysis further revealed the presence of turnerbactin and carotenoid gene clusters. Turnerbactin, known to contribute to nitrogen fixation in plants, highlights the strain's potential as a biofertilizer. Additionally, the carotenoid gene cluster suggests potential applications in industrial carotenoid production. The discovery of a trehalose synthase (treS) gene indicates the capability for one-step conversion of maltose into trehalose, underscoring its potential utility in trehalose production.},
}
@article {pmid40803399,
year = {2025},
author = {Jin, L and Lu, Y and Huang, J and Liu, J and Wei, X and Ma, G and Yu, H},
title = {Metabolism exploration of disinfection byproducts halonitromethanes (HNMs) by cytochrome P450 enzymes and toxicity evaluation.},
journal = {Environmental research},
volume = {285},
number = {Pt 4},
pages = {122575},
doi = {10.1016/j.envres.2025.122575},
pmid = {40803399},
issn = {1096-0953},
mesh = {*Cytochrome P-450 Enzyme System/metabolism ; *Disinfectants/toxicity/metabolism ; Animals ; Humans ; Rats ; *Nitroparaffins/toxicity/metabolism ; Disinfection ; Microsomes, Liver/metabolism ; },
abstract = {The nitrogen-contained disinfection by-products, halonitromethanes (HNMs), are known for their high cytotoxicity and genotoxicity. Although HNMs can be metabolized by cytochrome P450 enzymes (P450s), the specific mechanism has remained unclear. To shed light on this, density functional theory (DFT) calculations were performed to elucidate the potential oxidative P450-catalytic activation of the nine HNMs. Our findings reveal that active species of P450s (Cpd I) predominantly react with halogen-substituted nitromethanes via hydrogen abstraction and bromine atom abstraction, rather than chlorosylation. As a result of these reactions, oxidized HNMs are produced and can undergo further hydrolysis, leading to nitro-formaldehyde, nitro formyl halogen, halogen hydride, hypobromous acid, and nitroformic acid. To experimentally validate the computational predictions, in vitro experiments were conducted on five typical nitromethanes using human liver microsomes and the results reveal that DCNM, BCNM and DBCNM form nitroformyl chlorine (NO2CClO), while BCNM, DBNM and TBNM are transferred into nitroformyl bromide (NO2CBrO). Nitroformic acid is also identified as a metabolite in the TBNM metabolism reaction. Toxicity assessment reveals that metabolic transformation leads to an overall reduction in the ecological toxicity. However, metabolites showed similar toxicity to Fathead minnow and even higher acute toxicity to rat, as well as larger probability of hERG inhibition effects than HNMs, underscoring the need for caution in health risk assessment. By integrating in silico and in vitro approaches, this work has provided a comprehensive understanding of the metabolism of HNMs and offered potential toxicity data basis of these compounds.},
}
@article {pmid40805736,
year = {2025},
author = {Lu, F and Yi, B and Ma, JX and Wang, SN and Feng, YJ and Qin, K and Tu, Q and Bu, ZJ},
title = {Drought and Shrub Encroachment Accelerate Peatland Carbon Loss Under Climate Warming.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
pmid = {40805736},
issn = {2223-7747},
support = {U23A2003//The National Nature Science Foundation of China/ ; 42407354//The National Nature Science Foundation of China/ ; 42371050//The National Nature Science Foundation of China/ ; 20230203002SF and 20210402032GH//Jilin Provincial Science and Technology Development Project/ ; 2024QN1081//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Peatlands store substantial amounts of carbon (C) in the form of peat, but are increasingly threatened by drought and shrub encroachment under climate warming. However, how peat decomposition and its temperature sensitivity (Q10) vary with depth and plant litter input under these stressors remains poorly understood. We incubated peat from two depths with different degrees of decomposition, either alone or incubated with Sphagnum divinum shoots or Betula ovalifolia leaves, under five temperature levels and two moisture conditions in growth chambers. We found that drought and Betula addition increased CO2 emissions in both peat layers, while Sphagnum affected only shallow peat. Deep peat alone or with Betula exhibited higher Q10 than pure shallow peat. Drought increased the Q10 of both depths' peat, but this effect disappeared with fresh litter addition. The CO2 production rate showed a positive but marginal correlation with microbial biomass carbon, and it displayed a rather similar responsive trend to warming as the microbial metabolism quotient. These results indicate that both deep and dry peat are more sensitive to warming, highlighting the importance of keeping deep peat buried and waterlogged to conserve existing carbon storage. Additionally, they further emphasize the necessity of Sphagnum moss recovery following vascular plant encroachment in restoring carbon sink function in peatlands.},
}
@article {pmid40807726,
year = {2025},
author = {Ye, G and Yu, R},
title = {Spatiotemporal Mapping of Grazing Livestock Behaviours Using Machine Learning Algorithms.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {15},
pages = {},
pmid = {40807726},
issn = {1424-8220},
support = {Project No. 72104065//National Natural Science Foundation of China/ ; Project No. NHXXRCXM202303//Hainan New Star Projects/ ; Project No. KC20230018//Natural Resources Comprehensive Survey Command Centre Science and Technology Innovation Fund/ ; Project No. 2022KJCX04//Sanya Science and Technology Special Fund/ ; },
mesh = {Animals ; *Machine Learning ; *Livestock/physiology ; China ; Grassland ; Spatio-Temporal Analysis ; Algorithms ; Geographic Information Systems ; *Behavior, Animal/physiology ; *Herbivory/physiology ; Ecosystem ; },
abstract = {Grassland ecosystems are fundamentally shaped by the complex behaviours of livestock. While most previous studies have monitored grassland health using vegetation indices, such as NDVI and LAI, fewer have investigated livestock behaviours as direct drivers of grassland degradation. In particular, the spatial clustering and temporal concentration patterns of livestock behaviours are critical yet underexplored factors that significantly influence grassland ecosystems. This study investigated the spatiotemporal patterns of livestock behaviours under different grazing management systems and grazing-intensity gradients (GIGs) in Wenchang, China, using high-resolution GPS tracking data and machine learning classification. the K-Nearest Neighbours (KNN) model combined with SMOTE-ENN resampling achieved the highest accuracy, with F1-scores of 0.960 and 0.956 for continuous and rotational grazing datasets. The results showed that the continuous grazing system failed to mitigate grazing pressure when grazing intensity was reduced, as the spatial clustering of livestock behaviours did not decrease accordingly, and the frequency of temporal peaks in grazing behaviour even showed an increasing trend. Conversely, the rotational grazing system responded more effectively, as reduced GIGs led to more evenly distributed temporal activity patterns and lower spatial clustering. These findings highlight the importance of incorporating livestock behavioural patterns into grassland monitoring and offer data-driven insights for sustainable grazing management.},
}
@article {pmid40808268,
year = {2025},
author = {Xu, G and Guo, J and Yu, X and Zhao, N and Li, X and Yuan, T and Xu, Z and Zhao, T and Zhao, S and Li, X and Liu, X},
title = {Multi-Omics Analysis Reveals Adaptive Strategies of Meconopsis horridula to UV-B Radiation in the Qinghai-Tibet Plateau.},
journal = {Plant, cell &amp; environment},
volume = {48},
number = {11},
pages = {8249-8263},
doi = {10.1111/pce.70117},
pmid = {40808268},
issn = {1365-3040},
support = {//This study was supported by the Local Development Funds of the Science and Technology Department of Tibet (Grants XZ202001YD0028C and XZ202102YD0031C), and by the Graduate High-Level Talent Training Program of Tibet University (Grant 2025-GSP-B017)./ ; },
mesh = {*Ultraviolet Rays ; Flavonoids/biosynthesis ; Tibet ; *Adaptation, Physiological ; Transcriptome ; Gene Expression Regulation, Plant ; Altitude ; Arabidopsis/genetics ; Multiomics ; Acyltransferases ; Papaveraceae ; },
abstract = {Meconopsis horridula, an endemic medicinal and alpine horticultural species of the Qinghai-Tibet Plateau, exhibits remarkable adaptation to high-altitude UV-B radiation. Despite its ecological and medicinal significance, the mechanisms underlying its UV-B adaptation remain poorly understood. Here, we used a PacBio full-length transcriptome as a reference, integrating RNA-seq and metabolomic data from altitudinal populations, with field-based transcriptomic and microbiome profiling under shade-controlled UV-B gradients, to elucidate UV-B adaptive regulatory networks. KEGG enrichment and environmental correlation analyses highlighted flavonoid biosynthesis as a central pathway in UV-B adaptation at high altitudes. Controlled UV-B gradient experiments identified 10 conserved flavonoid biosynthesis genes, including chalcone synthase (CHS). Overexpression of CHS in Arabidopsis thaliana increased flavonoid content by approximately 1.2-fold. Co-expression analysis further revealed that CHS-associated regulatory factors mediate coordinated responses, including reduced light signalling, enhanced antioxidant capacity and suppression of defence genes and anthocyanin biosynthesis inhibitors. CHS, in coordination with immune regulation, modulates high-centrality microbes, contributing to differential network regulation and microbiome stability. Enriched key microbes may mitigate the growth-defence trade-off under UV-B stress through antimicrobial, growth-promoting and antioxidant activities. Collectively, our findings reveal a flavonoid-centred adaptation framework that deepens our understanding of UV-B resilience in alpine plants and offers potential resources for crop improvement.},
}
@article {pmid40808315,
year = {2025},
author = {Navratilova, HF and Whetton, AD and Geifman, N},
title = {Integrating Food Preference Profiling, Behavior Change Strategies, and Machine Learning for Cardiovascular Disease Prevention in a Personalized Nutrition Digital Health Intervention: Conceptual Pipeline Development and Proof-of-Principle Study.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e75106},
pmid = {40808315},
issn = {1438-8871},
mesh = {Humans ; *Cardiovascular Diseases/prevention &amp; control ; *Machine Learning ; *Food Preferences ; Female ; Male ; *Precision Medicine ; Middle Aged ; United Kingdom ; Digital Health ; },
abstract = {BACKGROUND: Personalized dietary advice needs to consider the individual's health risks as well as specific food preferences, offering healthier options aligned with personal tastes.<br><br>OBJECTIVE: This study aimed to develop a digital health intervention (DHI) that provides personalized nutrition recommendations based on individual food preference profiles (FPP), using data from the UK Biobank.<br><br>METHODS: Data from 61,229 UK Biobank participants were used to develop a conceptual pipeline for a DHIs. The pipeline included three steps: (1) developing a simplified food preference profiling tool, (2) creating a cardiovascular disease (CVD) prediction model using the subsequent profiles, and (3) selecting intervention features. The CVD prediction model was created using 3 different predictor sets (Framingham set, diet set, and FPP set) across 4 machine learning models: logistic regression, linear discriminant analysis, random forest, and support vector machine. Intervention functions were designed using the Behavior Change Wheel, and behavior change techniques were selected for the DHI features.<br><br>RESULTS: The feature selection process identified 14 food items out of 140 that effectively classify FPPs. The food preference profile prediction set, which did not include blood measurements or detailed nutrient intake, demonstrated comparable accuracy (across the 4 models: 0.721-0.725) to the Framingham set (0.724-0.727) and diet set (0.722-0.725). Linear discriminant analysis was chosen as the best-performing model. Four key features of the DHI were identified: food source and portion information, recipes, a dietary recommendation system, and community exchange platforms. The FPP and CVD risk prediction model serve as inputs for the dietary recommendation system. Two levels of personalized nutrition advice were proposed: level 1-based on food portion intake and FPP; and level 2-based on nutrient intake, FPP, and CVD risk probability.<br><br>CONCLUSIONS: This study presents proof of principle for a conceptual pipeline for a DHI that empowers users to make informed dietary choices and reduce CVD risk by catering to person-specific needs and preferences. By making healthy eating more accessible and sustainable, the DHI has the potential to significantly impact public health outcomes.},
}
@article {pmid40811794,
year = {2025},
author = {Shen, S and Qi, W and Zeng, J and Li, S and Liu, X and Zhu, X and Dong, C and Wang, B and Shi, Y and Yao, J and Wang, B and Lou, X and Gu, S and Li, P and Wang, J and Jiang, G and Cao, S},
title = {Passive Sensing for Mental Health Monitoring Using Machine Learning With Wearables and Smartphones: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e77066},
pmid = {40811794},
issn = {1438-8871},
mesh = {*Wearable Electronic Devices ; Humans ; *Machine Learning ; *Smartphone ; *Mental Health ; *Mental Disorders/diagnosis ; Monitoring, Physiologic ; },
abstract = {BACKGROUND: Mental health issues have become a significant global public health challenge. Traditional assessments rely on subjective methods with limited ecological validity. Passive sensing via wearable devices and smartphones, combined with machine learning (ML), enables objective, continuous, and noninvasive mental health monitoring.<br><br>OBJECTIVE: This study aimed to provide a comprehensive review of the current state of passive sensing-based and ML technologies for mental health monitoring. We summarized the technical approaches, revealed the association patterns between behavioral features and mental disorders, and explored potential directions for future advancements.<br><br>METHODS: This scoping review adhered to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines and was prospectively registered on the Open Science Framework. We systematically searched 7 databases (Web of Science, PubMed, IEEE Xplore, Embase, PsycINFO, Scopus, and ACM Digital Library) for studies published between January 2015 and February 2025. We included 42 peer-reviewed studies that used passive sensing from wearables or smartphones with ML to monitor clinically diagnosed mental disorders, such as depression and anxiety. Data were synthesized across technical dimensions (data collection, preprocessing, feature engineering, and ML models) and clinical associations, with behavioral features categorized into 8 domains.<br><br>RESULTS: The 42 included studies were predominantly cohort designs (23/42, 55%), with a median sample size of 60.5 (IQR 54-99). Most studies focused on depression (23/42, 55%) and anxiety (9/42, 21%) using primarily wrist-worn devices (32/42, 76%) collecting heart rate (28/42, 67%), movement index (25/42, 60%), and step count (17/42, 40%) as key biomarkers. Deep learning models (eg, convolutional neural networks and long short-term memory) showed high accuracy, while traditional ML (eg, random forest) remained prevalent due to better interpretability. We identified critical limitations, including small samples (32/42, 76% with N<100), short monitoring periods (19/42, 45% <7 days), scarce external validation (1/42, 2%), and limited reporting on data anonymization (6/42, 14%).<br><br>CONCLUSIONS: While passive sensing and ML demonstrate promising accuracy (eg, convolutional neural network-long short-term memory achieving 92.16% in anxiety detection), the evidence remains constrained by three key limitations: (1) methodological heterogeneity (32/42, 76% single-device studies; 19/42, 45% with <7-day monitoring), (2) high risk of bias from small samples (median 60.5, IQR 54-99 participants) and scarce external validation (1/42, 2%), and (3) ethical gaps (only 6/42, 14% addressing anonymization). These findings underscore the technology's potential to transform mental health care through objective, continuous monitoring-particularly for depression (heart rate and step count biomarkers) and anxiety (sleep and social interaction patterns). However, clinical translation requires standardized protocols, larger longitudinal studies (&#x2265;3 months), and ethical frameworks for data privacy. Future work should prioritize multimodal sensor fusion and explainable artificial intelligence to bridge the gap between technical performance and clinical deployability.},
}
@article {pmid40812171,
year = {2025},
author = {Lundberg, DS and Bergelson, J and Roux, F and Weigel, D and Karasov, TL},
title = {Lab to field: Challenges and opportunities for plant biology.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {8},
pages = {1212-1216},
doi = {10.1016/j.chom.2025.05.027},
pmid = {40812171},
issn = {1934-6069},
mesh = {*Plants/microbiology ; Plant Diseases/microbiology ; *Plant Physiological Phenomena ; },
abstract = {Plant-microbe research offers many choices of model and strain and whether a field-first or lab-first approach is best. However, differences between laboratory studies, offering control and repeatability, versus field experiments, revealing ecological relevance and environmental effects, should not be seen as failure but motivate further inquiry and allow complementary discovery.},
}
@article {pmid40814786,
year = {2026},
author = {Misono, S and Nguyen-Feng, VN and Lei, X and Feddema, E and Tella, A and Stockness, A and Frazier, PA and Kummerfeld, E and Lim, KO},
title = {Ecological Momentary Assessment of Voice &amp; Psychological Factors: Group &amp; Individual Mechanisms.},
journal = {The Laryngoscope},
volume = {136},
number = {1},
pages = {324-331},
pmid = {40814786},
issn = {1531-4995},
support = {K23DC016335/DC/NIDCD NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; UL1TR002494/TR/NCATS NIH HHS/United States ; KL2 TR000113/TR/NCATS NIH HHS/United States ; K23 DC016335/DC/NIDCD NIH HHS/United States ; KL2TR000113/TR/NCATS NIH HHS/United States ; //American College of Surgeons, Triological Society: Clinical Scientist Development Award/ ; },
mesh = {Humans ; Male ; Female ; Adult ; *Ecological Momentary Assessment ; Middle Aged ; *Dysphonia/psychology/physiopathology ; *Voice Quality ; Cross-Sectional Studies ; Anxiety/psychology ; Stress, Psychological ; Aged ; },
abstract = {OBJECTIVES: Cross-sectional associations between voice and psychological factors are known, but changes over time offer opportunities to refine our understanding of their interactions and consider customized treatment options. Study objectives were to measure relationships between voice and psychological factors using ecological momentary assessment and applying (1) group-level time series analysis and (2) group and (3) individual causal modeling to identify key psychological factors relevant for voice outcomes.<br><br>METHODS: Adults (N&#x2009;=&#x2009;32) with primary muscle tension dysphonia completed multiple assessments daily for 10&#x2009;days. Measures included items from the Voice Handicap Index-10, voice-adapted perceived present control scale, items from NIH PROMIS and the NIH Toolkit to assess distress, and the Positive and Negative Affect Scale. Group-level time series analysis was conducted using dynamic structural equation modeling; causal analysis utilized the Greedy Fast Causal Inference algorithm.<br><br>RESULTS: In group-level time series analyses, neither perceived control nor distress predicted subsequent timepoint voice handicap scores. In group-level causal modeling, anxiety was causal for voice handicap, but perceived control was not. Individual-level analyses identified various causal factors for voice handicap including perceived control and negative affect, and to a lesser extent, serenity, anxiety, somatic arousal, and stress.<br><br>CONCLUSIONS: Group-level analyses may obscure important heterogeneity that is identifiable using individual-level causal analyses. For example, perceived control was not identified as predictive or causal for voice handicap at the group level; but was a salient causal factor for voice handicap in some individuals. Causal modeling using intensive longitudinal datasets offers a potential avenue for individualized treatment approaches.},
}
@article {pmid40816181,
year = {2025},
author = {Xu, Z and Xu, D and Ma, J and Wang, J and Yan, S and Fu, R and Cui, Y},
title = {The risk assessment for metal(loid)s in soil-slag mixing systems: Coupling sequential extraction, leaching tests, and in vitro bioaccessibility assays.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139544},
doi = {10.1016/j.jhazmat.2025.139544},
pmid = {40816181},
issn = {1873-3336},
mesh = {Risk Assessment ; *Soil Pollutants/analysis/toxicity ; *Metalloids/analysis/toxicity ; Biological Availability ; Humans ; *Industrial Waste/analysis ; Soil/chemistry ; *Metals, Heavy/analysis ; *Metals/analysis ; Arsenic ; Metallurgy ; },
abstract = {The metals and metalloids (metal[loid]s) in the newly formed soil-slag mixing systems (SSMS), formed by the invasion of smelting slag into contaminated soils, may pose potential risks to environment and residents near the smelter sites. In this study, sequential extraction, leaching tests and in vitro bioaccessibility assays were conducted to assess the ecological and human health risk of metal(loid)s in SSMS. The results indicated that the contaminated soils and smelting slags were composed of more than 80 % silicate and oxide minerals, which served as the host phases for metal(loid)s in SSMS. Cd exhibited high mobility and availability, with its exchangeable fraction ranging from 0.15 % to 69.23 %. Leaching tests revealed high leachability and bioavailability of Cd, Mn and Zn. Moreover, metal(loid)s bioaccessibility varied amongst samples: 2.78-46.63 % of As, 11.87-95.25 % of Cd, 37.35-93.88 % of Mn, 1.97-87.84 % of Pb and 0-57.98 % of Zn. Risk assessment calculation results indicated potentially ecological risks posed by Cd, Mn, Pb, and Zn, and unfavorable carcinogenic risks associated with As and Cd, suggesting that remediation efforts were warranted. Overall, this study highlighted how the invasion of smelting slags can affect the accuracy of risk assessments, providing new guidance for risk control and environmental management at slag dumping sites.},
}
@article {pmid40817347,
year = {2025},
author = {Rajpal, H and Stengel, CV and Mediano, PAM and Rosas, FE and Viegas, E and Marquet, PA and Jensen, HJ},
title = {Information dynamics and the emergence of high-order individuality in ecosystems.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1231},
pmid = {40817347},
issn = {2399-3642},
support = {EP/W024020/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/X03870X/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/W007142/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; ES/T005319/2//RCUK | Economic and Social Research Council (ESRC)/ ; },
mesh = {*Ecosystem ; *Biological Evolution ; *Selection, Genetic ; Mutation ; Population Dynamics ; *Information Theory ; },
abstract = {At what level does natural selection occur? When considering the reproductive dynamics of interacting and mutating agents, it has long been debated whether selection is better understood by focusing on the individual or if hierarchical selection emerges as a consequence of joint adaptation. Despite longstanding efforts in theoretical ecology, there is still no consensus on this fundamental issue, most likely due to the difficulty in obtaining adequate data spanning a sufficient number of generations and the lack of adequate tools to quantify the effect of hierarchical selection. Here, we capitalise on recent advances in information-theoretic data analysis to advance this state of affairs by investigating the emergence of high-order structures- such as groups of species- in the collective dynamics of the Tangled Nature model of evolutionary ecology. Our results show that evolutionary dynamics can lead to clusters of species that act as a self-perpetuating group that exhibits greater information-theoretic agency than a single species for a broad range of stable mutation rates. However, this higher-order organization breaks down for mutation rates close to the error threshold, where increased information processing is observed at the level of a single species. For mutation rates higher than the error threshold, no stable population of species are observed in time, and all individuality is lost in the ecosystem. Overall, our findings provide quantitative evidence supporting the emergence of higher-order structures in evolutionary ecology from relatively simple processes of adaptation and reproduction.},
}
@article {pmid40818234,
year = {2025},
author = {Poudel, B and Xie, J and Guo, C and Watt, OE and Pulster, EL and Patel, RJ and Steevens, JA and Xu, D},
title = {Real-time oil spill concentration assessment through fluorescence imaging and deep learning.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139374},
doi = {10.1016/j.jhazmat.2025.139374},
pmid = {40818234},
issn = {1873-3336},
abstract = {Oil spills may pose severe ecological and socioeconomic threats, necessitating rapid and accurate environmental assessment. Traditional assessment methods used to determine the extent of a spill including gas chromatography-mass spectrometry, satellite imaging, and visual surveys, are often time-consuming, expensive, and limited by weather conditions or sampling constraints. Furthermore, these methods frequently struggle to provide real-time data crucial for prompt decision-making during spill emergencies. This study addresses these limitations by combining fluorescence imaging, deep learning, a mobile application, and a data management system for automated and real-time oil spill assessment. Our approach leverages a convolutional neural network architecture for feature extraction coupled with a custom regression model, trained and evaluated on a self-curated comprehensive dataset of 1530 fluorescence images from two distinct oil types, a napthalenic crude oil and an aromatic-napthalenic crude oil, at concentrations ranging from 0 to 500 mg/L. The proposed approach demonstrates superior performance compared to both traditional machine learning models and more complex deep learning architectures, achieving an R[2] score of 0.9958 and RMSE of 9.28. The application enables rapid, cost-effective field measurements with robust data tracking and analysis capabilities. This research advances oil spill monitoring technology with a scalable solution that balances accuracy, speed, and accessibility for real-time environmental assessment and emergency response.},
}
@article {pmid40819189,
year = {2025},
author = {Alhashmi, AA and Elhessewi, GMS and Ghaleb, M and Ahmad, N and Aljehane, NO and Alkhaldi, TM and Almansour, H and Al Zanin, S},
title = {Enhancing medical response efficiency in real-time large crowd environments via smart coverage and deep learning for stable ecological health monitoring.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30000},
pmid = {40819189},
issn = {2045-2322},
mesh = {*Deep Learning ; Humans ; Geographic Information Systems ; *Crowding ; Algorithms ; },
abstract = {Festivals and city-wide mass events are prevalent in human societies worldwide, drawing large crowds. Such events range from concerts with a dozen attendees to large-scale actions with thousands of viewers. It is the highest priority for each organizer of such an occasion to be capable of upholding a higher standard of safety and minimizing the danger of events, especially medical emergencies. Therefore, establishing sufficient safety measures is significant. There is a requirement for event organizers and emergency response personnel to identify developing, potentially critical crowd situations at an early stage during city-wide mass assemblies. In general, the localization of the global positioning system (GPS) and proximity-based tracking is employed to capture intricate crowd dynamics throughout an event. Recently, technology has been used in numerous diverse ways to achieve these large crowds. For example, computer vision-based models are employed to observe the flexibility and behaviour of crowds. In this manuscript, a model for Medical Response Efficiency in Real-Time Large Crowd Environments via Smart Coverage and Hiking Optimisation (MRELC-SCHO) is presented, aiming to maintain stable ecological health. The primary objective of this paper is to propose an effective method for enhancing medical response efficiency in large crowd environments by utilizing advanced optimization algorithms. Initially, the MRELC-SCHO model utilizes min-max normalization to transform the input data into a structured format. Furthermore, the Chimp Optimisation Algorithm (CHOA) model is employed for the feature selection (FS) process to select the most significant features from the dataset. Additionally, the MRELC-SCHO technique utilizes the bidirectional long short-term memory with an auto-encoder (BiLSTM-AE) method for classification. Finally, the parameter selection for the BiLSTM-AE model is performed by using the Hiking Optimisation Algorithm (HOA) model. The experimentation of the MRELC-SCHO approach is accomplished under the Ecological Health dataset. The comparison analysis of the MRELC-SCHO approach revealed a superior accuracy value of 98.56% compared to existing models.},
}
@article {pmid40820130,
year = {2025},
author = {Sehi, GT and Birhanie, SK and Hans, J and Brown, MQ and Parker, DM},
title = {Environmental correlates of Aedes aegypti abundance in the West Valley region of San Bernardino County, California, USA, from 2017 to 2023: an ecological modeling study.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {349},
pmid = {40820130},
issn = {1756-3305},
support = {U01 CK000649/CK/NCEZID CDC HHS/United States ; U01CK000649/ACL/ACL HHS/United States ; },
mesh = {Animals ; *Aedes/physiology/virology ; California/epidemiology ; *Mosquito Vectors/physiology/virology ; Geographic Information Systems ; Temperature ; *Environment ; Ecosystem ; Dengue/transmission ; Mosquito Control ; Humans ; },
abstract = {BACKGROUND: Aedes mosquitoes, particularly Aedes aegypti and Ae. albopictus, are major vectors of globally significant diseases such as dengue, Zika, and chikungunya. Since 2013, Ae. aegypti populations have rapidly expanded in California, making control efforts difficult due to their widespread, small-scale breeding sites and strong adaptation to urban environments.<br><br>METHODS: Remote sensing technologies, coupled with Geographic Information Systems (GIS), offer innovative solutions for mosquito surveillance and control. However, understanding the environmental drivers of mosquito abundance, particularly in California's diverse ecological settings, remains an important gap. To address this gap, we analyzed Ae. aegypti abundance (2017 to 2023) in relation to environmental variables, such as temperature, precipitation, surface water, elevation, and built environment. We applied hotspot analysis to identify spatial clusters of high mosquito abundance and used a generalized additive model (GAM) with a negative binomial distribution to assess environmental and meteorological influences on mosquito counts.<br><br>RESULTS: Hotspot analyses revealed clusters of Ae. aegypti hotspots near residential areas. Aedes aegypti counts increased with higher surface water availability and temperature.<br><br>CONCLUSIONS: Our study characterizes the spatial and temporal dynamics of Ae. aegypti mosquito abundance in the West Valley region of San Bernardino County from 2017 to 2023, shedding light on the influence of environmental factors and human activities on temporal trends. Our findings emphasize the critical role of temperature and water availability in shaping mosquito population dynamics, highlighting the need for proactive vector control strategies in response to environmental changes.},
}
@article {pmid40820776,
year = {2025},
author = {Stansberry, TT and Myers, CR and Tran, L and Roberson, PNE and Ahn, S},
title = {Impacts of Access to Hospital and Emergency Care on Rural Mortality in Tennessee, 2010-2019: A GIS-Informed Study.},
journal = {Journal of health care for the poor and underserved},
volume = {36},
number = {3},
pages = {787-814},
doi = {10.1353/hpu.2025.a967333},
pmid = {40820776},
issn = {1548-6869},
mesh = {Humans ; Tennessee/epidemiology ; *Health Services Accessibility/statistics &amp; numerical data ; Retrospective Studies ; *Rural Population/statistics &amp; numerical data ; Cross-Sectional Studies ; Middle Aged ; Geographic Information Systems ; Female ; Male ; COVID-19/epidemiology ; Adult ; Aged ; *Mortality/trends ; *Emergency Medical Services/statistics &amp; numerical data ; },
abstract = {Rural Tennessee's health and economic disparities have worsened since 2010 (while the state led the nation in hospital closures per capita). Guided by the Vulnerable Populations Conceptual Model, we examined the relationship between Tennessee's county-level rural mortality rates and declining access to hospital and emergency care in the decade preceding the COVID-19 pandemic (avoiding pandemic-related delayed data releases and potential statistical modeling issues). We conducted a retrospective, ecological correlational study using geographic information systems and annual cross-sectional secondary data, employing aspatial and spatial negative binomial generalized linear mixed-effects models (GLMMs). Our bivariate models revealed significant correlations between hospital and emergency care access and mortality rates, but the effect decreased when adjusted for rurality, median household income, age, and other covariates. While access to hospital and emergency care influences mortality, our findings indicate that socioeconomic and demographic factors have a greater impact, underscoring the strong health-wealth connection in rural Tennessee.},
}
@article {pmid40821442,
year = {2025},
author = {Motlagh, SH and Momtazi, F and Saeedi, H},
title = {Senckenberg dogger bank long-term monitoring: First dataset on amphipods.},
journal = {Data in brief},
volume = {62},
number = {},
pages = {111931},
pmid = {40821442},
issn = {2352-3409},
abstract = {This dataset includes unique occurrence records of amphipod specimens collected during the 2024 annual Senckenberg Long-Term Monitoring Project in Dogger Bank (a shallow sand bank in the central North Sea), Cruise DOG24. This cruise was part of an ongoing effort to monitor biodiversity, which has occurred annually from 1991 to 2024 by the Marine Zoology Department at the Senckenberg Research Institute and Natural History Museum. Amphipods, key components of marine benthic ecosystems, were sampled by beam trawl over the Dogger Bank's stable sandy substrate. A total of 8444 specimens of ten species belonging to 13 families and 14 genera were identified using morphological methods with Leica M60 and DM750 microscopes. This study presents the first species-level identification of benthic amphipods in the Dagger Bank, providing a taxonomically resolved dataset that serves as a reliable identification key for future monitoring efforts in the area. Data were structured and published to the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF) following the Darwin Core (DwC) standard. This dataset is the first-hand data ever published open-access from the Senckenberg Long Term Monitoring Project since 1991. This dataset also supports a broader research project aimed at (i) revealing the distribution pattern of amphipods in the North Sea, (ii) identifying environmental drivers of species distribution and diversity, and (iii) evaluating the response of the amphipod community to ecosystem changes.},
}
@article {pmid40822726,
year = {2025},
author = {Piršelová, B and Jakubčinová, J},
title = {Plant cyanogenic glycosides: from structure to properties and potential applications.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1612132},
pmid = {40822726},
issn = {1664-462X},
abstract = {Cyanogenic glycosides (CGs) represent an important group of secondary metabolites predominantly of plant origin, characterized by their ability to release hydrogen cyanide upon enzymatic hydrolysis. These compounds are widely distributed across the plant kingdom, where they play a crucial role in defense against herbivores and pathogens. In recent years, advanced analytical tools have greatly expanded our knowledge of CGs by enabling the identification of less abundant forms. Based on the latest data from published scientific studies, this review presents a comprehensive overview of CGs, with a focus on their structural variability, biosynthetic pathways, ecological functions, and inherent toxicity. Special attention is given to the quantity and distribution of significant CGs in plants, as the available data is often heterogeneous, fragmented, and dispersed across the literature. Furthermore, the review explores emerging evidence regarding the biomedical relevance of selected CGs, including their putative anticancer properties and broader therapeutic potential. The findings presented in this review may be applied in fields such as pharmacology, toxicology, food safety, and plant biotechnology - either to enhance CG content for crop protection or, conversely, to eliminate such content in order to improve food safety.},
}
@article {pmid40824055,
year = {2025},
author = {Grigson, SR and Bouras, G and Dutilh, BE and Olson, RD and Edwards, RA},
title = {Computational function prediction of bacteria and phage proteins.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {89},
number = {3},
pages = {e0002225},
pmid = {40824055},
issn = {1098-5557},
support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; DP250103825//Australian Research Council/ ; 865694/ERC_/European Research Council/International ; RC2DK116713/DK/NIDDK NIH HHS/United States ; 390713860//Deutsche Forschungsgemeinschaft/ ; DP220102915//Australian Research Council/ ; FL250100019//Australian Research Council/ ; },
mesh = {*Bacteriophages/genetics/metabolism ; *Computational Biology/methods ; *Viral Proteins/genetics/metabolism/chemistry ; *Bacteria/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism/chemistry ; Machine Learning ; Molecular Sequence Annotation/methods ; },
abstract = {SUMMARYUnderstanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advances in bioinformatics methods, ~30% of all bacterial and ~65% of all bacteriophage (phage) protein sequences cannot be confidently annotated. In this review, we examine state-of-the-art bioinformatics tools and methodologies for annotating bacterial and phage proteins, particularly those of unknown or poorly characterized function. We describe the process of identifying protein-coding regions and the systems to classify protein functionalities. Additionally, we explore a range of protein annotation methods, from traditional homology-based methods to cutting-edge machine learning models. In doing so, we provide a toolbox for confidently annotating previously unknown bacterial and phage proteins, advancing the discovery of novel functions and our understanding of microbial systems.},
}
@article {pmid40825407,
year = {2025},
author = {Tarandek, A and Boštjančić, LL and Francesconi, C and Bonassin, L and Schardt, L and Jussila, J and Kokko, H and Schwenk, K and Hudina, S and Lecompte, O and Theissinger, K},
title = {Characterisation of the noble crayfish immune response to oomycete-derived immunostimulants.},
journal = {Fish &amp; shellfish immunology},
volume = {166},
number = {},
pages = {110666},
doi = {10.1016/j.fsi.2025.110666},
pmid = {40825407},
issn = {1095-9947},
mesh = {Animals ; *Astacoidea/immunology/genetics/microbiology ; *Aphanomyces/chemistry/physiology/immunology ; *Adjuvants, Immunologic/pharmacology ; *Glucans/pharmacology ; *Immunity, Innate ; Hemocytes/immunology ; },
abstract = {The invasive oomycete pathogen Aphanomyces astaci significantly threatens native European crayfish populations, prompting investigations towards the effects of protective immunostimulation on the immune response of the vulnerable noble crayfish (Astacus astacus). Here, we evaluate the effect of three oomycete-derived immunostimulant treatments: laminarin (β-1,3-glucan found within the Ap. astaci cell wall), inactivated Ap. astaci spores and Ap. astaci hyphal homogenate. Our findings reveal immediate changes in the noble crayfish total haemocyte count (THC), differential haemocyte count (DHC), and gene expression. A short-term increase in the THC was observed in all treatments, with a gradual return to normal values 8 h post immunostimulation. Granular haemocytes seem to be involved in response to immunostimulation with inactivated Ap. astaci spores, while the number of semi-granular and hyaline haemocytes increased in response to laminarin and Ap. astaci hyphal homogenate. Analysis of the differentially expressed genes showed that the Prophenoloxidase pathway genes and Toll pathway genes are involved in the response to oomycete-derived immunostimulants. Prolonged effects of immunostimulation were reflected in the decreased C/EBP and Kr-h1 gene expression in the hyphal homogenate group as well as decreased Kr-h1 expression in the spore group. Taken together, our results indicate that immunostimulation causes a dynamic change in the noble crayfish immune system response, with similarities in the gene expression patterns between immunostimulated and Ap. astaci infected noble crayfish. As a future research focus, we highlight the importance of molecular characterisation of the genes involved in the anti-oomycete response which could provide valuable insights into pathogen resistance in freshwater crayfish. In the context of the Ap. astaci mediated downfall of the noble crayfish stocks across Europe, further exploration is needed regarding the benefits of the oomycete-derived immunostimulation that can potentially support conservation and aquacultural efforts.},
}
@article {pmid40826054,
year = {2025},
author = {Quintanilha, D and Moura, E and Xavier, D},
title = {Hospitalisations in Brazil: an ecological time series analysis of the impact of medical decision support data as an exogenous variable.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {2827},
pmid = {40826054},
issn = {1471-2458},
mesh = {Brazil/epidemiology ; Humans ; *Hospitalization/statistics &amp; numerical data ; *Decision Support Systems, Clinical/statistics &amp; numerical data ; *Public Health Surveillance/methods ; },
abstract = {PURPOSE: Public health surveillance depends on continuous monitoring to guide interventions and allocate resources effectively. This study aimed to evaluate whether structured medical search data from the Afya Whitebook®, a clinical decision-support platform, can serve as exogenous variables to enhance the explanatory capacity of time series models characterising hospitalisation patterns within Brazil's public health system.<br><br>METHODS: An ecological time series analysis was conducted using hospitalisation data (SIH/SUS) and Afya Whitebook&#xae; search volumes from 2021 to 2024. SARIMAX models assessed temporal associations between search activity and hospital admissions across Brazilian states, compared to univariate SARIMA models to evaluate the added value of search data.<br><br>RESULTS: In 278 of the 478 time series, SARIMAX models provided a better fit than univariate SARIMA models, particularly for conditions such as chronic obstructive pulmonary disease, dengue, urinary tract infections, type 2 diabetes, asthma, depression, and chronic kidney disease. Model fit varied by disease and region, underscoring the influence of contextual factors in the association between search behaviour and hospital admissions.<br><br>CONCLUSION: This study demonstrates that structured medical search data can serve as exogenous variables to improve the explanatory capacity of time series models of hospitalisation patterns. Despite variation between diseases and regions, this approach shows promise in supporting public health surveillance and could be strengthened by incorporating contextual data in future studies.},
}
@article {pmid40827702,
year = {2025},
author = {Chung, J and Moloney, ME and Seixas, AA and Jackson, CL},
title = {The environment around the sleeper is changing: a perspective.},
journal = {Sleep},
volume = {48},
number = {11},
pages = {},
pmid = {40827702},
issn = {1550-9109},
support = {5R01HL152453-05/GF/NIH HHS/United States ; },
mesh = {Humans ; *Sleep/physiology ; Weather ; *Environmental Exposure/adverse effects ; *Environment ; Circadian Rhythm/physiology ; Temperature ; },
abstract = {Sleep is shaped by a complex interplay of biological, behavioral, and environmental factors. While substantial attention has been paid to the first two factors, the role of environmental exposures, particularly weather patterns, ambient temperature variability, and other dynamic atmospheric conditions, remains relatively underexplored in sleep research. This gap is notable given the increasing availability of high-resolution environmental data and growing evidence that ambient conditions can influence circadian regulation, thermal comfort, and sleep continuity. This perspective paper reviews emerging evidence linking environmental factors to sleep patterns, highlighting both direct effects (e.g. thermal disruptions) and indirect pathways (e.g., displacement or stress from extreme weather events). Recent advances in environmental sensing, geospatial data, and real-time monitoring offer new opportunities to capture high-resolution environmental data relevant to sleep. This perspective highlights the need for data infrastructure capable of integrating these dynamic environmental inputs with sleep metrics from, for instance, wearables, surveys, and clinical records. We also examine the methodological and informatics challenges of integrating environmental data with sleep measures and suggest directions for future research. As environmental conditions evolve, understanding their influence on sleep holds promise for advancing both scientific knowledge and public health relevance, particularly in identifying affected populations, designing responsive interventions, and contextualizing sleep within broader ecological systems.},
}
@article {pmid40828274,
year = {2025},
author = {Ramos-Onsins, SE and Guirao-Rico, S and Hafez, A and Ferretti, L},
title = {npstat: An Efficient Tool to Explore the Population Genome Variability and Divergence Using Pool Sequencing Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {51-66},
pmid = {40828274},
issn = {1940-6029},
mesh = {*Software ; *Genetic Variation ; *Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; *Genetics, Population/methods ; *Computational Biology/methods ; },
abstract = {Pool sequencing has emerged as a valuable approach in ecological studies, particularly when dealing with very small organisms (with limited amount of DNA available), when distinguishing individual organisms is a challenge (e.g., in colonies, microbiome), when there is a trade-off between the sequencing cost and the number of individuals to sequence, when the main goal is to estimate nucleotide variability and variant frequency patterns at the population level (that is, when individual information is not required). Estimates of variability can be efficiently explored by analyzing sequences of pooled individuals sampled from the population. When using this approach, the number of pooled individuals and the mean read depth are key choices in the experimental design.The software npstat calculates different estimates of nucleotide variability and neutrality tests.It also calculates the number of synonymous and nonsynonymous variants and the proportion of beneficial substitutions (alpha) using the MKT approach when GTF annotation file and an outgroup is provided.},
}
@article {pmid40828279,
year = {2025},
author = {Vizueta, J and Pisarenco, VA and Rozas, J},
title = {Evolutionary Genomics of Gene Families: A Case Study of Insect Gustatory Receptors.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {179-209},
pmid = {40828279},
issn = {1940-6029},
mesh = {Animals ; *Genomics/methods ; *Evolution, Molecular ; *Multigene Family ; Phylogeny ; *Receptors, Cell Surface/genetics ; *Ants/genetics ; Computational Biology/methods ; *Insect Proteins/genetics ; Molecular Sequence Annotation ; },
abstract = {Gene families, which are groups of genes that share common ancestry and are often functionally related, constitute a substantial proportion of the protein-coding sequences within eukaryotic genomes. In insects, genes involved in chemoperception belong to gene families characterized by numerous copies that arise from episodic bursts of gene duplication. This biological process is crucial for insect survival, as it enables the perception of environmental chemical cues. In this chapter, we analyze the gustatory receptors in the fire ant Solenopsis invicta and present a protocol for bioinformatic analyses. First, we employ BITACORA to identify and annotate gene family members in the genome assembly, providing tools for the annotation and subsequent validation. Then, we use GALEON to explore the genomic arrangement of gene family members in the chromosome-level assembly and visualize the distribution of gene clusters. To gain insights into the evolution and function of these genes, we conduct multiple-sequence alignment and reconstruct the phylogeny, incorporating data from two other insects. Finally, we integrate physical and evolutionary distances of the gustatory receptors to further understand the dynamics of this gene family.},
}
@article {pmid40828283,
year = {2025},
author = {Aceto, S and Perrini, S and Varone, M and Lucibelli, F and Volpe, G and Di Lillo, P and Carfora, A and Mazzucchiello, SM and Saccone, G and Salvemini, M},
title = {Identification of Sex-Specific and Sex-Biased Transcripts for Genetic Sexing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {273-298},
pmid = {40828283},
issn = {1940-6029},
mesh = {Animals ; Male ; Female ; *Computational Biology/methods ; *Sex Determination Analysis/methods ; *Transcriptome ; },
abstract = {Sex-specific transcripts are RNA molecules expressed predominantly or exclusively in one sex, providing insights into molecular and physiological differences between males and females. This knowledge underpins the development of precise and efficient genetic sexing methods applicable in various contexts. In agriculture and livestock management, early sex determination could enhance resource management and productivity. In ecology and conservation, genetic sexing informs population monitoring and species management. In applied entomology, it could improve biological control strategies, such as the sterile insect technique. Here, we describe a bioinformatic framework to identify sex-specific transcripts using RNA-seq sequencing data in eukaryotic species with or without a sequenced reference genome.},
}
@article {pmid40828862,
year = {2025},
author = {Kubota, Y and Fukiage, T},
title = {Human-like monocular depth biases in deep neural networks.},
journal = {PLoS computational biology},
volume = {21},
number = {8},
pages = {e1013020},
pmid = {40828862},
issn = {1553-7358},
mesh = {Humans ; *Neural Networks, Computer ; *Depth Perception/physiology ; *Vision, Monocular/physiology ; Computational Biology ; Male ; Female ; Adult ; },
abstract = {Human depth perception from 2D images is systematically distorted, yet the nature of these distortions is not fully understood. By examining error patterns in depth estimation for both humans and deep neural networks (DNNs), which have shown remarkable abilities in monocular depth estimation, we can gain insights into constructing functional models of this human 3D vision and designing artificial models with improved interpretability. Here, we propose a comprehensive human-DNN comparison framework for a monocular depth judgment task. Using a novel human-annotated dataset of natural indoor scenes and a systematic analysis of absolute depth judgments, we investigate error patterns in both humans and DNNs. Employing exponential-affine fitting, we decompose depth estimation errors into depth compression, per-image affine transformations (including scaling, shearing, and translation), and residual errors. Our analysis reveals that human depth judgments exhibit systematic and consistent biases, including depth compression, a vertical bias (perceiving objects in the lower visual field as closer), and consistent per-image affine distortions across participants. Intriguingly, we find that DNNs with higher accuracy partially recapitulate these human biases, demonstrating greater similarity in affine parameters and residual error patterns. This suggests that these seemingly suboptimal human biases may reflect efficient, ecologically adapted strategies for depth inference from inherently ambiguous monocular images. However, while DNNs capture metric-level residual error patterns similar to humans, they fail to reproduce human-level accuracy in ordinal depth perception within the affine-invariant space. These findings underscore the importance of evaluating error patterns beyond raw accuracy, providing new insights into how humans and computational models resolve depth ambiguity. Our dataset and methodology provide a framework for evaluating the alignment between computational models and human perceptual biases, thereby advancing our understanding of visual space representation and guiding the development of models that more faithfully capture human depth perception.},
}
@article {pmid40828878,
year = {2025},
author = {Fong, LJM and Johnson, BD and Darolti, I and Sandkam, BA and Mank, JE},
title = {Genome report: Genome of the Amazon guppy (Poecilia bifurca) reveals conservation of sex chromosomes and dosage compensation.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {10},
pages = {},
pmid = {40828878},
issn = {2160-1836},
support = {//NSERC/ ; //UBC/ ; //BRC Informatics/ ; },
mesh = {Animals ; *Poecilia/genetics ; *Dosage Compensation, Genetic ; Male ; Female ; *Sex Chromosomes/genetics ; *Genome ; *Genomics/methods ; X Chromosome/genetics ; },
abstract = {The Amazon guppy, Poecilia bifurca, is a small live-bearing fish. The close relatives Poecilia reticulata, Poecilia picta, and Poecilia parae all share the same sex chromosome system, but with substantial diversity in the degree of Y degeneration and the extent of X chromosome dosage compensation. In order to identify if P. bifurca shares the same sex chromosome system, we built a female (XX) draft genome with 55X coverage of PacBio HiFi data, resulting in a 785 Mb assembly with 94.4% BUSCO completeness. We used this genome and found that P. bifurca shares the same sex chromosomes as related species and shows substantial Y chromosome degeneration. We combined this with RNA-Seq data and found similar expression of X-linked genes between sexes, revealing that P. bifurca also exhibits complete X chromosome dosage compensation. We further identify 11 putative autosome-to-Y gene duplications, 5 of which show gene expression in guppy male germ cells.},
}
@article {pmid40829560,
year = {2025},
author = {McKnight, JC and Solms, B and Jensen, M and Turnbull, J and Balfour, S and Laagland, M and Bronkhorst, M and Lee, HJ and Kang, G and Lee, JY and Bell, A and Hastie, G and Ilardo, M},
title = {Diving behaviour and physiology of the Korean Haenyeo.},
journal = {Current biology : CB},
volume = {35},
number = {16},
pages = {R797-R798},
doi = {10.1016/j.cub.2025.06.066},
pmid = {40829560},
issn = {1879-0445},
mesh = {Adult ; Female ; Humans ; *Diving/physiology ; Republic of Korea ; *Breath Holding ; },
abstract = {There is a long history of breath-hold diving cultures in East Asia, with references in Japanese chronicles as early as the third century BC. Given evidence of genetic adaptations for phenotypes associated with enhanced diving capacity within such populations[1], it is likely they hold the most prodigious human diving abilities - abilities that may be akin to semi-aquatic mammals, and even some marine mammals. Yet, a dearth of fine-scale information exists on the combined natural diving behaviour and physiological responses within these diving populations. One such extraordinary population is the all-female Haenyeo. Here, we assess the fine-scale diving behaviours and physiological responses of these women during natural harvest diving. Our results show that Haenyeo divers demonstrate the highest proportions of time underwater of any humans, also exceeding those of semi-aquatic mammals and being comparable with some marine mammals. Additionally, they do not exhibit an overt cardiovascular depression, or 'dive response', classically associated with consummate diving mammals.},
}
@article {pmid40833038,
year = {2026},
author = {De Neef, E and Velásquez-Zapata, V and Gordon, ERL and Narva, K and Mc Cahon, P and Mézin, L and Lester, PJ and Romeis, J and Fletcher, S and Mitter, N and Devisetty, UK and Sridharan, K},
title = {A bioinformatic ecological risk assessment framework for externally applied double-stranded RNA-based biopesticides.},
journal = {Integrated environmental assessment and management},
volume = {22},
number = {1},
pages = {116-131},
doi = {10.1093/inteam/vjaf116},
pmid = {40833038},
issn = {1551-3793},
mesh = {*RNA, Double-Stranded/toxicity ; Risk Assessment/methods ; *Computational Biology/methods ; *Biological Control Agents/toxicity ; *Pest Control, Biological/methods ; Animals ; *Pesticides/toxicity ; },
abstract = {Double-stranded RNA (dsRNA)-based biopesticides are a promising new method of pest management. These biopesticides leverage the endogenous RNA interference pathway to selectively regulate expression of key genes involved in growth and development in pests, providing the potential to minimize harmful environmental effects by highly specific targeting. As dsRNA-based biopesticides are presented for regulatory review, evaluating potential off-target effects on nontarget organisms (NTOs) in a manner that may be unique to this novel sequence-specific mode of action is crucial. To address this, we propose here a bioinformatics framework for consideration of sequence-specific off-target effects in NTOs. This framework includes careful consideration of NTOs based on potential exposure and susceptibility and recommends standardizing analyses to search for 21-nucleotide stretches of perfect identity and 80% overall identity between the dsRNA and off-target transcripts. We recommend a three-pronged approach to ensure a comprehensive risk assessment: (a) phylogenetic analysis of gene orthologs that defines the taxonomic scope of sequence similarity, (b) broad searches of large databases to identify potential unexpected similarity in distantly related species, and (c) full transcriptome analyses in NTO species of particular concern for a thorough understanding of all potential hazards. Finally, we recommend considering the results of bioinformatic analyses in the context of risk characterization, which means considering likely exposure to the dsRNA-based pesticide and potential susceptibility or barriers to dsRNA uptake. This approach enables a robust ecological risk assessment for dsRNA-based biopesticides and a regulatory path forward for this promising new pest management tool.},
}
@article {pmid40838167,
year = {2025},
author = {Boyes, D and Fletcher, C and Phillips, D and Sivess, L and Boyes, C and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Tortix moth, Archips podanus (Scopoli, 1763).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {189},
pmid = {40838167},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Archips podanus (Tortix moth; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 549.00 megabases. Most of the assembly (99.72%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.45 kilobases.},
}
@article {pmid40840423,
year = {2025},
author = {Bozeman, BB and Matson, PG and DeRolph, CR and DeNeale, ST},
title = {The HydroBio Dataset: a new data resource for evaluating existing and potential hydropower capacity and freshwater biodiversity in the conterminous United States.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127042},
doi = {10.1016/j.jenvman.2025.127042},
pmid = {40840423},
issn = {1095-8630},
mesh = {*Biodiversity ; Conservation of Natural Resources ; Ecosystem ; *Fresh Water ; *Power Plants ; Rivers ; United States ; *Datasets as Topic ; },
abstract = {Hydropower is a critical source of affordable and reliable electricity and energy system stability services in the United States. Opportunities to expand US hydropower production include retrofitting existing non-powered dams to produce power, retrofitting existing hydropower dams to improve efficiency or increase capacity, or constructing new hydropower infrastructure on currently unregulated river reaches. We created the HydroBio Dataset, which summarizes existing and potential hydropower capacity and freshwater biodiversity at the sub-basin scale in the conterminous US to contextualize existing and potential grid contributions with the freshwater ecosystems in which dams are situated. We demonstrate a use-case of this dataset by rescaling and comparing potential non-powered dam nominal capacity to rarity-threat-weighted freshwater species richness for sub-basins where both types of data exist. On average, normalized freshwater biodiversity exceeded normalized potential non-powered dam nominal capacity in these sub-basins. Potential non-powered dam nominal capacity was concentrated in sub-basins in the Upper Mississippi and Ohio hydrologic regions while freshwater biodiversity was concentrated in the South Atlantic-Gulf, Ohio, and Tennessee hydrologic regions. Additionally, non-powered dams and existing hydropower dams are located in sub-basins with similar indices of freshwater biodiversity. The HydroBio Dataset adds an additional ecological dimension of context to our understanding of current and potential future US hydropower capabilities and is a valuable decision support tool for stakeholders tasked with balancing gains in services to the US power grid with the public and environmental benefits of freshwater ecosystems.},
}
@article {pmid40840460,
year = {2025},
author = {Carlozzi, NE and Troost, J and Lombard, WL and Miner, JA and Graves, CM and Choi, SW and Wu, Z and Sen, S and Sander, AM},
title = {Completion and Compliance Rates for an Intensive mHealth Study Design to Promote Self-Awareness and Self-Care Among Care Partners of Individuals With Traumatic Brain Injury: Secondary Analysis of a Randomized Controlled Trial.},
journal = {JMIR mHealth and uHealth},
volume = {13},
number = {},
pages = {e73772},
pmid = {40840460},
issn = {2291-5222},
support = {K24 HL156896/HL/NHLBI NIH HHS/United States ; R01 HL146354/HL/NHLBI NIH HHS/United States ; R01 NR013658/NR/NINR NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Awareness ; *Brain Injuries, Traumatic/psychology/therapy ; *Caregivers/psychology/statistics &amp; numerical data ; Mobile Applications/statistics &amp; numerical data/standards ; *Patient Compliance/statistics &amp; numerical data/psychology ; *Self Care/methods/psychology/standards/statistics &amp; numerical data ; Surveys and Questionnaires ; Telemedicine/standards/statistics &amp; numerical data ; *Treatment Adherence and Compliance/statistics &amp; numerical data/psychology ; Secondary Data Analysis ; },
abstract = {BACKGROUND: Compliance rates for mobile health (mHealth) studies that involve intensive study designs are highly variable. Both person- and study-specific factors likely contribute to this variability. We were interested in understanding the impact that care partner characteristics and demographics have on study engagement, given that engagement is critical to the success of mHealth interventions.<br><br>OBJECTIVE: The primary objective of this report was to analyze the overall and component-specific completion and compliance rates for an intensive 6-month mHealth intervention (CareQOL app) designed to promote self-awareness and self-care among care partners of individuals with traumatic brain injury.<br><br>METHODS: This randomized controlled trial was designed to test the CareQOL app, an mHealth app designed to promote care partner self-awareness (through self-monitoring) and self-care (through personalized self-care push notifications). The study design consisted of a baseline assessment, a 6-month home-monitoring period that included 3 daily ecological momentary assessment (EMA) questions, monthly patient-reported outcome (PRO) surveys, continuous activity and sleep monitoring using a Fitbit, and 2 follow-up PRO surveys at 3 and 6 months posthome monitoring. Three participants withdrew prior to the initiation of the home-monitoring period, resulting in a final analytical sample size of 254. All participants had access to a self-monitoring dashboard (CareQOL app) that included graphical displays of the daily survey scores, as well as daily steps and sleep data from the Fitbit.<br><br>RESULTS: Overall compliance for the different aspects of the study was high. On average, the full-sample daily EMA PRO completion rate was 84% (SD 19%), Fitbit-based step count compliance was 90% (SD 21%), and Fitbit-based sleep duration compliance was 75% (SD 32%); there was no difference between the study arms for daily EMA PROs and Fitbit compliance rates. Completion rates for monthly and follow-up PRO surveys were even higher, with average end-of-month completion rates ranging from 97% to 100%, and follow-up completion rates of 95% for both time points. Again, these rates did not differ by study arm. The data were represented by 3 engagement groups: high-compliance-all data; high-compliance-PROs and steps only; and moderate PRO compliance-low Fitbit compliance. Group membership was predicted by both race (P<.001) and relationship to the care recipient (P=.001), but not by the other person-specific variables.<br><br>CONCLUSIONS: The compliance rates for this intensive study design are consistent, but at the high end, with what has been reported previously in the literature for studies with shorter time durations. Except for race and relationship to the care recipient, person-specific factors did not appear to be significantly associated with the engagement group. As such, we anticipate that the high compliance rates observed in this study are likely due to several study-specific design elements that were used to encourage study engagement.},
}
@article {pmid40840863,
year = {2025},
author = {Zong, Z and Sun, X and Chen, J and Yu, Y and Ni, Z and Wang, Y},
title = {Identification of the full-length GbERD7 gene family in Gossypium barbadense and functional analysis of the role of the GbERD7g gene in drought and salt tolerance.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {360},
number = {},
pages = {112715},
doi = {10.1016/j.plantsci.2025.112715},
pmid = {40840863},
issn = {1873-2259},
mesh = {*Gossypium/genetics/physiology ; Plant Proteins/genetics ; *Salt Tolerance/genetics/physiology ; Droughts ; Dehydration/genetics/metabolism ; *Stress, Physiological/genetics/physiology ; Computational Biology ; Genes, Plant ; *Acclimatization/genetics/physiology ; Sodium Chloride ; Polyethylene Glycols ; Hot Temperature ; Malondialdehyde/metabolism ; },
abstract = {ERD (early response to dehydration) genes are promptly upregulated under dehydration stress and are pivotal in plant development. Nonetheless, the precise impact of the ERD7 gene on the response of cotton to abiotic stress remains unclear. The physical and chemical characteristics, gene architecture, gene collinearity, and transcriptomic profiles were examined. Using bioinformatics techniques, we investigated the evolutionary relationships among the genes within the GbERD7 gene family of sea island cotton. The GbERD7 genes are unevenly distributed across the seven chromosomes of sea island cotton, with multiple gene duplications. The GbERD7 gene family was subjected to phylogenetic analysis, leading to the classification of its members into the SENA and SENB subfamilies. The expression of the GbERD7 genes was investigated in relation to heat, low-temperature, salt (NaCl), and polyethylene glycol (PEG) treatments. Some genes presented greater expression in specific organs and different periods of fiber development. The functional role of GbERD7g was subsequently investigated using molecular biological techniques. GbERD7g exhibited pronounced expression in sea island cotton leaves and was upregulated following exposure to PEG, NaCl, and ABA. Subcellular localization studies revealed that the GbERD7g protein is located within the nucleus as well as the plasma membrane of the cell. When the GbERD7g gene was silenced under drought and salt stress, the sea island cotton plants were significantly less resistant to drought and salinity and exhibited lower survival than the control plants. The proline levels, catalase activity, and superoxide dismutase activity were reduced, and the malondialdehyde and hydrogen peroxide levels were elevated. In addition, compared with those in the control plants, the expression of all three stress-responsive genes, namely, GbRD22, GbRD26, and GbCDPK1, was significantly lower in the mutant plants.},
}
@article {pmid40841201,
year = {2025},
author = {Sena, AVDS and Telles, L and Melo, PHM and Salomão, SL and Uzeda, TS and Pereira Lima, BL and Kratky, L and Mooney, DP and Bustorff-Silva, J},
title = {The management of cryptorchidism in Brazil: An ecological overview.},
journal = {Journal of pediatric urology},
volume = {21},
number = {6},
pages = {1813-1819},
doi = {10.1016/j.jpurol.2025.07.025},
pmid = {40841201},
issn = {1873-4898},
mesh = {Humans ; *Cryptorchidism/surgery/epidemiology ; Male ; Brazil/epidemiology ; *COVID-19/epidemiology ; Child ; Child, Preschool ; *Orchiopexy/statistics &amp; numerical data ; Infant ; Adolescent ; Infant, Newborn ; },
abstract = {INTRODUCTION: Cryptorchidism refers to the extra-scrotal location of the testicle and is the most common male genital anomaly. Although the recommended age ranges for both hormonal and surgical treatments are well-established, within the Brazilian Unified Health System (SUS), children with cryptorchidism undergo surgery at varying ages across the country. As a time-sensitive procedure, delayed orchidopexy has consequences such as an increased risk of infertility or even testicular cancer. Correlating data on cryptorchidism treatment in SUS with geographic and socioeconomic indicators may help to understand how a population's profile influences the public healthcare system. This study explores the potential relationship between the age at which orchiopexy is performed and the quality of public healthcare services in Brazil while also assessing the impact of the COVID-19 pandemic on this surgery's backlog.<br><br>METHODS: To achieve this, we collected data from the Department of Informatics of the Brazilian Public Health System (DATASUS) and indicators provided by the Brazilian Institute of Geography (IBGE) and the Institute for Applied Economic Research (IPEA). We cataloged and compiled the data for comprehensive analysis.<br><br>RESULTS: Between 2008 and 2022, 94,237 orchiopexies were performed in SUS in patients aged 0-15. Nationwide, this represents only 47.6 % of the expected procedures, ranging from 22.75 % in the North to 68.18 % in the South. The proportion of surgeries performed before age 2 was very low, ranging from 12 % in the North and Northeast to 24 % in the South. Most orchiopexies in Brazil were performed after the age of five. The COVID-19 pandemic significantly worsened this situation, causing a 44.45 % decline in surgeries in 2020 compared to 2019, disproportionately affecting all age groups and exacerbating the backlog of surgeries.<br><br>CONCLUSION: Our study indicates that many children with cryptorchidism remain undiagnosed or receive delayed treatment. The COVID-19 pandemic further worsened this scenario, temporarily reducing the number of operations. These findings underscore the urgent need for comprehensive public policies to improve healthcare access and prevent complications associated with untreated cryptorchism.},
}
@article {pmid40841825,
year = {2025},
author = {De Rovere, F and Mastropierro, M and Jungclaus, JH and Khodri, M and Rubino, A and Zanchettin, D},
title = {Future Atlantification of the European Arctic limited under sustained global warming.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30802},
pmid = {40841825},
issn = {2045-2322},
support = {2022CCRN7R, "ATTRACTION - ATlantificaTion dRiven by polAr-subpolar ConnecTIONs", CUP: H53D23001550006//Next-GenerationEU - PNRR - M.4 C.2, INVESTIMENTO 1.1 - PRIN22/ ; },
abstract = {Atlantification is an ongoing oceanic phenomenon characterised by the expansion of the typical Atlantic domain towards the Arctic, driving rapid oceanic and ecological changes in the European Arctic. Using reanalyses and a multi-model ensemble of unperturbed and transient preindustrial, historical and future-scenario simulations, this study shows that modern Atlantification possibly initiated in the late nineteenth century, preceded by several "Arctification" episodes in the preindustrial millennium. In the historical period, Atlantification and pan-Arctic warming superposed constructively to drive upper-ocean warming and salinification in the Barents Sea. Modern Atlantification is projected to continue in the next few decades, fully revealing its exceptional character in the context of the past millennium. However, Atlantification halts during the second half of the twenty-first century, decoupling from pan-Arctic warming. The northward expansion of the Atlantic domain is hindered by the onset of a damping mechanism where the Atlantic-Arctic density gradient increases progressively, which sustains a countercurrent by baroclinic adjustment pushing the Arctic polar front southward. As the evolution of this density gradient is intertwined with the retreat of the sea-ice edge, a late-summer ice-free Barents Sea may mark the end of modern Atlantification.},
}
@article {pmid40843346,
year = {2025},
author = {Xia, K and Hu, Y and Cai, S and Lin, M and Lu, M and Lu, H and Ye, Y and Lin, F and Gao, L and Xia, Q and Tian, R and Lin, W and Xie, L and Tan, D and Lu, Y and Lin, X and Yang, X and Zhong, L and Xu, L and Zhang, Z and Wang, L and Ren, J and Xu, H},
title = {GastritisMIL: An interpretable deep learning model for the comprehensive histological assessment of chronic gastritis.},
journal = {Patterns (New York, N.Y.)},
volume = {6},
number = {8},
pages = {101286},
pmid = {40843346},
issn = {2666-3899},
abstract = {The comprehensive histological assessment of chronic gastritis is imperative for guiding endoscopic follow-up strategies and surveillance of early-stage gastric cancer, yet rapid and objective assessment remains challenging in clinical workflows. We propose a powerful deep learning model (GastritisMIL) to effectively identify pathological alterations on H&amp;E-stained biopsy slides, thereby expediting pathologists' evaluation and improving decision-making regarding follow-up intervals. We have trained and tested GastritisMIL by using retrospective data from 2,744 patients and evaluated discriminative performance across three medical centers (467 patients). GastritisMIL attained areas under the receiver operating curve greater than 0.971 in four tasks (inflammation, activity, atrophy, and intestinal metaplasia) and superior performance comparable to that of two senior pathologists. Specifically, interpretable attention heatmaps generated by GastritisMIL effectively assist junior pathologists in locating suspicious lesion regions across the entire field and minimizing missed diagnosis risk. Moreover, the high generalizability of this developed model across multiple external cohorts demonstrates its potential translational value.},
}
@article {pmid40846910,
year = {2025},
author = {Lu, M and Wang, S and Zhou, Y and Wang, X and Su, H and Gong, Y and De, J},
title = {Multi-omics profiling reveals single-seed mutants of Ephedra saxatilis as dominant variants in high-altitude Xizang.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1118},
pmid = {40846910},
issn = {1471-2229},
support = {32060087//National Natural Science Foundation of China/ ; 32060087//National Natural Science Foundation of China/ ; 32060087//National Natural Science Foundation of China/ ; XZ202402ZD0005//Science and Technology Projects of Xizang Autonomous Region, China/ ; XZ202402ZD0005//Science and Technology Projects of Xizang Autonomous Region, China/ ; XZ202501ZY0101//Xizang Autonomous Region Science and Technology Department project, China/ ; XZ202501ZY0101//Xizang Autonomous Region Science and Technology Department project, China/ ; },
mesh = {*Altitude ; *Ephedra/genetics/metabolism/physiology ; Germination/genetics ; *Seeds/genetics/metabolism/ultrastructure/physiology ; Tibet ; Mutation ; Metabolomics ; Transcriptome ; Multiomics ; },
abstract = {Ephedra species, important Tibetan medicinal plants, are widely distributed across the Qinghai-Tibet Plateau at altitudes of 2700-5000 m. Their adaptation to high-altitude environments, such as low temperatures, strong UV radiation and low oxygen, is still poorly understood. This study investigated the morphological, metabolic, and genetic mechanisms underlying the reproductive advantage of a unique single-seed variant observed in high-germination-rate Ephedra species. Seeds from six Ephedra species were collected for germination assays and electron microscopic analysis. Results showed that E. saxatilis, E. intermedia, and E. monosperma exhibited significantly higher germination rates (Germination rates > 65%) and predominantly produced single-seed variants, while others mainly produced double seeds. Analysis of burr and fold numbers of phenotypic traits showed a significant positive correlation with germination rates. Time-course metabolomics analysis identified 762 KEGG annotated metabolites, and revealed E. saxatilis as the dominant species due to its faster metabolic rate, particularly simulated high-altitude conditions. Absolute hormone quantification highlighted the single-seed variant of E. saxatilis as the dominant type, with ABA content peaking in the shed seed coat. ABA exhibited antagonistic interactions with 2MeScZR, SA, IAA, GA7, IPR, and t-CA, suggesting a complex hormonal regulation network. Co-expression network analysis integrating transcriptome and hormone data predicted 23 key genes regulating seed germination adaptation. This study provides novel insights into the ecological and evolutionary significance of single-seed variation in high-altitude adaptation. The findings have potential applications in high-altitude plant breeding, conservation, and sustainable utilization of Ephedra species. Future research should focus on the genetic basis of single-seed variation and its role in other high-altitude plant species.},
}
@article {pmid40848298,
year = {2025},
author = {Jia, Y and Chen, L and Jin, LN and Zhang, P and Chen, L and Fan, C and Liu, H and Ji, Y and Li, D and Chen, J},
title = {Environmentally Relevant Levels of Ozone Enhance Klebsiella pneumoniae Pulmonary Colonization and Cross-Organ Translocation.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {35},
pages = {18424-18439},
doi = {10.1021/acs.est.5c02782},
pmid = {40848298},
issn = {1520-5851},
mesh = {*Klebsiella pneumoniae ; *Ozone/toxicity ; Animals ; Lung/microbiology ; Mice ; Klebsiella Infections ; },
abstract = {Ozone (O3) is a major global air pollutant. Recent epidemiological studies have suggested links between O3 exposure and outbreaks of infectious diseases. However, whether environmentally relevant levels of O3 exacerbate the colonization and infection of airborne pathogens remains unclear. This study demonstrated that exposure to environmentally relevant levels of O3 (0.15 and 0.60 ppm) significantly enhanced pulmonary colonization of low-dose Klebsiella pneumoniae (1 × 10[3] CFU/mouse) in mice, which failed to colonize without O3 exposure. Unexpectedly, in vivo and in vitro coculture experiments with BEAS-2B bronchial epithelial cells demonstrated that O3 exposure also enhanced the ability of K. pneumoniae to penetrate the lung-blood barrier, thereby inducing bacteremia that spread to the liver and caused severe liver injury. O3 exposure reduced the proportions of T cells, B cells, and macrophages in the lungs and altered the expression of key pulmonary genes (Tlr4, Il-18, Traf6, and Tgf-β1) involved in resisting K. pneumoniae colonization. In addition, lipid peroxidation product MDA in plasma acted as a mediator in the signal transmission along the lung-liver axis. This study underscores the critical role of air pollutants in pathogen colonization and infection, emphasizing the urgent need to address air quality to mitigate respiratory health risks.},
}
@article {pmid40851520,
year = {2025},
author = {Naseri, C and Hill, AM and Xu, D and Francis-Coad, J and Vaz, S and Garswood, L and Meakes, R and Umbella, J and O'Brien, G and Starling, T and Weselman, T},
title = {What influences older people to join a community hub to engage in healthy ageing programs? An exploratory study.},
journal = {Australasian journal on ageing},
volume = {44},
number = {3},
pages = {e70079},
pmid = {40851520},
issn = {1741-6612},
support = {//Royal Perth Hospital Medical Research Foundation/ ; //Australian Association of Gerontology Research Trust/ ; },
mesh = {Humans ; *Healthy Aging/psychology ; Aged ; Female ; Male ; Western Australia ; Aged, 80 and over ; Age Factors ; Middle Aged ; *Health Services for the Aged/organization &amp; administration ; Social Support ; Social Networking ; Interviews as Topic ; *Community Health Services ; *Health Promotion ; Qualitative Research ; *Community Networks/organization &amp; administration ; },
abstract = {OBJECTIVES: Most people seek to stay connected to their community as they age; this has been a major focus in the development of innovative community programs in Australia. This study aimed to explore what influences older people to join a community hub to engage in healthy ageing programs.<br><br>METHODS: Semi-structured interviews (n&#x2009;=&#x2009;29) were conducted during an Open Day in early 2023 at an urban community hub in Western Australia, followed by telephone interviews (n&#x2009;=&#x2009;9) of a purposive sample of older individuals, community hub facilitators and coordinators of national community hubs. Analysis used a socio-ecological framework.<br><br>RESULTS: Deductive content analysis identified social prescribing as an overarching influencer for older people to join and engage in healthy ageing programs and main themes of (i) supporting community hub facilitators to harness community assets, (ii) link-supports provided to older members by paid community hub concierges triggered positive outcomes at individual and community levels, (iii) online and in-person social and physical healthy ageing activities tailored to member interests and (iv) nurturing social networks and reciprocity between members sustained engagement in healthy ageing activities.<br><br>CONCLUSIONS: The dynamic process of social prescribing was a central influencer for older adults to engage in healthy ageing programs, and the social network perpetuated through community hubs was an immeasurable social investment that boosted the resilience of intergenerational populations in Australian communities. Policy support is required for communities to meet the challenge of being responsive to the needs of members who seek to remain independent as they age in place.},
}
@article {pmid40854001,
year = {2025},
author = {Khajehnejad, M and García, J and Meyer, B},
title = {Age polyethism can emerge from social learning: A game-theoretic investigation.},
journal = {PLoS computational biology},
volume = {21},
number = {8},
pages = {e1013415},
pmid = {40854001},
issn = {1553-7358},
mesh = {Animals ; *Social Learning/physiology ; *Game Theory ; Behavior, Animal/physiology ; Social Behavior ; Computational Biology ; Models, Biological ; },
abstract = {Age-polyethism-the age-based allocation of tasks in social insect colonies-is a key feature of division of labour. While its hormonal underpinnings have been studied extensively, the behavioural and environmental mechanisms driving age-polyethism remain poorly understood, especially under ecological stress. We present a novel modelling framework that integrates social learning with task-related environmental feedback to explain the emergence and breakdown of age-polyethism. We develop two models: a Social Learning (SL) model, in which individuals adapt task preferences by copying similar peers, and a Stimulus-Response Threshold Social Learning (SRT-SL) model, which extends this framework by incorporating task-related dynamic stimuli and response thresholds that regulate collective task demand. Our models demonstrate that age-polyethism can emerge from simple social imitation processes, without the need for fixed hormonal schedules. We show that under increasing environmental pressure (e.g., resource scarcity), age-polyethism collapses as younger individuals are forced into tasks typically handled by older workers. Importantly, we find that age-polyethism does not necessarily optimize immediate colony efficiency; instead, it appears to reflect a trade-off between environmental constraints and behavioural coordination. These findings provide a mechanistic and ecologically grounded explanation for empirical observations linking environmental stress to dysfunctional division of labour and colony collapse.},
}
@article {pmid40855644,
year = {2025},
author = {Panneerselvam, K and Tiwari, KK and Licata, L and Panni, S and Ricard-Blum, S and Balu, S and Huget, S and Medina Reyes, JJ and Ragueneau, E and Perfetto, L and Meldal, B and Orchard, S and Hermjakob, H},
title = {Mining Alzheimer's Interactomes, Macromolecular Complexes and Pathways for Drug Discovery.},
journal = {Proteomics},
volume = {25},
number = {21-22},
pages = {102-150},
pmid = {40855644},
issn = {1615-9861},
support = {203149/WT_/Wellcome Trust/United Kingdom ; 218294/WT_/Wellcome Trust/United Kingdom ; U24 HG012198/AOU_/AOU NIH HHS/United States ; U24 HG012198/HG/NHGRI NIH HHS/United States ; 3367/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //BBSRC - National Science Foundation/Directorate for Biological Sciences/ ; 212925/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; //European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) core funding/ ; },
mesh = {*Alzheimer Disease/metabolism/genetics/drug therapy ; Humans ; *Drug Discovery/methods ; Amyloid beta-Protein Precursor/metabolism/genetics ; Protein Interaction Maps ; MicroRNAs/metabolism/genetics ; Data Mining ; Mutation ; },
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder that leads to dementia. Many cases are diagnosed annually and there is no currently available cure. Understanding the underlying disease biology of AD through the study of molecular networks, particularly by mapping clinical variants to tissue-specific interactomes and regulatory macromolecular assemblies, offers a promising avenue to elucidate altered disease pathways. In this study, we applied differential interactome analysis using a manually curated AD dataset to identify how disease-associated mutations alter both transient and stable protein interactions. By focussing on variant-specific associations detected in brain-relevant tissues, we mapped disruptions in stable macromolecular assemblies and performed Reactome enrichment analysis to uncover perturbed pathways unique to each variant. Additionally, we explored therapeutic insights through the analysis of amyloid precursor protein (APP) physical interactors, identifying potential intervention points that influence amyloidogenic processing. Complementing protein-level data, we integrated microRNA (miRNA)-mediated regulatory interactions, revealing an additional layer of posttranscriptional control over key AD genes. Together, this multilayered strategy provides a framework for precision therapeutics in AD.},
}
@article {pmid40858627,
year = {2025},
author = {Ge, S and Li, J and Ma, H and Sánchez-Bermúdez, M and Wu, S and Lv, Q and Guo, F and Dong, J and Ma, G and Li, QQ and Satheesh, V and Lei, M},
title = {A cis-natural antisense RNA regulates alternative polyadenylation of SlSPX5 under Pi starvation in tomato.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7981},
pmid = {40858627},
issn = {2041-1723},
support = {U24A20385//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32270344//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2025JCXK01//Hangzhou Normal University (HNU)/ ; 2347540//National Science Foundation (NSF)/ ; },
mesh = {*Polyadenylation/genetics ; *Solanum lycopersicum/genetics/metabolism ; Gene Expression Regulation, Plant ; *RNA, Antisense/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Phosphates/deficiency/metabolism ; RNA, Messenger/metabolism/genetics ; Transcription Factors/metabolism/genetics ; RNA Polymerase II/metabolism ; },
abstract = {Alternative polyadenylation (APA) generates transcript diversity by producing mRNA isoforms with distinct 3' ends. Despite the critical roles that APA plays in various biological processes, the mechanisms regulating APA in response to stresses have remained poorly understood in plants. Here, we perform comprehensive analysis of APA in tomato, and focus on a phosphate (Pi)- regulated APA gene SlSPX5, encoding a putative Pi sensor protein. SlSPX5 interacts with and sequesters the transcription factor SlPHL1 in the cytosol, thereby inhibiting the expression of Pi starvation inducible genes. We discover that a cis-natural antisense RNA (cis-NAT) is activated from SlSPX5 to promote its proximal polyadenylation under Pi-depleted conditions. The transcription of this cis-NAT induces RNA Polymerase II pausing, generating Ser2 phosphorylation signals that recruit polyadenylation machinery to the 5' end of SlSPX5. Our findings demonstrate that a cis-NAT regulates APA of its cognate gene in response to Pi starvation.},
}
@article {pmid40862956,
year = {2025},
author = {Yoon, HJ and Seo, JH and Shin, SH and Abdelhamid, MAA and Pack, SP},
title = {Bioinformation and Monitoring Technology for Environmental DNA Analysis: A Review.},
journal = {Biosensors},
volume = {15},
number = {8},
pages = {},
pmid = {40862956},
issn = {2079-6374},
support = {RS-2021NR060107//the National Research Foundation of Korea funded by the Ministry of Science and ICT/ ; RS-2022-NR074662//the National Research Foundation of Korea funded by the Ministry of Education/ ; },
mesh = {*Environmental Monitoring/methods ; *DNA, Environmental/analysis ; *Computational Biology ; Ecosystem ; },
abstract = {Environmental DNA (eDNA) analysis has emerged as a transformative tool in environmental monitoring, enabling non-invasive detection of species and microbial communities across diverse ecosystems. This study systematically reviews the role of bioinformation technology in eDNA analysis, focusing on methodologies and applications across air, soil, groundwater, sediment, and aquatic environments. Advances in molecular biology, high-throughput sequencing, bioinformatics tools, and field-deployable detection systems have significantly improved eDNA detection sensitivity, allowing for early identification of invasive species, monitoring ecosystem health, and tracking pollutant degradation processes. Airborne eDNA monitoring has demonstrated potential for assessing microbial shifts due to air pollution and tracking pathogen transmission. In terrestrial environments, eDNA facilitates soil and groundwater pollution assessments and enhances understanding of biodegradation processes. In aquatic ecosystems, eDNA serves as a powerful tool for biodiversity assessment, invasive species monitoring, and wastewater-based epidemiology. Despite its growing applicability, challenges remain, including DNA degradation, contamination risks, and standardization of sampling protocols. Future research should focus on integrating eDNA data with remote sensing, machine learning, and ecological modeling to enhance predictive environmental monitoring frameworks. As technological advancements continue, eDNA-based approaches are poised to revolutionize environmental assessment, conservation strategies, and public health surveillance.},
}
@article {pmid40872272,
year = {2025},
author = {Bugingo, C and Infantino, A and Okello, P and Perez-Hernandez, O and Petrović, K and Turatsinze, AN and Moparthi, S},
title = {From Morphology to Multi-Omics: A New Age of Fusarium Research.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
pmid = {40872272},
issn = {2076-0817},
mesh = {*Fusarium/genetics/classification/pathogenicity ; Genomics/methods ; *Plant Diseases/microbiology ; Mycotoxins ; Humans ; Crops, Agricultural/microbiology ; Host-Pathogen Interactions ; *Fusariosis/microbiology ; Multiomics ; },
abstract = {The Fusarium genus includes some of the most economically and ecologically impactful fungal pathogens affecting global agriculture and human health. Over the past 15 years, rapid advances in molecular biology, genomics, and diagnostic technologies have reshaped our understanding of Fusarium taxonomy, host-pathogen dynamics, mycotoxin biosynthesis, and disease management. This review synthesizes key developments in these areas, focusing on agriculturally important Fusarium species complexes such as the Fusarium oxysporum species complex (FOSC), Fusarium graminearum species complex (FGSC), and a discussion on emerging lineages such as Neocosmospora. We explore recent shifts in species delimitation, functional genomics, and the molecular architecture of pathogenicity. In addition, we examine the global burden of Fusarium-induced mycotoxins by examining their prevalence in three of the world's most widely consumed staple crops: maize, wheat, and rice. Last, we also evaluate contemporary management strategies, including molecular diagnostics, host resistance, and integrated disease control, positioning this review as a roadmap for future research and practical solutions in Fusarium-related disease and mycotoxin management. By weaving together morphological insights and cutting-edge multi-omics tools, this review captures the transition into a new era of Fusarium research where integrated, high-resolution approaches are transforming diagnosis, classification, and management.},
}
@article {pmid40874445,
year = {2026},
author = {Liang, M and Pan, W and Feng, Z and Cui, Y and Su, H and Guo, C and He, J},
title = {IVCDB: a comprehensive database of iridoviruses for epidemiology, genetic evolution, and disease management.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D790-D800},
pmid = {40874445},
issn = {1362-4962},
support = {2022YFE0203900//National Key Research and Development Program of China/ ; CARS-46//Earmarked Fund for China Agriculture Research System/ ; 32473201//National Natural Science Foundation of China/ ; 2022B1111030001//Special Project for Research and Development in Key areas of Guangdong Province/ ; 2024B1212040007//Science and Technology Planning Project of Guangdong Province/ ; 2023A1515110395//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
mesh = {Animals ; *Iridovirus/genetics/classification/pathogenicity ; Phylogeny ; Genome, Viral ; *Databases, Genetic ; *Evolution, Molecular ; *DNA Virus Infections/epidemiology/virology/veterinary ; Viral Proteins/genetics ; },
abstract = {Iridoviruses, a globally distributed group of double-stranded DNA viruses, exhibit remarkable environmental adaptability and host-switching capabilities, infecting over 200 species of ectothermic vertebrates and invertebrates, including reptiles, amphibians, fish, crustaceans, and insects. These characteristics have led to substantial economic losses in global aquaculture and population declines in amphibian and invertebrate species. Despite accumulating genomic data, research progress remains constrained by three critical limitations: fragmented multidimensional data resources, ambiguous taxonomic levels, and insufficient spatiotemporal visualization tools. To address these challenges, we present the Iridovirus Comprehensive Database (IVCDB; https://www.iridovirus.com/), a comprehensive database consolidating multidimensional iridovirus-related data. IVCDB provides curated comprehensive information on 310 geographically distinct virus isolates complemented by an interactive geospatial visualization system and a nonredundant protein database containing 4378 viral proteins, including 162 core genes/proteins, derived from a standardized genome annotation pipeline. This database also contains phylogenetic relationships across various viral taxonomic levels within the family Iridoviridaeanda viral genome collinearity analysis tool, facilitating taxonomic analysis and supporting novel species identification. Furthermore, IVCDB integrates an application-oriented knowledge base including host range data, experimentally validated vaccines, and field-deployable visual detection methods. IVCDB offers substantial support for disease control and host conservation while addressing systemic bottlenecks in viral cross-species transmission research.},
}
@article {pmid40885803,
year = {2025},
author = {Simonienko, K and Jermakowicz, E and Szefer, P and Wróbel, K and Suprunowicz, U and Cwalina, U and Kostro-Ambroziak, A},
title = {The impact of urban flower meadows on the well-being of city dwellers provides hints for planning biophilic green spaces.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31981},
pmid = {40885803},
issn = {2045-2322},
support = {SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; },
mesh = {Humans ; Female ; Male ; *Flowers/growth &amp; development ; Adult ; Middle Aged ; Cities ; *Urban Population ; Emotions ; Young Adult ; Aged ; },
abstract = {Living surrounded by greenery has a relaxing effect and reduces physiological and psychological symptoms of stress. In view of the exponential growth of the urban population and disconnection with nature, supporting the physical and mental health of city dwellers is a huge challenge nowadays. In this context, urban flower meadows (UFMs), a relatively new management strategy cultivated in many cities, can be a very important component of urban greenery, which support human well-being. We investigated the emotional reception of UFMs, taking into account the features of different types of UFMs and the socio-demographic characteristics of respondents. Our research shows that urban flower meadows evoke positive emotions regardless of the age, gender and place of origin of respondents. While some structural variables of UFMs, particularly the proportion of green in relation to other colours, the representation of various flower colours, the proportion of yellow flowers, and the presence of alien plant species-influence people's perception. Fewer colours and the absence of alien plant species tend to shift perception towards less positive emotions. The dominance of yellow flowers evokes positive emotions. These results are helpful for the further planning of UFMs to better reinforce the well-being of all city dwellers.},
}
@article {pmid40886889,
year = {2025},
author = {Furxhi, I and Perucca, M and Baldi, G and Dami, V and Cioni, A and Koivisto, AJ and Bengalli, R and Mantecca, P and Motta, G and Carriere, M and Kose, O and Nicosia, A and Ravegnani, F and Burrueco-Subirà, D and Candalija, A and Cabellos, J and Vázquez-Campos, S and Lahive, E and Eagles, E and de Ipiña, JL and Oliveira, J and Conin, P and Zanoni, I and Brigliadori, A and Faccani, L and Syed, T and Haq, EU and O'Mahony, C and Serantoni, M and Blosi, M and Exner, T and Costa, A},
title = {The fruits of data shepherding: A collection of open FAIR datasets for titanium dioxide coated photocatalytic surfaces.},
journal = {NanoImpact},
volume = {39},
number = {},
pages = {100583},
doi = {10.1016/j.impact.2025.100583},
pmid = {40886889},
issn = {2452-0748},
mesh = {*Titanium/chemistry ; Catalysis ; *Databases, Factual ; Surface Properties ; *Nanostructures/chemistry ; Information Dissemination ; },
abstract = {This paper presents a large-scale collaborative effort within a multi-partner consortium, to systematically structure, curate, and openly share data in alignment with the FAIR principles. The data result from a case study of titanium dioxide (TiO2) nanomaterials (NMs) for photocatalytic depolluting surfaces, produced via various spray coating techniques under the Safe and Sustainable by Design (SSbD) approach. The data are publicly available through a dedicated Zenodo community (https://zenodo.org/communities/asina/records), comprising of individual records that separately host the data and the corresponding metadata. Each dataset is systematically named to reflect its context beginning with "ASINA dataset," followed by i) the relevant life cycle stage (LCS) from synthesis to end-of-life, ii) the SSbD dimension (i.e., functionality, safety, and environmental aspects), and iii) the assessed features (e.g., physicochemical properties, hazard evaluation, functionality assessment) facilitating searchability. The data files include "descriptors" excel tab, which is a harmonized version derived from primary data for visualization, data integration and future modeling applications. Metadata are provided in separate records and include detailed information such as contributor name and affiliations, experimental protocols, instrumentation, dictionary definitions, ontologies, and licensing terms. The data and metadata files are mutually paired in Zenodo using related identifiers, where each data file includes the DOI of its corresponding metadata file, and vice versa. In total, 43 interlinked records are provided capturing the case study, offering structured and machine-actionable resources that support modeling, data integration and harmonization efforts within the nanosafety and nanoinformatics communities. This effort was coordinated through dedicated data shepherding, which enabled trust-building, metadata alignment, and consistent FAIR implementation across partners.},
}
@article {pmid40887834,
year = {2025},
author = {Han, Y and Yu, J and Liu, X and Zhang, F and Huang, X and Lu, Y and Zhang, W and Zimmerman, R and Rudich, Y and Li, Q and Chen, J and Chen, Y and Jin, LN},
title = {Generation of More Potent Components at Higher Temperatures Offsets Toxicity Reduction despite Reduced Mass Emissions during Biomass Burning.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {36},
pages = {19244-19256},
doi = {10.1021/acs.est.5c05710},
pmid = {40887834},
issn = {1520-5851},
mesh = {*Biomass ; Humans ; Temperature ; Aerosols ; Air Pollutants/toxicity ; Reactive Oxygen Species ; },
abstract = {Biomass burning organic aerosols (BBOAs) represent a major global health hazard. Their toxicity varies significantly due to the diversity of combustion conditions, which shape mixtures of components with differing toxic potency. We quantified component-specific contributions to intracellular reactive oxygen species generation in human bronchial epithelial cells exposed to BBOAs produced under controlled combustion conditions. Elevated combustion temperatures substantially reduced organic carbon (OC) mass emissions (by 20-fold) but resulted in a more modest reduction in OC toxicity emissions (by 5-fold). The toxicity emission reduction was primarily attributed to water-extractable OC (WOC), while methanol-extractable OC (MOC) limited this effect. The reduced emission of WOC toxicity was driven by the decreased mass emission of polar compounds such as methoxylates, as the toxicity per unit mass of WOC showed negligible changes across temperatures. In contrast, the toxicity per unit mass of MOC increased 10-fold from low to high temperatures, partially due to the formation of more potent aromatic derivatives, despite their smaller mass contribution. These findings underscore the importance of identifying key toxicity drivers to guide targeted source apportionment and refine strategies for reducing toxic emissions.},
}
@article {pmid40888850,
year = {2026},
author = {Chasapi, MN and Chasapi, IN and Aplakidou, E and Baltoumas, FA and Karatzas, E and Iliopoulos, I and Stravopodis, DJ and Emiris, IZ and Buluç, A and Georgakopoulos-Soares, I and Kyrpides, NC and Pavlopoulos, GA},
title = {metagRoot: a comprehensive database of protein families associated with plant root microbiomes.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D1733-D1742},
pmid = {40888850},
issn = {1362-4962},
support = {23592//Hellenic Foundation for Research and Innovation/ ; //European Union's Horizon 2020/ ; 945405//Marie Sk&#x142;odowska-Curie/ ; //Penn State College of Medicine/ ; //Huck Innovative and Transformational Seed/ ; //Huck Institutes of the Life Sciences/ ; 16718-PRPFOR//Hellenic Foundation for Research and Innovation/ ; TAEDR-0539180//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//U.S. Department of Energy Office of Science/ ; //Nikos Kyrpides JGI-LBNL/ ; },
mesh = {*Plant Roots/microbiology ; *Microbiota/genetics ; *Databases, Protein ; Metagenomics ; Molecular Sequence Annotation ; Metagenome ; },
abstract = {The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.metagroot.org.},
}
@article {pmid40889349,
year = {2025},
author = {Moraitou, M and Richards, JL and Bolyos, C and Saliari, K and Gilissen, E and Timmons, Z and Kitchener, AC and Pauwels, OSG and Sabin, R and Kokkini, P and Portela Miguez, R and Guschanski, K},
title = {Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70039},
pmid = {40889349},
issn = {1755-0998},
support = {2019-00275//Svenska Forskningsr&#xe5;det Formas/ ; },
mesh = {*Metagenomics/methods ; *Dental Calculus/microbiology ; *Mammals/microbiology/classification ; Animals ; *Microbiota ; *Gene Library ; Metagenome ; Computational Biology ; },
abstract = {Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.},
}
@article {pmid40892020,
year = {2025},
author = {Ng, S and Brown, JP and Straub, L and Bateman, B and Gray, KJ and Huybrechts, KF and Hernández-Díaz, S},
title = {Leveraging Health Insurance Claims Data to Complement the Centers for Disease Control and Prevention Surveillance System for Birth Defects.},
journal = {Birth defects research},
volume = {117},
number = {9},
pages = {e2523},
pmid = {40892020},
issn = {2472-1727},
support = {R01 HD097778/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; United States/epidemiology ; *Congenital Abnormalities/epidemiology ; Female ; Prevalence ; Centers for Disease Control and Prevention, U.S. ; Infant, Newborn ; *Insurance, Health/statistics &amp; numerical data ; Pregnancy ; Databases, Factual ; Male ; Insurance Claim Review ; Population Surveillance/methods ; Infant ; Adult ; },
abstract = {BACKGROUND: Birth defect surveillance can help identify temporo-spatial clusters and teratogenic signals to inform subsequent investigations or interventions. In the United States, state surveillance systems exist but collect limited information, prompting a complementary use of health insurance claims data to describe national birth defect prevalence trends and investigate signals.<br><br>METHODS: The Merative MarketScan Commercial Claims and Encounters (MarketScan) database was used to identify liveborn infants from 2016 to 2022, with linkage to maternal health care records during pregnancy. Birth defects were identified using ICD-10-CM codes recorded in the first 3&#x2009;months of life, and prevalence estimates with 95% confidence intervals were generated for birth defect categories and select birth defects.<br><br>RESULTS: The study population included 943,855 liveborn infants. From 2016 to 2022, the prevalence increased for cardiac, central nervous system, ear, genital, urinary, musculoskeletal, and limb birth defect categories. Stable prevalence over the study period was observed for chromosomal, oral cleft, respiratory, gastrointestinal, vascular, and eye defects. For specific defects, we observed an increased prevalence of both ankyloglossia and lip-tie over the study period and a transient higher prevalence of omphalocele over 2017 and 2018. Within genital birth defects, we observed increasing prevalence trends for congenital malformations of the penis, while hypospadias and cryptorchidism remained relatively stable.<br><br>CONCLUSION: Health care utilization databases can complement existing surveillance systems by generating, confirming, or refuting signals based on ecological trends or clusters. The availability of patient information in claims databases can allow for further investigation of signals to inform birth defect etiology.},
}
@article {pmid40892908,
year = {2025},
author = {Araujo, G and Lurgi, M},
title = {Mutualism provides a basis for biodiversity in eco-evolutionary community assembly.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013402},
pmid = {40892908},
issn = {1553-7358},
mesh = {*Biodiversity ; *Symbiosis/physiology ; *Biological Evolution ; *Models, Biological ; *Ecosystem ; Computational Biology ; Animals ; Computer Simulation ; },
abstract = {Unveiling the ecological and evolutionary mechanisms underpinning the assembly of stable and complex ecosystems is a main focus of community ecology. Ecological theory predicts the necessity of structural constraints on the network of species interactions to allow for growth and persistence of multi-species communities. However, the mechanisms behind their emergence are not well understood. An understanding of how the coexistence of diverse species interaction types could influence the development of complexity and how a persistent composition of interactions could arise in nature is needed. Using an eco-evolutionary model, we investigate the assembly of complex species interaction networks with multiple interaction types and its consequences for ecosystem stability. Our results show that highly mutualistic communities promote complex and stable network configurations, thus resulting in a positive complexity-stability relationship. We show that evolution by speciation enhances the emergence of such conditions compared to a purely ecological assembly scenario of repeated invasions by migrating species. Furthermore, communities evolved in isolation promote a disproportionately higher complexity and a larger diversity of outcomes. Our results produce valuable theoretical insight into the mechanisms behind the emergence of ecological complexity and into the roles of mutualism and speciation in community formation.},
}
@article {pmid40892914,
year = {2025},
author = {Rowntree, LC and Allen, LF and Hagen, RR and McQuilten, HA and Quadeer, AA and Chaurasia, P and Kaewpreedee, P and Lee, KWK and Cohen, CA and Petersen, J and Littler, DR and Habel, JR and Zhang, W and Cheng, SMS and Chan, KKP and Kwok, JSY and Leung, KSM and Wu, JT and Lee, CK and Davies, J and Pannaraj, PS and Kaity Allen, E and Thomas, PG and Tosif, S and Crawford, NW and Lappas, M and Thevarajan, I and Lewin, SR and Kent, SJ and Juno, JA and Bond, KA and Williamson, DA and Holmes, NE and Smibert, OC and Gordon, CL and Trubiano, JA and Kotsimbos, TC and Cheng, AC and Efstathiou, C and Turtle, L and Thwaites, RS and Brightling, CE and , and Rossjohn, J and McKay, MR and Tian, J and Liu, WJ and Gao, GF and Xu, J and Sonehara, K and Ishii, KJ and Namkoong, H and Okada, Y and Peiris, M and Hui, DSC and Poon, LLM and Doherty, PC and Nguyen, THO and Valkenburg, SA and Kedzierska, K},
title = {HLA-B*15:01-positive severe COVID-19 patients lack CD8[+] T cell pools with highly expanded public clonotypes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {36},
pages = {e2503145122},
pmid = {40892914},
issn = {1091-6490},
support = {U01 AI144616/AI/NIAID NIH HHS/United States ; 1173871//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Humans ; *COVID-19/immunology/genetics ; *CD8-Positive T-Lymphocytes/immunology ; *SARS-CoV-2/immunology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Spike Glycoprotein, Coronavirus/immunology ; },
abstract = {Understanding host factors driving asymptomatic versus severe disease outcomes is of key importance if we are to control emerging and re-emerging viral infections. HLA-B*15:01 has been associated with asymptomatic SARS-CoV-2 infection in nonhospitalized individuals of European ancestry, with protective immunity attributed to preexisting cross-reactive CD8[+] T-cells directed against HLA-B*15:01-restricted Spike-derived S919-927 peptide (B15/S919[+]CD8[+] T-cells). However, fundamental questions remained on the abundance and clonotypic nature of CD8[+] T-cell responses in HLA-B*15:01-positive patients who succumbed to life-threatening COVID-19. Here, we analyzed B15/S919[+]CD8[+] T-cell responses in COVID-19 patients from independent HLA-typed COVID-19 patient cohorts across three continents, Australia, Asia and Europe. We assessed B15/S919[+]CD8[+] T-cells in COVID-19 patients across disease outcomes ranging from asymptomatic to hospitalized critical illness. We found that severe/critical COVID-19 patients mounted B15/S919[+]CD8[+] T-cell responses lacking a highly expanded key public B15/S919[+]CD8[+] T-cell receptor (TCR; TRAV9-2/TRBV7-2) which recurred across multiple individuals in COVID-19 patients with a mild disease. Instead, B15/S919[+]CD8[+] T-cell responses in life-threatening disease had a prevalence of an alternate TCR clonotypic motif (TRAV38-2/DV8/TRBV20-1), potentially contributing, at least in part, to why B15/S919[+]CD8[+] T-cells in severe COVID-19 patients were less protective. Interestingly, the frequency, memory phenotype, and activation profiles of circulating B15/S919[+]CD8[+] T-cells did not differ across disease severity. Moreover, B15/S919[+]CD8[+] T-cells were better maintained into convalescence compared to other SARS-CoV-2-specificities. Our study thus provides evidence on the differential nature of the TCR clonal repertoire in 22.37% of HLA-B*15:01-positive COVID-19 patients who developed severe or critical disease in our cohorts, comparing to HLA-B*15:01-expressing individuals with mild COVID-19.},
}
@article {pmid40894108,
year = {2025},
author = {de Goeij, JM and Mueller, B and Achlatis, M and Campana, S and Hudspith, M and Kornder, NA and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The scaffold-level genome sequence of an encrusting sponge, Halisarca caerulea Vacelet &amp; Donadey, 1987, and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {344},
pmid = {40894108},
issn = {2398-502X},
abstract = {We present a scaffold-level genome assembly from a Halisarca caerulea specimen (encrusting sponge; Porifera; Demospongiae; Chondrillida; Halisarcidae). The genome sequence is 195.70 megabases in span. The mitochondrial genome has also been assembled and is 19.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,722 protein-coding genes. The metagenome of the specimen was also assembled and four binned bacterial genomes related to the relevant sponge symbiont clades Alphaproteobacteria bacterium GM7ARS4 and Gammaproteobacteria bacterium AqS2 ((Tethybacterales) were identified.},
}
@article {pmid40894110,
year = {2025},
author = {Whiteford, S and , and , and , and , and , },
title = {The genome sequence of the virgin bagworm, Luffia ferchaultella (Stephens, 1850).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {108},
pmid = {40894110},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Luffia ferchaultella (the Virgin Bagworm; Arthropoda; Insecta; Lepidoptera; Psychidae). The genome sequence spans 645.30 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,416 protein-coding genes.},
}
@article {pmid40897756,
year = {2025},
author = {Zhang, F and Liang, Y and Hu, Z},
title = {Research on the inversion model of soil moisture content based on a novel ReMPDI index in mining areas.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32330},
pmid = {40897756},
issn = {2045-2322},
support = {N25XQD015//Basic Research Operations in Higher Education/ ; },
abstract = {The excavation of subterranean coal has led to a plethora of ecological and environmental issues, which seriously restrict the sustainable development of society. As one of the important physical indicators of soil, soil moisture content needs to be scientific, real-time, and comprehensively monitored. Due to the low efficiency of manual measurement, methods based on remote sensing data inversion have received widespread attention and in-depth research in recent years. In this study, a new ReMPDI index (Red edge Modified Perpendicular Drought Index) is constructed, and six retrieval models of soil moisture content based on machine learning algorithms are compared and analyzed, and the accuracy is verified by measured sampling data. The following conclusions were obtained: (1) Using the red edge band as the horizontal axis, and the near infrared band NIR as the vertical axis is the optimal spatial band combination of spectral characteristics for constructing soil lines; (2) The determination coefficient (R2) of ReMPDI index based on REdge-NIR spectral feature space and adding vegetation cover factor is the highest, which is-0. 798, and there is a significant correlation, which is better than MPDI and PDI index; (3) The model inversion accuracy of the RF is significantly higher than SVM, BPNN, PLSR, CNN, and RBFNN, with an error of only 9.52% compared to the measured results. The results of this study can provide a theoretical basis and technical support for the fine monitoring of surface soil moisture content on a large scale in mining areas.},
}
@article {pmid40897761,
year = {2025},
author = {Rodal, M and Luyssaert, S and Balzarolo, M and Campioli, M},
title = {A global database of net primary production of terrestrial ecosystems.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1534},
pmid = {40897761},
issn = {2052-4463},
mesh = {*Ecosystem ; *Databases, Factual ; *Biomass ; Soil ; Forests ; Grassland ; },
abstract = {Net primary production (NPP) is a fundamental measure of biomass production in ecosystems. In terrestrial biomes, NPP lacks standard measuring protocols and is difficult to measure. Thus, despite decades of research efforts, NPP data are limited and heterogenous. Moreover, there continues to be a lack of global NPP databases containing harmonized estimates for all major ecosystem types and which account for both above- and belowground production. We present a global database containing records for both above- and belowground production for forests, grasslands, arid shrublands, northern peatlands and tundra at 456 sites. The records are reported as annual production (g m[-2]yr[-1]). The NPP data are complemented with detailed site and methodological information, including a method specific estimate for the measurement uncertainty, as well as ancillary data on climatic conditions, soil fertility and management status. This database provides a basis for comparative studies on local, regional and global scales, and may serve as an important benchmarking dataset for the development of DGVMs.},
}
@article {pmid40899150,
year = {2025},
author = {Ürel, H and Benassou, S and Marti, H and Reska, T and Sauerborn, E and Pinheiro Alves De Souza, Y and Perlas, A and Rayo, E and Biggel, M and Kesselheim, S and Borel, N and Martin, EJ and Venegas, CB and Schloter, M and Schröder, K and Mittelstrass, J and Prospero, S and Ferguson, JM and Urban, L},
title = {Nanopore- and AI-empowered microbial viability inference.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40899150},
issn = {2047-217X},
support = {//Helmholtz Principal Investigator Grant/ ; HIDSS-006//Munich School for Data Science/ ; BB/M010996/1//BBSRC/ ; //STFC Food Network+ Scoping Grant/ ; //Helmholtz Association Initiative and Networking Fund/ ; 1336/2004//Vontobel-Stiftung/ ; //University of Zurich/ ; },
mesh = {*Microbial Viability ; *Nanopores ; *Artificial Intelligence ; *Nanopore Sequencing/methods ; Metagenomics/methods ; Escherichia coli/genetics ; Computational Biology/methods ; },
abstract = {BACKGROUND: The ability to differentiate between viable and dead microorganisms in metagenomic data is crucial for various microbial inferences, ranging from assessing ecosystem functions of environmental microbiomes to inferring the virulence of potential pathogens from metagenomic analysis. Established viability-resolved genomic approaches are labor-intensive as well as biased and lacking in sensitivity.<br><br>RESULTS: We here introduce a new fully computational framework that leverages nanopore sequencing technology to assess microbial viability directly from freely available nanopore signal data. Our approach utilizes deep neural networks to learn features from such raw nanopore signal data that can distinguish DNA from viable and dead microorganisms in a controlled experimental setting of UV-induced Escherichia cell death. The application of explainable artificial intelligence (AI) tools then allows us to pinpoint the signal patterns in the nanopore raw data that allow the model to make viability predictions at high accuracy. Using the model predictions as well as explainable AI, we show that our framework can be leveraged in a real-world application to estimate the viability of obligate intracellular Chlamydia, where traditional culture-based methods suffer from inherently high false-negative rates. This application shows that our viability model captures predictive patterns in the nanopore signal that can be utilized to predict viability across taxonomic boundaries. We finally show the limits of our model's generalizability through antibiotic exposure of a simple mock microbial community, where a new model specific to the killing method had to be trained to obtain accurate viability predictions.<br><br>CONCLUSIONS: While the potential of our computational framework's generalizability and applicability to metagenomic studies needs to be assessed in more detail, we here demonstrate for the first time the analysis of freely available nanopore signal data to infer the viability of microorganisms, with many potential applications in environmental, veterinary, and clinical settings.},
}
@article {pmid40900722,
year = {2025},
author = {Jones, OE and Beckett, H and Abraham, AJ and Makunga, NP and Midgley, GF},
title = {Endozoochory by Black Rhinoceroses Enhances Germination of a Key Arid Savanna Tree Species.},
journal = {Ecology and evolution},
volume = {15},
number = {9},
pages = {e71951},
pmid = {40900722},
issn = {2045-7758},
abstract = {Megaherbivores are typically regarded as agents of top-down control, limiting woody encroachment through destructive foraging. Yet they also possess traits and engage in behaviours that facilitate plant success. For example, megaherbivores can act as effective endozoochorous seed dispersers. However, studies on facilitative roles are heavily biased towards the African savanna elephant (Loxodonta africana), with little attention paid to other species or to effects beyond germination, across early ontogenic stages. The African black rhinoceros (Diceros bicornis), an obligate browser that exhibits frugivory and defecates in fixed dung middens, may offer ecologically distinct dispersal services. We conducted controlled experiments to test whether black rhino interactions with Vachellia erioloba, a leguminous tree of ecological importance in arid savannas, enhance germination, early seedling development or seedling resilience to herbivory. Germination was compared among dung-derived seeds, untreated controls and chemically scarified seeds. Seedling growth was assessed in dung versus sand and under simulated black rhino herbivory. Dung-derived seeds germinated most steadily and produced the highest cumulative germination (+40%) over the longest period (+13 days). Growth trials revealed that dung substrates did not enhance initial growth. Rather, seedlings being older conferred greater resilience to biomass loss than exposure to different substrate conditions. Our results provide the first experimental evidence of an apparent mutualism between black rhino and V. erioloba. This relationship is not driven by enhanced seedling development through legacy effects of gut passage, nor by dung conditions, as expected. Instead, it stems from gut passage effects on germination. In addition to increasing total germination, gut passage accelerates germination and extends the germination period, producing a seedling cohort with both older individuals and greater age variation-a population structure that may enhance persistence beyond the germination bottleneck. This research supports a more nuanced view of megaherbivores as both disturbance agents and mutualists in arid ecosystems.},
}
@article {pmid40904111,
year = {2025},
author = {Kupczok, A and Gavriilidou, A and Paulitz, E and Guerrero-García, L and Baumdicker, F},
title = {Gene co-occurrence and its association with phage infectivity in bacterial pangenomes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1934},
pages = {20240070},
pmid = {40904111},
issn = {1471-2970},
support = {//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Bacteriophages/physiology ; *Bacteria/genetics/virology ; *Genome, Bacterial ; Host Specificity ; *Genes, Bacterial ; Phylogeny ; },
abstract = {Phages infect bacteria and have recently re-emerged as a promising strategy to combat bacterial infections. However, there is a lack of methods to predict whether and why a particular phage can or cannot infect a bacterial strain based on their genome sequences. Understanding the complex interactions between phages and their bacterial hosts is thus of considerable interest. We recently developed Goldfinder, a phylogenetic method to discover gene co-occurrences across bacterial pangenomes. Here, we expand Goldfinder to infer which gene presences or absences influence bacterial sensitivity to phages. By integrating a bacterial pangenome with an experimentally determined host range matrix, we infer associations between phage infectivity and the presence of accessory genes in bacterial pangenomes. The presented approach can be applied to predict bacterial genes that potentially enable phage infection, bacterial genes that prevent phage infection, and potential interactions between particular bacterial and phage accessory genes. Finally, the predicted interactions are clustered and visualized with the software Cytoscape. Here, we present a method to identify candidate genes within the pool of mobile accessory genes that may contribute to phage-host interactions. This approach will help to set up follow-up experiments and to understand the complex interactions between phages and bacteria.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.},
}
@article {pmid40904416,
year = {2025},
author = {Hutchinson, F and Crowley, LM and Broad, GR and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Brown Moss-moth, Bryotropha terrella (Denis &amp; Schiffermüller), 1775.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {310},
pmid = {40904416},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Bryotropha terrella (Brown Moss-moth; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence has a total length of 756.35 megabases. Most of the assembly (99.62%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.29 kilobases.},
}
@article {pmid40904542,
year = {2025},
author = {Zhang, L and Xiong, A and Li, C and Liu, X and Zhang, X and Gong, S and Yan, M and Qin, X and Liu, Y and Hu, Z and Fang, JK and Duan, H and Liu, H and Chan, LL and Jin, LN},
title = {Ecological pattern of microalgal communities and associated risks in coastal ecosystems.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf109},
pmid = {40904542},
issn = {2730-6151},
abstract = {Eukaryotic harmful and toxic microalgae, along with their derived toxins, pose significant threats to seafood safety, human health, and marine ecosystems. Here, we developed a novel full-length 18S rRNA database for harmful and toxic microalgae and combined metabarcoding with toxin analyses to investigate the ecological patterns of phytoplankton communities and the underlying mechanism of associated toxic microalgae risks. We identified 79 harmful and toxic species in Hong Kong's coastal waters, with dinoflagellates and diatoms representing the majority of toxic and harmful taxa, respectively. Distinct seasonal succession patterns were observed in phytoplankton communities, driven by different ecological assembly processes. Deterministic processes dominated during the dry season, correlating with elevated toxic microalgae abundance and temperature stress. Seasonal shifts in temperature played a pivotal role in shaping toxic algal communities. The dominance of dinoflagellates, particularly Alexandrium spp., Dinophysis spp., Prorocentrum spp., and Karenia spp., during the dry season was consistent with elevated toxin concentrations. These toxin profiles highlight the heightened risk in a warming climate, where the prevalence and impacts of toxigenic algae are expected to intensify.},
}
@article {pmid40904625,
year = {2025},
author = {Hébert-Dufresne, L and Ahn, YY and Allard, A and Colizza, V and Crothers, JW and Dodds, PS and Galesic, M and Ghanbarnejad, F and Gravel, D and Hammond, RA and Lerman, K and Lovato, J and Openshaw, JJ and Redner, S and Scarpino, SV and St-Onge, G and Tangherlini, TR and Young, JG},
title = {One pathogen does not an epidemic make: a review of interacting contagions, diseases, beliefs, and stories.},
journal = {Npj complexity},
volume = {2},
number = {1},
pages = {26},
pmid = {40904625},
issn = {2731-8753},
support = {K23 AI175660/AI/NIAID NIH HHS/United States ; P20 GM125498/GM/NIGMS NIH HHS/United States ; },
abstract = {From pathogens and computer viruses to genes and memes, contagion models have found widespread utility across the natural and social sciences. Despite their success and breadth of adoption, the approach and structure of these models remain surprisingly siloed by field. Given the siloed nature of their development and widespread use, one persistent assumption is that a given contagion can be studied in isolation, independently from what else might be spreading in the population. In reality, countless contagions of biological and social nature interact within hosts (interacting with existing beliefs, or the immune system) and across hosts (interacting in the environment, or affecting transmission mechanisms). Additionally, from a modeling perspective, we know that relaxing these assumptions has profound effects on the physics and translational implications of the models. Here, we review mechanisms for interactions in social and biological contagions, as well as the models and frameworks developed to include these interactions in the study of the contagions. We highlight existing problems related to the inference of interactions and to the scalability of mathematical models and identify promising avenues of future inquiries. In doing so, we highlight the need for interdisciplinary efforts under a unified science of contagions and for removing a common dichotomy between social and biological contagions.},
}
@article {pmid40906521,
year = {2025},
author = {Selten, G and Gómez-Repollés, A and Lamouche, F and Radutoiu, S and de Jonge, R},
title = {SyFi: generating and using sequence fingerprints to distinguish SynCom isolates.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
pmid = {40906521},
issn = {2057-5858},
mesh = {*Microbiota/genetics ; *Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; *DNA Fingerprinting/methods ; Sequence Analysis, DNA/methods ; },
abstract = {The plant root microbiome is a complex community shaped by interactions among bacteria, the plant host and the environment. Synthetic community (SynCom) experiments help disentangle these interactions by inoculating host plants with a representative set of culturable microbial isolates from the natural root microbiome. Studying these simplified communities provides valuable insights into microbiome assembly and function. However, as SynComs become increasingly complex to better represent natural communities, bioinformatics challenges arise. Specifically, accurately identifying and quantifying SynCom members based on, for example, 16S rRNA amplicon sequencing becomes more difficult due to the high similarity of the target amplicon, limiting downstream interpretations. Here, we present SynCom Fingerprinting (SyFi), a bioinformatics workflow designed to improve the resolution and accuracy of SynCom member identification. SyFi consists of three modules: the first module constructs a genomic fingerprint for each SynCom member based on its genome sequence and, when available, raw genomic reads, accounting for both copy number and sequence variation in the target gene. The second module extracts the target region from this genomic fingerprint to create a secondary fingerprint linked to the relevant amplicon sequence. The third module uses these fingerprints as a reference to perform pseudoalignment-based quantification of SynCom member abundance from amplicon sequencing reads. We demonstrate that SyFi outperforms standard amplicon analysis by leveraging natural intragenomic variation, enabling more precise differentiation of closely related SynCom members. As a result, SyFi enhances the reliability of microbiome experiments using complex SynComs, which more accurately reflect natural communities. This improved resolution is essential for advancing our understanding of the root microbiome and its impact on plant health and productivity in agricultural and ecological settings. SyFi is available at https://github.com/adriangeerre/SyFi.},
}
@article {pmid40908443,
year = {2025},
author = {Kaplan, DM and Alvarez, SJA and Palitsky, R and Choi, H and Clifford, GD and Crozier, M and Dunlop, BW and Grant, GH and Greenleaf, MN and Johnson, LM and Maples-Keller, J and Levin-Aspenson, HF and Mascaro, JS and McDowall, A and Pozzo, NS and Raison, CL and Zarrabi, AJ and Rothbaum, BO and Lam, WA},
title = {Correction: Fabla: A voice-based ecological assessment method for securely collecting spoken responses to researcher questions.},
journal = {Behavior research methods},
volume = {57},
number = {10},
pages = {274},
doi = {10.3758/s13428-025-02818-9},
pmid = {40908443},
issn = {1554-3528},
}
@article {pmid40909344,
year = {2025},
author = {Polak, I and Stryiński, R and Paukszto, &#x141; and Jastrzębski, JP and Bogacka, I and Łopieńska-Biernat, E},
title = {Diversity, expression, and structural modeling of sugar transporters in Anisakis simplex s. s. L3 and L4 larvae: an in vitro and in silico study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1621051},
pmid = {40909344},
issn = {2235-2988},
mesh = {Animals ; Larva/genetics/metabolism ; *Anisakis/genetics/metabolism/growth &amp; development ; *Glucose Transport Proteins, Facilitative/genetics/metabolism/chemistry ; Computer Simulation ; Computational Biology ; Glucose/metabolism ; Phylogeny ; *Monosaccharide Transport Proteins/genetics/metabolism/chemistry ; Biological Transport ; *Helminth Proteins/genetics/metabolism/chemistry ; Gene Expression Profiling ; Models, Molecular ; },
abstract = {INTRODUCTION: Glucose transporter (GLUT) research in parasitic nematodes focuses on identifying and characterizing developmentally regulated isoforms, elucidating their regulatory and structural properties, and evaluating their potential as drug targets. While glucose transport mechanisms have been well characterized in the free-living nematode Caenorhabditis elegans, data on parasitic species remain limited. Anisakis simplex s. s., a parasitic nematode, relies on host-derived glucose to maintain energy metabolism. It is hypothesized that A. simplex s. s. utilizes specific glucose transporters to facilitate sugar uptake under varying nutritional conditions.<br><br>MATERIALS AND METHODS: In silico analysis identified five putative facilitated glucose transporter genes (fgt-1, fgt-2, fgt-3, fgt-5, fgt-9) and one Sugars Will Eventually be Exported Transporter (sweet-1) gene. The FGTs were classified as members of the solute carrier family 2 (SLC2), while sweet-1 belonged to the SWEET transporter family. Full-length cDNA sequences were obtained, and encoded proteins structurally characterized using bioinformatic modeling. Expression of transporter genes was assessed in A. simplex s. s. larvae at stages L3 and L4 cultured in vitro under different glucose concentrations and time points.<br><br>RESULTS: Structural and phylogenetic analyses revealed that fgt-1 and fgt-3 share high similarity with class I GLUTs found in nematodes and vertebrates. Gene expression profiling demonstrated differential regulation between larval stages. Most notably, FGT genes were stably expressed in L4 larvae, whereas in L3 larvae, gene activation was more variable and dependent on glucose concentration, showing a dynamic transcriptional response to nutrient levels. Sweet-1 was expressed in both stages, but its regulation differed over time and with glucose availability. Glucose supplementation altered trehalose and glycogen levels, and trehalase activity varied across stages and treatments, indicating stage-specific metabolic adaptation.<br><br>DISCUSSION: The observed transcriptional and biochemical differences between L3 and L4 larvae suggest a shift in glucose uptake mechanisms, from transcuticular absorption in L3 to intestinal glucose uptake in L4 following intestine activation. FGT1 and FGT3 are proposed as key facilitators of glucose uptake, with roles varying across developmental stages. These findings indicate that glucose transporters are regulated in response to changing environmental conditions and may represent targets for rational anthelmintic drug design.},
}
@article {pmid40910796,
year = {2025},
author = {Gaun, N and Pietroni, C and Martin-Bideguren, G and Lauritsen, J and Aizpurua, O and Fernandes, JM and Ferreira, E and Aubret, F and Sarraude, T and Perry, C and Wauters, L and Romeo, C and Spada, M and Tranquillo, C and Sutton, AO and Griesser, M and Warrington, MH and Pérez I de Lanuza, G and Abalos, J and Aguilar, P and de la Cruz, F and Juste, J and Alonso-Alonso, P and Groombridge, J and Louch, R and Ruhomaun, K and Henshaw, S and Cabido, C and Barrio, IG and Šunje, E and Hosner, P and Prates, I and While, GM and García-Roa, R and Uller, T and Feiner, N and Bonaccorso, E and Klein-Ipsen, P and Rotovnik, RM and Alberdi, A and Eisenhofer, R},
title = {The Earth Hologenome Initiative: Data Release 1.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40910796},
issn = {2047-217X},
support = {DNRF143//Danmarks Grundforskningsfond/ ; CF20-0460//Carlsbergfondet/ ; 101066225//HORIZON EUROPE Framework Programme/ ; PD/BD/150645/2020//Ag&#xea;ncia Regional para o Desenvolvimento da Investiga&#xe7;&#xe3;o, Tecnologia e Inova&#xe7;&#xe3;o/ ; 25925//Villum Fonden/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; Earth, Planet ; *Vertebrates/genetics/microbiology ; Databases, Genetic ; },
abstract = {BACKGROUND: The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from the systemic host-microbiota perspective, through the standardized generation and analysis of joint animal genomic and associated microbial metagenomic data.<br><br>RESULTS: The first data release of the EHI contains 968 shotgun DNA sequencing read files containing 5.2 TB of raw genomic and metagenomic data derived from 21 vertebrate species sampled across 12 countries, as well as 17,666 metagenome-assembled genomes reconstructed from these data.<br><br>CONCLUSIONS: The dataset can be used to address fundamental questions about host-microbiota interactions and will be available to the research community under the EHI data usage conditions.},
}
@article {pmid40911670,
year = {2025},
author = {Wan, N and Duan, Q and Cai, Z and Zhu, Z and Wang, J and Tian, Y and Shen, W and Li, B and Kuang, Z and Liang, X and Liu, S and An, X and Yang, X and Liu, X and Mao, L and Chen, J and Wang, Y and Feng, Z and Liu, W and Bu, Y and Nevo, E and Papa, R and Meyer, A and Liu, J and Li, K},
title = {Aplf/Dna2 variants drive chromosomal fission and accelerate speciation in zokors.},
journal = {Science advances},
volume = {11},
number = {36},
pages = {eadt2282},
pmid = {40911670},
issn = {2375-2548},
mesh = {Multiomics ; Chromosomes ; Animals ; *Rodentia/classification/genetics ; *DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics ; *DNA Helicases/genetics ; *Endodeoxyribonucleases/genetics ; Genome ; Molecular Sequence Annotation ; Synteny ; Genomic Structural Variation ; Genetic Speciation ; Genetics, Population ; Telomere ; Phylogeny ; Base Sequence ; Genetic Variation ; },
abstract = {Chromosomal fissions and fusions are common, yet the molecular mechanisms and implications in speciation remain poorly understood. Here, we confirm a fission event in one zokor species through multiple-omics and functional analyses. We traced this event to a mutation in a splicing enhancer of the DNA repair gene Aplf in the fission-bearing species, which caused exon skipping and produced a truncated protein that disrupted DNA repair. An intronic deletion in Dna2, known to facilitate neo-telomere formation when knocked out, reduced gene activity. These variants collectively drove chromosomal fission in this zokor species. The newly formed chromosome became fixed due to carrying essential genes and strong selective pressure. While geographic isolation likely initiated the divergence of this species and the sister one, the fission event and associated decline at the chromosome level in gene flow probably exacerbated the speciation process. Our work elucidates the genetic basis of chromosomal fission and underscores its role in speciation dynamics.},
}
@article {pmid40914230,
year = {2025},
author = {Xu, Y and Chevreul, K and Dindorf, C and Bismuth, &#xc9; and Carel, JC and Michel, M},
title = {Association of socioeconomic status and hospital efficiency in Type-1 diabetic patients with ketoacidosis or diabetic coma: a secondary data analysis comparing nation-wide paediatric and adult admissions in France.},
journal = {Diabetes research and clinical practice},
volume = {229},
number = {},
pages = {112450},
doi = {10.1016/j.diabres.2025.112450},
pmid = {40914230},
issn = {1872-8227},
mesh = {Humans ; France/epidemiology ; *Diabetes Mellitus, Type 1/complications/economics/epidemiology/therapy ; Adult ; Male ; Female ; *Diabetic Ketoacidosis/economics/epidemiology/therapy ; Child ; Adolescent ; Length of Stay/statistics &amp; numerical data/economics ; *Social Class ; Young Adult ; Middle Aged ; Child, Preschool ; *Diabetic Coma/economics/epidemiology/therapy ; *Hospitalization/statistics &amp; numerical data/economics ; Secondary Data Analysis ; },
abstract = {AIMS: To study the association between socioeconomic status (SES) and hospital efficiency in Type 1 diabetes mellitus patients admitted for ketoacidosis or diabetic coma in mainland France, overall and in adults versus children.<br><br>METHODS: An observational study was carried out using exhaustive national hospital discharge databases. It included all admissions discharged from 2013 to 2019. SES was assessed using an ecological measure divided into national quintiles, and efficiency by variations in patients' length of stay (LOS) compared to mean national LOS and a comparison of production costs and revenues. Multilevel multivariable analyses were carried out to study the association.<br><br>RESULTS: 67,100 admissions were included. Multivariable analyses found a significant association between efficiency outcomes, SES and age. Compared to other age groups, children under 5 had higher LOS than the national mean and incurred higher costs than what hospitals were paid regardless of SES. In adults, there was a significant interaction between SES and age group, leading to significantly increased LOS and costs in adults from intermediate and/or lower SES groups.<br><br>CONCLUSIONS: Current payment methods using diagnosis-related groups may not adequately reflect the burden of Type 1 diabetes mellitus patients admitted for ketoacidosis or diabetic coma on hospitals.},
}
@article {pmid40915583,
year = {2026},
author = {Zhang, Y and Wang, B and Hassan, M and Zhang, X},
title = {Biochar-calcium alginate composite immobilizing Pseudomonas sp. H6 for phosphate and ammonium recovery: Multi-omics insights and practical application evaluation.},
journal = {Bioresource technology},
volume = {439},
number = {},
pages = {133274},
doi = {10.1016/j.biortech.2025.133274},
pmid = {40915583},
issn = {1873-2976},
mesh = {*Alginates/chemistry ; *Charcoal/chemistry ; *Ammonium Compounds/isolation &amp; purification ; *Phosphates/isolation &amp; purification ; *Pseudomonas/metabolism ; Wastewater/chemistry ; Glucuronic Acid/chemistry ; Hexuronic Acids/chemistry ; Cells, Immobilized/metabolism ; Adsorption ; Water Purification/methods ; Biodegradation, Environmental ; Water Pollutants, Chemical/isolation &amp; purification ; Multiomics ; },
abstract = {Water eutrophication has emerged as a pervasive ecological challenge worldwide. To realize the resource utilization of waste and nutrients, a novel rape straw-derived biochar-calcium alginate composite (M-CA-RBC) immobilized Pseudomonas sp. H6 was synthesized to simultaneously remove phosphate (PO4[3-]) and ammonium (NH4[+]) from distillery wastewater. The removal performance of PO4[3-] and NH4[+] by M-CA-RBC were investigated. The removal mechanisms were explored by using different adsorption models combined with microbial degradation kinetics, analysis of dissolved organic matter components, electrochemical analysis, metagenomics, and metabolomics. The resource application potential of M-CA-RBC was evaluated. The results showed that M-CA-RBC had good removal performance for PO4[3-] (17.81 mg/g) and NH4[+] (25.78 mg/g). Surface precipitation, electrostatic attraction, Poly-P accumulation, microbial-induced calcium precipitation, and microbial assimilation were the main removal mechanisms of PO4[3-] by M-CA-RBC. The removal mechanisms of NH4[+] were micropore filling, ion exchange, electrostatic attraction, and heterotrophic nitrification-aerobic denitrification (HN-AD). M-CA-RBC had a good application potential in the practical distillery wastewater, with removal rates of PO4[3-] and NH4[+] reaching 88% and 65%, respectively. After adsorption saturation, M-CA-RBC exhibited good stability, which could be used as a slow-release fertilizer to promote the growth of mung beans. This study provides practical significance for the efficient removal and recovery of nitrogen and phosphorus in wastewater.},
}
@article {pmid40919732,
year = {2026},
author = {Milligan, PD and Rossiter, J and Zare, A and Palmer, TM and Lemboi, J and Mizell, GM and Mosiany, J and Riginos, C and Goheen, JR and Pringle, EG},
title = {Mutualism, herbivory, and invasive ants as seasonally dependent drivers of root surface area in a foundational savanna ant-plant.},
journal = {The New phytologist},
volume = {249},
number = {2},
pages = {777-791},
doi = {10.1111/nph.70553},
pmid = {40919732},
issn = {1469-8137},
support = {1556905//Division of Environmental Biology/ ; 1935498//Division of Environmental Biology/ ; 2010075//National Science Foundation Division of Biological Infrastructure/ ; },
mesh = {Animals ; *Acacia/growth &amp; development ; *Ants ; Convolutional Neural Networks ; Grassland ; *Herbivory ; *Introduced Species ; Mammals ; Models, Biological ; *Plant Roots/growth &amp; development ; Rain ; Seasons ; *Symbiosis ; *Myrmecophytes/growth &amp; development ; },
abstract = {Many plants are defended from herbivory by costly insect mutualists. Understanding positive associations between plants and mutualists requires a whole-plant perspective including roots. We hypothesized that root surface area increases with mutualist activity (to a saturation threshold) and recent rainfall but that this relationship shifts when herbivores are excluded. We also hypothesized that invasive ants limit root surface area and that mutualism breakdown driven by invaders blunts root responses to rainfall and herbivore exclusion. Using minirhizotrons (est. 2021), we surveyed root surface area of ant-acacias during a dry (2022) and then a wet (2023) season. Study plots either excluded or permitted vertebrate browsers, within a natural experiment comparing mutualist-defended ant-acacias to those invaded by a mutualism-disrupting ant. Root area increased with mutualist activity to a threshold, but this positive association was less apparent during rainy periods. Megabrowser exclusion increased overall root area but reduced the threshold for a positive association with mutualist activity and reduced the steepness of the root area-rainfall correlation. Ant-invaded acacias had smaller root areas that correlated less steeply with rainfall. Positive associations between insect defense and root area were thus contingent on rainfall, herbivory, and biotic invasion, drivers that are shifting under global change.},
}
@article {pmid40920239,
year = {2026},
author = {Kröger, K and Wiemes, K and Santosa, F and Böhner, H and Lax, H and Stolpe, S and Kowall, B and Stang, A},
title = {Prescription of lipid-lowering drugs and their association with hospitalization for ST-elevation myocardial infarction (STEMI) in Germany in 2010-2022.},
journal = {Clinical research in cardiology : official journal of the German Cardiac Society},
volume = {115},
number = {2},
pages = {313-321},
pmid = {40920239},
issn = {1861-0692},
mesh = {Humans ; Germany/epidemiology ; *ST Elevation Myocardial Infarction/epidemiology/therapy ; *Hospitalization/trends/statistics &amp; numerical data ; Male ; *Hypolipidemic Agents/therapeutic use ; Female ; Aged ; Middle Aged ; *Drug Prescriptions/statistics &amp; numerical data ; },
abstract = {OBJECTIVES: We investigated changes in lipid-lowering drug prescriptions in Germany as a whole and in the 16 federal states over the last 13 years and their association with hospitalization rates for acute myocardial infarction.<br><br>DESIGN: Ecological study.<br><br>SETTING: Nationwide German hospitalization, Diagnosis-Related Groups Statistic.<br><br>PATIENTS/PARTICIPANTS: German population in the years 2010 through 2022.<br><br>INTERVENTION: All prescriptions of lipid-lowering drugs in the years 2010 to 2022 by federal state in Germany.<br><br>MAIN OUTCOME MEASURES: Hospitalization rates for the treatment of transmural infarction per calendar year and federal state (STEMI&#x2009;=&#x2009;ST-elevation myocardial infarction).<br><br>RESULTS: The age-standardized prescription rates of lipid-lowering drugs per 1000 person-years increased from 77.4 in 2010 to 145.2 in 2022 (reference population: Germany 2011). Within the same period, the STEMI hospitalization rate per 100,000 person-years decreased from 143.7 to 100.1. Based on the prescription and hospitalization rates of the 16 federal states, it is shown that the STEMI hospitalization rate decreased the more the prescription rate of lipid-lowering drugs in a federal state increased over time (beta&#x2009;=&#x2009;0.38, 95% confidence interval&#x2009;-&#x2009;0.64;&#x2009;-&#x2009;0.12; adjusted explained variance 0.362).<br><br>CONCLUSION: Increasing prescription rates of lipid-lowering drugs have correlated with decreasing rates of hospitalized cases for STEMI in Germany in the last decade.},
}
@article {pmid40920446,
year = {2025},
author = {Jackson, K and Gabrielli, J and Colby, S and Wray, T and Janssen, T and Rogers, M and Delapaix, C},
title = {Real-Time Exposure to Alcohol Content in Digital Media in Adolescents: Protocol for a Multiburst Ecological Momentary Assessment Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e50649},
pmid = {40920446},
issn = {1929-0748},
support = {R01 AA027968/AA/NIAAA NIH HHS/United States ; },
mesh = {Humans ; Adolescent ; *Ecological Momentary Assessment ; Male ; Female ; *Social Media/statistics &amp; numerical data ; Prospective Studies ; *Alcohol Drinking/psychology ; *Adolescent Behavior/psychology ; Surveys and Questionnaires ; *Underage Drinking/psychology ; Digital Media ; },
abstract = {BACKGROUND: Digital media frequently contains positive portrayals of alcohol content, which has been shown to be associated with alcohol-related cognitions and behaviors. Because youth are heavy media consumers and have access to unsupervised, repeat viewing of media content on their personal mobile devices, it is critical to understand the frequency of encountering alcohol content in adolescents' daily lives and how adolescents engage with the content.<br><br>OBJECTIVE: This paper outlines the study protocol for examining adolescents' exposure to alcohol-related content in digital media within their natural environments.<br><br>METHODS: Adolescents (N=302; 31.8% boys, 16.2% nonbinary, 51.3% girls; 25.8% Asian, 3.6% American Indian, 21.5% Black, 4.6% other, 52% White, 25.8% Hispanic or Latinx; mean age 16.21, SD 0.77 y) enrolled in high school were recruited through social media to participate in a prospective study involving bursts of ecological momentary assessment (EMA) reports coupled with longer surveys. We conducted group orientation sessions via videoconference and online surveys, followed by a 21-day EMA period that included scheduled reports across 4 daily time blocks, as well as self-initiated reports on media exposure. Reports of alcohol content exposure included details about the platform, level of engagement, source characteristics, beliefs and perceived norms about the content, the viewing context, and whether the content was sponsored or branded. The participants submitted exposures to alcohol content as an image (screenshot or photo) or text description to be objectively coded. The participants completed a weekly online survey assessing alcohol use and related cognitions. EMA reports will be merged with coded image and text entries and with data from baseline, weekly, and follow-up surveys. Self-reported alcohol exposure will be explored descriptively, and differences in exposure tested across subgroups. Event-level data will be compared with random prompt data to examine differences at times of exposure versus nonexposure. Prospective associations between media alcohol content exposure and alcohol use will be explored over 1-week and 4-month time frames. Mediation of the association between media alcohol exposure and drinking will be tested to explore putative mechanisms.<br><br>RESULTS: EMA data collection took place from February 2022 to August 2023. Data management and preliminary analysis are ongoing. Preliminary data were disseminated through conference presentations in 2024-2025 and manuscripts are ongoing with full results anticipated to be published in 2025-2026.<br><br>CONCLUSIONS: By characterizing adolescents' real-world exposure to alcohol content in the media, the study provides critical information to develop and implement interventions to target youth behavior that are well suited to delivery via mobile devices. Next steps are to conduct focus groups to understand participants' lived experience of exposure to media alcohol content and reactions to proposed intervention targets. This study and subsequent qualitative work will launch a program of research to counter the effects of alcohol-related media exposure as experienced by adolescents in an effort to minimize underage alcohol involvement.<br><br>DERR1-10.2196/50649.},
}
@article {pmid40920559,
year = {2025},
author = {Abdugheni, R and Li, WJ},
title = {EzBioCloud 16S rRNA Gene Sequence Formatter: a Python-based sequence formatting tool for systematic microbiology.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.006890},
pmid = {40920559},
issn = {1466-5034},
mesh = {*RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Bacteria/classification/genetics ; *Software ; Sequence Analysis, DNA/methods ; *Computational Biology/methods ; },
abstract = {EzBioCloud is one of the practical reference databases and analytical platforms for systematic microbiology research. The EzBioCloud database provides convenient services in this regard, especially for performing sequence analysis using the 16S rRNA genes. However, '.fasta' files of 16S rRNA sequences obtained after the alignment in EzBioCloud need manual formatting for further analysis and phylogenetic tree construction, which is labourious and time-consuming. To address this issue, we have developed a Python-based tool, EzBioCloud 16S rRNA Gene Sequence Formatter (version 1.0), designed to assist in sequence formatting. Here, we report the development and application of the tool and present this tool publicly to support the researchers in the relevant field.},
}
@article {pmid40920814,
year = {2025},
author = {Bergman, DR and Jackson, T and Jain, HV and Norton, KA},
title = {An efficient and flexible framework for inferring global sensitivity of agent-based model parameters.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013427},
pmid = {40920814},
issn = {1553-7358},
support = {U01 CA243075/CA/NCI NIH HHS/United States ; },
mesh = {*Models, Biological ; Humans ; Computational Biology/methods ; Computer Simulation ; Cell Proliferation/physiology ; Algorithms ; Neoplasms/pathology ; Reproducibility of Results ; },
abstract = {Agent-based models (ABMs) have become essential tools for simulating complex biological, ecological, and social systems where emergent behaviors arise from the interactions among individual agents. Quantifying uncertainty through global sensitivity analysis is crucial for assessing the robustness and reliability of ABM predictions. However, most global sensitivity methods demand substantial computational resources, making them impractical for highly complex models. Here, we introduce SMoRe GloS (Surrogate Modeling for Recapitulating Global Sensitivity), a novel, computationally efficient method for performing global sensitivity analysis of ABMs. By leveraging explicitly formulated surrogate models, SMoRe GloS allows for comprehensive parameter space exploration and uncertainty quantification without sacrificing accuracy. We demonstrate our method's flexibility by applying it to two biological ABMs: a simple 2D in vitro cell proliferation model and a complex 3D vascular tumor growth model. Our results show that SMoRe GloS is compatible with simpler methods like the Morris one-at-a-time method, and more computationally intensive variance-based methods like eFAST. SMoRe GloS accurately recovered global sensitivity indices in each case while achieving substantial speedups, completing analyses in minutes. In contrast, direct implementation of eFAST amounted to several days of CPU time for the complex ABM. Remarkably, our method also estimates sensitivities for ABM parameters representing processes not explicitly included in the surrogate model, further enhancing its utility. By making global sensitivity analysis feasible for computationally expensive models, SMoRe GloS opens up new opportunities for uncertainty quantification in complex systems, allowing for more in depth exploration of model behavior, thereby increasing confidence in model predictions.},
}
@article {pmid40920894,
year = {2025},
author = {Kawam, B and Ostner, J and McElreath, R and Schülke, O and Redhead, D},
title = {A causal framework for the drivers of animal social network structure.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013370},
pmid = {40920894},
issn = {1553-7358},
mesh = {Animals ; Bayes Theorem ; *Behavior, Animal/physiology ; Computational Biology ; *Social Behavior ; Computer Simulation ; Models, Biological ; },
abstract = {A major goal of behavioural ecology is to explain how phenotypic and ecological factors shape the networks of social relationships that animals form with one another. This inferential task is notoriously challenging. The social networks of interest are generally not observed, but must be approximated from behavioural samples. Moreover, these data are highly dependent: the observed network edges correlate with one another, due to biological and sampling processes. Failing to account for the resulting uncertainty and biases can lead to dysfunctional statistical procedures, and thus to incorrect results. Here, we argue that these problems should be understood-and addressed-as problems of causal inference. For this purpose, we introduce a Bayesian causal modelling framework that explicitly defines the links between the target interaction network, its causes, and the data. We illustrate the mechanics of our framework with simulation studies and an empirical example. First, we encode causal effects of individual-, dyad-, and group-level features on social interactions using Directed Acyclic Graphs and Structural Causal Models. These quantities are the objects of inquiry, our estimands. Second, we develop estimators for these effects-namely, Bayesian multilevel extensions of the Social Relations Model. Third, we recover the structural parameters of interest, map statistical estimates to the underlying causal structures, and compute causal estimates from the joint posterior distribution. Throughout the manuscript, we develop models layer by layer, thereby illustrating an iterative workflow for causal inference in social networks. We conclude by summarising this workflow as a set of seven steps, and provide practical recommendations.},
}
@article {pmid40920919,
year = {2025},
author = {Li, Y and Meng, L and Richardson, AD and Lee, X and Menzel, A and Mao, J and Diehl, JL and Wang, A},
title = {Cooling outweighs warming across phenological transitions in the Northern Hemisphere.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {37},
pages = {e2501844122},
pmid = {40920919},
issn = {1091-6490},
mesh = {Seasons ; Forests ; Temperature ; *Climate Change ; *Global Warming ; Plant Leaves/physiology ; Trees ; },
abstract = {Vegetation phenology, i.e., seasonal biological events such as leaf-out and leaf-fall, regulates local climate through biophysical processes like evapotranspiration (ET) and albedo. However, the net surface temperature impact of these processes-whether ET cooling or albedo-induced warming predominates-and how the dominance changes across phenological transitions and regions remains poorly understood. Here, we investigated the effects of vegetation foliage on daytime land surface temperature (LST) following six phenological transitions, spanning from the start of season to end of season, in deciduous and mixed forests across the mid- to high-latitude Northern Hemisphere during 2013-2021 using multiple satellite products and ground observations. We quantified vegetation effect as the difference between observed LST and LST estimates from the Annual Temperature Cycle (ATC) model, representing a no-foliage scenario. We found that vegetation-induced cooling consistently outweighs warming following all phenological transitions except for the end of the season. Cooling intensity increased with vegetation greenness, ranging from 1.0 ± 0.5 °C (mean ± 0.15 SD) in 59% of forests after the start of the season (SOS) to 6.1 ± 0.8 °C in 89% of forests following the onset of maturity, before declining toward the end of the season. Over half of the regions experiencing cooling showed intensification of surface cooling with climate warming, suggesting an amplified vegetation-mediated cooling under future climate change. The findings provide a more precise understanding of the role of vegetation in modulating climate at the intraseasonal scale, highlighting the importance of integrating phenological impacts into climate adaptation strategies and Earth system modeling.},
}
@article {pmid40921753,
year = {2025},
author = {Wang, F and Xue, M and Zhou, L and Doughty, CE and Ciais, P and Reich, PB and Shang, J and Chen, JM and Liu, J and Green, JK and Hao, D and Tao, S and Su, Y and Liu, L and Xia, J and Wang, H and Yu, K and Zhu, Z and Zhu, P and Li, X and Liu, H and Zeng, Y and Yan, K and Liu, L and Lafortezza, R and Su, Y and Meng, Y and Pan, Y and Yang, X and Fu, YH and He, N and Yuan, W and Chen, X},
title = {Contrasting age-dependent leaf acclimation strategies drive vegetation greening across deciduous broadleaf forests in mid- to high latitudes.},
journal = {Nature plants},
volume = {11},
number = {9},
pages = {1748-1758},
pmid = {40921753},
issn = {2055-0278},
mesh = {*Plant Leaves/physiology/growth &amp; development ; *Forests ; *Acclimatization ; *Trees/physiology ; Seasons ; Climate Change ; Photosynthesis ; North America ; Europe ; },
abstract = {Increasing leaf area and extending vegetation growing seasons are two primary drivers of global greening, which has emerged as one of the most significant responses to climate change. However, it remains unclear how these two leaf acclimation strategies would vary across forests at a large spatial scale. Here, using multiple satellite-based datasets and field measurements, we analysed the temporal changes (Δ) in maximal leaf area index (LAImax) and length of the growing season (LOS) from 2002 to 2021 across deciduous broadleaf forests (DBFs) in the middle to high latitudes. Contrary to the widely held assumption of coordination, our results revealed a negative correlation between ΔLAImax and ΔLOS. Notably, the trade-offs between ΔLAImax and ΔLOS were strongly explained by stand age. Younger DBFs, with lower baseline LAImax, predominantly located in eastern Asia, displayed an increase in LAImax with small changes in LOS. This acquisitive strategy facilitated younger DBFs to grow more photosynthetically efficient leaves with low leaf mass per area, enhancing their light use efficiency. Conversely, older DBFs with a higher baseline LAImax, primarily located in North America and Europe, extended their LOS by increasing leaf mass per area. This conservative strategy facilitated older DBFs to produce thicker, but less photosynthetically efficient leaves, resulting in decreased light use efficiency. Our findings offer new insights into the contrasting changes in leaf area and growing season length and highlight their divergent impacts on ecosystem functioning.},
}
@article {pmid40923094,
year = {2025},
author = {Sze, JS and Sauls, LA},
title = {Prospects and perils in the geospatial turn of conservation.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {39},
number = {6},
pages = {e70145},
pmid = {40923094},
issn = {1523-1739},
support = {ES/Y002660/1//Economic and Social Research Council/ ; ERC-2021-ADG/ERC_/European Research Council/International ; CONDJUST/ERC_/European Research Council/International ; 101054259/ERC_/European Research Council/International ; },
mesh = {*Conservation of Natural Resources/methods ; *Biodiversity ; *Big Data ; },
abstract = {Conservation has embraced advances in big data and related digital technologies as key to preventing biodiversity loss, especially in the identification of areas of conservation priority based on spatial data, which we call the big geospatial data turn. This turn has led to the proliferation of useful methods and tools, including global geospatial maps. But these methods may also undermine moves toward rights-based and inclusive conservation approaches that consider plural values and perspectives. We built on the burgeoning literature to call for greater attention to be paid to the datasets, methodological choices, and the assumptions global mapping for biodiversity conservation is based on. In increasingly prioritizing the use of big geospatial data, conservation professionals risk forgetting that maps show only partial information and limit the diversity of ways of seeing and representing the world. Big geospatial data collected through remotely sensed technologies must still be situated in time and place and provided with appropriate political-economic and sociocultural contexts. Further, global mapping efforts remain primarily the purview of Global North researchers, even given the push to make data open access. Instead of uncritically calling for more data, we urge conservationists to contextualize and situate big geospatial data carefully so as to build a field that achieves socially just and ecologically effective conservation outcomes.},
}
@article {pmid40924543,
year = {2025},
author = {Baele, G and Carvalho, LM and Brusselmans, M and Dudas, G and Ji, X and McCrone, JT and Lemey, P and Suchard, MA and Rambaut, A},
title = {HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {10},
pages = {},
pmid = {40924543},
issn = {1367-4811},
support = {R01 AI153044/AI/NIAID NIH HHS/United States ; //Research Foundation-Flanders/ ; },
mesh = {*Software ; *Phylogeny ; *SARS-CoV-2/genetics/classification ; Bayes Theorem ; *Ebolavirus/genetics/classification ; Algorithms ; Humans ; *Computational Biology/methods ; COVID-19/virology ; },
abstract = {SUMMARY: In Bayesian phylogenetic and phylodynamic studies, it is common to summarize the posterior distribution of trees with a time-calibrated summary phylogeny. While the maximum clade credibility (MCC) tree is often used for this purpose, we here show that a novel summary tree method-the highest independent posterior subtree reconstruction, or (HIPSTR)-contains consistently higher supported clades over MCC. We also provide faster computational routines for estimating both summary trees in an updated version of TreeAnnotator X, an open-source software program that summarizes the information from a sample of trees and returns many helpful statistics such as individual clade credibilities contained in the summary tree.<br><br>RESULTS: HIPSTR and MCC reconstructions on two Ebola virus and two SARS-CoV-2 datasets show that HIPSTR yields summary trees that consistently contain clades with higher support compared to MCC trees. The MCC trees regularly fail to include several clades with very high posterior probability (&#x2265;0.95) as well as a large number of clades with moderate to high posterior probability (&#x2265;50%), whereas HIPSTR-in particular its majority-rule extension MrHIPSTR-achieves near-perfect performance in this respect. HIPSTR and MrHIPSTR also exhibit favourable computational performance over MCC in TreeAnnotator X. Comparison to the recent CCD0-MAP algorithm yielded mixed results and requires a more in-depth investigation in follow-up studies.<br><br>TreeAnnotator X is available as part of the BEAST X (v10.5.0) software package, available at https://github.com/beast-dev/beast-mcmc/releases, and on Zenodo (DOI: https://doi.org/10.5281/zenodo.4895234).},
}
@article {pmid40926576,
year = {2025},
author = {Achury, R and Staab, M and Seibold, S and Müller, J and Heidrich, L and Püls, M and Hacker, H and Fonseca, CR and Fischer, M and Blüthgen, N and Weisser, W},
title = {Habitat and land-use intensity shape moth community structure across temperate forest and grassland.},
journal = {The Journal of animal ecology},
volume = {94},
number = {11},
pages = {2308-2321},
pmid = {40926576},
issn = {1365-2656},
support = {//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Grassland ; *Moths/physiology ; *Forests ; Germany ; *Biodiversity ; Ecosystem ; },
abstract = {Land-use change and intensification are major drivers of biodiversity loss, yet their effects on diversity have usually been studied within a single habitat type or land-use category, limiting our understanding of cross-habitat patterns. Moths, a species-rich taxon worldwide, represent a significant portion of the biodiversity in both temperate forests and grasslands, functioning as pollinators and herbivores. While increasing land-use intensity (LUI) in both habitats is expected to negatively impact moth assemblages, the strength of this effect remains uncertain. Moreover, land-use intensification interacts with broader environmental factors, such as weather conditions and the spread of artificial light at night (ALAN), but their combined effects on moth community diversity and turnover across habitats remain poorly understood. We sampled moth communities across 150 grassland and 150 forest plots along land-use gradients in Germany. We quantified plot- and landscape-scale LUI and tested the role of plant diversity, temperature and precipitation during the night of sampling and the preceding season, and ALAN in shaping moth diversity (standardized by coverage) along Hill numbers. Forests supported significantly higher moth abundance, biomass and diversity than grasslands, with habitat type being the main driver of moth community composition. LUI at the plot scale had contrasting effects on moth abundance, increasing it in forests but reducing it in grasslands. Impacts of LUI were more pronounced at the landscape level, reducing moth diversity particularly in areas dominated by grasslands. Plant diversity and temperature were key determinants for moth communities, increasing alpha diversity across diversity metrics, that is Hill numbers. ALAN had no significant influence on moth abundance or biomass but significantly decreased Simpson diversity. Beta diversity increased with geographic distance, habitat change and LUI but decreased with weather differences among plots. Our results highlight the interplay between LUI, habitat type and abiotic factors in shaping moth communities across large spatial scales. Effective conservation strategies should consider maintaining habitat heterogeneity and promoting plant diversity, particularly in temperate habitats exposed to high land-use intensification.},
}
@article {pmid40927873,
year = {2025},
author = {Blackman Carr, LT and Ard, J and Shanks, CB and Forman, EM and Goldstein, SP and Haire-Joshu, D and Jastreboff, AM and Johnson, S and Kandula, NR and Katzmarzyk, PT and Keyserling, TC and Kumanyika, SK and Lee, BY and Lewis, KH and Martin, MY and Mozaffarian, D and Newton, RL and Odoms-Young, A and Panza, E and Pronk, NP and Rosas, LG and Samuel-Hodge, C and Schmidt, LA and Sherwood, NE and Spring, B and Cooksey Stowers, K and Baskin, ML},
title = {Toward Health Equity: A Workshop Report on the State of the Science of Obesity Interventions for Adults.},
journal = {Obesity (Silver Spring, Md.)},
volume = {33},
number = {12},
pages = {2235-2245},
doi = {10.1002/oby.70035},
pmid = {40927873},
issn = {1930-739X},
support = {P30 DK045735/DK/NIDDK NIH HHS/United States ; /HL/NHLBI NIH HHS/United States ; /NH/NIH HHS/United States ; //Office of Disease Prevention/ ; },
mesh = {Humans ; *Obesity/prevention &amp; control/epidemiology/therapy ; *Health Equity ; Adult ; United States ; Health Promotion ; },
abstract = {OBJECTIVE: From October 18 to 20, 2022, the National Institutes of Health held a workshop to examine the state of the science concerning obesity interventions in adults to promote health equity. The workshop had three objectives: (1) convene experts from key institutions and the community to identify gaps in knowledge and opportunities to address obesity, (2) generate recommendations for obesity prevention and treatment to achieve health equity, and (3) identify challenges and needs to address obesity prevalence and disparities and develop a diverse workforce.<br><br>METHODS: A three-day virtual convening.<br><br>RESULTS: Several key themes emerged from the workshop discussions that describe directions to build on the currently limited amount of research on obesity, disparities, and equity. Key themes centered on the determinants of health, leveraging technology, clinical, community, commercial, and policy approaches. Community-engaged work, particularly in populations that have received little focus (e.g., sexual gender minorities, Asian communities), was also discussed.<br><br>CONCLUSIONS: Future research may be impactful when multilevel approaches are undertaken that leverage equity-minded tools and can be scaled up to meet community-informed population needs in a variety of settings. Funding priorities and workforce development will be critical to realizing health equity.},
}
@article {pmid40928529,
year = {2025},
author = {Lawler, T and Kwekkeboom, K and Warren Andersen, S and Sethi, AK and Tevaarwerk, AJ and Litzelman, K and Pophali, PA and Gangnon, RE and Hampton, JM and LoConte, NK and Trentham-Dietz, A},
title = {Self-efficacy for cancer self-management in the context of COVID-19: a cross-sectional survey study.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {33},
number = {10},
pages = {843},
pmid = {40928529},
issn = {1433-7339},
support = {P30 CA014520/CA/NCI NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; P30CA014520/CA/NCI NIH HHS/United States ; UL1TR002373//National Institutes of Health, United States/ ; },
mesh = {Humans ; *Self Efficacy ; *COVID-19/epidemiology/psychology ; Middle Aged ; Male ; Female ; Cross-Sectional Studies ; Adult ; Aged ; *Neoplasms/therapy/psychology ; *Self-Management/psychology ; Adolescent ; *Cancer Survivors/psychology ; Aged, 80 and over ; Young Adult ; Surveys and Questionnaires ; },
abstract = {PURPOSE: For cancer survivors, self-efficacy is needed to manage the disease and the effects of treatment. The COVID-19 pandemic disrupted cancer-related healthcare, which may have impacted self-management self-efficacy. We investigated self-efficacy reported by cancer survivors during COVID-19, including associations with healthcare disruptions, distress, and general health.<br><br>METHODS: Between 2020 and 2021, 1902 individuals aged 18-80&#xa0;years with a recent cancer diagnosis completed a survey regarding the effects of COVID-19 on healthcare, self-efficacy for managing cancer and social interactions, cancer-related distress, and perceived general health. Linear and logistic models estimated odds ratios and 95% confidence intervals (CIs) between self-efficacy scores, healthcare disruptions, significant distress, and general health.<br><br>RESULTS: Mean self-efficacy for managing cancer was 7.58 out of 10. Greater self-efficacy was associated with lower odds for distress (OR 0.18 [95% CI 0.13-0.26], quartile 4 vs. 1) and for worse general health (0.05 [0.03-0.09]). Participants with disruptions to cancer-related healthcare had lower self-efficacy for managing cancer compared to those without (6.62 vs. 7.09, respectively, P&#x2009;<&#x2009;0.001) and higher odds for distress (1.70 [1.36-2.14]), but not worse general health (1.13 [0.39-1.44]). Lower self-efficacy mediated 27% of the association between healthcare disruptions and increased distress (15-47%). Associations with self-efficacy for managing social interactions trended in the same direction.<br><br>CONCLUSIONS: During COVID-19, disruptions to cancer-related healthcare were associated with lower self-efficacy, increased distress, and worse general health. Psychosocial interventions designed to overcome barriers and target self-efficacy may be important for enhancing outcomes among cancer survivors experiencing disruptions in healthcare access.},
}
@article {pmid40930298,
year = {2026},
author = {Slack, SD and Esquinca, E and Arehart, CH and Boorgula, MP and Szczesny, B and Romero, A and Campbell, M and Chavan, S and Rafaels, N and Watson, H and Landis, RC and Hansel, NN and Rotimi, CN and Olopade, CO and Figueiredo, CA and Ober, C and Liu, AH and Kenny, EE and Kammers, K and Ruczinski, I and Taub, MA and Daya, M and Gignoux, CR and Kechris, K and Barnes, KC and Mathias, RA and Johnson, RK},
title = {Prediction and characterization of genetically regulated expression of asthma tissues from African-ancestry populations.},
journal = {The Journal of allergy and clinical immunology},
volume = {157},
number = {1},
pages = {253-261},
doi = {10.1016/j.jaci.2025.07.035},
pmid = {40930298},
issn = {1097-6825},
mesh = {Female ; Humans ; Male ; *Asthma/genetics/immunology ; *Black People/genetics ; *CD4-Positive T-Lymphocytes/immunology ; Gene Expression Profiling ; *Gene Expression Regulation ; Genetic Predisposition to Disease ; *Nasal Mucosa/metabolism/immunology ; Transcriptome ; },
abstract = {BACKGROUND: Genetic control of gene expression in asthma-related tissues is not well characterized, particularly for African-ancestry populations, limiting advancement in our understanding of the increased prevalence and severity of asthma in these populations.<br><br>OBJECTIVE: We sought to create novel transcriptome prediction models for asthma tissues (nasal epithelium and CD4[+] T cells) and apply them in a transcriptome-wide association study (TWAS) to discover candidate asthma genes.<br><br>METHODS: We developed and validated gene expression prediction databases for unstimulated CD4[+] T cells and nasal epithelium using an elastic net framework. Combining these with existing prediction databases (N = 51), we performed a TWAS of 9284 individuals of African ancestry to identify tissue-specific and cross-tissue candidate genes for asthma.<br><br>RESULTS: Novel databases for CD4[+] T cells and nasal epithelial gene expression prediction contain 8,351 and 10,296 genes, respectively, including 4 asthma loci (SCGB1A1, MUC5AC, ZNF366, and LTC4S) not predictable with existing public databases. Prediction performance was comparable to existing databases and was most accurate for populations sharing ancestry with the training set (eg, African ancestry). From the TWAS, we identified 17 candidate causal asthma genes (adjusted P < .1), including genes with tissue-specific (IL33 in nasal epithelium) and cross-tissue (CCNC and FBXW7) effects.<br><br>CONCLUSIONS: Expression of IL33, CCNC, and FBXW7 may affect asthma risk in African- ancestry populations by mediating inflammatory responses. The addition of CD4[+] T cell and nasal epithelium prediction databases to the public sphere will improve ancestry representation and power to detect novel gene-trait associations from TWAS.},
}
@article {pmid40930573,
year = {2026},
author = {Orfanos, I and Vrijlandt, S and van der Walle, E and Tan, CD and Nieboer, D and Alfvén, T and Sotoca Fernandez, J and Elliver, M and Elfving, K and Martinón-Torres, F and Kohlmaier, B and Zenz, W and Emonts, M and Nijman, RG and Carrol, E and Eklund, E and Moll, HA and Oostenbrink, R},
title = {Validating the PECARN rule to identify febrile infants at low risk of serious bacterial infections: an international validation study.},
journal = {Archives of disease in childhood},
volume = {111},
number = {4},
pages = {299-305},
doi = {10.1136/archdischild-2024-328246},
pmid = {40930573},
issn = {1468-2044},
mesh = {Humans ; Infant ; C-Reactive Protein/analysis/metabolism ; *Bacterial Infections/diagnosis/epidemiology/blood/complications ; Male ; Female ; Procalcitonin/blood ; *Fever/diagnosis/etiology ; Infant, Newborn ; Sweden/epidemiology ; Europe/epidemiology ; *Clinical Decision Rules ; Biomarkers/blood ; Predictive Value of Tests ; Sensitivity and Specificity ; Emergency Service, Hospital ; Risk Assessment/methods ; },
abstract = {OBJECTIVE: To externally validate the Paediatric Emergency Care Applied Research Network (PECARN) rule for identifying febrile infants aged <60 days at low risk of serious bacterial infections (SBIs) and assess the utility of the rule with C reactive protein (CRP) instead of procalcitonin (PCT).<br><br>METHODS: Secondary analysis of data from the Management and Outcomes of Fever in Children in Europe (MOFICHE) study (12 paediatric emergency departments in eight European countries, January 2017 to April 2018) and a Swedish study (four paediatric emergency departments, January 2014 to December 2020). Previously healthy febrile infants aged &#x2264;60 days were included. We validated the original PECARN rule in a Swedish subcohort (2018-2020) and explored an adapted version using CRP in the full Swedish and MOFICHE cohorts.<br><br>RESULTS: The Swedish subcohort (2018-2020) included 536 febrile infants with an SBI prevalence of 11%. The original PECARN rule showed a sensitivity of 96.6% (95% CI 88.1 to 99.6), specificity of 61.9% (95% CI 57.4 to 66.3), negative predictive value (NPV) of 99.3% (95% CI 97.4 to 99.8) and positive predictive value (PPV) of 23.5% (95% CI 21.4 to 25.8). The full Swedish cohort (2014-2020) included 2237 infants and the MOFICHE cohort of 512 infants with 12% and 10% SBI prevalence, respectively. Using CRP <20&#x2009;mg/L instead of PCT, the adapted PECARN rule showed a sensitivity of 97.8% and NPV of 99.4% in the Swedish cohort, and sensitivity of 92.2% with an NPV of 98.3% in the MOFICHE cohort.<br><br>CONCLUSIONS: The PECARN rule demonstrated high NPV (similar to the derivation cohort) and high potential in ruling out SBIs in two new European cohorts. The rule maintained good performance with CRP instead of PCT, supporting the potential use of CRP in settings where PCT is unavailable.},
}
@article {pmid40931350,
year = {2025},
author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T},
title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {276},
pmid = {40931350},
issn = {1474-760X},
support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Databases, Genetic ; *Microbiota ; },
abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .},
}
@article {pmid40932046,
year = {2025},
author = {Matsumoto, Y and Okada, G and Ohta, M},
title = {Can Augmented Reality be Used as a Portion Size Estimation Aid Tool? A Pilot Randomized Controlled Trial.},
journal = {Journal of human nutrition and dietetics : the official journal of the British Dietetic Association},
volume = {38},
number = {5},
pages = {e70125},
doi = {10.1111/jhn.70125},
pmid = {40932046},
issn = {1365-277X},
support = {//This study was supported by PUH Research Grant Program./ ; },
mesh = {Humans ; Pilot Projects ; *Portion Size/psychology ; Female ; Male ; Young Adult ; Adult ; *Augmented Reality ; *Dietetics/education/methods ; Students ; Feasibility Studies ; },
abstract = {BACKGROUND: Evidence on the effectiveness of augmented reality (AR)-based tools for portion size estimation as an educational aid remains limited. In this pilot study, we developed a 3D food model using AR and assessed the feasibility of using this application to teach portion size estimation skills.<br><br>METHODS: This intervention study involved 43 students (including 38 females) from two dietetic education institutions. Participants were randomly assigned into four groups: (1) text only, (2) text and pictures, (3) food model and (4) AR. Learning effectiveness was evaluated using a pretest of 10 different foods, followed by a 10-min instructional session with the assigned tool, and then a post-test. Participants rated each learning tool for enjoyment, usefulness and recommendation to others on an 11-point Likert scale. Outcomes included the change in the number of correct answers within &#xb1;&#x2009;10% or &#xb1;&#x2009;20% of the true food weight.<br><br>RESULTS: Mean acceptability ratings for the text only, text and picture, food model and AR groups were enjoyment (4.1, 5.6, 7.0 and 7.9), usefulness (5.5, 7.4, 8.4 and 8.3) and recommendation to others (3.6, 6.3, 6.3 and 7.1), respectively. The mean changes in correct answers for text only, text and picture, food model and AR groups were 0.7, -1.1, 1.5 and 0.1, respectively, within a 10% error margin, and 1.2, -1.9, 2.0 and 0.8, respectively, within a 20% error margin.<br><br>CONCLUSIONS: This pilot study suggests that AR-based tools have potential as educational aids for portion size estimation among future dietitians, with acceptability ratings comparable to conventional methods, such as text only, text and pictures, and food models.<br><br>TRIAL REGISTRATION: The study was registered with the University Hospital Medical Information Network; UMIN000054307.},
}
@article {pmid40934430,
year = {2025},
author = {Tejada-Llacsa, PJ and Alarcón, GS and Ugarte-Gil, MF},
title = {Prevalence of systemic lupus erythematosus in Peru and its association with environmental and healthcare factors: An ecological study.},
journal = {Lupus},
volume = {34},
number = {13},
pages = {1406-1412},
doi = {10.1177/09612033251379313},
pmid = {40934430},
issn = {1477-0962},
mesh = {Humans ; Peru/epidemiology ; Female ; Male ; Adult ; *Lupus Erythematosus, Systemic/epidemiology ; Prevalence ; Middle Aged ; Young Adult ; Adolescent ; Altitude ; Child ; Temperature ; Registries ; Physicians/supply &amp; distribution ; Aged ; Sex Factors ; Risk Factors ; },
abstract = {ObjectiveTo estimate the prevalence of Systemic Lupus Erythematosus (SLE) in Peru in 2017 and its association with altitude, environmental temperature, and physician density.MethodsThis ecological study was performed using population data from the 2017 Peruvian census. The number of SLE cases for each department was obtained from the National Health Registries using the ICD-10 code M32. Altitude, environmental temperature and physician density were obtained for each department from the National Institute of Statistics and Informatic (Instituto Nacional de Estadística e Informática) registries. The prevalence for each department was calculated adjusting for age and sex. Then a negative binomial regression was performed to estimate the prevalence ratio (PR) and evaluate factors associated with the prevalence of SLE.ResultsThe national prevalence of SLE was 40.2 per 100,000 people. Two age groups had the highest prevalence: 12-17 years and 30-59 years. Females exhibited a higher prevalence than males, particularly in the 30-59 age group (113.9 vs 16.1 per 100,000, respectively). An inverse relationship was observed between the age- and sex-adjusted prevalence in each department and altitude (PR 0.97; 95% CI: 0.94-0.99). On the other hand, there was a direct relationship with physician density (PR: 1.04; 95% CI: 1.01-1.07). No association was found between the adjusted prevalence and environmental temperature or latitude.ConclusionThe prevalence of SLE in Peru aligns with global estimates. The inverse relationship with altitude and the direct association with physician density suggest that environmental and healthcare access factors may influence disease distribution. Further research is needed to explore the underlying mechanisms driving these associations.},
}
@article {pmid40936754,
year = {2025},
author = {Ward, EJ and English, PA and Rooper, CN and Ferriss, BE and Whitmire, CE and Wetzel, CR and Barnett, LAK and Anderson, SC and Thorson, JT and Johnson, KF and Indivero, J and Markowitz, EH},
title = {surveyjoin: a standardized database of scientific trawl surveys in the Northeast Pacific Ocean.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19964},
pmid = {40936754},
issn = {2167-8359},
mesh = {Pacific Ocean ; *Fisheries/statistics &amp; numerical data ; *Databases, Factual/standards ; Animals ; Gadiformes ; Biomass ; Surveys and Questionnaires ; Conservation of Natural Resources ; },
abstract = {Fisheries management faces challenges due to political, spatial, and ecological complexities, which are further exacerbated by variation or shifts in species distributions. Effective management depends on the ability to integrate fisheries data across political and geographic boundaries. However, such efforts may be hindered by inconsistent data formats, limited data sharing, methodological differences in sampling, and regional governance differences. To address these issues, we introduce the surveyjoin R package, which combines and provides public access to bottom trawl survey data collected in the Northeast Pacific Ocean by NOAA Fisheries and Fisheries and Oceans Canada. This initial database integrates over 3.3 million observations from 14 bottom trawl surveys spanning Alaska, British Columbia, Washington, Oregon, and California from the 1980s to present. This database standardizes variables such as catch-per-unit-effort (CPUE), haul data, and in-situ measurements of bottom temperature. We demonstrate the utility of this database through three case studies. Our first case study develops a coastwide biomass index for Pacific hake (Merluccius productus) using geostatistical index standardization, comparing results to independent acoustic survey estimates. The second case study examines spatial patterns in groundfish community structure, highlighting breakpoints between assemblages in their mixture of life histories and trophic compositions. Our third example applies spatially varying coefficient models to assess sablefish (Anoplopoma fimbria) biomass trends, identifying regional variability in increases in occurrence and biomass. Together, these case studies demonstrate how the surveyjoin R package and database may improve species and ecosystem assessments by providing insights into population trends across geopolitical boundaries. This database and package represent an important step toward offering a scalable framework that can be extended to include additional data types, surveys, and species. By fostering collaboration, transparency, and data-driven decision making, surveyjoin supports international efforts to sustainably manage shared marine resources under dynamic environmental conditions.},
}
@article {pmid40938934,
year = {2025},
author = {Attar, MI and Naseer, S and Pandey, Y and Khan, JN and Bangroo, SA and Hasan, MA and Khan, ZA and Khan, AH and Tantray, AM},
title = {Morphometric analysis for prioritizing critical areas of Urpash watershed in Sindh catchment of the lesser Himalayas using RS and GIS approach.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0330503},
pmid = {40938934},
issn = {1932-6203},
mesh = {*Geographic Information Systems ; *Rivers ; *Remote Sensing Technology ; Hydrology ; Conservation of Natural Resources ; Environmental Monitoring/methods ; Soil Erosion ; Himalayas ; },
abstract = {Effective soil and water conservation is critical in fragile watersheds prone to erosion. However, assessing erosion susceptibility in ungauged watersheds remains challenging due to the lack of observed hydrological data This study addresses this gap by employing a comprehensive morphometric analysis integrated with remote sensing (RS) and Geographic Information Systems (GIS) to prioritize erosion-prone sub-watersheds within the ecologically sensitive and data-scarce Urpash watershed. Shuttle Radar Topography Mission (SRTM) Digital Elevation Model (DEM) data and ArcGIS 10.7 were used to analyze a 21.37 km[2] area. Key morphometric parameters-including linear, areal, and relief aspects-were assessed to understand watershed hydrology and erosion susceptibility. A total of 32 streams were identified, categorized into 1st to 3rd orders. Watershed shape indices, such as elongation ratio (Re = 0.65), form factor (Rf = 0.33) and circularity ratio (Rc = 0.295), indicate an elongated shape, indicative of reduced surface runoff and erosion potential, along with higher sub-soil permeability. However, drainage parameters like drainage density (Dd = 1.67 km/km2), stream frequency (Fs = 1.49 km-2) and drainage intensity (Di = 0.89 km-1) pointed to the watershed's susceptibility to flooding, gully erosion, and landslides due to slow surface runoff dispersion. Relief parameters such as basin relief (H = 1742.87 m), relief ratio (Rh = 0.22) and ruggedness number (Rn = 2.9) reflect the watershed's high relief and steep terrain, indicating a greater susceptibility to erosion. Using a compound parameter approach, the sub-watershed prioritisation ranked WS3 as the highest priority, followed by WS4, WS5, WS6, WS2, and WS1. By using RS and GIS-based morphometric analysis in an ungauged Urpash watershed, this study provides a geospatial framework for targeted soil and water conservation strategies, contributing to more precise watershed management in data-scarce and erosion-vulnerable regions.},
}
@article {pmid40941648,
year = {2025},
author = {Pantelić, M and Cvetković, D and Jovankić, J and Soldatović, I and Pantelić, M and Dujović, M and Vučinić, T and Cvetković, A},
title = {Predictive Value of Serum HMGB1, NF-κB, and IL-17 Gene Expression in Acute Pancreatitis Outcomes.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {40941648},
issn = {2075-4418},
abstract = {Background/Objectives: This study investigated the gene expression levels of High Mobility Group Box 1 (HMGB1), nuclear factor kappa B (NF-κB) and interleukin-17 (IL-17) in the serum of patients with acute pancreatitis (AP) and analyzed the correlation of these three with the severity of AP, local and systemic complications, transfer to intensive care unit (ICU) and death. Methods: AP was diagnosed and stratified according to the revised Atlanta classification. The diagnosis of AP requires two of the following three features: abdominal pain (acute onset of persistent severe, epigastric pain often radiating to the back); serum lipase/or amylase activity at least three times higher than normal; characteristic findings of AP on computed tomography or abdominal ultrasonography. Results: This study confirmed that NF-kB is a significant marker of AP severity, as well as for ICU transfer, and correlates with acute respiratory distress syndrome (ARDS), while IL-17 is shown as a significant marker of systemic complications (pleural effusions, ARDS, and renal failure). HMGB1 correlates with pancreatic necrosis, systemic inflammatory response syndrome, and ICU transfer. Conclusions: Over the past years, the role of HMGB1, NF-kB, and IL-17 in the pathogenesis of AP has been under intense scrutiny, and they have been proposed as prognostic biomarkers for AP severity, poor prognosis, and death outcome. The advantage of this research is that changes in gene expression can be detected before the increase in serum concentrations of these biomarkers, and it allows early prediction of a severe form of AP, as well as the development of complications.},
}
@article {pmid40945060,
year = {2026},
author = {Zhang, M and Zhao, C and Zhang, W and Guo, Y and Han, F and Li, Y and Zhou, W},
title = {Stable ammonium assimilation mediates the metabolic adaptation of halophilic microbiome to hypo-osmotic stress in wastewater treatment.},
journal = {Water research},
volume = {288},
number = {Pt A},
pages = {124572},
doi = {10.1016/j.watres.2025.124572},
pmid = {40945060},
issn = {1879-2448},
mesh = {*Ammonium Compounds/metabolism ; *Wastewater/chemistry/microbiology ; *Water Purification/methods ; *Microbiota/physiology ; Osmotic Pressure ; Salinity ; Salt Tolerance ; Acclimatization ; Stress, Physiological/physiology ; Multiomics ; },
abstract = {Salinity barrier shapes distinct microbial ecology on earth, and applications of microbiomes are frequently hindered by trans-osmotic challenges. As a central nutrient metabolism, nitrogen transformations may contribute to conquering osmotic perturbations in microbiomes, and thus understanding the nitrogen metabolic responses to non-isosmotic exposure is crucial. Here we uncover that ammonium assimilation mediates the maintenance of physicochemical properties in a marine-derived halophilic microbiome when adapting to hypo-osmotic stress from salinity of 3 % to 0.5 %. An adaptive threshold at salinity approximately around 1 % is observed that reducing osmotic gradients disrupt ammonium assimilation and microbial community stability with decreasing specific ammonium assimilation rates from 2.34 to 0.62 mg-N/(g MLSS h). Multi-omics analysis demonstrates that enhancing ammonium-assimilating function prevents nitrogen metabolic differentiation and promotes production of amino acids and their derivatives recognized as osmoprotectants. Genes coding for transporter systems and mechanosensitive channels are also up-regulated. The results of this study suggest that maintaining stable ammonium assimilation could enhance the amino acid metabolism and subsequent osmoprotectant production, thus improving the metabolic adaptation of the halophilic microbiome to hypotonic conditions. Our findings provide insights into the adaptation of microbiomes to osmotic alterations, and highlight the importance of enhancing ammonium assimilation in engineering microbiomes under environmental stress.},
}
@article {pmid40946389,
year = {2025},
author = {Siuda, P and Aaltonen, M and Haasio, A and Bancroft, A and Nurmi, J and Shi, H and Harviainen, JT},
title = {Digital drug trading ecologies in context: Technological, geographic, and linguistic variation across darknet platforms.},
journal = {The International journal on drug policy},
volume = {145},
number = {},
pages = {104984},
doi = {10.1016/j.drugpo.2025.104984},
pmid = {40946389},
issn = {1873-4758},
mesh = {*Drug Trafficking ; Humans ; Datasets as Topic ; *Internet/economics ; Language ; *Illicit Drugs/economics ; Commerce ; Internationality ; },
abstract = {BACKGROUND: Previous research on darknet drug markets has primarily concentrated on large, English-language cryptomarkets, often overlooking regionally oriented platforms that operate in national languages. This study adopts a comparative, exploratory approach to examine how drug trade practices vary across linguistic, geographic, and technological contexts. We introduce the concept of "drug trading ecologies" to describe how platform features, communication norms, and localized settings together shape distinct trading environments.<br><br>METHODS: Using a mixed-methods approach, we analyzed web-crawled data from three Tor-based platforms: Tsatti (Finnish-language chat), Cebulka (Polish-language forum), and Nemesis (English-language cryptomarket). Data were collected through customized web scraping and analyzed using statistical tools and qualitative content coding to examine platform-specific patterns. Our comparative approach highlights structural and localization-specific variations without attempting exhaustive conceptual definitions.<br><br>RESULTS: Each platform displayed a distinct configuration shaped by its technical affordances and localization-specific user practices. Tsatti supported fast, hyperlocal, and highly anonymized exchanges with minimal user identity or community features. Cebulka enabled semi-public vendor-buyer interactions, trust-building through discourse, and diverse product bundling. Nemesis functioned as a transnational, professionalized cryptomarket with standardized listings, formalized trust mechanisms, and branding strategies.<br><br>CONCLUSIONS: Rather than attributing differences solely to local, transnational, or design factors in isolation, we argue that darknet drug trading ecologies emerge from the intersection of platform architecture, localization (geographic scope), and language. Our findings underscore the importance of considering these factors when conducting digital ethnography in illicit economies and providing concrete entry points for tailoring harm reduction interventions responsive to the diverse realities of online drug trading.},
}
@article {pmid40947031,
year = {2026},
author = {Onyeka, OC and Cheng, JS and Sanei, S and Clark, SL and Pinciotti, CM and Guzick, AG and Storch, EA and Stewart, S and Sandoval, JF and Taylor, L and Riddle, D and Garza, C and Liberzon, I and Rousseau, J and Shahidullah, JD and Newport, DJ and Wagner, KD and Nemeroff, C},
title = {Exploring resource profiles among trauma exposed youth: An identity-focused, cultural, and person-centered approach.},
journal = {Journal of affective disorders},
volume = {393},
number = {Pt A},
pages = {120298},
doi = {10.1016/j.jad.2025.120298},
pmid = {40947031},
issn = {1573-2517},
mesh = {Humans ; Female ; Male ; Adolescent ; *Resilience, Psychological ; *Stress Disorders, Post-Traumatic/psychology/ethnology ; Anxiety/psychology ; Depression/psychology ; Social Support ; Longitudinal Studies ; Texas ; *Social Identification ; Child ; },
abstract = {OBJECTIVE: Resilience is a multi-faceted construct comprised of both internal and external resources that support adaptive functioning following trauma exposure. The role of resilience in ameliorating internalizing symptoms may depend on its typology as opposed to its presence alone, suggesting the existence of distinct subpopulations with heterogeneous resource profiles. The current study employs Latent Profile Analysis (LPA) to identify and characterize profiles of resilience-related resources among youth exposed to trauma from an identity-focused, cultural lens.<br><br>METHOD: Patterns of resources were examined in 1,538 youth (Mage = 13.4, 51.9% female) from a large longitudinal registry of trauma exposed youth in Texas using LPA. Profiles were related to demographic variables and internalizing symptoms (post-traumatic stress symptoms [PTSS], depression, and anxiety) using multinomial regression.<br><br>RESULTS: Results demonstrated an optimal four-class solution (Low Social Support and Average ERI, 31.2&#xa0;%; Average Level of Protective Factors, 27.4&#xa0;%; Ethnic Identity Diffusion, 18.1&#xa0;%; Social Support Dominant, 23.2&#xa0;%). Depressive symptoms significantly differentiated between classes in the four-class model as well as youth race, age, and ethnicity. Anxiety symptoms and PTSS did not differentiate the classes as clearly.<br><br>CONCLUSION: Person-centered analyses such as LPA underscore the value of examining resilience as a multi-faceted and heterogenous pattern of resources shaped by socio-ecological and cultural contexts among trauma-exposed youth. Implications for clinical intervention are discussed.},
}
@article {pmid40950394,
year = {2025},
author = {Sambo, B and Sperotto, A and Aznarez, C and Terzi, S and Pittore, M and Critto, A and Torresan, S},
title = {Managing the water-energy-food nexus in the adige river basin: impacts of climate and land use change on ecosystem services bundles.},
journal = {Climatic change},
volume = {178},
number = {9},
pages = {168},
pmid = {40950394},
issn = {0165-0009},
abstract = {UNLABELLED: The Water-Energy-Food (WEF) nexus framework highlights the interdependencies among water, energy, and food systems. Integrating Ecosystem Services (ESs) enhances this approach by incorporating ecological benefits for more holistic assessments. This study applies a spatially explicit ESs-based WEF nexus analysis in the Adige River Basin (Northern Italy), focusing on five ESs: water provisioning, crop yield, sediment retention, carbon storage, and landscape diversity, under two future scenarios (SSP1-RCP 2.6 and SSP5-RCP 8.5) from 2018 to 2050. Using Self-Organizing Maps, sub-basins were clustered into ESs bundles enabling the identification of tailored management strategies. Results reveal spatial heterogeneity and shifts in ESs bundles, with synergies often found in upstream, forested areas. Under high-emission scenarios, regulating services decline and provisioning services face trade-offs, especially with intensified agriculture. Key strategies suggested include maintaining environmental flows, reducing synthetic fertilizers, promoting reforestation, crop diversification, and expanding protected areas. These are structured into physical, economic, and climatic pathways aligned with EU restoration goals. Findings demonstrate the value of an ESs-bundles approach for optimizing synergies and managing trade-offs across the WEF nexus.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10584-025-04013-3.},
}
@article {pmid40951316,
year = {2025},
author = {Zhang, B and Sheng, Z and Bu, C and Wang, L and Lv, W and Wang, Y and Xu, Y and Yan, G and Gong, M and Liu, L and Hu, W},
title = {Whipworm infection remodels the gut microbiome ecosystem and compromises intestinal homeostasis in elderly patients revealed by multi-omics analyses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663666},
pmid = {40951316},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome ; Animals ; Humans ; *Homeostasis ; RNA, Ribosomal, 16S/genetics ; Aged ; Metabolomics/methods ; Metagenomics ; *Trichuriasis/parasitology/microbiology ; *Trichuris ; Female ; Male ; Bacteria/classification/genetics/isolation &amp; purification ; Metabolic Networks and Pathways ; Aged, 80 and over ; Metabolome ; *Intestines/microbiology ; Multiomics ; },
abstract = {INTRODUCTION: Whipworm (Trichuris trichiura) coexists with symbiotic microbiota in the gastrointestinal ecosystem. There is a paucity of data on the association between whipworm infection and the gut microbiota composition in elderly individuals. This study was designed to investigate changes in gut microbiota and function and its metabolite profile in patients with whipworm infection.<br><br>METHODS: We used 16S rRNA gene sequencing to identify microbial signatures associated with whipworm infection. Subsequently, shotgun metagenomic sequencing revealed functional changes that highlighted disruptions in microbial gene expression and metabolic pathways influencing host health. Ultraperformance liquid chromatography-mass spectrometry metabolomics was used to characterize whipworm infectioninduced metabolic perturbations and elucidate metabolite dynamics linked to microbial activity. Collectively, this multi-omics approach deciphered structural, functional, and metabolic remodeling of the gut ecosystem that distinguished whipworm-infected patients from healthy controls.<br><br>RESULTS: Analyses of the gut microbiome in patients with whipworm infection revealed significantly increased observed species richness and ACE indices, along with an enrichment of Prevotella 9-driven enterotypes. Additionally, metagenomic and metabolomic analyses indicated enrichment in metabolic pathways related to amino acid, energy and carbohydrate metabolism. Metabolic network analysis further suggested that the upregulated Prevotella copri and Siphoviridae sp. were positively correlated with elevated levels of myristic acid and DL-dipalmitoylphosphatidylcholine.<br><br>CONCLUSION: These findings suggest that whipworm infection significantly remodels the gut microbiome ecosystem and compromises intestinal homeostasis.},
}
@article {pmid40952002,
year = {2025},
author = {Guan, R and Garrido-Oter, R},
title = {Integrated diversity and network analyses reveal drivers of microbiome dynamics.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0056425},
pmid = {40952002},
issn = {2379-5077},
support = {2048/1//German Excellence Strategy/ ; },
mesh = {*Microbiota/genetics ; *Biodiversity ; *Plants/microbiology ; Ecosystem ; Microbial Interactions ; Bacteria/genetics/classification ; Computational Biology/methods ; },
abstract = {UNLABELLED: Microbial communities are key components of ecosystems, where interactions among microbes drive biodiversity and productivity. An increased number of microbiome data sets are available, owing to advances in sequencing; however, standard analyses often focus on community composition, neglecting the complex interactions between co-occurring microbes. To address this, we developed a computational framework integrating compositional and co-occurrence network analyses. We applied this approach to extensive microbial amplicon data sets, focusing on plant microbiota, which typically exhibits high diversity and remains challenging to characterize due to the large number of low-abundance taxa. We show that identifying a subset of representative microbial taxa captures the overall community structure and increases the statistical power. From these taxa, we inferred a large-scale co-occurrence network and clustered microbes with co-varying abundances into units for diversity measurement. This approach not only reduces unexplained variance in diversity assessments but also captures the key microbe-microbe relationships that govern assembly patterns. Furthermore, we introduced a bootstrap- and permutation-based statistical approach to compare microbial networks from diverse conditions. Our method robustly distinguishes meaningful differences and pinpoints specific microbes and features driving those differences. These results highlight the importance of incorporating microbe-microbe interactions in microbiota studies, leading to more accurate and ecologically meaningful insights. Our framework, available as an R package ("mina"), enables researchers to identify condition-specific interactions via network comparison and gain a deeper understanding of community ecology. With broad applicability beyond plant systems, this package provides a valuable tool for leveraging microbiome data across disciplines, from agriculture to ecosystem resilience and human health.<br><br>IMPORTANCE: Understanding microbiome dynamics requires capturing not only changes in microbial composition but also interactions between community members. Traditional approaches frequently overlook microbe-microbe interactions, limiting their ecological interpretation. Here, we introduce a novel computational framework that integrates compositional data with network-based analyses, significantly improving the detection of biologically meaningful patterns in community variation. By applying this framework to a large data set from the plant microbiota, we identify representative groups of interacting microbes driving differences across microhabitats and environmental conditions. Our analysis framework, implemented in an R package "mina," provides robust tools allowing researchers to assess statistical differences between microbial networks and detect condition-specific interactions. Broadly applicable to microbiome data sets, our framework is aimed at enabling advances in our understanding of microbial interactions within complex communities.},
}
@article {pmid40952102,
year = {2025},
author = {Guillén Matus, DG and Donaghy, CM and Vijayan, N and Lane, ZT and Howell, M and Glavin, GG and Angeles-Boza, AM and Nyholm, SV and Balunas, MJ},
title = {Multi-omics analysis reveals important role for microbial-derived metabolites from Botryllus schlosseri in metal interactions.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0079325},
pmid = {40952102},
issn = {2379-5077},
support = {Convergence Awards for Research in Interdisciplinary Centers (CARIC)//University of Connecticut/ ; DGE-1747453//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; },
mesh = {*Urochordata/microbiology/metabolism ; Animals ; *Microbiota ; *Metals/metabolism ; *Metabolome ; *Bacteria/metabolism/classification ; Metabolomics/methods ; Multiomics ; },
abstract = {Marine microbial communities govern many of the biological and chemical processes in the ocean, including element cycles, ecosystem health, and disease. Marine organisms are surrounded by microbes, with complex molecular interactions occurring between bacterial symbionts, eukaryotic hosts, and their pathogens or prey. Trace metals in the ocean can be either beneficial or detrimental to marine life depending on their concentrations and bioavailability. Multiple marine tunicate species are known to bioaccumulate trace metals in their mantel, and research suggests that tunicate microbiota plays an important role in this process. Botryllus schlosseri, a marine colonial tunicate, has become a model organism for cellular and developmental studies, yet its ecological interactions are still not well understood. Using an integrated multidisciplinary approach, we established a comprehensive baseline and explored correlations between members of the B. schlosseri microbiome, metabolome, and metallome to elucidate the ecological effects of trace metals in host-microbe-pathogen interactions. We identified significant correlations between metals, including manganese, nickel, cerium, zinc, and cobalt, with various metabolites and bacterial taxa. These findings offer insights into B. schlosseri's biological and chemical interactions with microorganisms and their environment, contributing to bridging the knowledge gap of host-microbiome-environment interactions and establishing a foundation for continuing research on the ecological effects of trace metals in these biological systems.IMPORTANCEGiven the importance of marine invertebrates and their microbial communities in marine ecosystems, we sought to characterize the largely unknown microbial associates, metal sequestration, and metabolite production of the marine colonial tunicate, Botryllus schlosseri, a model organism for cellular and developmental studies. Using an integrated multidisciplinary approach, we identified significant correlations between metals, metabolites, and bacterial taxa. B. schlosseri tissue was highly enriched in metals compared to seawater, and B. schlosseri microbiome beta-diversity was significantly different from seawater. We also introduced the concept of the pan-metabolome to classify metabolites based on their presence or absence across complex samples and found microbial metabolites in both the core and flexible metabolome. These findings offer insights into B. schlosseri's biological and chemical interactions with microorganisms and their environment, bridging the knowledge gap of host-microbiome-environment interactions and establishing a foundation for continuing research on the ecological effects of trace metals in these biological systems.},
}
@article {pmid40954274,
year = {2025},
author = {Moore, TR and Krobath, DM and Chang Chusan, YA and Sanga, U and Webb, P and Pachucki, M and Cuevas, A and Roland, HB and Grant, B and Economos, CD and Nicholson, V and Kumanyika, S},
title = {Systems science methods reveal and address links between discrimination and health disparities in US food systems.},
journal = {Nature food},
volume = {6},
number = {9},
pages = {821-826},
pmid = {40954274},
issn = {2662-1355},
support = {K99 HD109456/HD/NICHD NIH HHS/United States ; P30 DK092950/DK/NIDDK NIH HHS/United States ; K99HD109456//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; },
abstract = {Discriminatory practices are well documented and deeply rooted in food systems. Systems science methods such as social network analysis, system dynamics modeling, and agent-based modeling can help elicit how discriminatory processes arise, interact, and accumulate to contribute to diet-related health disparities. Such methodological approaches can reveal leverage points for advancing equity driven solutions.},
}
@article {pmid40957742,
year = {2026},
author = {Seven, OF and Bicer, M and Adli, MA},
title = {Experimental insights into muscle and joint roles in stumble recovery: A scoping review.},
journal = {Gait &amp; posture},
volume = {123},
number = {},
pages = {109963},
doi = {10.1016/j.gaitpost.2025.08.081},
pmid = {40957742},
issn = {1879-2219},
mesh = {Humans ; Biomechanical Phenomena ; *Muscle, Skeletal/physiology ; *Accidental Falls ; *Gait/physiology ; *Walking/physiology ; Electromyography ; *Joints/physiology ; Lower Extremity/physiology ; Recovery of Function ; },
abstract = {INTRODUCTION: A major concern, often resulting in serious injuries and loss of independence, is caused by falls due to stumbling. Previous works, investigating stumble recovery responses isolated to joint or muscle responses, lacks a comprehensive view of coordinated whole-body recovery.<br><br>METHODS: A scoping review, on Web of Science, Scopus and PubMed, was conducted using keywords related to recovery from anteriorly-directed stumbles induced by physical obstruction of the swing limb during healthy human walking. Extracted data were experimental cohort, swing phase during stumble, perturbation apparatus, recovery strategies, biomechanical responses including joint kinematics, kinetics and muscle activity. A narrative synthesis was provided to summarize findings across studies.<br><br>RESULTS: 23 of 337 identified studies met inclusion criteria. Limited focus on older adults or comparing them to young adults were found. Rigid and stationary obstacles were commonly used, while compliant/movable obstacles were rarely examined, limiting ecological validity. Recovery strategies varied by perturbation timing: foot elevation and lowering in early/mid-swing and late swing stumbles, respectively. Rare responses like delayed lowering and reaching were underexplored. Sagittal plane lower-limb kinematics were frequently reported, with often missing trunk motion, joint moments and EMG from proximal muscles.<br><br>CONCLUSION: This review highlights the importance of rapid and coordinated whole-body responses in stumble recovery, particularly involving the support limb and trunk. Findings suggest rehabilitation should target hip extensor strength, trunk control and support limb engagement to improve recovery. Future research should investigate underexplored strategies, trunk and upper-limb involvement and age-related adaptations to enhance intervention design.},
}
@article {pmid40958166,
year = {2025},
author = {Ghaly, TM and Rajabal, V and Russell, D and Colombi, E and Tetu, SG},
title = {EcoFoldDB: Protein Structure-Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale.},
journal = {Environmental microbiology},
volume = {27},
number = {9},
pages = {e70178},
pmid = {40958166},
issn = {1462-2920},
support = {CE200100029//ARC Centre of Excellence in Synthetic Biology/ ; //Macquarie University Research Fellowship/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism ; Soil Microbiology ; Phylogeny ; *Microbiota/genetics ; Computational Biology/methods ; *Bacterial Proteins/genetics/chemistry ; *Databases, Protein ; Protein Conformation ; },
abstract = {Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes and accelerate discoveries in microbial ecology.},
}
@article {pmid40959203,
year = {2025},
author = {Beene, D and Lin, Y and Hoover, JH and Shi, X},
title = {Deconstructing rurality to better "place" health data.},
journal = {International journal of geographical information science : IJGIS},
volume = {},
number = {},
pages = {},
pmid = {40959203},
issn = {1365-8816},
support = {P42 ES025589/ES/NIEHS NIH HHS/United States ; UH3 OD023344/OD/NIH HHS/United States ; UG3 OD023344/OD/NIH HHS/United States ; P30 ES032755/ES/NIEHS NIH HHS/United States ; P50 MD015706/MD/NIMHD NIH HHS/United States ; P30 ES006694/ES/NIEHS NIH HHS/United States ; },
abstract = {Rural-urban classification schemes are frequently used in ecological studies of population health. However, the algorithms used to produce these classifications as well as their underlying assumptions may not match their intended use in health research. Here, we focus on the spatial distribution of features of the physical environment that are related to health - such as healthcare - to examine the extent to which eight classification schemes capture the heterogeneous context of rural places. We further explore how well rural-urban classifications distinguish between different types of rural places by comparing rural Tribal reservations with other rural areas in the American southwest. Because health services and infrastructure are often distributed through state and federal programs to underserved populations in rural areas, this approach speaks to the broader political implications in how rural communities are defined and represented. Results indicate that rural-urban classifications do not adequately reflect heterogeneous contexts within and across rural places. We advocate for more appropriate population health models that explain contextual differences in the relationship between health and place.},
}
@article {pmid40962773,
year = {2025},
author = {Zhao, ZL and Jiang, X and Su, Y and Yin, LJ and Luo, T and Zhao, WQ and Luo, JH},
title = {[Analysis of Vegetation Changes and Influencing Factors in Guiyang City over the Past 33 Years Based on the kNDVI and OPGD Model].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {9},
pages = {5839-5849},
doi = {10.13227/j.hjkx.202408129},
pmid = {40962773},
issn = {0250-3301},
mesh = {China ; *Ecosystem ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; Cities ; *Models, Theoretical ; *Conservation of Natural Resources ; *Plant Development ; Geographic Information Systems ; Satellite Imagery ; },
abstract = {The vegetation index is a critical indicator for monitoring changes in terrestrial ecosystems， and understanding the spatiotemporal characteristics of vegetation changes and their potential driving factors is essential for improving regional ecological protection and management. This study utilized eight periods of Landsat remote sensing images from 1990 to 2023 to calculate the kernel normalized difference vegetation index （kNDVI） for Guiyang City using the Google Earth engine （GEE） platform. The Theil-Sen + Mann-Kendall trend analysis method was applied to assess the trends and significance levels of kNDVI changes， and the Hurst index was used to evaluate the persistence and future trends of kNDVI. Additionally， the optimal parameters geographic detector （OPGD） was employed to analyze the driving mechanisms behind the spatial differentiation of kNDVI. The study produced the following results： ① From 1990 to 2023， the kNDVI in Guiyang City exhibited a fluctuating upward trend over four distinct phases， with significant spatial differentiation， generally displaying a north-high， south-low distribution pattern. ② Over the 33 years， 74.62% of the area in Guiyang City experienced improvement in vegetation cover， while 25.14% showed signs of degradation. ③ The average Hurst index was 0.610 2， indicating weak persistence and suggesting a trend of continued improvement into the future for vegetation kNDVI in Guiyang City. ④ The land-use type factor （0.231 2） showed the strongest explanatory power for the spatial differentiation of vegetation kNDVI. The interactions between factors exhibited both nonlinear enhancement and bi-factor enhancement， with the combination of land use and other factors synergistically explaining the spatial differentiation of kNDVI more effectively.},
}
@article {pmid40963762,
year = {2025},
author = {Dey, D and Lateef, HA and Leroux, A and Zipunnikov, V and Merikangas, K},
title = {Associations Between Daily Outdoor Temperature and Subjective Real-time Ratings of Emotional States and Sleep in Mood Disorder Subtypes.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40963762},
support = {Z01 MH002804/ImNIH/Intramural NIH HHS/United States ; ZIA MH002804/ImNIH/Intramural NIH HHS/United States ; ZIA MH002954/ImNIH/Intramural NIH HHS/United States ; },
abstract = {Growing evidence for the influence of weather on mental health at both the aggregate level indices of mental health statistics of hospitalizations, morbidity, and mortality, and individual level dynamics of mood states. Most research on this topic has focused on light exposure and depressed mood as the sole indicators of seasonal fluctuations of mood disorders. This paper evaluates the association between daily maximum outdoor temperature (DMOT) and contemporaneously reported mood, energy, anxiousness, and sleep quality assessed with Ecological Momentary Assessment (EMA) in a community-based sample of 452 people, aged 11 to 85 years, comprising people with or without a history of mood disorders. After controlling for demographics, daily activity levels, and daytime cloud coverage as an index of light exposure, we found that higher DMOT was associated with better mood, increased energy, and better sleep quality among those with with a history of mood disorders, particularly in the spring among people with a history of Bipolar Disorder (BD) who tended to exhibit more seasonal changes than controls. These findings suggest that the dynamics of mood, energy, and sleep may underlie the aggregate population-level influences of temperature and correlated environmental influences on negative mental health outcomes, particularly among those with BD. Therefore, the conceptualization of risk and intervention for mood disorders should consider both the aggregate influences of temperature and light and associated environmental conditions, as well as individual-level sleep quality and energy as potential mechanisms for seasonal patterns of emotional states.},
}
@article {pmid40965023,
year = {2025},
author = {Li, S and Chen, P and Zhang, J and Wang, B},
title = {MBLEformer: Multi-Scale Bidirectional Lesion Enhancement Transformer for Cervical Cancer Image Segmentation.},
journal = {Current medical imaging},
volume = {21},
number = {},
pages = {e15734056357180},
pmid = {40965023},
issn = {1573-4056},
mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/diagnostic imaging ; Neural Networks, Computer ; *Image Interpretation, Computer-Assisted/methods ; Deep Learning ; Colposcopy ; Iodides ; *Image Processing, Computer-Assisted/methods ; },
abstract = {BACKGROUND: Accurate segmentation of lesion areas from Lugol's Iodine Staining images is crucial for screening pre-cancerous cervical lesions. However, in underdeveloped regions lacking skilled clinicians, this method may lead to misdiagnosis and missed diagnoses. In recent years, deep learning methods have been widely applied to assist in medical image segmentation.<br><br>OBJECTIVE: This study aims to improve the accuracy of cervical cancer lesion segmentation by addressing the limitations of Convolutional Neural Networks (CNNs) and attention mechanisms in capturing global features and refining upsampling details.<br><br>METHODS: This paper presents a Multi-Scale Bidirectional Lesion Enhancement Network, named MBLEformer, which employs the Swin Transformer encoder to extract image features at multiple stages and utilizes a multi-scale attention mechanism to capture semantic features from different perspectives. Additionally, a bidirectional lesion enhancement upsampling strategy is introduced to refine the edge details of lesion areas.<br><br>RESULTS: Experimental results demonstrate that the proposed model exhibits superior segmentation performance on a proprietary cervical cancer colposcopic dataset, outperforming other medical image segmentation methods, with a mean Intersection over Union (mIoU) of 82.5%, accuracy, and specificity of 94.9% and 83.6%.<br><br>CONCLUSION: MBLEformer significantly improves the accuracy of lesion segmentation in iodine-stained cervical cancer images, with the potential to enhance the efficiency and accuracy of pre-cancerous lesion diagnosis and help address the issue of imbalanced medical resources.},
}
@article {pmid40965697,
year = {2025},
author = {Serpico, J and Choi, KH and Zambrano-Luna, BA and Wang, TX and Wang, H},
title = {Decoding the spatial spread of cyanobacterial blooms in an epilimnion.},
journal = {Journal of mathematical biology},
volume = {91},
number = {4},
pages = {44},
pmid = {40965697},
issn = {1432-1416},
support = {Individual Discovery Grant RGPIN-2020-03911//Natural Sciences and Engineering Research Council of Canada/ ; Discovery Accelerator Supplement Award RGPAS-2020-00090//Natural Sciences and Engineering Research Council of Canada/ ; Tier 1 Canada Research Chair Award//Canada Research Chairs/ ; },
mesh = {*Cyanobacteria/growth &amp; development ; *Lakes/microbiology ; *Models, Biological ; Ecosystem ; Biomass ; Mathematical Concepts ; Geographic Information Systems ; *Eutrophication ; Computer Simulation ; Environmental Monitoring/statistics &amp; numerical data ; *Harmful Algal Bloom ; },
abstract = {Cyanobacterial blooms (CBs) pose significant global challenges due to their harmful toxins and socio-economic impacts, with nutrient availability playing a key role in their growth, as described by ecological stoichiometry (ES). However, real-world ecosystems exhibit spatial heterogeneity, limiting the applicability of simpler, spatially uniform models. To address this, we develop a spatially explicit partial differential equation model based on ES to study cyanobacteria in the epilimnion of freshwater systems. We establish the well-posedness of the model and perform a stability analysis, showing that it admits two linearly stable steady states, leading to either extinction or a spatially uniform positive equilibrium where cyanobacterial biomass stabilizes at its carrying capacity. Further, we discuss the possibility of long-term spatially nonuniform solution with small diffusion and space-dependent parameters. We use the finite elements method (FEM) to numerically solve our system on a real lake domain derived from Geographic Information System (GIS) data and realistic wind conditions extrapolated from ERA5-Land. Additionally, we use a cyanobacteria estimation (CE) obtained from Sentinel-2 to set initial conditions, and we achieve strong model validation metrics. Our numerical results highlight the importance of lake shape and size in bloom monitoring, while global sensitivity analysis using Sobol Indices identifies light attenuation and intensity as primary drivers of bloom variation, with water movement influencing early bloom stages and nutrient input becoming critical over time. This model supports continuous water-quality monitoring, informing agricultural, recreational, economic, and public health strategies for mitigating CBs.},
}
@article {pmid40966233,
year = {2025},
author = {Lee, J and Suh, Y},
title = {Physical activity and its associated factors among adults with chronic kidney disease in a community setting: A secondary data analysis.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0332604},
pmid = {40966233},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Renal Insufficiency, Chronic/physiopathology/epidemiology ; *Exercise/physiology ; Middle Aged ; Adult ; Aged ; Republic of Korea/epidemiology ; Nutrition Surveys ; Glomerular Filtration Rate ; Quality of Life ; Secondary Data Analysis ; },
abstract = {BACKGROUND: Physical activity in patients with chronic kidney disease is important as it helps lowers blood pressure, reduces inflammatory markers, improves cognitive function, and improves health-related quality of life. However, there is a lack of studies accurately assess physical activity levels in this population.<br><br>OBJECTIVE: This study aimed to examine the characteristics of chronic kidney disease patients across eGFR stages, assess the proportion of Korean adults with chronic kidney disease meeting recommended physical activity levels, and identify the factors associated with meeting the weekly physical activity recommendation.<br><br>METHODS: We conducted a secondary analysis of data from the 2016-2020 Korean National Health and Nutrition Examination Survey. Descriptive statistics and logistic regression were used to examine physical activity patterns and associated factors.<br><br>RESULTS: Among CKD patients, 79.5% engaged in insufficient physical activity. Factors significantly associated with sufficient activity included sex, smoking status, activity limitation, and eGFR.<br><br>CONCLUSIONS: Tailoring physical activity interventions is crucial, considering the patient's clinical condition, physical performance, and demographic factors.},
}
@article {pmid40968609,
year = {2025},
author = {Kim, EM and Koh, DH and Sung, S and Hong, Y and Moon, S and Lee, JE and Ko, KP and Park, SK and Min, J and Choi, S and Park, JH and Lee, SG and Kim, HC and Park, DU and Kim, I},
title = {Fraction of Cancer Attributable to Occupational Carcinogens in Korea between 2015 and 2030.},
journal = {Cancer research and treatment},
volume = {},
number = {},
pages = {},
doi = {10.4143/crt.2025.193},
pmid = {40968609},
issn = {2005-9256},
abstract = {PURPOSE: To estimate the contribution of occupational carcinogens to cancer incidence and mortality in the Korean population between 2015 and 2030.<br><br>MATERIALS AND METHODS: We selected occupational carcinogens classified as International Agency for Research on Cancer (IARC) Group 1 and estimated the prevalence of exposure using data from the Korean CARcinogen EXposure (K-CAREX) and previous studies. Relative risks were calculated using published literature through a meta-analysis. Levin's formula was used to estimate population attributable fraction (PAF) while considering a 15-year latency period between exposure, cancer incidence, and death. Additionally, trends in cancer PAF were calculated up to 2030, assuming constant relative risks and a 15-year latency period.<br><br>RESULTS: In 2015, the PAFs for occupational carcinogen-related cancer incidence and mortality were 1.00% (men: 1.75%, women: 0.15%) and 1.97% (men: 2.97%, women: 0.33%), respectively, with asbestos being the largest contributor (incidence: 0.48%; mortality: 0.98%). In 2030, the PAFs for occupational carcinogen-related cancer incidence and mortality were 0.34% (men: 0.62%, women: 0.07%) and 0.80% (men: 1.22%; women: 0.15%), respectively, with diesel engine exhaust being projected to become the largest contributor by 2030 (incidence: 0.16%, mortality: 0.41%).<br><br>CONCLUSION: The PAFs of occupational carcinogens in Korea between 2015 and 2030 were estimated to be very low in the general population, and the values are expected to decrease over time owing to various regulations to prevent exposure to occupational carcinogens. Therefore, while regulating well-known occupational carcinogens, efforts should be made to monitor newly identified ones to ensure prompt implementation of preventive measures.},
}
@article {pmid40970218,
year = {2024},
author = {Finn, RD and Balech, B and Burgin, J and Chua, P and Corre, E and Cox, CJ and Donati, C and Dos Santos, VM and Fosso, B and Hancock, J and Heil, KF and Ishaque, N and Kale, V and Kunath, BJ and Médigue, C and Nogueira, T and Pafilis, E and Pesole, G and Richardson, L and Santamaria, M and Strepis, N and Van Den Bossche, T and Vizcaíno, JA and Zafeiropoulos, H and Willassen, NP and Pelletier, E and Batut, B},
title = {Establishing the ELIXIR Microbiome Community.},
journal = {F1000Research},
volume = {13},
number = {},
pages = {},
pmid = {40970218},
issn = {2046-1402},
mesh = {Computational Biology ; *Metagenomics/methods ; *Microbiota ; },
abstract = {Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and identifying solutions to the computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine microbiome studies, but are broadly applicable to other biomes. Thus, expanding this Marine Metagenomics Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broader range of biomes and link expertise across 'omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.},
}
@article {pmid40971328,
year = {2025},
author = {Bock, O and Huang, JY and Wigge, M and Bieche, C and Kehm, C and Richter, N and Fink, GR and Onur, OA},
title = {Route-following deficits in amnestic mild cognitive impairment: Is the dual encoding of route-following strategies impaired?.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {108},
number = {2},
pages = {606-615},
doi = {10.1177/13872877251378658},
pmid = {40971328},
issn = {1875-8908},
mesh = {Case-Control Studies ; Virtual Reality ; Cues ; *Mental Recall/physiology ; *Orientation, Spatial/physiology ; *Amnesia/physiopathology/psychology ; *Cognitive Dysfunction/physiopathology/psychology ; *Maze Learning/physiology ; Humans ; Male ; Female ; Aged ; Aged, 80 and over ; },
abstract = {BackgroundOne of the earliest signs of amnestic mild cognitive impairment (MCI) and neurodegenerative dementia (ND) is spatial disorientation, e.g., getting lost on previously familiar routes. Healthy individuals often follow routes by combining two strategies, serial recall of directions and cue-direction associations, but the integration of these two strategies may be degraded in amnestic MCI and ND.ObjectiveTo evaluate whether impaired integration of the two strategies (dual encoding) contributes to the route-following deficits in amnestic MCI.MethodsTwenty-five patients with amnestic MCI and 25 age-matched healthy controls (HC) followed routes through virtual mazes that allowed the use of the serial order strategy only (maze S), the associative cue strategy only (maze A), or both strategies (maze SA).ResultsFor longer routes, accuracy in maze SA exceeded that in mazes S and A, confirming the existence of a dual encoding benefit. The magnitude of this benefit was comparable in both groups. In contrast, performance on an additional dual-task test was poorer in MCI than in HC.ConclusionsWe attribute the dissociation between preserved dual encoding and impaired dual-tasking in amnestic MCI not to fundamental differences in the underlying mechanisms, but rather to the different ecological validity of the two experimental paradigms. Our findings suggest that spatial orientation training in amnestic MCI need not target dual encoding.},
}
@article {pmid40971701,
year = {2025},
author = {Schumann, PG and Bundy, J and Haggard, DE and Everett, L and Harrill, JA and Harris, F and Ryoo, D and Collins, J and Rivetti, C and Campos, B and Hodges, G and LaLone, CA},
title = {Zebrafish cell lines and high-throughput transcriptomics: advancing in vitro and bioinformatics methods for supporting environmental risk assessment.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {208},
number = {2},
pages = {343-356},
pmid = {40971701},
issn = {1096-0929},
support = {//Cooperative Research and Development Agreement/ ; # 1289-20//Unilever Global IP Limited/ ; },
mesh = {*Zebrafish/genetics ; Animals ; Risk Assessment ; *Computational Biology/methods ; Cell Line ; *Transcriptome/drug effects ; *High-Throughput Screening Assays ; *Gene Expression Profiling ; *Toxicity Tests/methods ; *Water Pollutants, Chemical/toxicity ; },
abstract = {Historic animal-based toxicity testing methods cannot keep pace with the need for prioritizing new and existing chemicals for comprehensive risk assessment. New approach methodologies such as high-throughput in vitro transcriptomics screening have emerged to address this challenge. However, most in vitro methods were developed using mammalian cell lines, including human, and may not adequately represent environmental species, potentially limiting the utility of this methodology for supporting environmental risk assessment. The objective of this study was to evaluate whether zebrafish cell lines can generate biologically meaningful chemical effects data in a high-throughput transcriptomics pipeline that is protective of toxicologically relevant aquatic apical endpoints. Forty-two test chemicals were screened in 2 commercially available zebrafish cell lines (ZFL liver and ZEM2S embryonic fibroblast) using the TempO-Seq zS1500+ platform. Transcriptomic points-of-departure (tPODs) were derived using 2 methods: Gene-level analysis (tPODgenes) with BMDExpress software and biological pathway-altering concentrations (BPACs/tPODsignatures) from signature-based dose-response analysis. When converted to predicted external water concentrations using quantitative in vitro-in vivo extrapolation models, tPODs were generally protective of aquatic in vivo endpoints from the ECOTOX Knowledgebase. Differential gene expression and biological pathway analysis revealed potential cell-type-specific effects for several chemicals, highlighting the value of using multiple cell types for capturing tissue-specific responses. Lastly, the biological pathway information was used to extrapolate the chemical effects data across species through an integration of protein-protein interaction network analysis and the Sequence Alignment to Predict Across Species Susceptibility tool, which has significant implications for improving the ecological relevance of these methods.},
}
@article {pmid40971902,
year = {2025},
author = {Gontjes, KJ and Singh, A and Sansom, SE and Boyko, JD and Smith, SA and Lautenbach, E and Snitkin, E},
title = {Phylogenetic Context of Antibiotic Resistance Provides Insights into the Dynamics of Resistance Emergence and Spread.},
journal = {The Journal of infectious diseases},
volume = {232},
number = {6},
pages = {e992-e1002},
pmid = {40971902},
issn = {1537-6613},
support = {F31-AI186288//National Institute of Allergy and Infectious Diseases/ ; KL2 TR002387/TR/NCATS NIH HHS/United States ; U19AI181767//National Institute of Allergy and Infectious Diseases/ ; T32-HG000040/HG/NHGRI NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; 2217116//National Science Foundation/ ; U19 AI181767/AI/NIAID NIH HHS/United States ; 5R01AI148259//National Institute of Allergy and Infectious Diseases/ ; F31 AI186288/AI/NIAID NIH HHS/United States ; R01 AI148259/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Phylogeny ; *Anti-Bacterial Agents/pharmacology ; *Klebsiella pneumoniae/drug effects/genetics/classification/isolation &amp; purification ; *Klebsiella Infections/microbiology/epidemiology/transmission/drug therapy ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Carbapenems/pharmacology ; Male ; *Drug Resistance, Bacterial/genetics ; Female ; Drug Resistance, Multiple, Bacterial/genetics ; Aged ; Middle Aged ; },
abstract = {BACKGROUND: To ameliorate the antibiotic resistance crisis, the drivers of resistance emergence and resistance spread must be better understood.<br><br>METHODS: Whole-genome sequencing and susceptibility testing were performed on clinical carbapenem-resistant Klebsiella pneumoniae isolates collected from August 2014 to July 2015 across 12 long-term acute care hospitals. Ancestral state reconstruction partitioned patients with resistant strains into those that likely acquired resistance via de novo evolution or cross-transmission. Logistic regression was used to evaluate the associations between patient characteristics/exposures and these 2 pathways: resistance due to predicted within-host emergence of resistance and resistance due to predicted cross-transmission. This framework is available in the user-friendly R package, phyloAMR (https://github.com/kylegontjes/phyloAMR).<br><br>RESULTS: Phylogenetic analysis of 386 epidemic lineage carbapenem-resistant K. pneumoniae sequence type 258 isolates revealed differences in the relative contribution of de novo evolution and cross-transmission to the burden of resistance to 5 antibiotics. Clade-specific variations in rates of resistance emergence and their frequency and magnitude of spread were detected for each antibiotic. Phylogenetically informed regression modeling identified distinct clinical risk factors associated with each pathway. Exposure to the cognate antibiotic was an independent risk factor for resistance emergence (trimethoprim-sulfamethoxazole, colistin, and novel beta-lactam/beta-lactamase inhibitors) and resistance spread (trimethoprim-sulfamethoxazole, amikacin, and colistin). In addition to antibiotic exposures, comorbidities (eg, stage IV + decubitus ulcers) and indwelling medical devices (eg, gastrostomy tubes) were detected as unique risk factors for resistance spread.<br><br>CONCLUSIONS: Phylogenetic contextualization generated insights and hypotheses into how bacterial genetic background, patient characteristics, and clinical practices influence the emergence and spread of antibiotic resistance.},
}
@article {pmid40972996,
year = {2025},
author = {Paladan, S and Kumbar, B and Govindasamy, D and Patil, S and Chethan Kumar, HB and Yogisharadhya, R and Yadav, P and Vivian, TJW and Gaekwad, SS and Kumar, N and Gulati, BR and Shivachandra, SB and Chanda, MM},
title = {Unravelling ecological factors influencing phylodynamics of Kyasanur Forest Disease in India.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {135},
number = {},
pages = {105831},
doi = {10.1016/j.meegid.2025.105831},
pmid = {40972996},
issn = {1567-7257},
mesh = {India/epidemiology ; *Kyasanur Forest Disease/epidemiology/virology/transmission ; Phylogeny ; *Encephalitis Viruses, Tick-Borne/genetics/classification ; Humans ; Genome, Viral ; Animals ; },
abstract = {Kyasanur Forest Disease Virus (KFDV) is a tick-borne flavivirus endemic to the Western Ghats region of India, with increasing reports of geographic expansion. This study employs phylogenetic analysis and spatial diffusion modeling to understand the evolutionary dynamics and transmission patterns of KFDV. Whole genome and E-gene sequences were analysed to identify major phylogenetic clusters, transmission velocity, and environmental factors influencing viral spread. The analysis revealed two primary phylogenetic clusters: Cluster A, originating in Karnataka, and linked to initial outbreaks (1957-1972) and subsequent re-emergence post-2010 in Karnataka, Kerala, and Goa; and Cluster B, which expanded from Maharashtra in the late 1970s into Tamil Nadu, Karnataka, and Kerala. Phylogenetic findings indicated a slow mutation rate, indicative of long-term viral persistence in sylvatic reservoirs rather than sustained human-human transmission. Spatial diffusion analysis estimated a median transmission velocity of 59.67 km/year. Environmental factors such as deforestation, land cover change, and livestock density acted as facilitators of viral spread, while urbanization, open water bodies, and precipitation served as resistance factors. The findings underscore the need for enhanced surveillance, ecological monitoring, and public health interventions to mitigate the increasing risk of KFD outbreaks. This study provides a comprehensive framework for understanding KFDV transmission and evolution, integrating phylogenetic and ecological data to improve risk assessment and guide control strategies in both endemic and emerging regions.},
}
@article {pmid40976215,
year = {2025},
author = {Kakuma, M and Wada, T and Murakami, M and Tatsuno, T and Ishii, N and Kobayashi, NI and Kurosawa, T and Sayama, Y and Nihei, N and Ohte, N},
title = {Environmental and biological drivers of [137]Cs accumulation in freshwater fish across forested and downstream sites in Fukushima.},
journal = {Journal of environmental radioactivity},
volume = {290},
number = {},
pages = {107810},
doi = {10.1016/j.jenvrad.2025.107810},
pmid = {40976215},
issn = {1879-1700},
mesh = {Animals ; *Cesium Radioisotopes/analysis/metabolism ; *Fukushima Nuclear Accident ; *Water Pollutants, Radioactive/metabolism/analysis ; *Radiation Monitoring ; *Fishes/metabolism ; Japan ; Forests ; Rivers ; Fresh Water ; },
abstract = {To elucidate ecological factors governing [137]Cs accumulation in freshwater fish, we examined 10 species collected from forested headwater streams and downstream reaches of rivers flowing through the Fukushima evacuation zone between 2020 and 2022. By integrating land cover data with isotopic and body size metrics, our study clarifies mechanisms shaping radiocesium distribution across fish communities in post-accident environments. Individuals exceeding the Japanese regulatory limit of 100 Bq/kg-wet were found at all sites, and fish/water concentration ratios of [137]Cs varied widely, from 9.7 × 10 L/kg-wet in a sea-run masu salmon to 1.2 × 10[6] L/kg-wet in a Japanese dace. White-spotted charr and masu salmon, both typical stream-dwelling salmonids, exhibited significantly higher concentration ratios than the other species. Fish from areas with greater forest cover exhibited consistently elevated [137]Cs concentrations, indicating that forests serve as persistent sources of radiocesium to aquatic food webs more than a decade after the accident. Stable isotope analysis showed a significant positive association between terrestrial carbon contribution and [137]Cs concentration, demonstrating that individuals assimilating more terrestrial-derived resources tended to accumulate higher contamination. A positive relationship was also observed between relative body size and [137]Cs concentration, suggesting that growth-related traits influence accumulation. These results suggest that forest connectivity, dietary reliance on allochthonous resources, and individual growth characteristics collectively influence the accumulation of [137]Cs in freshwater fish. The approach and findings provide quantitative evidence for species- and site-specific processes underlying long-term radiocesium dynamics in forested river networks, informing risk assessment and fisheries management in radiologically impacted landscapes.},
}
@article {pmid40979437,
year = {2025},
author = {Atagong, SD and Tonnang, H and Senagi, K and Wamalwa, M and Agboka, KM and Odindi, J},
title = {A review on knowledge and information extraction from PDF documents and storage approaches.},
journal = {Frontiers in artificial intelligence},
volume = {8},
number = {},
pages = {1466092},
pmid = {40979437},
issn = {2624-8212},
abstract = {INTRODUCTION: Automating the extraction of information from Portable Document Format (PDF) documents represents a major advancement in information extraction, with applications in various domains such as healthcare, law, or biochemistry. However, existing solutions face challenges related to accuracy, domain adaptability, and implementation complexity.<br><br>METHODS: A systematic review of the literature was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology to examine approaches and trends in PDF information extraction and storage approaches.<br><br>RESULTS: The review revealed three dominant methodological categories: rule-based systems, statistical learning models, and neural network-based approaches. Key limitations include the rigidity of rule-based methods, the lack of annotated domain-specific datasets for learning-based approaches, and issues such as hallucinations in large language models.<br><br>DISCUSSION: To overcome these limitations, a conceptual framework is proposed comprising nine core components: project manager, document manager, document pre-processor, ontology manager, information extractor, annotation engine, question-answering tool, knowledge visualizer, and data exporter. This framework aims to improve the accuracy, adaptability, and usability of PDF information extraction systems.},
}
@article {pmid40980745,
year = {2024},
author = {Boyes, D and Broad, GR and Sivess, L and Holt, S and Holland, PWH and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Brown China-mark moth, Elophila nymphaeata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {155},
pmid = {40980745},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Elophila nymphaeata (the Brown China-mark moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 734.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,079 protein coding genes.},
}
@article {pmid40986480,
year = {2025},
author = {Constant, A and Paquin, V and Ackerman, RA and Depp, CA and Moore, RC and Harvey, PD and Pinkham, AE},
title = {Exploring the clinical utility of rhythmic digital markers for schizophrenia.},
journal = {PLOS digital health},
volume = {4},
number = {9},
pages = {e0001010},
pmid = {40986480},
issn = {2767-3170},
abstract = {This study investigates the clinical utility of rhythmic digital markers (RDMs) in schizophrenia. RDMs are digital markers capturing behavioral rhythms over different timescales - within 24 hours span (ultradian), at a span of 24 hours (circadian), or over cycles of more than 24 hours (infradian). While previous research has explored digital markers for schizophrenia, the focus has primarily been on sensor data variability rather than rhythmic patterns. This study introduces two RDMs: an entropy RDM, which quantifies uncertainty in activity distribution over the infradian cycles, and a dynamic RDM, which is derived from models of transitions in entropy and psychotic symptom intensity using Markov chain analysis. Data were ecological momentary assessments (EMAs) of 39 activities collected from 390 individuals diagnosed with schizophrenia (N = 153) or bipolar disorder (N = 192) and controls (N = 45). We assessed associations between RDMs and symptom severity and whether participants could be differentiated based on these RDMs. We found that participants with schizophrenia significantly differed on dynamic RDMs, suggesting a potential diagnostic utility. However, dynamic RDMs were not associated with symptom severity, and entropy RDM had no significant clinical correlate. Our findings contribute to the growing evidence on digital markers in psychiatry and highlight the potential of rhythmic digital markers (RDMs) in characterizing digital phenotypes for schizophrenia.},
}
@article {pmid40986865,
year = {2025},
author = {Sun, Y and Jaiswal, A and Slade, C and Phillips, KT and Benzo, RM and Washington, P},
title = {Associations Between Social Determinants of Health and Adherence in Mobile-Based Ecological Momentary Assessment: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e69831},
pmid = {40986865},
issn = {1438-8871},
mesh = {Humans ; Male ; *Ecological Momentary Assessment ; Mobile Applications ; *Patient Compliance ; *Social Determinants of Health ; Telemedicine ; },
abstract = {BACKGROUND: Ecological momentary assessment (EMA) involves repeated prompts to capture real-time self-reported health outcomes and behaviors via mobile devices. With the rise of mobile health (mHealth) technologies, EMA has been applied across diverse populations and health domains. However, the extent to which EMA engagement and data quality vary across social determinants of health (SDoH) remains underexplored. Emerging evidence suggests that EMA adherence and data completeness may be sometimes associated with participant characteristics such as socioeconomic status, race/ethnicity, and education level. These associations may sometimes influence who engages with EMA protocols and the types of contextual data captured. Despite growing interest in these patterns, no review to date has synthesized evidence on how SDoH relate to EMA compliance and engagement.<br><br>OBJECTIVE: We conducted a scoping review to study two research questions: (R1) how EMA compliance rates in health studies can differ across SDoH and (R2) what types of SDoH have been identified through EMA health studies.<br><br>METHODS: Following PRISMA-ScR guidelines, we searched PubMed, Web of Science, and EBSCOhost using two sets of queries targeting EMA and its relationship to SDoH. Eligible studies were peer reviewed, were published in English between 2013 and 2024, and used mobile-based EMA methods. Studies were included if they (1) reported on differences in EMA compliance by SDoH or (2) reported at least one SDoH observed or uncovered during an EMA study. We used the social ecological model (SEM) as a guiding framework to categorize and interpret SDoH across individual, interpersonal, community, and societal levels. A qualitative thematic synthesis was conducted to iteratively and collaboratively extract, categorize, and review determinants.<br><br>RESULTS: We analyzed 48 eligible studies, of which 35 addressed R1 by examining compliance patterns across various SDoH. Using the SEM, we identified 13 determinants categorized across 4 levels: individual (eg, daily routine, biological sex, age, socioeconomic status, language, education, and race or ethnicity), interpersonal (eg, social support), community and organizational (eg, social context, social acceptance, stigmatization, and youth culture), and policy or societal (eg, systemic and structural barriers). These studies described differences in EMA response rates, compliance, and dropout associated with these determinants, often among vulnerable populations. The remaining 13 studies addressed R2, demonstrating examples of the types of SDoH that EMA research can uncover, including family culture, social support, social contexts, stigmatization, gender norms, heroic narratives, LGBTQ+ culture, racial discrimination, and systematic and structural barriers.<br><br>CONCLUSIONS: This scoping review illustrates how EMA compliance rates can differ across SDoH and highlights the potential of EMA to uncover social and cultural factors linked to health behaviors and outcomes. Our findings underscore the importance of integrating SDoH considerations into EMA study designs to capture context-specific sociocultural dynamics.},
}
@article {pmid40990718,
year = {2025},
author = {Sabino, AU and Guerreiro, DM and Kim, AR and Ramos, AF and Reinitz, J},
title = {Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {10},
pages = {},
pmid = {40990718},
issn = {1367-4811},
support = {R01 OD010936/OD/NIH HHS/United States ; R01 OD010936/NH/NIH HHS/United States ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior-Brasil (CAPES)/ ; //Programa Unificado de Bolsas-USP/ ; },
mesh = {Thermodynamics ; Animals ; Transcription Factors/metabolism ; *Transcription, Genetic ; Drosophila/genetics ; *Gene Expression Regulation ; Enhancer Elements, Genetic ; Drosophila Proteins/genetics/metabolism ; Binding Sites ; *Models, Genetic ; *DNA/chemistry/genetics ; *Sequence Analysis, DNA/methods ; Computational Biology/methods ; Base Sequence ; },
abstract = {MOTIVATION: Understanding how the genome encodes the regulatory logic of transcription is a main challenge of the post-genomic era, and can be overcome with the aid of customized computational tools.<br><br>RESULTS: We report an automated framework for analyzing an ensemble of fits to data of a thermodynamics-based sequence-level model for transcriptional regulation. The fits are clustered accordingly with their intrinsic regulatory logic. A multiscale analysis enables visualization of quantitative features resulting from the deconvolution of the regulatory profile provided by multiple transcription factors interacting with the locus of a gene. Quantitative experimental data on reporters driven by the whole locus of the even-skipped gene in the blastoderm of Drosophila embryos was used for validating our approach. A few clusters of highly active DNA binding sites within the enhancers collectively modulate even-skipped gene transcription. Analysis of variable enhancers' length shows the importance of bound protein-protein interactions for transcriptional regulation. The interplay between activation and quenching enables function conservation of enhancers despite length variations.<br><br>The transcription factor level data used for performing the reported study is accessible in the input files in Zenodo and GitHub as well the full code. Additional data from formerly FlyEx database will be available under request.},
}
@article {pmid40991430,
year = {2025},
author = {Pascal, LV and Chadès, I and Adams, MP and Helmstedt, KJ},
title = {Developing new technologies to protect ecosystems: Planning with adaptive management.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {39},
pages = {e2422002122},
pmid = {40991430},
issn = {1091-6490},
support = {DE200101791//Department of Education and Training | Australian Research Council (ARC)/ ; DE200100683//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {*Conservation of Natural Resources/methods ; *Ecosystem ; Climate Change ; Biodiversity ; Australia ; Coral Reefs ; },
abstract = {Technology development is an essential investment for policymakers to address contemporary global crises, including climate change, biodiversity loss, the energy transition, and emergent infectious diseases. However, investing limited resources in the development of new technologies is risky. The research and development process is unpredictable, with unknown timelines and outcomes. In addition, even after successful development, the effects of deploying a new technology remain uncertain. When confronted with these uncertainties, policymakers must determine how long they should allocate resources to developing new technologies. Informed decisions require anticipating possible successes and failures of both technology development and deployment, which is a challenging optimization task when managing dynamic systems, such as threatened ecological systems. Using an adaptive management approach from AI, we find a time limit new technologies should be developed for, which balances costs, benefits, and uncertainties during development and deployment. We extract clear and transparent general rules for investing in new technologies, building on an analytical approximation. Using Australia's Great Barrier Reef as a case study, we demonstrate that the development time limit ranges between 0 to 45 y before surrendering. We also show how characteristics of an ecological system influence the optimal investment strategy. Our approach can inform the development of new technologies in multiple domains including biodiversity conservation, public health, energy production, and the technology industry more broadly.},
}
@article {pmid40993501,
year = {2025},
author = {Garnier, &#xc9; and Delalandre, L and Segrestin, J and Barkaoui, K and Kazakou, E and Navas, ML and Vile, D and Violle, C and Bernard-Verdier, M and Birouste, M and Blanchard, A and Bumb, I and Cruz, P and Debain, S and Fayolle, A and Fortunel, C and Grigulis, K and Laurent, G and Lavorel, S and Lloret, F and Pérez-Ramos, IM and Prieto, I and Roumet, C},
title = {FAIRTraits: An enriched, FAIR-compliant database of plant traits from Mediterranean populations of 240 species.},
journal = {Ecology},
volume = {106},
number = {9},
pages = {e70219},
pmid = {40993501},
issn = {1939-9170},
support = {AAPFNSO2019OpenMetaPaper-14026//Minist&#xe8;re de l'Enseignement sup&#xe9;rieur et de la Recherche (FNSO Project)/ ; },
mesh = {*Plants/classification ; Mediterranean Region ; *Databases, Factual ; *Plant Physiological Phenomena ; },
abstract = {Trait-based ecology relies on high-quality, well-documented data to explore how plant traits relate to environmental conditions, community assembly, and ecosystem functioning. However, the reuse and synthesis of trait data across studies remain limited by several constraints: a lack of detailed metadata, heterogeneous protocols, absence of individual-level measurements, and underrepresentation of certain trait types-particularly below-ground traits. Many existing datasets also lack the environmental details necessary to investigate trait-environment relationships at local scales. Here, we present FAIRTraits, a comprehensive dataset that addresses these limitations by compiling 189,452 records of quantitative trait measurements collected between 1997 and 2023 from 1955 populations of 240 vascular plant species in the Northern Mediterranean Basin, a region known both for its exceptional biodiversity and as a climate change hotspot. All data were collected by a single research group using consistent and well-documented field and laboratory protocols, ensuring internal consistency across traits, species, sites, and years. FAIRTraits includes 180 traits measured at the individual or replicate level, with no aggregation. It features an unprecedented diversity of traits spanning all major plant organs-leaves, stems, roots, and reproductive parts. These include widely used traits such as specific leaf area and plant height, but also traits that are rarely reported, especially below-ground traits related to root morphology, as well as mechanical properties, phenology, and microbial associations. In addition to raw measurements, species are annotated with categorical descriptors (e.g., life form, photosynthetic pathway, and successional status), and species-level values taken from a Mediterranean flora, for key traits such as reproductive phenology and maximum height. To support analyses that account for environmental variability, each observation is linked to detailed descriptors of the plot where the individual was sampled, including climate data, soil physicochemical properties, and disturbance regime. Full metadata on sampling protocols and measurement methods are provided for every trait and environmental variable. FAIRTraits was built in compliance with the FAIR principles of data management (Findable, Accessible, Interoperable, and Reusable). Metadata are described using the Ecological Metadata Language (EML); trait definitions are standardized using community-endorsed semantic resources. The data are archived across two interoperable repositories: GBIF (via Darwin Core and trait-specific extensions) for taxon-trait associations and InDoRES for environmental and contextual data. These efforts ensure long-term preservation, data traceability, and seamless integration with plant trait databases such as BROT or TRY, and cross-organism initiatives such as the Open Traits Network or the Encyclopedia of Life. FAIRTraits offers a robust, richly documented, and reusable resource for investigating plant functional strategies, trait-environment relationships, and scaling from individuals to communities and ecosystems. It also provides a concrete example of how trait datasets can meet the highest standards of data quality and interoperability-serving as a model for future community-led initiatives in functional ecology. The FAIRTraits database is released under the CC-BY Attribution 4.0 International license.},
}
@article {pmid40995615,
year = {2025},
author = {Kuhara, S and Matsugaki, R and Itoh, H and Oginosawa, Y and Fushimi, K and Matsuda, S and Saeki, S},
title = {Factors Influencing the Availability of Cardiopulmonary Exercise Testing for Patients Undergoing Cardiac Resynchronization Therapy in Japan.},
journal = {Journal of arrhythmia},
volume = {41},
number = {5},
pages = {e70198},
pmid = {40995615},
issn = {1880-4276},
abstract = {BACKGROUND: This study aimed to investigate the implementation rate of cardiopulmonary exercise testing (CPET) in patients undergoing cardiac resynchronization therapy (CRT) or cardiac resynchronization therapy-defibrillator (CRT-D), as well as the associated factors, using real-world data.<br><br>METHODS AND RESULTS: Data from the Diagnostic Procedure Combination System in Japan (2014-2018) was analyzed. The participants were cardiac patients who underwent CRT or CRT-D device implantation (n&#x2009;=&#x2009;3859). The primary outcome was whether CPET was performed after device implantation. Unpaired t-tests and chi-squared tests were used to compare the characteristics of the CPET (+) and CPET (-) groups. Multivariate analysis was used to identify factors associated with CPET performance. CPET was performed in 134 patients (3%). The CPET (-) group was older and had lower Barthel Index (BI) scores at discharge. CPET (+) patients had a higher rate of cardiac rehabilitation. Multivariate analysis revealed that age&#x2009;<&#x2009;70&#x2009;years and BI score&#x2009;&#x2265;&#x2009;85 at discharge were associated with CPET implementation. In-hospital cardiac rehabilitation is also an important determinant.<br><br>CONCLUSIONS: The CPET implementation after CRT or CRT-D was low. Emphasizing the importance of CPET may improve these rates. Future studies should explore strategies to increase its use in this patient population.},
}
@article {pmid40996703,
year = {2025},
author = {Sierra, MA and Ryon, K and Arikatla, MR and Elshafey, R and Bhaskar, H and Proszynski, J and Bhattacharya, C and Shaaban, H and Danko, DC and Ambrose, P and Spaulding, SA and Zambrano, MM and Consortium, TMD and Mason, CE},
title = {The Microbe Directory: a centralized database for biological interpretation of microbiome data.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
pmid = {40996703},
issn = {1758-0463},
support = {U01DA053941/NH/NIH HHS/United States ; U54AG089334/NH/NIH HHS/United States ; R01AI151059/NH/NIH HHS/United States ; 80NSSC24K0728/NASA/NASA/United States ; 80NSSC24K1052/NASA/NASA/United States ; //WorldQuant Foundation/ ; },
mesh = {*Microbiota/genetics ; Humans ; *Databases, Genetic ; Data Curation ; Metadata ; Animals ; Metagenomics ; },
abstract = {The Microbe Directory (TMD) is a centralized database of metadata for microbes from all domains that helps with the biological interpretation of metagenomic data. The database comprises phenotypical and ecological traits of microorganisms, which have been verified by independent manual annotations. This effort has been possible by the help of a community of volunteer students worldwide who were trained in manual curation of microbiology data. To summarize this information, we have built an interactive browser that makes the database accessible to everyone, including non-bioinformaticians. We used the TMD data to analyse microbiome samples from different projects such as MetaSUB, TARA Oceans, Human Microbiome Project, and Sponge Microbiome Project, showcasing the utility of TMD. Furthermore, we compare our microbial annotations with annotations collected by artificial intelligence (AI) and demonstrate that despite the high speed of AI in reviewing and collecting microbial data, annotation requires domain knowledge and therefore manual curation. Collectively, TMD provides a unique source of information that can help to interpret microbiome data and uncover biological associations. Database URL: www.themicrobedirectory.com/.},
}
@article {pmid40996715,
year = {2025},
author = {Fruggiero, I and Maisto, A and Passaro, S and Gentile, D and Nunziata, A and D'Agostino, N},
title = {A new database of chestnut DNA fingerprints for genetic diversity assessment, precise varietal identification, and traceability.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
pmid = {40996715},
issn = {1758-0463},
support = {//Italy-Rural Development Programme/ ; //Italian Ministry of Agriculture/ ; },
mesh = {*Fagaceae/genetics ; *Genetic Variation ; Polymorphism, Single Nucleotide ; *DNA Fingerprinting ; *Databases, Genetic ; *DNA, Plant/genetics ; },
abstract = {The European chestnut (Castanea sativa Mill., Fagaceae) is ecologically and economically important, particularly in countries like Italy, Greece, Spain, and Turkey, where it supports rural economies and ecosystems. Accurate varietal recognition is crucial for managing chestnut groves but is hindered by the limitations of traditional methods, which require costly expertise and struggle to identify young, dormant, or scion trees. Recent advances in molecular tools, particularly single nucleotide polymorphism (SNP) markers identified through Kompetitive Allele-Specific PCR (KASP) technology, have transformed cultivar identification. To harness this potential, we developed KASTRACKdb, a genetic fingerprinting database for European chestnut that now integrates genotypic and phenotypic data for 150 chestnut accessions. Designed to translate KASP analysis results into practical and actionable insights, KASTRACKdb serves as a powerful tool for cultivar identification and management. The database offers three primary query modes and is designed for continuous upgrades, serving a crucial role in cataloguing the genetic diversity of chestnut trees, characterized by broad geographic distributions and significant genetic variation. This diversity is critical for conservation and breeding programs, enabling precise varietal identification and traceability to protect intellectual property, verify authenticity, and support the commercialization of high-value cultivars. Database URL: KASTRACKdb is available online at https://kastrack.crea.gov.it/kastrackdb/?lang=en.},
}
@article {pmid40996892,
year = {2025},
author = {Njoroge, SM and Kulohoma, BW and Falzon, LC and Kamanu, TK and Momanyi, K and Muinde, P and Murungi, MK and Ogendo, A and Ogola, J and Wambua, L and Kangethe, E and Rushton, J and Woolhouse, M and Thomson, NR and Kariuki, S and von Mentzer, A and Fèvre, EM},
title = {Genomic profiling of enterotoxigenic Escherichia coli toxins and adhesins in livestock isolates from Kenya.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001515},
pmid = {40996892},
issn = {2057-5858},
mesh = {*Enterotoxigenic Escherichia coli/genetics/isolation &amp; purification/pathogenicity ; Kenya/epidemiology ; Animals ; *Livestock/microbiology ; *Escherichia coli Infections/microbiology/veterinary ; *Enterotoxins/genetics ; *Escherichia coli Proteins/genetics ; *Adhesins, Bacterial/genetics ; *Bacterial Toxins/genetics ; Virulence Factors/genetics ; Whole Genome Sequencing ; Humans ; Feces/microbiology ; Cattle ; *Adhesins, Escherichia coli/genetics ; },
abstract = {Enterotoxigenic Escherichia coli (ETEC) is a significant cause of diarrhoea in livestock and humans. The epidemiology of ETEC in animals remains understudied, prompting an investigation into the virulence factors and associated adhesins of ETEC in livestock from Western Kenya. Also, there is limited evidence supporting the role of livestock as possible zoonotic reservoirs for ETEC. ETEC strains harbour colonization factors/adhesins and enterotoxins, with animal ETECs exhibiting various adhesins (F4, F5, F6, F17, F18 and F41). Enterotoxins include heat-labile (LT) and heat-stable (ST) toxins and are further divided into LT-I and LT-II and STa and STb, respectively. Additional toxin combinations occur, with ETEC and Shiga toxin-producing E. coli (STEC) hybrids garnering public health significance. Here, we analysed faecal and mesenteric lymph node samples from diverse livestock across three Western Kenyan counties (Busia, Bungoma and Kakamega), using whole-genome sequencing. In silico screening determined the presence of AB5 and A2B5-like toxin genes, including cytolethal distending toxin (cdtABC) along with associated adhesins. To broaden the screening panel, adhesin genes identified were further characterized to identify both known and novel alleles, particularly focusing on human-ETEC colonization factors. Two estA alleles (estA-4-06, estA-6-02) and six eltAB-II toxin alleles (eltAB-II-a2-01, eltAB-II-a3-01, eltAB-II-c1-02, eltAB-II-c6-03, eltAB-II-c6-04 and eltAB-II-c7-02) were identified in livestock. Hybrid ETECs identified were ETEC/STEC present in 6.7% (4/60) of ETEC strains and ETEC with cdtABC type I. An A2B5-like tripartite toxin, potentially resembling the typhoid toxin, was detected in 8.7% (4/46) of the eltAB-II-positive strains. It may have unique effects on enterocytes distinct from known toxins. These findings expand our understanding of ETEC pathogenicity and genetic diversity in animal reservoirs, while also highlighting potential zoonotic risks. They broaden the toxin repertoire, offer adhesin-based vaccine candidates for livestock and provide valuable insights for future vaccine development and public health strategies in the Lake Victoria Crescent ecosystem and beyond.},
}
@article {pmid40997692,
year = {2025},
author = {Zang, H and Feng, Y and Yang, F and Gao, S and Su, M and Li, H},
title = {Multi-media distribution, partitioning behavior, and environmental risk of per- and polyfluoroalkyl substances (PFASs) in the southern coastal zone of Shandong Peninsula, China.},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107562},
doi = {10.1016/j.marenvres.2025.107562},
pmid = {40997692},
issn = {1879-0291},
abstract = {Per- and polyfluoroalkyl substances (PFASs) pose significant ecological threats due to their persistence and toxicity. This study investigates the occurrence, partitioning behavior, and environmental risks of 33 legacy and emerging PFASs in the southern coastal zone of Shandong Peninsula, China. Paired water and sediment samples were collected from 55 sites across groundwater, river, estuarine, tourist beaches and marine ranches. PFASs were ubiquitously detected, with total concentrations (∑PFASs) ranging from 23.41 to 80.62 ng/L in water and 0.38-6.49 ng/g dry weight (dw) in sediment. Except perfluorooctanoic acid (PFOA), perfluorobutanoic acid (PFBA) (6.42 ± 2.26 ng/L) and perfluorobutanesulfonic acid (PFBS) (3.03 ± 1.44 ng/L) dominated aqueous phases, reflecting phased-out replacements of long-chain homologs. Sediments accumulated long-chain compounds (e.g., Perfluorohexanoic acid (PFHxA): 0.92 ± 1.08 ng/g dw; perfluorooctane sulfonic acid (PFOS): 0.45 ± 0.28 ng/g dw), driven by hydrophobic partitioning. Strong positive correlations among long-chain PFASs (e.g., Perfluorododecanoic acid (PFDoDA)- perfluorotetradecanoic acid (PFTeDA), r = 0.882) indicated co-accumulation in organic-rich sediments. Spatial analysis revealed land-to-sea concentration gradients, with maxima in estuaries (52.72 ng/L) and industrial-adjacent sediments (6.48 ng/g dw). Groundwater infiltration (up to 51.53 ng/L) highlighted subsurface transport risks. Sediment-water partition coefficients (log Kd) increased with carbon chain length and salinity, consistent with salting-out effects and reduced electrostatic repulsion. Organic carbon-normalized log Koc values (Kow method) aligned with model predictions for most PFASs. Risk assessment identified high ecological risk for sediment-bound PFOS (RQ > 1) near river discharges, while PFOA posed greater aqueous-phase risks. Emerging PFASs (e.g., 6:2 chlorinated polyfluoroalkyl ether sulfonic acid (6:2 Cl-PFESA)) showed negligible risks. Coastal sediments act as significant PFASs reservoirs, with resuspension potential enabling secondary pollution.},
}
@article {pmid40997859,
year = {2025},
author = {Hu, J and Bao, G and Wu, J and Chen, S and Xu, Y and Wang, H and Tian, L and Fu, Z and Li, N and Yuan, Y},
title = {Freeze-Thaw Cycles Accelerate Plastic Pollution Invasion in Agriculture: Trojan Horse Effect of Microplastic-Plasticizer Contamination Revealed in Rye via Computational Chemistry and Multiomics.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {40},
pages = {25285-25300},
doi = {10.1021/acs.jafc.5c08155},
pmid = {40997859},
issn = {1520-5118},
mesh = {*Soil Pollutants/chemistry/metabolism/toxicity ; *Microplastics/metabolism/chemistry/toxicity/analysis ; *Secale/metabolism/drug effects/chemistry/genetics/growth &amp; development ; *Plasticizers/metabolism/chemistry/toxicity ; Freezing ; Phthalic Acids/metabolism/chemistry/toxicity ; Bacteria/genetics/metabolism/isolation &amp; purification/classification/drug effects ; Agriculture ; Plant Roots/metabolism/drug effects/microbiology ; Multiomics ; },
abstract = {Climate change-related freeze-thaw (FT) cycles intensify combined contamination from diethyl phthalate (DEP) and microplastics (MPs) in agricultural systems. This study examines their synergistic phytotoxicity in hydroponic rye using multidisciplinary approaches, including physiology, transcriptomics, and computational modeling. FT dramatically increased cocontamination risks. Notably, DEP promoted MP uptake into plants by elevating MP surface charge─an effect intensified by FT─resulting in disrupted root function and nutrient absorption. Molecular analyses showed that DEP binds strongly to key proteins (e.g., HSP70; ΔG = -7.6 kcal/mol), inhibiting photosynthesis (net rate reduced by 20.1-64.5%) and altering antioxidant activity. MPs adsorbed DEP, reducing its mobility, while simultaneously reshaping the root microbiome to favor DEP-degrading bacteria (e.g., Rhizobium). Transcriptomic changes were observed in stress-responsive and phytohormone pathways. These results demonstrate that FT cycles exacerbate combined pollutant toxicity through surface charge modification, molecular disruption, and microbial community adaptation, offering important insights for assessing ecological risks under climate-induced stressors.},
}
@article {pmid40997916,
year = {2025},
author = {Zhong, H and Chi, S and Magaña, AA and Fordwour, OB and Foster, LJ},
title = {Integrative Omics and AI-Driven Systems Biology: Multilayer Networks Decoding Apis mellifera Health and Resilience.},
journal = {Journal of proteome research},
volume = {24},
number = {11},
pages = {5305-5318},
pmid = {40997916},
issn = {1535-3907},
mesh = {Bees/physiology/metabolism/genetics ; Animals ; *Systems Biology/methods ; *Artificial Intelligence ; *Proteomics/methods ; *Metabolomics/methods ; Lipidomics/methods ; Machine Learning ; Multiomics ; },
abstract = {Honey bees (Apis mellifera) are vital pollinators essential for maintaining ecosystem stability and global food production, but they face escalating threats from pathogens, agrochemicals, and climate change. Although proteomics has advanced our understanding of bee physiology, single-omics approaches are insufficient to capture the complexity of colony health. This review highlights the rise of integrative multiomics frameworks─combining proteomics, metabolomics, and lipidomics─with artificial intelligence (AI)-based strategies to decode molecular resilience in bees. We summarize recent advances in omics technologies, including spatial and single-cell platforms, mass spectrometry innovations, and customized computational pipelines. Furthermore, we highlight how AI-enhanced multiomics integration facilitates biomarker discovery, elucidates regulatory networks, especially in nonmodel organisms like honey bees. Emerging computational methods such as deep learning, graph neural networks, and multilayer network models offer predictive, scalable, and interpretable insights. Despite challenges like limited sample input and cross-omics heterogeneity, the convergence of omics and machine learning represents a transformative paradigm for decoding complex biological systems. These integrative approaches offer not only a deeper molecular understanding of bee biology but also generalizable frameworks for systems biology in other ecologically relevant species.},
}
@article {pmid40998880,
year = {2025},
author = {Le Scornec, E and Chimienti, M and Corbeau, A and Pajot, A and Weimerskirch, H and Collet, J},
title = {Predicting fisheries from albatross movements requires accounting for individual variability in interaction.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32807},
pmid = {40998880},
issn = {2045-2322},
mesh = {Animals ; *Fisheries ; *Birds/physiology ; Geographic Information Systems ; *Animal Migration ; },
abstract = {Fisheries have major ecological impacts including bycatch of foraging seabirds, but it is often difficult to obtain comprehensive information on the presence of fishing vessels. Automatic Identification System (AIS) data can be used to monitor fisheries and their interactions with GPS-tracked seabirds, but not all vessels have their AIS operational. Bird-tied radar detectors can overcome this limit and complement monitoring, but the technology is recent and costly. We used both methods combined as a training dataset for classification algorithms, to extend the identification of interactions to GPS tracks without radar detectors nor AIS. We studied over 3 years wandering albatrosses from the French Southern Territories, interacting with toothfish and tuna longliners. We used 196 GPS tracks combined with radar detectors, to calculate different movement variables over various scales (time spent in an area, sinuosity, speed) and used a Random Forest to distinguish behaviour in presence or absence of fishing vessels. Our model reached high classification accuracy (ca. 85%) for individual birds included in the training dataset. However, we lost predictive power (around 72% of accuracy, with a drop of specificity from 76 to 59%) when predicting on individuals not included in the training dataset. Our results emphasize the importance of documenting and accounting for individual variations to use animals as sentinels. We discuss the pros and cons of different research avenues (data sampling, classification model, bird species, etc.) to eventually get to predict fisheries from bird movements only.},
}
@article {pmid41000208,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Brown House-moth, Hofmannophila pseudospretella (Stainton, 1849).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {230},
pmid = {41000208},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Hofmannophila pseudospretella (the Brown House-moth; Arthropoda; Insecta; Lepidoptera; Oecophoridae). The genome sequence is 406.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.},
}
@article {pmid41001448,
year = {2025},
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 = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {41001448},
support = {R01 AG046938/AG/NIA NIH HHS/United States ; T32 MH016880/MH/NIMH NIH HHS/United States ; U01 AG009740/AG/NIA NIH HHS/United States ; },
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. 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 estimate time- or age-specific genetic effects, 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.},
}
@article {pmid41001881,
year = {2026},
author = {Rutz, A and Probst, D and Aguilar, C and Akiyama, DY and Alberti, F and Augustijn, HE and Avalon, NE and Beemelmanns, C and Barbieri, HB and Biermann, F and Bridge, AJ and Girón, EC and Cox, R and Crüsemann, M and D'Agostino, PM and Feuermann, M and Gerke, J and García, KG and Holme, JE and Hwang, JY and Iacovelli, R and Jeronimo Barbosa, JC and Kaur, N and Klapper, M and Köhler, AM and Korenskaia, A and Kubach, N and Lee, BT and Loureiro, C and Mantri, S and Narula, S and Meijer, D and Navarro-Muñoz, JC and Nguyen, GS and Paliyal, S and Panghal, M and Rao, L and Sieber, S and Sokolova, N and Sowa, ST and Szenei, J and Terlouw, BR and Weddeling, HG and Yu, J and Ziemert, N and Weber, T and Blin, K and van der Hooft, JJJ and Medema, MH and Zdouc, MM},
title = {MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D635-D642},
pmid = {41001881},
issn = {1362-4962},
support = {101 072 485//Marie Sk&#x142;odowska-Curie/ ; //German Research Foundation/ ; 102 029 187//SINTEF/ ; 2023/06874-4//S&#xe3;o Paulo Research Foundation/ ; //Department of Biotechnology/ ; 101 000 392//Horizon 2020/ ; //National Agri-Food and Biomanufacturing Institute (NABI)/ ; //University Grants Commission/ ; //the Werner Siemens Foundation/ ; //DFG/ ; KICH1.LWV04.21.013//Netherlands Organisation for Scientific Research/ ; F32AT011475/GF/NIH HHS/United States ; //NWO/ ; //State Secretariat for Education, Research and Innovation/ ; 948770-DECIPHER/ERC_/European Research Council/International ; //Horizon Europe programme/ ; //Danish National Research Foundation/ ; MR/V022334/1//UKRI/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; 102 022 750//SINTEF/ ; NNF23OC0086472//Novo Nordisk Foundation/ ; //Hans-Fischer-Gesellschaft/ ; //German Center for Infection Research/ ; 495740318//German Research Foundation/ ; 802736, MORPHEUS//Horizon 2020/ ; 239748522//Deutsche Forschungsgemeinschaft/ ; 2021/08947-3//S&#xe3;o Paulo Research Foundation/ ; 101 072 485//Horizon Europe Marie Sk&#x142;odowska-Curie/ ; 21/07038-0//S&#xe3;o Paulo Research Foundation/ ; 102 029 407//SINTEF/ ; 102024676-14//SINTEF/ ; F32 AT011475/AT/NCCIH NIH HHS/United States ; 862 923//Horizon 2020/ ; 101 081 957//Horizon 2020/ ; },
mesh = {*Enzymes/metabolism/chemistry/genetics ; Substrate Specificity ; *Software ; Humans ; Machine Learning ; Computational Biology/methods ; Internet ; *Databases, Protein ; },
abstract = {Secondary or specialized metabolites show extraordinary structural diversity and potent biological activities relevant for clinical and industrial applications. The biosynthesis of these metabolites usually starts with the assembly of a core 'scaffold', which is subsequently modified by tailoring enzymes to define the molecule's final structure and, in turn, its biological activity profile. Knowledge about reaction and substrate specificity of tailoring enzymes is essential for understanding and computationally predicting metabolite biosynthesis, but this information is usually scattered in the literature. Here, we present MITE, the Minimum Information about a Tailoring Enzyme database. MITE employs a comprehensive set of parameters to annotate tailoring enzymes, defining substrate and reaction specificity by the expressive reaction SMARTS (Simplified Molecular Input Line Entry System Arbitrary Target Specification) chemical pattern language. Both human and machine readable, MITE can be used as a knowledge base, for in silico biosynthesis, or to train machine-learning applications, and tightly integrates with existing resources. Designed as a community-driven and open resource, MITE employs a rolling release model of data curation and expert review. MITE is freely accessible at https://mite.bioinformatics.nl/.},
}
@article {pmid41003170,
year = {2025},
author = {Francesconi, L and Conti, M and Martellos, S and Di Nuzzo, L and Gheza, G and Nimis, PL and Pistocchi, C and Nascimbene, J},
title = {Dolichens: An Information System on the Lichens of the Dolomites.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
pmid = {41003170},
issn = {2309-608X},
support = {DOT199RYN9-2//Ministero dell'universit&#xe0; e della ricerca/ ; },
abstract = {Lichens, despite their key role as environmental indicators and their ecological importance, remain underrepresented in conservation policies, largely due to fragmented exploration of several areas, as well as limited availability of data in digital platforms. The UNESCO World Heritage area of the Dolomites (N Italy) is well-investigated as far as lichen diversity is concerned, with a long history of lichenological exploration since the 19th century. However, the relevant amount of data produced by these efforts was scattered and often not accessible in digital format, thus hindering data accessibility and usability. In this paper, we present Dolichens, a novel web platform designed to aggregate data about lichen diversity in the Dolomites. The platform aims at making available a comprehensive resource to support research, monitoring, and conservation of lichen diversity in the Dolomites, while ensuring data interoperability with the most relevant global repositories.},
}
@article {pmid41004955,
year = {2025},
author = {Qin, J and Wang, Q and Li, W},
title = {Incorporating regional green spaces into greenspace exposure assessment: A nationwide study of 244 Chinese cities.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127369},
doi = {10.1016/j.jenvman.2025.127369},
pmid = {41004955},
issn = {1095-8630},
mesh = {Cities ; China ; Urbanization ; Humans ; Ecosystem ; Transportation ; *Conservation of Natural Resources ; },
abstract = {Green spaces are essential components of urban ecosystems, offering ecological services that support environmental sustainability and enhance human well-being. However, rapid urbanization has caused substantial declines in green space, particularly in rapidly growing cities. In this context, regional green spaces (RGSs), which are defined as green areas located beyond the boundaries of built-up areas, have gained attention for their ecological value and strategic role in enhancing urban resilience. Despite their importance, RGSs remain underrepresented in current greenspace exposure assessment frameworks. To fill this gap, we propose a novel transportation-weighted global greenspace exposure model that integrates RGSs, urban green spaces, and transportation proximity. Using greenspace exposure (GE) as an indicator, the model assesses the spatial distribution and exposure contribution of RGSs. We applied this model to 244 Chinese cities and obtained the following findings: (1) Incorporating RGSs significantly improves GE levels in many cities, particularly in southern and western regions, while also amplifying spatial disparities; (2) The compensatory effect of RGSs was validated, as substantial GE increases were observed under larger RGSs buffer zones; (3) Nighttime light intensity, elevation, and land surface temperature correlate strongly with GE, indicating the influence of both anthropogenic and natural factors. The proposed framework enhances the accuracy of GE assessments by integrating RGSs and transportation networks. Its scalable structure and moderate data requirements enable its application across diverse regions, supporting international efforts toward sustainable urban development.},
}
@article {pmid41006295,
year = {2025},
author = {van Galen, LG and Smith, GR and Margenot, AJ and Waldrop, MP and Crowther, TW and Peay, KG and Jackson, RB and Yu, K and Abrahão, A and Ahmed, TA and Alatalo, JM and Anslan, S and Anthony, MA and Araujo, ASF and Ascher-Jenull, J and Bach, EM and Bahram, M and Baker, CCM and Baldrian, P and Bardgett, RD and Barrios-Garcia, MN and Bastida, F and Beggi, F and Benning, LG and Bragazza, L and Broadbent, AAD and Cano-Díaz, C and Cates, AM and Cerri, CEP and Cesarz, S and Chen, B and Classen, AT and Dahl, MB and Delgado-Baquerizo, M and Eisenhauer, N and Evgrafova, SY and Fanin, N and Fornasier, F and Francisco, R and Franco, ALC and Frey, SD and Fritze, H and García, C and García-Palacios, P and Gómez-Brandón, M and Gonzalez-Polo, M and Gozalo, B and Griffiths, R and Guerra, C and Hallama, M and Hiiesalu, I and Hossain, MZ and Hu, Y and Insam, H and Jassey, VEJ and Jiang, L and Kandeler, E and Kohout, P and Kõljalg, U and Krashevska, V and Li, X and Lu, JZ and Lu, X and Luo, S and Lutz, S and Mackie-Haas, KA and Maestre, FT and Malmivaara-Lämsä, M and Mangelsdorf, K and Manjarrez, M and Marhan, S and Martin, A and Mason, KE and Mayor, J and McCulley, RL and Moora, M and Morais, PV and Muñoz-Rojas, M and Murugan, R and Nottingham, AT and Ochoa, V and Ochoa-Hueso, R and Oja, J and Olsson, PA and Öpik, M and Ostle, N and Peltoniemi, K and Pennanen, T and Pescador, DS and Png, GK and Poll, C and Põlme, S and Potapov, AM and Priemé, A and Pritchard, W and Puissant, J and Rocha, SMB and Rosinger, C and Ruess, L and Sayer, EJ and Scheu, S and Sinsabaugh, RL and Slaughter, LC and Soudzilovskaia, NA and Sousa, JP and Stanish, L and Sugiyama, SI and Tedersoo, L and Trivedi, P and Vahter, T and Voriskova, J and Wagner, D and Wang, C and Wardle, DA and Whitaker, J and Yang, Y and Zhong, Z and Zhu, K and Ziolkowski, LA and Zobel, M and van den Hoogen, J},
title = {A global database of soil microbial phospholipid fatty acids and enzyme activities.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1568},
pmid = {41006295},
issn = {2052-4463},
support = {DEB-1845544//National Science Foundation (NSF)/ ; DEB-1926335//National Science Foundation (NSF)/ ; DGE 1450271//National Science Foundation (NSF)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; 305069/2018-7//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (National Council for Scientific and Technological Development)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; CZ.02.01.01/00/22_008/0004635//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy (Ministry of Education, Youth and Sports)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; PICT 2014-2838//Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (National Agency for Science and Technology, Argentina)/ ; 315260_149807//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; BIPD_01_2021_FCT-PTDC/BIA-CBI/2340/2020, UIDB/05937/2020, UIDP/05937/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816, Ei 862/29-1 and Ei 862/31-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 316045089//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 315415//Academy of Finland (Suomen Akatemia)/ ; PTDC/BIA-CBI/2340/2020//Ministry of Education and Science | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (Portuguese Science and Technology Foundation)/ ; ANR; MIXOPEAT; ANR-17-CE01-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; 31872994//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41922056//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32101286//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32061143027//National Natural Science Foundation of China (National Science Foundation of China)/ ; CIDEGENT/2018/041//Generalitat Valenciana (Regional Government of Valencia)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; NE/T012226//National Eye Research Centre (NERC)/ ; PRG1065, PRG1789, PSG784//Ministry of Education and Research | Estonian Research Competency Council (Research Competency Council)/ ; 2021M693360//China Postdoctoral Science Foundation/ ; },
mesh = {*Soil Microbiology ; *Phospholipids ; *Fatty Acids ; *Databases, Factual ; *Enzymes ; Soil/chemistry ; Ecosystem ; },
abstract = {Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.},
}
@article {pmid41007943,
year = {2025},
author = {Zhu, Y and Zhao, Y and He, Y and Wu, B and Su, X},
title = {YOLO-WildASM: An Object Detection Algorithm for Protected Wildlife.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {18},
pages = {},
pmid = {41007943},
issn = {2076-2615},
support = {QNTD202308//Outstanding Youth Team Project of Central Universities/ ; 2023YFD2201700//National Key R&amp;D Program of China/ ; },
abstract = {Wild animals are an essential component of natural ecosystems, and the accurate identification of wildlife targets plays a critical role in ecological conservation and species monitoring. However, the effectiveness of conventional object detection algorithms is often limited by the challenges posed by complex outdoor environments, small target sizes, and group occlusions. To address these issues, this study constructs a dataset comprising over 8000 images of 10 protected wildlife species and investigates effective detection methods for wildlife in natural habitats. We propose a novel deep learning-based detection framework, YOLO-WildASM, which incorporates three key improvements to the YOLOv8 architecture: a P2 detection layer for small objects, a multi-head self-attention (MHSA) mechanism, and a bidirectional feature pyramid network (BiFPN). Experimental results demonstrate that YOLO-WildASM significantly outperforms YOLOv8 and other state-of-the-art models on the custom wildlife dataset, achieving a mAP50 of 94.1%, which is 2.8% higher than the baseline model and superior to the latest YOLOv12 model (92.2%). Furthermore, ablation and generalization experiments validate the model's enhanced performance and adaptability in multi-scale wildlife detection tasks. The proposed deep learning-based detection framework provides an efficient and robust solution for wildlife monitoring and ecological conservation in complex natural ecosystems.},
}
@article {pmid41009797,
year = {2025},
author = {Cheng, L and Shi, N and Du, X and Huang, T and Zhang, Y and Zhao, C and Zhao, K and Lin, Z and Ma, D and Li, Q and Wang, F and Yao, H and Shen, H},
title = {Bioinformatics Analysis and Expression Profiling Under Abiotic Stress of the DREB Gene Family in Glycyrrhiza uralensis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {18},
pages = {},
pmid = {41009797},
issn = {1422-0067},
support = {KY2025JBGS03//the Science and Technology Plan Project of the Third Division/ ; 32260083//the National Natural Science Foundation of China/ ; 2023AB052 and 2023CB008-17//a Science and Technology Project of Bingtuan/ ; RCZK202595//Scientific Research Startup Project for High-Level Talents, Shihezi University/ ; },
mesh = {*Gene Expression Regulation, Plant ; *Glycyrrhiza uralensis/genetics/metabolism ; *Stress, Physiological/genetics ; *Plant Proteins/genetics/metabolism ; *Computational Biology/methods ; Phylogeny ; *Transcription Factors/genetics/metabolism ; Gene Expression Profiling ; Droughts ; *Multigene Family ; Promoter Regions, Genetic ; Transcriptome ; },
abstract = {Glycyrrhiza uralensis is an important medicinal plant exhibiting strong tolerance to abiotic stresses, including drought and salinity. DREB (Dehydration-Responsive Element-Binding) transcription factors, key members of the AP2/ERF family, play crucial roles in plant growth, development, and stress responses. Based on transcriptome data, we identified 18 DREB transcription factors in G. uralensis, designated GuDREB1 to GuDREB18. Bioinformatics analysis revealed genomic sequences ranging from 534 to 2864 bp and coding sequence (CDS) lengths between 525 and 1509 bp. All GuDREB proteins contain a single AP2 domain, including the conserved YRG and RAYD elements, and were predicted to localize to the nucleus. Phylogenetic analysis clustered the G. uralensis DREBs with 61 Arabidopsis thaliana DREBs into five subgroups, indicating evolutionary conservation. Promoter analysis detected seventeen stress-responsive cis-acting elements, encompassing hormone-responsive and abiotic stress-responsive motifs, suggesting diverse biological functions. Tissue-specific expression profiling revealed GuDREB transcription in both aerial and underground parts. Drought stress induced varying degrees of GuDREB expression, confirming their involvement in stress responses. Notably, GuDREB10 expression increased significantly in underground parts, while GuDREB15 showed pronounced upregulation in aerial parts under drought; the GuDREB15 promoter contained the highest number of light-responsive elements (23), potentially explaining its aerial tissue specificity. Drought stress significantly increased abscisic acid (ABA) content. Underground parts exhibited higher initial sensitivity to drought, whereas aerial parts displayed a more sustained response; ABA levels overall showed an initial increase followed by a decline. This study expands the G. uralensis DREB gene database, provides a foundation for selecting stress-resistance genes, and offers insights into DREB functional roles in abiotic stress responses in this key medicinal species.},
}
@article {pmid41011672,
year = {2025},
author = {Song, C and Yan, M and Lin, S and Li, J and Zou, H and Hu, Z and Yan, X},
title = {Dual-Ionization SPME-GC-HRMS Metabolomic Profiling of Broccoli Volatiles for the Construction of a Broccoli Metabolic Database.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {18},
pages = {},
pmid = {41011672},
issn = {1420-3049},
support = {2022YFE0108300//National Key R&amp;D Program of China/ ; N20220013//the Basic Agricultural Research Project of Wenzhou/ ; },
mesh = {*Volatile Organic Compounds/analysis/metabolism/chemistry ; *Brassica/metabolism/chemistry ; Gas Chromatography-Mass Spectrometry/methods ; *Metabolomics/methods ; Solid Phase Microextraction/methods ; *Metabolome ; Principal Component Analysis ; Databases, Factual ; },
abstract = {Volatile organic compounds (VOCs) play critical roles in broccoli's sensory attributes, defense mechanisms, and ecological interactions, yet comprehensive profiling of its volatilome remains limited. This study aimed to construct a robust and inclusive volatile metabolite database for broccoli using advanced analytical techniques. A pooled sample comprising florets from 191 cultivars was prepared to capture broad chemical diversity and analyzed using solid-phase microextraction-gas chromatography-high-resolution mass spectrometry (SPME-GC-HRMS) under dual ionization modes: electron ionization (EI) and chemical ionization (CI). A total of 206 VOCs spanning nine chemical classes were detected, with 37 compounds further confirmed through synchronized CI analysis. To validate the database, broccoli florets from seven distinct cultivars were analyzed using the same workflow. Of the 206 compounds, 187 (90.78%) were detected in at least one cultivar, while 38 were consistently found across all samples, indicating a conserved core volatilome. Principal component analysis revealed distinct VOC profiles among cultivars, and freeze-dried samples were found suitable for reproducible large-scale analysis. This study demonstrates that a pooled-sample strategy coupled with dual-ionization GC-HRMS provides comprehensive and reliable VOC coverage. The resulting database offers a valuable resource for metabolomics studies in Brassica, with applications in cultivar differentiation, flavor research, and environmental response profiling.},
}
@article {pmid41013625,
year = {2025},
author = {Li, M and Yang, H},
title = {Exploring spatial-temporal heterogeneity in new-type urbanization's impact on health expenditure: a GTWR analysis.},
journal = {International journal of health geographics},
volume = {24},
number = {1},
pages = {26},
pmid = {41013625},
issn = {1476-072X},
mesh = {Humans ; *Urbanization/trends ; *Health Expenditures/trends/statistics &amp; numerical data ; China/epidemiology ; *Spatio-Temporal Analysis ; *Geographic Information Systems/trends ; },
abstract = {BACKGROUND: To address challenges arising from rapid urban development, China has formulated and implemented the New-Type Urbanization strategy. However, empirical research on the specific impacts between New-Type Urbanization and health expenditures remains limited.<br><br>METHODS: Using panel data from 31 Chinese provinces (2012-2019), this study constructed a comprehensive evaluation index system for New-Type Urbanization across four dimensions: demographic, economic, social, and ecological. Geographically and Temporally Weighted Regression was employed to examine the spatial effects, influencing factors, and spatial heterogeneity of New-Type Urbanization's impact on health expenditures.<br><br>RESULTS: The results show that China's health expenditures primarily exhibit High-High and Low-Low clustering patterns with spatial fluctuations. Meanwhile, the impact of New-Type Urbanization on health expenditures demonstrates spatiotemporal heterogeneity and non-stationarity. As urbanization levels increase, the negative effects of health expenditure clustering expand, while the influence of economic urbanization weaken.<br><br>CONCLUSIONS: Our findings fill the research gap regarding the impacts between New-Type Urbanization and health expenditures, while also providing direction for New-Type Urbanization development to support the implementation of health policies aimed at controlling health expenditure growth.},
}
@article {pmid41013991,
year = {2025},
author = {Formanack, A and Ogle, K and Peltier, D},
title = {Flashy, decoupled, or declining? Single theories fail to explain the diversity of drought mortality signals in tree rings.},
journal = {The New phytologist},
volume = {248},
number = {6},
pages = {2795-2808},
doi = {10.1111/nph.70605},
pmid = {41013991},
issn = {1469-8137},
mesh = {*Droughts ; *Trees/growth &amp; development/physiology ; Bayes Theorem ; Species Specificity ; Models, Biological ; Climate ; },
abstract = {Growth patterns recorded in tree rings may predict drought 'winners' and 'losers'. Past studies of drought-killed trees have produced conflicting evidence. Some show killed trees were highly responsive to climate, while others suggest killed trees were climate-insensitive or became less sensitive over time. We leveraged ring width data from 2934 drought-killed and -surviving trees of seven species to compute growth sensitivity to seasonal climate variables via a Bayesian mixed effects model. Aided by clustering analyses, we evaluated how species conformed to three alternative hypotheses (theories): relative to surviving trees, killed trees (H1) have 'flashy' climate responses, (H2) are 'decoupled' from climate, or (H3) have 'declining' sensitivity over time. Differences in growth patterns were not consistent across species or status (surviving/killed). Drought-killed subalpine fir and Engelmann spruce exhibited 'flashy' growth - higher sensitivity of growth to climate over time - compared with survivors. Drought-killed aspen, Scots pine, and Norway spruce showed stable, climate-insensitive growth compared with survivors, suggesting 'decoupling' from climate. Most species showed nonstationary sensitivities, but rather than declining, some sensitivities increased, even in surviving trees. Our flashy-decoupled-declining framework links predictions for future drought-induced mortality to potential mechanisms, enhancing ecological and physiological understanding of growth-climate patterns preceding drought mortality events.},
}
@article {pmid41020379,
year = {2025},
author = {Vázquez, E and Duong, I and Rabin, BA and Stadnick, NA and Watson, PL and Cain, KL and Pozar, M and Cheney, A},
title = {Ripple Effects Mapping: Evaluating Multilevel Perspectives and Impacts of a Statewide Community-Academic Partnership Network on Covid-19 Health Disparities.},
journal = {Health expectations : an international journal of public participation in health care and health policy},
volume = {28},
number = {5},
pages = {e70446},
pmid = {41020379},
issn = {1369-7625},
support = {//This paper was supported by the following funding NIH/NHLBI CEAL grant #21-312-0217571-66106L./ ; },
mesh = {Humans ; *COVID-19/epidemiology/ethnology ; *Health Status Disparities ; California/epidemiology ; Community-Based Participatory Research ; *Community-Institutional Relations ; Universities/organization &amp; administration ; *Community Networks/organization &amp; administration ; SARS-CoV-2 ; Female ; },
abstract = {INTRODUCTION: Community-academic partnerships played an important role in addressing Covid-19-related health disparities in historically marginalised groups such as racial ethnic minorities and low-income and rural communities in the pandemic. Part of the federal response involved establishing regional community academic networks that engaged highly impacted communities in health disparities research. The statewide Share, Trust, Organize, Partner COVID-19 California Alliance (STOP COVID-19 CA) network was part of the federal response.<br><br>METHODS: In spring 2024, ripple effects mapping (REM), a participatory action research method, was used to conduct an evaluation of the impact of the STOP COVID-19 network on the capacity of community-academic partnerships to carry out Covid-19-related health disparities research. This method uses group interviews to capture direct and indirect outcomes, that is, ripples, of community-based programmes. Short-, medium- and long-term changes and conditions related to community-academic partnerships in the statewide network were mapped onto the spheres of influence of the social ecological model.<br><br>RESULTS: A total of 24 participants took part in one of three REM sessions. Community and academic partners were represented in all sessions, and most had been involved in community-engaged research for 3 to 10+&#x2009;years. Most identified as female, Hispanic/Latino, and between the ages of 40 and 49. Qualitative analysis of sessions indicated that most changes occurred at the individual and interpersonal levels and involved medium-term changes (e.g., increased capacity to partner in research and shared understanding). Neighbourhood- or community-level changes included identification of culturally and linguistically responsive intervention and dissemination efforts (e.g., promotora model). Policy and built environment conditions reveal the inequities in higher education and the need for structural-level changes to university infrastructure and grant administration.<br><br>CONCLUSION: Most outcomes were observed at the individual and interpersonal (group) levels and involved primarily medium-term changes. However, the network itself served as a platform to discuss the need for structural-level changes within university infrastructure to facilitate community-engaged scholarship. Such networks have the potential to facilitate capacity building for community-academic partnerships to collaborate in health disparities research that can generate evidence to move forward public health policy change.<br><br>Community partners, including grassroots leaders and staff of community-based organisations, were involved in the development of the research questions, the design of the study, and data collection, analysis and interpretation of the findings. Community partners also contributed to manuscript development.},
}
@article {pmid41021230,
year = {2025},
author = {Muzekari, B and Cooper, N and Resnick, A and Paul, AM and Torres-Grillo, OE and Andrews, ME and Mattan, B and Scholz, C and Johnson, D and Carreras-Tartak, J and Cakar, ME and Hao, S and Zhou, E and Beard, E and Mesquiti, S and Sayed, F and Fichman, MA and Lydon-Staley, DM and Barnett, IJ and Strasser, AA and Kirchner, TR and Henriksen, L and Falk, EB},
title = {Naturalistic Tobacco Retail Exposure and Smoking Outcomes in Adults Who Smoke Cigarettes Daily.},
journal = {JAMA network open},
volume = {8},
number = {9},
pages = {e2530132},
pmid = {41021230},
issn = {2574-3805},
support = {R01 CA229305/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; Adult ; Middle Aged ; *Tobacco Products/economics/statistics &amp; numerical data ; Craving ; *Commerce/statistics &amp; numerical data ; Aged ; *Cigarette Smoking/epidemiology/psychology ; Cohort Studies ; Young Adult ; Ecological Momentary Assessment ; New Jersey/epidemiology ; *Tobacco Industry ; },
abstract = {IMPORTANCE: The tobacco industry spends more than $8 billion annually in the US on marketing at the point of sale. Exposure to tobacco retail has been associated with smoking outcomes, but substantially less is known about how objectively logged everyday tobacco retail exposure is associated with smoking outcomes.<br><br>OBJECTIVE: To assess preregistered hypotheses that individuals would report (1) greater craving and (2) more cigarettes smoked on days when their exposure to tobacco retail is higher than usual.<br><br>This multimodal, within-person cohort study combined objectively logged geolocation tracking, public tobacco retail location records, and ecological momentary assessment data. Eligible participants recruited from the GeoSmoking Study were aged 21 to 65 years, smoked at least 5 cigarettes per day over the previous 6 months, owned a smartphone, and were a resident of Pennsylvania, New Jersey, or Delaware. Data were collected from May 25, 2022, to June 10, 2024.<br><br>EXPOSURE: Exposure to tobacco retail stores was assessed using mobility data matched with locations of tobacco retailers across Pennsylvania, New Jersey, and Delaware.<br><br>MAIN OUTCOMES AND MEASURES: Daily mean craving and daily number of cigarettes smoked were computed using ecological momentary assessment.<br><br>RESULTS: A total of 273 participants were included in the final analyses (mean [SD] age, 42.5 [10.7] years; 151 women [55.3%]). Multilevel models revealed support for both preregistered hypotheses. On days when individuals had more tobacco retail exposure than their own average, they reported significantly higher levels of craving (b&#x2009;=&#x2009;0.04; 95% CI, 0.01-0.07; t3457&#x2009;=&#x2009;2.72; P&#x2009;=&#x2009;.01) and smoking significantly more cigarettes (b&#x2009;=&#x2009;0.01; 95% CI, 0.0002-0.01; t3469&#x2009;=&#x2009;2.05; P&#x2009;=&#x2009;.04).<br><br>CONCLUSIONS AND RELEVANCE: In this cohort study of individuals who smoke cigarettes daily, exposure to tobacco retail in their everyday lives was associated with increases in craving and smoking. These findings highlight the importance of retail exposure and smoking outcomes, information that is critical for developing effective tobacco control interventions and lays the foundation for broader health research on environmental factors that shape health behaviors.},
}
@article {pmid41021637,
year = {2025},
author = {Maity, B and Banerjee, S and Senapati, A and Pitchford, J and Chattopadhyay, J},
title = {Coupling plankton and cholera dynamics: Insights into outbreak prediction and practical disease management.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013523},
pmid = {41021637},
issn = {1553-7358},
mesh = {*Cholera/epidemiology/transmission/microbiology/prevention &amp; control ; *Disease Outbreaks/statistics &amp; numerical data/prevention &amp; control ; Humans ; Vibrio cholerae/pathogenicity ; Animals ; *Plankton/microbiology ; Zooplankton/microbiology ; Models, Biological ; Phytoplankton ; Computational Biology ; },
abstract = {Despite extensive control efforts over the centuries, cholera remains a globally significant health issue. Seasonal emergence of cholera cases has been reported, particularly in the Bengal delta region, which is often synchronized with plankton blooms. This phenomenon has been widely attributed to the commensal interaction between Vibrio cholerae and zooplankton in aquatic environments. The role of plankton dynamics in cholera epidemiology has been acknowledged but remains poorly understood, and consequently, its importance in effective policymaking is largely overlooked. To this end, we propose and analyze a novel compartment-based transmission model that integrates phytoplankton-zooplankton interactions into a human-bacteria cholera framework. Our study shows that, beyond the reproduction number, the relative contribution of bacterial versus zooplankton-mediated transmission plays a crucial role in shaping epidemic progression and severity. In presence of zooplankton-mediated transmission, an outbreak with a delayed and lower peak may still result in a larger overall outbreak size. Additionally, contrary to common intuition, even for a large and early outbreak, the epidemic overshoot may intensify due to the maintenance of lower-level infections during the post-peak phase. Furthermore, our analysis reveals that the timing of filtration-like interventions can be strategically guided by ecological indicators, such as phytoplankton blooms. Our study underscores the importance of incorporating ecological aspects in epidemiological research to better predict and manage disease outbreaks.},
}
@article {pmid41026600,
year = {2025},
author = {Liu, L and Han, P and Wang, J and Xiuqin, S and Xu, G and Wang, L and Liu, R and Shen, X and Chen, F},
title = {Approaches to the water environment and aquatic ecology governance in basin systems.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {6},
pages = {894-902},
pmid = {41026600},
issn = {0273-1223},
support = {ZR2024MD117//Natural Science Foundation of Shandong Province/ ; No.0031504//The Shandong Top Talent Special Foundation/ ; X20192Z//The Doctoral research fund project of Shandong Jianzhu University/ ; 42107496//The National Science Fund for Distinguished Young Scholars-Construction and application of remote sensing ecological index model of Tamarix shrubbery forest/ ; },
mesh = {*Ecology ; *Conservation of Natural Resources ; Ecosystem ; Sustainable Development ; },
abstract = {With the development of human civilization and the rapid progress of urbanization, the water environment and aquatic ecology need more systematic treatment to support the construction of ecological civilization and sustainable development. Based on a large number of research results and from the four dimensions including governance concept, governance technology, management and control platform and engineering strategy suggestions, this study systematically analysed the cutting-edge concepts such as reverse-driven governance, explored the application of key technologies such as remote sensing in the water environment and water ecological governance, put forward strategic suggestions on building an intelligent analysis and decision-making platform and avoiding great leap forward-style vanity projects in the water environment and aquatic ecology governance. Finally, six cutting-edge governance concepts, four key technologies, two types of governance and control platforms and two engineering strategies were sorted out and formed a governance system covering concept guidance, technical support, platform integration and application, and engineering strategy guarantee. The research enriches the theory of the water environment and aquatic ecology governance, and has important reference value for policy-making and engineering practice of watershed water environment and aquatic ecology governance.},
}
@article {pmid41028195,
year = {2025},
author = {Yang, M and Wang, M and Cao, L and Zhang, H},
title = {Integrating trade-offs and supply-demand into ecosystem service zoning management to provide more targeted management strategies from the water-food-ecosystem nexus perspective.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33957},
pmid = {41028195},
issn = {2045-2322},
support = {42401384//National Natural Science Foundation of China/ ; 41971241//National Natural Science Foundation of China/ ; 24YJCZH376//Humanities and Social Sciences Youth Foundation, Ministry of Education/ ; 24YJCZH376//Humanities and Social Sciences Youth Foundation, Ministry of Education/ ; 25IRTSTHN008//Higher Education Institutions Scientific and Technological Innovation Team Support Program in Henan Province/ ; 25A170008//Key Scientific Research Projects of Colleges and Universities in Henan Province/ ; 24B170003//Key Scientific Research Projects of Colleges and Universities in Henan Province/ ; },
abstract = {The water-food-ecosystem nexus (WFE nexus) forms the foundation for achieving sustainable development. Managing ecosystem services (ESs) from this perspective is crucial for maintaining and enhancing ecosystem sustainability. However, synchronously mitigating trade-offs and supply-demand conflicts among ESs poses a significant challenge for sustainable ecosystem management. This study proposes a spatial management zoning framework integrating information on ESs trade-offs and supply-demand relationships from the perspective of the WFE nexus. This framework aims to precisely distinguish regional differences in ESs trade-off characteristics and supply-demand risk levels. We applied this framework to China's Loess Plateau (LP) in China, where the simultaneous safeguarding of water, food, and ecological security has become a major challenge for local sustainable development. Based on analyzing ESs trade-offs and supply-demand matching relationships, our framework divided the LP into ten management zones. Each of these zones faces similar ecological issues internally, while different zones confront distinct ecological problems. Consequently, we propose targeted management strategies for each zone based on their unique ecological issues. Our framework deepens the research on the WFE nexus and provides a new perspective for simultaneously resolving ESs trade-offs and supply-demand conflicts.},
}
@article {pmid41028231,
year = {2026},
author = {Ging-Jehli, NR and Pine, DS},
title = {From symptom-based heterogeneity to mechanism-based profiling in youth ADHD: the promise of computational psychiatry.},
journal = {Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology},
volume = {51},
number = {1},
pages = {234-243},
pmid = {41028231},
issn = {1740-634X},
support = {P500PS_214223//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; ZIA-MH002781//U.S. Department of Health &amp; Human Services | NIH | National Institute of Mental Health (NIMH)/ ; },
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/diagnosis/therapy ; Models, Theoretical ; *Psychiatry/methods ; *Diagnosis, Computer-Assisted ; },
abstract = {Mental health conditions such as attention-deficit/hyperactivity disorder (ADHD) and mood disorders show marked symptom heterogeneity, complicating diagnosis and treatment. Computational psychiatry offers a way forward by using mathematical models, such as sequential sampling models, applied to trial-by-trial behavior in well-defined neurocognitive tasks, to infer latent mechanisms underlying behavior. In ADHD, this approach has revealed consistent alterations in information integration (reduced drift rates) in attention-demanding tasks and also indicates that combinations of different model parameters (increased drift rate and longer nondecision time) distinguish the different neurocomputational mechanisms that underlie symptom dimensions. Early work in ADHD also suggests that drift rate predicts illness trajectories and provides insights into treatment response. Yet current applications remain preliminary, limited by task constraints, assumptions in model specification, and questions of reliability and generalizability of the derived parameters. Integrating mechanistic modeling with naturalistic tasks, physiological measures, and longitudinal designs may help to disentangle context-specific from generalizable processes. Ultimately, shifting from symptom descriptions to mechanistic models of belief and behavioral adaptation in dynamic environments may pave the way for next-generation assessments in ADHD, and help to support interventions that are ecologically valid, developmentally informed, and adaptive to patients' changing needs across time and context.},
}
@article {pmid41029229,
year = {2025},
author = {Nagy, KN and Károlyi, CE and Bakacsy, L},
title = {Multiscale assessment of conservation management for Amorpha fruticosa invasion in a marsh meadow.},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {97},
pmid = {41029229},
issn = {2730-7182},
support = {7616//University of Szeged Open Access Found/ ; 7616//University of Szeged Open Access Found/ ; 7616//University of Szeged Open Access Found/ ; },
mesh = {*Introduced Species ; *Wetlands ; *Conservation of Natural Resources/methods ; Biodiversity ; Animals ; Cattle ; *Fabaceae/physiology ; },
abstract = {This study examined the ecological impact of the invasive shrub Amorpha fruticosa in marsh meadows and assessed the effectiveness of combined conservation management practices, i.e., mowing and cattle grazing, in on restoring native vegetation. Conducted in the Mártély Landscape Protection Area (Hungary), the research used a multiscale approach to compare treated non-invaded and treated invaded wetland vegetation. Information theory-based diversity metrics were employed to evaluate the impact of A. fruticosa on structural complexity and species composition. Results revealed that although A. fruticosa can significantly altered plant community structure, the implemented management strategies effectively reduced its impact. The treated invaded vegetation exhibited diversity levels compareable to native marshland communities, suggesting that mowing and grazing contributed to decreasing A. fruticose dominance. However, in the absence of untreated control stands, this pattern must be interpreted cautiously, as the observed similarity could be conclusively attributed to the applied management alone. A slight, but non-significant shift in structural diversity was also observed, implying a residual effect of invasion. This study underscores the value of active, combined conservation strategies in maintaining biodiversity and ecosystem resilience in wetland habitats. The results contribute to broader discussions on invasive species control, emphasizing the role of traditional land-use practices in mitigating the ecological effects of biological invasions.},
}
@article {pmid41030122,
year = {2025},
author = {Robinson, JM and Brame, J and Cando-Dumancela, C and Deshmukh, S and Fickling, NW and Hawken, S and Hayward, C and Kuhn, E and Lee, K and Liddicoat, C and Ramesh, S and Robinson, K and Sun, X and Breed, MF},
title = {Mapping and Cataloguing Microbial and Biochemical Determinants of Health: Towards a 'Database of Salutogenic Potential'.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70243},
pmid = {41030122},
issn = {1751-7915},
support = {//National Environmental Science Program/ ; 32361143523//National Natural Science Foundation of China/ ; UOWX2101//New Zealand Ministry of Business Innovation and Employment/ ; 322GJHZ2022028FN//International Partnership Program of Chinese Academy of Sciences/ ; 2023YFF1304600//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Environmental Microbiology ; *Databases, Factual ; *Bacteria/metabolism/classification/genetics ; },
abstract = {Microbial and biochemical research has historically focused on pathogenic agents due to their clear association with disease. This is a perspective that has saved countless lives but encourages a skewed, threat-centered view of microbes and biogenic compounds. Emerging evidence shows that exposure to diverse environmental microbiomes and natural biochemical products is also salutogenic-promoting health and resilience. Here we introduce the 'Database of Salutogenic Potential', a prototype relational repository cataloguing environmental microbes and biochemical compounds linked to health benefits. Drawing from more than 200 articles, we identified 124 potentially salutogenic microbial taxa, 14 biochemical compounds and 63 associated benefits. By creating a structured and open platform, we aim to shift the balance between pathogen-centric and salutogenic perspectives, potentially enabling future applications in public health, urban planning and ecosystem restoration. While the current iteration of the database primarily centers on human health outcomes, it is designed to expand into ecosystem health domains, embedding salutogenic thinking into One Health frameworks. We present this as a first step, not a ready-to-use tool, and invite collaborative refinement from the scientific community.},
}
@article {pmid41030989,
year = {2025},
author = {Carroll, RA and Ricemeyer, ES and Hillier, LW and DaCosta, JM and Osipova, E and Smith, S and Jamie, GA and Martinez, JG and Molina-Morales, M and Marques-Bonet, T and Manthey, JD and Haddad, D and Fuxjager, MJ and Lynch, KS and Wood, JMD and Jarvis, E and Masterson, P and Thibaud-Nissen, F and Hauber, M and Spottiswoode, CN and Sackton, TB and Balakrishnan, CN and Sorenson, MD and Warren, WC},
title = {Genomic resources for comparative analyses of obligate avian brood parasitism.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41030989},
issn = {2692-8205},
support = {U54 MD017979/MD/NIMHD NIH HHS/United States ; },
abstract = {Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental care behaviors, has evolved independently in seven different lineages, though little is known about the genetic basis of the complex suite of traits associated with this rare life history strategy. We generated genome assemblies for ten brood parasitic species plus eight species representatives of their parental/nesting outgroups. This includes nine long-read chromosome-level assemblies, with scaffold N50 sizes ranging from 38.1 to 72.6 MB, and gene representation completeness measures >97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6 to 4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species.},
}
@article {pmid41032366,
year = {2026},
author = {Liu, S and Crawford, CM and Fisher, ZF and Gates, KM},
title = {Dynamic Fit Index Cutoffs for Time Series Network Models.},
journal = {Multivariate behavioral research},
volume = {61},
number = {1},
pages = {94-115},
doi = {10.1080/00273171.2025.2561943},
pmid = {41032366},
issn = {1532-7906},
mesh = {Humans ; Computer Simulation ; *Models, Statistical ; Data Interpretation, Statistical ; Time Factors ; },
abstract = {In this study, we extend the dynamic fit index (DFI) developed by McNeish and Wolf to the context of time series analysis. DFI is a simulation-based method for deriving fit index cutoff values tailored to the specific model and data characteristics. Through simulations, we show that DFI cutoffs for detecting an omitted path in time series network models tend to be closer to exact fit than the popular benchmark values developed by Hu and Bentler. Moreover, cutoff values vary by number of variables, network density, number of time points, and form of misspecification. Notably, using 10% as the upper limit of Type I and Type II error rates, the original DFI approach fails to identify cutoffs for detecting an omitted path when effect size and/or sample size is small. To address this problem, we propose two alternatives that allow for the derivation of cutoffs using more lenient criteria. DFIA extends the original DFI approach by removing the upper limit of Type I and Type II error rates, whereas DFIB aims at maximizing classification quality measured by the Matthews correlation coefficient. We demonstrate the utility of these approaches using simulation and empirical data and discuss their implications in practice.},
}
@article {pmid41032510,
year = {2025},
author = {Zhang, C and Teng, J and Liu, P and Liu, C},
title = {Ecological suitability evaluation of traditional village locations in Jiangxi Province based on multi-model integration using artificial intelligence.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0332375},
pmid = {41032510},
issn = {1932-6203},
mesh = {*Artificial Intelligence ; China ; *Ecosystem ; Humans ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Neural Networks, Computer ; *Ecology ; Support Vector Machine ; },
abstract = {Traditional villages have evolved over time to adapt to their environmental characteristics, demonstrating high ecological suitability. Ideal village locations not only provide comfortable living spaces but also ensure safety and sustainability, reflecting the ancestors' profound understanding of the natural environment and ecological wisdom. This study employs an artificial intelligence-based multi-model integration approach to evaluate the ecological suitability of 413 traditional village sites in Jiangxi Province. Key influencing factors are identified, and the ecological wisdom of ancestral site selection is analyzed, resulting in an ecological suitability evaluation map for traditional village locations in Jiangxi Province. The study draws upon environmental characteristic data of Jiangxi Province, including topography, climate, habitat quality, land use, air quality, vegetation cover, and river network density. GIS technology is utilized for spatial analysis and result visualization, with raster data being extracted and standardized. Machine learning methods, such as Random Forest, Support Vector Machine, and Gradient Boosting Decision Trees, along with deep learning methods like Convolutional Neural Networks and Multilayer Perceptrons, are applied. Multi-model integration techniques combine diverse predictive outputs, thereby enhancing the overall accuracy and robustness of ecological suitability evaluations. Experimental results indicate that elevation, slope, habitat quality, actual distance to water bodies, and average temperature are the main influencing factors for village site selection. The multi-model integration method performs excellently in evaluating ecological suitability, effectively identifying key ecological factors. The model's accuracy and reliability are verified through confusion matrix, feature importance analysis, and ROC curve. By analyzing the impact weights of various ecological factors, this study constructs a Composite Suitability Index (CSI) and generates an ecological suitability evaluation map that clearly displays suitability levels. This provides a scientific basis for the protection and rational development of traditional villages and serves as a reference for ecological site selection studies in other regions.},
}
@article {pmid41032589,
year = {2025},
author = {Yang, M and Adegbite, O and Chang, P and Cheng, J and Wang, Y and Held, M and Zhu, X and Li, Y and Dykes, GF and Chen, Y and Savage, N and Zhang, YZ and Gao, J and Hinton, JCD and Lian, LY and Liu, LN},
title = {Molecular basis of the biogenesis of a protein organelle for ethanolamine utilization.},
journal = {Science advances},
volume = {11},
number = {40},
pages = {eadx9774},
pmid = {41032589},
issn = {2375-2548},
mesh = {*Ethanolamine/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; *Organelles/metabolism ; *Salmonella/metabolism ; },
abstract = {Many pathogenic bacteria use proteinaceous ethanolamine utilization microcompartments (Eut BMCs) to catabolize ethanolamine. This ability gives pathogens a competitive edge over commensal microbiota, which can drive virulence in the inflamed gut. Despite such a critical function, the molecular mechanisms underlying the synthesis of Eut BMCs remain elusive. We report a systematic study for dissecting the molecular basis underlying Eut BMC assembly in Salmonella. We determined the functions of individual constituent proteins in the structure and function of Eut BMCs and demonstrated that EutQ is essential for cargo encapsulation and Eut BMC formation through specific association with the shell and cargo enzymes. We found that Eut proteins can self-assemble to form cargo and shell aggregates independently in vivo and that the biogenesis of Eut BMCs follows a "shell-initiated" pathway. Cargo enzymes exhibit dynamic liquid-like organization within the Eut BMC. Our findings provide mechanistic insights into the structure and assembly of the Eut BMC that serves as a paradigm for membraneless organelles.},
}
@article {pmid41034648,
year = {2025},
author = {Weingarten, A and Häusler, M and Serangeli, J and Verheijen, I and Reiter, E and Radzevičiūtė, R and Stoessel, A and Krause, J and Spyrou, MA and Conard, NJ and Nieselt, K and Posth, C},
title = {Mitochondrial genomes of Middle Pleistocene horses from the open-air site complex of Schöningen.},
journal = {Nature ecology &amp; evolution},
volume = {9},
number = {12},
pages = {2248-2258},
pmid = {41034648},
issn = {2397-334X},
mesh = {Animals ; Horses/genetics ; *Genome, Mitochondrial ; Phylogeny ; Fossils ; DNA, Ancient/analysis ; Germany ; DNA, Mitochondrial/genetics ; Biological Evolution ; },
abstract = {Deep-time palaeogenomics offers rare insights into macroevolutionary events for both extant and extinct species. Aside from a Middle Pleistocene genome from North American permafrost (780-560 ka) and a number of Late Pleistocene specimens, most ancient horse DNA studies have focused on tracing the origins of domestication and subsequent periods. Here we present mitochondrial genomes from two Equus mosbachensis specimens from Schöningen, Germany, a Middle Pleistocene archaeological site complex with direct and repeated evidence of hominin-horse interactions on the shore of a palaeolake. Using petrous bone sampling, targeted enrichment and damage-aware and polarization-free mitochondrial DNA reconstruction methods, we extend the range of genome recovery in open-air sites to ~300,000 years ago. Phylogenetic analyses position these mitochondrial DNAs in two distinct, deeply divergent lineages, basal to both previously sequenced ancient Eurasian specimens and all modern-day horses. The Schöningen horse mitochondrial DNA data reveal a previously unrecognized diversification event within the clade, ultimately giving rise to modern-day horses, that is molecularly dated to ~570 ka and provides genetic support for the morphological species assignment. By extending the recoverable limits of ancient DNA from Middle Pleistocene open-air sites, our molecular findings bridge a temporal and geographic gap, providing insights on early evolutionary events within the genus Equus.},
}
@article {pmid41038931,
year = {2025},
author = {Nganso, BT and Agboka, KM and Atagong, SD and Topé, SF and Massing, T and Landmann, T and Sevgan, S and Mwiza, W and Odera, F and Piiru, ED and Otieno-Ayayo, ZN and Soroker, V and Guimapi, RA},
title = {A Geospatial atlas of honey bee forage plants and their distribution patterns in Africa and beyond.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34384},
pmid = {41038931},
issn = {2045-2322},
support = {70054//JRS Biodiversity Foundation/ ; },
mesh = {Animals ; Africa ; *Bees/physiology ; Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Ecosystem ; Pollination ; *Plants ; },
abstract = {Honey bee forage plants are essential for bee nutrition and wellbeing, and they also sustain multifunctional landscapes that support human livelihoods and biodiversity. Despite the critical need to conserve them, information on their identity and distribution across Africa remains limited. Through a systematic literature review, we compiled the first continental database of 1,248 honey bee forage plant species from 91 families and retrieved 1,572,790 occurrence records of these species from open-access biodiversity databases like iNaturalist and the Global Biodiversity Information Facility (GBIF). The database includes native and exotic species, with georeferenced records from Africa and beyond. An interactive web-based dashboard accompanies the database, allowing users to visualize species distributions. The dashboard reveals floral report gaps in Western, Central and Northern Africa, helping inform future conservation priorities. In Southern and Eastern Africa where considerable data exists, this resource promotes pollinator-friendly land management practices, supporting honey bees and other pollinators vital for ecosystem resilience. Overall, this resource provides a foundation for future integration with high-resolution imagery, climate models and field-collected data on plant-pollinator interactions to contextualize species distributions under varying land-use and climatic conditions. It offers a valuable tool to support pollinator conservation and climate-resilient strategies for agriculture and beekeeping across Africa.},
}
@article {pmid41040647,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Sycamore-seed Pygmy moth, Ectoedemia decentella (Herrich-Schäffer, 1855) van Nieukerken, 1986.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {182},
pmid = {41040647},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Ectoedemia decentella (Sycamore-seed Pygmy; Arthropoda; Insecta; Lepidoptera; Nepticulidae). The genome sequence has a total length of 418.14 megabases. Most of the assembly (99.59%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.25 kilobases.},
}
@article {pmid41040651,
year = {2025},
author = {Boyes, D and Lees, DC and Boyes, C and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Triangle-marked Roller, Ancylis achatana (Denis &amp; Schiffermüller), 1775.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {128},
pmid = {41040651},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Ancylis achatana (Triangle-marked Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 547.27 megabases. Most of the assembly (99.25%) is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.0 kilobases.},
}
@article {pmid41040654,
year = {2025},
author = {Boyes, D and Broad, GR and Lees, DC and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Brindled White-spot moth, Parectropis similaria (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {179},
pmid = {41040654},
issn = {2398-502X},
abstract = {We present a genome assembly from a female Parectropis similaria (Brindled White-spot; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 574.79 megabases. Most of the assembly (99.92%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.94 kilobases.},
}
@article {pmid41041147,
year = {2024},
author = {Botham, M and , and , and , and , and , },
title = {The genome sequence of the Small Argent and Sable moth, Epirrhoe tristata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {541},
pmid = {41041147},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Small Argent and Sable moth Epirrhoe tristata (Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence spans 313.80 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.92 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,469 protein-coding genes.},
}
@article {pmid41041439,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Hoile, A and , },
title = {The genome sequence of the Brick, Agrochola circellaris (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {44},
pmid = {41041439},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Agrochola circellaris (the Brick; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 572 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 18,319 protein coding genes.},
}
@article {pmid41042792,
year = {2025},
author = {Chapman, D and Occhibove, F and Bullock, JM and Beck, PSA and Navas-Cortes, JA and White, SM},
title = {Modelling plant disease spread and containment: Simulation and approximate Bayesian Computation for Xylella fastidiosa in Puglia, Italy.},
journal = {PLoS computational biology},
volume = {21},
number = {10},
pages = {e1013539},
pmid = {41042792},
issn = {1553-7358},
mesh = {*Xylella/pathogenicity/physiology ; *Plant Diseases/microbiology/statistics &amp; numerical data/prevention &amp; control ; Italy ; Bayes Theorem ; Computer Simulation ; Disease Outbreaks ; *Models, Biological ; Olea/microbiology ; Computational Biology ; },
abstract = {Mathematical and computational models play a crucial role in understanding the epidemiology of economically important plant disease outbreaks, and in evaluating the effectiveness of surveillance and disease management measures. A case in point is Xylella fastidiosa, one of the world's most deadly plant pathogens. Since its European discovery in olives in Puglia, Italy in 2013, there remain key knowledge gaps that undermine landscape-scale containment efforts of the outbreak, most notably concerning the year of introduction, the rate of spread, dispersal mechanisms and control efficacy. To address this, we developed a spatially explicit simulation model for the outbreak spreading among olive groves coupled to a simulation of the real surveillance and containment measures. We used Approximate Bayesian Computation to fit the model to surveillance and remote-sensing infection data, comparing the fits for three alternative dispersal mechanisms (isotropic, wind and road). The model accurately explained the rate and spatiotemporal pattern of the outbreak and found weak support for the wind dispersal model over the isotropic model. It suggests that the bacterium may have been introduced as early as 2003 (95% CI [2000, 2009]), earlier than previous estimates and congruent with anecdotal evidence. The isotropic model estimates the pathogen is spreading at 5.7 km y-1 (95% CI [5.4-5.9]) under containment measures, down from 7.2 km y-1 (95% CI [6.9-7.5]) without containment measures. Our estimate of an approximately 10-year lag between introduction and detection highlights the need for stronger biosecurity and surveillance for earlier detection of emerging plant pathogens. The outputs from simulations without any disease management also suggest that while containment measures have caused some slowing of X. fastidiosa spread, stronger measures will be required to contain the outbreak fully.},
}
@article {pmid41042793,
year = {2025},
author = {Du, H and Zahn, MV and Loo, SL and Alleman, TW and Truelove, S and Patenaude, B and Gardner, LM and Papageorge, N and Hill, AL},
title = {Improving policy design and epidemic response using integrated models of economic choice and disease dynamics with behavioral feedback.},
journal = {PLoS computational biology},
volume = {21},
number = {10},
pages = {e1013549},
pmid = {41042793},
issn = {1553-7358},
mesh = {Humans ; *COVID-19/epidemiology/economics/transmission/prevention &amp; control ; Pandemics/economics ; SARS-CoV-2 ; Choice Behavior ; Decision Making ; *Policy Making ; Computational Biology ; *Health Policy ; },
abstract = {Human behavior plays a crucial role in infectious disease transmission, yet traditional models often overlook or oversimplify this factor, limiting predictions of disease spread and the associated socioeconomic impacts. Here we introduce a feedback-informed epidemiological model that integrates human behavior with disease dynamics in a credible, tractable, and extendable manner. From economics, we incorporate a dynamic decision-making model where individuals assess the trade-off between disease risks and economic consequences, and then link this to a risk-stratified compartmental model of disease spread taken from epidemiology. In the unified framework, heterogeneous individuals make choices based on current and future payoffs, influencing their risk of infection and shaping population-level disease dynamics. As an example, we model disease-decision feedback during the early months of the COVID-19 pandemic, when the decision to participate in paid, in-person work was a major determinant of disease risk. Comparing the impacts of stylized policy options representing mandatory, incentivized/compensated, and voluntary work abstention, we find that accounting for disease-behavior feedback has a significant impact on the relative health and economic impacts of policies. Including two crucial dimensions of heterogeneity-health and economic vulnerability-the results highlight how inequities between risk groups can be exacerbated or alleviated by disease control measures. Importantly, we show that a policy of more stringent workplace testing can potentially slow virus spread and, surprisingly, increase labor supply since individuals otherwise inclined to remain at home to avoid infection perceive a safer workplace. In short, our framework permits the exploration of avenues whereby health and wealth need not always be at odds. This flexible and extendable modeling framework offers a powerful tool for understanding the interplay between human behavior and disease spread.},
}
@article {pmid41047557,
year = {2025},
author = {Rausch, P and Ratjen, I and Tittmann, L and Enderle, J and Wacker, EM and Jaeger, K and Rühlemann, MC and Franzpötter, K and Ellul, P and Kruse, R and Halfvarson, J and Roggenbuck, D and Ellinghaus, D and Jacobs, G and Krawczak, M and Schreiber, S and Bang, C and Lieb, W and Franke, A},
title = {First insights into microbial changes within an Inflammatory Bowel Disease Family Cohort study.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2559119},
pmid = {41047557},
issn = {1949-0984},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/epidemiology ; Male ; Female ; Adult ; *Bacteria/classification/isolation &amp; purification/genetics ; *Dysbiosis/microbiology ; Prospective Studies ; *Gastrointestinal Microbiome ; Middle Aged ; Cohort Studies ; Feces/microbiology ; Germany/epidemiology ; Young Adult ; },
abstract = {The prospective Kiel Inflammatory Bowel Disease (IBD) Family Cohort Study (KINDRED cohort) was initiated in 2013 to systematically and extensively collect data and biosamples from index IBD patients and their relatives, a population at high risk for IBD development. Regular follow-ups were conducted to collect updated health and lifestyle information, to obtain new biosamples, and to capture the incidence of IBD during development. By combining microbial data collected at successive time points with extensive anthropometric, medical, nutritional, and social information, this study aimed to characterize the factors influencing the microbiota in health and disease via detailed ecological analyses. Using a microbial dysbiosis metric based on the German KINDRED cohort, we identified strong and generalizable gradients within and across different external IBD cohorts for validation. These community gradients correspond strongly with IBD pathologies, physiological manifestations of inflammation (e.g. Bristol stool score, ASCA IgA, ASCA IgG), and genetic risk for IBD. Anthropometric and medical factors influencing fecal transit time strongly modify bacterial communities. Various Enterobacteriaceae (e.g. Klebsiella sp.) and opportunistic Clostridia pathogens (e.g. C. XIVa clostridioforme), characterize in combination with ectopically colonizing oral taxa (e.g. Veillonella sp. Cand. Saccharibacteria sp. Fusobacterium nucleatum) the distinct and chaotic IBD-specific communities. Weak community and physiological changes are further traceable in a small number of individuals, who developed IBD in the study's runtime. Our findings demonstrate broad-scale ecological patterns which indicate drastic state transitions of communities in IBD patients. These patterns appear to be universal across cohorts and influence physiological signs of inflammation, display increased resilience, but show only limited heritability/intrafamily transmission.},
}
@article {pmid41047562,
year = {2025},
author = {Takata, K and Ogawa, M and Takahashi, T},
title = {Temporal Trends and Determinants of Low-Dose Estrogen-Progestin Prescription in Japan During 2014-2022: An Ecological Study Using a Nationwide Claims Database.},
journal = {The journal of obstetrics and gynaecology research},
volume = {51},
number = {10},
pages = {e70093},
doi = {10.1111/jog.70093},
pmid = {41047562},
issn = {1447-0756},
support = {24K13368//Japan Society for the Promotion of Science/ ; },
mesh = {Female ; Humans ; Adult ; Middle Aged ; Adolescent ; Japan ; Young Adult ; Child ; *Estrogens/administration &amp; dosage ; *Progestins/administration &amp; dosage ; Databases, Factual ; *Drug Prescriptions/statistics &amp; numerical data ; *Practice Patterns, Physicians'/statistics &amp; numerical data/trends ; *Estrogen Replacement Therapy/trends/statistics &amp; numerical data ; },
abstract = {AIM: This study aimed to evaluate the trends and regional disparities in low-dose estrogen-progestin (LEP) prescription in Japan from 2014 to 2022 and the factors contributing to these disparities.<br><br>METHODS: LEP prescription data were obtained from the National Health Insurance Claims and Specific Health Examination Database; the prescriptions per 1000 women aged 10-54&#x2009;years were calculated. Trends were analyzed in terms of the overall volume, age group distribution, and formulation type. The regional distribution in 2022 was also examined; the factors influencing regional differences were identified using multiple regression analysis.<br><br>RESULTS: LEP prescriptions showed a significant annual increase (p&#x2009;<&#x2009;0.05), rising approximately five-fold over 9&#x2009;years. A significant increase was observed in all age groups, except for those in their 50s (p&#x2009;<&#x2009;0.05). Ethinylestradiol 0.035&#x2009;mg/norethisterone 1&#x2009;mg (p&#x2009;<&#x2009;0.005) and ethinylestradiol 0.02&#x2009;mg/drospirenone 3&#x2009;mg (cyclic dosing regimen) (p&#x2009;<&#x2009;0.001) usage declined. Conversely, ethinylestradiol 0.02&#x2009;mg/drospirenone 3&#x2009;mg (continuous dosing regimen) and ethinylestradiol 0.02&#x2009;mg/levonorgestrel 0.09&#x2009;mg usage increased significantly (p&#x2009;<&#x2009;0.05). In 2022, regional disparities in LEP prescriptions reached a maximum of 2.7-fold. These disparities were not associated with the number of obstetricians and gynecologists and women's health specialists. However, the prescription of EE 0.02&#x2009;mg/drospirenone 3&#x2009;mg (continuous dosing regimen) showed a significant association with the number of women's health specialists (p&#x2009;=&#x2009;0.002).<br><br>CONCLUSION: This study provides the first comprehensive analysis of real-world LEP prescription patterns in Japan, revealing significant regional disparities.},
}
@article {pmid41047667,
year = {2025},
author = {Liang, S and Wang, W and Tan, C and Zhou, L and Ou, Z and Qu, Y},
title = {Multi-omics analysis reveals the potential role of MbDDC in tissue-specific alkaloid biosynthesis and distribution in Meconopsis betonicifolia.},
journal = {The Plant journal : for cell and molecular biology},
volume = {124},
number = {1},
pages = {e70515},
doi = {10.1111/tpj.70515},
pmid = {41047667},
issn = {1365-313X},
support = {32160404//National Natural Science Foundation of China/ ; 31460218//National Natural Science Foundation of China/ ; 202501BD070001-084//Yunnan Fundamental Research Projects- the General Program of the Agriculture Joint Special Project/ ; YNWR-QNBJ-2019-211//Ten Thousand Talent Plans for Young Top-notch Talents of Yunnan Province/ ; 2025Y0844//Scientific Research Fund Project of Yunnan Provincial Department of Education/ ; },
mesh = {*Alkaloids/biosynthesis/metabolism ; *Plant Proteins/metabolism/genetics ; Plant Roots/metabolism ; Plant Leaves/metabolism ; Gene Expression Regulation, Plant ; Nicotiana/metabolism/genetics ; Flowers/metabolism ; Plant Stems/metabolism ; Metabolomics ; Transcriptome ; Multiomics ; Papaveraceae ; },
abstract = {Plants of the Meconopsis (Meconopsis spp.), endemic to the Qinghai-Tibet Plateau, are prized in traditional Tibetan medicinal herbs for their bioactive alkaloids, particularly their antispasmodic and analgesic properties. To elucidate the mechanisms underlying tissue-specific alkaloid accumulation in Meconopsis betonicifolia, we integrated metabolomic and transcriptomic analyses across four organs (roots, stems, leaves, and flowers) and functionally characterized the rate-limiting enzyme MbDDC-3. Our results demonstrate that roots are the primary site of alkaloid accumulation, with codeinone and salutaridine identified as key intermediates in the isoquinoline pathway. Eleven differentially expressed genes (DEGs) were strongly correlated with these metabolites. Heterologous overexpression of MbDDC-3 in tobacco (Nicotiana tabacum) significantly increased total alkaloid by 274% in roots (P < 0.05), with (S)-cis-N-methylstylopine and its precursors (tyramine/dopamine) significantly enriched. Notably, MbDDC-3 protein contains a non-classical nuclear localization signal (NLS)-RLKPAAIFNRKLG-located near its C-terminal region and exhibits key residue substitutions compared to lowland species, suggesting adaptive evolution under high-altitude stress. Collectively, this study reveals how M. betonicifolia optimizes alkaloid distribution for ecological fitness, while offering a genetic tool for metabolic engineering of medicinal alkaloids.},
}
@article {pmid41052097,
year = {2025},
author = {Teitelbaum, CS and Casazza, ML and Overton, CT and Matchett, EL and Prosser, DJ},
title = {Host responses and viral traits interact to shape the impacts of climate warming on highly pathogenic avian influenza in migratory waterfowl.},
journal = {PLoS computational biology},
volume = {21},
number = {10},
pages = {e1013451},
pmid = {41052097},
issn = {1553-7358},
mesh = {Animals ; *Influenza in Birds/virology/epidemiology/transmission ; *Animal Migration ; *Climate Change ; Disease Outbreaks ; *Influenza A virus/pathogenicity ; Birds/virology ; Models, Biological ; Computational Biology ; Computer Simulation ; Host-Pathogen Interactions ; Animals, Wild/virology ; },
abstract = {Emerging infectious diseases pose threats to wildlife populations, as exemplified by recent outbreaks of avian influenza viruses in wild birds. Climate change can affect infection dynamics in wildlife through direct effects on pathogens (e.g., environmental decay rates) and changes to host ecology, including shifting migration patterns. Here, we adapt an existing mechanistic model that couples migration and infection to study how traits of highly pathogenic avian influenza (HPAI) viruses contribute to HPAI outcomes in migratory waterfowl, then apply this model to explore potential impacts of climate change on HPAI dynamics. We find that the simulated impacts of HPAI on the host population under baseline climate conditions varied from no impact to 100% mortality, depending on viral traits. In most cases, traits related to transmission (i.e., contact rates, shedding rates) were more important for HPAI establishment probability, infection prevalence, and mortality than were other viral traits (e.g., environmental temperature sensitivity, cross-protective immunity). We then simulated the effects of climate change (i.e., altered temperature regimes) on HPAI dynamics both via viral environmental decay and via changes in bird migration phenology. In these simulations, we found that a 9-day advancement in spring migration timing increased the duration of HPAI outbreaks by increasing time birds spent at their breeding grounds, leading to higher mortality and fewer infections. In contrast, increased viral decay in warmer years had a smaller, but opposite impact. These patterns depended on the primary transmission mode of HPAI (i.e., direct vs. environmental) and its sensitivity to environmental temperatures. Together, these results suggest that climate change is likely to increase the impacts of HPAI on waterfowl populations if HPAI relies strongly on direct transmission and birds advance their spring migration. Further integrating host-viral co-evolution and other climatic changes (e.g., salinity, humidity) could provide more precise predictions of how HPAI dynamics could change in the future.},
}
@article {pmid41052276,
year = {2025},
author = {Sherwani, MK and Ruuskanen, MO and Feldner-Busztin, D and Nisantzis Firbas, P and Boza, G and Móréh, &#xc1; and Borman, T and Putu Erawijantari, P and Scheuring, I and Gopalakrishnan, S and Lahti, L},
title = {Multi-omics time-series analysis in microbiome research: a systematic review.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {5},
pages = {},
pmid = {41052276},
issn = {1477-4054},
support = {952914//European Union's Horizon 2020 research and innovation programme/ ; },
mesh = {*Microbiota ; Humans ; *Computational Biology/methods ; Machine Learning ; *Genomics/methods ; Multiomics ; },
abstract = {Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and characterizing temporal variation simultaneously across multiple scales, from specific molecular interactions to entire ecosystems, is crucial for uncovering biological mechanisms and understanding the emergence of complex phenotypes. With the increasing number of studies incorporating multi-omics data sampled over time, it has become clear that integrated approaches are pivotal for these efforts. However, standard data analytical practices in longitudinal multi-omics are still shaping up and many of the available methods have not yet been widely evaluated and adopted. To address this gap, we performed the first systematic literature review that comprehensively categorizes, compares, and evaluates computational methods for longitudinal multi-omics integration, with a particular emphasis on four categories of the studies: (i) host and host-associated microbiome studies, (ii) microbiome-free host studies, (iii) host-free microbiome studies, and (iv) methodological framework studies. Our review highlights current methodological trends, identifies widely used and high-performing frameworks, and assesses each method across performance, interpretability, and ease of use. We further organize these methods into thematic groups-such as statistical modeling, machine learning, dimensionality reduction, and latent factor approaches-to provide a clear roadmap for future research and application. This work offers a critical foundation for advancing integrative longitudinal data science and supporting reproducible, scalable analysis in this rapidly evolving field.},
}
@article {pmid41053814,
year = {2025},
author = {Huebner, C and Huebner, NO and Goerig, T and Flessa, S},
title = {A regional One Health approach to mapping antimicrobial resistance interactions via systems thinking.},
journal = {One health outlook},
volume = {7},
number = {1},
pages = {46},
pmid = {41053814},
issn = {2524-4655},
abstract = {BACKGROUND: Antimicrobial resistance (AMR), as an original One Health problem, combines inextricable interactions between the human, animal and environmental dimensions. Addressing this challenge requires systemic thinking and coordinated networking between different levels of society and regional institutions. Knowledge of causal relationships, their mutual influence and the ability to assess the impact of possible interventions are prerequisites for coherent action to combat the further spread of antimicrobial resistance in a region. An integrated regional approach has not yet been addressed in One Health research on antimicrobial resistance.<br><br>METHODS: This study is based on a systems thinking approach and uses a causal loop diagram to visualise the relationships between human, animal and ecological components in a circular AMR system map for a One Health model region. The participatory approach actively involved regional stakeholders in the data collection and modelling process through surveys, semi structured interviews and interactive workshops. Based on the developed causal loop diagram, leverage point analysis is applied to estimate which types of interventions would have the greatest ability to address antimicrobial resistance in the One Health region.<br><br>RESULTS: Our results show that the system mapping tool is suitable for demonstrating the relationships regarding AMR in the One Health context for a defined region. It provides an opportunity to identify and visualise important risk factors that are direct or indirect drivers of AMR. Specifically, two amplifying and two balancing loops have been constructed in the model, covering antibiotic stewardship, public awareness, regional data management and environmental impact. Interdisciplinary and intersectoral collaboration, homogeneity of data and public awareness were identified as important leverage points. The graphical illustration of the causal loop diagram enables political and economic decision-makers to develop a deeper understanding of regional resistance patterns and the rational use of antibiotics from a One Health perspective.<br><br>CONCLUSION: This study is one of the first applications of a participatory systems thinking approach to the topic of AMR in the context of a One Health region.<br><br>TRAIL REGISTRATION: Not applicable.},
}
@article {pmid41053825,
year = {2025},
author = {Villette, R and Ortís Sunyer, J and Novikova, PV and Aho, VTE and Petrov, VA and Hickl, O and Busi, SB and De Rudder, C and Kunath, BJ and Heintz-Buschart, A and Trezzi, JP and Halder, R and Jäger, C and Lebrun, LA and Daujeumont, A and Schade, S and Janzen, A and Jehmlich, N and von Bergen, M and Laczny, CC and May, P and Trenkwalder, C and Oertel, W and Mollenhauer, B and Wilmes, P},
title = {Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {200},
pmid = {41053825},
issn = {2049-2618},
support = {863664//HORIZON EUROPE European Research Council/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; CORE/15/BM/10404093//Fonds National de la Recherche Luxembourg/ ; FNR11264123//Fonds National de la Recherche Luxembourg/ ; MJFF-019228//Michael J. Fox Foundation for Parkinson's Research/ ; MCI-BIOME_2019//Institute for Advanced Studies, Universit&#xe9; of Luxembourg/ ; 101038088//European Union's Horizon 2020 Widening Fellowships/ ; INTER/DFG/19/14429377//DFG Research Unit FOR2488/ ; },
mesh = {*Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Metabolomics/methods ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; Metabolome ; Prodromal Symptoms ; Multiomics ; },
abstract = {BACKGROUND: Parkinson's disease (PD) is associated with gut microbiome shifts. These shifts are mainly described at taxonomic level, but the functional consequences remain unclear. To obtain insight into the functional disruptions of the gut microbiome in PD, we used an integrated multi-omics approach, comparing gut microbiomes of individuals with PD, prodromal PD, and healthy controls.<br><br>RESULTS: Meta-metabolomics, the most discriminatory and robust omics&#xa0;level, was selected to Guide the analysis. We identified 11 metabolites that were differentially abundant between the groups, among which &#x3b2;-glutamate was increased in PD and prodromal PD, and correlated with the transcriptional activities of Methanobrevibacter smithii and Clostridium spp. We identified decreases in transcripts, but not in gene abundances, related to glutamate metabolism, bile acids biosynthesis, chemotaxis, and flagellar assembly in PD, particularly in keystone genera such as Roseburia, Agathobacter, and Blautia. Our findings, integrated into the Expobiome map, reveal multifactorial microbiome alterations which converge with PD pathways.<br><br>CONCLUSION: Our study highlights the apparent disruption of microbial gene expression in PD, particularly in genes associated to mobility. Moreover, we showcase the importance of investigating the gut microbiome's functional dimensions to better resolve microbiome-host interactions in health and disease.},
}
@article {pmid41056132,
year = {2026},
author = {Kourtesis, P and Lizarraga, A and MacPherson, SE},
title = {Immersive virtual reality assessments of working memory and psychomotor skills: A comparison between immersive and non-immersive assessments.},
journal = {Journal of neuropsychology},
volume = {20},
number = {1},
pages = {115-131},
pmid = {41056132},
issn = {1748-6653},
mesh = {Humans ; *Virtual Reality ; Male ; Female ; *Memory, Short-Term/physiology ; *Psychomotor Performance/physiology ; Adult ; Young Adult ; Reaction Time/physiology ; *Neuropsychological Tests ; Adolescent ; User-Computer Interface ; Reproducibility of Results ; },
abstract = {OBJECTIVE: Immersive virtual reality (VR) enhances ecological validity and facilitates intuitive and ergonomic hand interactions for performing neuropsychological assessments. However, its comparability to traditional computerized methods remains unclear. This study investigates the convergent validity, user experience and usability of VR-based versus PC-based assessments of short-term and working memory, as well as psychomotor skills, while also examining how demographic and IT-related skills influence performance in both modalities.<br><br>METHODS: Sixty-six participants performed the Digit Span Task (DST), Corsi Block Task (CBT) and Deary-Liewald Reaction Time Task (DLRTT) in both VR- and PC-based formats. Participants' experience in using computers and smartphones, and playing videogames, was considered. User experience and system usability of the formats were also evaluated.<br><br>RESULTS: While performance on DST was similar across modalities, PC assessments enabled better performance on CBT and faster reaction times in DLRTT. Significant correlations between VR and PC versions supported convergent validity. Regression analyses revealed that performance on PC versions was influenced by computing and gaming experience, whereas performance on VR versions was largely independent of these factors, except for gaming experience predicting performance on CBT backward recall. Moreover, VR assessments received higher ratings for user experience and usability than PC-based assessments.<br><br>CONCLUSION: Immersive VR assessments provide an engaging alternative to traditional computerized methods, with minimal reliance on prior IT experience and demographic factors. This resilience to individual differences suggests that VR may offer a more equitable and accessible platform for automated cognitive assessment. Future research should explore the long-term reliability of VR-based assessments.},
}
@article {pmid41057836,
year = {2025},
author = {Rangachari, P and Al Arkoubi, K and Shindi, R},
title = {A multi-level framework for advancing digital health equity in learning health systems: aligning practice and theory with the Quintuple Aim.},
journal = {International journal for equity in health},
volume = {24},
number = {1},
pages = {253},
pmid = {41057836},
issn = {1475-9276},
mesh = {Humans ; *Health Equity/standards ; *Learning Health System/organization &amp; administration ; Social Determinants of Health ; Electronic Health Records ; Digital Health ; },
abstract = {Achieving digital health equity is essential to realizing the transformative goals of the Quintuple. Aim: optimizing patient experience, improving population health, supporting provider well-being, reducing costs, and advancing health equity. Yet significant disparities persist in access to digital tools, driven by both traditional and digital social determinants of health (SDOH), such as housing instability and limited broadband access. Health system responses often focus on downstream interventions to meet immediate needs, such as referrals for housing assistance or smartphone distribution, while upstream strategies, like partnerships to expand access to affordable housing or advocacy to improve broadband access, remain underutilized. Similarly, targeted tools for specific populations often lack corresponding universal strategies like digital literacy campaigns. The absence of systematic Electronic Health Record (EHR) integration of SDOH data further limits health systems' ability to identify disparities, tailor interventions, and support structural change. This paper introduces a theoretically grounded, multi-level framework for advancing digital health equity within Learning Health Systems (LHS). Drawing on insights from information systems theories, socio-ecological models, organizational learning, implementation science, and systems thinking, the framework supports alignment of equity-centered strategies across micro- (individual), meso- (organizational), and macro- (policy) levels. The framework is organized around three strategic domains: (1) building equity-driven data infrastructure through SDOH-EHR integration, (2) designing scalable, equity-centered interventions that balance targeted and universal approaches, and (3) leveraging strategic starting points to transition from downstream efforts to upstream reforms. Grounded in the U.S. context yet informed by international evidence, this framework offers a roadmap for aligning theory and practice to advance digital health equity in LHS. It is both actionable and adaptable, translating evidence and theory into a structured approach that healthcare systems can use to guide health equity initiatives. It illustrates how SDOH data can inform person-centered care, how targeted tools like multilingual telehealth apps can be integrated with universal strategies such as digital literacy campaigns, and how enabling services, community partnerships, and policy advocacy can catalyze longer-term structural reforms. Emphasizing continuous learning through feedback loops and multi-level alignment, the framework equips stakeholders to embed equity into LHS design and function, ultimately advancing sustainable progress toward the Quintuple Aim.},
}
@article {pmid41061878,
year = {2025},
author = {William, G and Qadir, A and Saqib, Z},
title = {Urbanization and pollution pressures drive functional homogenization in bird feeding guilds.},
journal = {Environmental research},
volume = {286},
number = {Pt 3},
pages = {123029},
doi = {10.1016/j.envres.2025.123029},
pmid = {41061878},
issn = {1096-0953},
mesh = {*Urbanization ; *Environmental Pollution/statistics &amp; numerical data ; Ecosystem ; Animals ; *Birds/physiology ; Pakistan ; Feeding Behavior/physiology ; Biodiversity ; },
abstract = {Urbanization and pollution are rapidly transforming ecosystems across the Global South, yet their impacts on functional biodiversity remain underexplored. Birds, as ecologically diverse and responsive taxa, are valuable indicators of environmental change and functional simplification. We examined how urbanization and pollution jointly influence the functional structure of avian communities across an urban-rural gradient in Sialkot District, a rapidly industrializing region of northeastern Pakistan. Using standardized point counts across 18 sites stratified by urban intensity and pollution levels, we quantified bird community composition and feeding guilds. We applied multidimensional indices of functional diversity (FRic, FEve, FDis, RaoQ) and ordination methods to assess trait-based filtering. Functional richness and divergence contracted markedly with increasing pollution and urbanization. Functionally specialized guilds particularly insectivores, piscivores, and carnivores were absent from the most polluted urban sites, which were dominated by ecological generalists such as omnivores and scavengers. Trait dissimilarity and redundancy declined sharply with pollution, and ordination revealed clear guild turnover along the pollution gradient, indicating homogenization of trophic roles. Functional evenness and dispersion showed weaker responses, suggesting selective persistence of a few tolerant guilds in urban cores. Feeding guild richness also declined with pollution, reflecting a strong loss of trophic diversity under anthropogenic stress. These findings provide rare empirical evidence from South Asia linking environmental contamination to multidimensional losses of avian functional diversity. By integrating trait-based metrics with ecological gradients, this study highlights the need to incorporate functional indicators into conservation planning, particularly in rapidly urbanizing regions where ecological data remain limited.},
}
@article {pmid41061883,
year = {2025},
author = {de Oliveira, FG and Palmeiro, AS and Brito, PEM and Motta, WG and Cestari, MM and de Assis, HCDS and Dos Santos, LD},
title = {Environmental assessment of three southern Brazilian rivers using an integrated biomarker response index in Hypostomus ancistroides applied to GIS.},
journal = {Environmental research},
volume = {286},
number = {Pt 3},
pages = {123028},
doi = {10.1016/j.envres.2025.123028},
pmid = {41061883},
issn = {1096-0953},
mesh = {Animals ; Brazil ; Rivers/chemistry ; *Environmental Monitoring/methods ; *Catfishes/metabolism ; *Water Pollutants, Chemical/analysis/toxicity ; Biomarkers/metabolism/analysis ; Geographic Information Systems ; Oxidative Stress ; },
abstract = {This study evaluated the effects of contaminants, particularly metals and pesticides, in three rivers in Southern Brazil - São Camilo, Santa Fé, and Pioneiro - using the catfish Hypostomus ancistroides as a bioindicator. Biomarkers of oxidative stress, neurotoxicity, and genotoxicity were employed and integrated into an Integrated Biomarker Response (IBR) index, spatial analysis conducted using Geographic Information Systems (GIS). Sampling occurred during two seasons, winter (2022) and summer (2023), with sediments and fish collected from three sites per river. Detected concentrations of metals, including Cu, Zn, K, and Mn, were below Brazilian regulatory thresholds. Biomarker responses revealed significant biological effects associated with oxidative stress, particularly at intermediate and downstream sites. These included acetylcholinesterase inhibition, increased activity of superoxide dismutase (SOD) and catalase (CAT), elevated levels of metallothionein's (MET) and lipid peroxidation (LPO), indicating neurotoxicity and oxidative damage. Site SF2 (Santa Fé River) exhibited the greatest impact, likely due to the urban and industrial influences. Nuclear morphological alterations revealed localized genotoxic effects. Despite the low contaminant levels, the results highlight notable sublethal effects on fish health and ecological integrity. The integration of biomarkers proved effective in identifying critical areas and informing environmental management strategies.},
}
@article {pmid41063755,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Treble Lines, Charanyca trigrammica (Hufnagel, 1766) (Lepidoptera: Noctuidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {520},
pmid = {41063755},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Charanyca trigrammica (Treble Lines; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 546.43 megabases and 546.58 megabases. Most of haplotype 1 (99.97%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.44 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 {pmid41063758,
year = {2025},
author = {Sivell, O and Sivell, D and Mitchell, R and Webb, JA and Falk, S and , and , and , and , and , and , and , and , },
title = {The genome sequence of a snipefly, Rhagio lineola Fabricius, 1794.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {154},
pmid = {41063758},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Rhagio lineola (snipefly; Arthropoda; Insecta; Diptera; Rhagionidae). The genome sequence has a total length of 1,654.96 megabases. Most of the assembly (97.13%) is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.64 kilobases.},
}
@article {pmid41064473,
year = {2024},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Pale Oak Beauty, Hypomecis punctinalis (Scopoli, 1763).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {531},
pmid = {41064473},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Hypomecis punctinalis (the Pale Oak Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 741.20 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,897 protein-coding genes.},
}
@article {pmid41066464,
year = {2025},
author = {O'Neill, X and White, A and Northrup, GR and Saad-Roy, CM and White, PS and Boots, M},
title = {Superspreading and the evolution of virulence.},
journal = {PLoS computational biology},
volume = {21},
number = {10},
pages = {e1013517},
pmid = {41066464},
issn = {1553-7358},
mesh = {Virulence/genetics ; Humans ; *COVID-19/transmission/epidemiology/virology ; *SARS-CoV-2/pathogenicity/genetics ; Animals ; *Biological Evolution ; Computer Simulation ; Computational Biology ; Host-Pathogen Interactions ; Models, Biological ; },
abstract = {Superspreading, where a small proportion of a population can cause a high proportion of infection transmission, is well known to be important to the epidemiology of a wide range of pathogens, including SARS-CoV-2. However, despite its ubiquity in important human and animal pathogens, the impact of superspreading on the evolution of pathogen virulence is not well understood. Using theory and both deterministic and stochastic simulations we examine the evolution of pathogen virulence under a range of different distributions of infection transmission for the host. Importantly, for many pathogens, superpreader events may be associated with increased tolerance to infection or asymptomatic infection and when we account for this superspreading selects for higher virulence. In contrast, in animal populations where highly connected individuals, that are linked to superspreader events, also have fitness benefits, superspreading may select for milder pathogens. In isolation, the transmission distribution of the host does not impact selection for pathogen virulence. However, superspreading reduces the rate of pathogen evolution and generates considerable variation in pathogen virulence. Therefore, the adaptation of an emerging infectious disease, that exhibits superspreading, is likely to be slowed and characterised by the maintenance of maladaptive variants. Taken as a whole, our results show that superspreading can have important impacts on the evolution of pathogens.},
}
@article {pmid41070261,
year = {2025},
author = {Câmara, J and de Aguiar, SC and Paulino, T and Faria, AL and Bermúdez I Badia, S and Vilar, M and Fermé, E},
title = {Comparing adaptive tablet-based cognitive training and paper-and-pencil cognitive training: a pilot randomized controlled trial with community-dwelling stroke survivors.},
journal = {International journal of clinical and health psychology : IJCHP},
volume = {25},
number = {3},
pages = {100627},
pmid = {41070261},
issn = {2174-0852},
abstract = {INTRODUCTION: This study explored the feasibility and the preliminary efficacy of adaptive tablet-based cognitive training (CT) and paper-and-pencil CT approaches for mitigating multidomain post-stroke cognitive and noncognitive deficits.<br><br>METHODS: In this two-arm pilot randomized controlled trial, participants were randomly assigned to the NeuroAIreh@b (NAIr; adaptive tablet-based CT inspired by activities of daily living) and the Task Generator (TG; adaptive paper-and-pencil CT). A non-randomized passive control group was recruited for comparative purposes. Interventions comprised 12 bi-weekly 30-minute sessions. Primary outcomes explored training effects on several cognitive (e.g., global cognition, episodic memory), and noncognitive domains (e.g., quality of life, functional abilities).<br><br>RESULTS: A total of 20 participants were randomized (NAIr: n = 10; TG = 10). Within-group analysis revealed that the NAIr group presented significant improvements in more cognitive domains than the TG, and reported less functional disability, increased quality of life and greater motivation for rehabilitation at post-intervention. At follow-up, the NAIr group further improved in several cognitive domains and reported greater quality of life, while TG only improved in global cognition. Between-group analysis exhibited a pattern of superior performance in the adaptive CT groups over passive controls.<br><br>CONCLUSIONS: Findings suggest that adaptive CT interventions are feasible to implement and lead to cognitive and noncognitive improvements in community-dwelling stroke survivors. However, while both training approaches yield different short and medium/long-term benefits, the NAIr - a more ecologically valid method - was the only to promote generalization of training effects to functionality and quality of life at post-intervention and three-month follow-up, respectively.<br><br>TRIAL REGISTRATION: The trial is registered at ClinicalTrials.gov, number NCT05929287. Registered July 3rd, 2023 (cf. https://classic.clinicaltrials.gov/ct2/show/NCT05929287).},
}
@article {pmid41070750,
year = {2025},
author = {Seah, BKB},
title = {Database Release: PPSDB, a Linked Open Data Knowledge Base for Protist-Prokaryote Symbioses.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {6},
pages = {e70049},
pmid = {41070750},
issn = {1550-7408},
mesh = {*Symbiosis ; *Eukaryota/physiology/classification/genetics ; *Knowledge Bases ; *Archaea/physiology/genetics ; *Databases, Factual ; *Prokaryotic Cells/physiology ; *Bacteria/genetics/classification ; Software ; },
abstract = {As the ecological and evolutionary importance of symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea) is better appreciated, keeping an overview of their diversity and the literature becomes a growing and ongoing challenge. Here I present the Protist-Prokaryote Symbiosis Database (PPSDB), comprising 1146 manually curated interaction statements sourced from 443 publications, where biological taxonomy, anatomical localization, and analytical methods applied have been annotated and mapped to external databases and ontologies, such as Wikidata, NCBI Taxonomy, and Gene Ontology. I describe how its data model deals practically with challenges such as incomplete information and inconsistent taxon concepts, which will be applicable to similar projects. Both the model and underlying Wikibase software platform are highly extensible, so new items and properties can easily be added. Unlike a static table or list of citations, PPSDB is a structured knowledge base that enables programmatic access and powerful, integrated semantic queries. The database is available at https://ppsdb.wikibase.cloud/.},
}
@article {pmid41072345,
year = {2026},
author = {Liu, D and Yuan, J and Ren, P and Shi, L and Zhu, Z and Zhang, C and Dong, H and Liu, D},
title = {Electrochemical ammonia recovery from wastewater: The critical roles of electrode engineering toward scale-up.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124708},
doi = {10.1016/j.watres.2025.124708},
pmid = {41072345},
issn = {1879-2448},
mesh = {*Ammonia ; *Wastewater/chemistry ; Electrodes ; *Electrochemical Techniques ; Waste Disposal, Fluid/methods ; Water Purification/methods ; },
abstract = {Ammonia is indispensable for producing fertilizers that sustain the global population, yet its agricultural application contributes significantly to water pollution. Electrochemical technologies offer a renewable-energy-driven and chemical-free pathway for recovering ammonia directly from wastewater, representing a critical step toward a circular nitrogen economy and net-zero emissions in the wastewater sector. Nevertheless, translating lab-scale advances to industrialization remains constrained by technological hurdles. Emerging electrode-engineering strategies promise scalable, membrane-less electrochemical systems, but a systematic and comparative assessment is lacking. In this review, we first present the electrochemical ammonia recovery pathway and elucidate the mechanisms of various electrode materials in this process. Secondly, we critically evaluate state-of-the-art scalable electrode systems for electrochemical ammonia recovery. Thirdly, we comparatively analyze the ammonia recovery performance at both the electrode-material and electrode-system levels, comprehensively discussing the current challenges and future research opportunities toward technological scale-up. Finally, we outline key research targets toward next-generation electrochemical engineering for sustainable ammonia recovery and wastewater treatment.},
}
@article {pmid41074313,
year = {2025},
author = {Lv, J and Wang, Y and Zhou, L and Zhang, S and Song, W and Dong, R and Liu, T and Wang, G and Shi, L},
title = {Multi-omics investigation unveils the role of Eurotium cristatum fermentation in potentiating thinned young apple pomace for colitis-induced liver disorders amelioration.},
journal = {Food research international (Ottawa, Ont.)},
volume = {220},
number = {},
pages = {117095},
doi = {10.1016/j.foodres.2025.117095},
pmid = {41074313},
issn = {1873-7145},
mesh = {*Malus/microbiology ; *Fermentation ; Animals ; *Liver Diseases/etiology/prevention &amp; control ; Gastrointestinal Microbiome ; Oxidative Stress ; *Fermented Foods ; Humans ; Male ; Mice ; Liver/metabolism ; *Colitis/complications ; Multiomics ; },
abstract = {Liver disorders are the most prevalent extraintestinal manifestations observed in patients with ulcerative colitis, impacting millions of individuals worldwide. The present study elucidated the novel role of Eurotium cristatum (E. cristatum) -fermented thinned young apples (E.YAP) in preventing colitis associated liver disorders and dissected potential mechanisms through multi-omics integration. Specifically, E.YAP exhibited superior efficacy in alleviating colitis symptoms, liver damage, lipid accumulation, inflammation cytokines and oxidative stress, compared to the unfermented sample and the anti-colitis drug mesalazine. Hepatic transcriptomics demonstrated that E.YAP suppressed genes belonging to the cytochrome P450 family, CXC chemokine ligands and pro-inflammatory cytokines while enhancing PPAR signaling and oxidative phosphorylation. E.YAP exclusively elevated hepatic levels of metabolites involved in glycerophospholipid metabolism, linoleic acid metabolism, biosynthesis of unsaturated fatty acids and glutathione metabolism, whereas suppressing urobilin, a microbial metabolite implicated in fatty liver disease. Moreover, E.YAP increased α-diversity and relative abundances of Lactobacillus, Akkermansia, Muribaculum, Blautia and Faecalibaculum, concurrently increasing short-chain fatty acids. Multi-omics integration revealed robust links between E.YAP- affected hepatic genes, metabolites and gut bacteria that were associated with liver health. Furthermore, E.YAP outperformed unfermented samples in mitigating palmitic acid-induced inflammation, dyslipidemia and ROS overproduction in HepG2 cells. Additionally, network pharmacology identified key metabolites enriched by E. cristatum fermentation, particularly flavonoids, polyphenols and indole derivatives, which may synergistically inhibit hepatic inflammation and oxidative stress. Collectively, our study establishes the novel function of E.YAP in preventing colitis associated liver disorders, providing a sustainable strategy to valorize apple thinning waste into functional foods.},
}
@article {pmid41077897,
year = {2025},
author = {Rachtman, E and Jiang, Y and Mirarab, S},
title = {Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70055},
pmid = {41077897},
issn = {1755-0998},
support = {2138296//National Science Foundation (ACCESS Program)/ ; CNS-2100237//National Science Foundation (NRP/Natulius Program)/ ; OAC-1826967//National Science Foundation (NRP/Natulius Program)/ ; ACI-1541349//National Science Foundation (NRP/Natulius Program)/ ; 2137603//National Science Foundation (ACCESS Program)/ ; CNS-2120019//National Science Foundation (NRP/Natulius Program)/ ; //Minderoo Foundation/ ; ACI-1540112//National Science Foundation (NRP/Natulius Program)/ ; CNS-1730158//National Science Foundation (NRP/Natulius Program)/ ; OAC-2112167//National Science Foundation (NRP/Natulius Program)/ ; R35 GM142725/GM/NIGMS NIH HHS/United States ; 2138259//National Science Foundation (ACCESS Program)/ ; 2138286//National Science Foundation (ACCESS Program)/ ; 2138307//National Science Foundation (ACCESS Program)/ ; 1R35GM142725/NH/NIH HHS/United States ; //Schmidt Foundation/ ; },
mesh = {*Phylogeny ; *Machine Learning ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {A key application of phylogenetics in ecological studies is identifying unknown sequences with respect to known ones. This goal can be formalised as assigning taxonomic labels or inserting sequences into a reference phylogenetic tree (phylogenetic placement). Much attention has been paid to the phylogenetic placement of short fragments used in amplicon sequencing or metagenomics. However, placing longer pieces of DNA, such as assembled genomes, contigs, or long reads, is less studied. Placing long sequences should be easier than short reads due to their increased signal. However, handling larger inputs poses its own challenges including finding homologues and the computational burden. Here, we explore a phylogenetic placement method that uses k-mer frequencies to measure distances between long query sequences and reference genomes. Our proposed method, kf2vec, requires no alignment and can work on any region of the genome (needs no marker genes), thus simplifying analysis pipelines. A rich literature exists on using short k-mers frequencies to measure distances that correlate with phylogeny. Existing methods, however, have had moderate practical success despite enjoying strong theory. Instead of using predefined metrics, we train a deep neural network to estimate a distance from k-mer frequency vectors such that those distances match the path lengths on the reference phylogeny. The trained model is then used to characterise new samples. We demonstrate that kf2vec outperforms existing k-mer-based approaches in distance calculation and allows accurate phylogenetic placement and taxonomic identification of new samples from various types of long sequences.},
}
@article {pmid41079487,
year = {2025},
author = {Owens, JBB and Wüster, W and Mulley, J and Graham, S and Morgan, R and Barlow, A and , and , and , and , and , },
title = {The genome sequence of the common adder, Vipera berus (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {11},
pmid = {41079487},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Vipera berus (common adder; Chordata; Lepidosauria; Squamata; Viperidae). The haplotype-resolved assembly contains two haplotypes with total lengths of 1,695.0 megabases and 1,476.7 megabases, respectively. Most of haplotype 1 (98.45%) is scaffolded into 19 chromosomal pseudomolecules, while haplotype 2 is assembled to scaffold level. Haplotype 1 achieves the Earth Biogenome Project reference standard of 6.C.Q52. The mitochondrial genome has also been assembled and is 17.35 kilobases in length.},
}
@article {pmid41081996,
year = {2025},
author = {Yetişgin, SO and Bagci, HR and Coban, HO and Goktepe, S},
title = {From grazing to green: unraveling the ecological consequences of transhumance decline in Turkey's Mediterranean mountains.},
journal = {Tropical animal health and production},
volume = {57},
number = {8},
pages = {435},
pmid = {41081996},
issn = {1573-7438},
mesh = {Animals ; Turkey ; *Goats/physiology ; Geographic Information Systems ; *Animal Husbandry/methods ; *Ecosystem ; *Conservation of Natural Resources ; *Animal Migration ; },
abstract = {Transhumance, a millennia-old pastoral practice, has been instrumental in shaping the cultural, ecological and socio-economic fabric of Turkey's Mediterranean mountains while providing a range of ecosystem services. However, profound socio-economic shifts, policy constraints, and land-use changes have led to its rapid decline, triggering cascading environmental consequences. This study investigates the spatial and temporal associations between transhumance decline and land use/cover changes (LULC) along four transhumance migration routes in Turkey's Mediterranean Mountains over the past three decades. The migration routes of transhumant goat flocks were recorded using GPS collars. Digital Elevation Model data were sourced from the U.S. Geological Survey and analyzed using ArcGIS software to produce comprehensive maps illustrating the geographical and elevational characteristics of the study area. Furthermore, CORINE (Coordination of Information on the Environment) land cover maps derived from satellite imagery were employed to assess existing land cover and temporal shifts within the region. Through Geographic Information Systems (GIS), we conducted an in-depth analysis of land use/cover changes across the years 1990 and 2018, employing the Dynamic Degree Index to quantify the rate and extent of spatial transformations. Using Geographic Information Systems (GIS) and remote sensing, the findings reveal a loss of grasslands (- 9.96%) and shrublands (- 13.19%), while forests (+ 23.81%), agricultural land (+ 13.11%), and urban areas (+ 37.03%) expanded. Although direct causality cannot be confirmed, the spatial overlap between declining grazing areas and vegetation transitions suggests a strong association. Informal conversations with herders supported the observation that reduced grazing pressure contributed to shrub encroachment and forest expansion. These findings underscore the necessity of holistic rangeland governance strategies that reconcile conservation imperatives with the cultural and economic sustainability of pastoral communities. Ensuring the resilience of these landscapes requires a nuanced approach that acknowledges transhumance as a dynamic socio-ecological system rather than a relic of the past.},
}
@article {pmid41082884,
year = {2025},
author = {, },
title = {The burden of bacterial antimicrobial resistance in the WHO Eastern Mediterranean Region 1990-2021: a cross-country systematic analysis with forecasts to 2050.},
journal = {The Lancet. Public health},
volume = {10},
number = {11},
pages = {e955-e970},
doi = {10.1016/S2468-2667(25)00201-4},
pmid = {41082884},
issn = {2468-2667},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Humans ; World Health Organization ; *Drug Resistance, Bacterial ; Mediterranean Region/epidemiology ; Disability-Adjusted Life Years ; Forecasting ; *Bacterial Infections/mortality/drug therapy/epidemiology ; *Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is an urgent global crisis and one of the world's most complex challenges. Although there is increasing evidence of its impact on human mortality and morbidity, precise burden estimation has many challenges, and thus far has been elusive for the Eastern Mediterranean Region. Here, we present a comprehensive time-trend analysis of regional and country-level AMR burden estimates in the WHO Eastern Mediterranean Region (EMR), between 1990 and 2021, with forecasts up to 2050.<br><br>METHODS: We estimated deaths and disability-adjusted life-years (DALYs) attributable to and associated with AMR for 11 infectious syndromes, 22 bacterial pathogens, and 84 pathogen-drug combinations for the WHO EMR and each of its countries from 1990 to 2021. Data were obtained from mortality registries, surveillance systems, hospital records, systematic literature reviews, and other sources. We based our modelling approach on five broad components: the number of deaths in which infection had a role, the proportion of infectious deaths attributable to a given infectious syndrome, the proportion of infectious syndrome deaths attributable to a given pathogen, the percentage of a given pathogen resistant to an antimicrobial drug of interest, and the excess risk of mortality (or duration of an infection) associated with this resistance. These components were then used to estimate the disease burden by using two counterfactual scenarios: deaths and DALYs attributable to AMR (considering an alternative scenario where drug-resistant infections are replaced with susceptible infections), and deaths and DALYs associated with AMR (considering an alternative scenario where infections would not occur at all). Predictive statistical modelling was applied to generate estimates of AMR burden for each country. We also generated AMR burden forecasts up to 2050. We generated 95% uncertainty intervals (UIs) for the final estimates by taking the 2&#xb7;5th and 97&#xb7;5th percentiles across 500 draws through the multistage computational pipeline, and models were cross-validated for out-of-sample predictive validity.<br><br>FINDINGS: We estimated 380&#x2009;000 deaths (95% UI 332&#x2009;000-426&#x2009;000) associated with bacterial AMR and 92&#x2009;800 deaths (78&#x2009;300-111&#x2009;000) attributable to bacterial AMR in the EMR in 2021. In the past 31 years, there was considerable variation in AMR mortality trends across countries of the region and different age groups. Between 1990 and 2021, associated deaths among children younger than 5 years decreased by 50&#xb7;0% (38&#xb7;2-62&#xb7;0), while those among adults aged 70 and older rose by over 85&#xb7;7% (95% UI 57&#xb7;0-115&#xb7;7). Six pathogens were identified as the primary generators of burden: Streptococcus pneumoniae, Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Acinetobacter baumannii, and Pseudomonas aeruginosa. A substantial increase in the AMR burden due to S aureus was observed between 1990 (28&#x2009;200 deaths [21&#x2009;600-34&#x2009;000]) and 2021 (49&#x2009;500 deaths [43&#x2009;100-56&#x2009;200]); consequently, in 2021, methicillin-resistant S aureus was a leading pathogen-drug combination for most countries in the region for deaths and DALYs attributable to, and associated with AMR. Somalia had the highest age-standardised mortality rates in the region: for deaths attributable to and associated with AMR per 100&#x2009;000 population in both 1990 and 2021; conversely, the country with the lowest burden in the EMR was Qatar. By 2050, the number of deaths attributable to AMR in region is forecasted to reach 187&#x2009;000 (157&#x2009;000-223&#x2009;000) and deaths associated with AMR were projected to reach 752&#x2009;000 (629&#x2009;000-879&#x2009;000).<br><br>INTERPRETATION: Our study shows that bacterial AMR has been a serious public health threat in the EMR for more than 30 years, with a substantial fatal and non-fatal burden for priority bacterial pathogens and pathogen-drug combinations. The magnitude of this issue, future projects, and the inadequate response capacity in many countries underscore the need for more stringent regional leadership in this field. The insights gained from this study can direct targeted mitigation strategies for individual countries within the region, aiding in resource allocation and funding decisions, and emphasising the need for collaborative multisectoral endeavours among nations to address this issue.<br><br>FUNDING: Wellcome Trust, and the UK Department of Health and Social Care using aid funding managed by the Fleming Fund.},
}
@article {pmid41085718,
year = {2025},
author = {Karaarslan, F and Güneri, FD and Özen, H and Odabaşı, E},
title = {The evaluation of medical mud pack treatment from the patient's perspective in different musculoskeletal disorders- A prospective study.},
journal = {International journal of biometeorology},
volume = {69},
number = {12},
pages = {3587-3596},
pmid = {41085718},
issn = {1432-1254},
mesh = {Humans ; Male ; Female ; Middle Aged ; Patient Satisfaction ; Prospective Studies ; Adult ; *Mud Therapy ; Aged ; *Musculoskeletal Diseases/therapy ; Low Back Pain/therapy ; *Osteoarthritis, Knee/therapy ; *Myofascial Pain Syndromes/therapy ; Pain Measurement ; },
abstract = {This study evaluated patient satisfaction and expectation levels in individuals with chronic low back pain (LBP), myofascial pain syndrome (MPS), and knee osteoarthritis (KOA) who received mud pack therapy (MPT). It also investigated the relationship between these conditions and pain levels, global assessment results, and side effects. We assessed 250 patients (n = 74 for LBP, n = 75 for MPS, n = 101 for KOA) who underwent twelve sessions of MPT at 43 °C, lasting 30 min each. Patients continued their routine care and completed surveys on satisfaction and expectations, as well as measures of pain (VAS-pain), global assessment (VAS-PGA), and acceptable symptom state (PASS). Satisfaction levels were reported as "satisfied" or "definitely satisfied" by 93.1% to 96% of patients. Expectations were met by 86.7% to 89.2% of patients. Both VAS-pain and VAS-PGA showed statistically significant improvements after treatment (p < 0.001), though there were no differences between groups (p = 0.794 for VAS-pain, p = 0.234 for VAS-PGA). The PASS evaluation showed no significant group differences (p = 0.274). No serious side effects were reported, except for mild, short-term increases in pain. MPT is an effective treatment providing significant pain relief for LBP, MPS, and KOA patients, with high satisfaction and expectation fulfillment among participants.},
}
@article {pmid41087306,
year = {2025},
author = {Tang, Y and Qiu, S and Li, B and Sui, D and Jiang, K and Zheng, J and Zou, J and Lian, J and Wang, L and Yuan, Y},
title = {Integrative Physiological and Multi-Omics Insights: Salt Stress Adaptation and Functional Specialization in Suaeda salsa L.},
journal = {Physiologia plantarum},
volume = {177},
number = {5},
pages = {e70581},
doi = {10.1111/ppl.70581},
pmid = {41087306},
issn = {1399-3054},
support = {LYKJ[2023]01//Research on Breeding of Native Tree Species for Carbon Sequestration Afforestation in Jiangsu Coast/ ; Su[2024]TG14//Central Finance Forestry Science and Technology Extension Project/ ; JAF-2025-01//Youth Fund of Jiangsu Academy of Forestry Sciences/ ; LYKJ[2021]08//Long-Term Scientific Research Base for Cultivation of Salt-Tolerant Native Tree Species in Jiangsu/ ; },
mesh = {*Chenopodiaceae/physiology/genetics/metabolism ; Plant Leaves/physiology/metabolism/genetics ; Plant Roots/physiology/metabolism/genetics ; *Salt Stress/physiology ; Gene Expression Regulation, Plant ; Salt Tolerance/physiology ; Salt-Tolerant Plants/physiology/genetics ; Transcriptome ; Adaptation, Physiological ; Gene Expression Profiling ; Metabolomics ; Multiomics ; },
abstract = {Soil salinization, a major abiotic stress, severely limits plant growth and reduces crop yields. Understanding the salt tolerance mechanisms of halophytes is essential for the effective utilization of saline soils and improving crop resilience. Suaeda salsa L., a saline-alkali pioneer species with significant ecological and economic value, was investigated using physiological, metabolomic, and transcriptomic approaches under low, medium, and high soil electrical conductivities to elucidate its salt adaptation mechanisms. Physiological assays demonstrated that the responses were predominantly leaf-centered, with measurements of antioxidant enzymes, oxidative stress indicators, and osmolytes indicating that leaves play a key role in salt stress responses. Transcriptomic analysis revealed that the metabolic pathways were the most enriched across all conductivity comparisons. Metabolomic profiling showed that differential metabolites in the roots and leaves were enriched in starch and sucrose metabolism, whereas phenylpropanoid biosynthesis exhibited contrasting enrichment patterns in the roots and leaves under low- and high conductivity conditions. Based on these pathways, tissue-specific regulatory networks were constructed, revealing coordinated carbon allocation and the establishment of an efficient salt-tolerance network. Most genes exhibited divergent expression patterns between roots and leaves as conductivity increased, reflecting functional specialization. This study proposed that S. salsa uses a metabolic regulatory network characterized by gradient responses, functional differentiation, and energy optimization, providing a theoretical foundation for enhancing halophyte adaptation and improving crop salt tolerance.},
}
@article {pmid41087389,
year = {2025},
author = {Jiang, C and Wu, Q and Su, F and Cui, W and Chen, T and Sun, L},
title = {Chromosome-level genome assembly of the sea cucumber, Colochirus anceps.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1643},
pmid = {41087389},
issn = {2052-4463},
mesh = {Animals ; *Chromosomes ; *Genome ; Molecular Sequence Annotation ; *Sea Cucumbers/genetics ; Datasets as Topic ; },
abstract = {Colochirus anceps is a benthic sea cucumber recognized for its striking aposematic coloration, ecological role in nutrient recycling, and biomedical potential. In this study, we utilized Illumina short-read, PacBio HiFi long-read, and Hi-C sequencing technologies to assemble the chromosome-level genome of C. anceps. This represents the first genome assembly for the order Dendrochirotida within the class Holothuroidea. The assembled genome has a total size of 2,238.33 Mb, with a contig N50 of 15.09 Mb, and 95.09% of the assembly sequences have been anchored to 23 chromosomes. Annotation identified 24,102 protein-coding genes and revealed a high repeat content of 70.95%. The genome achieved a completeness score of 94.3%, as evaluated through BUSCO analysis. This genome assembly provides valuable insights into the genomic architecture and evolutionary dynamics of sea cucumbers, laying a foundation for exploring their unique biological traits, adaptability, and diversity.},
}
@article {pmid41087423,
year = {2025},
author = {Li, Z and Liu, J and Li, J and Zhou, Z and Huang, X and Gopinath, D and Luo, P and Wang, Q and Shan, D},
title = {Fusobacterium in the microbiome: from health to disease across the oral-gut axis and beyond.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {200},
pmid = {41087423},
issn = {2055-5008},
mesh = {Humans ; *Fusobacterium/physiology/pathogenicity/genetics ; *Mouth/microbiology ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Microbiota ; Animals ; Neoplasms/microbiology ; *Fusobacterium Infections/microbiology ; },
abstract = {Fusobacterium functions as both commensal and pathogen, linking the oral-gut axis to diverse diseases, including cancer. Evidence shows it modulates microbial balance, promotes dysbiosis, and contributes to carcinogenesis by driving inflammation, proliferation, invasion, and immune evasion. This review integrates ecological, molecular, and clinical insights, highlighting its roles in oral and systemic disease and discussing therapeutic potential, underscoring Fusobacterium's dualistic nature and implications for microbiome-targeted interventions.},
}
@article {pmid41090561,
year = {2026},
author = {Zhang, T and Luo, D and Li, G and Wang, H and Cao, Q and Zhang, R and Li, Y and Zhu, Y and Ma, C and Liston, A and Sun, H and Qiao, Q},
title = {Multi-omics analyses shed lights on the evolution and fruit development of Chinese raspberries (Rubus spp.).},
journal = {Journal of integrative plant biology},
volume = {68},
number = {4},
pages = {1032-1048},
pmid = {41090561},
issn = {1744-7909},
support = {202301AS070071//Yunnan Fundamental Research Projects/ ; 202505AS350015//Yunnan Fundamental Research Projects/ ; 202501AS070177//Yunnan Fundamental Research Projects/ ; 32260094//National Natural Science Foundation of China/ ; 32372655//National Natural Science Foundation of China/ ; 82260739//National Natural Science Foundation of China/ ; 2024YFF1306702//National Key Research and Development Program of China/ ; },
mesh = {*Rubus/genetics/growth &amp; development/metabolism ; *Fruit/growth &amp; development/genetics/metabolism ; Genome, Plant/genetics ; *Genomics ; Phylogeny ; Transcriptome/genetics ; Multiomics ; },
abstract = {Rubus (raspberries and blackberries) is a large genus of over 700 species well known for its taxonomic challenges. Many of its species hold significant economic value as important edible and medicinal plants. Here, near-complete genomes for four wild diploid raspberry species were assembled, including R. ellipticus, R. niveus, as well as the highly heterozygous diploid red raspberry (R. idaeus), and its closely related species R. sachalinensis. Pan-genome analysis of Rubus identified 10,243 core gene families (64% of total), and highlights expansions of flavonoid/terpenoid pathways in Rubus, correlating with fruit bioactive compound diversity. Our discovery of shared ancestral components between R. idaeus and R. sachalinensis subgenomes provides evidence for their homoploid hybrid origin. The centromere sequence characteristics could serve as markers for subgenome assignment in R. idaeus and R. sachalinensis. Moreover, population genomic studies of 125 accessions from ca. 80 species uncovered widespread genetic introgression, particularly in red raspberries, with centromeric haplotype signatures tracing ancestral contributions to cultivated varieties. By integrating metabolome and transcriptome data, we explore the fruit quality regulatory network of Chinese raspberries. We identified a glutathione S-transferase gene that may inhibit the successful transport of anthocyanins into the vacuole and appears to be a limiting factor for the anthocyanin pigmentation in R. ellipticus fruits. In summary, this research sheds new light on the genetic intricacies of raspberry species and their cultivars, and provides a robust foundation for horticultural improvement and genomic selection in raspberry breeding.},
}
@article {pmid41092926,
year = {2025},
author = {, },
title = {Burden of 375 diseases and injuries, risk-attributable burden of 88 risk factors, and healthy life expectancy in 204 countries and territories, including 660 subnational locations, 1990-2023: a systematic analysis for the Global Burden of Disease Study 2023.},
journal = {Lancet (London, England)},
volume = {406},
number = {10513},
pages = {1873-1922},
pmid = {41092926},
issn = {1474-547X},
support = {P01 HD031921/HD/NICHD NIH HHS/United States ; R01 AG044917/AG/NIA NIH HHS/United States ; R01 AG030153/AG/NIA NIH HHS/United States ; HHSN271201300071C/AG/NIA NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R03 AG043052/AG/NIA NIH HHS/United States ; R01 AG034479/AG/NIA NIH HHS/United States ; R01 AG018016/AG/NIA NIH HHS/United States ; R21 AG032572/AG/NIA NIH HHS/United States ; U01 AG009740/AG/NIA NIH HHS/United States ; R01 AG031716/AG/NIA NIH HHS/United States ; R21 AG034263/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Global Burden of Disease/trends ; *Life Expectancy/trends ; Risk Factors ; Male ; Female ; Disability-Adjusted Life Years ; *Wounds and Injuries/epidemiology ; Middle Aged ; Adult ; Global Health/statistics &amp; numerical data ; Child ; Aged ; Adolescent ; Infant ; Child, Preschool ; Young Adult ; Infant, Newborn ; COVID-19/epidemiology ; Persons with Disabilities/statistics &amp; numerical data ; Quality-Adjusted Life Years ; Aged, 80 and over ; },
abstract = {BACKGROUND: For more than three decades, the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) has provided a framework to quantify health loss due to diseases, injuries, and associated risk factors. This paper presents GBD 2023 findings on disease and injury burden and risk-attributable health loss, offering a global audit of the state of world health to inform public health priorities. This work captures the evolving landscape of health metrics across age groups, sexes, and locations, while reflecting on the remaining post-COVID-19 challenges to achieving our collective global health ambitions.<br><br>METHODS: The GBD 2023 combined analysis estimated years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs) for 375 diseases and injuries, and risk-attributable burden associated with 88 modifiable risk factors. Of the more than 310&#x2008;000 total data sources used for all GBD 2023 (about 30% of which were new to this estimation round), more than 120&#x2008;000 sources were used for estimation of disease and injury burden and 59&#x2008;000 for risk factor estimation, and included vital registration systems, surveys, disease registries, and published scientific literature. Data were analysed using previously established modelling approaches, such as disease modelling meta-regression version 2.1 (DisMod-MR 2.1) and comparative risk assessment methods. Diseases and injuries were categorised into four levels on the basis of the established GBD cause hierarchy, as were risk factors using the GBD risk hierarchy. Estimates stratified by age, sex, location, and year from 1990 to 2023 were focused on disease-specific time trends over the 2010-23 period and presented as counts (to three significant figures) and age-standardised rates per 100&#x2008;000 person-years (to one decimal place). For each measure, 95% uncertainty intervals [UIs] were calculated with the 2&#xb7;5th and 97&#xb7;5th percentile ordered values from a 250-draw distribution.<br><br>FINDINGS: Total numbers of global DALYs grew 6&#xb7;1% (95% UI 4&#xb7;0-8&#xb7;1), from 2&#xb7;64 billion (2&#xb7;46-2&#xb7;86) in 2010 to 2&#xb7;80 billion (2&#xb7;57-3&#xb7;08) in 2023, but age-standardised DALY rates, which account for population growth and ageing, decreased by 12&#xb7;6% (11&#xb7;0-14&#xb7;1), revealing large long-term health improvements. Non-communicable diseases (NCDs) contributed 1&#xb7;45 billion (1&#xb7;31-1&#xb7;61) global DALYs in 2010, increasing to 1&#xb7;80 billion (1&#xb7;63-2&#xb7;03) in 2023, alongside a concurrent 4&#xb7;1% (1&#xb7;9-6&#xb7;3) reduction in age-standardised rates. Based on DALY counts, the leading level 3 NCDs in 2023 were ischaemic heart disease (193 million [176-209] DALYs), stroke (157 million [141-172]), and diabetes (90&#xb7;2 million [75&#xb7;2-107]), with the largest increases in age-standardised rates since 2010 occurring for anxiety disorders (62&#xb7;8% [34&#xb7;0-107&#xb7;5]), depressive disorders (26&#xb7;3% [11&#xb7;6-42&#xb7;9]), and diabetes (14&#xb7;9% [7&#xb7;5-25&#xb7;6]). Remarkable health gains were made for communicable, maternal, neonatal, and nutritional (CMNN) diseases, with DALYs falling from 874 million (837-917) in 2010 to 681 million (642-736) in 2023, and a 25&#xb7;8% (22&#xb7;6-28&#xb7;7) reduction in age-standardised DALY rates. During the COVID-19 pandemic, DALYs due to CMNN diseases rose but returned to pre-pandemic levels by 2023. From 2010 to 2023, decreases in age-standardised rates for CMNN diseases were led by rate decreases of 49&#xb7;1% (32&#xb7;7-61&#xb7;0) for diarrhoeal diseases, 42&#xb7;9% (38&#xb7;0-48&#xb7;0) for HIV/AIDS, and 42&#xb7;2% (23&#xb7;6-56&#xb7;6) for tuberculosis. Neonatal disorders and lower respiratory infections remained the leading level 3 CMNN causes globally in 2023, although both showed notable rate decreases from 2010, declining by 16&#xb7;5% (10&#xb7;6-22&#xb7;0) and 24&#xb7;8% (7&#xb7;4-36&#xb7;7), respectively. Injury-related age-standardised DALY rates decreased by 15&#xb7;6% (10&#xb7;7-19&#xb7;8) over the same period. Differences in burden due to NCDs, CMNN diseases, and injuries persisted across age, sex, time, and location. Based on our risk analysis, nearly 50% (1&#xb7;27 billion [1&#xb7;18-1&#xb7;38]) of the roughly 2&#xb7;80 billion total global DALYs in 2023 were attributable to the 88 risk factors analysed in GBD. Globally, the five level 3 risk factors contributing the highest proportion of risk-attributable DALYs were high systolic blood pressure (SBP), particulate matter pollution, high fasting plasma glucose (FPG), smoking, and low birthweight and short gestation-with high SBP accounting for 8&#xb7;4% (6&#xb7;9-10&#xb7;0) of total DALYs. Of the three overarching level 1 GBD risk factor categories-behavioural, metabolic, and environmental and occupational-risk-attributable DALYs rose between 2010 and 2023 only for metabolic risks, increasing by 30&#xb7;7% (24&#xb7;8-37&#xb7;3); however, age-standardised DALY rates attributable to metabolic risks decreased by 6&#xb7;7% (2&#xb7;0-11&#xb7;0) over the same period. For all but three of the 25 leading level 3 risk factors, age-standardised rates dropped between 2010 and 2023-eg, declining by 54&#xb7;4% (38&#xb7;7-65&#xb7;3) for unsafe sanitation, 50&#xb7;5% (33&#xb7;3-63&#xb7;1) for unsafe water source, and 45&#xb7;2% (25&#xb7;6-72&#xb7;0) for no access to handwashing facility, and by 44&#xb7;9% (37&#xb7;3-53&#xb7;5) for child growth failure. The three leading level 3 risk factors for which age-standardised attributable DALY rates rose were high BMI (10&#xb7;5% [0&#xb7;1 to 20&#xb7;9]), drug use (8&#xb7;4% [2&#xb7;6 to 15&#xb7;3]), and high FPG (6&#xb7;2% [-2&#xb7;7 to 15&#xb7;6]; non-significant).<br><br>INTERPRETATION: Our findings underscore the complex and dynamic nature of global health challenges. Since 2010, there have been large decreases in burden due to CMNN diseases and many environmental and behavioural risk factors, juxtaposed with sizeable increases in DALYs attributable to metabolic risk factors and NCDs in growing and ageing populations. This long-observed consequence of the global epidemiological transition was only temporarily interrupted by the COVID-19 pandemic. The substantially decreasing CMNN disease burden, despite the 2008 global financial crisis and pandemic-related disruptions, is one of the greatest collective public health successes known. However, these achievements are at risk of being reversed due to major cuts to development assistance for health globally, the effects of which will hit low-income countries with high burden the hardest. Without sustained investment in evidence-based interventions and policies, progress could stall or reverse, leading to widespread human costs and geopolitical instability. Moreover, the rising NCD burden necessitates intensified efforts to mitigate exposure to leading risk factors-eg, air pollution, smoking, and metabolic risks, such as high SBP, BMI, and FPG-including policies that promote food security, healthier diets, physical activity, and equitable and expanded access to potential treatments, such as GLP-1 receptor agonists. Decisive, coordinated action is needed to address long-standing yet growing health challenges, including depressive and anxiety disorders. Yet this can be only part of the solution. Our response to the NCD syndemic-the complex interaction of multiple health risks, social determinants, and systemic challenges-will define the future landscape of global health. To ensure human wellbeing, economic stability, and social equity, global action to sustain and advance health gains must prioritise reducing disparities by addressing socioeconomic and demographic determinants, ensuring equitable health-care access, tackling malnutrition, strengthening health systems, and improving vaccination coverage. We live in times of great opportunity.<br><br>FUNDING: Gates Foundation and Bloomberg Philanthropies.},
}
@article {pmid41092928,
year = {2025},
author = {, },
title = {Global burden of 292 causes of death in 204 countries and territories and 660 subnational locations, 1990-2023: a systematic analysis for the Global Burden of Disease Study 2023.},
journal = {Lancet (London, England)},
volume = {406},
number = {10513},
pages = {1811-1872},
pmid = {41092928},
issn = {1474-547X},
support = {P01 HD031921/HD/NICHD NIH HHS/United States ; R01 AG044917/AG/NIA NIH HHS/United States ; R01 AG030153/AG/NIA NIH HHS/United States ; HHSN271201300071C/AG/NIA NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R03 AG043052/AG/NIA NIH HHS/United States ; R01 AG034479/AG/NIA NIH HHS/United States ; R01 AG018016/AG/NIA NIH HHS/United States ; R21 AG032572/AG/NIA NIH HHS/United States ; U01 AG009740/AG/NIA NIH HHS/United States ; R01 AG031716/AG/NIA NIH HHS/United States ; R21 AG034263/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Global Burden of Disease/trends ; Cause of Death/trends ; Male ; Female ; Aged ; Middle Aged ; Adult ; Infant ; Child ; Child, Preschool ; Adolescent ; Life Expectancy/trends ; Global Health/statistics &amp; numerical data ; Young Adult ; Infant, Newborn ; Aged, 80 and over ; Risk Factors ; Mortality/trends ; },
abstract = {BACKGROUND: Timely and comprehensive analyses of causes of death stratified by age, sex, and location are essential for shaping effective health policies aimed at reducing global mortality. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2023 provides cause-specific mortality estimates measured in counts, rates, and years of life lost (YLLs). GBD 2023 aimed to enhance our understanding of the relationship between age and cause of death by quantifying the probability of dying before age 70 years (70q0) and the mean age at death by cause and sex. This study enables comparisons of the impact of causes of death over time, offering a deeper understanding of how these causes affect global populations.<br><br>METHODS: GBD 2023 produced estimates for 292 causes of death disaggregated by age-sex-location-year in 204 countries and territories and 660 subnational locations for each year from 1990 until 2023. We used a modelling tool developed for GBD, the Cause of Death Ensemble model (CODEm), to estimate cause-specific death rates for most causes. We computed YLLs as the product of the number of deaths for each cause-age-sex-location-year and the standard life expectancy at each age. Probability of death was calculated as the chance of dying from a given cause in a specific age period, for a specific population. Mean age at death was calculated by first assigning the midpoint age of each age group for every death, followed by computing the mean of all midpoint ages across all deaths attributed to a given cause. We used GBD death estimates to calculate the observed mean age at death and to model the expected mean age across causes, sexes, years, and locations. The expected mean age reflects the expected mean age at death for individuals within a population, based on global mortality rates and the population's age structure. Comparatively, the observed mean age represents the actual mean age at death, influenced by all factors unique to a location-specific population, including its age structure. As part of the modelling process, uncertainty intervals (UIs) were generated using the 2&#xb7;5th and 97&#xb7;5th percentiles from a 250-draw distribution for each metric. Findings are reported as counts and age-standardised rates. Methodological improvements for cause-of-death estimates in GBD 2023 include a correction for the misclassification of deaths due to COVID-19, updates to the method used to estimate COVID-19, and updates to the CODEm modelling framework. This analysis used 55&#x2008;761 data sources, including vital registration and verbal autopsy data as well as data from surveys, censuses, surveillance systems, and cancer registries, among others. For GBD 2023, there were 312 new country-years of vital registration cause-of-death data, 3 country-years of surveillance data, 51 country-years of verbal autopsy data, and 144 country-years of other data types that were added to those used in previous GBD rounds.<br><br>FINDINGS: The initial years of the COVID-19 pandemic caused shifts in long-standing rankings of the leading causes of global deaths: it ranked as the number one age-standardised cause of death at Level 3 of the GBD cause classification hierarchy in 2021. By 2023, COVID-19 dropped to the 20th place among the leading global causes, returning the rankings of the leading two causes to those typical across the time series (ie, ischaemic heart disease and stroke). While ischaemic heart disease and stroke persist as leading causes of death, there has been progress in reducing their age-standardised mortality rates globally. Four other leading causes have also shown large declines in global age-standardised mortality rates across the study period: diarrhoeal diseases, tuberculosis, stomach cancer, and measles. Other causes of death showed disparate patterns between sexes, notably for deaths from conflict and terrorism in some locations. A large reduction in age-standardised rates of YLLs occurred for neonatal disorders. Despite this, neonatal disorders remained the leading cause of global YLLs over the period studied, except in 2021, when COVID-19 was temporarily the leading cause. Compared to 1990, there has been a considerable reduction in total YLLs in many vaccine-preventable diseases, most notably diphtheria, pertussis, tetanus, and measles. In addition, this study quantified the mean age at death for all-cause mortality and cause-specific mortality and found noticeable variation by sex and location. The global all-cause mean age at death increased from 46&#xb7;8 years (95% UI 46&#xb7;6-47&#xb7;0) in 1990 to 63&#xb7;4 years (63&#xb7;1-63&#xb7;7) in 2023. For males, mean age increased from 45&#xb7;4 years (45&#xb7;1-45&#xb7;7) to 61&#xb7;2 years (60&#xb7;7-61&#xb7;6), and for females it increased from 48&#xb7;5 years (48&#xb7;1-48&#xb7;8) to 65&#xb7;9 years (65&#xb7;5-66&#xb7;3), from 1990 to 2023. The highest all-cause mean age at death in 2023 was found in the high-income super-region, where the mean age for females reached 80&#xb7;9 years (80&#xb7;9-81&#xb7;0) and for males 74&#xb7;8 years (74&#xb7;8-74&#xb7;9). By comparison, the lowest all-cause mean age at death occurred in sub-Saharan Africa, where it was 38&#xb7;0 years (37&#xb7;5-38&#xb7;4) for females and 35&#xb7;6 years (35&#xb7;2-35&#xb7;9) for males in 2023. Lastly, our study found that all-cause 70q0 decreased across each GBD super-region and region from 2000 to 2023, although with large variability between them. For females, we found that 70q0 notably increased from drug use disorders and conflict and terrorism. Leading causes that increased 70q0 for males also included drug use disorders, as well as diabetes. In sub-Saharan Africa, there was an increase in 70q0 for many non-communicable diseases (NCDs). Additionally, the mean age at death from NCDs was lower than the expected mean age at death for this super-region. By comparison, there was an increase in 70q0 for drug use disorders in the high-income super-region, which also had an observed mean age at death lower than the expected value.<br><br>INTERPRETATION: We examined global mortality patterns over the past three decades, highlighting-with enhanced estimation methods-the impacts of major events such as the COVID-19 pandemic, in addition to broader trends such as increasing NCDs in low-income regions that reflect ongoing shifts in the global epidemiological transition. This study also delves into premature mortality patterns, exploring the interplay between age and causes of death and deepening our understanding of where targeted resources could be applied to further reduce preventable sources of mortality. We provide essential insights into global and regional health disparities, identifying locations in need of targeted interventions to address both communicable and non-communicable diseases. There is an ever-present need for strengthened health-care systems that are resilient to future pandemics and the shifting burden of disease, particularly among ageing populations in regions with high mortality rates. Robust estimates of causes of death are increasingly essential to inform health priorities and guide efforts toward achieving global health equity. The need for global collaboration to reduce preventable mortality is more important than ever, as shifting burdens of disease are affecting all nations, albeit at different paces and scales.<br><br>FUNDING: Gates Foundation.},
}
@article {pmid41093042,
year = {2025},
author = {Noordzij, HT and Wortel, MT and Heintz-Buschart, A and Petrikonyte, P and de Muinck, EJ and Trosvik, P},
title = {Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids.},
journal = {Plasmid},
volume = {134},
number = {},
pages = {102761},
doi = {10.1016/j.plasmid.2025.102761},
pmid = {41093042},
issn = {1095-9890},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Plasmids/genetics ; Infant ; Feces/microbiology ; Infant, Newborn ; Bacteroides/genetics ; Longitudinal Studies ; Female ; Computational Biology/methods ; Male ; Clostridium/genetics ; },
abstract = {Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant Bacteroides plasmid pBI143. Overall, the genus Bacteroides had the highest plasmid carriage, while the highest plasmid diversity was observed in Clostridium, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.},
}
@article {pmid41093232,
year = {2025},
author = {Lei, W and Guo, J and Liang, X and Wang, H and Qi, W and Mao, Z and He, S},
title = {Occurrence characteristics and environmental fate of neonicotinoid insecticides in mountain agricultural soils and river waters.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {386},
number = {},
pages = {127269},
doi = {10.1016/j.envpol.2025.127269},
pmid = {41093232},
issn = {1873-6424},
abstract = {Neonicotinoid insecticides (NNIs) have been widely detected in terrestrial ecosystems and may pose potential threats to ecosystem functions. Yet comprehensive evaluation of their occurrence characteristics, influencing factors, and soil-water connections remains limited. This study investigated NNIs occurrence patterns, transport dynamics, and ecological risks in soils and river waters of mountainous agricultural areas. The results revealed that NNIs were detected in soils and waters with a 100 % detection rate. Imidacloprid (IMI) was the predominant compound in soils (84.8 %), whereas river waters exhibited multi-component coexistence, with IMI, thiamethoxam (THIA), dinotefuran (DIN), and clothianidin (CLO) accounting for 30.9 %, 14.3 %, 12.9 %, and 11.8 % of NNIs, respectively. The mean concentration of eight NNIs (∑8NNIs) in stem mustard fields (11.45 ng/g) was higher than in forest soils (0.17 ng/g). The ∑8NNIs in water bodies near towns (102.65 ng/L) was 3.4 times higher than that in forest background areas. Additionally, A significant negative correlation between soil and water NNIs concentrations suggests that soil NNIs influence water NNIs levels. SEM and SHAP analyses identified soil NNIs concentration, bulk density, and elevation as primary factors regulating NNIs in adjacent waters. Ecological risk assessment outcomes indicate that the overall ecological risk in the study area was low. There were 13 % of soil sites with an α (risk entropy) exceeding 1, and 28 % of water sites with a risk coefficient surpassing the chronic HC5. These results provide theoretical support for understanding the occurrence characteristics and transfer trends of NNIs in soils and waters of agricultural areas.},
}
@article {pmid41093395,
year = {2025},
author = {Men, C and Cai, HJ and Fu, H and Zuo, JE},
title = {[Occurrence Characteristics， Ecological Risks， and Main Sources of Antibiotics in Rivers in Tongzhou District， Beijing].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {10},
pages = {6264-6273},
doi = {10.13227/j.hjkx.202408216},
pmid = {41093395},
issn = {0250-3301},
mesh = {Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; *Anti-Bacterial Agents/analysis ; *Environmental Monitoring ; China ; Beijing ; Risk Assessment ; Ecosystem ; Geographic Information Systems ; Wastewater/chemistry ; },
abstract = {China is a major producer and consumer of antibiotics. Because humans and animals have difficulty fully metabolizing antibiotics and the limited degradation efficiency of antibiotics in current wastewater treatment plants， antibiotic pollution is common in rivers in China， threatening the health of river ecosystems. Tongzhou District， Beijing， is the sub-center of Beijing， and all of the rivers flowing through the main urban area of Beijing converge in this district. A total of 16 antibiotics in the rivers of Tongzhou District， Beijing， were used as research objects， an analysis of the antibiotic concentration and spatial distribution characteristics was performed based on the geographic information system （GIS）， the ecological risk of the antibiotics and its uncertainty were evaluated by the coupling risk quotient method and Monte Carlo method， and the main sources of antibiotics were identified using the principal component analysis method. The results showed that the total concentrations of the 16 target antibiotics ranged from 69.52 to 1 913.05 ng·L[-1]. Ofloxacin （OFL） had the highest concentration among all antibiotics， with an average concentration of 279.95 ng·L[-1]， accounting for 50.07% of the total antibiotic concentration. Spatially， the concentrations of most of the antibiotics were relatively high in the Beiyun River and relatively low in the Wenyu River and Yunchaojian River. Compared to the Hai， Yangtze， Yellow， Pearl， Huai， and Liao Rivers， the concentrations of antibiotics in the rivers in Tongzhou District were low. The results of the ecological risk assessment showed that the ecological risk levels of sulfadimethoxine （SDM） and OFL were higher than those of the other antibiotics. The upper limits of the 90% confidence interval of the probability distribution of ecological risk for these antibiotics were 132.04 and 86.58 times the threshold of the high-risk class， respectively， and the probability of SDM leading to high ecological risk was higher than 95%. The results of source identification showed that the main sources of antibiotics were effluents of wastewater treatment plants， aquaculture， and livestock farming. Among these， effluent of wastewater treatment plants was the most dominant source， explaining 41.38% of the antibiotics. This study comprehensively explored the occurrence， ecological risks， and major sources of antibiotics in the rivers in Tongzhou District， Beijing， which is of great significance for targeted antibiotic pollution control and ecosystem health protection.},
}
@article {pmid41093425,
year = {2025},
author = {Guo, JX and Xie, Y and Qi, WX and Liao, YJ and Cao, XF and Peng, JF},
title = {[Pollution Characteristics and Identification of Risk Zones of Polycyclic Aromatic Hydrocarbons and Their Derivatives in Sediments and Soils of Chagan Lake].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {10},
pages = {6593-6602},
doi = {10.13227/j.hjkx.202409321},
pmid = {41093425},
issn = {0250-3301},
abstract = {Sediments and soils are primary reservoirs and potential secondary sources of polycyclic aromatic hydrocarbons （PAHs）. Investigating the pollution characteristics of PAHs and their derivatives in these environments is of significant environmental， health， and ecological relevance. In this study， Chagan Lake， a typical lake in the agricultural region of northeast China， was selected as the research area. Thirteen surface sediment and soil samples were collected in July 2021 to analyze the pollution characteristics， influencing factors， and ecological risks of 19 PAHs and 11 derivatives. The results showed that the contents of 19 PAHs in sediments ranged from 106.7 to 915.0 ng·g[-1]， higher values than those in soils， which ranged from 251.7 to 718.1 ng·g[-1]. The average contents of parent PAHs （PPAHs）， methylated PAHs （MPAHs）， oxygenated PAHs （OPAHs）， and nitro PAHs （NPAHs） in sediments and soils were 327.6， 57.7， 59.7， and 21.1 ng·g[-1]， respectively. The dominant congeners were primarily 3-ring （38%）， 2-ring （91%）， 3-ring （72%） and 2-ring （81%）， PAHs. An examination of derivatives of Nap， Flu， Ant， and BaA revealed that 2-MN and BA-7，12-D were the main derivatives of Nap and BaA， respectively， with contents lower than their parent compounds. In contrast， the contents of derivatives such as 9-FL， 2-NF， AQ， and 2-MAQ were higher than those of their parent compounds Flu and Ant. Quantitative results from the linear mixing model indicated that the sand ratio had a greater influence on the contents of PPAHs and MPAHs than TOC， particularly for 2-3 ring PPAHs， whereas the effect on 4-6 rings was opposite. Ecological risk assessments indicated that the contents of Nap and Phe in sediments and surrounding soils exceeded the threshold for adverse ecological effects， with 28% of the Chagan Lake area classified as a high-risk zone for overlapping Nap and Phe contamination.},
}
@article {pmid41094481,
year = {2025},
author = {Karami, H and Bleichrodt, A and Luo, R and Chowell, G},
title = {BayesianFitForecast: a user-friendly R toolbox for parameter estimation and forecasting with ordinary differential equations.},
journal = {BMC medical informatics and decision making},
volume = {25},
number = {1},
pages = {385},
pmid = {41094481},
issn = {1472-6947},
mesh = {Bayes Theorem ; Humans ; Forecasting/methods ; *Software ; *Models, Theoretical ; },
abstract = {BACKGROUND: Mathematical models based on ordinary differential equations (ODEs) are essential tools across various scientific disciplines, including biology, ecology, epidemic modeling, and healthcare informatics, where they are used to simulate complex dynamic systems and inform decision-making. However, implementing Bayesian calibration and forecasting typically requires substantial coding in Stan or similar tools. To support Bayesian parameter estimation and forecasting for such systems, we introduce BayesianFitForecast, a user-friendly R toolbox specifically developed to streamline Bayesian parameter estimation and forecasting in ODE models, making it particularly relevant to health informatics and public health decision-making (https://github.com/gchowell/BayesianFitForecast/).<br><br>RESULTS: This toolbox enables automatic generation of Stan files, allowing users to configure models, define priors, and analyze results with minimal programming expertise. By eliminating manual coding, BayesianFitForecast significantly lowers the technical barrier to Bayesian inference with dynamical systems. We demonstrate its flexibility and usability through applications to historical epidemic datasets (e.g., the 1918 influenza pandemic in San Francisco and the 1896-1897 Bombay plague) and simulated data, showing robust parameter estimation and forecasting performance under Poisson and negative binomial observation error structures. The toolbox also provides robust tools for evaluating model performance, including convergence diagnostics, posterior distributions, credible intervals, and performance metrics.<br><br>CONCLUSION: By improving the accessibility of advanced Bayesian methods, BayesianFitForecast broadens the application of Bayesian inference in time-series modeling, healthcare forecasting, and epidemiological applications. In addition to the R scripting interface, a built-in Shiny web application is included, enabling interactive model configuration, visualization, and forecasting. A tutorial video demonstrating the toolbox's functionality is also available (https://youtu.be/jnxMjz3V3n8).},
}
@article {pmid41096595,
year = {2025},
author = {Sakaguchi, T and Irifune, Y and Kamada, R and Sakaguchi, K},
title = {Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
pmid = {41096595},
issn = {1422-0067},
support = {25K00273//Japan Society for the Promotion of Science/ ; 24K01633//Japan Society for the Promotion of Science/ ; 23K17966//Japan Society for the Promotion of Science/ ; 23H02098//Japan Society for the Promotion of Science/ ; JPMJSP2119//Japan Science and Technology Agency/ ; none//the Photo-excitonix Project at Hokkaido University/ ; },
mesh = {*Systems Biology/methods/trends ; *Multiomics/methods/trends ; *Genomics/methods/trends ; Genome-Wide Association Study ; *Genome, Bacterial ; Protein Interaction Mapping ; Spatial Transcriptomics ; Single-Cell Gene Expression Analysis ; Proteomics/methods ; Quantitative Trait Loci ; Bacterial Proteins/genetics/metabolism ; Polymorphism, Single Nucleotide ; Microfluidics/methods ; Gene Editing ; Machine Learning ; Metabolic Engineering ; Drug Discovery ; },
abstract = {The field of bacterial systems biology is rapidly advancing beyond static genomic analyses, and moving toward dynamic, integrative approaches that connect genetic variation with cellular function. This review traces the progression from genome-wide association studies (GWAS) to multi-omics frameworks that incorporate transcriptomics, proteomics, and interactome mapping. We emphasize recent breakthroughs in high-resolution transcriptomics, including single-cell, spatial, and epitranscriptomic technologies, which uncover functional heterogeneity and regulatory complexity in bacterial populations. At the same time, innovations in proteomics, such as data-independent acquisition (DIA) and single-bacterium proteomics, provide quantitative insights into protein-level mechanisms. Experimental and AI-assisted strategies for mapping protein-protein interactions help to clarify the architecture of bacterial molecular networks. The integration of these omics layers through quantitative trait locus (QTL) analysis establishes mechanistic links between single-nucleotide polymorphisms and systems-level phenotypes. Despite persistent challenges such as bacterial clonality and genomic plasticity, emerging tools, including deep mutational scanning, microfluidics, high-throughput genome editing, and machine-learning approaches, are enhancing the resolution and scope of bacterial genetics. By synthesizing these advances, we describe a transformative trajectory toward predictive, systems-level models of bacterial life. This perspective opens new opportunities in antimicrobial discovery, microbial engineering, and ecological research.},
}
@article {pmid41098171,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Yellow-barred Brindle, Acasis viretata (Hübner, 1799) (Lepidoptera: Geometridae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {516},
pmid = {41098171},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Acasis viretata (Yellow-barred Brindle; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 297.68 megabases. Most of the assembly (99.98%) is scaffolded into 17 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.01 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 {pmid41102232,
year = {2025},
author = {Fassoni, AC and Yong, ASM and Clark, RE and Roeder, I and Glauche, I},
title = {Predicting treatment-free remission in chronic myeloid leukemia patients using an integrated model of tumor-immune dynamics.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {115},
pmid = {41102232},
issn = {2056-7189},
mesh = {Humans ; *Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology/drug therapy/therapy ; Killer Cells, Natural/immunology ; Remission Induction ; Treatment Outcome ; Models, Biological ; },
abstract = {The interactions between tumor and the immune system are main factors in determining cancer treatment outcomes. In Chronic Myeloid Leukemia (CML), considerable evidence shows that the dynamics between residual leukemia and the patient's immune system can result in either sustained disease control, leading to treatment-free remission (TFR), or disease recurrence. The question remains how to integrate mechanistic and data-driven models to support prediction of treatment outcomes. Starting from classical ecological modeling concepts, which allow to explicitly account for immune interactions at the cellular level, we incorporate time-course data on natural killer (NK) cell number, function, and their tumor-induced suppression into our general model of CML treatment. We identify relevant time scales governing treatment and immune response, enabling refined model calibration using tumor and NK cell time courses from different datasets. While the model successfully describes patient-specific response dynamics, critical parameters for predicting treatment outcome remain uncertain. However, by explicitly incorporating tumor load changes in response to TKI dose alterations, these parameters can be estimated and used to derive model predictions for treatment cessation. Further exploring dynamic changes in the number of functional immune cells, we suggest specific measurement strategies of immune effector cell populations to enhance prediction accuracy for CML recurrence following treatment cessation. The generalizability and flexibility of our approach represent a significant step towards quantitative, personalized medicine that integrates tumor-immune dynamics to guide clinical decisions and optimize dynamic cancer therapies.},
}
@article {pmid41102527,
year = {2025},
author = {Pei, Y and Forstmeier, W and Suh, A and Bambach, L and Borges, I and Low, GW and Dion-Côté, AM and Knief, U and Wolf, J and Kempenaers, B},
title = {Evolution of Large Polymorphic Inversions in a Panmictic Songbird.},
journal = {Molecular biology and evolution},
volume = {42},
number = {11},
pages = {},
pmid = {41102527},
issn = {1537-1719},
support = {//Max Planck Society/ ; //Lillawski/ ; RGPIN-2019-05744//NSERC Discovery/ ; //New Brunswick Innovation Foundation/ ; },
mesh = {Animals ; *Chromosome Inversion ; *Finches/genetics ; *Evolution, Molecular ; Polymorphism, Single Nucleotide ; *Songbirds/genetics ; Polymorphism, Genetic ; Male ; },
abstract = {Chromosomal inversions have long been appreciated as an important source of genetic diversity, local adaptation, and speciation. However, selection pressures maintaining ancestral and derived alleles at high frequency over extended periods of time remain poorly characterized. Using genome-wide single-nucleotide polymorphism markers and shared barcodes of linked-read sequences from 20 wild and 7 captive zebra finches Taeniopygia guttata, we systematically scanned a high-quality zebra finch reference genome and identified all large polymorphic inversions that segregate at high minor allele frequencies. Apart from the known polymorphic inversions on chromosomes Tgu5, Tug11, Tgu13, and TguZ, we characterized two inversions on microchromosomes Tgu26 and Tgu27 and identified another eight putative inversions, located mostly on microchromosomes and ranging in size from 0.42 to 65.22 Mb. Population genomic analyses show that most of the six bona fide inversions are complex, containing short nested inversions. The early inversions emerged an estimated 0.6 to 2.2 million years ago and segregate at relatively high frequencies in the wild (minor haplotype frequency range: 0.289 to 0.429). Based on fitness-related measures of about 5,000 captive zebra finches, we conclude that three of the inversion polymorphisms (Tgu11, Tgu27, and TguZ) may be maintained by net heterosis. In the youngest of the six inversions (Tgu13), the derived haplotype showed weak positive additive effects on various fitness components. In combination with previous discoveries, we provide a comprehensive overview of the genomic distribution and evolutionary dynamics of large polymorphic inversions in the panmictic zebra finch. Our findings highlight (i) that microchromosomes may harbor quite a few additional inversion polymorphisms, (ii) that most of the inversions contain smaller nested or overlapping inversions, and (iii) that inversions were most likely maintained by weak heterosis with small fitness effects requiring large sample sizes to be detected.},
}
@article {pmid41103550,
year = {2025},
author = {McLean, BS and Bloom, D and Davis, EB and Guralnick, RP and Santana, SE and Allen, JM and Amarilla-Stevens, H and Bell, KC and Blackburn, DC and Bradley, JE and Bradley, RD and Carling, MD and Coconis, A and Colella, JP and Conroy, CJ and Cook, JA and de Bastos Cruz Machado, H and Demboski, JR and Derieg, KM and Doll, A and Dumbacher, JP and Duncan, WD and Dunnum, JL and Feldman, C and Ferguson, AW and Fitzgerald, KE and Flannery, ME and Hood, K and Hornsby, AD and Krejsa, D and LaFrance, R and Light, JE and Pavan, SE and Peterson, S and Raniszewski, A and Rickart, EA and Robson, S and Rowe, RJ and Rowsey, DM and Semerdjian, A and Stankowich, T and Steger, L and Stevens, R and Thibault, KM and Thompson, CW and Upham, NS and Wilkins, A and Wommack, EA},
title = {Extending mammal specimens with their essential phenotypic traits.},
journal = {Journal of mammalogy},
volume = {106},
number = {5},
pages = {1282-1291},
pmid = {41103550},
issn = {0022-2372},
support = {R35 GM156919/GM/NIGMS NIH HHS/United States ; },
abstract = {Natural history collections are repositories of biodiversity specimens that provide critical infrastructure for studies of mammals. Over the past 3 decades, digitization of collections has opened up the temporal and spatial properties of specimens, stimulating new data sharing, use, and training across the biodiversity sciences. These digital records are the cornerstones of an "extended specimen network," in which the diverse data derived from specimens become digital, linked, and openly accessible for science and policy. However, still missing from most digital occurrences of mammals are their morphological, reproductive, and life-history traits. Unlocking this information will advance mammalogy, establish richer faunal baselines in an era of rapid environmental change, and contextualize other types of specimen-derived information toward new knowledge and discovery. Here, we present the Ranges Digitization Network (Ranges), a community effort to digitize specimen-level traits from all terrestrial mammals of western North America, append them to digital records, publish them openly in community repositories, and make them interoperable with complimentary data streams. Ranges is a consortium of 23 institutions with an initial focus on non-marine mammal species (both native and introduced) occurring in western Canada, the western United States, and Mexico. The project will establish trait data standards and informatics workflows that can be extended to other regions, taxa, and traits. Reconnecting mammalogists, museum professionals, and researchers for a new era of collections digitization will catalyze advances in mammalogy and create a community-curated trait resource for training and engagement with global conservation initiatives.},
}
@article {pmid41105870,
year = {2025},
author = {Astill Wright, L and Majid, M and Moore, M and Momoh, G and Patil, R and Shajan, G and Purewal, D and Patel, S and Morriss, R},
title = {The User Experience of Ambulatory Assessment and Mood Monitoring in Bipolar Disorder: Systematic Review and Meta-Synthesis of Qualitative Studies.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e71525},
pmid = {41105870},
issn = {1438-8871},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Bipolar Disorder/psychology/diagnosis ; Humans ; Qualitative Research ; *Affect ; *Monitoring, Ambulatory ; },
abstract = {BACKGROUND: Mood monitoring and ambulatory assessment hold promise for supporting self-management and data collection in bipolar disorder (BD), but the effectiveness of these depends crucially on the preferences and perspectives of those who use them. To date, these user experiences have not been systematically synthesized.<br><br>OBJECTIVE: This study aimed to explore and synthesize qualitative evidence on the user experience of mood monitoring and ambulatory assessment in BD, with a focus on identifying barriers and facilitators for both individuals with BD and clinicians, as well as the intended purposes of these tools.<br><br>METHODS: We conducted a systematic review and meta-synthesis of qualitative and mixed-methods studies reporting on ambulatory assessment and mood monitoring in BD (PROSPERO CRD42023396473). A total of 8 electronic databases were searched. Studies were appraised using established criteria for qualitative research. First- and second-order constructs were extracted, and a third-order synthesis was developed using the Noblit and Hare meta-ethnographic approach.<br><br>RESULTS: A total of 20 studies comprising 2365 participants met inclusion criteria. We identified 9 overarching themes: adverse effects, barriers to use, facilitators to use, perceived purpose, sharing with others (positive and negative), clinician concerns, clinician suggestions, and desired features. Users reported both benefits and harms. Some experienced increased insight, behavioral change, and relapse prevention skills, while others reported emotional burden, repetitive content, and worsened mood or anxiety. Preferences varied widely, but a strong, consistent emphasis was placed on personalization, including the ability to control what is tracked, when and how it is shared, and the level of engagement with health care providers. Passive data collection was often seen as less intrusive and more sustainable. Sharing data was sometimes seen as empowering, especially when it enabled communication with trusted individuals or clinicians, but also raised concerns around autonomy, misinterpretation, and privacy. Clinicians echoed many user views but raised additional concerns about liability and interpretability of data. Participants also highlighted the need for onboarding or support to aid comprehension and effective use.<br><br>CONCLUSIONS: This review highlights the complexity and diversity of user experiences with ambulatory assessment and mood monitoring in BD. While many found these tools valuable for fostering insight, self-management, and relapse prevention, others found them burdensome or confronting. User engagement appears closely tied to perceived control, relevance, and personal fit. These findings underscore the need for flexible, user-centered design in future interventions. Customizability should be prioritized-including what is monitored, how feedback is delivered, and whether data is shared externally. Incorporating onboarding and adaptive feedback could help users better understand and apply their data to better self-manage. By aligning interventions more closely with user preferences and lived experience, ambulatory assessment and mood monitoring protocols may achieve greater uptake, engagement, and ultimately, a more effective intervention.},
}
@article {pmid41106000,
year = {2025},
author = {Kang, X and Wang, X and Zhang, Y and Ju, F},
title = {Multi-omics-guided discovery of broad-spectrum plasticizer degrader Rhodococcus sp. SPR1 and key enzymes driving tris(2-ethylhexyl) trimellitate (TOTM) degradation.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140086},
doi = {10.1016/j.jhazmat.2025.140086},
pmid = {41106000},
issn = {1873-3336},
mesh = {*Plasticizers/metabolism ; *Rhodococcus/metabolism/enzymology/genetics ; Biodegradation, Environmental ; Animals ; Bacterial Proteins/metabolism ; *Environmental Pollutants/metabolism ; Larva/microbiology ; Multiomics ; },
abstract = {Plastic pollution has garnered global attention, yet the environmental threats posed by plasticizers remain largely understudied. Emerging plasticizers, such as tris(2-ethylhexyl) trimellitate (TOTM), are increasingly prevalent in anthropogenically impacted environmental reserviros, but their biodegradation mechanism and associated strains and enzymes are poorly understood. Here, we discovered Rhodococcus strain SPR1 from the gut of polyvinyl chloride (PVC)-consuming insect larvae, which exhibits broad-spectrum degradation capabilities across five representative plasticizers, including both traditional and emerging types. SPR1 achieved up to 63.07 % degradation of TOTM in 120 h, with two enzymes TOTMaseA (linear primary-alkylsulfatase) and TOTMaseB (α/β hydrolase), validated as key contributors. Enzyme kinetics revealed that TOTMaseA exhibited a Vmax of 2.655 mM and Km of 0.3821 µM/min, while TOTMaseB showed a Vmax of 0.9664 mM and Km of 0.2245 µM/min, confirming that TOTMaseA has superior catalytic throughput and serves as the dominant contributor to TOTM degradation. Notably, TOTMaseA also displayed consistently greater abundance compared to TOTMaseB under TOTM exposure. The widespread presence of homologous strains and enzymes of TOTM-degrading SPR1 in environmental samples underscores the ecological relevance and bioremediation potential. This study provides quantitative and mechanistic insights into the microbial degradation of TOTM and advances our understanding of enzymatic strategies that enable the breakdown of emerging plasticizers.},
}
@article {pmid41106353,
year = {2026},
author = {Asteraye, GB and Jobling, R and Jemberu, WT and Pinchbeck, G and Knight-Jones, TJD and Critchlow, R and Rushton, J and Chaters, GL},
title = {Classification of donkey systems in Ethiopia.},
journal = {Preventive veterinary medicine},
volume = {246},
number = {},
pages = {106719},
doi = {10.1016/j.prevetmed.2025.106719},
pmid = {41106353},
issn = {1873-1716},
mesh = {Animals ; Ethiopia ; *Equidae ; *Animal Husbandry/classification/methods/statistics &amp; numerical data ; Ownership/statistics &amp; numerical data ; Surveys and Questionnaires ; Animal Welfare ; Female ; },
abstract = {Working donkeys play a critical role in transportation, agriculture and household resilience in low- and middle-income countries. Other animals that are kept for production purposes, such as cattle, are often grouped into broad production system classes, such as dairy or pastoral, for comparison between and better understanding of the needs and outputs of animals within specific sectors. Despite the importance of working donkeys for sustaining livelihoods there are no systematic classifications of these populations. The aim of this study was to classify and characterise donkey systems in Ethiopia using household-level questionnaire data which included donkey ownership, husbandry, use and local environment data, through multiple factor and hierarchical cluster analysis. Household questionnaire data from 241 donkey-owning households in three districts of Ethiopia were used. Three distinct clusters of donkey ownership were identified: 'Domestic-Pastoral'; 'Domestic-Agricultural' and 'Commercial'. Differences between systems are primarily influenced by donkey purpose, environmental (agro-ecological) factors, and husbandry practices. Constraints associated with donkey ownership varied across clusters: households in the commercial system reported higher incidence of injuries and welfare concerns, in the pastoral system the main constraints were drought and feed shortage, and domestic-agricultural households reported infectious diseases as the main challenge. This new classification of donkey systems provides a framework for analysing donkey health and welfare data, enabling more context-specific needs assessments and facilitating the design of targeted interventions to improve equid health and household livelihoods.},
}
@article {pmid41106617,
year = {2026},
author = {Losiewicz, OM and Cohen, ZD and Akre, S and Welborn, A and Craske, MG},
title = {Daily spread of positive affect is associated with subsequent well-being: A study of idiographic network analysis and emotional inertia.},
journal = {Journal of affective disorders},
volume = {393},
number = {Pt B},
pages = {120461},
doi = {10.1016/j.jad.2025.120461},
pmid = {41106617},
issn = {1573-2517},
mesh = {Humans ; Female ; Male ; Adult ; Ecological Momentary Assessment ; *Affect ; Middle Aged ; Cross-Sectional Studies ; *Emotions ; Longitudinal Studies ; Young Adult ; *Personal Satisfaction ; },
abstract = {Emotional inertia, or the persistence of affect over time, and emotion network density, a measurement of the interconnected or relatedness of one's emotions, both capture dynamics of emotional experiences. Previous research has found that higher levels of negative emotional inertia and network density are associated with anxiety and depression. However, there is a dearth of research examining inertia and density of positive emotions and prospective associations between emotion dynamics and subsequent wellbeing. This study sought to address these limitations by examining both cross-sectional and longitudinal associations between emotional inertia and network density and well-being. We examined inertia and density of both positive and negative emotions. Adults with moderate-to-severe depression (N = 333) completed two 8-day epochs of ecological momentary assessment (EMA) five times daily. Emotional inertia and idiographic networks were calculated separately for EMA measures of negative and positive affect, and associations with self-reported well-being were examined using nested comparison tests and Bayesian multilevel models. In partial support of hypotheses, contemporaneous network density of positive emotions was positively associated with self-reported well-being six months later. Conversely, inertia of positive affect was inversely associated with well-being six months later. Neither inertia nor network density of negative affect was associated with subsequent well-being. These results suggest that inertia and network density of positive affect may indicate likelihood of experiencing changes in well-being in the future. Future research should investigate the underlying mechanisms, discern differences between emotional inertia and emotion network density, and explore potential implications for treatment.},
}
@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 &amp; purification ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics/isolation &amp; 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.},
}
@article {pmid41114939,
year = {2026},
author = {Castro-Alvarez, S and Bringmann, LF and Back, J and Liu, S},
title = {The many reliabilities of psychological dynamics: An overview of statistical approaches to estimate the internal consistency reliability of intensive longitudinal data.},
journal = {Psychological methods},
volume = {31},
number = {2},
pages = {281-296},
doi = {10.1037/met0000778},
pmid = {41114939},
issn = {1939-1463},
support = {//Hellman Foundation/ ; },
mesh = {Humans ; Reproducibility of Results ; *Psychology/methods/standards ; Longitudinal Studies ; *Psychometrics/methods/standards ; Data Interpretation, Statistical ; *Models, Statistical ; },
abstract = {[Correction Notice: An Erratum for this article was reported in Vol 31(2) of Psychological Methods (see record 2027-65824-001). The authors discovered an error in the computation of the reliability coefficients according to the 2RDM. Upon correcting this, several results required minor updates. Specifically, the corrections affect a couple of sentences in the Results and Discussion sections, Figure 3, and the corresponding parts of the Supplementary Material. While the overall conclusions of the paper remain unchanged, the article has been updated to accurately reflect the corrected computations. The article was published with the impact statement from an unrelated paper. The impact statement has been replaced with correct version. All versions of this article have been corrected] Reliability is a key concept in psychology that has been broadly studied since the introduction of Cronbach's α, which is a measure of internal consistency. Despite its importance, reliability has been relatively understudied when dealing with intensive longitudinal data. Although intensive longitudinal measurements are often considered more ecologically valid and less prone to recall bias than survey data collected using traditional methods, there is no warranty that they are more reliable. Hence, empirical researchers need tools to study and report the reliability of the scales used in intensive longitudinal research. In recent years, psychologists have proposed different approaches to estimate the reliability of scales and items used when studying psychological dynamics. However, it is unclear how these approaches compare to one another, making it difficult to determine what options researchers have given a particular data set and specific research questions. Specifically, these approaches estimate reliability indices based on different statistical models, such as linear multilevel analysis, vector autoregressive models, and dynamic factor models. Furthermore, while some methods involve estimating one reliability index for the scores that applies to the whole sample, others estimate person-specific reliability indices. This wide variety of approaches can provoke some confusion. In this article, we aim to bridge this gap by reviewing and highlighting the similarities and differences of different methods used to estimate the reliability of intensive longitudinal data. We also showcase their application with empirical data. (PsycInfo Database Record (c) 2026 APA, all rights reserved).},
}
@article {pmid41115518,
year = {2026},
author = {Seneci, L and Suranse, V and Mancuso, M and Senoner, T and Xie, B and Koludarov, I and Sunagar, K and Fry, BG},
title = {Deadly innovations: Molecular phylogenetics and evolution of phospholipase A2 toxins in viperid snake venoms.},
journal = {Biochimie},
volume = {240},
number = {},
pages = {137-152},
doi = {10.1016/j.biochi.2025.10.010},
pmid = {41115518},
issn = {1638-6183},
mesh = {*Viperidae/genetics ; Animals ; *Phospholipases A2/chemistry/genetics ; Evolution, Molecular ; *Viper Venoms/chemistry/genetics ; Phylogeny ; Bayes Theorem ; Cluster Analysis ; Mutation ; Aspartic Acid/analysis/genetics ; Lysine/analysis/genetics ; },
abstract = {Snake venoms have surged as model systems in evolutionary biology thanks to the dynamic diversification and accelerated evolution of many toxin families. Among these, phospholipase A2 (PLA2) constitute a prime example as they are ubiquitous across the venomous snake radiation and have evolved a wide variety of pathophysiological activities. This is especially true in vipers (family Viperidae), one of the most successful and medically significant venomous snake lineages worldwide. In this study, we gathered publicly available sequences of viper venom PLA2s to recreate the molecular phylogeny and toxicological evolution of this toxin family to date. Furthermore, we determined the selection regimes regulating the evolution of these toxins with a comparative approach that combines multiple methodologies of phylogenetic reconstruction and analysis of selection signatures. Our phylogeny confirms the basal position of Asp49 PLA2s (proteins with Asp at position 49), while derived clades, such as the non-enzymatic Lys49 myotoxins and the poorly characterised Ser49 type, are nested within. Neurotoxicity arose on multiple independent occasions (all within the Asp49 clade), with monomeric and dimeric forms only distantly related to each other. Positive Darwinian selection was widespread across the viper PLA2 tree, in line with previous research. However, purifying selection was also preponderant (perhaps due to structural constraints imposed by the pathophysiological targets of these toxins) and relatively neutral substitutions were observed in certain clades. Overall, this study provides novel insights into the evolutionary history of viper venom PLA2s through a comprehensive phylogenetic framework and highlights the need for complementary genomic and functional research into these toxins.},
}
@article {pmid41120627,
year = {2025},
author = {Zhong, X and Zheng, R and Chen, W and Lv, L and Wei, Z},
title = {Regional differences, dynamic evolution, and driving factors of ecological resilience in China's urban agglomerations.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36791},
pmid = {41120627},
issn = {2045-2322},
support = {Grant No. 22XTY006//Western Program of the National Social Science Foundation of China/ ; Grant No. 23FYJ024//Philosophy and Social Science Planning Project of Guangxi, China/ ; Grant No. XYCSR2024025//Graduate Innovation Project of School of Economics and Management, Guangxi Normal University/ ; },
abstract = {With the ongoing progress of urbanization, the urban ecosystem is becoming increasingly fragile, exacerbated further by the emergence of urban agglomerations. Based on the 'Pressure-State-Response' model and panel data covering the period from 2010 to 2021, the step-by-step vertical and horizontal tiered evaluation method is employed to calculate the scores of ecological resilience in China's urban agglomerations. The Dagum's Gini coefficient, global and local Moran's index, unite strength and unite threshold, Markov chain, and geographic detector are utilized to reveal regional disparities, dynamic evolution, and driving factors of ecological resilience in China's urban agglomerations. The results reveal several significant findings: (1) The ecological resilience in Chinese urban agglomerations exhibited a fluctuating yet upward trend. (2) Although disparities in the ecological resilience of China's urban agglomerations are decreasing, differences between them remain significant. (3) Spatial correlation is evident in the ecological resilience of China's urban agglomerations. High-high clusters are primarily found in the eastern and upgrading urban agglomerations, while low-low clusters are concentrated in the western and fostering urban agglomerations. (4) The number of cities exceeding the ecological resilience threshold is gradually increasing, with core cities playing a pivotal role. (5) The probability of transition in a city is affected by the ecological resilience states of adjacent cities. (6) Driving factors such as Internet penetration rate, informatization level, and innovation capacity have significant but heterogeneous effects on ecological resilience. This paper enlightens that spatial co-governance and zoning management of ecological resilience are crucial for achieving regional ecological security.},
}
@article {pmid41121164,
year = {2025},
author = {Yang, YA and Huang, YH and Weng, YH and Chiu, YW},
title = {Socioeconomic factors in relation to dental caries among children aged 5-14 years: a cross-national comparative study using secondary data analyses.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {1640},
pmid = {41121164},
issn = {1472-6831},
support = {CMRPG1N0032//Chang Gung Memorial Hospital, Linkou/ ; NSTC 112-2314-B-037-098-MY3, NSTC 112-2314-B-182A-106 -MY3//National Science and Technology Council/ ; NSTC 112-2314-B-037-098-MY3, NSTC 112-2314-B-182A-106 -MY3//National Science and Technology Council/ ; },
mesh = {Humans ; *Dental Caries/epidemiology ; Child ; Child, Preschool ; Adolescent ; *Socioeconomic Factors ; Fluoridation/statistics &amp; numerical data ; Male ; Female ; Risk Factors ; Prevalence ; Global Health ; Tooth, Deciduous ; Income ; Cross-Sectional Studies ; Secondary Data Analysis ; },
abstract = {BACKGROUND: Dental caries is a preventable non-communicable disease. Untreated caries in deciduous teeth may contribute to the development of caries in permanent teeth. Nevertheless, limited research has focused specifically on the risk factors in children. The current study examined the association between dental caries and socioeconomic risk factors among children aged 5-14 years across countries worldwide.<br><br>METHODS: An ecological survey was conducted using nation-based, publicly available online databases from six reputable organizations: the World Health Organization, the Food and Agriculture Organization of the United Nations, the World Bank, the British Fluoridation Society, the United Nations Development Programme, and the Global Burden of Disease Project. Data were collected from these sources between 2014 and 2017. Independent variables included density of dental personnel, parental education, family income, water fluoridation, and sugar consumption. The dependent variables were the prevalence of caries in deciduous and permanent teeth. Data were analyzed using descriptive statistics, univariate analysis, and multinomial logistic regression.<br><br>RESULTS: After eliminating countries without complete information, this study enrolled 120 countries with complete data for both dependent and independent variables. Univariate analysis revealed significant differences by parental education, income level, and water fluoridation. We further conducted multivariate logistic regression analysis, indicating that countries with low fluoridation (<&#x2009;50%) had significantly higher odds of caries in permanent teeth (OR: 13.23; 95% CI: 1.22-143.53; p&#x2009;=&#x2009;0.03); shorter years of parental schooling was associated with lower prevalence of caries in permanent teeth (OR: 0.12; 95% CI: 0.03-0.47; p&#x2009;=&#x2009;0.002); and middle-income countries showed increased risk in both deciduous teeth (OR: 3.44; 95% CI: 1.26-9.43; p&#x2009;=&#x2009;0.02) and permanent teeth (OR: 6.93; 95% CI: 1.75-27.38; p&#x2009;=&#x2009;0.01) than high-income countries. Sugar consumption and density of dental personnel were not significantly associated.<br><br>CONCLUSION: This ecological study provides valuable insights into the global patterns of dental caries in children aged 5-14 years and their associations with selected socioeconomic indicators. Our results reveal significant correlations of dental caries with income level, water fluoridation coverage, and parental education. However, these associations should be interpreted with caution due to the ecological nature of the data and several important limitations.},
}
@article {pmid41127944,
year = {2026},
author = {Misono, S and Kummerfeld, E and Lim, KO},
title = {In Response to Ecological Momentary Assessment of Voice and Psychological Factors: Group and Individual Mechanisms.},
journal = {The Laryngoscope},
volume = {136},
number = {3},
pages = {E46},
doi = {10.1002/lary.70204},
pmid = {41127944},
issn = {1531-4995},
}
@article {pmid41128050,
year = {2025},
author = {Ben Mocha, Y and Woith, M and Scemama de Gialluly, S and Bruscagnin, L and Kestel, N and Markman, S and Drobniak, SM and Baglione, V and Boersma, J and Cousseau, L and Covas, R and Braga de Miranda, GH and Dey, CJ and Doutrelant, C and Gula, R and Heinsohn, R and Keynan, O and Kingma, SA and Leitão, AV and Li, J and Makuya, L and Middleton, KM and Pruett-Jones, S and Radford, AN and Restrepo, C and Rubenstein, DR and Schradin, C and Theuerkauf, J and Warrington, MH and Williams, DA and Woxvold, IA and Griesser, M},
title = {An integrative, peer-reviewed and open-source cooperative-breeding database (Co-BreeD).},
journal = {The Journal of animal ecology},
volume = {94},
number = {12},
pages = {2597-2614},
pmid = {41128050},
issn = {1365-2656},
support = {//Zukunftskolleg, Universit&#xe4;t Konstanz/ ; //Oxford Brookes Emerging Leaders Research Fellowship/ ; //SAVE Wildlife Conservation Fund/ ; 2018/29/B/NZ8/023123//Polska Akademia Nauk/ ; 4650/2-1//Deutsche Forschungsgemeinschaft/ ; EXC 2117-422037984//Deutsche Forschungsgemeinschaft/ ; //Ministerium f&#xfc;r Wissenschaft, Forschung und Kunst Baden-W&#xfc;rttemberg/ ; //Klaus Tschira Stiftung gGmbH/ ; },
mesh = {Animals ; *Mammals/physiology ; *Birds/physiology ; *Databases, Factual ; *Cooperative Behavior ; *Reproduction ; *Breeding ; },
abstract = {Large-scale, cross-species comparative analyses on cooperative breeding-where individuals care for the offspring of other group members-are important for understanding sociality and cooperation. However, the datasets that facilitate these analyses are often limited in precision. To advance comparative research on cooperative breeding, we hereby introduce the Cooperative-Breeding Database (Co-BreeD) for birds and mammals. We describe key features of Co-BreeD's structure: (i) integration of complementary datasets, each presenting a biological parameter relevant to cooperative-breeding research; (ii) sample-based (i.e. multiple samples per species linked to an exact sampling location and period); and (iii) open-source. Respectively, these features enable: (a) comprehensive identification of cooperative-breeding species according to the user's chosen definition, (b) linking intra- and inter-specific variation in traits with fine-scale environmental parameters and (c) enabling the research community to correct and expand this database. We present the initial Co-BreeD dataset, which estimates the prevalence of breeding events involving potential alloparents in 460 populations of 324 species, including 6 human populations (No. total = 43,247 breeding events). We conclude by demonstrating: (i) how Co-BreeD can improve comparative research (e.g. by enabling the study of cooperative breeding as a continuous rather than a binary trait); and (ii) that cooperative breeding is probably more prevalent than previously estimated in birds and mammals.},
}
@article {pmid41128166,
year = {2025},
author = {Campbell, C and Wang, T and Stockdale, AJ and Todd, S and Jaworski, J and Glampson, B and Papadimitriou, D and Mayer, E and Salih, H and Roadknight, G and Little, S and Noble, T and Várnai, KA and Davis, C and Heinson, AI and George, M and Borca, F and Roberts, T and Ribeyre, BB and English, L and Zhu, L and , and Woods, K and Davies, J and Cooke, GS and Nastouli, E and Khakoo, SI and Gelson, W and Elsharkawy, AM and Barnes, E and Matthews, PC},
title = {Hepatitis B Virus (HBV) Treatment Eligibility in the UK: Retrospective Longitudinal Cohort Data to Explore the Impact of Changes in Clinical Guidelines.},
journal = {Journal of viral hepatitis},
volume = {32},
number = {11},
pages = {e70098},
pmid = {41128166},
issn = {1365-2893},
support = {//National Institute for Health Research (NIHR) Health Informatics Collaborative (HIC)/ ; //National Institute for Health and Care Research/ ; //University College London/ ; },
mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; *Antiviral Agents/therapeutic use ; *Hepatitis B, Chronic/drug therapy ; Longitudinal Studies ; Retrospective Studies ; United Kingdom/epidemiology ; Aged ; Practice Guidelines as Topic ; Young Adult ; Hepatitis B virus/drug effects ; Hepatitis B e Antigens/blood ; Alanine Transaminase/blood ; Adolescent ; },
abstract = {Nucleos/tide analogue (NA) drugs are used for long-term treatment of chronic hepatitis B virus (HBV) infection, with treatment eligibility criteria changing rapidly amidst globally evolving clinical guidelines. We aimed to quantify the prescription of NA drugs to date, and to undertake a preliminary assessment of the impact of relaxing treatment eligibility thresholds, leveraging a unique large real-world secondary care dataset. We assimilated longitudinal clinical data, collected between February 1997 and April 2023 from adults with chronic HBV infection from six centres in England through the UK NIHR Health Informatics Collaborative (HIC) Viral Hepatitis and Liver Disease theme. We describe factors currently associated with the receipt of NA treatment and determine the proportion of the population who would become treatment eligible as thresholds change. Across 7558 adults with a mean follow-up of 4.0 years (SD 3.9), NA treatment was prescribed in 2014/7558 (26.6%), and as expected according to guidelines at the time, was associated with HBV e-antigen (HBeAg) positivity and alanine transferase (ALT) above the upper limit of normal (> ULN). Treatment was more likely in males, older adults, in Asian and Other ethnicities (compared to White), and less likely in socioeconomically deprived individuals. The proportion of treatment-eligible individuals was 32.3% based on 2 records of ALT > ULN over 6-12 months, 41.7% based on ALT > ULN and viral load (VL) > 2000 IU/mL, and 95.1% based on detectable VL and either ALT > ULN or age > 30 years. Evolving clinical guidelines will lead to substantial increases in the proportion of individuals living with HBV who are eligible for treatment, underlining the need for services to adapt rapidly to the changing clinical environment.},
}
@article {pmid41129719,
year = {2025},
author = {Astill Wright, L and Monk-Cunliffe, J and Guo, B and Morriss, R},
title = {Adverse Events of Mood Monitoring and Ambulatory Assessment in Depression and Bipolar Disorder: Systematic Review and Meta-Analysis.},
journal = {JMIR mental health},
volume = {12},
number = {},
pages = {e79500},
pmid = {41129719},
issn = {2368-7959},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Bipolar Disorder/diagnosis/psychology ; *Monitoring, Ambulatory/adverse effects ; *Affect ; *Depression/diagnosis ; *Depressive Disorder/diagnosis ; },
abstract = {BACKGROUND: Mood monitoring and ambulatory assessment offer improvements in measuring mood and behavior for mental health research and clinical practice. However, concerns about adverse effects and usability may hinder their implementation.<br><br>OBJECTIVE: This systematic review and meta-analysis assessed the prevalence of adverse events, barriers and facilitators to use, and suggestions for improvement in quantitative mood monitoring studies involving people with depression and bipolar disorder.<br><br>METHODS: We conducted a systematic review and meta-analysis of 77 quantitative studies that used mood monitoring or ambulatory assessment in depression and bipolar disorder, assessing adverse events, barriers and facilitators to use, and suggestions for improvement. Adverse events data were pooled to identify prevalence.<br><br>RESULTS: Of the 77 studies, 15 (19%) reported adverse events, and 20 (26%) reported usability issues. Pooled prevalence of adverse events was 0.04 (95% CI 0.03-0.06; P<.001). Specific adverse effects included increased burden or stress (0.04, 95% CI 0.02-0.07; P<.001), mood worsening (0.02, 95% CI 0.01-0.02; P=.001), self-harm (0.05, 95% CI-0.02 to 0.10; P=.007), and hospitalization (0.06, 95% CI 0.04-0.09; P=.26). The top facilitators were perceived helpfulness and ease of use, the top barriers included technical challenges and the time-consuming nature of the interventions, and the top suggested improvement was personalization.<br><br>CONCLUSIONS: A small number of mood monitoring or ambulatory assessment users experienced negative psychological effects; however, we were unable to infer causality. Due to the severe underreporting of adverse events as well as heterogeneity and publication bias in the included studies, there was limited certainty in the prevalence, duration, and severity of these adverse events. More systematic monitoring of adverse events is needed to optimize safety and usability. Many mood monitoring protocols may require additional development to decrease adverse events and improve acceptability.},
}
@article {pmid41130938,
year = {2025},
author = {Li, L and Simopoulos, CMA and Mayne, J and Ning, Z and Zhang, X and Hamada, M and Butcher, J and Serrana, JM and Wang, L and Cheng, K and Qin, H and Walker, K and Zhang, X and Stintzi, A and Figeys, D},
title = {Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9383},
pmid = {41130938},
issn = {2041-1723},
support = {32370050//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; *Proteomics/methods ; Bacteria/drug effects/metabolism/genetics/classification ; *Proteome/metabolism/drug effects ; Bacterial Proteins/metabolism ; },
abstract = {Therapeutic compounds exert impacts on gut microbiota; however, how they affect the community functional ecology, especially as reflected at the protein level, remains largely unexplored. In this study, we systematically map metaproteomic responses of ex vivo human gut microbiota to 312 compounds, generating 4.6 million microbial protein responses, available as an interactive resource (https://shiny.imetalab.ca/MPR_Viz/). Protein-level analyses identify significant metaproteomic shifts induced by 47 compounds, with neuropharmaceuticals as the sole drug class significantly enriched among these hits. Further analyses on the community level reveal a tri-stability pattern in microbial composition and the emergence of three distinct functional states, based on a functional beta-diversity metric. Notably, neuropharmaceuticals cause particularly strong effects on the microbiomes, lowering the proteome-level functional redundancy and raising the level of antimicrobial resistance proteins, ultimately pushing the microbiome into an alternative functional state. Preliminary validation suggests that enhancing functional redundancy may contribute to maintaining microbiota resilience against neuropharmaceutical-induced antimicrobial resistance. Overall, this work establishes a comprehensive view of how drugs influence gut microbiome function and ecology at the protein level, proposes a landscape-based framework for interpreting community resilience, and highlights the need to consider protein-level and ecological responses in the evaluation of therapeutic interventions.},
}
@article {pmid41130983,
year = {2025},
author = {Tang, C and Chen, X and Ke, S and Han, W and Chang, X and Li, X and Wang, Z and Chen, K and Bao, L and Hu, J and Wang, S and Bao, Z},
title = {A draft genome assembly of the mushroom coral Podabacia crustacea (Pallas, 1766).},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1677},
pmid = {41130983},
issn = {2052-4463},
support = {2024M763096//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Genome ; Phylogeny ; Datasets as Topic ; },
abstract = {Coral reefs are facing significant environmental changes that greatly impact biodiversity, including species such as the widely distributed coral Podabacia. In particular, Podabacia crustacea is notable for its high abundance and broad distribution. Despite its ecological importance, comprehensive genomic studies of this species have been limited, even though such data are crucial for the conservation of coral ecosystems. In this study, we generated a high-quality genome assembly of P. crustacea, the type species of the genus Podabacia, to provide a foundation for further genomic research on the genus. Using PacBio HiFi long reads, we assembled a genome of 853.9 Mb with a contig N50 of 2.9 Mb. BUSCO analysis revealed a completeness score of 97.0%. Additionally, we identified 29,342 protein-coding genes, 95.6% of which were functionally annotated through comparisons with established protein databases. This genomic resource advances our understanding of coral phylogeny and serves as an important reference for coral conservation studies.},
}
@article {pmid41131611,
year = {2025},
author = {Zhong, F and Zhou, W and Gao, X and Li, D and Zeng, J and Xiong, X and Lu, T and Gong, X and Xiao, Y and Li, J},
title = {Development and validation of a machine learning-based model for predicting radiation-induced hypothyroidism in nasopharyngeal carcinoma.},
journal = {Radiation oncology (London, England)},
volume = {20},
number = {1},
pages = {158},
pmid = {41131611},
issn = {1748-717X},
support = {20212BAB216064//Natural Science Foundation of Jiangxi Province/ ; 20224BAB206065//Natural Science Foundation of Jiangxi Province/ ; 82103478//National Natural Science Foundation of China/ ; 2021K01//Open Fund for Scientific Research of Jiangxi Cancer Hospital/ ; 2021&#x2009;J13//Open Fund for Scientific Research of Jiangxi Cancer Hospital/ ; 20232BBG70025//Jiangxi Province Key R&amp;D Program (Key Program)/ ; WCDJ2024YQ01//"Five-level Progressive" talent cultivation project of Jiangxi Cancer Hospital &amp; Institute/ ; },
mesh = {Humans ; *Machine Learning ; *Nasopharyngeal Carcinoma/radiotherapy ; *Hypothyroidism/etiology/diagnosis ; Male ; Female ; Middle Aged ; *Nasopharyngeal Neoplasms/radiotherapy ; *Radiotherapy, Intensity-Modulated/adverse effects ; Adult ; Nomograms ; Aged ; *Radiation Injuries/etiology ; },
abstract = {BACKGROUND AND PURPOSE: This study aims to develop a robust and user-friendly prediction model for radiation-induced hypothyroidism (RIHT) in nasopharyngeal carcinoma (NPC) patients.<br><br>MATERIALS AND METHODS: NPC patients treated with IMRT between Jan. 2019 and Dec. 2021 were randomly assigned to a training cohort (n&#x2009;=&#x2009;328) and a validation cohort (n&#x2009;=&#x2009;141) at a ratio of 7:3. A total of 33 clinical and dose-volume variables were collected. Significant variables (p&#x2009;<&#x2009;0.05) were identified through univariate Cox analysis and further refined using a 101-combination machine learning (ML) framework to develop a robust predictive model. The model was subsequently simplified through multivariate Cox analysis and a nomogram. Finally, the performance of the model was evaluated using the C-index, calibration plots, and decision curve analysis.<br><br>RESULTS: Using a 101-combination ML framework, we developed a predictive model for RIHT in NPC. The Coxboost&#x2009;+&#x2009;RSF method with 11 predictors achieved the best performance (C-index: 0.91 [training], 0.71 [validation]). A simplified five-variable model (pre-treatment TSH, TSH-to-thyroid-volume ratio, age, V45, V20) was created via multi-cox regression, with a C-index of 0.80 [training] and 0.71 [validation]. High-risk patients had significantly higher three-year RIHT incidences (72.3% vs. 18.6%, p&#x2009;<&#x2009;0.0001) in the training cohort, and 67.9% versus 24.4% (p&#x2009;<&#x2009;0.0001) in the validation cohort. The model showed strong calibration and confirmed clinical utility through decision curve analysis, supporting its use in personalized treatment planning.<br><br>CONCLUSION: We developed a ML framework to identify key predictive factors for RIHT, which was simplified into a five-variable model for clinical use, offering a robust tool for predicting RIHT risk in decision-making.},
}
@article {pmid41138377,
year = {2025},
author = {You, W and Xu, H and Duan, J and Zhou, Y and Li, J and He, D and Kizos, T},
title = {Assessing spatial differences of perceptions of cultural ecosystem services for coastal cultural landscape management: A case study from rural and urban areas in Quanzhou, China.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127674},
doi = {10.1016/j.jenvman.2025.127674},
pmid = {41138377},
issn = {1095-8630},
mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; Humans ; Surveys and Questionnaires ; Rural Population ; Urbanization ; Perception ; Culture ; Geographic Information Systems ; },
abstract = {Coastal cultural landscapes are critical ecosystems that provide essential cultural, social, and ecological services, supporting dense populations and contributing to global ecosystem functions. However, rapid urbanization and environmental degradation are transforming these landscapes, posing significant challenges for sustainable management. This study examines the spatial distribution of Cultural Ecosystem Services (CES) in urban and rural context of coastal cultural landscapes of Quanzhou. Using questionnaire surveys and Participatory Geographic Information Systems (PPGIS), we analyzed public perceptions of CES across different infrastructure types, including grey, blue, and green infrastructure. Results show that urban areas, especially the historic areas are hotspots for CES such as cultural heritage, religious values, and sense of place. In contrast, rural areas emphasize landscape appreciation and recreation. Grey infrastructure, particularly historic buildings, and blue-green infrastructure, such as urban parks and historic villages, are major contributors to CES perceptions. Significant differences in CES perceptions were observed between urban and rural contexts, shaped by socio-economic factors and local multiple landscape features and infrastructures. This study highlights the importance of integrating urban and rural perspectives in the sustainable management of coastal cultural landscapes and offers recommendations for enhancing the protection and utilization of cultural and natural heritage to foster socio-ecological sustainability in coastal regions.},
}
@article {pmid41138856,
year = {2026},
author = {Krutikov, M and Price, JR and Fry, Z and Longstaff, V and Meacock, K and Stephenson, C and O'Reilly, K and Singer, A and Shallcross, L},
title = {The hidden iceberg: can wastewater transform infection surveillance and prevention in care homes?.},
journal = {The Journal of hospital infection},
volume = {167},
number = {},
pages = {187-191},
doi = {10.1016/j.jhin.2025.09.022},
pmid = {41138856},
issn = {1532-2939},
}
@article {pmid41140115,
year = {2025},
author = {Symonová, R and Jůza, T and Tesfaye, M and Brabec, M and Sajdlová, Z and Brabec, J and Kubečka, J},
title = {Differential activity of transcription factors and neuronal effectors during the development of pikeperch brain.},
journal = {Biology open},
volume = {14},
number = {11},
pages = {},
pmid = {41140115},
issn = {2046-6390},
support = {LM2023055//ELIXIR CZ/ ; MEYS CR//ELIXIR CZ/ ; RVO 67985807//Akademie V&#x11b;d &#x10c;esk&#xe9; Republiky/ ; },
mesh = {Animals ; *Brain/metabolism/growth &amp; development ; *Transcription Factors/metabolism/genetics ; *Perches/growth &amp; development/genetics/metabolism ; Transcriptome ; *Neurons/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Computational Biology/methods ; Body Size ; },
abstract = {Juvenile pikeperch (Sander lucioperca) undergo several ontogenetic shifts, the timing of which determines the survival of their first winter. The shift from planktivory to a more active piscivorous phenotype involves moving from pelagic to demersal habitat with more stimuli and hence potential brain functional reorganizations. During two consecutive years, we collected planktivores and piscivores with different body sizes between the years, recording distinct stages relative to the shift, and analyzed their whole-brain transcriptomes in an ecological context. We identified a distinct non-overlapping group of transcription factors (TFs) significantly upregulated in each phenotype: TFs upregulated in planktivores correspond to initial establishment of brain regions and overall architecture; TFs upregulated in piscivores correspond to the refinement of neurons and the formation of specific neuronal circuits. The planktivores independently of body size were characterized by interconnected activity of two TFs, fosab and junba. Gene set enrichment revealed extracellular matrix and collagen-related transcripts in piscivores from both years. A high activity of solute carrier (Slc) transporters was identified in the smaller-bodied piscivores. The neurotranscriptomics results reflected differences in body size and matched with ecological data and survival rates. The brain regulome indicated that body size differences translate into the specific gene activity of juvenile pikeperch.},
}
@article {pmid41140638,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Shy Cosmet Moth, Limnaecia phragmitella Stainton, 1851 (Lepidoptera: Cosmopterigidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {509},
pmid = {41140638},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Limnaecia phragmitella (Shy Cosmet Moth; Arthropoda; Insecta; Lepidoptera; Cosmopterigidae). The assembly contains two haplotypes with total lengths of 539.22 megabases and 553.78 megabases. Most of haplotype 1 (98.9%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.26 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 {pmid41141935,
year = {2025},
author = {Montecino-Latorre, D and Pruvot, M and Shimabukuro, PHF and Barker, CM and Gallo, S and Palmer, J and Kutz, SJ and Cayol, C and Dórea, F and Noguera, LP and Joly, DO and Walzer, C and Keatts, L and Fine, AE and Olson, SH},
title = {A community-of-practice-built database to support the implementation and operation of national and subnational wildlife health surveillance systems.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101227},
pmid = {41141935},
issn = {2352-7714},
abstract = {Historically, poor data management has hampered the establishment and operation of wildlife health surveillance (WHS) systems and limited the integration of environmental data into One Health frameworks. Effective WHS purpose-built databases are key to solve this problem, yet the few options available remain inaccessible or narrow in scope. To address this gap, an international partnership is developing the Health and Wildlife Knowledge (HAWK) database. HAWK supports the management of diverse data generated by multiple actors and methodologies, all within a harmonized structure and vocabulary facilitating data access, analysis, communication, and reuse. Data are secured through compartmentalization across organizations and users, while supporting compliance of FAIR and CARE data principles. Slated for release in late 2025, HAWK is envisioned as a global public good to encourage data compatibility and best practices in the wildlife conservation and One Health communities, independent of languages and location, with minimal to no cost for users.},
}
@article {pmid41143093,
year = {2025},
author = {Liu, J and Liu, S},
title = {HealthBench: Advancing AI evaluation in healthcare, but not yet clinically ready.},
journal = {Digital health},
volume = {11},
number = {},
pages = {20552076251390447},
pmid = {41143093},
issn = {2055-2076},
abstract = {Large language models (LLMs) are increasingly applied in healthcare, yet their evaluation remains inconsistent and often disconnected from clinical practice. OpenAI's HealthBench represents an important advancement, encompassing 5000 multiturn synthetic clinical conversations benchmarked against 48,562 clinician-developed criteria across accuracy, completeness, context awareness, communication, and instruction-following. Key strengths include broad scenario coverage, contributions from 262 clinicians across 60 countries, and automated grading methods that show high concordance with physician ratings. HealthBench provides a scalable and globally relevant framework. Nevertheless, important limitations constrain its clinical applicability. Exclusive reliance on synthetic dialogs limits ecological validity, and model-based graders may reinforce shared blind spots. Moreover, HealthBench assesses static, offline interactions while omitting multimodal inputs, longitudinal care, and patient outcomes-factors critical to real-world decision-making. Without external validation, strong benchmark performance may not translate into improved diagnostic accuracy, workflow efficiency, or patient safety. To ensure safe and effective integration of LLMs into practice, future benchmarks must incorporate authentic clinical data, longitudinal outcomes, and system-level considerations. HealthBench is a valuable step, but evaluation strategies must evolve to capture the complexity and demands of frontline care.},
}
@article {pmid41145216,
year = {2025},
author = {Peel, N and Martin, S and Heavens, D and Yu, DW and Clark, MD and Leggett, RM},
title = {Real-time analysis and visualization of nanopore metagenomic samples with MARTi.},
journal = {Genome research},
volume = {35},
number = {11},
pages = {2488-2500},
pmid = {41145216},
issn = {1549-5469},
mesh = {*Metagenomics/methods ; *Software ; *Nanopore Sequencing/methods ; *Nanopores ; Metagenome ; Humans ; Computational Biology/methods ; },
abstract = {The emergence of nanopore sequencing technology has the potential to transform metagenomics by offering low-cost, portable, and long-read sequencing capabilities. Furthermore, these platforms enable real-time data generation, which could significantly reduce the time from sample collection to result, a crucial factor for point-of-care diagnostics and biosurveillance. However, the full potential of real-time metagenomics remains largely unfulfilled due to a lack of accessible, open-source bioinformatic tools. We present Metagenomic Analysis in Real-Time (MARTi), an innovative open-source software designed for the real-time analysis, visualization, and exploration of metagenomic data. MARTi supports various classification methods, including BLAST, Centrifuge, and Kraken2, letting users customize parameters and utilize their own databases for taxonomic classification and antimicrobial resistance analysis. With a user-friendly, browser-based graphical interface, MARTi provides dynamic, real-time updates on community composition and AMR gene identification. MARTi's architecture and operational flexibility make it suitable for diverse research applications, ranging from in-field analysis to large-scale metagenomic studies. Using both simulated and real-world data, we demonstrate MARTi's performance in read classification, taxon detection, and relative abundance estimation. By bridging the gap between sequencing and actionable insights, MARTi marks a significant advance in the accessibility and functionality of real-time metagenomic analysis.},
}
@article {pmid41148369,
year = {2025},
author = {Kuannaxiaer, A and Liu, J and Kasthuri, N},
title = {Integrating machine learning and geospatial approaches for multi-hazard vulnerability mapping: implications for environmental health and contaminant risk in fragile ecosystems.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {12},
pages = {526},
pmid = {41148369},
issn = {1573-2983},
mesh = {*Machine Learning ; *Ecosystem ; Geographic Information Systems ; India ; *Environmental Monitoring/methods ; *Environmental Health ; Humans ; Risk Assessment ; },
abstract = {High-altitude ecosystems face growing threats from natural hazards and human activities, intensifying socio-economic and environmental risks. The Nilgiris District, Tamil Nadu, is a hotspot where steep terrain, fragile ecosystems, climate variability, and anthropogenic pressures converge. This study integrates geospatial technologies and machine learning (XGBoost) to map multi-hazard risk zones and assess their implications for ecosystem stability and contaminant susceptibility. The GIS-based multi-moderated evaluation was applied using slope, elevation, land use/land cover (LULC), drainage density and proximity to roads and settlements. Improved the accuracy of the XGBoost classification by capturing complex spatial relationships. The multi-hazard risk zone map identified five classes with very low-risk zones with high-risk zones cantered near Coonoor and Kotagiri, which are associated for landslides and contaminated mobility, while in the lower-way areas cluster around AU. Combining crisis weakness with environmental fragility, this structure supports durable land-use management, ecosystem conservation and reducing pollution. The integration of geospatial analytics and machine learning provides a strong tool for disaster preparedness, risk reducing and elasticity in ecological sensitive hill districts.},
}
@article {pmid41150182,
year = {2025},
author = {Jones, L and Lay, M and Seneci, L and Hodgson, WC and Koludarov, I and Senoner, T and Soria, R and Fry, BG},
title = {Neurotoxic Sleight of Fang: Differential Antivenom Efficacy Against Mamba (Dendroaspis spp.) Venom Spastic-Paralysis Presynaptic/Synaptic vs. Flaccid-Paralysis Postsynaptic Effects.},
journal = {Toxins},
volume = {17},
number = {10},
pages = {},
pmid = {41150182},
issn = {2072-6651},
support = {DP210102406//Australian Research Council/ ; },
mesh = {Animals ; *Antivenins/pharmacology ; *Elapid Venoms/toxicity/genetics/chemistry ; *Dendroaspis ; Chickens ; *Paralysis/chemically induced/drug therapy ; *Neurotoxins/toxicity ; },
abstract = {Mamba (Dendroaspis species) snakebites are critical medical emergencies across sub-Saharan Africa. Envenomings can result in the rapid onset of complex neurotoxic symptoms, often leading to high rates of mortality without timely intervention with antivenom. The ancestral state of mambas is the green coloured, forest dwelling type, with the tan/grey coloured, savannah dwelling D. polylepis (Black Mamba) representing a derived state both ecologically and morphologically. However, it has not been tested whether these changes are paralleled by changes in venom biochemistry or if there are differential molecular evolutionary patterns. To fill these knowledge gaps, this study evaluated the neurotoxic effects of all Dendroaspis species venoms using the chick biventer cervicis nerve-muscle preparation, assessed the neutralizing efficacy of three antivenoms commercially available in Africa, and reconstructed the molecular evolutionary history of the toxin types to ascertain whether some were unique to particular species. All Dendroaspis venoms demonstrated potent flaccid-paralysis due to postsynaptic neurotoxicity. The only exception was D. angusticeps venom, which conversely exhibited spastic-paralysis due to presynaptic/synaptic neurotoxicity characterised by potentiation of acetylcholine presynaptic release and sustained synaptic activity of this neurotransmitter. Antivenom efficacy varied significantly. All three antivenoms neutralized to some degree the flaccid-paralysis postsynaptic effects for all species, with D. viridis venom being the best neutralized, and this pattern extended to all the antivenoms. However, neutralisation of flaccid-paralysis postsynaptic effects unmasked spastic-paralysis presynaptic/synaptic neurotoxicity within non-angusticeps venoms. Spastic-paralysis presynaptic effects were poorly neutralized for all species by all antivenoms, consistent with prior clinical reports of poor neutralisation of spastic-paralytic effects. Geographic variation in D. polylepis venom was evident for the relative neutralisation of both spastic-paralysis presynaptic/synaptic and flaccid-paralysis postsynaptic/synaptic neurotoxic pathophysiological effects, with differential neutralization capabilities noted between the Kenyan and South African populations studied. Molecular phylogenetic analyses confirmed spastic-paralysis and flaccid- paralysis toxins to be a trait that emerged in the Dendroaspis last common ancestor, with all species sharing all toxin types. Therefore, differences in venoms' pathophysiological actions between species are due to differential expression of toxin isoforms rather than the evolution of species-specific novel toxins. Our findings highlight the synergistic nature of flaccid-paralysis postsynaptic and spastic-paralysis presynaptic/synaptic toxins, while contributing significant clinical and evolutionary knowledge of Dendroaspis venoms. These data are crucial for the continued development of more effective therapeutic interventions to improve clinical outcomes and for evidence-based design of clinical management strategies for the envenomed patient.},
}
@article {pmid41154259,
year = {2025},
author = {Dabic, M and Djordjevic, G and Radovanovic, S and Mihaljevic, O and Stepovic, M and Zdravkovic, M and Zdravkovic, N and Stojic, V and Milojevic, S and Zdravkovic, D and Djonovic, N and Knezevic, D and Popovic, S and Janicijevic, K and Selakovic, V and Radovanovic, J},
title = {Disparities in Healthcare Utilization by Settlement Type in Serbia.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {20},
pages = {},
pmid = {41154259},
issn = {2227-9032},
abstract = {Background and Objectives: Urban-rural health disparities reflect differences in health outcomes, healthcare access, and socio-economic conditions between populations. In Serbia, limited research has quantified how socio-demographic and socio-economic characteristics influence settlement type and healthcare utilization. The aim of this study was to examine the relationship between settlement type and socio-demographic/socio-economic factors, and to assess whether these differences are reflected in patterns of healthcare utilization. Materials and Methods: Data were drawn from the 2019 Serbian National Health Survey, a nationally representative, stratified, two-stage random sample including 12,439 adults aged ≥20 years. Settlement type (urban vs. rural) was the primary dependent variable. Descriptive statistics, Chi-square and t-tests, and bivariate and multivariate logistic regression models were used to assess associations. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated, with significance set at p < 0.05. Results: Urban residence was more likely among unmarried individuals, those living in Šumadija/Central Serbia, and those with higher education. Primary or lower education reduced the odds of urban residence, and middle-income groups were less likely to live in urban areas compared to the richest. Settlement type was not significantly associated with hospital or day hospital use. However, rural residents had lower use of prescribed medicines, higher use of non-prescribed medicines, and more frequent physiotherapy visits. Private practice use was over twice as likely in urban settlements. Conclusions: To address urban-rural healthcare disparities in Serbia, targeted strategies could include enhancing health literacy in rural areas, incentivizing physicians to work in underserved regions, expanding telemedicine and mobile health services, improving access to prescribed medications, and strengthening public-private healthcare integration to ensure equitable access across all settlement types.},
}
@article {pmid41156942,
year = {2025},
author = {Gao, L and Zhao, H and Guo, N and Jiang, X and Zhang, Y},
title = {Mechanical and Environmental Properties of Cemented Paste Backfill Prepared with Bayer Red Mud as an Alkali-Activator Substitute.},
journal = {Materials (Basel, Switzerland)},
volume = {18},
number = {20},
pages = {},
pmid = {41156942},
issn = {1996-1944},
abstract = {This study developed a sustainable high-strength coal gangue backfill material for underground mining applications using coal gangue, fly ash, and cement as primary raw materials, with red mud (RM) as an alternative alkali activator. The mechanical properties of the backfill material were systematically optimized by adjusting coal gangue particle size and alkali activator dosage. The optimized formulation (coal gangue/fly ash/cement = 5:4:1, 3-6 mm coal gangue particle size, 5% RM, which named BF-6-5RM) achieved superior compressive strengths of 8.23 MPa (7 days) and 10.5 MPa (28 days), significantly exceeding conventional backfill requirements and outperforming a CaO-activated reference system (coal gangue/fly ash/cement = 5:4:1, 3-6 mm coal gangue particle size, 2% CaO, which named BF-6-2CaO). Microstructural and physicochemical analyses revealed that both formulations produced calcium silicate hydrate gels (C-S-H gels) and ettringite (AFt) as key hydration products, though BF-6-5RM exhibited a denser microstructure with well-developed ettringite networks and no detectable portlandite (CH), explaining its enhanced early-age strength. Environmental assessments confirmed effective heavy metal immobilization via encapsulation, adsorption, precipitation and substitution, except for arsenic (As), which exceeded Class III groundwater thresholds (DZ/T 0290-2015) due to elevated raw material content, displaying "surface wash-off, diffusion and depletion" leaching behavior. The findings confirm that red mud-based alkali activation is a viable technology for underground backfilling, provided it is coupled with arsenic control strategies like chemical stabilization or the selection of low-arsenic raw materials. This approach not only enables the resource utilization of hazardous industrial waste but also facilitates the production of backfill materials that combine both mechanical strength and environmental compatibility, thereby delivering dual economic and ecological benefits for sustainable mining practices.},
}
@article {pmid41160887,
year = {2026},
author = {Guo, S and Jiang, Y and Zou, J and Lu, M and Li, D and Zhang, Q and Li, W and Mao, L and Xu, Z and Liu, S},
title = {GPSAdb 2.0: an expanded atlas of gene-perturbation transcriptomes with enhanced tools for regulatory gene discovery.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D1082-D1086},
pmid = {41160887},
issn = {1362-4962},
support = {82403086//National Natural Science Foundation of China/ ; CSTB2022NSCQ-BHX0698//Natural Science Foundation of Chongqing/ ; //Chongqing Medical Scientific Research Project/ ; 2025DBXM005//Chongqing Health Commission and Science and Technology Bureau/ ; CYYY-DSTDXM202502//Chongqing Medical University/ ; },
mesh = {Humans ; *Transcriptome ; *Software ; *Gene Expression Profiling/methods ; Gene Knockdown Techniques ; *Gene Expression Regulation ; Cell Line ; *Databases, Genetic ; },
abstract = {Gene perturbation is essential for uncovering gene function and its involvement in various biological processes and diseases. GPSAdb 2.0 (https://www.gpsadb.com/) presents a significantly expanded and improved platform for exploring gene expression changes following gene knockdown across diverse cell lines. Compared to GPSAdb 1.0, this new version offers several key upgrades: (i) a substantial increase in data coverage, now featuring 7665 gene knockdown groups, 42 235 samples, and 2810 perturbation genes across a broader array of cell lines and biological conditions; (ii) the introduction of new tools, including "BioTrigger" for flexible gene set enrichment analysis and "fastGPSA" for rapid, advanced differential expression analysis. With these enhancements, GPSAdb 2.0 provides researchers with a powerful resource for investigating gene perturbation effects and gaining deeper insights into transcriptional regulation, making it an invaluable resource for studies on gene regulation, disease mechanisms, and potential therapeutic targets.},
}
@article {pmid41161774,
year = {2025},
author = {Khaing, PT and Han, YMZ and Zaww, K and Kyaw, MS and Thwin, KM and Orui, M and Kunii, Y and Hamaie, Y and Kyaw, SS and Tsuboi, M and Egawa, S},
title = {A Remote Access Qualitative Study Protocol to Investigate the Coping Strategies in the Mindset of the Affected Adults after the 2025 Myanmar Earthquake.},
journal = {The Tohoku journal of experimental medicine},
volume = {267},
number = {3},
pages = {263-272},
doi = {10.1620/tjem.2025.J130},
pmid = {41161774},
issn = {1349-3329},
mesh = {Humans ; Myanmar ; *Adaptation, Psychological ; *Earthquakes ; Qualitative Research ; Adult ; Middle Aged ; Female ; Male ; Young Adult ; Adolescent ; Social Support ; Coping Skills ; },
abstract = {On March 28, 2025, a 7.7-magnitude earthquake struck central Myanmar (GLIDE #EQ-2025-000043-MMR), compounding the country's existing political instability, economic fragility, and infrastructural weaknesses. Although seismic events have recurred throughout history, limited knowledge exists regarding how working-age adults (18-60), who play a central role in recovery, mobilize personal, cultural, and community resources to cope with adversity and reconstruct their lives. This is a protocol clarification for a remote access qualitative study using semi-structured interviews with 30 purposively sampled participants, half from heavily impacted zones (Sagaing, Mandalay) and half from nearby regions experiencing secondary disruption (Yangon). Using a remote system, interviews will be audio-recorded, transcribed verbatim, and analyzed thematically following Graneheim and Lundman's approach. This study aims to identify key coping strategies, including social support networks, spiritual practices, and local initiatives of working-age adults in Myanmar, and to compare how exposure severity shapes adaptive responses. Anticipated themes based on existing disaster and resilience literature include community-led resilience, hope through faith, and resource-sharing practices. Findings are expected to offer in-depth, culturally grounded insights that can inform disaster recovery programs, psychosocial support services, and policy frameworks aimed at strengthening resilience in Myanmar and similar low-resource, low-accessibility, crisis-affected settings.},
}
@article {pmid41162384,
year = {2025},
author = {Outhwaite, CL and Cocker, L and Comont, RF and White, HJ and Powney, GD and Turvey, K and Roy, HE and Brown, PMJ},
title = {A database of traits for the ladybird species of the United Kingdom.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1708},
pmid = {41162384},
issn = {2052-4463},
support = {Open Access Fund//Anglia Ruskin University/ ; NE/V006533/1//RCUK | Natural Environment Research Council (NERC)/ ; Algorithm studentship//RCUK | Natural Environment Research Council (NERC)/ ; NE/V006878/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/V006878/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/R016429/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/Y006208/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/V007548/1//RCUK | Natural Environment Research Council (NERC)/ ; },
mesh = {Animals ; United Kingdom ; *Coleoptera ; Ecosystem ; Databases, Factual ; },
abstract = {Trait-based approaches have become common in ecological research as they can contribute to an understanding of ecosystem functioning and how species, communities and systems may respond to environmental change. However, trait datasets are difficult and time-consuming to compile and consequently not commonly available, particularly for insects. Ladybirds, beetles in the family Coccinellidae, are an important insect group that provide key ecosystem services, primarily through predation of pest insects such as aphids and coccids. Here, we have compiled information on species traits, ecological preferences and distribution metrics for 48 species considered resident in the United Kingdom (UK) (including the harlequin ladybird) using published sources, a recently published field guide, and biological records. Species traits may inform analyses useful for conservation purposes. This database provides researchers with access to the most up-to-date assessment of UK ladybird species, promoting research into this important insect group.},
}
@article {pmid41162447,
year = {2025},
author = {Sayed, E and Ali, AM and Alrashdi, I and Sallam, KM and Abdel-Basset, M and Ismail, MM},
title = {A robust framework for evaluating green mines towards sustainable development.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37739},
pmid = {41162447},
issn = {2045-2322},
abstract = {The development of green mines is essential for promoting sustainability in the mining sector due to the significant ecological impacts of resource extraction. This study proposes a novel hybrid multi-criteria decision-making (MCDM) framework that integrates Spherical Fuzzy Sets (SFSs) with SWOT analysis, the CRITIC method, and Grey Relational Analysis (GRA). The framework introduces several innovations: it applies SFS-based MCDM for the first time to green mine evaluation in Egypt, structures 37 sustainability-related criteria under SWOT dimensions, and employs SF-CRITIC for objective weighting without subjective comparisons. The model is applied to assess 20 gold mines, where the SF-GRA method is used to rank alternatives based on proximity to an ideal solution. The results show that GME20 consistently ranks highest, while GME5 ranks lowest. A sensitivity analysis is conducted by varying the Grey relational coefficient and simulating 37 weight scenarios, demonstrating stable rankings and strong model resilience. Comparative analysis against ten SFS-based MCDM methods confirms the consistency of results, with Spearman correlation coefficients exceeding 0.77. In addition to its methodological novelty, the framework supports interpretable decision outcomes by identifying key sustainability drivers such as renewable energy adoption and land reclamation. This contributes actionable insights for policymakers and stakeholders, enabling informed green investment and regulatory decisions. The study offers a transparent, reproducible, and scalable tool for sustainability evaluation in resource-intensive industries. The proposed model introduces a structured integration of SWOT-based criteria classification, objective weight computation via SF-CRITIC, and robust alternative ranking using SF-GRA. Furthermore, it contributes uniquely by applying the methodology to the underexplored context of green mine evaluation in Egypt. These distinctions articulate the methodological and application-based novelties of the proposed framework.},
}
@article {pmid41163577,
year = {2025},
author = {Fujiwara, K and Toyoda, A and Katsuki, T and Sato, Y and Biswa, BB and Kishida, T and Tsuruta, M and Nakamura, Y and Mochizuki, T and Kimura, N and Kawamoto, S and Ohta, T and Nonomura, KI and Niki, H and Yano, H and Umehara, K and Suzuki, C and Koide, T},
title = {Chromosome-scale genomes of two wild flowering cherries (Cerasus itosakura and Cerasus jamasakura) provide insights into structural evolution in Cerasus.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {32},
number = {6},
pages = {},
pmid = {41163577},
issn = {1756-1663},
support = {//ROIS/ ; },
mesh = {*Genome, Plant ; *Chromosomes, Plant/genetics ; *Evolution, Molecular ; Japan ; },
abstract = {Flowering cherries (genus Cerasus) are iconic trees in Japan, celebrated for their cultural and ecological significance. Despite their prominence, high-quality genomic resources for wild Cerasus species have been limited. Here, we report chromosome-level genome assemblies of two representative Japanese cherries: Cerasus itosakura, a progenitor of the widely cultivated C. ×yedoensis "Somei-yoshino," and Cerasus jamasakura, a traditional popular wild species endemic to Japan. Using deep PacBio long-read and Illumina short-read sequencing, combined with reference-guided scaffolding based on near-complete C. speciosa genome, we generated assemblies of 259.1 Mbp (C. itosakura) and 312.6 Mbp (C. jamasakura), with both >98% BUSCO completeness. Consistent with their natural histories, C. itosakura showed low heterozygosity, while C. jamasakura displayed high genomic diversity. Comparative genomic analyses revealed structural variations, including large chromosomal inversions. Notably, the availability of both the previously published C. speciosa genome and our new C. itosakura genome enabled the reconstruction of proxy haplotypes for both parental lineages of "Somei-yoshino." Comparison with the phased genome of "Somei-yoshino" revealed genomic discrepancies, suggesting that the cultivar may have arisen from genetically distinct or admixed individuals, and may also reflect intraspecific diversity. Our results offer genomic foundations for evolutionary and breeding studies in Cerasus and Prunus.},
}
@article {pmid41163612,
year = {2025},
author = {Belgaid, Y and Helal, M and Lakmeche, A and Venturino, E},
title = {A model for the interactions of wild boars and park rangers.},
journal = {Mathematical biosciences and engineering : MBE},
volume = {22},
number = {11},
pages = {2780-2806},
doi = {10.3934/mbe.2025102},
pmid = {41163612},
issn = {1551-0018},
mesh = {Animals ; *Sus scrofa/physiology ; Computer Simulation ; Population Dynamics ; Ecosystem ; Conservation of Natural Resources ; Swine ; Parks, Recreational ; Population Density ; *Models, Biological ; },
abstract = {Boars, being one of the most widely spread ungulates worldwide, have a widely recognized important role in the balance of natural environment and forests. Since large boar populations severely damage crops and cause serious traffic accidents, they are widely hunted, thereby also representing a relevant economic resource. In the model presented here, the species is at times considered ravaging, enabling it to be kept in check, while on the other hand, it must be preserved from extinction as a protected species. We considered an idealized, relatively simple situation in which rangers of the park where the boars are hosted manage this animal population size when they extrude into the surrounding areas through the woods perimeter. Modeling this situation involves considering not the whole boar population, but only those that are involved in the spillover, i.e., those living in proximity of the woods edge. The theoretical investigation and the simulations revealed the existence of a transcritical bifurcation relating the two viable equilibria, coexistence, and the ranger-free point. Also, the possible onset of persistent oscillations via a Hopf bifurcation is shown, leading to periodic recalling of rangers to contain the spillovers. On the other hand, a better regime was obtained by reducing the environment's resources for the wild boars, which stabilized the the boar population at constant level, with a reduced presence of the rangers, reducing the costs of their periodic recalling.},
}
@article {pmid41165898,
year = {2025},
author = {Doležel, M and Lískovec, R},
title = {Reference and Solution Architecture for GenAI- and GIS-Enhanced Physical Activity Interventions: Towards Implementing the AI4Motion Platform.},
journal = {Journal of medical systems},
volume = {49},
number = {1},
pages = {150},
pmid = {41165898},
issn = {1573-689X},
mesh = {Humans ; *Geographic Information Systems ; *Exercise ; *Mobile Applications ; Ecological Momentary Assessment ; },
abstract = {Digital Behaviour Change Interventions (DBCIs) aim at improving individual health by engaging various means of Information and Communication Technology (ICT), including mobile apps and wearables. Participant intervention fatigue may happen when DBCIs become too frequent, repetitive, demanding, or lack perceived relevance, and this may result in participants' reduced motivation and adherence over time. Advancing technology-supported engagement mechanisms is therefore of utmost importance. To address this problem, we present a reference and solution architecture based on open-source technologies and open Application Programming Interfaces (Open APIs). First, we integrated a Large Language Model (LLM) component into the DBCI design. Second, to support context-awareness, we enhanced this integration by adding a Geographic Information Systems (GIS) element. Our pilot implemented AI4Motion platform targets both personalization and contextualization aspects of DBCIs. Our work contributes to the emerging discussion on LLM/GIS-related system design patterns for digital platforms supporting Ecological Momentary Assessment (EMA), Experience Sampling Method (ESM), and Just-in-Time Adaptive Interventions (JITAIs).},
}
@article {pmid41166222,
year = {2026},
author = {Boot, J and van den Ende, MWJ and Wiers, RW and Lees, MH and van der Maas, HLJ},
title = {Integrating dual-process decision making and social dynamics: A formal modeling framework for addiction.},
journal = {Psychological review},
volume = {133},
number = {4},
pages = {864-891},
doi = {10.1037/rev0000584},
pmid = {41166222},
issn = {1939-1471},
support = {//Horizon Europe Framework Programme/ ; },
mesh = {Humans ; *Decision Making ; *Behavior, Addictive/psychology/physiopathology ; *Models, Psychological ; *Social Behavior ; Group Dynamics ; },
abstract = {Currently, formal models of addiction focus either on the complex individual decision-making processes involved in addiction or on the social dynamics of addiction. They do not integrate these two levels, which has been identified as a key shortcoming of current formal models of addiction. To address this, we propose a nonlinear dynamical modeling framework of addiction integrating both the individual level and social level of addictive behavior. The individual level of our modeling framework is a formalization of a dual-process theory, where one type of process increases the consumption of addictive goods, and another type of process limits consumption. For our formalization, we build on a well-studied model from ecology, originally used to model periodic outbreaks of the spruce budworm population. To this model, we add the process of incentive sensitization at the individual level and at the social level, we incorporate the critical processes of selection homophily and peer influence. We show that our integrated modeling framework can be used to explain key phenomena identified in addiction literature: a gradual transition to heavy use, sudden relapse and sudden quitting, relatively stable use states over time (i.e., abstinence moderate use, and heavy use), social contagion and sudden outbreaks, clustering of users, and social aid in recovery. In addition, we demonstrate how our modeling framework can be extended to include mutualistic, competitive, and more complex interactions between different addictive behaviors. Finally, we show how our framework can lead to new insights and predictions and suggest avenues for future research. (PsycInfo Database Record (c) 2026 APA, all rights reserved).},
}
@article {pmid41168455,
year = {2025},
author = {Oka, SO and Tomass, Z and Takele, S and Megaze, A and Kano, JK},
title = {Habitat suitability assessment for hippopotamus (Hippopotamus amphibius) conservation using GIS-based multi-criteria decision analysis in Ethiopia's Southern Rift Valley.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {11},
pages = {1276},
pmid = {41168455},
issn = {1573-2959},
mesh = {Ethiopia ; Geographic Information Systems ; *Conservation of Natural Resources/methods ; *Ecosystem ; Animals ; *Environmental Monitoring/methods ; *Artiodactyla/physiology ; Decision Support Techniques ; },
abstract = {The hippopotamus (Hippopotamus amphibius) is a keystone species inhabiting freshwater ecosystems across sub-Saharan Africa but is increasingly threatened by habitat loss, fragmentation, and human-wildlife conflict. This study assessed habitat suitability for hippopotamus conservation in Ethiopia's southern Rift Valley, focusing on Lakes Abaya and Chamo, using a Geographic Information System (GIS)-based multi-criteria decision analysis (MCDA). Data from October to December 2024 included satellite imagery, bathymetry, rainfall records, a digital elevation model (DEM), focus group discussions, and farmer interviews. Six socio-ecological criteria-land use/land cover (LULC), lake depth, slope, elevation, rainfall, and distance from settlements-were integrated through a weighted overlay. Results show that 26% of the study area is highly suitable, 23% suitable, 39% moderately suitable, and 12% unsuitable. Wetlands and shallow waters emerged as the most critical habitats, while croplands, settlements, and steep or upland areas were least favorable. Human-hippo conflicts were strongly linked to cropland encroachment near lakeshores, consistent with local reports and previous studies. Compared to other Ethiopian hippo ranges, the Abaya-Chamo system supports a relatively higher proportion of suitable habitat, attributed to persistent wetlands and aquatic-terrestrial connectivity. However, threats from wetland degradation, agricultural expansion, and settlement growth continue to reduce habitat quality. These findings highlight the urgent need for wetland restoration, buffer zones, and community-based conflict mitigation strategies to sustain hippopotamus populations in the region.},
}
@article {pmid41171124,
year = {2026},
author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S},
title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D813-D825},
pmid = {41171124},
issn = {1362-4962},
support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&amp;T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&amp;D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; },
mesh = {Metagenome ; *Databases, Genetic ; *Microbiota/genetics ; Metagenomics/methods ; *Aquatic Organisms/genetics/classification ; Oceans and Seas ; *Seawater/microbiology ; Biodiversity ; Ecosystem ; Bacteria/genetics/classification ; Molecular Sequence Annotation ; Software ; Multiomics ; },
abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.},
}
@article {pmid41171134,
year = {2026},
author = {Sun, Y and Chen, Q and Fan, G and Sun, Q and Zhou, Q and Zhang, J and Nie, J and Ma, J and Wu, L},
title = {gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D724-D733},
pmid = {41171134},
issn = {1362-4962},
support = {2021YFA0717001//National Key R&amp;D Program of China/ ; XDB0830000//Chinese Academy of Sciences/ ; 153211KYSB201900211//Chinese Academy of Science/ ; //Chinese Academy of Sciences/ ; },
mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Databases, Genetic ; Humans ; *Ecosystem ; Animals ; Molecular Sequence Annotation ; Bacteria/genetics/classification ; },
abstract = {The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportunities for microbial discovery and functional characterization. Yet, full utilization of these resources has been constrained by heterogeneous data generation practices and inconsistent analytical pipelines. The gcMeta database addresses this gap by compiling MAGs through both public acquisition and de novo assembly. This release integrates over 2.7 million MAGs from 104 266 samples spanning various biomes, covering human, animal, plant, marine, freshwater, and extreme environments. It establishes 50 biome-specific MAG catalogues comprising 109 586 species-level clusters, of which 63% (69 248) represents previously uncharacterized taxa, and annotates >74.9 million novel genes. By linking functional traits with microbial co-occurrence networks, gcMeta identifies keystone taxa central to biogeochemical cycling and environmental adaptation. The platform further supports cross-ecosystem functional comparisons, revealing niche-specific metabolic pathways and stress-response genes. Moreover, gcMeta provides standardized, AI-ready datasets encompassing microbial enzymes, anti-phage defense systems, and other functional modules, enabling advanced machine learning applications. By bridging microbial "sequence discovery" with "functional utilization," gcMeta establishes a foundation for ecological research, industrial biotechnology, and novel gene mining. The platform is freely accessible at https://gcmeta.wdcm.org/.},
}
@article {pmid41171142,
year = {2026},
author = {Lyu, B and Wu, K and Huang, Y and Anton, M and Li, X and Viknander, S and Anwer, D and Yang, Y and Lu, D and Kerkhoven, E and Zelezniak, A and Gao, D and Chen, Y and Li, F},
title = {GotEnzymes2: expanding coverage of enzyme kinetics and thermal properties.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D583-D592},
pmid = {41171142},
issn = {1362-4962},
support = {2024YFA0920300//National Key R&amp;D Program of China/ ; 22478223//National Natural Science Foundation of China General Project/ ; A2403013//National Natural Science Foundation of China General Project/ ; JC2024004//Tsinghua Shenzhen International Graduate School/ ; DCE-iBHE-2023-1//Tsinghua Shenzhen International Graduate School/ ; 2023-04254//Swedish Research Council/ ; 2019-05356//Swedish Research Council/ ; 2019-01403//Formas grant/ ; BB/Y000730/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Kinetics ; *Enzymes/chemistry/metabolism ; *Databases, Protein ; Temperature ; Enzyme Stability ; Humans ; },
abstract = {Enzyme kinetics are fundamental for understanding metabolism, yet experimentally measured parameters remain scarce. To address this gap, we introduce GotEnzymes2, a substantially expanded resource covering 10 765 species, 7.3 million enzymes, and 59.6 million unique entries. Compared with the first version, GotEnzymes2 now integrates both catalytic and thermal parameters, enabling unified predictions of kcat, Km,kcat/Km, optimal temperature, and melting temperature. This expansion markedly broadens species and enzyme coverage, creating the most comprehensive database of enzyme kinetic and stability parameters to date. To construct the resource, we systematically benchmarked state-of-the-art models for catalytic and thermal parameter prediction, and incorporated the best-performing strategies to ensure accuracy and generalizability. Altogether, GotEnzymes2 provides the community with a powerful resource for data-driven enzyme discovery, design, and engineering, with broad applications in systems biology, metabolic engineering, and synthetic biology. GotEnzymes2 is publicly accessible at https://metabolicatlas.org/gotenzymes.},
}
@article {pmid41172900,
year = {2026},
author = {Kou, X and Yang, S and Zou, J and Chen, S and Wu, J and Sun, B and Yan, Z and Liu, D and Tan, H},
title = {Rapid spectrophotometric method for the selective determination of peracetic acid in water with cobalt-mediated oxidation decolorization of rhodamine B.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {348},
number = {Pt 1},
pages = {127082},
doi = {10.1016/j.saa.2025.127082},
pmid = {41172900},
issn = {1873-3557},
abstract = {Recently, increasing attention had been paid for using peracetic acid (PAA) as an efficient disinfectant or a strong oxidant in wastewater treatment. In this study, a rapid and simple spectrophotometric method for the selective determination of PAA in aqueous solution was established, based on the oxidative decolorization of rhodamine B (RhB) by reactive species generated from the combination of PAA and Co(II). Under the optimized conditions (20 μmol L[-1] RhB, 1.0 mmol L[-1] Co(II), pH = 5.0 buffered with 10 mM acetate acid buffer, and reaction time = 40 s), the extent of RhB decolorization at the characteristic wavelength of 552 nm was found to be proportional to the concentration of PAA in the aqueous solution. A strong linear correlation was observed between the consumption of RhB and the concentration of PAA in the range of 0.25-25 μmol L[-1] (R[2] = 0.9991), and the sensitivity for PAA was as high as 2.99 × 10[4] M[-1] cm[-1]. The RhB spectrophotometric method is effectively tolerant to interference the coexistent H2O2 in PAA solution, the common coexisting species in practical water samples (KCl, MgSO4, NaNO3, NaHCO3, DCF and humic acid) and even the added reducing substances such as hydroxylamine and ascorbic acid. As a selective colorimetric agent, RhB is resistant to interference from reducing substances and water bodies, enabling accurate determination of PAA concentration in actual water environments. Overall, the RhB spectrophotometric method could be used as an alternative method for the cheap, rapid and selective determination of PAA in water samples.},
}
@article {pmid41173371,
year = {2025},
author = {Mehta, S and Allen, LH and Bailey, RL and Boushey, CJ and Duggan, CP and Crouter, SE and Engle-Stone, R and Fahim, SM and Gibbs, K and Hernandez, E and Huey, SL and Owino, VO and Prado, EL and Proaño, GV and Savage, JS and Steiber, AL and Zemel, BS and Raiten, DJ},
title = {Application of an Ecological Approach to Assessment of Nutrition in School-Aged Children-A Report from the "Biomarkers of Nutrition for Development: Knowledge Indicating Dietary Sufficiency (BOND-KIDS)" Project Working Group 3.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
pmid = {41173371},
issn = {1541-6100},
support = {T32 HD087137/HD/NICHD NIH HHS/United States ; U01 CA215834/CA/NCI NIH HHS/United States ; },
abstract = {The global health community must extend its attention beyond the "first 1000 d" to include school-aged children (i.e., the "next 7000 d") given the critical windows of development during this period. An opportunity exists to leverage school settings to implement programs for supporting child health and nutrition. Historically, many school-based programs evaluate "learning" or academic achievement as a priority outcome, with less attention paid to the "learner." This has left gaps in studying the impact school nutrition programs and interventions may have on children's health and development, and how to measure these outcomes. The "Biomarkers of Nutrition for Development: Knowledge Indicating Dietary Sufficiency (BOND-KIDS)" Project primarily focused on these gaps-specifically, the need for better tools to measure the functional impact of school-based nutritional interventions on the health and development of school-aged children aged 5-19 y. Functionally, BOND-KIDS applied an ecological approach via the organization of 4 interacting thematic working groups (WG): 1) biology (internal environment), 2) environment (external; home, school, physical), 3) assessment, and 4) translation and implementation. This report represents the work of WG 3: assessment, which addresses the specific need for better assessment tools, and also includes general considerations for nutritional assessment in children. We included the evidence, relevance, and feasibility of current approaches in assessing dietary intake, nutritional status, and key functional outcomes for the developing school-aged children. The findings will help to determine context-specific approaches to assess the need for and impact of interventions designed to improve the diet, nutrition, and health of school-aged children. To increase utility and accessibility, the data contained in this report are accessible via a self-service online dashboard. The current version of this dashboard is hosted at https://www.cpnh.cornell.edu/bond-kids-1, via the Cornell Joan Klein Jacobs Center for Precision Nutrition and Health at Cornell University.},
}
@article {pmid41175080,
year = {2026},
author = {Carroll, RA and Ricemeyer, ES and Hillier, LW and DaCosta, JM and Osipova, E and Smith, S and Jamie, GA and Martinez, JG and Molina-Morales, M and Marques-Bonet, T and Manthey, JD and Haddad, D and Fuxjager, MJ and Lynch, KS and Wood, JMD and Jarvis, E and Masterson, P and Thibaud-Nissen, F and Hauber, ME and Spottiswoode, CN and Sackton, TB and Balakrishnan, CN and Sorenson, MD and Warren, WC},
title = {Genomic resources for comparative analyses of avian obligate brood parasitism.},
journal = {The Journal of heredity},
volume = {117},
number = {3},
pages = {545-556},
doi = {10.1093/jhered/esaf087},
pmid = {41175080},
issn = {1465-7333},
support = {U54 MD017979/MD/NIMHD NIH HHS/United States ; 1754311//National Science Foundation/ ; 1754397//National Science Foundation/ ; 1754406//National Science Foundation/ ; 1754546//National Science Foundation/ ; 1754643//National Science Foundation/ ; 1940624//National Science Foundation/ ; IOS 1456524//National Science Foundation/ ; 1456612//National Science Foundation/ ; },
mesh = {Animals ; *Birds/genetics/classification/physiology ; *Nesting Behavior ; *Genomics/methods ; *Genome ; Synteny ; Phylogeny ; Biological Evolution ; },
abstract = {Examples of convergent evolution, wherein distantly related organisms evolve similar traits, including behaviors, underscore the adaptive power of natural selection. In birds, obligate brood parasitism, and the associated loss of parental care behaviors, has evolved independently in seven different lineages, though little is known about the genetic basis of the complex suite of traits associated with this rare life history strategy. We generated genome assemblies for ten brood parasitic species plus eight species representatives of their parental/nesting outgroups. This includes nine long-read chromosome-level assemblies, with scaffold N50 sizes ranging from 38.1 to 72.6 MB, and gene representation completeness measures >97%. Leveraging this new catalog of avian genomes, we constructed clade-level alignments that reveal variation in chromosomal synteny, provide first-time or improved annotations of protein-coding and non-coding genes, and define cross-species ortholog reference sets. We also refine estimates for the timing of the seven independent origins of brood parasitism, ranging from recent events such as 1.6-4.5 million years ago in Molothrus cowbirds to much earlier origins over 30 million years ago in two of the three cuckoo lineages. These genomic resources lay the foundation for investigating the genetic and genomic underpinnings of brood parasitism, including the loss of parental care, shifts in mating systems, perhaps resulting in heightened sperm competition, elevated annual fecundity, improved spatial cognition related to nest-finding, and the diverse adaptations shaped by intense coevolution with host species.},
}
@article {pmid41175854,
year = {2025},
author = {Schor, J and Schulze, T and Ulrich, N and Mutlu, &#x130; and Krauss, M and Brack, W and Doan, T and Bingert, S and Bumberger, J and Busch, W and Hackermüller, J},
title = {Chemical mixture risk drivers and their heterogeneity in European freshwaters.},
journal = {Environment international},
volume = {205},
number = {},
pages = {109881},
doi = {10.1016/j.envint.2025.109881},
pmid = {41175854},
issn = {1873-6750},
mesh = {Europe ; Fresh Water/chemistry ; *Water Pollutants, Chemical/analysis/toxicity ; *Environmental Monitoring/methods ; Risk Assessment/methods ; Water Pollution, Chemical/statistics &amp; numerical data ; Quantitative Structure-Activity Relationship ; Models, Chemical ; },
abstract = {Chemical pollution of aquatic environments involves diverse substance combinations that can provoke combined biological and toxicological effects even when individual concentrations remain below effect thresholds. Multiple efforts are ongoing to better consider mixture effects in chemical safety regulation, but debate continues over whether a few substances drive aquatic mixture risks or whether a large heterogeneous set of drivers must be considered. We employed a data re-use strategy to investigate the heterogeneity of chemical mixture risk drivers to aquatic species in Europe. Initially, we derived 201 risk-driving chemicals from a single measurement campaign, allowing driver comparisons between sites based on consistently measured substances. We then extended our analysis to extensive chemical monitoring data of the NORMAN network, originating from different campaigns focusing on diverging substance sets measured at different times and locations. Data were aggregated quarterly and sites clustered per quarter according to measured substances. Using a robust definition of risk drivers (the most significant chemicals whose cumulative toxic units contribute ≥75% of total risk), our study concludes that at least 580 different substances drive chemical mixture risks in European freshwaters, with high heterogeneity between locations. Notably, mixture risk drivers were species-specific, exhibited temporal variability, and belonged to different chemical use groups considered in various safety regulations. We also found that monitoring data gaps prevented more precise analysis, particularly regarding temporal variability. These findings have important implications for future chemical monitoring strategies and mixture risk regulation in Europe, highlighting the complexity and heterogeneity of chemical mixture risks in aquatic environments.},
}
@article {pmid41178269,
year = {2026},
author = {Ono, S and Takebe, K and Tosa, I and Nishiya, Y and Nakayama, M and Wada, T and Takashiba, S and Ohara, N},
title = {PGN_0298 in the Assembly and Insertion Machinery (Aim) Operon Is Essential for the Viability of Porphyromonas gingivalis.},
journal = {Microbiology and immunology},
volume = {70},
number = {1},
pages = {9-14},
pmid = {41178269},
issn = {1348-0421},
support = {//JSPS KAKENHI Grant Number JP24K02614 (NO), JP23K15970 (SO), JP21K09842 (MN), JP24K23551 (KT)./ ; },
mesh = {*Porphyromonas gingivalis/genetics/physiology ; *Operon ; Gingipain Cysteine Endopeptidases ; Virulence Factors/genetics/metabolism ; Adhesins, Bacterial/metabolism/genetics ; Cysteine Endopeptidases/metabolism/genetics ; *Microbial Viability ; *Bacterial Proteins/genetics/metabolism ; Computational Biology ; Humans ; Bacterial Secretion Systems/genetics ; },
abstract = {Porphyromonas gingivalis is a typical periodontal pathogen, and one of its key virulence factors is the powerful protease gingipains. Gingipains are secreted via the type IX secretion system (T9SS) and are associated with the assembly and insertion machinery (Aim) operon (PGN_0296 to PGN_0301), which encodes both T9SS components and non-T9SS proteins. In this study, we investigated PGN_0298, a gene of unknown function within this operon, to elucidate its role in P. gingivalis and to gain insights into its potential function through bioinformatics analyses. Our results demonstrated that PGN_0298 is essential for the viability of P. gingivalis, despite having limited direct association with T9SS. Sequence homology and structure predictions indicate that PGN_0298 encodes a putative isoprenyl transferase. The essentiality of PGN_0298 underscores its potential as a novel drug target for the treatment of periodontal disease.},
}
@article {pmid41180493,
year = {2025},
author = {Choi, JM and Wu, X and Zhang, L},
title = {FastST: an efficient tool for inferring decomposition and directionality of microbial communities.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20161},
pmid = {41180493},
issn = {2167-8359},
mesh = {*Microbiota ; Humans ; Bayes Theorem ; Computer Simulation ; *Software ; *Computational Biology/methods ; },
abstract = {Microbiomes play crucial roles in human health, disease development, and global ecosystem functioning. Understanding the origins, movements, and compositions of microbial communities is essential for unraveling the principles governing microbial ecology. Microbial source tracking (MST) approaches have emerged as valuable tools for quantifying the proportions of different microbial sources within target communities, enabling researchers to track transmissions between hosts and environments, identify similarities between microbiome samples, and determine sources of contamination in various settings. Current MST methods like SourceTracker2 and FEAST have advanced the field by employing Bayesian and expectation-maximization approaches, respectively, but are limited by computational inefficiency with high-dimensional data and inability to infer directionality in source-sink relationships. This study presents a novel computational framework for microbial source tracking called FastST. FastST infers the relative contributions of source environments to sink microbiomes while also determining directionality when source-sink relationships are not predefined. Through extensive simulation studies with varying numbers of sources and complexity, FastST demonstrates superior performance in both accuracy and computational efficiency compared to FEAST and SourceTracker2, maintaining consistent execution times even as the number of source environments increases. Furthermore, the proposed method achieved over 90% accuracy in directionality inference across all tested scenarios, even when multiple major sources are present, broadening its applicability in practical microbiome research and environmental monitoring. FastST and data simulation codes are publicly available at https://github.com/joungmin-choi/FastST.},
}
@article {pmid41184333,
year = {2025},
author = {Ghosh, A and Maile, A and Nagarajaram, HA},
title = {Prokaryotic co-occurrence patterns in diverse Indian mangrove ecosystems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38283},
pmid = {41184333},
issn = {2045-2322},
mesh = {India ; *Wetlands ; Biodiversity ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Soil Microbiology ; },
abstract = {Mangrove ecosystems are unique coastal zones known to harbour a rich biodiversity of flora and fauna, including microbial communities. These microorganisms play a crucial role in nutrient cycling and sustain the primary productivity driven by plants within this ecosystem. Recent advancements in microbial ecology research emphasise that microbial community structure and composition are critical for an ecosystem to thrive. Studies have focused on the microbial diversity within Indian mangrove forests; however, there is a limited understanding of the co-occurrence patterns and functional roles of microbial communities in these ecosystems. This study explores prokaryotic diversity, primarily focusing on community interactions across three major Indian mangrove forests: the Bhitarkanika mangrove forest in Odisha, the Goan mangroves, and the Sundarbans in West Bengal. By analysing the publicly available 16 S rRNA amplicon datasets of the Indian mangrove microbiomes and performing co-occurrence network analysis on these datasets, we identified positively correlated genera and their predicted functional roles. Furthermore, the findings revealed the co-occurrence of several pathogenic bacteria in two of the mangrove ecosystems. Overall, our study highlights the shared functional roles adopted by co-occurring microbes in three major Indian mangrove ecosystems and suggests the need for large-scale studies in these understudied Indian ecosystems.},
}
@article {pmid41184763,
year = {2025},
author = {Jiao, Y and Hu, N and Xia, H and Li, X and Li, J and Liu, Y and Wang, J},
title = {Multi-omics approaches investigate the bitter flavor in the shoot of Bambusa oldhamii Munro.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1501},
pmid = {41184763},
issn = {1471-2229},
support = {32101606//National Natural Science Foundation of China/ ; },
mesh = {*Plant Shoots/genetics/metabolism/chemistry ; *Bambusa/genetics/metabolism ; Taste ; Genome, Plant ; Genomics ; Transcriptome ; Multiomics ; },
abstract = {BACKGROUND: Bamboo, widely distributed in Southeast Asian and East Asia, is a palatable food resource, with its nutritional and low-fat properties, and functions in economic and ecological balance. As an important food source, some bamboo shoots often synthesize bitter chemicals in a special developing period or in a particular position of the shoot, which depends on the edible bamboo species. In this research, we focus on a sympodium bamboo, Bambusa oldhamii Munro, located in Southeast China, which has special biological properties. When the shoots are harvested underground, the shoots taste tender and tasty enough, but when the shoots erupt out of the soil surface with sunlight for days, the shoot has a little bitterness in the tip portion. This research conducts multi-omics approaches to investigate the bitter flavor formation with multiple developing phases of the shoot in B. oldhamii Munro.<br><br>RESULTS: The PacBio and Hi-C technologies were used to sequence the hexaploid species, B. oldhamii Munro, for de novo genome assembly. The assembled genome size of B. oldhamii is 1,446&#xa0;Mb, with a scaffold-level N50 equal to 38,936,033&#xa0;bp. A total of 88,140 genes in the genome were acquired, and about 53.89% of the genome is occupied by repeat components. The BUSCO score is 96.59%, suggesting a relatively complete and reliable assembly. Three subgenomes (ABC) include 35 pseudo-chromosomes based on the synteny analysis with another hexaploid species, Dendrocalamus latiflorus. The technologies of transcriptome analysis on the genome level and widely targeted metabolome were used to classify the key transcription factors and key bitter metabolites that account for the bamboo shoot flavor transition of B. oldhamii from underground to above ground, especially in the multiple developing phases. We finally mined out several bitter metabolites belonging to amino acids, flavonoids, terpenoids, purines, and other families, and several related pathways of Circadian rhythm, plant hormone signal transduction, flavonoid biosynthesis, and flavone and flavonol biosynthesis. Additionally, from joint analysis between bitter metabolites and transcription factors, we found that the family of bHLH and HB- transcription factors might influence the shoot bitter flavor transition and formation via influencing the accumulation of bitter metabolites in B. oldhamii.<br><br>CONCLUSIONS: In this research, we used Multi-omics methods to investigate the bitter flavor formation and transition in the shoot of B. oldhamii and hypothesized a simple model about this biological process. In a suitable circumstance (warm temperature and sunlight), the environment signals transduction influences the expression of transcription factor (bHLH, HB-, and others) which activate or suppress the expression level of genes or enzymes in the bitter flavor metabolites related pathways (biosynthesis of secondary metabolites, amino acid metabolism, biosynthesis of flavonoid, flavone, flavonol and isoflavonoid, plant hormone signal transduction and others), then causing the contents of bitter flavor metabolites (flavonoids, amino acids, terpenoids, cyanogenic glycosides and others) increase or decrease. This phenomenon influences the bitter flavor formation or transition in the shoot of B. oldhamii.},
}
@article {pmid41187144,
year = {2025},
author = {Mercan, &#xc7; and Acıbuca, V},
title = {Utilizing FUCOM and AHP methods to identify the optimal beekeeping lands: A case study from Mardin, Türkiye.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0335784},
pmid = {41187144},
issn = {1932-6203},
mesh = {*Beekeeping/methods ; Geographic Information Systems ; Bees ; Animals ; Conservation of Natural Resources ; },
abstract = {Beekeeping plays a vital role in agricultural sustainability and biodiversity conservation, yet identifying ecologically suitable areas for apiculture remains challenging. The objective of this study is to evaluate and compare two Multi-Criteria Decision-Making (MCDM) methods-the Analytical Hierarchy Process (AHP) and the Full Consistency Method (FUCOM)-within a Geographic Information Systems (GIS) framework to identify optimal beekeeping areas in Mardin Province, Türkiye. Nine environmental, climatic, topographical, logistic, and socio-economic factors were selected through literature review, legal regulations, expert consultation, and field observations. Suitability maps were generated and validated using field-verified hive locations and Receiver Operating Characteristic-Area Under the Curve (ROC-AUC) analysis. The results show that land use/cover, proximity to water sources, and precipitation were the most influential factors. Overall, 83% of hive locations coincided with areas classified as moderately suitable or higher. AHP achieved slightly higher predictive accuracy (AUC = 0.774) than FUCOM (AUC = 0.754), while FUCOM required substantially fewer pairwise comparisons, underscoring its efficiency. These findings confirm the robustness of the framework and provide a practical tool for sustainable apicultural land-use planning, offering transferable insights for policymakers, decision-makers, and beekeepers in Türkiye and other regions with similar ecological conditions.},
}
@article {pmid41189536,
year = {2025},
author = {Hagan Brown, W and Gloor, E and Fyfe, R and MacKenzie, AR and Harper, NJ and Ganderton, P and Hart, K and Curioni, G and Quick, S and Davidson, SJ and Yetton, E and Diehl, JL and Fauset, S},
title = {Elevated CO2 Increases the Canopy Temperature of Mature Quercus robur (Pedunculate Oak).},
journal = {Global change biology},
volume = {31},
number = {11},
pages = {e70565},
pmid = {41189536},
issn = {1365-2486},
support = {//John Horseman Trust/ ; //Ecological Continuity Trust, UK/ ; //Royal Forestry Society, UK/ ; NE/S015833/1//Natural Environmental Research Council/ ; NE/V008366/1//Natural Environmental Research Council/ ; //University of Birmingham/ ; //Jabbs Foundation/ ; },
mesh = {*Quercus/physiology ; *Carbon Dioxide/metabolism ; Temperature ; Climate Change ; England ; Plant Leaves/physiology ; Forests ; },
abstract = {The canopy thermal response of natural forests to elevated CO2 (eCO2) is an understudied biophysical feedback in the global climate system. We investigated the effects of eCO2 (150 μmol mol[-1] above ambient) on canopy temperature (Tcan) dynamics of mature (> 175 years) Quercus robur (oak) at the Birmingham Institute for Forest Research Free Air CO2 Enrichment (BIFoR-FACE) facility in Staffordshire, England, during the growing seasons of 2021, 2022 and 2023. We employed long-term, high-frequency thermal infrared (TIR) imaging to measure Tcan. Our results show that daily maximum oak Tcan under eCO2 was, on average, approximately 1.3°C higher than under ambient (aCO2) conditions (21.5°C ± 4.4°C for aCO2 vs. 22.8°C ± 5.2°C for eCO2 oaks). Moreover, daily maximum Tcan-air temperature (Tair) differences were significantly higher under eCO2, resulting from more frequent extreme temperature excursions. These differences appear primarily to be driven by reduced stomatal conductance under eCO2, which limits transpirational cooling and alters the surface energy balance. This effect was evident in the different relationship between Tcan-Tair and vapour pressure deficit (VPD) for eCO2 compared to aCO2, showing a reduction in transpirational cooling under high VPD. Also, CO2-induced leaf structural and anatomical modifications, such as increased leaf mass per area, may have enhanced solar radiation absorption, thereby enabling greater canopy warming under high radiation conditions. Thus, eCO2 could likely cause a reduction in leaf transpiration in oaks, reducing its contribution to processes such as humidification of the lower atmosphere and precipitation in local and regional climates. Our findings highlight how high CO2 conditions may intensify thermal stress in temperate forests, influencing water and carbon cycles and potentially impacting forest resilience. Furthermore, Tcan will be essential for refining global Earth system models, which often use Tair as a proxy for Tcan, despite the latter's direct influence on carbon and hydrological cycles.},
}
@article {pmid41189540,
year = {2026},
author = {Inoue, J and Hirai, J and Ikeba, K and Yu, Z and Ahmed, SI and Lin, Z and Lin, Y and Wong, MK and Shinzato, C and Itoh, S and Ito, SI and Saito, H and Hyodo, S},
title = {eDNAmap: A Metabarcoding Web Tool for Comparing Marine Biodiversity, With Special Reference to Teleost Fish.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70066},
pmid = {41189540},
issn = {1755-0998},
support = {21H04922//Japan Society for the Promotion of Science/ ; //The University of Tokyo - FSI Project &#x201b;Ocean DNA'/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Internet ; *DNA, Environmental/genetics ; *Computational Biology/methods ; *Aquatic Organisms/classification/genetics ; *Metagenomics/methods ; *Software ; },
abstract = {Marine environmental DNA (eDNA) metabarcoding data are beginning to accumulate, even for remote and poorly studied areas, such as marine environments. These data enable us to identify distributions of target organisms and then to compare biological compositions between different marine areas. However, there is no platform to effectively utilise and accumulate these data. In this study, we developed eDNAmap, a web-based platform designed to analyse and store marine eDNA metabarcoding data. By uploading species or sequence composition data with location information, eDNAmap users can automatically (1) plot sampling locations on a map, (2) generate a heatmap to evaluate potential batch effects arising from methodological differences and (3) perform nonmetric multidimensional scaling and cluster analyses using similarity indices. Furthermore, users can specify scientific names to display species distributions and upload species lists to assess species compositions of the target sea area. As an example, fish sequence composition data obtained from 55 stations around the Watase line-believed to exist along a geographic canyon known as the Tokara Gap-were used to verify its existence using eDNAmap. The platform includes a database primarily consisting of teleost fish data from the Northwestern Pacific, which users can analyse similarly to their own uploads. Although originally designed for fish, eDNAmap is flexible enough to handle data from other marine organisms. Analysing multiple taxa enables the detection of concordant biogeographic patterns across different groups, which can strengthen ecological interpretations and lay the groundwork for identifying environmental drivers shaping community structures. eDNAmap is available at https://github.com/jun-inoue/eDNAmap.},
}
@article {pmid41190312,
year = {2025},
author = {Liuzzo, M and Utevsky, S and Marrone, F},
title = {Predictive Distribution Modeling of the Medicinal Leech Hirudo verbana Carena, 1820 (Hirudinea, Hirudinidae) in Sicily: Implications for Conservation.},
journal = {Ecology and evolution},
volume = {15},
number = {11},
pages = {e72410},
pmid = {41190312},
issn = {2045-7758},
abstract = {Hirudo verbana, a medicinal leech species of conservation concern, has long been considered rare and fragmented across its distribution range due to overexploitation and habitat alteration. In this study, we present the first predictive distribution model for H. verbana in Sicily, combining field occurrence data (time: 1980-2024) with environmental variables using an ensemble species distribution modeling (SDM) framework. Unlike its typical occurrence in temperate lowland wetlands of central-eastern Europe, the species in Sicily shows a marked shift toward upper hill and montane zones. Species presence was strongly associated with high NDVI values, reflecting a preference for areas with dense and structurally complex vegetation. In contrast, presence probability declined sharply with increasing terrestrial human footprint (THF), indicating a notable sensitivity to anthropogenic disturbance. Aquatic habitat type also emerged as a key predictor: the species was most likely to occur in lentic environments such as standing water bodies, and least likely in lotic systems or areas lacking aquatic habitats. Notably, most high-suitability areas overlapped with sites in the Natura 2000 network, emphasizing the importance of existing protected areas as refugia for the species. Moreover, some previously undocumented areas of high habitat suitability were identified, providing a spatially basis for refining monitoring strategies and informing conservation planning for this ecologically sensitive freshwater invertebrate.},
}
@article {pmid41192043,
year = {2026},
author = {Kumar, A and Xu, C and Dakal, TC},
title = {Microbiome based precision medicine through integrated multiomics and machine learning.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128384},
doi = {10.1016/j.micres.2025.128384},
pmid = {41192043},
issn = {1618-0623},
mesh = {Humans ; *Machine Learning ; *Precision Medicine/methods ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Metabolomics/methods ; Proteomics/methods ; Dysbiosis/microbiology ; Inflammatory Bowel Diseases/microbiology ; Multiomics ; },
abstract = {Gut microbiome (GME) is a dynamic ecosystem composed of diverse microorganisms with extensive functional potential that influence host physiology, endocrinology, and neurology. This review explores how multiomics (m[OMICS]) and machine learning (ML) enhance understanding of the GME and its implications for human disease and therapy. Integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics with ML enables the linkage of microbial composition and function to clinical outcomes. Combined m[OMICS] approaches elucidate species and strain dynamics, metabolic pathways, and metabolite production within the gut environment. Techniques such as shotgun metagenomics, metagenome-assembled genomes, and pathway mapping reveal associations between dysbiosis and diseases including inflammatory bowel disease, colorectal cancer, cardiometabolic, and neurological disorders. Mechanistic insights highlight short-chain fatty acids in immune regulation, bile acid transformations in metabolic signaling, and trimethylamine N-oxide in cardiovascular risk. ML models trained on heterogeneous datasets identify disease-related microbial modules, improve patient stratification, and predict therapeutic responses, such as differentiating IBD subtypes and detecting cancer-linked microbial signatures. Network analyses uncover gut microbial interaction patterns influencing host physiology. Emerging integrative tools like MOFA+ , DIABLO, and MintTea strengthen cross-modal analysis and biomarker discovery. Standardized workflows addressing quality control, assembly, binning, annotation, and visualization ensure reproducibility. Together, m[OMICS] and ML establish a robust framework for translating GME ecology into clinically relevant biomarkers and precision interventions. To enhance reliability, GME studies should adopt uniform sampling protocols, correct compositional biases, employ interpretable models, and validate findings across multi-site cohorts to advance microbiome-based diagnostics and therapeutics in precision medicine.},
}
@article {pmid41192332,
year = {2025},
author = {Zhou, L and She, J and Li, Q and Zheng, Q and Yang, J and Cui, M and Chen, T and Sun, S and Tang, F and Liu, Y},
title = {Integrated multi-omics and network pharmacology reveals antioxidant-active metabolites and health benefits of Camellia oleifera seed oil.},
journal = {Food chemistry},
volume = {496},
number = {Pt 3},
pages = {146913},
doi = {10.1016/j.foodchem.2025.146913},
pmid = {41192332},
issn = {1873-7072},
mesh = {*Antioxidants/metabolism/chemistry/pharmacology ; *Plant Oils/metabolism/chemistry/pharmacology ; *Camellia/chemistry/metabolism ; Metabolomics ; *Seeds/chemistry/metabolism ; Network Pharmacology ; Fatty Acids/metabolism/chemistry ; Humans ; Multiomics ; },
abstract = {The antioxidant properties of camellia oil (CO) remain insufficiently characterized. Here, multi-omics profiling combined with ABTS, DPPH, and FRAP assays was applied to identify antioxidant-active metabolites (AAMs). Widely-targeted metabolomics detected 2110 metabolites, while fatty acid, tocopherol, and elemental analyses revealed key nutritional contributors. Oleic acid dominated the fatty acid fraction (68.2-82.7 %), α-tocopherol was the major tocopherol (139.78-337.20 mg/kg), and selenium and zinc were the most relevant trace elements. A total of 160 AAMs were defined by OPLS-DA and WGCNA, with over 42 % being non-phenolics. Antioxidant assays indicated ABTS activity was mainly phenolic-driven, whereas DPPH involved both phenolics and amino acids. Network pharmacology linked core AAMs to targets in neurological, cardiovascular, hepatic, and respiratory systems. An integrated metabolic pathway network highlighted the multi-dimensional basis of CO's antioxidant potential. These findings reveal a broader antioxidant architecture beyond phenolics and provide a mechanistic foundation for developing CO as a functional nutraceutical oil.},
}
@article {pmid41194777,
year = {2024},
author = {Boyes, D and Crowley, LM and Wawman, DC and , and , and , and , and , and , and , },
title = {The genome sequence of the September Thorn moth, Ennomos erosaria (Denis &amp; Schiffermüller), 1775.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {287},
pmid = {41194777},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Ennomos erosaria (the September Thorn moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 423.1 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 16.3 kilobases in length.},
}
@article {pmid41195458,
year = {2025},
author = {Davis, AJS and Dawson, W and Essl, F and Kreft, H and Lenzner, B and Pergl, J and Pyšek, P and Weigelt, P and Winter, M and van Kleunen, M},
title = {The updated Global Naturalized Alien Flora (GloNAF 2.0) database.},
journal = {Ecology},
volume = {106},
number = {11},
pages = {e70245},
doi = {10.1002/ecy.70245},
pmid = {41195458},
issn = {1939-9170},
support = {//Czech Science Foundation/ ; RVO 67985939//Czech Academy of Sciences/ ; 202548816//German Research Foundation/ ; 264740629//German Research Foundation/ ; 379417748//German Research Foundation/ ; 52112243//German Research Foundation/ ; },
mesh = {*Plants/classification ; *Introduced Species ; *Databases, Factual ; },
abstract = {GloNAF is a continuously updated, curated compilation of alien naturalized vascular plant inventories for geographic regions worldwide. Building on its predecessor, GloNAF 2.0 now contains 16,429 taxa and introduces major updates, including the standardization of taxonomic names using the World Checklist of Vascular Plants (WCVP), removal of outdated records, and the net addition of 117,229 new records. These new entries have substantially increased the size of GloNAF, resulting in a 26% increase in the number of naturalized taxa in the database and a 31% increase in the number of geographic regions compared to GloNAF 1.2. We provide an overview of GloNAF 2.0, highlighting its expanded geographic and taxonomic coverage. In addition, we have aligned GloNAF with FAIR data principles through improvements in data accessibility, metadata standards, and support for data reuse. GloNAF 2.0 represents a significant and comprehensive resource for researchers aiming to advance our understanding of the drivers and consequences of biological invasions and naturalization success. The dataset is published under a CC-BY 4.0 license; thus, when using these data, please give credit to this paper.},
}
@article {pmid41198686,
year = {2025},
author = {Adde, A and Rey, PL and Külling, N and Chauvier-Mendes, Y and Fopp, F and Popp, MR and Broennimann, O and Petitpierre, B and Strebel, N and Gross, A and Stofer, S and Lehmann, A and Zimmermann, NE and Pellissier, L and Guisan, A and Altermatt, F},
title = {SDMapCH: a Comprehensive database of &gt;7,500 modelled species habitat suitability maps for Switzerland.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1752},
pmid = {41198686},
issn = {2052-4463},
mesh = {Switzerland ; *Ecosystem ; *Biodiversity ; *Databases, Factual ; Conservation of Natural Resources ; Software ; },
abstract = {Conserving natural ecosystems requires consistent and standardized biodiversity data to advance scientific research and ecological understanding. Despite several national initiatives to develop databases of species habitat suitability maps, even well-studied countries often lack comprehensive, standardized databases that cover a wide range of taxonomic groups modelled using a consistent framework. Using Switzerland as a case study, we demonstrate how these gaps can be addressed by introducing SDMapCH (v1.3), a nationwide raster database of species habitat suitability maps at 25-meter resolution. SDMapCH provides maps for about 7,500 species under both present conditions and future climate scenarios. SDMapCH was developed using the N-SDM software, an end-to-end platform based on a spatially-nested hierarchical framework. N-SDM allows multi-level integration of species and covariate data, helping to address niche truncation. SDMapCH outputs were evaluated using a state-of-the-art cross-validation procedure, and all layers passed a systematic data integrity check. By providing standardized, high-resolution habitat suitability maps for diverse species across various taxonomic and functional groups, SDMapCH stands as a key resource for scientific research and biodiversity assessments.},
}
@article {pmid41198702,
year = {2025},
author = {Cartereau, M and Biffoni, G and Baumel, A and Bacchetta, G and Brousset, L and Calvia, G and Casazza, G and Costanzo, A and Guerrina, M and Modaffari, A and Noble, V and Peruzzi, L and Pavon, D and Porceddu, M and Šegota, V and Silva, E and Todaro, F and Vuković, N and Leriche, A},
title = {WOODIV v2, more occurrences, functional traits, and a time-calibrated phylogeny for Euro-Mediterranean trees.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1756},
pmid = {41198702},
issn = {2052-4463},
mesh = {*Phylogeny ; *Trees/classification/anatomy &amp; histology ; Biodiversity ; *Databases, Factual ; Mediterranean Region ; Europe ; },
abstract = {The WOODIV v1 database provided occurrences at 10 km spatial resolution, traits and phylogenetic data for all 210 species (and 35 subspecies, totalling 245 taxa) in the Euro-Mediterranean Basin. While this reliable and readily accessible database has been of crucial help to investigate macro-ecological and biodiversity conservation questions, important knowledge gaps remained. To fill these gaps, we present an updated and extended version of the WOODIV database. (i) Occurrence data were updated from sources already considered in v1, three additional sources and an intensive field work campaign in Italy where occurrence data were scarce in v1, allowing to highly increase spatial coverage and data completeness. (ii) Besides increasing taxonomic coverage of traits already considered in v1, the traits data set has been extended to 15 new functional traits encompassing morpho-anatomy, reproduction and phenology, using new traits measurements from the field and data compilation from botanical literature not available in other databases. (iii) Finally, a new time-calibrated phylogeny for all 210 tree species was built and made available.},
}
@article {pmid41200470,
year = {2025},
author = {Maldonado, M and Pita, L 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 sponge, Corticium candelabrum Schmidt, 1862 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {535},
pmid = {41200470},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Corticium candelabrum (sponge; Porifera; Homoscleromorpha; Homosclerophorida; Plakinidae). The genome sequence has a total length of 185.49 megabases. Most of the assembly (99.4%) is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,198 protein-coding genes. The metagenome of the specimen was also assembled, and 53 binned bacterial genomes were identified, including 44 high-quality MAGs that were typical of high microbial abundance sponge and included, besides the phyla Chloroflexota (class Dehalococcoidia), Acidobacteriota (order Acidomicrobiales), Alpha- and Gammaproteobacteria, also representatives of several candidatus phyla (Candidatus Latescibacterota, Binatota, Poribacteria).},
}
@article {pmid41202092,
year = {2025},
author = {Sundh, J and Granqvist, E and Iwaszkiewicz-Eggebrecht, E and Manoharan, L and van Dijk, LJA and Goodsell, R and Godeiro, NN and Bellini, BC and Orsholm, J and Łukasik, P and Miraldo, A and Roslin, T and Tack, AJM and Andersson, AF and Ronquist, F},
title = {HAPP: High-accuracy pipeline for processing deep metabarcoding data.},
journal = {PLoS computational biology},
volume = {21},
number = {11},
pages = {e1013558},
pmid = {41202092},
issn = {1553-7358},
mesh = {*DNA Barcoding, Taxonomic/methods ; Algorithms ; Animals ; Computational Biology/methods ; Biodiversity ; DNA, Mitochondrial/genetics ; Software ; Insecta/genetics/classification ; Sequence Analysis, DNA/methods ; },
abstract = {Deep metabarcoding offers an efficient and reproducible approach to biodiversity monitoring, but noisy data and incomplete reference databases challenge accurate diversity estimation and taxonomic annotation. Here, we introduce a novel algorithm, NEEAT, for removing spurious operational taxonomic units (OTUs) originating from nuclear-embedded mitochondrial DNA sequences (NUMTs) or sequencing errors. It integrates 'echo' signals across samples with the identification of unusual evolutionary patterns among similar DNA sequences. We also extensively benchmark current tools for chimera removal, taxonomic annotation and OTU clustering of deep metabarcoding data. The best performing tools/parameter settings are integrated into HAPP, a high-accuracy pipeline for processing deep metabarcoding data. Tests using CO1 data from BOLD and large-scale metabarcoding data on insects demonstrate that HAPP significantly outperforms existing methods, while enabling efficient analysis of extensive datasets by parallelizing computations across taxonomic groups.},
}
@article {pmid41203782,
year = {2025},
author = {Baghbanzadeh, M and Dawson, T and Sayoldin, B and Frazer, SA and Oakley, TH and Crandall, KA and Rahnavard, A},
title = {deepBreaks identifies and prioritizes genotype-phenotype associations using machine learning.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39095},
pmid = {41203782},
issn = {2045-2322},
support = {2109688//National Science Foundation/ ; 2109688//National Science Foundation/ ; 1754770//National Science Foundation/ ; 1754770//National Science Foundation/ ; 2109688//National Science Foundation/ ; 2109688//National Science Foundation/ ; },
mesh = {*Machine Learning ; *Software ; Algorithms ; *Genetic Association Studies/methods ; Humans ; Genotype ; Phenotype ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; },
abstract = {Sequence data, such as nucleotides or amino acids, are crucial in advancing our understanding of biology. However, investigating and analyzing sequencing data and genotype-phenotype associations present several challenges, including noise components that arise from the sequencing, nonlinear genotype-phenotype associations, collinearity between input features, and high dimensionality of the input data. Machine learning (ML) algorithms have proven to be effective in detecting intricate and nonstructural patterns, making them a valuable tool for studies focused on genotype-phenotype associations. Yet, there needs to be more user-friendly ML implementations that leverage the unique features of high-volume DNA sequence data. Here, we introduce deepBreaks, a generic approach that detects important positions (genotypes) in sequence data that are associated with phenotypic traits. deepBreaks compares the performance of multiple ML algorithms and prioritizes positions based on the best-fit models. It is open-source software with online documentation and examples available at https://github.com/omicsEye/deepBreaks .},
}
@article {pmid41203806,
year = {2025},
author = {Yang, J and Li, J and Liang, B and Zhao, N and Zhang, P and Fang, C and Xie, T and Xiang, P and Liu, H},
title = {Network toxicology, transcriptomics, and cytotoxic validation reveal TDCPP-induced pterygium mechanisms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39077},
pmid = {41203806},
issn = {2045-2322},
support = {ZKF2024042//National Clinical Key Specialty Ophthalmology Open Foundation/ ; ZKF2024041//National Clinical Key Specialty Ophthalmology Open Foundation/ ; YNQR-QNRC-2018-049//Yunnan Xingdian Youth Talent Program/ ; XDYC-MY-2024//Yunnan Xingdian Youth Talent Program/ ; 82460201//National Natural Science Foundation of China/ ; YDYXJJ2024-0003//Yunnan University Medical Research Foundation/ ; 202205AC160016//Yunnan Young and middle-aged Academic and Technical Leader Project/ ; 2024YNLCYXZX0343//Key Project of the Provincial Clinical Medical Center of Yunnan Province/ ; },
mesh = {Humans ; *Pterygium/chemically induced/genetics/pathology/metabolism ; Matrix Metalloproteinase 3/metabolism/genetics/chemistry ; *Transcriptome/drug effects ; Molecular Docking Simulation ; Gene Expression Profiling ; Fibroblasts/drug effects/metabolism ; Gene Regulatory Networks/drug effects ; Cell Proliferation/drug effects ; *Organophosphorus Compounds/toxicity ; Computational Biology ; },
abstract = {Pterygium, a common ocular surface disorder, is associated with environmental factors such as ultraviolet exposure and air pollution. Tris(1,3-dichloro-2-propyl) phosphate (TDCPP), a widely used organophosphate flame retardant, has been detected in environmental and biological samples, yet its role in pterygium pathogenesis remains unclear. This study employed an integrative approach combining network toxicology, transcriptome sequencing, and in vitro cytotoxicity assays to elucidate the molecular mechanisms linking TDCPP exposure to pterygium development. Bioinformatics analysis identified 273 TDCPP-related targets and 1,078 pterygium-associated genes, with 43 overlapping candidates. Weighted gene co-expression network analysis (WGCNA) revealed two key modules correlated with pterygium phenotypes, highlighting MMP3 as a central regulator. Molecular docking and dynamics simulations confirmed stable interactions between TDCPP and MMP3 (binding energy: -5.9 kcal/mol), supported by RMSD, RMSF, and hydrogen bonding analyses. In vitro experiments demonstrated that low-dose TDCPP (0.5 µM) upregulated MMP3 expression in immortalized human conjunctival fibroblasts, enhancing cell proliferation, while higher concentrations (50 µM) induced cytotoxicity. These findings suggest that TDCPP promotes pterygium pathogenesis via MMP3-mediated extracellular matrix remodeling and fibroblast proliferation. This study provides novel insights into the environmental etiology of pterygium and identifies MMP3 as a potential therapeutic target for TDCPP-associated ocular surface disorders.},
}
@article {pmid41205483,
year = {2026},
author = {Ma, X and Wang, Z and Ishida, Y and Kobayashi, H},
title = {Land-cover-based indoor gamma-ray dose after a nuclear accident: location factor mapping via Monte Carlo simulation, GIS, and remote sensing.},
journal = {Journal of environmental radioactivity},
volume = {291},
number = {},
pages = {107853},
doi = {10.1016/j.jenvrad.2025.107853},
pmid = {41205483},
issn = {1879-1700},
mesh = {*Radiation Monitoring/methods ; Monte Carlo Method ; Gamma Rays ; Geographic Information Systems ; *Air Pollutants, Radioactive/analysis ; Remote Sensing Technology ; Fukushima Nuclear Accident ; *Air Pollution, Indoor/analysis/statistics &amp; numerical data ; Cesium Radioisotopes/analysis ; *Radioactive Hazard Release ; Radiation Dosage ; },
abstract = {Long-term indoor dose prediction is critical for health risk assessment and disaster management of accidental radionuclide releases. The gamma rays emitted from the ground deposition of [137]Cs are the primary concern in this context. This deposition exhibits variations in the relative initial source strength, ecological half-life, and vertical migration depending on the ground material. The dose response is further influenced by the attenuation within the ground, air, and building structures. Therefore, evaluating indoor doses in complex urban environments is challenging, particularly when accounting for directional variations in factors such as building density and ground materials. To address this issue, this study draws on the Local Climate Zone (LCZ) concept to propose a universal urban classification method suited to areas with mixed land cover and low-rise detached wooden structures, such as Fukushima. Monte Carlo simulations are then used to identify time-dependent indoor dose location factors across various environment type combinations. A mapping approach referencing LCZ recognition is developed using geographic information systems and remote sensing.},
}
@article {pmid41206013,
year = {2025},
author = {Yuan, R and Zhang, J},
title = {Testing the Mother's Curse Hypothesis in Human Mitochondrial Genome Evolution.},
journal = {Genome biology and evolution},
volume = {17},
number = {11},
pages = {},
pmid = {41206013},
issn = {1759-6653},
support = {R35 GM139484/GM/NIGMS NIH HHS/United States ; },
mesh = {*DNA, Mitochondrial/genetics ; Humans ; *Maternal Inheritance/genetics ; Male ; Female ; Mutation ; *Genetic Fitness ; United Kingdom ; UK Biobank ; Sex Factors ; *Disease/genetics ; Haplotypes ; },
abstract = {In species where mitochondrial DNA (mtDNA) is maternally inherited such as vertebrates, mtDNA mutations harming males only are not subject to purifying selection and thus can spread in a population, especially when these mutations benefit females. Therefore, the mother's curse hypothesis (MCH) posits a greater mtDNA mutation load in males than in females. MCH is potentially important for human health, disease, and evolution, but a systematic test that considers the vast human mtDNA variation is lacking. Analyzing the genotypic and phenotypic data of approximately 0.5 million British participants in the UK Biobank, we estimate the reproductive fitness of mtDNA variants in each sex. Contradicting MCH, a positive intersexual correlation in the number of offspring exists across mitochondrial haplogroups. While a significant variation in the number of opposite-sex sexual partners-a proxy for reproductive fitness in premodern societies-is present among mitochondrial haplogroups, no significant intersexual correlation in this quantity is detected. The frequencies of a few mtDNA variants differ significantly between males and females, suggesting that these variants differentially affect the survival in the two sexes, but the number of such variants with lower male frequencies is not significantly different from that with lower female frequencies. Analysis of disease associations also finds no enrichment of male disease-associated mtDNA variants despite the discovery of multiple sex-biased disease associations. Together, these findings provide no genomic support to MCH in humans and suggest no difference in mtDNA mutation load between the two sexes that is detectable in the UK Biobank.},
}
@article {pmid41207298,
year = {2026},
author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J},
title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D763-D775},
pmid = {41207298},
issn = {1362-4962},
support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Metagenome ; *Databases, Genetic ; Molecular Sequence Annotation ; Bacteria/genetics/classification ; Software ; Internet ; },
abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.},
}
@article {pmid41208809,
year = {2026},
author = {Lee, K and Kummerfeld, E and McMorris, BJ and Looman, WS and Burns, MK and Delaney, CW},
title = {Causal Pathways to Risk and Protective Factors for Partial-Day School Absenteeism for Secondary School Students.},
journal = {Journal of adolescence},
volume = {98},
number = {2},
pages = {450-460},
doi = {10.1002/jad.70073},
pmid = {41208809},
issn = {1095-9254},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Absenteeism ; Adolescent ; Male ; Female ; *Students/psychology/statistics &amp; numerical data ; Schools ; Risk Factors ; Protective Factors ; Minnesota ; Surveys and Questionnaires ; Sleep Deprivation/psychology ; Child ; },
abstract = {INTRODUCTION: Chronic absenteeism, defined as missing 10% or more school days annually, negatively impacts academic achievement and correlates with long-term risks like poverty, poor health, and criminal behavior. While prior research has focused on full-day absences, partial-day absences, missing portions of the school day, are more prevalent and may have detrimental effects on academic outcomes. Despite this significance, PDAs are underexplored, leaving gaps in understanding their prevalence, causes, and impact. This study seeks to address these gaps and provide insights to guide comprehensive absenteeism interventions.<br><br>METHODS: In this study we used the Kids and Teens at School framework and causal discovery analysis to model the factors causally associated with partial-day absences using secondary school student-level data (n&#x2009;=&#x2009;125,375) from the 2019 Minnesota Student Survey. The discovered model indicate specified factors as causes of PDAs and broader absenteeism patterns.<br><br>RESULTS AND CONCLUSIONS: The findings highlighted a pattern of partial-day absences directly affecting full-day absences. Additional factors influencing school absences were discovered including (a) a positive association of sleep deprivation with mental health difficulties, and (b) a negative association between school engagement and partial-day absences. These findings emphasize the need for targeted policies addressing the behavioral and structural factors influencing absenteeism. Implications for practice include strategies to enhance engagement and mitigate the impact of sleep deprivation on attendance.},
}
@article {pmid41210100,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the March moth, Alsophila aescularia (Denis &amp; Schiffermüller).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {50},
pmid = {41210100},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Alsophila aescularia (the March moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 901.6 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.67 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,618 protein coding genes.},
}
@article {pmid41212859,
year = {2025},
author = {Hendawy, E and Belal, AA and Rebouh, NY and Shokr, MS and Sheta, AEAS and Saleh, AM and Abou-Hadid, AF},
title = {Health risk assessment of heavy metals in arid soils of the Nile Delta, Egypt using GIS and multivariate statistical analyses.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0335394},
pmid = {41212859},
issn = {1932-6203},
mesh = {Egypt ; *Metals, Heavy/analysis/toxicity ; *Geographic Information Systems ; Humans ; *Soil Pollutants/analysis/toxicity ; Risk Assessment ; *Soil/chemistry ; Multivariate Analysis ; Environmental Monitoring/methods ; },
abstract = {Economic expansion has led to an increase in new toxins in the environment, creating a global problem for managing both environmental and human health. This study aimed to quantify the concentration of heavy metals (HMs) in soils of the Kafr El-Sheikh Governorate, located in the northern Nile Delta, Egypt, and to evaluate potential health risks by integrating Geographic Information Systems (GIS) with multivariate statistical analyses. Soil samples from 27 sites were analysed for potentially toxic elements (As, Cd, Co, Cu, Fe, Mn, Ni, Pb, and Zn) using Inductively Coupled Plasma Mass Spectrometry. Soil pollution indices such as enrichment factor (EF), contamination factor (CF), and geoaccumulation index (Igeo) were assessed. In addition, non-carcinogenic and cancer risk indices were calculated. To identify the origins of HMs in the research area, Pearson's bivariate correlation, principal component, and hierarchical cluster analyses (PCA) were used. The findings revealed that the mean HM concentrations (mg kg-1) were in the following order: Fe (10706 ± 2855)>Mn (697.53 ± 138.46)> As(210.07 ± 20.23)> Zn (207.40 ± 216.76)>Ni(112.43 ± 13.68)> Cu (87.15 ± 47.69)> Pb(31.11 ± 8.66)> Co(23.97 ± 5.96)> Cd (6.50 ± 5.62). The EF, CF, and Igeo indices indicated that the soils in the study area were contaminated with metals. The risk index values indicated moderate, considerable, and very high ecological risk, with a median value of 2060.40 (range: 192.95-5006.97). From PCA results, the possible sources of the metals in the arid soils included pesticides and chemical fertilizers, except for Mn, which appeared to originate from geogenic sources. Both children and adults had hazard quotient and Hazard index values less than one in all three exposure pathways, except for As in the ingestion pathway for children.. Furthermore, the total cancer risk (sum of ingestion, inhalation, and dermal contact pathways for each element) associated with children's exposure to the elements under investigation was as follows: Pb (4.5E-02)> As (4.1E-03)> Ni (2.6E-03)> Cd (4.7E-05). Consequently, the largest cancer risk was determined to be from Pb. These results provide valuable information that emphasizes the need to mitigate pollution from potentially toxic elements in the Nile delta and minimize health concerns for the local population.},
}
@article {pmid41213900,
year = {2025},
author = {Bu, C and Zhang, H and Zhang, F and Liang, W and Gao, H and Zhao, J and Lv, F and Xue, R and Liu, Q and Zhang, Z and Jin, Z and Xiao, J},
title = {PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9865},
pmid = {41213900},
issn = {2041-1723},
support = {32170669//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Software ; *Genome, Bacterial/genetics ; *Genomics/methods ; Genetic Variation ; *Computational Biology/methods ; Phylogeny ; },
abstract = {Pan-genome analysis is a crucial method for studying genomic dynamics. By creating pan-genome maps for prokaryotic organisms, we can gain valuable insights into their genetic diversity and ecological adaptability. However, current analytical methods often struggle to balance accuracy and computational efficiency, and they tend to provide primarily qualitative results. This study introduces PGAP2, an integrated software package that simplifies various processes, including data quality control, pan-genome analysis, and result visualization. PGAP2 facilitates the rapid and accurate identification of orthologous and paralogous genes by employing fine-grained feature analysis within constrained regions. Our systematic evaluation with simulated and gold-standard datasets demonstrates that PGAP2 is more precise, robust, and scalable than state-of-the-art tools for large-scale pan-genome data. Furthermore, PGAP2 introduces four quantitative parameters derived from the distances between or within clusters, enabling detailed characterization of homology clusters. Finally, we validate our quantitative findings by applying PGAP2 to construct a pan-genomic profile of 2794 zoonotic Streptococcus suis strains. This analysis offers new insights into the genetic diversity of S. suis, thereby enhancing our understanding of its genomic structure. PGAP2 is freely available at https://github.com/bucongfan/PGAP2 .},
}
@article {pmid41214799,
year = {2025},
author = {Ahuekwe, EF and Taiwo, DI},
title = {Performance assessment of Bayesian meta-analytic predictive model on kdr mutation in insecticide-resistant malarial vectors in sub-Saharan Africa.},
journal = {Malaria journal},
volume = {24},
number = {1},
pages = {391},
pmid = {41214799},
issn = {1475-2875},
mesh = {Africa South of the Sahara ; Bayes Theorem ; *Insecticide Resistance/genetics ; *Anopheles/genetics/drug effects ; *Mosquito Vectors/genetics/drug effects ; Animals ; *Mutation ; Malaria/transmission ; *Insecticides/pharmacology ; Pyrethrins/pharmacology ; },
abstract = {Mosquito populations' selective pressure arising from the widespread and prolonged use of insecticides, especially pyrethroids, for both agricultural usages and public health outcomes, has immensely contributed to the emergence and heavily spread of insecticide resistance. In this study, a systematic review identified eight eligible case-control or cohort studies published between 2015 and 2025 across sub-Saharan Africa that reported both allele and/or genotype frequencies of L1014F and L1014S. The predictive performance and inferential robustness of a Bayesian meta-analytic model were applied and evaluated on two knockdown resistance (kdr) mutations, L1014F and L1014S, in the Anopheles mosquito populations. Using the Markov Chain Monte Carlo (MCMC) sampling to compute pooled concordance statistics, odds ratios, and perform funnel plot asymmetry tests (Egger, Macaskill, Debray). The results revealed that L1014F showed a stronger and more consistent association with phenotypic resistance compared to L1014S, with odds ratios (OR) as high as 4.44 (95% CI 3.40-5.80). However, concordance statistics for both mutations demonstrated wide confidence intervals (L1014F: 0.141; CI - 0.095 to 0.459; L1014S: 0.169; CI - 0.399 to 0.688), indicating moderate predictive reliability. The Bayesian framework effectively synthesized complex and heterogeneous resistance data, confirming the operational relevance of KDR mutations in resistance surveillance. The global significance of these results enhances the predictive analytics in resistance management, such that resistance evolution is temporally and spatially dynamic. The integration of Bayesian modelling into existing entomological surveillance systems shifts the paradigm towards more adaptive and anticipatory management. Although data sparsity and regional heterogeneity warrant cautious interpretation, integrating ecological and thermodynamic variables into predictive models is essential for enhancing future resistance forecasting.},
}
@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.},
}
@article {pmid41216995,
year = {2026},
author = {Trepel, J and Atkinson, J and le Roux, E and Abraham, AJ and Aucamp, M and Greve, M and Greyling, M and Kalwij, JM and Khosa, S and Lindenthal, L and Makofane, C and Mokoena, L and Oosthuizen, A and Rech, BJ and Lundgren, E and Svenning, JC and Buitenwerf, R},
title = {Large herbivores are linked to higher herbaceous plant diversity and functional redundancy across spatial scales.},
journal = {The Journal of animal ecology},
volume = {95},
number = {1},
pages = {230-242},
pmid = {41216995},
issn = {1365-2656},
support = {DNRF173//Danmarks Grundforskningsfond/ ; 0135-00225B//Danmarks Frie Forskningsfond/ ; },
mesh = {*Herbivory ; Animals ; South Africa ; *Biodiversity ; Grassland ; *Food Chain ; *Plants/classification ; },
abstract = {Large herbivores can strongly influence plant communities. However, these effects are highly variable, potentially depending on the herbivore regime, that is, herbivore diversity and density. However, the role of the herbivore regime has been challenging to evaluate across spatial scales due to widespread defaunation and a lack of data on herbivore communities and their densities. Here, we investigated the effects of large herbivores along a gradient of trophic complexity (low to high herbivore diversity) and herbivory intensity (estimated from herbivore biomass and visitation frequency) on plant taxonomic and functional diversity at different scales (plot [n = 250], site [n = 50] and landscape [n = 10]) in 10 reserves in the savanna biome in South Africa. We found higher total plant species richness, driven by higher herbaceous (but not woody) plant species richness, in areas with higher herbivory intensity across multiple scales. While herbivores had no significant relationship with plant functional richness, we observed higher functional redundancy at all scales in areas more frequently visited by herbivores. Overall, herbivore-vegetation relationships were largely consistent across scales, and the strongest effects emerged at the largest scale. Our results show a positive relationship between large herbivores and both herbaceous plant species richness and plant functional redundancy, the latter suggesting higher vegetation resilience (the capacity of ecosystems to quickly recover from disturbances as different species compensate for the loss or decline of others). These effects are largely consistent across scales, indicating that the impact of herbivore regimes on plant communities is predominantly scale-independent and that large herbivores drive vegetation dynamics at both local and large scales. However, the stronger effects observed at the landscape scale imply that herbivore impacts manifest most prominently at larger scales. Altogether, our results suggest that restoring large herbivore populations can be expected to promote herbaceous plant diversity and ecosystem resilience.},
}
@article {pmid41219229,
year = {2025},
author = {Berto, D and Fanelli, E and Vizzini, S and Rampazzo, F and Da Ros, Z and Noventa, S and Fortibuoni, T and Antonini, C and Cilluffo, G and Signa, G and Premici, A and Bardelli, R and Raicevich, S},
title = {ISOMED - A Stable ISOtope database of MEDiterranean marine food web components.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1768},
pmid = {41219229},
issn = {2052-4463},
support = {101059877//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101059877//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101059877//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Food Chain ; Nitrogen Isotopes/analysis ; Carbon Isotopes/analysis ; Mediterranean Sea ; Databases, Factual ; Animals ; },
abstract = {Marine food webs shape the ecological dynamics of energy flows and predator-prey relationships. Their study is crucial to understanding human impacts that are monitored within environmental policies, such as the European Marine Strategy Framework Directive. One of the most used methods to assess the structure and functioning of marine food webs relies on the use of carbon and nitrogen stable isotopes (δ[13]C and δ[15]N), which are particularly useful for a vast range of taxa whose diet composition may be impractical to evaluate through traditional approaches (i.e., stomach content analysis). However, such data are sparse and have not been consistently collected, making it often difficult to assess the status of marine food webs. Here, we present ISOMED, a georeferenced database of published δ[13]C and δ[15]N values and carbon and nitrogen elemental composition of basal sources of organic matter and consumers collected in the Mediterranean Sea. The information reported includes estimates for 4959 records. ISOMED provides a unique tool for investigating trophic interactions and energy flow within Mediterranean food web components.},
}
@article {pmid41223204,
year = {2025},
author = {Bateux, Q and Koss, J and Sweeney, PW and Edwards, E and Rios, N and Dollar, AM},
title = {Improving the accuracy of automated labeling of specimen images datasets via a confidence-based process.},
journal = {PLoS computational biology},
volume = {21},
number = {11},
pages = {e1013650},
pmid = {41223204},
issn = {1553-7358},
mesh = {Humans ; *Image Processing, Computer-Assisted/methods ; Neural Networks, Computer ; Computational Biology/methods ; Machine Learning ; Algorithms ; Databases, Factual ; Deep Learning ; },
abstract = {The digitization of natural history collections over the past three decades has unlocked a treasure trove of specimen imagery and metadata. There is great interest in making this data more useful by further labeling it with additional trait data, and modern "deep learning" machine learning techniques utilizing convolutional neural nets (CNNs) and similar networks show particular promise to reduce the amount of required manual labeling by human experts, making the process much faster and less expensive. However, in most cases, the accuracy of these approaches is too low for reliable utilization of the automatic labeling, typically in the range of 80-85% accuracy. In this paper, we present and validate an approach that can greatly improve this accuracy, essentially by examining the "confidence" that the network has in the generated label as well as utilizing a user-defined threshold to reject labels that fall below a chosen level. We demonstrate that a naive model that produced 86% initial accuracy can achieve improved performance - over 95% accuracy (rejecting about 40% of the labels) or over 99% accuracy (rejecting about 65%) by selecting higher confidence thresholds. This gives flexibility to adapt existing models to the statistical requirements of various types of research and has the potential to move these automatic labeling approaches from being unusably inaccurate to being an invaluable new tool. After validating the approach in a number of ways, we annotate the reproductive state of a large dataset of over 600,000 herbarium specimens. The analysis of the results points at under-investigated correlations as well as general alignment with known trends. By sharing this new dataset alongside this work, we want to allow biologists to gather insights for their own research questions, at their chosen point of accuracy/coverage trade-off.},
}
@article {pmid41225921,
year = {2025},
author = {Alrhmoun, M and Sulaiman, N and Bajrami, A and Hajdari, A and Pieroni, A and Sõukand, R},
title = {The Resilience and Change in the Biocultural Heritage of Wild Greens Foraging Among the Arbëreshë Communities in Argolis and Corinthia Areas, Peloponnese, Greece.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41225921},
issn = {2223-7747},
abstract = {The transformation of Local Ecological Knowledge (LEK) among minority populations undergoing cultural and linguistic assimilation over time is poorly understood. Arbëreshë communities in Greece, who have preserved Albanian-derived traditions for centuries, offer a unique opportunity to examine how folk plant knowledge adapts over time. This study examines the linguistic labels and culinary uses of wild greens among Arbëreshë (or Arvanites), an ethno-linguistic minority traditionally speaking Arbërisht or Arvanitika, the Tosk dialect of Albanian, who have resided in the Argolis and Corinthia regions of the Peloponnese for several centuries. In 2025, fieldwork was conducted in four rural Arbëreshë villages in the Argolis and Corinthia regions of Greece, combining semi-structured interviews with 24 elderly participants, participant observation, and the collection and identification of botanical specimens. The contemporary dataset was compared with historical ethnobotanical records from the 1970s to assess temporal changes in the use of wild vegetables and folk plant nomenclature. Our results reveal that current Arbëreshë ethnobotanical heritage has undergone profound Hellenisation, with 62% of folk plant names of Greek origin, 14% Albanian, and 24% hybrid, reflecting strong linguistic and cultural assimilation over the past half-century. The traditional boiled green mix (lakra in Arbëreshë, chorta in Greek) remains central to the local cuisine, which is rooted in foraged plants, although its culinary applications have diversified. In total, 37 taxa of wild vegetables across 37 genera and 14 families were documented in 2025, compared with 21 taxa across 21 genera in the filtered 1970 dataset. Core families, such as Asteraceae and Brassicaceae, remained dominant, while new families, like Malvaceae and Portulacaceae, appeared, possibly indicating both ecological and culinary changes. These findings raise questions about whether the Arbëreshë wild vegetable heritage was strongly influenced by the surrounding Greek majority or primarily acquired after migration, potentially facilitated by intermarriages and shared Orthodox Christian affiliation. Overall, our study highlights a largely Hellenised Arbëreshë biocultural heritage and underscores the urgent need for national and regional stakeholders to recognise and celebrate the remaining minority's linguistic and ethnobotanical diversity. The transformation of local ethnobotanical knowledge over the past fifty years appears influenced by ecological availability, socio-cultural dynamics, and changing taste preferences.},
}
@article {pmid41227447,
year = {2025},
author = {Götz, S and Reiter, K and Wensch-Dorendorf, M and von Borell, E and Raoult, CMC},
title = {Role of Illumination and Light Colour Temperature in the Preference Behaviour of Weaned Piglets.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227447},
issn = {2076-2615},
support = {820 204, 2017//German Government's Special Purpose Fund (Landwirtschaftliche Rentenbank)/ ; },
abstract = {This study investigated the preference behaviour of 24 four-week-old weaned piglets under different lighting conditions (0 lux with 0 Kelvin vs. 80 lux with 3000 Kelvin vs. 6500 Kelvin). Two trials with 12 piglets each were conducted over five weeks in a room with four interconnected pens, allowing free movement between the pens. Pens A and B were nearly dark (~0 lux), while pen C (80 lux, 3000 Kelvin) and pen D (80 lux, 6500 Kelvin) were illuminated. On three days in weeks 1, 3 and 5, behaviour (lying, eating and activity) was recorded using video observations and a 5 min time sampling method. Cleanliness was also monitored daily. In the first week, piglets in the first batch preferred the darkened pens, whereas piglets in the second batch preferred illuminated pens, especially when the colour temperature was 3000 Kelvin. By the third week, piglets in the second batch now preferred darker areas. In the fifth week, the piglets spent more time in the dark in the mornings and evenings but showed no preference for colour temperature. The darkened pens remained mostly clean, whereas pen D, which had a light colour temperature of 6500 Kelvin, was the most soiled. The results show that piglet behaviour changes with age and the time of day, suggesting that lighting concepts can be adapted to improve both animal welfare and pen hygiene.},
}
@article {pmid41228769,
year = {2025},
author = {Tanabe, R and Kikuchi, R and Zou, M and Suehiro, K and Takahashi, N and Saito, H and Kobayashi, T and Satake, H and Sato, N and Kageyama, Y},
title = {Emotion Recognition Using Temporal Facial Skin Temperature and Eye-Opening Degree During Digital Content Viewing for Japanese Older Adults.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {21},
pages = {},
pmid = {41228769},
issn = {1424-8220},
support = {JP22K12215//JSPS KAKENHI/ ; JP25K15297//JSPS KAKENHI/ ; },
mesh = {Humans ; *Emotions/physiology ; *Skin Temperature/physiology ; Female ; Male ; Aged ; Thermography/methods ; *Eye Movements/physiology ; Facial Expression ; Face/physiology ; Japan ; Middle Aged ; East Asian People ; },
abstract = {Electroencephalography is a widely used method for emotion recognition. However, it requires specialized equipment, leading to high costs. Additionally, attaching devices to the body during such procedures may cause physical and psychological stress to participants. These issues are addressed in this study by focusing on physiological signals that are noninvasive and contact-free, and a generalized method for estimating emotions is developed. Specifically, the facial skin temperature and eye-opening degree of participants captured via infrared thermography and visible cameras are utilized, and emotional states are estimated while Japanese older adults view digital content. Emotional responses while viewing digital content are often subtle and dynamic. Additionally, various emotions occur during such situations, both positive and negative. Fluctuations in facial skin temperature and eye-opening degree reflect activities in the autonomic nervous system. In particular, expressing emotions through facial expressions is difficult for older adults; as such, emotional estimation using such ecological information is required. Our study results demonstrated that focusing on skin temperature changes and eye movements during emotional arousal and non-arousal using bidirectional long short-term memory yields an F1 score of 92.21%. The findings of this study can enhance emotion recognition in digital content, improving user experience and the evaluation of digital content.},
}
@article {pmid41230929,
year = {2026},
author = {Chen, Z and Vončina, K and Sigwart, JD},
title = {Evaluating Probe Design for Phylogenomics Across Taxonomic Scales: First Steps for Applying Ultraconserved Elements in an Understudied Class (Mollusca: Polyplacophora).},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70076},
pmid = {41230929},
issn = {1755-0998},
support = {P123//Leibniz project PHENOME/ ; },
mesh = {Animals ; *Phylogeny ; *Genomics/methods ; *Conserved Sequence ; *Mollusca/genetics/classification ; Transcriptome ; Computational Biology/methods ; },
abstract = {Ultraconserved elements (UCEs) have become a powerful tool for phylogenomics, but probe sets optimized for one lineage often perform inconsistently when applied in others. Here, we designed and tested new UCE probe sets derived from both genome and transcriptome data of an understudied molluscan class, Polyplacophora (chitons). In this study, we identified 5730 ultra-conserved elements (UCEs) from available chiton genomes and transcriptomes, and designed a set of 19,080 probes. These probes showed an average efficiency of 55% in the genome and 20% in transcriptomes, significantly outperforming available molluscan probe sets. A coalescence-based phylogenetic tree based on in silico extractions of UCEs from transcriptome and genome data successfully resolved chiton phylogeny at the species level. Relatively shorter flanking regions performed best. Where genome and transcriptome data were available for the same species, they did not always resolve as sister taxa in non-optimized methods; instead, genome- and transcriptome-derived sequences tended to form separate clades. This offers a caution for combining data harvested from published datasets. Quantifying phylogenetic signal at individual UCE loci demonstrates that the dataset retains topological stability across a range of filtering stringencies. This resource provides a foundation for integrating new genomic and transcriptomic datasets and has the potential to enable targeted sequencing of historical museum specimens. More broadly, our study highlights the importance of tailored probe design for phylogenomic studies in understudied lineages and the challenges of combining diverse molecular data types.},
}
@article {pmid41231440,
year = {2025},
author = {Lee, J and Nam, KH and Suh, Y and Lee, Y and Lee, D},
title = {Factors Associated With Patient Safety Activities of Clinical Nurses: A Cross-Sectional Secondary Data Analysis.},
journal = {International nursing review},
volume = {72},
number = {4},
pages = {e70127},
pmid = {41231440},
issn = {1466-7657},
support = {2022-22-0274//Ministry of Education/ ; //National Research Foundation of Korea/ ; },
mesh = {Humans ; Cross-Sectional Studies ; *Patient Safety ; Republic of Korea ; *Nursing Staff, Hospital/psychology/education ; Female ; Male ; Adult ; Organizational Culture ; Middle Aged ; Surveys and Questionnaires ; *Clinical Competence ; *Safety Management ; Secondary Data Analysis ; },
abstract = {AIMS: To examine the associations between patient safety silence, culture, competency, and activities among clinical nurses.<br><br>BACKGROUND: Patient safety ensures harm prevention and quality of care. Factors such as silence, culture, and competency are widely recognized as significantly associated with patient safety activities, but limited research has examined their interrelationships.<br><br>DESIGN: Cross-sectional secondary data analysis.<br><br>METHODS: This study used data from a study that investigated the patient safety educational needs of 291 nurses from general hospitals located in the Busan, Ulsan, and Gyeongsangnamdo regions of South Korea. To assess patient safety activities, silence, culture, and competency, the study employed the Patient Safety Activities Questionnaire, Patient Safety Silence Scale, Hospital Survey on Patient Safety Culture, and Patient Safety Competency Self-Evaluation Tool, respectively. The analysis involved descriptive statistics, correlation analysis, and multiple regression using SPSS 27.0.<br><br>RESULTS: The factors of silence and receiving patient safety education only once were negatively associated with patient safety activities. Positive associations were found for teamwork within the culture subdomain, skills within the competency subdomain, and hospital size.<br><br>CONCLUSIONS: These findings provide a basis for educational programs to improve nursing skills and highlight the need to build an open and collaborative organizational culture.<br><br>IMPLICATIONS FOR NURSING: Clinical nurses should develop patient safety skills, report patient safety incidents, and collaborate with team members to foster an open and cooperative organizational culture.<br><br>To minimize silence, while strengthening teamwork, organizations actively foster a culture of openness and collaboration. Education should be managed to meet minimum standards, and hospital-specific policies should be tailored according to each institution's size and characteristics.},
}
@article {pmid41231796,
year = {2025},
author = {Baral, T and Maile, A and Adimurthy, NH and Saravu, K and Kudru, CU and Singh, J and Mukhopadhyay, C and Rao, M and Manu, MK and Sekhar Miraj, S},
title = {Exploring gut microbiota and its predicted functions in pulmonary tuberculosis: A multi-regional study using public 16S datasets.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336337},
pmid = {41231796},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Tuberculosis, Pulmonary/microbiology/drug therapy ; Phylogeny ; *RNA, Ribosomal, 16S/genetics ; Antitubercular Agents/therapeutic use ; Male ; Female ; Mycobacterium tuberculosis/genetics ; Middle Aged ; Adult ; },
abstract = {BACKGROUND: Pulmonary tuberculosis, caused by the bacillus Mycobacterium tuberculosis, remains a major global health challenge, particularly in developing countries. In this study, we analyzed publicly available 16S amplicon sequencing datasets from four geographical locations using a single workflow.<br><br>METHODS: We employed Quantitative Insights Into Microbial Ecology v.2 for microbial diversity analysis and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States v.2 for functional pathway predictions of the gut microbiota in patients with PTB and antitubercular therapy.<br><br>RESULTS: Our analysis revealed statistically significant alpha diversity differences in West Africa with decreased microbial diversity in pulmonary tuberculosis patients after two months of antitubercular therapy. Additionally, there were no statistically significant differences observed in pairwise comparisons within the same location or in the aggregate beta diversity of the datasets. The predicted microbial metabolic pathways related to vitamin biosynthesis, amino acid synthesis, and energy production were depleted in pulmonary tuberculosis patients following antitubercular therapy.<br><br>CONCLUSIONS: The observed alterations of gut microbial diversity and predicted functional profile underscores the influence of antitubercular therapy on gut health, suggesting that longer treatment durations may aggravate these alterations in gut microbial function. Moreover, geographical location exerts a more significant impact on microbial diversity than the disease state in a specific location, highlighting the potential for precision medicine to tailor interventions based on individual or regional microbiome characteristics.},
}
@article {pmid41232106,
year = {2025},
author = {Wang, LC and Pike, KC and Conway, M and Chen, AT},
title = {Identifying Stigma Phenotypes in Social Media Narratives of Substance Use: Observational Study.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e68695},
pmid = {41232106},
issn = {1438-8871},
support = {R21 DA056684/DA/NIDA NIH HHS/United States ; },
mesh = {Humans ; *Substance-Related Disorders/psychology ; *Social Stigma ; *Social Media ; Phenotype ; Narration ; },
abstract = {BACKGROUND: Individuals with substance use problems experience stigma in different contexts. Identifying characteristic situations in which stigma occurs or manifests-stigma phenotypes-can serve as important leverage points for future intervention.<br><br>OBJECTIVE: This paper aims to (1) identify stigma phenotypes expressed in social media narratives related to substance use stigma and (2) explore the similarities and differences between the stigma phenotypes from a social ecological perspective.<br><br>METHODS: We collected Reddit posts pertaining to 3 substances-alcohol, cannabis, and opioids. We performed feature engineering using a combination of content analysis, machine learning, and keyword-based methods to predict variables at different levels of the social ecological framework. Leveraging these features, we applied the fuzzy c-means clustering algorithm on the subset of posts containing stigma to extract stigma phenotypes, where a phenotype is defined by four main dimensions: (1) the stigma mechanism present (eg, internalized stigma, anticipated stigma, or enacted stigma), (2) the substance used (eg, alcohol, cannabis, or opioids), (3) the settings involved (eg, work, school, or home), and (4) the actors involved (eg, family, friends, or partners). Finally, we used Kruskal-Wallis and Dunn post hoc tests to examine the differences between stigma phenotypes with respect to specific ecological factors.<br><br>RESULTS: We derived 7 stigma phenotypes from stigma-related posts by 8627 authors. The phenotypes can be categorized into 4 groups: internalized stigma-only, anticipated stigma, enacted stigma-only, and mixed-stigma phenotypes. Narratives on internalized stigma phenotypes focused on the self, with minimal reference to settings and actors. One phenotype focused on anticipated stigma and was characterized by a high proportion of opioid use mentions (707/1217, 58.09% of the authors) and references to the health care setting (647/1217, 53.16% of the authors). Posts associated with the enacted stigma-only phenotypes included substantial representation of settings and actors. Narratives in the mixed-stigma phenotypes often involved more than one stigma mechanism, setting, and actor, with home and family being the most salient factors. The phenotypes differed from one another with respect to social ecological factors, including loneliness and social isolation, use of treatment services, presence of health care providers, community and support groups, society, and legalization.<br><br>CONCLUSIONS: These findings provide valuable insights that help inform the design and development of interventions targeted at different stigma phenotypic groups from a social ecological perspective.},
}
@article {pmid41234513,
year = {2025},
author = {Crowley, LM and Boyes, D and , and , and , and , and , and , and , },
title = {The genome sequence of the Tawny Oak Tortrix, Acleris ferrugana (Denis &amp; Schiffermüller), 1775 (Lepidoptera: Tortricidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {507},
pmid = {41234513},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Acleris ferrugana (Tawny Oak Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 480.03 megabases. Most of the assembly (99.03%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.58 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 {pmid41235392,
year = {2024},
author = {Ravenswater, HM and Greco, F and Burthe, SJ and Cunningham, EJA and , and , and , and , and , and , },
title = {The genome sequence of the European shag, Gulosus aristotelis (previously Phalacrocorax aristotelis) (Linnaeus, 1761).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {144},
pmid = {41235392},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Gulosus aristotelis, previously known as Phalacrocorax aristotelis, (the European shag; Chordata; Aves; Pelecaniformes; Phalacrocoracidae). The genome sequence is 1,279.1 megabases in length. Most of the assembly is scaffolded into 36 chromosomal pseudomolecules, including the Z and W sex chromosomes. Gene annotation of this assembly on Ensembl identified 16,474 protein coding genes. The mitochondrial genome has also been assembled and is 18.61 kilobases in length.},
}
@article {pmid41237195,
year = {2025},
author = {Kertesz, SG and Varley, AL and Hoge, AE and Joiner, TE and Darnall, BD and Nicholson, KM and Fuqua, LA and Gilmore, MF and Riggs, KR and Gamble, SA and Gordon, AJ and Dwivedi, Y and Flower, M and Veasley, CS and Patton, CS and Leal, AS and Gibson, DM and Elliott, JE and McCullough, MB},
title = {Protocol for research examination of individual suicides occurring in chronic pain: A qualitative approach to psychological autopsy methodology.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0329874},
pmid = {41237195},
issn = {1932-6203},
mesh = {Humans ; *Chronic Pain/psychology/drug therapy ; *Suicide/psychology ; Analgesics, Opioid/therapeutic use/adverse effects ; United States ; Male ; Female ; Autopsy/methods ; Qualitative Research ; Risk Factors ; Veterans/psychology ; Adult ; Middle Aged ; },
abstract = {INTRODUCTION: In the United States, taper and discontinuation of opioids prescribed for long-term pain have emerged as statistical correlates of suicidal events. Suicide is a complex and multidetermined event reflecting a combination of risks occurring over time in a particular narrative context. Prevention of suicides should be informed by a detailed understanding of life events, pain-related and other risk factors contributing to these tragedies. To date, there have been no efforts to qualitatively profile these suicides through interview of bereaved survivors or review of medical records. This method is usually termed "psychological autopsy.".<br><br>AIMS: This paper summarizes the protocol for the Clinical Context of Suicide Following Opioid Transitions (CSI:OPIOIDs) study. The study seeks to qualitatively characterize patient and clinical context factors associated with suicide among persons who died by suicide in the context of opioid stoppage or reduction, and to compare findings between Veteran and non-Veteran decedents.<br><br>METHODS: In the United States, there is no master list for suicide deaths linked to an antemortem health care event. For this reason, recruitment requires public advertising followed by screening of bereaved individuals who wish to participate. Data collection and interpretation are guided by the Social-Ecological Model for suicide. The study involves a collaboration of persons with lived experience and disciplinary experts in suicide, primary care, pain, health services, and medical anthropology.<br><br>CONCLUSIONS: This study aims to deliver the first in-depth analysis of suicide events occurring in persons with chronic pain who died by suicide in the context of a prescription opioid reduction or stoppage. The results should provide insights that can guide alterations to care by health systems and by individual practitioners.},
}
@article {pmid41237217,
year = {2025},
author = {Billings, WZ and Ge, Y and Skarlupka, AL and Miller, SL and Hemme, H and John, M and Dean, NE and Cobey, S and Cowling, BJ and Shen, Y and Ross, TM and Handel, A},
title = {Different antigenic distance metrics generate similar predictions of influenza vaccine response breadth despite moderate correlation.},
journal = {PLoS computational biology},
volume = {21},
number = {11},
pages = {e1013720},
pmid = {41237217},
issn = {1553-7358},
support = {R01 AI139761/AI/NIAID NIH HHS/United States ; R01 AI170116/AI/NIAID NIH HHS/United States ; 75N93019C00052/AI/NIAID NIH HHS/United States ; R35 GM146612/GM/NIGMS NIH HHS/United States ; U01 AI150747/AI/NIAID NIH HHS/United States ; },
mesh = {*Influenza Vaccines/immunology ; Humans ; *Influenza, Human/immunology/prevention &amp; control/virology ; *Antigens, Viral/immunology ; Computational Biology ; Bayes Theorem ; Antibodies, Viral/immunology ; Vaccine Efficacy ; Influenza A Virus, H3N2 Subtype/immunology ; Antigenic Variation/immunology ; Influenza A Virus, H1N1 Subtype/immunology ; },
abstract = {INTRODUCTION: Influenza continuously evolves to escape population immunity, which makes formulating a vaccine challenging. Antigenic differences between vaccine strains and circulating strains can affect vaccine effectiveness (VE). Quantifying the antigenic difference between vaccine strains and circulating strains can aid interpretation of VE, and several antigenic distance metrics have been discussed in the literature. Here, we compare how the predicted breadth of vaccine-induced antibody response varies when different metrics are used to calculate antigenic distance.<br><br>METHODS: We analyzed data from a seasonal influenza vaccine cohort that collected serum samples from 2013/14 - 2017/18 at three study sites. The data include pre- and post-vaccination HAI titers to the vaccine strains and a panel of heterologous strains. We used that data to calculate four different antigenic distance measures between assay strains and vaccine strains: difference in year of isolation (temporal), p-Epitope (sequence), Grantham's distance (biophysical), and antigenic cartography distance (serological). We analyzed agreement between the four metrics using Spearman's correlation and intraclass correlation. We then fit Bayesian generalized additive mixed-effects models to predict the effect of antigenic distance on post-vaccination titer after controlling for confounders and analyzed the pairwise difference in predictions between metrics.<br><br>RESULTS: The four antigenic distance metrics had low or moderate correlation for influenza subtypes A(H1N1), B/Victoria, and B/Yamagata. A(H3N2) distances were highly correlated. We found that after accounting for pre-vaccination titer, study site, and repeated measurements across individuals, the predicted post-vaccination titers conditional on antigenic distance and subtype were nearly identical across antigenic distance metrics, with A(H3N2) showing the only notable deviation between metrics, despite higher agreement for that subtype.<br><br>DISCUSSION: Despite moderate correlation among metrics, we found that different antigenic distance metrics generated similar predictions about breadth of vaccine response. Costly titer assays for antigenic cartography may not be needed when simpler sequence-based metrics suffice for quantifying vaccine breadth.},
}
@article {pmid41238729,
year = {2025},
author = {Lee, KY and Shin, SH and Park, G and Kang, SH and Kang, HJ and Kim, J and Lee, JJ and Son, GH and Hong, JY},
title = {Shotgun metagenomics of the vaginal microbiome in cervical shortening and preterm birth risk.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39988},
pmid = {41238729},
issn = {2045-2322},
support = {HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; RS-2023-00252948//Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health &amp; Welfare, the Ministry of Food and Drug Safety)/ ; },
mesh = {*Premature Birth/epidemiology/microbiology/physiopathology/prevention &amp; control ; *Vagina/microbiology ; *Cervix Uteri/microbiology/physiopathology ; Humans ; Female ; Microbiota/genetics ; *Metagenomics ; Cervical Length Measurement ; Risk Factors ; East Asian People/statistics &amp; numerical data ; Risk Assessment/methods ; Prospective Studies ; DNA, Bacterial/genetics/isolation &amp; purification ; Pregnancy ; Adult ; },
abstract = {Preterm birth (PTB), a leading cause of neonatal morbidity and mortality, is frequently associated with premature cervical remodeling and vaginal microbiome dysbiosis. Cervical shortening in mid-pregnancy is a well-established risk factor for spontaneous PTB (sPTB), yet the microbial signatures underlying this condition remain underexplored, especially in Asian populations. In this study, we conducted shotgun metagenomic analysis of vaginal samples from 35 East Asian pregnant women with a short cervix and 12 with normal cervical length. Species-level taxonomic profiling and functional pathway analysis revealed reduced Lactobacillus dominance, increased microbial diversity, and enrichment of non-optimal CST IV species, such as Fannyhessea vaginae, Bifidobacterium breve, and Mycobacterium canetti in the short cervix group. Functional profiling showed group differences in pathways related to folate biosynthesis, carbohydrate metabolism, and epithelial barrier regulation. Among women with a short cervix, those who delivered preterm had vaginal microbiomes enriched in opportunistic pathogens, including Peptoniphilus equinus, Treponema spp., and Staphylococcus hominis. Conversely, B. breve, Lactobacillus gasseri, and Lactobacillus paragasseri were associated with full-term delivery. Functions related to glycosylation, structural stability, and degradation of cervical mucin were enriched in the sPTB group. Network analysis identified distinct microbial interactions between Lactobacillus-dominated clusters and CST IV-associated taxa, providing ecological insights that may reflect competitive dynamics and potential influences on cervicovaginal barrier integrity. These findings enhance our understanding of the taxonomic and functional profiles of the vaginal microbiome linked to cervical shortening and sPTB, contributing to improved risk stratification and management strategies for PTB, particularly in women with cervical shortening.},
}
@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.<br><br>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.<br><br>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.<br><br>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.},
}
@article {pmid41246445,
year = {2025},
author = {Crnobrna, B and Champagne, PS and Williams, HF and Turner, H and Panduro Pisco, G},
title = {Occurrence dataset of reptiles and amphibians from two old-growth forest localities along the Las Piedras River, Tambopata Province, Peru.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e154136},
pmid = {41246445},
issn = {1314-2828},
abstract = {BACKGROUND: This study presents the first watershed-wide checklist and geo-referenced dataset of amphibians and reptiles from two primary forest localities along the Las Piedras River, Madre de Dios, Peru. Compiled from pitfall traps, quadrats, transects and opportunistic observations between 2004 and 2024, the dataset contains 2,327 records across 165 species, including several new distribution records from the central basin near the Huascar River. The Madre de Dios region in south-eastern Peru is renowned for its biodiversity and old-growth rainforests, hosting diverse flora and fauna. Protected areas like the Tambopata National Reserve and Manu National Park are vital refuges for wildlife and research hubs. The region faces threats from deforestation and illegal mining, necessitating urgent conservation efforts. Despite being one of the most diverse regions for herpetofauna globally, biogeography reports from the Las Piedras River are limited. Notably, sixty non-volant mammal species and 144 fish species have been documented, along with 59 frog and 11 reptile species at the Las Piedras Biodiversity Station (LPBS). However, a comprehensive review of reptile diversity in the watershed is lacking. This study presents a survey and occurrence dataset for reptile and amphibian species at LPBS and the Amazon Research and Conservation Centre (ARCC), including opportunistic records to provide complete taxonomic coverage. Furthermore, we review and compile other reported occurrences. This dataset and review offer detailed species and geographical information, supporting further research on herpetofauna biogeography and ecology and aiding conservation efforts on the Las Piedras River.<br><br>NEW INFORMATION: This list of reptile and amphibian species from the Las Piedras River in Peru includes new records from the basin's central area, near the Huascar River's confluence. It unifies data from early efforts to find herpetofauna at the Las Piedras Biodiversity Station spanning more than ten years. Over a decade of sampling, combined with opportunistic records, comprehensive taxonomic coverage of herpetofauna on the tributary has been provided. Our dataset contains 2,327 distinct geo-referenced records, categorised into Anura (1788), Crocodilia (10), Gymnophiona (1), Squamata (517) and Testudines (11). These records span 165 identified species, along with one entry recorded at the genus level (Chironius). This dataset was structured and managed using Microsoft Excel, where geo-referenced species occurrence data were organised into standardised formats compatible with GBIF publishing requirements. The dataset was subsequently validated and formatted as a Darwin Core Archive (DwC-A), the standard format for biodiversity data sharing, using GBIF's Integrated Publishing Toolkit (IPT). This structured approach ensures interoperability and compliance with global biodiversity informatics standards, supporting its integration into herpetofauna biogeography and conservation efforts. This dataset also includes new records from the central basin of the Las Piedras River near the Huascar River confluence. By offering 2,327 distinct geo-referenced records, this dataset (https://doi.org/10.15468/sa8m3q) supports ongoing research into herpetofauna biogeography and conservation efforts in a region under increasing pressure from deforestation and other human activities.Based on our dataset and an accompanying review of historical records and publications, we document a total of 175 herpetofauna species in the Las Piedras River watershed. This total includes 96 reptile species (ARCC = 70, LPBS = 76) and 79 amphibian species (ARCC = 64, LPBS = 69), from both geo-referenced and literature-confirmed sources.},
}
@article {pmid41247083,
year = {2026},
author = {Galtier, N and Belkhir, K and Antoine, PO and Bibal, C and Boëte, C and Delsuc, F and Huchard, E and Kéfi, S and Maeder, C and Paradis, L and Puechmaille, SJ and Queffelec, A and Scornavacca, C and Smadja, CM},
title = {Time to publish responsibly: DAFNEE, a database of academia-friendly journals in ecology and evolutionary biology.},
journal = {Journal of evolutionary biology},
volume = {39},
number = {2},
pages = {190-199},
doi = {10.1093/jeb/voaf143},
pmid = {41247083},
issn = {1420-9101},
support = {//CNRS Ecology &amp; Environment/ ; //University of Montpellier/ ; //DAFNEE/ ; },
mesh = {*Biological Evolution ; *Periodicals as Topic ; *Publishing ; *Ecology ; *Databases, Factual ; Academia ; },
abstract = {The current economics of scientific publishing reveal a profound imbalance: academia pays prices far exceeding the actual costs of publication. Rather than supporting research, much of this expenditure sustains the profits of a few dominant commercial publishers. Transitioning to responsible publishing is a collective challenge that requires raising awareness among scientists about the problem and the solutions available. We present DAFNEE, a database of academia-friendly journals in ecology, evolutionary biology and archaeology (https://dafnee.isem-evolution.fr/). DAFNEE includes information on over 600 journals (co)run by academic or non-profit institutions, aiming at helping to keep publishing funds within the academic community. The database details these journal's business models, article processing charges, citation rates and partnerships. We show that DAFNEE journals compare favourably to non-DAFNEE ones in terms of editorial and financial policy, while offering similar citation rates. Finally, we offer several recommendations aimed at encouraging authors, reviewers, and evaluators to adopt more responsible publishing practices.},
}
@article {pmid41248381,
year = {2025},
author = {Norris, LE and Lemin, M and Kelly-Hope, LA},
title = {Spatial-temporal analysis of natural hazards and disasters in the Greater Horn of Africa between 2010 and 2024 to inform disaster risk reduction, and surveillance and control strategies for climate and environmentally sensitive diseases.},
journal = {BMJ open},
volume = {15},
number = {11},
pages = {e104998},
pmid = {41248381},
issn = {2044-6055},
mesh = {Humans ; Retrospective Studies ; Cross-Sectional Studies ; Spatio-Temporal Analysis ; *Disasters/statistics &amp; numerical data ; *Disease Outbreaks/prevention &amp; control ; Floods/statistics &amp; numerical data ; *Natural Disasters ; Ethiopia ; Climate Change ; Somalia ; Droughts/statistics &amp; numerical data ; },
abstract = {OBJECTIVE: To determine the spatial-temporal patterns of natural hazards and disasters in the Greater Horn of Africa, including climate and environmentally sensitive diseases, and compare the reporting consistencies across multiple open-access databases.<br><br>DESIGN: Cross-sectional retrospective secondary analysis of natural hazard and disaster data.<br><br>SETTING: Djibouti, Eritrea, Ethiopia, Kenya, Somalia, Sudan, South Sudan and Uganda.<br><br>DATA SOURCES: Primary data from Emergency Events Database (EM-DAT), and comparative data from ReliefWeb, WHO Disease Outbreak News (WHO-DON), FloodList and Global Unique Disaster Identifier Number (GLIDE).<br><br>RESULTS: EM-DAT reported 228 natural hazards and disasters affecting 145.7&#x2009;million people; highest numbers reported in Uganda (n=48), Kenya (n=46), Somalia (n=38) and Ethiopia (n=35); 175 geophysical, hydrological, meteorological and climatological hazards reported, including 118 floods, 26 droughts, 11 storms and 17 landslides; 46 epidemics reported, primarily bacterial (eg, cholera) or viral (eg, yellow fever, measles) diseases, with 20% preceded by a flood, drought or landslide within the previous 3&#x2009;months. Reporting consistency and content varied considerably across the five databases.<br><br>CONCLUSION: Natural hazards and disasters affect millions of people. There is an urgent need to improve database connectedness to facilitate better monitoring and mapping, which can inform disease forecasting and decision tools to develop preparedness and intervention strategies.},
}
@article {pmid41249177,
year = {2025},
author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y},
title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {209},
pmid = {41249177},
issn = {2055-5008},
support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&amp;D Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; },
abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.},
}
@article {pmid41253877,
year = {2025},
author = {Wang, C and Lu, Y and Fang, C and Gan, X and Yang, L and He, S},
title = {Chromosome-level genome assembly of the Chinese algae eater Gyrinocheilus aymonieri.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1805},
pmid = {41253877},
issn = {2052-4463},
support = {91731301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170438//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {China ; *Chromosomes ; *Genome ; Molecular Sequence Annotation ; *Cypriniformes/genetics ; Animals ; Datasets as Topic ; },
abstract = {Gyrinocheilus aymonieri is endemic to Yunnan Province, China. Its mouth has evolved a specialized sucker-like structure as an adaptation to fast-flowing aquatic habitats, representing a remarkable evolutionary example of environmental adaptation. Here, we present a chromosome-level genome assembly of G. aymonieri (507 Mb) integrating HiFi, Illumina, and Hi-C sequencing data. The assembly comprises 24 chromosomes with 92.3% anchoring efficiency. Genome annotation revealed 23.02% repetitive elements, 24,078 protein-coding genes, and 55,943 transcript isoforms. The good genomic collinearity also demonstrates the accuracy of the G. aymonieri genome assembly at the macroscale. This high-quality genome will provide a crucial resource for understanding cypriniform evolution and different ecological adaptation mechanisms.},
}
@article {pmid41253964,
year = {2025},
author = {Yang, F and Wang, Z and Yang, X and Sun, Y and Wang, Q and Yu, X},
title = {Analyzing and predicting the effects of urban spatial planning on the gradient differentiation of production-living-ecological land and carbon storage.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40605},
pmid = {41253964},
issn = {2045-2322},
support = {ZR2021QD128//Shandong Provincial Natural Science Foundation/ ; },
abstract = {Carbon storage (CS) of terrestrial ecosystems is strongly associated with space utilization changes. However, effects of urban spatial planning on the spatio-temporal heterogeneity of production-living-ecological land (PLEL) and CS remain unclear. To bridge this gap, we developed a new PGIP framework that combines PLEL theory, gradient analysis, the InVEST model, and the PLUS model. This integrated approach offers a comprehensive tool for assessing and simulating how urban planning influences CS. We applied this framework in Jinan, China, where we defined four urban gradient zones to examine the gradient differentiation of PLEL and CS. By integrating dynamic driving factors and urban spatial planning, the PLEL and CS in 2030 were simulated under different scenarios. Results revealed significant gradient-based variations in PLEL between 1980 and 2020. The urban living land (ULL) within 10 km of the city center increased by 117.60%. The CS has decreased by 8.14 × 10[6] t, and the spatial heterogeneity of CS in the southeastern gradient zone was the strongest. More than 50% of the rise in CS resulted from the shift of rural living land to cultivated production land (CPL), while over 41% of the decrease in CS was caused by the conversion of CPL to ULL. By 2030, urban spatial planning is projected to significantly affect CS pattern, especially in downtown, far suburban, and southeastern gradient zone. Compared with unconstrained development scenario, under spatial planning-guided scenario, high-value clusters of CS will increase by 14.86 km[2], while low-value clusters will decrease by 3.99 km[2]. This study provides a spatially explicit, policy-relevant framework for understanding and planning CS across urban-rural gradients, integrating planning scenarios and mechanistic insights to support low-carbon land use strategies.},
}
@article {pmid41255279,
year = {2025},
author = {Mack, JM and Bely, AE},
title = {Regeneration physiology of invertebrates.},
journal = {The Journal of experimental biology},
volume = {228},
number = {22},
pages = {},
doi = {10.1242/jeb.250750},
pmid = {41255279},
issn = {1477-9145},
support = {//University of Maryland/ ; //University of Maryland/ ; IOS-1923429//National Science Foundation/ ; },
mesh = {Animals ; *Invertebrates/physiology ; *Regeneration/physiology ; },
abstract = {One of the great puzzles in biology is to understand the mechanisms underlying animal regeneration. Most recent efforts have used developmental and informatics approaches to understand how regenerated structures are formed, framing regeneration as a developmental outcome. However, regeneration is a complex process that also involves dynamic physiological mechanisms that support and fuel the rebuilding of lost structures. To develop a full understanding of regeneration, including how it relates to the ecology and evolution of organisms, it is essential to understand regeneration physiology. Despite the importance of physiological processes for regeneration, studies of regeneration focused on energetics, metabolism and environmental effects are scarce and have not been synthesized. This Review discusses the current understanding of regeneration physiology, focusing specifically on data from invertebrate animals where such information is especially dispersed and in need of synthesis. Considering data from diverse animal phyla, we review evidence for the consumption of different nutritional substrates during regeneration, summarize how aerobic and anaerobic metabolism appear to be broadly important to regeneration across animal phyla, and discuss how environmental and biotic factors can affect regeneration outcomes. We also introduce the concept of the 'physiological regeneration niche', describing the abiotic and biotic parameters where regeneration is possible, to expand consideration of regeneration in an ecological context. Significant gaps remain in understanding the physiological processes that underlie invertebrate regeneration, and we highlight some of these, including the need for broader taxonomic sampling, assessments of anaerobic metabolism during regeneration, investigations of multiple stressor effects on regeneration and comparisons between regenerators and non-regenerators.},
}
@article {pmid41256502,
year = {2025},
author = {Castillo-Neyra, R and Díaz, EW and Bellotti, BR and Morucci, K and De la Puente-León, M and Ortiz-Cam, L and Levy, MZ},
title = {Cave dogs around major urban areas threaten rabies elimination program.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41256502},
issn = {2692-8205},
support = {D43 TW012741/TW/FIC NIH HHS/United States ; K01 AI139284/AI/NIAID NIH HHS/United States ; R01 AI168291/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: In the city of Arequipa, Peru, the government has implemented control measures against dog rabies virus since the detection of its reintroduction in 2015. The city was previously considered free of animal reservoirs other than owned and stray dogs within its urban boundaries. However, multiple reports from peri-urban residents have suggested the presence of feral dogs living in caves on the city's outskirts. We aim to document the presence and dietary patterns of feral dogs adjacent to the city margins.<br><br>METHODS: We conducted monthly field visits to four peri-urban localities in eastern Arequipa, an area where the presence of feral dogs had been previously reported. Dog caves were identified by tracking footprints and other field signs left by dogs, and their locations were georeferenced. Each cave was revisited monthly three times to record the presence of live and dead dogs, and puppies. Fecal samples collected around the caves were analyzed to assess dietary patterns.<br><br>RESULTS: We observed that feral dogs use caves for resting, hiding, and reproduction-some of which appear to be constructed by the dogs themselves. The high number of puppies and dead adult dogs indicates a high population turnover. Dietary analysis revealed that these dogs feed on local fauna, including birds, rodents, cats, sheep, and, notably, other dogs.<br><br>CONCLUSIONS: These unowned, cave-dwelling dogs are not reached by mass rabies vaccination or sterilization programs. Moreover, they exist outside the jurisdiction of health inspectors responsible for rabies surveillance, resulting in a lack of data on rabies infection in this subpopulation. Our findings highlight the need for integrated One Health strategies to address the challenges posed by feral dog populations in rabies elimination efforts.},
}
@article {pmid41257449,
year = {2025},
author = {Wei, Y and Siddique, J and Spring, B and Hedeker, D},
title = {A Bayesian Two-Step Multiple Imputation Approach Based on Mixed Models for Missing EMA Data.},
journal = {Statistics in medicine},
volume = {44},
number = {25-27},
pages = {e70325},
pmid = {41257449},
issn = {1097-0258},
support = {P30 ES027792/ES/NIEHS NIH HHS/United States ; R01DK125414/DK/NIDDK NIH HHS/United States ; },
mesh = {Bayes Theorem ; Humans ; *Models, Statistical ; Computer Simulation ; *Ecological Momentary Assessment ; Data Interpretation, Statistical ; Linear Models ; Longitudinal Studies ; Logistic Models ; },
abstract = {Ecological Momentary Assessments (EMA) capture real-time thoughts and behaviors in natural settings, producing rich longitudinal data for statistical analyses. However, the robustness of these analyses can be compromised by the large amount of missing data in EMA studies. To address this, multiple imputation, a method that replaces missing values with several plausible alternatives, has become increasingly popular. In this article, we introduce a two-step Bayesian multiple imputation framework which leverages the configuration of mixed models. We adopt and compare: (1) the Random Intercept Linear Mixed model; (2) the Mixed-effect Location Scale (MELS) model which accounts for subject variance influenced by covariates and random effects; and (3) the Shared Parameter MELS model which additionally links the missing data to the response variable through a random intercept logistic model. Each of these three can be used to complete the posterior distribution within the framework. In the simulation study, we extend this two-step Bayesian multiple imputation strategy to handle simultaneous missing variables in EMA data and compare the effectiveness of the multiple imputations across the three mixed models. Our analyses highlight the advantages of multiple imputations over single imputations and underscore the importance of selecting an appropriate model for the imputation process. Specifically, modeling within-subject variance and linking the missingness mechanism to the response will greatly improve the performance in certain scenarios. Furthermore, we applied our techniques to the "Make Better Choices 1 (MBC1)" study, highlighting the distinction, in particular, of imputation results between the Random Intercept Linear Mixed model and the two MELS models in terms of modeling within-subject variance.},
}
@article {pmid41257544,
year = {2025},
author = {Agany, DD and Callegari, EA and Paez, MD and Pietri, JE},
title = {Multi-omics of cockroaches infected with Salmonella Typhimurium identifies molecular signatures of vector colonization.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {1118},
pmid = {41257544},
issn = {1471-2164},
support = {P20GM103443/NH/NIH HHS/United States ; R01 AI171014/AI/NIAID NIH HHS/United States ; R21 AI183477/AI/NIAID NIH HHS/United States ; P20 GM103443/GM/NIGMS NIH HHS/United States ; R01AI171014/NH/NIH HHS/United States ; },
mesh = {Animals ; *Salmonella typhimurium/physiology ; *Cockroaches/microbiology/genetics/metabolism ; *Proteomics/methods ; Host-Pathogen Interactions ; Transcriptome ; Gene Expression Profiling ; *Insect Vectors/microbiology/genetics ; Multiomics ; },
abstract = {BACKGROUND: German cockroaches (Blattella germanica) are prevalent indoor pests that have long been associated with the spread of enteric human pathogens. Recent work investigating the relationship between these insects and Salmonella enterica serovar Typhimurium (S. Typhimurium), a model pathogen of global concern, demonstrated that S. Typhimurium colonizes the cockroach gut. S. Typhimurium has a broad host range, but mechanistic molecular insight into how ecologically relevant invertebrate hosts interact with this pathogen is lacking. Here, we applied a multi-omic (transcriptomic and proteomic) approach to infected cockroaches to examine the molecular variables that govern cockroach-borne S. Typhimurium transmission.<br><br>RESULTS: Our results reveal enriched monocarboxylic acid transport and metabolism, increased long-chain fatty acid transport, increased triglyceride metabolism, and an increased response to reactive oxygen species and free radicals as host signatures of a metabolic shift in the cockroach gut during infection. Surprisingly, downregulation of the immune deficiency (IMD) pathway transcription factor relish, and upregulation of xenobiotic detoxification (glutathione-s-transferase) and known allergens (Blag5 &amp; Blag8, myosin, tropomyosin) were also evident in infected guts.<br><br>CONCLUSIONS: To our knowledge, this study is both the first omics study of enteric human pathogen infection in a cockroach vector and the first omics study of S. Typhimurium in an ecologically relevant insect host, representing a seminal contribution to the field of vector-borne infectious disease. This work provides novel fundamental knowledge regarding the response of insect hosts to S. Typhimurium infection and the evolution of vector-pathogen relationships with the potential to inform mitigation of the public health impacts of cockroaches.},
}
@article {pmid41258717,
year = {2025},
author = {Cheng, R and Lv, T and Ji, P and Ma, B and Wang, M and Matsumoto, H},
title = {Multi-omics analyses reveal the virulence differentiation underlying natural variation in Burkholderia gladioli.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {12},
pages = {e0168525},
pmid = {41258717},
issn = {1098-5336},
support = {2024SZRZDC130001//Natural Science Foundation of Hangzhou/ ; LD25C140002//Zhejiang Provincial Natural Science Foundation of China/ ; U21A20219//National Natural Science Foundation of China/ ; W2533054//National Natural Science Foundation of China/ ; 2024M762853//China Postdoctoral Science Foundation/ ; },
mesh = {*Burkholderia gladioli/genetics/pathogenicity ; *Oryza/microbiology ; Virulence/genetics ; *Plant Diseases/microbiology ; *Genetic Variation ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; Transcriptome ; Multiomics ; },
abstract = {UNLABELLED: Burkholderia gladioli is a critical pathogen causing bacterial panicle blight in rice, severely threatening global rice yield and grain quality. Here, B. gladioli strains were isolated and identified from two rice fields exhibiting markedly different severities of bacterial panicle blight. Although the two strains belong to the same species, they displayed significant differences in phenotype and pathogenicity. Comparative genomic and transcriptomic analyses revealed that natural variation between the strains not only arose from 79 single-nucleotide polymorphisms (SNPs), 12 insertions/deletions (INDELs), and 3 structural variations (SVs) across 27 mutated genes, which may affect protein function and stability, but also coincided with the significant downregulation of genes in multiple virulence-associated pathways, such as two-component systems, bacterial chemotaxis, quorum sensing, and flagellar assembly at the transcriptional level. The combined effects of genetic variation and transcriptional regulation ultimately contributed to the observed differences in pathogenicity. This study uncovers the potential mechanisms by which natural variation in B. gladioli influences pathogenicity, providing a theoretical basis and potential molecular targets for the precise control of rice bacterial panicle blight.<br><br>IMPORTANCE: This study demonstrates that natural variation in Burkholderia gladioli, a major pathogen responsible for bacterial panicle blight in rice, has a significant impact on its pathogenicity and further explores the underlying mechanisms. These findings expand our understanding of how phytopathogens' virulence differentiates conditions of natural variation, and provide potential molecular targets for the development of novel bactericides. The identification of low-virulence strains and their associated gene variations in this study offers both theoretical and practical foundations for ecological disease management and biocontrol of rice bacterial diseases, highlighting their importance for promoting precision agriculture and sustainable development.},
}
@article {pmid41259569,
year = {2025},
author = {Pereira, JFG and Nascimento, LFC},
title = {Preventable neonatal mortality in the state of São Paulo: a spatial approach.},
journal = {Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo},
volume = {43},
number = {},
pages = {e2024294},
pmid = {41259569},
issn = {1984-0462},
mesh = {Humans ; Brazil/epidemiology ; Infant, Newborn ; *Infant Mortality/trends ; Female ; Pregnancy ; Spatial Analysis ; Infant ; Socioeconomic Factors ; Prenatal Care/statistics &amp; numerical data ; Adolescent ; Apgar Score ; },
abstract = {OBJECTIVE: Identify spatial patterns for preventable neonatal deaths in municipalities in the state of São Paulo between the years of 2015 and 2019, looking for possible correlations with socioeconomic and demographic indices.<br><br>METHODS: This is an ecological study, with data obtained from the Department of Informatics of the Unified Health System (DATASUS), from the of Mortality Information System (SIM) and Live Birth Information System (SINASC), regarding preventable deaths due to adequate care for women during pregnancy, childbirth and for the newborns, were analysed. Proportions per thousand live births were built. The independent variables used were the proportion of adolescent mothers; insufficient number of antenatal consultations (0-6 consultations); low birthweight (500-2499 g); low Apgar score in the 1st and 5th minute of life (0-7), all of which were used to calculate the Univariate Moran Index (IMU). The Social Vulnerability Index (SVI) and the Municipal Human Development Index (MHDI) were used to calculate the Bivariate Moran Index (IM). The Univariate and Bivariate Moran's indexes were calculated, thematic maps and box maps were constructed, and a significance level of &#x3b1; < 5% was adopted.<br><br>RESULTS: There were four thematic maps, and three box maps created to analyse the dependent variables, mentioned above. SVI and MHDI, inadequate antenatal care and reduced Apgar score at the 1st and 5th minute showed IM significant with preventable deaths in the neonatal population. A concentration of preventable deaths was identified in the southern region of the state.<br><br>CONCLUSIONS: The data presented can support municipal managers, demonstrating the need for investment in maternal and child health.},
}
@article {pmid41260397,
year = {2026},
author = {Abbasi, E},
title = {Metagenomic surveillance of emerging viruses in mosquito populations from high-risk regions of Iran.},
journal = {Journal of virological methods},
volume = {340},
number = {},
pages = {115301},
doi = {10.1016/j.jviromet.2025.115301},
pmid = {41260397},
issn = {1879-0984},
mesh = {Animals ; Iran/epidemiology ; *Culicidae/virology ; *Metagenomics ; Phylogeny ; *Arboviruses/genetics/classification/isolation &amp; purification ; *Mosquito Vectors/virology ; *Virome ; High-Throughput Nucleotide Sequencing ; Epidemiological Monitoring ; Computational Biology ; RNA, Viral/genetics ; },
abstract = {BACKGROUND: Mosquito-borne arboviruses pose a growing threat to public health, particularly in ecologically vulnerable and climatically dynamic regions. This study aimed to investigate the diversity of emerging arboviruses in mosquito populations from high-risk provinces in southern and southeastern Iran using a metagenomic surveillance approach.<br><br>METHODS: Adult mosquitoes were collected from 36 sites across Hormozgan, Sistan and Baluchestan, and Khuzestan provinces. Specimens were pooled by species and location, followed by RNA extraction and high-throughput sequencing. Bioinformatics analysis was performed to identify viral taxa and assess phylogenetic relationships.<br><br>RESULTS: A total of 4275 mosquitoes representing six species were analyzed. Virome analysis revealed 43 viral taxa, including medically important arboviruses such as dengue virus serotype 2 (DENV-2), chikungunya virus (CHIKV), and West Nile virus (WNV). Multiple novel viral sequences were also detected, including putative members of Phenuiviridae and Orthomyxoviridae. Viral diversity was highest in Hormozgan province and positively correlated with ambient temperature.<br><br>CONCLUSION: This study provides the first comprehensive metagenomic insight into mosquito viromes in Iran, revealing both endemic and potentially novel arboviruses. These findings underscore the need for integrated genomic surveillance and regional vector-borne disease preparedness.},
}
@article {pmid41261182,
year = {2025},
author = {Prusty, G and Prasad, BR and Polaki, S and Mereddy, S},
title = {Integrative multi-omics characterization of the gut microbiome in Pila globosa: functional insights into nutrient cycling and detoxification potential.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {12},
pages = {464},
pmid = {41261182},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metagenomics/methods ; Proteomics/methods ; *Snails/microbiology ; Phylogeny ; Metagenome ; Multiomics ; },
abstract = {Pila globosa, a freshwater snail endemic to Indian aquatic ecosystems, plays a pivotal role in nutrient cycling and organic matter turnover. In this study, we present the first integrative multi-omics characterization of its gut microbiome using shotgun metagenomics, metaproteomics, and genome-resolved analyses. The gut microbiota was taxonomically diverse yet compositionally stable, dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with core genera including Pseudomonas, Clostridium, Bacillus, and Streptomyces. Alpha diversity metrics (Shannon = 4.22 ± 0.15; Simpson = 0.90 ± 0.01) and low Bray-Curtis dissimilarity (0.12-0.15) indicated a conserved core microbiome across replicates. Functional profiling through HUMAnN2 and metaproteomic validation revealed enrichment of pathways related to carbohydrate metabolism, short-chain fatty acid (SCFA) synthesis, amino-acid biosynthesis, and oxidative phosphorylation, reflecting the community's contribution to host nutrition and metabolic balance. Genes and proteins associated with xenobiotic degradation (benzoate, toluene metabolism) and oxidative stress response (superoxide dismutase, catalase, glutathione S-transferase) were abundant, suggesting microbial support for redox regulation and detoxification. Twelve high-quality metagenome-assembled genomes (MAGs) reconstructed from dominant taxa encoded traits for secondary metabolite production, metal resistance, and stress tolerance, underscoring their ecological versatility. Together, these results establish a foundational reference for understanding the functional potential of the P. globosa gut microbiome and its possible role in nutrient transformation and pollutant processing in freshwater systems. The study provides baseline data for future comparative and ecotoxicological investigations of gastropod holobionts.},
}
@article {pmid41261732,
year = {2026},
author = {Fullam, A and Letunic, I and Maistrenko, OM and Castro, AA and Coelho, LP and Grekova, A and Schudoma, C and Khedkar, S and Robbani, M and Kuhn, M and Schmidt, TSB and Bork, P and Mende, DR},
title = {proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D852-D857},
pmid = {41261732},
issn = {1362-4962},
support = {FT230100724//Australian Research Council/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; LIBIS/de.NBI//Ministry of Science, Research and Art Baden-W&#xfc;rttemberg/ ; //MEXT/ ; //Keio University/ ; },
mesh = {*Molecular Sequence Annotation/methods ; *Genome, Bacterial ; *Software ; *Databases, Genetic ; *Genomics/methods ; *Genome, Archaeal ; *Genome, Microbial ; Multigene Family ; },
abstract = {The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands robust quality control and consistent annotation pipelines to ensure meaningful biological insights. proGenomes4 (prokaryotic Genomes v4) addresses this challenge by providing a resource of nearly 2 million high-quality microbial genomes, a doubling in scale from previous versions, encompassing over 7 billion genes. Each genome underwent rigorous quality assessment and comprehensive functional annotation by applying multiple standardized annotation workflows, including the systematic identification of mobile genetic elements and biosynthetic gene clusters. proGenomes4 contains 32 887 species with ecological habitat metadata as well as precomputed pan-genomes. This substantially expanded resource provides the microbiology community with a foundation for large-scale comparative studies and is freely accessible via a newly developed command line interface and at https://progenomes.embl.de/.},
}
@article {pmid41261971,
year = {2025},
author = {Ye, JF and Liu, PL and Guo, H},
title = {Disparities in Healthcare Services Efficiency and Patient-Provider Communication Quality Among Deaf and Hard-of-Hearing Patients in the U.S.: A Multi-Year Cross-Sectional Analysis (2017-2020).},
journal = {Health communication},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/10410236.2025.2589346},
pmid = {41261971},
issn = {1532-7027},
abstract = {The marginalization of the Deaf and Hard of Hearing (D/HH) group arises from barriers at multiple levels of the socio-ecological matrix. This is primarily reflected in challenges related to effective healthcare services delivery and high-quality patient-provider communication. Utilizing national data from the Health Information National Trends Survey (HINTS) from 2017 to 2020, we examined the difference between D/HH adults and hearing-abled adults in terms of healthcare services efficiency, patient-provider communication quality, health self-efficacy, and psychological health. The findings revealed that D/HH adults consistently exhibited lower levels than hearing adults in healthcare services efficiency, health self-efficacy, and psychological health, and these differences remained evident from 2017 to 2020. However, the difference in patient-provider communication quality between the two groups was not significant. The study further investigates health self-efficacy as a potential mediator influencing the efficiency of healthcare services and quality of patient-provider communication in their relationship with psychological health. Our findings highlight the imperative to devise specialized communication strategies and enhance healthcare services for the D/HH group.},
}
@article {pmid41262554,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Dot Moth, Melanchra persicariae (Linnaeus, 1761).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {190},
pmid = {41262554},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Melanchra persicariae (the Dot Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 647.9 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 15.4 kilobases in length.},
}
@article {pmid41263111,
year = {2026},
author = {Feng, X and Li, Y and Zheng, J and Chen, X and Yang, S and Chen, Y and Li, SC},
title = {MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D842-D851},
pmid = {41263111},
issn = {1362-4962},
support = {C2004-23Y//Young Collaborative Research/ ; JCYJ20220818101201004//Shenzhen Science and Technology Program/ ; 32300527//National Natural Science Foundation of China/ ; 32470695//National Natural Science Foundation of China/ ; 2022A1515110784//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303040004//Key-Area Research and Development Program of Guangdong Province/ ; TC2024JC43//Basic Research Programs of Taicang, 2024/ ; //Shenzhen-Hong Kong Institute of Brain Science/ ; //SIAT-HKUST Joint Laboratory of Brain Science/ ; },
mesh = {*Molecular Sequence Annotation ; Archaea/genetics ; *Databases, Genetic ; Fungi/genetics ; Genome, Viral ; Genome, Archaeal ; Bacteria/genetics ; Viruses/genetics ; *Genomics/methods ; *Software ; Genome, Fungal ; Genome, Bacterial ; Computational Biology/methods ; Metagenome ; },
abstract = {Microorganisms, including bacteria, archaea, fungi, and viruses, are the most taxonomically diverse and ecologically dominant life forms on Earth, playing critical roles in ecosystems, human health, and industrial applications. While existing microbial databases such as BV-BRC and IMG archive both monoisolate and metagenome-assembled genomes (MAGs) across domains, challenges remain in standardized, multi-level annotations and interactive tools for all microbial groups. Here, we present MicrobialScope (https://microbial.deepomics.org/), a comprehensive microbial genomic platform that integrates large-scale genome collections, multilevel annotations, and interactive visualizations. MicrobialScope harbors 2 411 503 bacterial, 24 472 archaeal, 20 203 fungal, and 188 267 viral genomes derived from both monoisolate assemblies and MAGs. Integrating 15 state-of-the-art bioinformatics tools and 10 specialized databases, MicrobialScope provides extensive annotations encompassing basic genomic features, genomic element prediction (e.g., genes, tRNAs, tmRNAs, CRISPR-Cas and anti-CRISPR elements, secondary metabolite biosynthetic clusters, signal peptides, and transmembrane proteins), and functional and structural annotations. This includes 1 072 114 935 proteins with diverse annotations, 24 640 186 tRNAs and tmRNAs, 140 888 CRISPR-Cas systems, 173 256 anti-CRISPR elements, 105 121 secondary metabolite biosynthetic clusters, 13 235 096 signal peptides, and 50 811 729 transmembrane proteins. In addition, MicrobialScope offers unrestricted access to all data resources, interactive visualization tools, and built-in online analytical modules for intuitive exploration and comparative analysis. With its extensive genome collection, comprehensive annotations, and user-friendly interface, MicrobialScope serves as a scalable platform to advance genome research across diverse microbial domains.},
}
@article {pmid41264985,
year = {2026},
author = {Singh, CL and Spuur, K and Rose, L and Jones, D and Irwin, P and Yun, J},
title = {Documentation of contrast hypersensitivity reactions: a socio-ecological scoping review.},
journal = {European journal of radiology},
volume = {194},
number = {},
pages = {112539},
doi = {10.1016/j.ejrad.2025.112539},
pmid = {41264985},
issn = {1872-7727},
mesh = {Humans ; *Contrast Media/adverse effects ; *Documentation/statistics &amp; numerical data/standards ; *Drug Hypersensitivity/epidemiology/diagnosis ; },
abstract = {PURPOSE: To investigate the critical yet often overlooked challenge of documentation of hypersensitivity reactions to contrast media. Inaccurate documentation not only informs future imaging events but also impacts other areas in medicine. This study applies Bronfenbrenner's adapted socio-ecological model to examine the literature related to contrast hypersensitivity documentation, highlighting systemic issues that perpetuate suboptimal practice.<br><br>METHOD: A scoping review was conducted following the Arksey and O'Malley framework with adaptations for a socio-ecological lens. A search was conducted across Ovid MEDLINE, SCOPUS, ProQuest and CINAHL Plus (2000-present), identifying 673 articles. Seven studies met the inclusion criteria and were analysed using NVIVO software to identify key themes across Bronfenbrenner's system levels of micro, meso, exo, macro and chrono.<br><br>RESULTS: Findings revealed inconsistencies in documentation practices across all levels of healthcare. At the micro level, patient-practitioner communication is often hindered by the patient's inability to provide an accurate history. At the meso and macro levels, fragmented systems, lack of interoperability and inconsistent terminology contribute to the problem. At the chrono level, the impact of the evolution of documentation practices, standards, and policies over time have influenced current practices. This includes perpetuating a cycle of inaccurate information being utilised in clinical decision making, compromising patient outcomes and increasing healthcare costs.<br><br>CONCLUSION: This review is the first to highlight the systemic nature of contrast hypersensitivity documentation challenges using the socio-ecological lens. All medical and allied professionals who document and communicate medical histories can break this self-perpetuating cycle with simple actions such as accurately recording of contrast agent name, details of the reaction, severity, treatment and timelines. Further research is required to develop strategies to drive systemic change, ultimately to benefit patient safety.},
}
@article {pmid41266326,
year = {2025},
author = {Stanislawski, MA and Litkowski, E and Arehart, CH and Luo, K and Gilmore, N and Lange, LA and Lange, EM and Barnes, K and Avery, CL and Meyer, KA and Holguin, F and North, KE and Burk, RD and Kaplan, RC},
title = {Relationships among host genetics, gut microbiota, and asthma in US Hispanic/Latino adults.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10223},
pmid = {41266326},
issn = {2041-1723},
support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; R01 DK120870/DK/NIDDK NIH HHS/United States ; N01 HC065236/HL/NHLBI NIH HHS/United States ; K01HL157658//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01 HL105756/HL/NHLBI NIH HHS/United States ; R61 HL157069/HL/NHLBI NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; N01 HC065237/HL/NHLBI NIH HHS/United States ; R01HL136266//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HHSN268200625235C//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R33 HL157069/HL/NHLBI NIH HHS/United States ; N01 HC065233/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; N01 HC065235/HL/NHLBI NIH HHS/United States ; R01 DK119268/DK/NIDDK NIH HHS/United States ; R01HL157069//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI152504//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 1OT3HL14715//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; OT3 HL147154/HL/NHLBI NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; N01 HC065234/HL/NHLBI NIH HHS/United States ; R01 AI152504/AI/NIAID NIH HHS/United States ; R01 DK134672/DK/NIDDK NIH HHS/United States ; R01 AG085320/AG/NIA NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; K01 HL157658/HL/NHLBI NIH HHS/United States ; R01 HL136266/HL/NHLBI NIH HHS/United States ; R01MD011389//U.S. Department of Health &amp; Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; },
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Asthma/genetics/microbiology/epidemiology/ethnology ; Body Mass Index ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Hispanic or Latino/genetics ; Obesity/microbiology/genetics/complications ; Risk Factors ; United States/epidemiology ; },
abstract = {Asthma is a heterogeneous condition that is often comorbid with obesity and influenced by diverse risk factors. Elucidating the association of gut microbial characteristics with asthma could improve our understanding of the pathophysiology. Here, we investigate relationships of host genetics and stool microbiota characteristics with asthma among US Hispanic/Latino adults, while considering the influence of obesity status, using host whole genome sequencing and stool shotgun metagenomic microbiota data from participants of the Hispanic Community Health Study/Study of Latinos. We evaluate cross-sectional associations of microbiota characteristics with asthma and analyse whether they are modified by obesity status (body mass index≥30 kg/m[2]). We assess differences in alpha diversity, beta diversity, and taxonomic abundance with asthma, independent of obesity, and interactions between asthma and obesity using covariate-adjusted regression-based methods. We generate an asthma polygenic risk score (PRS) and compare the classification accuracy of genetic and microbial factors for asthma status. We report that asthma is associated with differences in overall taxonomic composition (beta diversity; p = 0.001), which is not dependent on obesity status (p = 0.31). Asthma is not associated with alpha diversity metrics (p > 0.17), though obesity is associated with lower alpha diversity (p < 0.01). We identify multiple taxa that are associated with asthma, including decreased abundance of Lactobacillus and Enterococcus species, and some taxonomic associations vary by obesity status. Compared to models including baseline risk factors and an asthma PRS, microbial information improves classification accuracy of asthma (p = 0.04). Our results support that there are microbiota characteristics associated with asthma in Hispanic/Latino adults independent of obesity.},
}
@article {pmid41270500,
year = {2025},
author = {Li, C and Chen, Z and Chen, L and Yu, J and Wang, Z and Wang, G},
title = {Multi-omics insight into the adaptation mechanism of desert cyanobacterium Chroococcidiopsis sp. ASB-02 under salinity stress.},
journal = {Plant physiology and biochemistry : PPB},
volume = {229},
number = {Pt D},
pages = {110769},
doi = {10.1016/j.plaphy.2025.110769},
pmid = {41270500},
issn = {1873-2690},
mesh = {*Cyanobacteria/metabolism/genetics/physiology ; *Salt Stress ; Desert Climate ; *Adaptation, Physiological ; Salt Tolerance ; Salinity ; Phylogeny ; Multiomics ; },
abstract = {Soil salinity is an environmental stress severely restricting organism growth and causing ecological deterioration. However, Chroococcidiopsis sp. can grow in various salt-rich deserts and is known for extreme environmental tolerance. Currently, there is little information about its salt adaptation mechanism. To address this issue, we conducted investigation at multiple levels, including phylogenetics, physiology, transcriptomics, and metabolomics, to gain understanding of its evolution, degree of salt tolerance, and study salt adaptation mechanism of Chroococcidiopsis sp. ASB-02. The results showed that Chroococcidiopsis sp. ASB-02 exhibited high survival rates under high salt stress and could grow even in 600 mM NaCl, which is 3-6 times than the salt limit of other desert cyanobacteria. Multi-omics analyses revealed that high salt enhanced the expression of PSII repair genes, activated SuS sucrose synthesis and TreS trehalose synthesis pathways, which help to reduce PSII damage, maintaining stable PSII activity, and facilitating osmoregulation. In addition, in response to higher salt concentration (600 mM NaCl), Chroococcidiopsis sp. ASB-02 activated Na[+]/H[+] transporters and ion channel genes to regulate intracellular ion concentrations. To counter salt-induced oxidative stress, Chroococcidiopsis sp. ASB-02 employed distinct antioxidant strategies based on salt concentration. At 300 mM NaCl, sodA2 and katG genes mainly played roles, whereas at 600 mM NaCl, gor2 and grxB of glutaredoxin system, as well as trxB and ntrC of thioredoxin system played key roles in mitigating oxidative damage. This study clarified the salt adaptation mechanism of Chroococcidiopsis sp. ASB-02 and revealed crucial biological pathways with multi-omics insight, which may be helpful to develop salinization bioremediating with cyanobacteria.},
}
@article {pmid41271865,
year = {2025},
author = {Pottier, P and Oh, RRY and Pollo, P and Rivera-Villanueva, AN and Yang, Y and Varon, S and Longo, AV and Burke, S and Lin, HY and Valdebenito, JO and Amano, T and Drobniak, SM and Nakagawa, S and Claunch, N},
title = {AmphiTherm: a comprehensive database of amphibian thermal tolerance and preference.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1987},
pmid = {41271865},
issn = {2052-4463},
support = {Scientia PhD Scholarship//University of New South Wales (UNSW Australia)/ ; Scientia PhD scholarship//University of New South Wales (UNSW Australia)/ ; DP230101248//Department of Education and Training | Australian Research Council (ARC)/ ; FT220100276//Department of Education and Training | Australian Research Council (ARC)/ ; FT180100354//Department of Education and Training | Australian Research Council (ARC)/ ; DE180100202//Department of Education and Training | Australian Research Council (ARC)/ ; UPD2024-0239//Wenner-Gren Foundation (Wenner-Gren Foundation for Anthropological Research, Inc.)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; IOS-2011278//National Science Foundation (NSF)/ ; 2109663//National Science Foundation (NSF)/ ; 3220722//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (National Fund for Scientific and Technological Development)/ ; },
mesh = {Animals ; *Amphibians/physiology ; *Thermotolerance ; Biodiversity ; Databases, Factual ; },
abstract = {Thermal traits are crucial to our understanding of the ecology and physiology of ectothermic animals. While rising global temperatures have increasingly pushed research towards the study of upper thermal limits, lower thermal limits and thermal preferences are essential for defining the thermal niche of ectotherms. Through a systematic review of the literature in seven languages, we expanded an existing database of amphibian heat tolerance by adding 1,009 estimates of cold tolerance and 816 estimates of thermal preference across 375 species. AmphiTherm is a comprehensive and reproducible database that contains 4,899 thermal trait estimates from a diverse sample of 659 species (~7.5% of all described amphibians) spanning 38 families. Despite its broad geographic coverage, we report evident gaps across amphibian biodiversity hotspots in Africa, most regions of Asia, central South America, and Western Australia. By providing a more holistic understanding of amphibian thermal tolerance and preferences, AmphiTherm is a valuable resource for advancing research in evolutionary biology, ecophysiology, and biogeography of amphibians, offering insights that are increasingly needed in changing climates.},
}
@article {pmid41275375,
year = {2025},
author = {Su, Z and Zhang, X and Wang, Q and Tang, Q and Yang, D and Liu, Y},
title = {amplysis: an R package for microbial composition and diversity analysis using 16S rRNA amplicon data.},
journal = {Briefings in functional genomics},
volume = {24},
number = {},
pages = {},
pmid = {41275375},
issn = {2041-2657},
support = {//Guangxi Education Agency/ ; //Guangxi Province Talent Project/ ; 42377012//National Natural Science Foundation of China/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Software ; *Microbiota/genetics ; *Computational Biology/methods ; Biodiversity ; Bacteria/genetics/classification ; },
abstract = {The downstream analysis of 16S rRNA sequencing data remains a significant challenge for researchers lacking extensive bioinformatics expertise, often requiring proficiency in diverse tools and methodologies. To address this, we present amplysis, an R package designed to streamline the analysis and visualization of 16S rRNA amplicon sequencing data through an intuitive, code-light workflow. amplysis integrates data importing, processing, statistical analysis, and visualization into a unified framework. Key features include data normalization, microbial composition profiling, alpha/beta diversity analysis, ordination methods (e.g. Principal Component Analysis), and publication-ready visualization tools. The package's utility was demonstrated through three case studies, one of which analyzed microbial community responses to hexachlorocyclohexane (HCH) degradation in groundwater environments. Using amplysis, we efficiently generated phylum/genus-level abundance plots, alpha-diversity indices, and Principal Coordinates Analysis ordination, revealing significant shifts in community structure and diversity under HCH stress. The other case studies utilized publicly available data from published studies by other researchers. These results underscore the package's ability to simplify complex analyses while ensuring reproducibility and high-quality output. By integrating modular, user-friendly functions, amplysis lowers the barrier to robust microbiome data exploration. The package is available on GitHub (https://github.com/min-perilla/amplysis), offering a valuable resource for researchers in microbial ecology and environmental genomics.},
}
@article {pmid41276033,
year = {2026},
author = {Liu, XY and He, FX and Qu, TC and Weng, ZH and Li, PF and Ye, J and Fu, HY},
title = {Integrated physiological and multi-omics insights into Chlorella mutagenized by atmospheric and room temperature plasma for enhanced saline aquaculture wastewater treatment and bioresource production.},
journal = {Bioresource technology},
volume = {442},
number = {},
pages = {133694},
doi = {10.1016/j.biortech.2025.133694},
pmid = {41276033},
issn = {1873-2976},
mesh = {*Chlorella/genetics/physiology/metabolism/drug effects ; *Wastewater/chemistry ; *Aquaculture/methods ; *Water Purification/methods ; *Mutagenesis ; *Plasma Gases/pharmacology ; Nitrogen ; Salinity ; Photosynthesis ; Temperature ; Biological Oxygen Demand Analysis ; Phosphorus ; *Metabolomics/methods ; Chlorophyll/metabolism ; Multiomics ; },
abstract = {The salinity of aquaculture wastewater varies considerably across farming systems, limiting the applicability of conventional Chlorella strains. To enhance salt tolerance and application potential, atmospheric and room temperature plasma (ARTP) mutagenesis was employed for its high mutation efficiency and ability to generate genetically stable mutants via a non-thermal plasma process. Among five mutant strains evaluated, strain AMC-2 exhibited the best performance, with enhanced growth, photosynthesis, nutrient removal, and bioresource accumulation. Within 8 days, strain AMC-2 removed over 90 % of total nitrogen (TN) and total phosphorus (TP) and chemical oxygen demand (COD), with algal density and chlorophyll content increased by 110 % and 134 %, respectively. The maximum quantum yield of PSII photochemistry reached 0.78, and the maximum electron transport rate increased by 69 %. Protein, polysaccharide, and lipid contents were also elevated by 83 %, 32 %, and 12 %, respectively. Compared to the wild-type, transcriptomic and metabolomic analyses of AMC-2 revealed coordinated upregulation of key genes (e.g., LHCB1, rbcS, ALDO, GOT2, Nrt, and NR) and elevated levels of metabolites such as citric acid, isocitric acid, γ-aminobutyric acid, and glycerophospholipids. These changes indicate systemic reprogramming of photosynthesis, carbon and nitrogen metabolism, and membrane composition. Functional validation in saline aquaculture wastewater demonstrated that AMC-2 sustained stable growth, photosynthetic activity, and nutrient removal at salinities up to 15 ppt, confirming its enhanced environmental adaptability. Collectively, these results highlight AMC-2 as a promising microalgal candidate for integrated bioremediation and bioresource production in brackish aquaculture systems, and exemplify the effectiveness of ARTP mutagenesis for improving microalgal performance under challenging conditions.},
}
@article {pmid41276529,
year = {2025},
author = {Martin, C and Gitter, A and Anantharaman, K},
title = {Protein Set Transformer: a protein-based genome language model to power high-diversity viromics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11123},
pmid = {41276529},
issn = {2041-1723},
support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; R35GM143024//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Genome, Viral/genetics ; *Genomics/methods ; *Viruses/genetics ; *Viral Proteins/genetics/chemistry/metabolism ; Capsid Proteins/genetics ; },
abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperforms other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrates protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.},
}
@article {pmid41277831,
year = {2025},
author = {Rahmdel, S and Türkoglu, T and Nikjoo, N and Babaali, E and Moradi Mirhesari, D and Nega, M and Brüggemann, H and Huang, L and Witte Paz, M and Nieselt, K and Götz, F},
title = {Beyond commensalism: genomic insights into micrococcin P1-producing Staphylococcus chromogenes.},
journal = {mSphere},
volume = {10},
number = {12},
pages = {e0073325},
pmid = {41277831},
issn = {2379-5042},
support = {Germany's Excellence Strategy-EXC 2124-390838134 'Controlling Microbes to Fight Infections' (CMFI)//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Bacteriocins/genetics/biosynthesis/pharmacology ; *Staphylococcus/genetics/metabolism ; Animals ; *Genome, Bacterial ; Multigene Family ; Whole Genome Sequencing ; Female ; Symbiosis ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Genomics ; Staphylococcal Infections/microbiology/veterinary ; Cattle ; Virulence/genetics ; Microbial Sensitivity Tests ; },
abstract = {UNLABELLED: Staphylococcus chromogenes (S. chromogenes) is a predominant non-aureus staphylococcal species colonizing the teat skin and mammary gland of dairy ruminants. Although often linked to mild or subclinical mastitis, specific strains may also play protective roles against major udder pathogens. In this study, we characterized two S. chromogenes isolates (4S77 and 4S90) that displayed antimicrobial activity against Gram-positive bacteria. Complete genome sequencing revealed a conserved, plasmid-encoded biosynthetic gene cluster for the thiopeptide bacteriocin micrococcin P1 (MP1). All genes necessary for MP1 biosynthesis, modification, export, and immunity were identified, and compound production was confirmed by high-performance liquid chromatography and liquid chromatography-mass spectrometry. Comparative analysis with publicly available S. chromogenes genomes revealed that the MP1 cluster appears unique to these isolates. Both strains showed full phenotypic susceptibility to tested antibiotics, despite 4S90 carrying the lnuA gene, which did not confer detectable resistance under standard conditions. Classical staphylococcal toxin genes were also absent. Virulence gene profiling revealed a conserved repertoire of colonization- and persistence-associated genes, including factors involved in adhesion, capsule formation, and iron acquisition, but no markers of aggressive pathogenicity. Mobile genetic elements, including prophages and genomic islands, were common but did not carry antimicrobial resistance or virulence genes, suggesting a low risk of transmission of new pathogenic traits to the endogenous microbiome, including opportunistic bacteria. These findings suggest that MP1-producing S. chromogenes strains combine antimicrobial functionality with low virulence potential, highlighting their potential ecological role as protective commensals on the teat skin and in the broader mammary ecosystem of dairy ruminants.<br><br>IMPORTANCE: Staphylococcus chromogenes is one of the most prevalent bacteria isolated from the mammary glands of dairy animals and is primarily considered a causative agent of subclinical mastitis. However, certain strains may also act as microbial competitors that inhibit more harmful pathogens. In this study, we identified two goat-derived S. chromogenes strains that produce micrococcin P1 (MP1), a potent antimicrobial compound effective against Gram-positive bacteria, including major mastitis pathogens. Genomic and phenotypic analyses revealed that these strains possess low virulence potential and retain antibiotic susceptibility, suggesting a possible protective role within the mammary microbiome. This is the first report of MP1 production in this species. Our findings highlight the functional diversity within S. chromogenes and suggest its potential application in microbiota-based strategies for mastitis prevention and antimicrobial stewardship in livestock.},
}
@article {pmid41278531,
year = {2024},
author = {Morales, HE and van Oosterhout, C and Whitford, H and Tatayah, V and Ruhomaun, K and Groombridge, JJ and Gilbert, MTP and , and , and , and , },
title = {The genome sequence of the Pink Pigeon, Nesoenas mayeri (Prévost, 1843).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {336},
pmid = {41278531},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Nesoenas mayeri (the Pink Pigeon; Chordata; Aves; Columbiformes; Columbidae). The genome sequence is 1,183.3 megabases in span. Most of the assembly is scaffolded into 40 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.97 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,730 protein coding genes. The primary assembly achieves the Earth Biogenome Project reference standard of 6.C.Q62.},
}
@article {pmid41278536,
year = {2025},
author = {Petrovič, M and Bartas, M and Garratt, AN and Pečinka, P and Dobrovolná, M and Koňaříková, K and Trenz, O and Brázda, V and Šťastný, J},
title = {Z-DNA Hunter tool for straightforward detection of Z-DNA forming regions and a case study in Drosophila.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf166},
pmid = {41278536},
issn = {2631-9268},
mesh = {Animals ; *Drosophila melanogaster/genetics ; *Software ; Algorithms ; Genome, Insect ; DNA ; },
abstract = {Z-DNA is a left-handed DNA conformation linked to gene regulation, chromatin dynamics, and immunity. Despite its importance, genome-wide prediction of Z-DNA forming sequences (ZFS) remains limited by the absence of fast and accessible tools. Here, we present Z-DNA Hunter, a user-friendly web server for genome-scale ZFS prediction utility. The algorithm employs a pattern-based approach optimized for canonical motifs such as (GC)n and (CA)n repeats, with adjustable parameters for detection stringency. Compared with existing methods, Z-DNA Hunter achieves similar or higher accuracy while reducing runtime from hours to seconds, making large-scale analyses feasible. To demonstrate its application, we analyzed the Drosophila melanogaster genome and uncovered a pronounced enrichment of long ZFS on the X chromosome, contrasting with their near absence on the satellite repeat- and transposable element-rich Y chromosome. These findings illustrate both the scalability of Z-DNA Hunter and its potential to reveal biologically meaningful patterns of non-B-DNA. The tool provides direct visualization and export options (e.g. BedGraph for UCSC Genome Browser) and is freely available at https://bioinformatics.ibp.cz/#/analyse/zdna.},
}
@article {pmid41278887,
year = {2025},
author = {Rühlemann, M and Szánthó, LL and Waschina, S and Moitinho-Silva, L and Mews, LK and Camarena, JF and Jebens, H and Costa, J and Juimo, V and Fezeu, A and Agyei, A and Afihene, MY and Asibey, SO and Awuku, YA and Duah, A and Nartey, YA and Ibrahim, F and Lim, YAL and Pin, TM and Onyekwere, C and Rusine, J and Mwikarago, IE and Baines, J and Franke, A and Szöllősi, GJ and Xavier, R and Alm, EJ and Groussin, M and Poyet, M},
title = {Convergent genomic responses of human gut bacteria to variations in industrialization.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41278887},
issn = {2692-8205},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; },
abstract = {To what extent gut bacteria respond to the distinct ecological pressures imposed by human lifestyle remains unclear. Here, we investigate how genomic adaptation in gut bacteria differ between industrialized and non-industrialized human populations. We generated a broad collection of isolate genomes spanning diverse host geographies, lifestyles, species, and strains. We first found that compared to MAGs, paired isolate genomes recover more functional elements and signals of horizontal gene transfers (HGTs). Leveraging isolate genomes from multiple species, we find that strains from industrialized hosts experience an expansion of proteome size and harbor greater pangenome fluidity, driven by recent events of HGTs. Gene- and variant-level analyses reveal convergent patterns of lifestyle-specific adaptation in functions that are critical for ecological adaptation, such as stress response, cell envelope remodeling and central metabolism. Our results demonstrate that industrialization imprints evolutionary signatures on gut bacterial genomes, illuminating the effects of rapidly changing environments on human biology.},
}
@article {pmid41279534,
year = {2025},
author = {McCrone, JT and Baele, G and Omah, IF and Kinganda-Lusamaki, E and Brew, JA and Carvalho, LM and Dudas, G and Mbala-Kingebeni, P and Suchard, MA and Rambaut, A},
title = {Evidence of latency reshapes our understanding of Ebola virus reservoir dynamics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41279534},
issn = {2692-8205},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; },
abstract = {Ebola virus (EBOV) has caused severe outbreaks of haemorrhagic fever in Central and West Africa since the first observed zoonotic epidemic in the late 1970s. While recent outbreaks have revealed much about the epidemiological dynamics that sustain human-to-human transmission, the mechanisms by which the virus persists between outbreaks are unknown. Previously, phylogenetic approaches have been used to characterise the EBOV reservoir from the evolutionary relationships among observed human outbreaks. We here employ a novel phylogenetic latency model - inspired by recent observations of extreme EBOV evolutionary rate heterogeneity in humans - to characterise the natural history of EBOV and by extension its reservoir. We find the prevailing model of EBOV reservoir dynamics is deficient, and the long-term EBOV evolutionary rate is slower than previously believed. The hypothesis that EBOV diversity dates back to a bottleneck event just prior to the first human outbreak is not supported by the data. Further, our results suggest that EBOV undergoes extended periods of quiescence in the reservoir, similar to that observed in a small fraction of human infections. These findings have significant implications for understanding the source of EBOV outbreaks, characterising the EBOV reservoir, and uncovering the factors that contribute to EBOV outbreaks in humans.},
}
@article {pmid41279688,
year = {2025},
author = {Tchourine, K and Carballo-Pacheco, M and Vitkup, D},
title = {Macroecological Laws Can Naturally Arise from Chaotic Internal Species Dynamics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41279688},
issn = {2692-8205},
support = {R01 DK118044/DK/NIDDK NIH HHS/United States ; R35 GM131884/GM/NIGMS NIH HHS/United States ; },
abstract = {Macroecological relationships that connect various statistical descriptors of long-term and short-term species dynamics represent some of the most general laws in ecology and biology. These macroecological laws have been observed across diverse ecologies of plants and animals, and more recently, also in microbiota. Yet it remains unclear why strikingly similar macroecological relationships often arise in very different biological communities and various environmental contexts. Here, we investigated whether chaotic internal dynamics in spatially heterogeneous communities could underlie multiple macroecological relationships. Our analyses reveal that very general constraints on species interactions and spatial migration parameters can simultaneously lead to multiple macroecological laws found in microbial ecosystems without requiring external sources of noise. Our study also identifies the mechanistic origins of many empirically observed macroecological relationships, such as Taylor's law, anomalous abundance diffusion, the Laplace distribution of short-term abundance changes, and the distribution of species residence times. Overall, we demonstrate how macroecological laws can arise from interaction-driven chaotic dynamics and common ecological constraints, thereby providing a unifying explanation for their widespread prevalence in nature.},
}
@article {pmid41280341,
year = {2025},
author = {Ma, J and Xu, L and Han, Q and Gao, J and Yuan, H and Dong, K and Huang, C and Zhou, C and Ji, JS and Zhang, C and Zeng, H and Guo, Y and Luo, L and Zhang, X and Luo, Y and Liu, Q and Stenseth, NC and Liang, W},
title = {The Indian Ocean Dipole drives imported-dominated dengue outbreaks in China: Mechanisms and predictions.},
journal = {PNAS nexus},
volume = {4},
number = {11},
pages = {pgaf350},
pmid = {41280341},
issn = {2752-6542},
abstract = {Dengue fever, influenced by climate dynamics and human mobility in nonendemic regions, remains poorly understood. We assessed the effects of large-scale climate features on domestic dengue outbreaks using data from China (2013-2021) and projections for 2023-2028, incorporating climate, human mobility, and environmental factors. A significant positive correlation (r = 0.89, P < 0.01) was found between domestic dengue incidence and overseas imported cases. Significant associations were also noted with domestic (F 2.96, 25.78 = 518.03, P < 0.01) and international human mobility (F 2.77, 25.78 = 66.84, P < 0.01), the Indian Ocean Dipole (IOD) index (F 2.98, 25.78 = 522.84), and vectorial capacity (F 2.92, 25.78 = 338.74, P < 0.01). IOD is the most influential climate feature, with a trend of intensification over time. The Extreme Gradient Boosting (XGBoost) algorithm incorporating IOD (r [2] = 0.56) predicted outbreaks in 2025, 2026, and 2028. Our findings reveal that large-scale climate phenomenon, notably the IOD, and human mobility significantly influence dengue domestic outbreaks in China through a "dislocated impact."},
}
@article {pmid41281954,
year = {2025},
author = {Johnston, PI and Chizani, K and Chirwa, E and Dale, H and Patel, P and Silungwe, N and Mkwangwanya, C and Kachala, T and Mhango, C and Nyirenda, G and Diness, Y and Mpesi, S and Wachepa, R and Shumba, F and Mwakiseghile, F and Rashid, V and Misiri, T and Ashton, PM and Chunga, A and Cocker, D and Cunningham-Oakes, E and Jewell, C and Feasey, N and Gordon, MA and Nyirenda, T},
title = {Transmission dynamics for invasive Non-Typhoidal S almonella serovars (TiNTS): protocol for a household study of transmission and immune response to non-typhoidal Salmonella in Malawi.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {581},
pmid = {41281954},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {BACKGROUND: Invasive non-typhoidal Salmonella (iNTS) disease is a leading cause of community-onset bloodstream infection in Africa, driving high morbidity in young children. The World Health Organization has published preferred product characteristics for an iNTS vaccine, but lack of transmission data is an impediment to vaccine licensure. Enteric NTS (eNTS) is the asymptomatic carriage of NTS in stool that precedes invasive disease. We do not know how long eNTS shedding lasts, how often infection spreads in endemic settings, or how an eNTS episode shapes immunity against later invasion. These gaps make it difficult to define trial sites, select cohorts, refine target product profiles, and build reliable models of vaccine impact. Here we describe TiNTS, a prospective household study in Blantyre, Malawi, which will measure real-time eNTS incidence, transmission, and antibody responses to close these evidence gaps and accelerate rational vaccine deployment.<br><br>METHODS: We will recruit all members of at least 60 households in Ndirande, Blantyre, Malawi. Stool samples will be collected every other day for at least four weeks and tested for NTS using culture and pan- Salmonella PCR on growth media. Environmental samples collected at enrolment will be tested using the same methods. Symptoms and exposure risks will be recorded throughout.We will collect blood samples at enrolment, after four weeks, and four weeks after the first eNTS episode in each household. We will measure serum IgG responses to Salmonella Typhimurium and Enteritidis LPS antigens. We will extend follow-up if participants continue shedding or if the first household case occurs with fewer than 14 days of follow-up remaining.All culture-positive isolates and PCR-positive broths will undergo Illumina sequencing to enable genome and metagenome reconstruction for transmission inference.<br><br>CONCLUSIONS: TiNTS will define the burden, transmission patterns, and immune response to eNTS. Findings will inform vaccine modelling, trial design, and targeted introduction strategies.},
}
@article {pmid41283812,
year = {2025},
author = {Shang, J and Peng, C and Guan, J and Cai, D and Wang, D and Sun, Y},
title = {From genomic signals to prediction tools: a critical feature analysis and rigorous benchmark for phage-host prediction.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
pmid = {41283812},
issn = {1477-4054},
support = {//Hong Kong Research Grants Council/ ; 11209823//General Research Fund/ ; 9667256//City University of Hong Kong/ ; 9678241//City University of Hong Kong/ ; 217310019//Open Research Fund of Guangdong Provincial Key Laboratory of Wastewater Information Analysis and Early Warning/ ; },
mesh = {*Bacteriophages/genetics/physiology ; *Genomics/methods ; *Computational Biology/methods ; Benchmarking ; *Host-Pathogen Interactions ; Genome, Viral ; },
abstract = {Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct performance comparison challenging due to inconsistent benchmarks and varying usability. Here, we provide a systematic review and a rigorous benchmark of 27 virus-host prediction tools. We formulate the host prediction task into two primary frameworks-link prediction and multi-class classification-and construct two benchmark datasets to evaluate tool performance in distinct scenarios: a database-centric dataset (RefSeq-VHDB) and a metagenomic discovery dataset (MetaHiC-VHDB). Our results reveal that no single tool is universally optimal. Performance is highly context-dependent, with tools like CHERRY and iPHoP demonstrating robust, broad applicability, while others, such as RaFAH and PHIST, excel in specific contexts. We further identify a critical trade-off between predictive accuracy, prediction rate, and computational cost. This work serves as a practical guide for researchers and establishes a standardized benchmark to drive future innovation in deciphering complex virus-host interactions.},
}
@article {pmid41285720,
year = {2025},
author = {Li, J and Liao, Q and Zhou, H and Hu, R and Li, Y and Hu, Z and Yu, B and Liu, P and Zheng, Q and Pu, W and Sheng, S and Liu, Y and Wu, S and Liu, T and Xiao, Q and Duan, S and Gao, J and Li, X and Wang, S and Xiao, H and Zhou, Z and Lu, Z and Yang, J and Yan, J},
title = {Multi-omics analyses reveal regulatory networks underpinning metabolite biosynthesis in Nicotiana tabacum.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10339},
pmid = {41285720},
issn = {2041-1723},
support = {32425011//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32502746//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Nicotiana/genetics/metabolism ; Gene Expression Regulation, Plant ; *Gene Regulatory Networks ; Metabolomics/methods ; Plant Leaves/metabolism/genetics ; Transcriptome ; Plant Proteins/genetics/metabolism ; Metabolome ; Metabolic Networks and Pathways/genetics ; Gene Expression Profiling ; Metabolic Engineering ; Multiomics ; },
abstract = {Tobacco is a significant industrial crop, serving as a model for plant science and a promising specie for the production of proteins and small molecules. However, system biology studies of tobacco under natural field cultivation conditions remain scarce. Here, we construct a genome-scale metabolic regulatory network through integration of dynamic transcriptomic and metabolomic profiles from field-grown tobacco leaves across two ecologically distinct regions. We map 25,984 genes and 633 metabolites into 3.17 million regulatory pairs using multi-algorithm integration. This network reveals three pivotal transcriptional hubs, including NtMYB28 (promoting hydroxycinnamic acids synthesis by modifying Nt4CL2 and NtPAL2 expression), NtERF167 (amplifying lipid synthesis via NtLACS2 activation) and NtCYC (driving aroma production through NtLOX2 induction). These transcriptional hubs achieve substantial yield improvements of target metabolites by rewiring metabolic flux. The present work provides a systems-level atlas of tobacco metabolic regulation and may help to guide metabolic engineering.},
}
@article {pmid41285770,
year = {2025},
author = {Gamaarachchi, H and Stevanovski, I and Hammond, JM and M Reis, AL and Rapadas, M and Jayasooriya, K and Russell, T and Yeow, D and Hort, Y and Patel, C and Mallett, AJ and Stackpoole, E and Roman, L and Silver, LW and Hogg, CJ and Streeting, LM and Bogdanovic, O and Coelho Rodrigues Noronha, R and Santos do Nascimento, LA and Lima Cardoso, A and Georges, A and Cheng, H and Patel, HR and Kumar, KR and Mallawaarachchi, AC and Deveson, IW},
title = {Targeted sequencing and iterative assembly of near-complete genomes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10406},
pmid = {41285770},
issn = {2041-1723},
mesh = {Humans ; *Genome, Human/genetics ; *Nanopore Sequencing/methods ; Animals ; *Sequence Analysis, DNA/methods ; Algorithms ; High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; },
abstract = {Advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability, and assembly quality and completeness. 'Cornetto' is a new strategy in which we use programmable selective nanopore sequencing to focus LRS data production onto the unsolved regions of a nascent assembly. This improves assembly quality and streamlines the process, both for humans and non-human vertebrates. Cornetto enables us to generate highly complete diploid human genome assemblies using only nanopore LRS data, surpassing the quality of previous efforts at a fraction of the cost. Cornetto enables genome assembly from challenging sample types like human saliva. Finally, we obtain accurate assemblies for clinically-relevant repetitive loci at the extremes of the genome, demonstrating valid approaches for genetic diagnosis in facioscapulohumeral muscular dystrophy (FSHD) and MUC1-autosomal dominant tubulointerstitial kidney disease (MUC1-ADTKD).},
}
@article {pmid41285897,
year = {2025},
author = {Dalisay, DS and Mateo, JC and Teodosio, JJR and Jusa, LMS and Baladjay, DMS and de Guzman, LS and Balida, LAP and Jamal, JA},
title = {Identification of SARS-CoV-2 3CLpro inhibitors from marine actinomycetes through integrated phylogeny-based metabolomics with functional screening and bioinformatic analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41503},
pmid = {41285897},
issn = {2045-2322},
mesh = {*Actinobacteria/chemistry/metabolism/genetics/classification ; *SARS-CoV-2/drug effects/enzymology ; Phylogeny ; Metabolomics/methods ; *Antiviral Agents/pharmacology/chemistry ; Computational Biology/methods ; *Coronavirus 3C Proteases/antagonists &amp; inhibitors/metabolism/chemistry ; Humans ; COVID-19/virology ; Molecular Docking Simulation ; *Protease Inhibitors/pharmacology/chemistry ; COVID-19 Drug Treatment ; },
abstract = {As the acute threat of the COVID-19 pandemic diminishes globally, advancing the research and development of antiviral agents remains crucial for ensuring preparedness for future outbreaks. This study investigates the inhibitory effects of marine sediment-derived actinomycetes on the SARS-CoV-2 main protease (3CLpro), a key enzyme involved in viral replication and transcription. Extracts of 75 actinomycete strains from two locations, Nogas Island in Antique and Tubbataha Reefs Natural Park in Palawan, Philippines, were evaluated for their ability to inhibit 3CLpro, with 36% of the extracts showing more than 90% inhibition. Further examination of 27 extracts revealed IC50 values between 2 and 8 µg/mL, suggesting notable inhibitory strength. Phylogenetic analysis grouped the active strains into seven distinct clades, with Clades 1, 5, and 6, closely related to Streptomyces enissocaesilis, S. geysiriensis, S. ardesiacus, and S. indicus, exhibiting antiviral activity. Metabolomic profiling using LCMS-QTOF, coupled with principal component analysis (PCA) and hierarchical clustering, revealed that metabolic signatures were consistent with clade classification. Shared features among the active clades included a biohopanoid, fatty acid amides, diketopiperazines, lipid derivatives, and aromatic compounds. Supervised analysis using orthogonal partial least squares discriminant analysis (OPLS-DA) identified 17 discriminant metabolites produced by Streptomyces strains associated with antiviral activity, including a bicyclic sesquiterpenoid, an aromatic polyketide, an alkylphenol, fatty acid derivatives, alkylated aromatic amines, lipid-derived metabolites, and a carbazole alkaloid. Among the identified compounds, streptocarbazole C showed a strong predicted binding affinity to SARS-CoV-2 3CLpro (- 9.8 ± 0.30 kcal/mol) in molecular docking analysis, with favorable interactions at the enzyme's catalytic dyad (HIS41 and CYS145). In silico toxicity predictions suggested a generally favorable safety profile, although some limitations were noted. These findings highlight the biosynthetic and functional potential of marine sediment-derived Streptomyces against SARS-CoV-2 3CLpro, providing a framework for the discovery of antiviral natural products through the integration of ecological, phylogenetic, metabolomics, and computational analyses.},
}
@article {pmid41285988,
year = {2025},
author = {Li, M and Li, Z and Xu, C and Chen, Y},
title = {Semi-supervised medical image segmentation of bladder tumors based on supervised branches and uncertainty estimation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41517},
pmid = {41285988},
issn = {2045-2322},
support = {No. 2019YFC0117800//National Key Research and Development Program of China/ ; No. 2019YFC0117800//National Key Research and Development Program of China/ ; No. 2019YFC0117800//National Key Research and Development Program of China/ ; No. 2019YFC0117800//National Key Research and Development Program of China/ ; },
mesh = {*Urinary Bladder Neoplasms/diagnostic imaging/pathology ; Humans ; Uncertainty ; Algorithms ; *Image Processing, Computer-Assisted/methods ; *Supervised Machine Learning ; *Image Interpretation, Computer-Assisted/methods ; Reproducibility of Results ; },
abstract = {Supervised learning has excellent segmentation performance in bladder tumor segmentation, but it relies on a large amount of labeled data. To learn the features of bladder tumors from limited labeled data and obtain accurate segmentation results, we propose a semi-supervised segmentation method for bladder tumors, UDS-MT. The method consists of a Mean Teacher network and a guided branch, which respectively undertake the tasks of segmentation prediction and supervision of prediction results. Mean teacher network uses the exponential moving average (EMA) mechanism to update the teacher network parameters to achieve fine-grained capture of the target shape; the guided branch uses uncertainty estimation to filter out pixel blocks with high confidence to obtain more reliable masks, and it suppresses overfitting on some certain extent. In addition, we propose a defend loss term that only calculates the loss for pixels with high prediction confidence of the model, thereby improving the reliability of the pseudo-label. After evaluation on a bladder tumor clinical medical image dataset, when the labeled data is limited to 15%, the Dice coefficient of the network segmentation target shape can reach up to 80.04%, which is at least 2.81% higher than other methods.},
}
@article {pmid41288576,
year = {2025},
author = {Li, J and Cai, X and Li, M and Zhang, D and Li, B and Jin, LN and Luo, C and Zhang, G},
title = {In situ degradation of 2-methylnaphthalene by a soil Penicillium strain associated with fungal-bacterial interactions.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41288576},
issn = {1751-7370},
support = {42192513//National Natural Science Foundation of China/ ; 42277210//National Natural Science Foundation of China/ ; 42477262//National Natural Science Foundation of China/ ; 2023B1515020038//Natural Science Foundation of Guangdong Province, China/ ; 2023B1212060049//Guangdong Foundation for Program of Science and Technology Research/ ; 2023368//Youth Innovation Promotion Association CAS/ ; },
mesh = {*Penicillium/metabolism/genetics/isolation &amp; purification/classification ; Biodegradation, Environmental ; *Soil Microbiology ; *Naphthalenes/metabolism ; *Bacteria/metabolism/genetics ; *Microbial Interactions ; *Soil Pollutants/metabolism ; Metabolic Networks and Pathways/genetics ; },
abstract = {Fungi play critical but underappreciated roles comparing to bacteria in the bioremediation of organic pollutants, particularly emerging contaminants. Numerous fungal species, along with their functional genes and metabolic pathways, remain largely unexplored. Here, we integrate single-cell Raman-activated cell sorting with stable isotope probing to identify and characterize in situ active fungi involved in emerging contaminant degradation. This approach enabled the isolation of a Penicillium sp. strain LJD-20, previously unreported, which acts as an active degrader of 2-methylnaphthalene, a model emerging pollutant. Genomic analyses revealed that LJD-20 harbors a diverse repertoire of degradation-related genes, including those encoding dioxygenases, methyl hydroxylases, and cytochrome P450 monooxygenases, highlighting its versatile metabolic potential. Single-cell genome sequencing also uncovered a potential close fungal-bacterial co-occurrence, suggesting possible ecological or metabolic interactions. In bioaugmentation trials, strain LJD-20 independently degraded 2-methylnaphthalene and simultaneously promoted the enrichment of other microorganisms involved in its removal. These findings highlight the metabolic versatility and ecological importance of fungi in pollutant degradation and demonstrate the utility of combining single-cell and isotopic approaches to explore microbial function and interaction in complex environments.},
}
@article {pmid41289307,
year = {2025},
author = {Guang, A and Dunn, CW and Novitsky, V and Howison, M and Kantor, R},
title = {T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters.},
journal = {PLoS computational biology},
volume = {21},
number = {11},
pages = {e1013676},
pmid = {41289307},
issn = {1553-7358},
support = {K24 AI134359/AI/NIAID NIH HHS/United States ; P20 GM109035/GM/NIGMS NIH HHS/United States ; P30 AI042853/AI/NIAID NIH HHS/United States ; R01 AI136058/AI/NIAID NIH HHS/United States ; },
mesh = {*HIV-1/genetics/classification ; *Phylogeny ; Humans ; *HIV Infections/transmission/virology/epidemiology ; *Genome, Viral/genetics ; *Sequence Alignment/methods ; Computational Biology/methods ; Cluster Analysis ; Algorithms ; },
abstract = {Molecular epidemiology and HIV-1 transmission networks reconstruction can provide insights into transmission dynamics and inform public health strategies. Long HIV sequences, such as near full-length (nFL) genomes, can improve the accuracy of phylogenetic inference. However, relatively short pol sequences are still broadly used for inferring molecular HIV clusters. Whether a mix of long and short HIV-1 sequences can improve phylogenetic inference of molecular HIV clusters remains unknown. We propose a flexible approach called T-shaped alignments that incorporates both nFL HIV-1 genomes and partial pol sequences, and investigate whether this approach improves phylogenetic reconstruction of molecular clusters. Under the assumption that clustering from 100% of long sequences is the most accurate, we obtained 1196 subtype B nFL HIV-1 sequences from the Los Alamos National Laboratory Database and a single-study subset, varied the proportion of long and short sequences in our T-shape alignments, systematically masked all non-pol regions with missing characters in proportional increments, and compared tree similarity and cluster inference among datasets. With the full dataset, we found that when more than 50% of available sequences are nFL, the T-shaped alignment gradually yields results closer to the 100% n, with more and larger clusters identified. However, below the 50% threshold accuracy did not increase. Stringent bootstrap thresholds decreased cluster accuracy gaps but also decreased number of clusters found and mean cluster size. For the subset dataset, we found that the introduction of nFL sequences to the T-shaped alignment improves accuracy in clustering either after a 30% threshold or immediately depending on bootstrap choice. Our new approach and results suggest that using T-shape alignments to mix HIV-1 sequences of different lengths can improve phylogenetic and clustering accuracy, with needed nFL proportion depending on analysis goals. The T-shape alignment provides a straightforward method for utilizing all available sequences to improve phylogenetic analysis.},
}
@article {pmid41289675,
year = {2026},
author = {Zou, D and Fancello, G and Montanari, A and Zhou, S and Chaix, B},
title = {Momentary associations between time-varying social contacts and depressive symptomatology in older adults: A GPS-based mobility survey study.},
journal = {Social science &amp; medicine (1982)},
volume = {389},
number = {},
pages = {118834},
doi = {10.1016/j.socscimed.2025.118834},
pmid = {41289675},
issn = {1873-5347},
mesh = {Humans ; Male ; Female ; Aged ; *Depression/psychology/epidemiology ; France/epidemiology ; Ecological Momentary Assessment ; Bayes Theorem ; Geographic Information Systems/statistics &amp; numerical data ; Surveys and Questionnaires ; Aged, 80 and over ; Time Factors ; Middle Aged ; *Interpersonal Relations ; },
abstract = {Studies often investigate the long-term impact of social contacts on mental health in older adults, neglecting momentary effects. This research, grounded in the consideration of daily activity, explores how time-varying social contacts associate with momentary depressive symptoms among 216 older adults in the Île-de-France region. Employing a geographically-explicit ecological momentary assessment approach (GEMA), we collected participants' depressive symptoms, mobility locations, and social contacts data via smartphone surveys, GPS receivers, and mobility survey over 7 days. Bayesian mixed models with random effects at individual and daily levels, considering time autocorrelation, were employed. Participants engaging with social contacts exhibited lower depression not only immediately but also in the following hours. Interestingly, a longer duration of time spent with social contacts did not lead to a sharper decrease in depression levels. Notably, larger decreases were observed when the number of social contacts increased from one to two, especially with friends or family members.},
}
@article {pmid41290171,
year = {2025},
author = {Becker, JA and Ortega, AC and Beck, J and Buchanan, CB and Bills, T and Hall, LE and Hennig, JD and Hnilicka, P and Huggler, K and Kauffman, M and Middleton, A and Mong, TW and Monteith, KL and Reinking, A and Sawyer, H and Scasta, J and Scurlock, BM and Merkle, JA},
title = {The role of spatiotemporal variation in resources in the diverse movement strategies of temperate ungulates.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2059},
pages = {20251973},
pmid = {41290171},
issn = {1471-2954},
support = {//Wyoming Governor's Big Game License Coalition/ ; //U.S. Geological Survey/ ; //George B. Storer Foundation/ ; //Wyoming Game and Fish Department/ ; //University of Wyoming-Reclamation and Restoration Center/ ; //Memorial Resource Development/ ; //Pinedale Anticline Project Office/ ; //National Geographic Society/ ; //University of Wyoming-School of Energy Resources/ ; //Bureau of Land Management/ ; //University of Wyoming-Haub School/ ; //Wyoming Sage Grouse Conservation Funds/ ; //Native Range Capture Services/ ; //Marathon Oil/ ; //Anadarko Petroleum Company/ ; //Petro-Canada/ ; //PacifiCorp/ ; //L. Floyd Clarke Greater Yellowstone Scholarship/ ; //Grand Teton Association/ ; //Samson Resources/ ; //Rawlins Field Office/ ; //Wyoming State Legislature/ ; //The Greater Yellowstone Coordinating Committee/ ; //Knobloch Family Foundation/ ; //Nature Conservancy/ ; //Brucellosis-Feedground-Habitat Program/ ; //Black Diamond Minerals LLC/ ; //The Greater Yellowstone Coalition/ ; //British Petroleum North America/ ; //Rocky Mountain Elk Foundation/ ; //Wyoming Chapter of The Wildlife Society/ ; //Sky Aviation/ ; //Leading Edge Aviation, LLC/ ; //Warren Resources/ ; //Wyoming Animal Damage Management Board/ ; //Linn Energy/ ; //University of Wyoming/ ; //Devon Energy Corporation/ ; //Community Forestry and Environmental Research Partnership Fellowship/ ; //Yellowstone Center for Resources/ ; //Greater Yellowstone Interagency Brucellosis Committee/ ; },
mesh = {Animals ; *Animal Migration ; *Deer/physiology ; Wyoming ; Seasons ; Climate ; Geographic Information Systems ; *Antelopes/physiology ; },
abstract = {Animal movement strategies are thought to be determined by the spatiotemporal variation of resources in an environment. Observations of various species indicate that the occurrence of migratory versus resident movements depends on resource predictability and the associated costs and benefits of tracking resource availability versus remaining in a familiar range. Here, we use 21 years of GPS data from seven populations (n = 239) of pronghorn (Antilocapra americana) and 12 populations (n = 283) of elk (Cervus canadensis) across Wyoming, USA to test if resource-based hypotheses predict individual movement strategies within a common geographic range. We identified three distinct movement strategies in each species-residents, dual-range migrants and multi-range migrants. Spatiotemporal variation in resources did explain variation in strategies in both pronghorn and elk, with residents experiencing less spatial and greater year-to-year variation than migratory individuals. However, spatiotemporal variation did not predict differentiation between dual- and multi-range migrants in either species. Climatic conditions were also important, especially in elk, where individuals were less likely to be resident when they experienced worse winters. Our findings demonstrate that the movement strategies of temperate ungulates are consistently linked to spatiotemporal resource variation across scales, but additional mechanisms can also facilitate localized behavioural differences.},
}
@article {pmid41290686,
year = {2025},
author = {Niedostatek, M and Baptista, A and Yamamoto, J and Kurths, J and Sanchez Garcia, R and MacArthur, BD and Bianconi, G},
title = {Mining higher-order triadic interactions.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11613},
pmid = {41290686},
issn = {2041-1723},
mesh = {Humans ; Algorithms ; Leukemia, Myeloid, Acute/genetics/metabolism ; *Data Mining/methods ; Neural Networks, Computer ; },
abstract = {Complex systems often involve higher-order interactions that go beyond pairwise networks. Triadic interactions, where one node regulates the interaction between two others, are a fundamental form of higher-order dynamics found in many biological systems, from neuron-glia communication to gene regulation and ecosystems. However, triadic interactions have so far been mostly neglected. In this article, we propose the Triadic Perceptron Model (TPM) which shows that triadic interactions can modulate the mutual information between the dynamical states of two connected nodes. Leveraging this result, we formulate the Triadic Interaction Mining (TRIM) algorithm to extract triadic interactions from node metadata, and we apply this framework to gene expression data, finding new candidates for triadic interactions relevant for Acute Myeloid Leukemia. Our findings highlight crucial aspects of triadic interactions that are often ignored, offering a framework that can deepen our understanding of complex systems across biology, ecology, and climate science.},
}
@article {pmid41291465,
year = {2025},
author = {Leber, W and Farooq, HZ and Panovska-Griffiths, J and Larvin, H and Baggaley, RF and Divall, P and Haigh, D and Davies, EA and Choudhry, S and Hicks, SR and Goodwin, L and Foster, GR and Orkin, CM and Zenner, D and Vickerman, P and Hickman, M and Reid, L and Worrall, S and Pareek, M and Lais, S and Anderson, J and Robson, J and Griffiths, CJ},
title = {Risk prediction models for targeted testing of HIV, hepatitis B and hepatitis C: a systematic review and meta-analysis.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1648},
pmid = {41291465},
issn = {1471-2334},
abstract = {BACKGROUND: Diagnosing human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) infections in general population settings is challenging. We conducted a systematic review and meta-analysis of prediction tools designed to help identify individuals at risk of these blood-borne viruses.<br><br>METHODS: We included studies on individuals of any age at risk of blood-borne viruses from healthcare, community settings, and national databases. We searched the Web of Science, MEDLINE, EMBASE, and CENTRAL databases (from database inception to 2023) and used the Prediction model Risk Of Bias ASsessment Tool (PROBAST) to evaluate the quality and systematic risk of bias of these studies. We extracted model accuracy using the area under the receiver operating characteristic curve (AUC), sensitivity, and specificity. A mixed-effects model (for AUC) and bivariate random-effects model (for sensitivity/specificity) were used to generate pooled values for these studies.<br><br>RESULTS: Of the 41,585 records, 71 were included, covering over 31 million participants and more than 65,000 cases of blood-borne viruses. We examined 67 models: 47 for HIV, 13 for HCV, 5 for HBV, and 2 from studies that assessed multiple viruses separately. The studies were conducted in 41 low- and middle-income and 30 high-income countries. They covered 11 different populations (including men who have sex with men, the general population, and women), 8 types of settings (including sexual health, secondary care, and primary care) and 7 types of risk factors (behavioural, clinical, and demographic). The methods comprised traditional regression (n&#x2009;=&#x2009;50), machine-learning models (n&#x2009;=&#x2009;17), and others (n&#x2009;=&#x2009;4). The risk of bias was high in 64 studies and low in seven. Among 33 studies reporting mean and 95% CI, pooled AUC values were 0.73 (95% CI:0.67&#x2013;0.80, [Formula: see text]&#x2009;=&#x2009;74%) across HIV studies (including 8 machine-learning models), 0.80 (0.73&#x2013;0.86, [Formula: see text]&#x2009;=&#x2009;86%) for HCV (including 2 machine-learning models) and 0.79 (0.76&#x2013;0.81, [Formula: see text]&#x2009;=&#x2009;93%) for HBV (including 3 machine-learning models).<br><br>CONCLUSIONS: Significant heterogeneity exists in blood-borne virus prediction accuracy across diverse settings and populations, with a high risk of bias. Contributions from primary care were limited, and evaluation and reporting were inconsistent. Developing and evaluating effective models for the combined risk assessment of HIV, HBV, and HCV in general population settings remains a priority.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-11921-3.},
}
@article {pmid41293580,
year = {2025},
author = {Siminiuc, R and Țurcanu, D and Siminiuc, S},
title = {Energy intake and dietary fiber as principal determinants of obesity in Eastern Europe, 2010-2022: an ecological panel study.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1698838},
pmid = {41293580},
issn = {2296-2565},
mesh = {*Dietary Fiber/administration &amp; dosage ; Humans ; *Obesity/epidemiology ; *Energy Intake ; Europe, Eastern/epidemiology ; Female ; Male ; Adult ; Exercise ; Prevalence ; Overweight/epidemiology ; Middle Aged ; Diet/statistics &amp; numerical data ; },
abstract = {BACKGROUND: Obesity is a major global health challenge, with Eastern Europe standing out for rapid nutrition transitions and persistent social and economic inequalities. Despite its high prevalence, longitudinal ecological evidence on the structural determinants of obesity in this region remains limited.<br><br>OBJECTIVE: To examine population-level associations between dietary energy availability, dietary fiber intake, macronutrient composition, and insufficient physical activity with obesity and overweight prevalence in Eastern Europe during 2010-2022.<br><br>METHODS: Data from FAOSTAT and the World Health Organization were assembled into a balanced panel of 130 country-year observations. Analyses combined descriptive statistics and Pearson correlations with two-way fixed-effects regressions (country and year), using robust standard errors and one-year lagged predictors to test for robustness.<br><br>RESULTS: Higher energy availability was positively associated with both obesity and overweight, while dietary fiber consistently showed a protective effect. Marginal estimates indicated that an additional 100&#x202f;kcal/day predicted an increase of nearly one percentage point in obesity, whereas +5&#x202f;g/day of fiber corresponded to an approximate two-percentage-point reduction. Neither macronutrient shares nor insufficient physical activity showed significant associations.<br><br>CONCLUSION: Dietary energy and fiber emerge as the primary structural correlates of obesity in Eastern Europe. These findings underscore the need for region-specific, data-driven nutrition and public health policies to address obesogenic environments and reduce socio-economic disparities in diet quality.},
}
@article {pmid41293965,
year = {2026},
author = {Navarro, D and Latch, EK and Tallon, AK and Ott-Conn, CN and DeYoung, RW and Walsh, DP and Euclide, PT and R G, C and Larson, WA and Seetharam, AS and Severin, AJ and Reecy, JM and Hu, ZL and Cantrell, JR and Carstensen, M and Caudell, JN and Killmaster, CH and Lockwood, ML and McKinley, WT and Norton, AS and Schuler, KL and Storm, DJ and Sumners, JA and Walter, WD and Blanchong, JA},
title = {Development of High-Throughput Genomic Resources to Inform White-Tailed Deer Population and Disease Management.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70085},
pmid = {41293965},
issn = {1755-0998},
support = {//State of Iowa/ ; //Michigan Department of Natural Resources/ ; //Association of Fish and Wildlife Agencies/ ; //Michigan State University/ ; T32 GM140935/GM/NIGMS NIH HHS/United States ; //Iowa State University/ ; },
mesh = {Animals ; Male ; *Deer/genetics ; Genetic Variation ; *Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; United States ; Whole Genome Sequencing ; Wasting Disease, Chronic/genetics ; },
abstract = {White-tailed deer (Odocoileus virginianus) are the most abundant and widespread cervid in North America. Genetic data are used as a tool to monitor populations and make management decisions for this game species. However, the development and use of genomic tools that can generate a set of markers suitable for longitudinal genomic data collection, whether for management purposes or to study the demographic and evolutionary processes of widely distributed species, have been challenging. This is mainly due to the cost required to fully implement and interpret the data produced. Here, we generated whole genome resequencing data for 44 free-ranging deer from three regions in their central and eastern North American range and identified over 89 million single nucleotide polymorphisms (SNPs). We used a subset of these SNPs to develop two nested SNP tools, a high-density array (702,183 SNPs) and a medium-density array (72,723 SNPs) to support deer and chronic wasting disease (CWD) management and research. SNPs were selected to ensure an even distribution across scaffolds of the reference genome and include SNPs associated with CWD susceptibility. Using genotyping results for 469 deer from 15 states in the US and Mexico generated by the high-density array and 1335 deer from 18 states generated by the medium-density array, we assessed genotyping success across different populations and explored some insights into population structure. These genomic tools offer a standard set of markers that will enable researchers and managers to address important questions related to white-tailed deer and CWD management. Our SNP arrays also offer the opportunity to examine aspects of white-tailed deer ecology and evolutionary history that were previously difficult to address.},
}
@article {pmid41294456,
year = {2025},
author = {Jacobs, S and Zhang, J and Wolf, E and Porter, E and Bohn, SJ and Sparks, AM and Eggermont, M and Summers, M and Rivera Cárdenas, CI and Clitheroe, H and Gillis, D and Smith, MA and Benessaiah, K and Jones, A and Davies, A and Helms, M and Bazely, D and Lipton, M and Dowhaniuk, D and van Vierssen Trip, N and Zampaki, N and Karpouzou, P and Wanieck, K},
title = {Are Ecosystem Services Replaceable by Technology Yet? Bio-Inspired Technologies for Ecosystem Services: Challenges and Opportunities.},
journal = {Biomimetics (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {41294456},
issn = {2313-7673},
support = {2022-00491//New Frontiers in Research - Canadian Federal Government/ ; },
abstract = {As ecological collapse accelerates under the pressures of anthropogenic climate change, adaptation strategies increasingly include technological proxies for nature's functions. But can ecosystem services (ES) be meaningfully replaced by technology? Revisiting this urgent question first posed by Fitter (2013), we assess the extent to which bio-inspired design-particularly biomimetics-has advanced the capacity to support, enhance, or replace natural ES. We convened an interdisciplinary team to synthesize and refine a comprehensive list of 22 ecosystem services, integrating often-overlooked cultural and relational dimensions. Using this framework, we conducted a large-scale analysis of over 68,000 peer-reviewed publications from the biomimetics and bio-inspired design literature between 2004 and 2025, applying AI-assisted classification to evaluate whether, and how, these technologies map onto specific ES functions and benefits. Our findings reveal both promise and profound limitations. Bio-inspired research engages with 20 of the 22 ES, but over 78% of this work concentrates on five technologically tractable functions-biochemicals, disease regulation, waste treatment, fibre/hide/wood, and fuel. Foundational supporting and regulating services such as pollination, soil formation, and nutrient cycling are almost entirely absent. Moreover, only 3% of technologies described in the academic literature aim to support existing systems; the overwhelming emphasis on enhancement (39%) and replacement (58%) suggests a design paradigm skewed toward substitution rather than coexistence. Intangible, co-produced services-particularly those related to culture, identity, and meaning-remain outside the current reach of biomimetic design. This skew reveals a dangerous imbalance: while certain ES can be technologically approximated, the relational, emergent, and systemic qualities of ecosystems elude replication. Technological replacement must not become a substitute for preservation. Instead, bio-inspired design should be mobilized as a tool for adaptation that amplifies and protects the living systems on which human and more-than-human futures depend.},
}
@article {pmid41295546,
year = {2025},
author = {Calvo, A and Hall, S and Melgar Cossich, VB and Andreadakis, J and López Castillo, H and Pinto, D and Hewitt, I},
title = {HPV Vaccine Uptake and Cervical Cancer Trends in Panama: A Reference Point for Future Impact Studies.},
journal = {Vaccines},
volume = {13},
number = {11},
pages = {},
pmid = {41295546},
issn = {2076-393X},
abstract = {Background: Cervical cancer (CC) continues to be an important public health concern in Latin America, where it is the second cause of cancer-related deaths among women. With its strong culture of vaccination, Panama was the first country to implement the HPV vaccine as part of its Essential Program on Immunization (EPI). Recently, the government implemented the 90:70:90 PAHO/WHO strategy to reach milestones toward CC elimination. Objective: This analysis triangulates and assesses national data on HPV vaccination coverage, screening practices, and cervical cancer incidence and mortality in Panama, to understand historical tendencies to date and establish a comprehensive foundation for future impact evaluations and research studies. The analysis aims to identify trends and gaps in prevention efforts and to serve as a reference point for future research on HPV-associated cancers. Methods: Population-based, descriptive, observational, ecological study where four, aggregate, de-identified data sources by various curators in Panama were match-merged by year, sex, and administrative division. Reported outcomes include HPV vaccine coverage, CC incidence and mortality rates, screening Pap tests, and CC behavior at diagnosis (in situ vs. invasive). Results: Panama has high HPV vaccine uptake (≥85% most years) in spite of low Pap test coverage (~10%). A decreasing trend in CC incidence has been observed continuously since the 1990s, counterintuitively to significantly increasing CC mortality rates, with most cases diagnosed as invasive and among younger women (30-69 years old). Conclusions: This report provides a comprehensive foundation for understanding trends in HPV vaccination coverage, cervical cancer incidence and mortality, and screening practices in Panama. While high vaccine uptake and declining incidence trends are encouraging, persistent low screening rates and elevated mortality-particularly at invasive stages among younger women-highlight critical gaps in prevention efforts. The need for integrated strategies that strengthen data systems, improve early detection, and address structural and sociocultural barriers are discussed, framed within Panama's progress toward achieving the 90:70:90 targets. Future studies should focus on understanding non-medical influences on health and further vaccine impact with patient-level data, and other forms of HPV-related cancers in immunosuppressed populations. Public strategies would benefit from the implementation of real-life data and efficient data management, consolidation systems, systematic health promotion interventions, and an increase in resource allocation for women at the highest risk.},
}
@article {pmid41297421,
year = {2025},
author = {Yang, H and Luo, X and Liao, Z and Gu, Y and Qian, J and Wang, Y and Guo, H and Shi, L and Peng, J and Liu, M and Wan, X and Chen, L and He, F and Huang, X},
title = {Integrative multi-omics reveal the regulatory mechanism of golden-thread wood color in Phoebe zhennan.},
journal = {Plant physiology and biochemistry : PPB},
volume = {229},
number = {Pt E},
pages = {110781},
doi = {10.1016/j.plaphy.2025.110781},
pmid = {41297421},
issn = {1873-2690},
mesh = {*Wood/genetics/metabolism ; Gene Expression Regulation, Plant ; Plant Proteins/genetics/metabolism ; Flavonoids/metabolism/biosynthesis ; *Pigmentation/genetics ; *Poaceae/genetics/metabolism ; Color ; Genome, Plant ; Metabolomics ; Multiomics ; },
abstract = {Wood color serves as a crucial indicator of timber quality and economic value. Phoebe zhennan is well known for its golden-thread wood color. Nonetheless, the absence of genomic information precludes a comprehensive understanding of the genetic basis of wood color development in this species. In this study, we produced a chromosome-scale genome sequence for P. zhennan, investigated the molecular processes associated with the development of golden-thread wood color, and examined population dynamics over evolutionary time. The genome, with a size of 1001.05 Mb (contig N50 = 4.32 Mb, 2n = 24), comprises 27,284 protein-coding genes. Metabolomic studies revealed seven flavonoids, including cycloheterophyllin, astraganoside, and licoricone, that contribute to the development of golden-thread wood color. Additionally, we reconstructed the flavonoid biosynthetic pathway, which plays a significant role in the development of golden-thread wood color. In this process, transcription factors such as PzMYB2, PzNAC6, and PzWRKY12 were identified as core regulators that activate the expression of crucial enzyme-encoding genes, including PzGT2, PzGT3, and PzF2H3. Moreover, PzNAC6 may regulate flavonoid accumulation during wood development through direct interactions with PzHSF3, PzC3H8 and PzMYB2. In summary, comprehensive genome assembly, metabolomic, transcriptomic, and population genomic data will significantly enhance Phoebe genomic resources, aid in conservation biology studies, and offer vital insights for a deeper understanding of the mechanisms that drive wood color development.},
}
@article {pmid41297621,
year = {2025},
author = {Houmenou, CT and Sokhna, C and Fenollar, F and Mediannikov, O},
title = {Advancements and challenges in bioinformatics tools for microbial genomics in the last decade: Toward the smart integration of bioinformatics tools, digital resources, and emerging technologies for the analysis of complex biological data.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {136},
number = {},
pages = {105859},
doi = {10.1016/j.meegid.2025.105859},
pmid = {41297621},
issn = {1567-7257},
mesh = {*Computational Biology/methods ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Humans ; Animals ; },
abstract = {Over the past decade, microbial genomics has been transformed by advances in sequencing technologies and bioinformatics, enabling the transition from targeted gene markers to complete genome assemblies and ecological scale metagenomic surveys. This review presents a comprehensive overview of the bioinformatics pipelines that structure this field, from sample preparation, PCR amplification, and next-generation sequencing (NGS) to read preprocessing, genome assembly, polishing, structural and functional annotation, and submission to public databases. We highlight the major tools that have become standards at each stage, including FastQC, SPAdes, Prokka, Bakta, CARD, GTDB-Tk, QIIME 2, and Kraken2, while also emphasizing recent innovations such as hybrid assemblers, ontology-driven annotation frameworks, and automated workflows (nf-core, Bactopia). Applications extend across microbiology, from antimicrobial resistance surveillance and phylogenetic classification to ecological studies, exemplified here by three case studies: termite gut microbiota profiling by 16S metabarcoding, the description of new Bartonella species from bats, and the genomic characterization of rare Salmonella enterica serovars from primates. Despite these advances, persistent challenges remain, including incomplete and biased reference databases, computational bottlenecks, and economic disparities in sequencing and storage capacities. In response, international initiatives increasingly promote open, interoperable, and reusable bioinformatics infrastructures. Conforming to the Findable, Accessible, Interoperable, Reusable (FAIR) principles and global frameworks such as Global Alliance for Genomics and Health (GA4GH), these efforts are driving greater standardization, transparency, and data sharing across the microbial genomics community. Future perspectives point toward the integration of artificial intelligence, long-read and telomere-to-telomere (T2T) sequencing, cloud-native infrastructures, and even quantum computing, paving the way for a predictive, reproducible, and globally inclusive microbial genomics.},
}
@article {pmid41298300,
year = {2025},
author = {Wang, ZQ and Gong, LX and Si, M and Huang, ZL and Wu, H and Feng, J and Jiang, TL},
title = {Seasonal changes in 3D space use and foraging strategies in the avivorous bat Ia io.},
journal = {Zoological research},
volume = {46},
number = {6},
pages = {1465-1476},
pmid = {41298300},
issn = {2095-8137},
mesh = {Animals ; *Chiroptera/physiology ; *Seasons ; *Feeding Behavior/physiology ; Ecosystem ; Geographic Information Systems ; },
abstract = {To cope with seasonal changes in food availability, animals need to optimize their behaviors, including shifts in temporal activity patterns and spatial use in habitats. Most studies focused on the temporal activity pattern or habitat use in two-dimensional (2D) space. However, studies on the simultaneous changes in temporal activity patterns and habitat use in three-dimensional (3D) space are limited. In this study, we used the great evening bat (Ia io) to investigate differences in the activity pattern and space use during the summer and autumn. We collected and analyzed the Global Positioning System (GPS) data and activity data obtained from accelerometers. The results showed that bats displayed seasonal variations in their movement patterns. Specifically, compared with summer, I. io individuals were found to extend their foraging duration and adopt a low-energy consumption pattern of activity in autumn. Furthermore, there was a notable increase in the vertical extent of the 3D habitat utilization range for these bats, although the 2D habitat size in autumn remained similar to that in summer. These changes manifested both temporally and spatially, potentially as a response to the reduced availability of insect resources from summer to autumn, and the arrival of migratory birds in autumn as an alternative food source. Our results suggest that I. io seasonally adjust their foraging strategies and spatial use from two to three dimensions. Our study provides important insights into the seasonal behaviour dynamics of bats during summer and autumn, which may contribute to understanding their ecological strategies and inform conservation efforts.},
}
@article {pmid41298935,
year = {2025},
author = {Farooq, MA and Hannan, F and Zou, HX and Zhou, W and Zhao, DS and Ayyaz, A and Ullah Asad, MA and Ahmad, R and Yan, X},
title = {Microplastics in soil-plant systems: impacts on soil health, plant toxicity, and multiomics insights.},
journal = {Plant cell reports},
volume = {44},
number = {12},
pages = {283},
pmid = {41298935},
issn = {1432-203X},
support = {2022YFE0108300//Key Technologies Research and Development Program/ ; },
mesh = {*Microplastics/toxicity ; *Soil/chemistry ; *Soil Pollutants/toxicity ; *Plants/drug effects/metabolism ; Proteomics ; Metabolomics ; Oxidative Stress/drug effects ; Multiomics ; },
abstract = {Microplastic pollution has emerged as a critical environmental concern, particularly in agricultural soils, where various MP types, including polyethylene, polystyrene and polyvinyl chloride accumulate due to plastic mulch degradation, irrigation, and biosolid application. This review synthesizes current knowledge on the impacts of MPs on soil integrity and function, highlighting the degradation of soil structure, disruption of nutrient cycles and shifts in microbial community composition and enzymatic activity. Furthermore, MPs can be taken up by plants, with submicrometer sized particles infiltrating root tissues, triggering phytotoxic effects such as oxidative stress, impaired growth, and reduced photosynthesis. In response plants deploy tolerance mechanisms involving antioxidant defense and altered nutrient metabolism to mitigate MP-induced stress. Advanced omics technologies, including transcriptomics, metabolomics, and proteomics provide valuable insights into the molecular responses of plants to MP exposure, uncovering stress responsive genes, metabolite shifts and protein alterations linked to MP toxicity. This review synthesizes current knowledge on MP contamination in agricultural soil, its impact on soil health and plant physiology, and the application of multiomics approaches to elucidate MP-induced toxicity, paving the way for sustainable strategies to mitigate MP pollution in agroecosystems.},
}
@article {pmid41299059,
year = {2025},
author = {Sharma, AK and Jani, AD and Brunnengraeber, E and Choi, J and Fife, R and Gandhok, S and Huie, K and Ilano, AB and Lopez, E and Lopez, M and McMillan, O and Parra, A and Pollock, T and Woodbridge, D and Young, R},
title = {Deep learning classification of INSV-associated weeds in Monterey county using a curated RGB image dataset.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {45395},
pmid = {41299059},
issn = {2045-2322},
mesh = {*Deep Learning ; *Plant Weeds/classification/virology ; *Image Processing, Computer-Assisted/methods ; *Convolutional Neural Networks ; Plant Diseases/virology ; Malva ; Sonchus ; California ; Datasets as Topic ; },
abstract = {Weeds, defined by their ecological and economic impact rather than taxonomy, present a major challenge to agriculture by competing with crops for limited resources and serving as vectors for disease. In Monterey County, California, one of the most productive farming regions in the United States, Sonchus oleraceus (annual sowthistle) and Malva parviflora (little mallow) have been linked to over $150 million in crop losses due to their role in spreading Impatiens Necrotic Spot Virus (INSV). As precision agriculture becomes more important in high-value production systems, deep learning and image-based classification offer promising tools for early weed detection and disease prevention. To address the absence of region-specific image datasets, this study presents the first curated, high-resolution image collection of INSV-associated weeds from Monterey County, captured under greenhouse conditions designed to mimic field variability. This dataset fills a documented gap in existing global repositories such as PlantCLEF and DeepWeeds, which lack representation of California's high-value crop systems. This study compares three convolutional neural networks-ResNet-50, ResNet-101, and DenseNet-121-for classifying these visually similar weeds under controlled conditions that approximate real field environments. RGB images were augmented to improve model robustness, and training was conducted across ten independent stratified data splits.Among the tested architectures, ResNet-101 achieved the highest median classification accuracy (91%) and Cohen's Kappa (0.87), while DenseNet-121 demonstrated the strongest F1-score and AUC values exceeding 0.99. These results confirm that dataset augmentation substantially enhanced model generalization. The results demonstrate that deep learning can support accurate and reliable weed identification, paving the way for real-time detection systems and more targeted, sustainable weed control practices in precision agriculture.},
}
@article {pmid41302669,
year = {2025},
author = {de Freitas, PP and Lopes, MS and Ferreira, NL and Peixoto, SV and Lopes, ACS},
title = {Community Food Environment in Brazilian Medium-Sized Municipality After the Ore Dam Break: Database Creation and Diagnosis.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {11},
pages = {},
pmid = {41302669},
issn = {1660-4601},
support = {Processo 25000.127551/2019-69//Minist&#xe9;rio da Sa&#xfa;de/ ; Productivity Scholarship SVP and ACSL//National Council for Scientific and Technological Development/ ; },
mesh = {Brazil ; *Databases, Factual ; *Food Supply/statistics &amp; numerical data ; Humans ; Mining ; Cities ; },
abstract = {This study proposed a methodology for obtaining a valid database of food retail establishments and characterized the community food environment, understood as the distribution and type of food outlets, in a Brazilian medium-sized municipality after the collapse of a mining tailings dam. An ecological study was conducted with establishments selling food for home consumption (butcher shops, fish markets; fruit and vegetable specialty markets; large- and small-chain supermarkets; bakeries and local markets) and immediate consumption (bars, snack bars, and restaurants). For home-consumption establishments, data were requested from governments and completed with website/app searches, virtual audits (Google Street View), and on-site audits. For immediate-consumption establishments, only on-site audit was used due to the low quality of the secondary databases. Agreement between databases was assessed with the Kappa statistic. Density (d) was calculated by the area (in km[2]) of the sampling stratum. Public databases presented low validity (23.0%; Kappa -0.388; p = 1.000), even after virtual auditing (31.4%; Kappa 0.37; p < 0.001). 96 establishments for home consumption and 261 for immediate consumption were identified, with predominance of local markets (35.4%), bars (35.2%), and snack bars (29.1%). The region with the highest density of establishments was the "Other Areas" stratum (d = 4.7 for home-consumption establishments and d = 13.2 for immediate-consumption establishments). Audit proved most effective, especially for small establishments. The lack of governmental databases and the identified food environment should inform municipal policies to promote food and nutrition security and reduce inequalities after the disaster.},
}
@article {pmid41304309,
year = {2025},
author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN},
title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
pmid = {41304309},
issn = {2076-2607},
support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; },
abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.},
}
@article {pmid41307322,
year = {2025},
author = {Baima, G and Dabdoub, S and Thumbigere-Math, V and Ribaldone, DG and Caviglia, GP and Tenori, L and Fantato, L and Vignoli, A and Romandini, M and Ferrocino, I and Aimetti, M},
title = {Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.},
journal = {Journal of periodontal research},
volume = {60},
number = {12},
pages = {1237-1253},
pmid = {41307322},
issn = {1600-0765},
support = {CUP B83C22004800006//Next Generation EU/ ; DM 1557 11.10.2022//Next Generation EU/ ; Prot. P2022YEX5R//Next Generation EU Program and the Italian Ministry of University and Research/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Saliva/microbiology ; *Periodontitis/microbiology/therapy/metabolism ; Male ; Feces/microbiology ; Female ; Metabolomics ; Adult ; Middle Aged ; *Mouth/microbiology ; Multiomics ; },
abstract = {AIM: To characterize the impact of periodontitis and of Steps I-II of periodontal therapy on microbiome composition, function, and metabolic output across the oral and gut environments.<br><br>METHODS: A multi-omics analysis was performed on saliva and stool samples collected from 50 systemically healthy individuals with and without Stage III-IV periodontitis. For participants with periodontitis, samples were analyzed both at baseline and 3&#x2009;months after Steps I-II of periodontal therapy. High-throughput whole metagenome sequencing was used to profile microbial taxa and functional genes, NMR-based metabolomics profiled host-microbial metabolites. Single-omic differential abundance analysis between healthy samples and periodontitis samples was performed with MaAsLin2, while analysis between pre- and post-treatment was conducted with timeOmics. Variable selection and subsequent supervised multivariate analysis to determine group-separating markers utilized multi-level sparse Partial Least Squares Discriminant Analysis (sPLS-DA) through mixOmics. KEGG pathway enrichment was analyzed using clusterProfiler, whereas multi-omic data integration was performed with multi-block Partial Least Squares regression analysis.<br><br>RESULTS: Periodontitis was associated with significant compositional and functional changes in both saliva and stool, with increased abundance of pathobionts and loss of health-associated taxa in both niches. A subset of species was shared across oral and gut habitats, with detectable differences across clinical groups. As functional potential, periodontitis enriched microbial pro-inflammatory pathways (lipopolysaccharide biosynthesis, bacterial motility) and depleted beneficial short-chain fatty acid (SCFA)- and vitamin-producing functions. Metabolomic profiles revealed reduced SCFAs and amino acids in periodontitis, with elevated pro-inflammatory metabolites (succinate, trimethylamine) in both saliva and stool. Following therapy, microbial communities and their metabolic output partially reverted toward health-associated profiles, particularly in saliva. Stool samples showed subtler but consistent shifts, including a decrease in some typically oral species and decreased succinate and methylamine and restoration of amino acid and SCFA-related metabolites.<br><br>CONCLUSIONS: Periodontitis is associated with coordinated microbial and metabolic signatures across the oral and gut environments. Non-surgical periodontal therapy promotes partial ecological restoration in both niches, supporting the view of oral health as a modifiable target for influencing systemic microbial homeostasis.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.},
}
@article {pmid41307499,
year = {2025},
author = {Campbell, R and Mevers, E},
title = {Structural Characterization and Multiomics Analysis Reveal Extensive Diversity and Global Distribution of Kurstakin Lipopeptides.},
journal = {Journal of natural products},
volume = {88},
number = {12},
pages = {2960-2967},
pmid = {41307499},
issn = {1520-6025},
support = {R35 GM146740/GM/NIGMS NIH HHS/United States ; },
mesh = {*Lipopeptides/chemistry ; Molecular Structure ; *Bacillus cereus/chemistry ; Multiomics ; },
abstract = {Bacillus species, particularly those investigated as biocontrol agents, are known to produce a cocktail of bioactive lipopeptides that act synergistically to shape the ecological function of these beneficial microbes. However, while certain families of lipopeptides are well-characterized, others remain elusive. Herein, we describe the characterization of the kurstakins, a family of lipopeptides associated with promising biocontrol properties but that lack adequate characterization. Metabolomic analyses of a semipurified Bacillus cereus EM195W extract fraction revealed the presence of approximately 50 cyclic- and linear-peptide analogs. Deeper analyses revealed that the chemical diversity stems from the diverse lipid tails, including linear, iso-, and anteiso-lipid tails ranging from C8-C18, along with several hydroxylated lipid tails. Isolation and complete structural analysis of two new analogs represented the first kurstakin analogs characterized by NMR and provided the first experimental analyses for deducing their absolute configuration. Finally, analysis of publicly available genomic and MS data provided insights into the true chemical diversity and distribution of the kurstakins. These results expand our understanding of this family of compounds, opening the door for determining their ecological functions and the role they play in the broader activity of biocontrol agents.},
}
@article {pmid41308887,
year = {2026},
author = {Ouyang, X and Deng, W and Li, Y and Zou, Y and Yan, W and Yang, F and Zhu, J and Tong, F},
title = {Analysis of depression status and influencing factors in older women with cardiometabolic-based chronic disease under Health Ecology Model.},
journal = {Journal of affective disorders},
volume = {395},
number = {Pt B},
pages = {120774},
doi = {10.1016/j.jad.2025.120774},
pmid = {41308887},
issn = {1573-2517},
mesh = {Humans ; Female ; *Depression/epidemiology/psychology ; Middle Aged ; Aged ; Datasets as Topic ; *Metabolic Syndrome/epidemiology/psychology ; *Cardiovascular Diseases/epidemiology/psychology ; Chronic Disease ; Longitudinal Studies ; Multilevel Analysis ; Models, Theoretical ; China/epidemiology ; Cross-Sectional Studies ; Life Style ; },
abstract = {BACKGROUND: Depression among older women with cardiometabolic-based chronic disease (CMBCD) is influenced by both biological mechanisms but complex social and environmental determinants.<br><br>OBJECTIVE: To examine multilevel factors associated with depression among older women with CMBCD in China within the framework of the Health Ecology Model (HEM), and to identify key determinants for targeted interventions.<br><br>METHODS: Using mixed cross-sectional data from 2015 and 2018 waves of the China Health and Retirement Longitudinal Study (CHARLS), 2961 women aged &#x2265;60 with CMBCD were included. Guided by the five levels of the HEM, univariable and multivariable linear regressions were conducted, with robustness verified through logistic regression and E-values. Heterogeneity analyses were performed on region, residence, education level, and medical service satisfaction.<br><br>RESULTS: Depression was primarily driven by midstream (social network level, living and working conditions level) and downstream (behavioral lifestyle level) factors. Heterogeneity analysis revealed significant variation in depression determinants across region, residence, education level, and medical service satisfaction. The protective effect of "with spouse" was more pronounced among rural and western populations, whereas the benefits of higher education and pension insurance were particularly evident in urban and central regions. The mitigating effect of higher medical service satisfaction on depression was particularly evident among women with higher education levels.<br><br>CONCLUSION: The HEM provides a valuable framework for designing multilevel, precision interventions. Effective strategies should focus on enhancing physical activity, improving medical service satisfaction, and strengthening community networks to reduce depression risk in older women with CMBCD.},
}
@article {pmid41309085,
year = {2025},
author = {Berrocal, A and Concepcion, W and Wac, K},
title = {A 6-Month Evaluation of the Peer-Ceived Momentary Assessment Method in a Small Sample of Liver Transplant Patients and Their Support Persons: Longitudinal Observational Study.},
journal = {JMIR formative research},
volume = {9},
number = {},
pages = {e55907},
pmid = {41309085},
issn = {2561-326X},
mesh = {Humans ; Longitudinal Studies ; Female ; Male ; Middle Aged ; *Liver Transplantation/psychology ; *Ecological Momentary Assessment ; Reproducibility of Results ; Adult ; *Patient Reported Outcome Measures ; Aged ; *Caregivers/psychology ; *Peer Group ; },
abstract = {BACKGROUND: Patient-reported outcomes, including ecological momentary assessments (EMAs), are acquired from patients via repeated self-reports of their perceived momentary physical and emotional states before and after medical procedures. Patient-reported outcomes are used to measure health outcomes and quality of care. However, certain observable states or behaviors (eg, moods such as fatigue, hope, or medication adherence), or behaviors suggestive of health decline (eg, depression, cognitive decline), are not easily measured via self-reports in certain situations (eg, patients undergoing certain medical procedures, patients with dementia, and others). The peer-ceived momentary assessment (PeerMA) method involves support persons or peers (eg, family members and friends) to report their perception of a patient's subjective physical and emotional states and has been validated in healthy populations.<br><br>OBJECTIVE: We examined the value of the PeerMA method in assessing the disease progression and recovery pathways of patients undergoing liver transplantation. Herein, the PeerMA method is operationalized via the patient's informal caregivers and the patient-based EMA, and wearable-based physical activity datasets from the patients. We report the feasibility results and human factors influencing the acceptance and reliability of the PeerMA method in a small study comprising 8 patients and support persons.<br><br>METHODS: We conducted a longitudinal observational study of 6 months (autumn 2019 to spring 2020), collecting EMA/self-reports from 8 patients (at the liver transplant clinic at Stanford University Hospital, California) about their perceived levels of hope, sleep, fatigue, depression, and pain in addition to PeerMA-based reports of the same aspects from 7 caregivers. We collected physical activity records from 5 patients using a Fitbit bracelet. Participants completed pre- and poststudy surveys, contributing qualitative data. We implemented the PeerMA method using a smartphone app, making it easy to use by both patients and support persons.<br><br>RESULTS: We collected 1142 patient-days and 976 support person-days. On average, each patient received 103 EMAs and responded to 64 (63%) of them, while support persons received 87 PeerMAs and responded to 64 (74%) of them. We report empirical evidence about the methodological feasibility of PeerMA, showing its dual and unique information streams unavailable by EMA alone. We show examples where support person assessments and physical activity data can inform health professionals about the actual state of a patient regarding outcomes such as hope, sleep quality, fatigue, pain, and depression. We discuss human factors influencing the acceptance of the method and make methodological recommendations.<br><br>CONCLUSIONS: It is possible to leverage data acquired via the PeerMA method and a wearable activity monitor to complement EMA. The PeerMA method incorporates frequent observations from support persons in patients' daily lives, which can be compared and analyzed next to the patient's self-reports. Such data may help to study and assist patients during disease recovery, which is beneficial for patients recovering from an organ transplant.},
}
@article {pmid41312302,
year = {2025},
author = {Steindler, L and Maldonado, M and Pita, L and Riesgo, A 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 stone sponge Petrosia ficiformis (Poiret, 1789) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {450},
pmid = {41312302},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Petrosia ficiformis (stone sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence is 191.3 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.89 kilobases in length. Gene annotation of the host organism assembly identified 18,339 protein coding genes. The metagenome of the specimen was also assembled, and 112 binned bacterial genomes were identified, including 57 high-quality MAGs. Besides MAGs characteristic of HMA sponge symbionts (i.e., Chloroflexota, Acidobacteriota), the P. ficiformis specific symbiont Candidatus Synechococcus feldmanni (formerly Aphanocapsa feldmanni (Cyanobacteriota) was recovered, as well as notably MAGs of several candidate phyla (Candidatus Latescibacteria, Poribacteria, Tectomicrobia, Dadabacteria, Kapabacteria and Binatia).},
}
@article {pmid41312645,
year = {2026},
author = {Fiamenghi, MB and Camargo, AP and Chasapi, IN and Baltoumas, FA and Roux, S and Egorov, AA and Aplakidou, E and Ndela, EO and Vasquez, YM and Chen, IA and Palaniappan, K and Reddy, TBK and Mukherjee, S and Ivanova, NN and Schulz, F and Woyke, T and Eloe-Fadrosh, EA and Pavlopoulos, GA and Kyrpides, NC},
title = {Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D801-D812},
pmid = {41312645},
issn = {1362-4962},
support = {FWP 70880//BER's Genomic Sciences Program/ ; 1U01DE034196-01/GF/NIH HHS/United States ; //Royal Physiographic Society of Lund/ ; 45379//Natural Sciences, Medicine and Technology/ ; //Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//US DOE/ ; U01 DE034196/DE/NIDCR NIH HHS/United States ; },
mesh = {*Genome, Viral ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Phylogeny ; Biodiversity ; Genetic Variation ; Metagenome ; Software ; },
abstract = {Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.},
}
@article {pmid41313826,
year = {2026},
author = {Xu, QQ and Wang, QQ and Lv, QL and Liu, ZG and Guo, Z},
title = {Anchoring single-atom iron sites onto carbon spheres for boosting electrochemical sensing of bisphenol A.},
journal = {Talanta},
volume = {300},
number = {},
pages = {129158},
doi = {10.1016/j.talanta.2025.129158},
pmid = {41313826},
issn = {1873-3573},
abstract = {Bisphenol A (BPA), a common endocrine-disrupting chemical, poses serious threats to both ecological systems and human health even at trace concentrations. However, the accurate detection of BPA in complex matrices remains challenging due to the low sensitivity and poor selectivity of conventional electrochemical sensing platforms. The saturated N4-coordinated single-atom sites derived from metal phthalocyanines exhibit high catalytic specificity and atomic utilization efficiency, enabling selective recognition of BPA. These characteristics enhance adsorption and electron transfer processes, potentially overcoming the limitations of traditional sensing materials and offering a feasible route for the ultra-sensitive detection of trace BPA in complex environments. In this study, we have developed a highly efficient electrochemical sensor for BPA by anchoring saturated N4-coordinated single-atom sites of metal phthalocyanine onto carbon spheres (MPc/CSs, where M = Fe, Co, and Ni). The carbon spheres (CSs) serve as substrates to support the metal phthalocyanine molecules, improving the stability of the active sites and preventing aggregation. Among the materials tested, FePc/CSs exhibited the highest sensitivity (0.53 μA μM[-1]) and the lowest limit of detection (0.031 μM), exhibiting better performance than other modified electrodes, including CoPc/CSs, NiPc/CSs, and metal-free phthalocyanine-loaded CSs (H2Pc/CSs). Structural analysis revealed that the Fe-N4 single-atom sites possess higher charge density than the Co-N4 and Ni-N4 single-atom sites, resulting in their superior catalytic activity. Practical validation of the FePc/CSs modified glassy carbon electrode (GCE) in real samples, such as supermarket receipts and plastic products, yielded satisfactory recovery rates (97.5-103.4 %), confirming the sensor's reliability in complex matrices. These results demonstrate that electrodes based on CSs-supported single-atom iron sites can serve as highly sensitive, selective, and cost-effective electrochemical sensors for BPA. Overall, this work provides an efficient strategy for designing high-performance environmental sensors based on engineered electronic microenvironments and offers valuable insights for the sensitive analysis of environmental pollutants.},
}
@article {pmid41315389,
year = {2025},
author = {Demetriou, J and Martinou, AF and Bowler, D and Peyton, J and Pescott, OL and Michailidis, N and Mountford, O and Onete, M and Stoumboudi, M and Rathod, B and van Breda, J and Roy, HE and Zenetos, A},
title = {The Cyprus Database of Alien Species (CyDAS).},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1881},
pmid = {41315389},
issn = {2052-4463},
mesh = {Cyprus ; *Introduced Species ; *Databases, Factual ; *Biodiversity ; Animals ; },
abstract = {Invasive alien species (IAS) are a direct driver of global biodiversity loss, and can also affect societies, economies and human health. Maintaining up-to-date alien species inventories is important for informing policy and management decisions. Here we present the Cyprus Database of Alien Species (CyDAS), an openly accessible, online dataset providing informational resources on alien species on the island of Cyprus. The dataset (up to end of December 2023) includes information on 1,293 terrestrial, freshwater and marine introduced taxa, with species profiles being constantly updated to keep track of new arrivals. The CyDAS aims to catalogue and supplement our knowledge on the alien species of Cyprus; to help develop and enhance early warning and rapid response systems; to raise public awareness of the risks posed by the IAS subset; to strengthen and enhance engagement and public participation in surveys in the field of biological invasions; and to inform IAS policy. CyDAS is a free, online database and we would like to encourage other researchers and decision-makers to provide information on IAS.},
}
@article {pmid41315930,
year = {2025},
author = {Chaussard, A and Bonnet, A and Le Corff, S and Sokol, H},
title = {TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {1},
pmid = {41315930},
issn = {1471-2105},
mesh = {*Metadata ; Humans ; *Gastrointestinal Microbiome ; Machine Learning ; *Microbiota ; *Software ; *Computational Biology/methods ; Algorithms ; },
abstract = {BACKGROUND: The gut microbiome plays a crucial role in human health, making it a cornerstone of modern biomedical research. To study its structure and dynamics, machine learning models are increasingly used to identify key microbial patterns associated with disease and environmental factors, but their performance is often limited by the intrinsic complexity of microbiome data and the small size of available cohorts. In this context, data augmentation has emerged as a promising strategy to overcome these challenges by generating artificial microbiome profiles.<br><br>RESULTS: We introduce TaxaPLN, a data augmentation method based on PLN-Tree generative models, which leverages the taxonomy and a data-driven sampler to generate realistic synthetic microbiome compositions. Additionally, we propose a conditional extension based on feature-wise linear modulation, enabling covariate-aware generation. Experiments on diverse curated microbiome datasets show that TaxaPLN preserves ecological properties and generally improves or maintains predictive performances, outperforming state-of-the-art baselines on most tasks. Furthermore, the conditional variant of TaxaPLN establishes a new benchmark for metadata-aware microbiome augmentation.<br><br>CONCLUSION: TaxaPLN provides a model-based framework for augmenting microbiome datasets while preserving their ecological and clinical relevance. By integrating taxonomic structure and host metadata, it enhances predictive modeling across diverse real-world settings. To facilitate reproducible and scalable microbiome analysis using our method, TaxaPLN is released as an open-source Python package available on PyPI (plntree), with MIT-licensed source code hosted at https://github.com/AlexandreChaussard/PLNTree-package .},
}
@article {pmid41316548,
year = {2026},
author = {Wang, S and Li, J and Wang, Z and Yu, M and Liu, C and Liu, D and Wang, R},
title = {Multi-Omics Combined With Mitochondrial Feeding Assays Reveal a Novel Energy Metabolism Strategy for Floral Thermogenesis in Magnolia Driven by Synergistic Supply of Multiple Substrates.},
journal = {Plant biotechnology journal},
volume = {24},
number = {4},
pages = {2169-2183},
pmid = {41316548},
issn = {1467-7652},
support = {32370391//National Natural Science Foundation of China/ ; 2025XJ06//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Magnolia/metabolism/genetics/physiology ; *Energy Metabolism/genetics/physiology ; *Thermogenesis/physiology/genetics ; *Flowers/metabolism/physiology/genetics ; *Mitochondria/metabolism ; Citric Acid Cycle/genetics ; Fatty Acids/metabolism ; Gene Expression Profiling ; Oxidative Phosphorylation ; Gene Expression Regulation, Plant ; Multiomics ; },
abstract = {The high demand for energy during floral thermogenesis drives the synergistic operation of multiple energy substrates for the rapid temperature rise and successful reproduction of flowers. However, how thermogenic plants precisely regulate substrate supply and metabolic pathways within a short time to support large-scale energy and heat release remains a mystery. This study revealed the elaborate synergistic supply mechanism of multi-source substrates in Magnolia denudata during thermogenesis. Transcriptome analysis showed that genes related to the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS) were significantly upregulated during the thermogenic stage (S2). Mitochondrial feeding assays using isotopically labelled substrates revealed that during the thermogenic stage, both the amount of pyruvate imported via the mitochondrial pyruvate carrier (MPC) and NAD-malic enzyme (NAD-ME) increased, and their synergistic effect accelerated the metabolic flow of the TCA cycle. Targeted lipidomics analysis indicated that the content of 63.6% fatty acids in the fatty acid degradation pathway decreased, while the key enzyme genes involved in triacylglycerol lipase (TGL) and fatty acid β-oxidation pathways were highly expressed during the thermogenic stage. In addition, enhanced expression of genes related to alanine aminotransferase (AlaAT) and glutamate dehydrogenase (GDH) suggested that amino acid metabolism might provide additional substrates for thermogenesis. This study clarifies the synergistic energy supply of carbohydrate, fatty acid and amino acid metabolism during thermogenesis in M. denudata, providing new evidence for understanding the metabolic regulatory flexibility of floral thermogenesis in plants.},
}
@article {pmid41316726,
year = {2026},
author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P},
title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D902-D911},
pmid = {41316726},
issn = {1362-4962},
support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; },
mesh = {*Genome, Viral ; *Virome/genetics ; *Metagenome ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Open Reading Frames ; Microbiota/genetics ; Humans ; Software ; Molecular Sequence Annotation ; },
abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.},
}
@article {pmid41316784,
year = {2025},
author = {Wu, ZQ and Yu, XC and Ning, YJ and Lin, F and Niu, JJ and Zhao, L and Luo, JY},
title = {[Multi-scale Ecosystem Services Trade-off/Synergy and Ecological Function Zoning in Taiyuan City].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {11},
pages = {7234-7245},
doi = {10.13227/j.hjkx.202410223},
pmid = {41316784},
issn = {0250-3301},
mesh = {*Ecosystem ; China ; *Conservation of Natural Resources/methods ; Cities ; Soil ; Forests ; Geographic Information Systems ; Agriculture ; Ecology ; Sustainable Development ; },
abstract = {A thorough understanding of the relationships between ecosystem services and ecological functional zoning is crucial for ecological restoration, land spatial planning, resource management, and sustainable economic development. We evaluated four types of ecosystem services-water yield, carbon storage, food production, and soil conservation-of Taiyuan City from 2000 to 2020 using the InVEST model. We also employed R language, GIS technology, and self-organizing maps to identify trade-offs and synergies between ecosystem services at three scales: whole regional, pixel and county, and ecological functional zoning. The results showed that: ① Between 2000 and 2020, significant changes occurred in land use and ecosystem services in Taiyuan City, including a decrease in cultivated land and grassland area and an increase in construction land and forest area. An enhancement in soil conservation, food production, and water yield value was observed, while carbon storage service value declined slightly. ② At the whole scale, trade-offs were predominant among ecosystem services, while weak synergistic effects were found at the pixel scale, and regional heterogeneity was observed at the county scale. ③ Three ecosystem service clusters were identified, which were divided into three ecological functional areas: ecological conservation, agricultural production, and ecologically vulnerable, with the largest proportion being the ecological conservation area. Based on these divisions, differentiated management recommendations were proposed. The findings may provide scientific guidance for the sustainable management of ecosystem services in Taiyuan City.},
}
@article {pmid41318529,
year = {2025},
author = {Wang, Y and Zhou, K and Lin, Z and Shen, H and Liu, R and Su, Z and Womer, FY and Wang, Y and Wei, Y and Zhu, R and Zheng, J and Zhang, X and Wang, F},
title = {Evaluation of the efficacy of group cognitive behavioral therapy on anxiety in college students based on wearable devices and mobile applications: a randomized controlled trial.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {6},
pmid = {41318529},
issn = {1471-244X},
mesh = {Humans ; Male ; Female ; *Cognitive Behavioral Therapy/methods ; *Students/psychology ; *Psychotherapy, Group/methods ; Young Adult ; Universities ; *Mobile Applications ; *Anxiety Disorders/therapy ; *Wearable Electronic Devices ; Adult ; Heart Rate/physiology ; Treatment Outcome ; Ecological Momentary Assessment ; Adolescent ; *Anxiety/therapy ; },
abstract = {BACKGROUND: Anxiety disorders are highly prevalent worldwide and have significant comorbidities including depression and substance use disorders. The global burden of anxiety disorders necessitates early intervention for high-risk populations, including college students facing stress during major life transitions. Objective measures and ecological momentary assessments may advance the development of early interventions.<br><br>OBJECTIVE: To test the efficacy of group cognitive-behavioral therapy (GCBT) intervention by implementing a randomized controlled trial and identifying potential objective measures.<br><br>METHODS: College students with a Generalized Anxiety Disorder Scale 7 scores &#x2265; 5 were randomized into GCBT (n&#x2009;=&#x2009;31) and wait-list control (WLC; n&#x2009;=&#x2009;28) groups. For both groups, self-reported symptom severity was assessed at baseline and follow-up in weeks 4, 8, and 28. Continuous heart rate and step counts measurements were captured by wearable sensors, along with ecological momentary assessments of mood and energy, which were obtained within 4&#x2009;weeks of treatment.<br><br>RESULTS: Compared to the WLC group, the GCBT group showed significant improvements in anxiety symptoms at week 28. Moreover, the GCBT group had significantly increased step counts and faster heart rates, more stable moods in the morning and evening, and better energy in the morning. Improvements in anxiety symptoms were closely associated with increases in step counts in the GCBT group.<br><br>CONCLUSION: Preliminary findings suggest that GCBT is associated with improvements in anxiety symptoms in college students over the long term. Changes in daily heart rates and step counts were correlated with mood and energy levels, suggesting that physiological markers may be useful in assessing treatment response.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov (NCT05913349), trial registration date: June 13, 2023 (retrospectively registered).},
}
@article {pmid41318763,
year = {2025},
author = {Turek, S and Skarzyńska-Łyżwa, A and Aparna, A and Pląder, W and Riewe, D and Junker, A and Altmann, T and Pawełkowicz, M},
title = {Multi-omics integration of transcriptome, miRNA, and metabolome uncovers molecular mechanisms of male flower development in cucumber line B10 (Cucumis sativus L.).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {45734},
pmid = {41318763},
issn = {2045-2322},
support = {UMO-2020/37/B/NZ9/00586//Narodowe Centrum Nauki/ ; CUC_GC-MS//European Plant Phenotyping Network - EPPN/ ; },
mesh = {*Cucumis sativus/genetics/growth &amp; development/metabolism ; *Flowers/genetics/growth &amp; development/metabolism ; *MicroRNAs/genetics/metabolism ; Gene Expression Regulation, Plant ; *Transcriptome ; *Metabolome ; Gene Expression Profiling ; Metabolomics/methods ; Multiomics ; },
abstract = {Male flower development in cucumber (Cucumis sativus L.) is a highly coordinated and genetically regulated process, yet the full complexity of its molecular underpinnings remains incompletely understood. In this study, we present a comprehensive, multi-omics analysis of male flower development in the cucumber line B10, integrating transcriptomic (RNA-seq), small RNA (miRNA) profiling, and metabolomic data across key tissues, including leaves, shoot apex, and floral buds at distinct developmental stages. Our analyses reveal dynamic gene expression changes and novel regulatory miRNAs, several of which have not previously been linked to male bud formation in cucumber. Functional enrichment analyses using GO and KEGG highlight critical pathways, including starch and sucrose metabolism, carbohydrate utilization, sporopollenin biosynthesis, and lignin catabolism. An integrative analysis combining miRNA-target interactions, transcriptomic shifts, and differential metabolite accumulation revealed coherent regulatory cascades linking transcription factors, carbohydrate metabolism, and cell wall dynamics. This study provides novel insights into the intricate genetic and metabolic networks shaping male flower morphogenesis and provides a valuable resource for advancing cucumber reproductive biology and crop improvement strategies.},
}
@article {pmid41319542,
year = {2026},
author = {Chen, X and Tie, Y and Zhu, M and Wu, Z and Xu, W and Zhang, Z and Ju, F and Zhang, W},
title = {Unraveling microbial synergy in blended Daqu: A multi-omics approach to decoding the unique flavor profile of Jiuliangxiang baijiu.},
journal = {Food chemistry},
volume = {499},
number = {},
pages = {147314},
doi = {10.1016/j.foodchem.2025.147314},
pmid = {41319542},
issn = {1873-7072},
mesh = {*Flavoring Agents/metabolism/chemistry ; *Bacteria/genetics/metabolism/isolation &amp; purification/classification ; Gas Chromatography-Mass Spectrometry ; Taste ; *Alcoholic Beverages/analysis/microbiology ; Volatile Organic Compounds/chemistry/metabolism ; *Wine/analysis/microbiology ; Microbial Consortia ; Metabolomics ; Multiomics ; },
abstract = {This study deciphers the microbial-ecological basis of Jiuliangxiang Baijiu's (JLX) unique flavor through blended Daqu multi-omics. GC-MS comparative analysis of five market-representative Baijiu types identified 25 aroma-active compounds (OAV ≥ 1) in JLX, with ethyl palmitate (OAV = 2) established as a potential characteristic marker. Subsequent investigation of its blended Daqu revealed how microbial consortia govern flavor formation. Physicochemical and microbial analyses demonstrated that Daqu blending elevated enzymatic capacities, including saccharification (+227.5 % vs single Daqu), esterification (+27.4 %), and liquefaction (+15.4 %), while enhancing microbial diversity. Metabolomic profiling identified glycerophospholipid Gpgro (14:0/16:0) as the ethyl palmitate precursor. Metagenomic tracking revealed that the core ester-producing taxa-primarily Bacillus licheniformis (from high-temperature Daqu) and Kroppenstedtia eburnea (from bacterial Daqu)-harbor complementary genetic potential for both esterase and acyltransferase pathways. The results provide a microbial-ecological framework for rational Daqu blending, offering actionable strategies to engineer microbial consortia for flavor-directed liquor innovation.},
}
@article {pmid41324251,
year = {2025},
author = {Ruiz Cuenca, P and Souza, FN and Coutinho do Nascimento, R and Goncalves da Silva, A and Eyre, MT and Santana, JO and de Oliveira, D and Ribeiro de Souza, EV and Palma, FG and de Carvalho Santiago, DC and Dos Santos Ribeiro, P and Ferreira Dos Santos, PE and Khalil, H and Read, JM and Cremonese, C and Costa, F and Giorgi, E},
title = {Using step selection functions to analyse human mobility using telemetry data in infectious disease epidemiology: a case study of leptospirosis.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {41324251},
issn = {2050-084X},
support = {PhD studentship/MRC_/Medical Research Council/United Kingdom ; R01 AI160780/AI/NIAID NIH HHS/United States ; Fellowship//Reckitt Global Hygiene Institute/ ; 150142/2024-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 10.35802/218987/WT_/Wellcome Trust/United Kingdom ; 1R01AI160780-01//National Institute of Allergy and Infectious Diseases/ ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Leptospirosis/epidemiology/transmission ; Female ; Male ; Brazil/epidemiology ; *Telemetry/methods ; Adult ; Middle Aged ; Young Adult ; Adolescent ; Risk Factors ; Aged ; Geographic Information Systems ; Movement ; },
abstract = {BACKGROUND: Human movement plays a critical role in the transmission of infectious diseases, especially those with environmental drivers like leptospirosis-a zoonotic bacterial infection linked to mud and water contact. Using GPS loggers, we collected detailed telemetry data to understand how fine-scale movements can be analysed in the context of an infectious disease.<br><br>METHODS: We recruited individuals living in urban slums in Salvador, Brazil, to analyse how they interact with environmental risk factors such as domestic rubbish piles, open sewers, and a local stream. We aimed to identify differences in movement patterns inside the study areas by gender, age, and leptospirosis serological status. Step selection functions, a spatio-temporal model used in animal movement ecology, estimated selection coefficients to represent the likelihood of movement toward specific environmental factors.<br><br>RESULTS: With 128 participants wearing GPS devices for 24-48 hr, recording locations every 35 s during active daytime hours, we segmented movements into morning, midday, afternoon, and evening. Our results suggested women moved closer to the central stream and farther from open sewers compared to men, while serologically positive individuals avoided open sewers.<br><br>CONCLUSIONS: This study introduces a novel method for analysing human telemetry data in infectious disease research.<br><br>FUNDING: Funding provided by Wellcome Trust, UK Medical Research Council, Brazilian National Research Council, Reckitt Global Hygiene Institute, and National Institute of Allergy and Infectious Diseases.},
}
@article {pmid41324682,
year = {2025},
author = {Koç, &#x130;},
title = {Predicting the potential geographic distribution of Fagus orientalis Lipsky under climate change using an ensemble model approach in Türkiye.},
journal = {Die Naturwissenschaften},
volume = {112},
number = {6},
pages = {93},
pmid = {41324682},
issn = {1432-1904},
mesh = {*Climate Change ; *Fagus/physiology ; Ecosystem ; Models, Theoretical ; Models, Biological ; },
abstract = {Oriental beech (Fagus orientalis Lipsky) is an ecologically and economically significant species, covering 8.5% of Türkiye's total forest area. However, climate change threatens its distribution due to increasing temperatures and decreasing precipitation. This study integrates geospatial informatics and ensemble modeling (EM) to predict the potential geographic distribution (PGD) of F. orientalis under future climate scenarios using Biomod2 within the ShinyBIOMOD framework. An EM model has been developed from six models [Generalized Boosting Model (GBM), Generalized Linear Model (GLM), Multivariate Adaptive Regression Splines (MARS), Generalized Additive Model (GAM), Artificial Neural Networks (ANN), and Maximum Entropy (MaxEnt)] using 76 validated occurrence records and 19 environmental predictors. Model validation achieved high predictive accuracy (AUC = 0.96, TSS = 0.85). Spatial projections for SSP2-45 and SSP5-85 scenarios indicate significant shifts in PGD. Notably, high-suitability habitats will decline under SSP2-45 but expand under SSP5-85. Bio2 [Mean Diurnal Range (mean of monthly (maximum temperature - minimum temperature))] and Bio4 [Seasonal temperature fluctuation (temperature seasonality (standard deviation x 100))] emerged as the dominant drivers of distribution changes. Based on geospatial analyses, F. orientalis is expected to migrate to higher altitudes in the Black Sea region and expand into southern and inner Türkiye. This shift reflects a broader trend of temperate forest adaptation to climate change. This study underscores the power of ensemble modeling for ecological forecasting and conservation planning, demonstrating the value of computational tools in assessing climate-driven species distribution changes. The findings contribute to predictive modeling for biodiversity conservation and ecosystem management.},
}
@article {pmid41325459,
year = {2025},
author = {Paredes-Vázquez, A and Balsa-Canto, E and Banga, JR},
title = {Identification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013204},
pmid = {41325459},
issn = {1553-7358},
mesh = {*Microbiota/physiology ; *Models, Biological ; Computational Biology/methods ; Workflow ; Humans ; Computer Simulation ; },
abstract = {Microbial communities, complex ecological networks crucial for human and planetary health, remain poorly understood in terms of the quantitative principles governing their composition, assembly, and function. Dynamic modeling using ordinary differential equations (ODEs) is a powerful framework for understanding and predicting microbiome behaviors. However, developing reliable ODE models is severely hampered by their nonlinear nature and the presence of significant challenges, particularly critical issues related to identifiability. Here, we address the identification problem in dynamic microbial community models by proposing an integrated methodology to tackle key challenges. Focusing on nonlinear ODE-based models, we examine four critical pitfalls: identifiability issues (structural and practical), unstable dynamics (potentially leading to numerical blow-up), underfitting (convergence to suboptimal solutions), and overfitting (fitting noise rather than signal). These pitfalls yield unreliable parameter estimates, unrealistic model behavior, and poor generalization. Our study presents a comprehensive workflow incorporating structural and practical identifiability analysis, robust global optimization for calibration, stability checks, and rigorous predictive power assessment. The methodology's effectiveness and versatility in mitigating these pitfalls are demonstrated through case studies of increasing complexity, paving the way for more reliable and mechanistically insightful models of microbial communities.},
}
@article {pmid41325472,
year = {2025},
author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Cornet, D and Beurier, G and Rouan, L and Estarague, A and Kazakou, E and Mahaut, L and Munoz, F and Weigel, D and Exposito-Alonso, M and Bossdorf, O and Chevin, LM and Vasseur, F},
title = {Divergent and stabilizing selection shape the phenotypic space of Arabidopsis thaliana.},
journal = {PLoS biology},
volume = {23},
number = {12},
pages = {e3003536},
pmid = {41325472},
issn = {1545-7885},
mesh = {*Arabidopsis/genetics/physiology ; Phenotype ; *Selection, Genetic ; Genetic Variation ; Arabidopsis Proteins/genetics ; Flowers/genetics ; Genome, Plant ; Transcription Factors/genetics ; },
abstract = {Why do we observe some plant phenotypes but not others? The multivariate phenotypic space occupied by individuals or species often reveals both limits and phenotypes strikingly deviating from main syndromes. These observations are usually thought to indicate, respectively, inviable trait combinations and unique phenotypes adapted to specific environments. However, the evolutionary drivers underlying trait covariations often remain unclear. Here, we characterized the phenotypic space of Arabidopsis thaliana by comparing 713 wild accessions collected across the globe with 2,544 artificially-created recombinant individuals. This, combined with the detection of adaptive processes operating within species, allowed us to elucidate the roles of natural selection as a driver of phenotypic (co)variations within A. thaliana. We found that the phenotypic space of this species is constrained and driven by varying levels of divergent and stabilizing selection across different traits. Moreover, at the margins of the European geographic range, strong directional selection favored outlier phenotypes characterized by very late flowering and variation in a WRKY transcription factor gene. Genome analyses revealed that these extreme phenotypes may be explained by hybridization between ancestral and modern lineages of A. thaliana. Our findings demonstrate how interplays between population history and natural selection shape phenotypic diversity in a plant species.},
}
@article {pmid41327539,
year = {2026},
author = {Mabuchi, K and Mai, JZ and Yauseyenka, VV and Brenner, AV and Little, MP and Minenko, VF and Veyalkin, I and Kukhta, TS and Trofimik, S and Drobyshevskaya, V and Vij, V and Ostroumova, E and Hatch, M and Drozdovitch, V and Cahoon, EK and Rozhko, AV},
title = {Thyroid nodules after prenatal exposure to chernobyl radioactive fallout in Belarus.},
journal = {International journal of radiation biology},
volume = {102},
number = {1},
pages = {20-26},
doi = {10.1080/09553002.2025.2588398},
pmid = {41327539},
issn = {1362-3095},
mesh = {Humans ; *Chernobyl Nuclear Accident ; Republic of Belarus/epidemiology ; Female ; Pregnancy ; *Thyroid Nodule/epidemiology/etiology ; Adult ; *Prenatal Exposure Delayed Effects/epidemiology ; *Radioactive Fallout/adverse effects ; Male ; Iodine Radioisotopes/adverse effects ; *Radiation Exposure/adverse effects ; Young Adult ; Radiation Dosage ; Dose-Response Relationship, Radiation ; },
abstract = {PURPOSE: To assess the risk of thyroid nodules associated with prenatal radiation exposure.<br><br>MATERIALS AND METHODS: Thyroid screening was conducted among 1,439 Belarusians who were prenatally exposed to radioactive fallout from the Chernobyl nuclear plant accident. Estimated thyroid doses (mean, 0.14; median, 0.02 gray [Gy]) were predominately from intake of [131]I. Binary logistic regression models were used to estimate excess odds ratios (EORs) for thyroid nodules associated with radiation dose.<br><br>RESULTS: A total of 258 screening participants had one or more nonneoplastic thyroid nodules. Among all participants, there was a linear dose response with an EOR/Gy of 0.44 (95% CI: -0.01, 1.38) of borderline significance (p = .06). This was driven by a significant EOR/Gy of 0.84 (95% CI: 0.07, 2.45; p = .02) among participants who were in the third trimester at the time of the accident (ATA). No significant associations with radiation were found among those who were in the second or first trimester ATA, but there were considerable uncertainties. No significant differences in dose response were found by nodule size or multiplicity.<br><br>CONCLUSIONS: The significant risk of thyroid nodules associated with exposure in the third trimester indicates the presence of a vulnerable subgroup of pregnant women at the time of an accidental radioiodine release. Because of the strong correlation between gestational age and [131]I dose in the fetal thyroid, the extent to which this excess risk is attributable to elevated [131]I dose and/or radiosensitivity of the thyroid in later stage of fetal development remains unclear.},
}
@article {pmid41327808,
year = {2026},
author = {Li, XD and Wu, QJ and Guo, YW and Chang, YJ and Chu, J},
title = {Treatment of acid coal gangue leaching wastewater with constructed wetland based on ceramsite substrate.},
journal = {Environmental technology},
volume = {47},
number = {5},
pages = {657-672},
doi = {10.1080/09593330.2025.2593569},
pmid = {41327808},
issn = {1479-487X},
mesh = {*Wetlands ; *Wastewater/chemistry ; *Water Pollutants, Chemical/analysis/chemistry ; *Waste Disposal, Fluid/methods ; *Coal ; Industrial Waste/analysis ; Biodegradation, Environmental ; },
abstract = {This study investigates the use of constructed wetlands (CWs) with ceramsite derived from surplus sludge pyrolysis ash for acid mine drainage (AMD) remediation. The system, incorporating ceramsite, limestone, and gravel, used soybean wastewater as a microbial carbon source. Results showed that the ceramsite-based system effectively raised pH from 3.5 to 8.0, achieving removal rates of 99.96% for Fe, 96.53% for Mn, 94.84% for Cu, 99.26% for Zn, and 96.02% for total phosphorus. Metal ion removal was primarily through ceramsite adsorption, with minor plant-mediated adsorption. Microbial analysis revealed that pH and metal concentrations influenced bacterial composition, with dominant genera including Trichococcus, Clostridium_Sensu_Stricto_1, and Citrobacter. Sulfate-reducing bacteria such as Desulfovibrio and Desulfobulbus played crucial roles in sulfate reduction. This study demonstrates a sustainable AMD treatment method that not only improves metal ion removal but also addresses sludge disposal challenges, highlighting the environmental benefits of using waste-derived materials for pollution control and resource recovery.},
}
@article {pmid41330108,
year = {2025},
author = {Casagrande, S and Pham, HV and Rufo, O and Critto, A},
title = {Unravelling the influence of projected land use/land cover on surface water ecological status in Italian watersheds.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181003},
doi = {10.1016/j.scitotenv.2025.181003},
pmid = {41330108},
issn = {1879-1026},
abstract = {This research examines the influence of land use and land cover (LULC) on water quality in Italian watersheds, with a focus on predicting the likelihood of achieving good surface water ecological status (SWES) under future scenarios (SSP2-RCP4.5 and SSP5-RCP8.5) for the years 2050 and 2100. The developed methodology includes remapping future LULC, conducting Principal Component Analysis to examine the interactions between land use classes and the impact of upstream LULC on downstream SWES, and regression analysis to predict future SWES. Future projections indicate a decline in SWES in human-influenced areas, but potential improvements in natural regions with conservation efforts. For both scenarios, over 60 % of Italian watersheds are expected to fail to achieve good SWES by 2050 and 2100, emphasizing the need for targeted land management strategies to mitigate these effects. This analysis represents valuable support for the development of adaptive strategies that safeguard water resources and ensure the long-term sustainability of freshwater ecosystems.},
}
@article {pmid41330243,
year = {2026},
author = {Bénézech, M and Drouineau, H and Bornarel, V and Briand, C and Díaz, E and Mateo, M and Beaulaton, L},
title = {Shifts in the European eel recruitment distribution: the impact of changing environmental conditions?.},
journal = {Marine environmental research},
volume = {214},
number = {},
pages = {107723},
doi = {10.1016/j.marenvres.2025.107723},
pmid = {41330243},
issn = {1879-0291},
mesh = {Animals ; *Anguilla/physiology ; Europe ; *Animal Migration ; Population Dynamics ; *Environmental Monitoring ; *Environment ; Ecosystem ; },
abstract = {The European eel (Anguilla anguilla) is a facultative catadromous migratory species that spawns in the Sargasso Sea, and grows over a wide continental range from the Barents Sea (72°N) to the southern limit of Morocco (30°N). Recruitment refers to the arrival of glass eels on continental shelves after an oceanic larval drift from the spawning ground. Although recruitment trends used to be quite consistent across European regions, recent modelling exercises have highlighted regional variations. At the European scale, we examined the relative contributions of six regions to overall recruitment over time using trend analysis methods. Variations in these contributions may be related to changes in environmental conditions. We identified the ecological processes preceding recruitment and their associated spatial and temporal scopes (e.g., spawning in the Sargasso Sea from March to May) to propose hypotheses regarding the potential influence of environmental factors on these processes. Using short- and long-term correlation strategies, we examined the relationships between recruitment and selected environmental variables. Our findings support the existence of spatial heterogeneity in recruitment distribution across Europe, which may inform management decisions at both local and broader levels for this species.},
}
@article {pmid41331158,
year = {2025},
author = {Castellano, S and Clarke, M and D'Acunto, L and Romañach, S and Cadaval, S},
title = {Restoring the Florida Everglades: Insights on Integrating Sea Level Rise into Decision-Support Tools.},
journal = {Environmental management},
volume = {76},
number = {1},
pages = {28},
pmid = {41331158},
issn = {1432-1009},
support = {G22AC00433-00//U.S. Geological Survey/ ; G22AC00433-00//U.S. Geological Survey/ ; G22AC00433-00//U.S. Geological Survey/ ; G22AC00433-00//U.S. Geological Survey/ ; G22AC00433-00//U.S. Geological Survey/ ; },
mesh = {Florida ; Climate Change ; *Conservation of Natural Resources/methods ; *Sea Level Rise ; *Decision Support Techniques ; Ecosystem ; Models, Theoretical ; *Wetlands ; },
abstract = {Although coastal ecosystems are impacted by climate change and sea-level rise, many ecological and hydrological models do not yet incorporate sea-level rise projections in their modeling outputs. Therefore, this research examined the various challenges that may prevent sea-level rise from being effectively incorporated in modeling and decision-support tools. We conducted semi-structured interviews with twenty-six professionals involved in Florida's Everglades restoration. We applied the Diffusions of Innovations Theory to better understand factors that can impact practitioners' adoption of newly designed decision-support tools that examine sea-level rise in the freshwater Everglades. The Diffusions of Innovations Theory provided insights into practitioners' perceptions of these tools. We found that these practitioners have a strong interest in using dynamic decision-support tools to plan for sea-level rise impacts on Everglades restoration, particularly when they receive information at appropriate geographic and temporal scales and are given hands-on tools and training. However, challenges that prevent developing these tools include outdated data, limited organizational capacity and funding, limited use of long-term indicators, uncertainty about climate change impacts on local ecosystems, and lack of integration between hydrological and ecological models. Our research also highlights that greater availability of different types of tools can help to meet the needs of the scientific and non-scientific audiences involved in Everglades restoration.},
}
@article {pmid41335619,
year = {2025},
author = {Yoshimura, M and Suwabe, M and Tsuji, K and Baba, Y and Kakazu, H and Miyagi, T and Ogasawara, M and Uematsu, J and Economo, EP and Ono, K},
title = {Maximum effect with minimum impact: A new selective control strategy for the Browsing ant Lepisiota frauenfeldi (Formicidae: Formicinae) minimize the impact on non-target species.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337230},
pmid = {41335619},
issn = {1932-6203},
mesh = {Animals ; *Ants/physiology ; *Introduced Species ; Japan ; *Insect Control/methods ; Biodiversity ; Ecosystem ; },
abstract = {Early-stage control of invasive ants provides an opportunity to suppress establishment while conserving existing biodiversity. We developed and tested a selective control strategy targeting the Browsing ant Lepisiota frauenfeldi, an emerging omnivorous, polygynous, and polydomous invader, during its initial establishment in an urban area of Okinawa Island, Japan. Because the local ant community was still present when the invasion was detected, the trial aimed at reducing the competitive advantage of the target species while preserving biotic resistance from resident species. We hypothesized that weakening L. frauenfeldi through selective chemical treatment would allow existing species to occupy its vacant niches, thereby accelerating eradication. Species-specific baits were formulated using a growth regulator with protein- and carbohydrate-based substrates. Baits were placed near nest entrances identified through monthly surveys over an area of approximately 1.6 hectares. Ant community dynamics were monitored for 44 months using hand-collection and sticky-trap surveys. The invasive ant showed a strong negative response to treatment, with an estimated 92% reduction in occurrence probability, ultimately disappearing from the treated area. Several non-target ant species increased in frequency, consistent with expectation of the niche reoccupation, while most other species remained stable, indicating minimal impact on the broader community. Compared to conventional methods, this approach used drastically less chemical while achieving high efficacy. Implementation through cross-organizational collaboration enabled parallel treatment in adjacent restricted areas and contributed to the program's success. These results highlight the practical and ecological value of nest-targeted, community-collaborative selective baiting as a strategy for managing omnivorous invasive ants during early establishment.},
}
@article {pmid41337153,
year = {2025},
author = {Mustri, MP and Duan, Q and Pawar, S},
title = {Accuracy of the Lotka-Volterra model fails in strongly coupled microbial consumer-resource systems.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013719},
pmid = {41337153},
issn = {1553-7358},
mesh = {*Models, Biological ; Computational Biology ; *Microbial Interactions/physiology ; Ecosystem ; *Microbiota/physiology ; Computer Simulation ; },
abstract = {The generalized Lotka-Volterra (GLV) model is a cornerstone of theoretical ecology for modeling the dynamics emerging from species interactions within complex ecological communities. The GLV is also increasingly being used to infer species interactions and predict dynamics from empirical data on microbial communities, in particular. However, despite its widespread use, the accuracy of the GLV's pairwise interaction structure in capturing the unseen dynamics of microbial consumer-resource interactions-arising from resource competition and metabolite exchanges-remains unclear. Here, we rigorously quantify how well the GLV can represent the dynamics of a general mathematical model that encapsulates key consumer-resource processes in microbial communities. We find that the GLV significantly misrepresents the feasibility, stability, and reactivity of microbial communities above a threshold biologically feasible level of consumer-resource coupling, because it omits higher-order nonlinear interactions. We show that the probability of the GLV making inaccurate predictions can be quantified by a simple, empirically accessible measure of timescale separation between consumers and resources. These insights advance our understanding of the temporal dynamics of resource-mediated microbial interactions and provide a method for gauging the GLV's reliability across various empirical and theoretical scenarios.},
}
@article {pmid41339386,
year = {2025},
author = {Camilo Fagua, J and Jantz, P and Burns, P and Jantz, SM and Kilbride, JB and Goetz, SJ},
title = {Maps of forest vertical structure for Colombia, a megadiverse country.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {1},
pmid = {41339386},
issn = {2052-4463},
mesh = {Colombia ; *Forests ; Ecosystem ; },
abstract = {Vegetation vertical structure refers to the 3D distribution of vegetation aboveground biomass. Vegetation vertical structure of tropical forests influences other ecological and environmental variables that are essential for the functioning of the ecosystems. Integrating over 5.9 million Globel Ecosystem Dynamics Investigation (GEDI) LiDAR (Light Detection and Ranging) footprints, multispectral, and synthetic aperture radar (SAR) imagery, we built five national maps at 25 m resolution of five forest structural metrics for Colombia, South America, for the year 2020. We mapped canopy height, the height of half the cumulative returned energy from GEDI (RH50), total canopy cover, foliage height diversity, and total plant area index. The resulting maps tended to have the highest errors in the Amazon and Andean regions. Total cover had the highest relative error. Interrelationship curves between forest structural metrics of GEDI footprints are maintained across mapped metrics, indicating that the predictive models preserve structural relationships observed in GEDI data. Due to the medium-high spatial resolution and national coverage of the forest structural maps presented in this work, these maps will be useful for evaluating and mapping other ecological variables and conservation priorities in Colombia.},
}
@article {pmid41339657,
year = {2025},
author = {Yao, G and Cai, X and Liu, J and Ding, S and Chen, X and Lin, C and Li, X and Yang, D},
title = {Chromosome-level genome assembly of Anastoechus asiaticus (Diptera: Bombyliidae).},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {10},
pmid = {41339657},
issn = {2052-4463},
support = {31970435//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32300372//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Chromosomes, Insect ; *Diptera/genetics ; *Genome, Insect ; Molecular Sequence Annotation ; Datasets as Topic ; },
abstract = {The genus Anastoechus plays a crucial role in ecosystems, functioning both as a pollinator and as a natural enemy, with its larvae parasitizing grasshopper egg masses and adults visiting flowers. Despite its ecological significance, research on Anastoechus remains limited. In this study, we present a chromosomal-level genome assembly of Anastoechus asiaticus, utilizing BGI sequencing, PacBio sequencing and High-throughput chromosome conformation capture (Hi-C) technology. This represents the first genomic data for the genus Anastoechus, with a final genome size of 512.14 Mb and a scaffold N50 of 82.71 Mb. Genome annotation identified 12,751 protein-coding genes, of which functional annotations are available for 11,305. Additionally, non-coding RNA annotation revealed 1,753 tRNAs, 56 miRNAs, 79 rRNAs, and 49 snRNAs. Repetitive elements account for 290.64 Mb, constituting 56.75% of the genome. This high-quality genome provides valuable data for future studies on population genetics, ecological adaptation, and the evolution of Bombyliidae and other related insect groups.},
}
@article {pmid41339692,
year = {2025},
author = {Hmidi, S and Cassir, N and Colson, P and Ruimy, R and Chaudet, H},
title = {Haemophilus influenzae and Staphylococcus aureus population shifts during social distancing as monitored by MALDI-TOF MS.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {920},
pmid = {41339692},
issn = {2045-2322},
mesh = {Humans ; *Staphylococcus aureus/isolation &amp; purification ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Haemophilus influenzae/isolation &amp; purification ; *COVID-19/epidemiology/virology/prevention &amp; control ; *Staphylococcal Infections/epidemiology/microbiology ; SARS-CoV-2/isolation &amp; purification ; *Haemophilus Infections/epidemiology/microbiology ; Physical Distancing ; },
abstract = {The COVID-19 pandemic prompted widespread public health interventions, including lockdowns and social distancing measures, which influenced microbial transmission dynamics. This study evaluates the evolution of the hospital incidence and spectral diversity of Haemophilus influenzae and Staphylococcus aureus associated with these measures using MALDI-TOF mass spectrometry-based epidemiological surveillance. MALDI-TOF MS spectra analyses of routine clinical bacterial identifications were used as proxies for strain typing. Spectra from lockdown and reference periods were compared using unsupervised classification methods. A total of 251 main spectrum profiles of H. influenzae, 2079 main spectrum profiles of S. aureus for respiratory tract and blood samples, and 414 main spectrum profiles for skin samples of S. aureus were examined. The data were analyzed using hierarchical clustering and binary discriminant analysis. Spectral diversity of H. influenzae showed a transient shift, reverting to pre-lockdown patterns by 2021, whereas S. aureus exhibited a spectral shift that persisted post-lockdown. Clustering analyses revealed statistically significant grouping of lockdown strains, suggesting selection pressures due to containment measures. Social distancing measures were associated with modifications in bacterial population structures, with distinct post-lockdown recovery patterns. MALDI-TOF MS fingerprints proved to be a valuable tool for real-time epidemiological surveillance. This full-size experiment of social distancing highlights the complex interactions involving human behavior, bacterial ecology, and population dynamics and suggests different effects for different bacterial species.},
}
@article {pmid41340097,
year = {2025},
author = {Wang, L and Zhou, N and Jaffe, NM and Pidvirny, K and Tierney, AO and Fisher, HB and Morfini, F and Forbes, EE and Pizzagalli, DA and Cai, T and Webb, CA},
title = {Multimodal prediction of future depressive symptoms in adolescents.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {21},
pmid = {41340097},
issn = {1471-244X},
support = {K23 MH108752/MH/NIMH NIH HHS/United States ; P50 MH119467/MH/NIMH NIH HHS/United States ; P50MH119467/MH/NIMH NIH HHS/United States ; K23MH108752/MH/NIMH NIH HHS/United States ; },
abstract = {BACKGROUND: Depression rates surge during adolescence. Early identification of youth at increased risk for depression is crucial for timely intervention and, ideally, prevention. This study aims to improve the prediction of future depressive symptoms in adolescents by using a multimodal approach that integrates relevant clinical, demographic, behavioral, and neural characteristics.<br><br>METHODS: 103 adolescents (ages 12&#x2013;18; 72.8% female) underwent a baseline assessment including self-report questionnaires, ecological momentary assessment, a clinical interview, and behavioral and neural measures of reward responsiveness. We used nested cross-validation to compare machine learning approaches as well as conventional linear regression in predicting depressive symptoms (Center for Epidemiological Studies Depression Scale [CES-D] and the Mood and Feelings Questionnaire [MFQ]) at a 3-month follow-up.<br><br>RESULTS: For the prediction of CES-D depression scores, the best performing model was a multivariable linear regression using as predictors five principal component scores from a principal component analysis of baseline variables (RMSE&#x2009;=&#x2009;6.501, R[2]&#x2009;=&#x2009;0.688). For the MFQ, the best performing model was a univariable linear regression with baseline MFQ scores as the sole predictor (RMSE&#x2009;=&#x2009;8.054, R[2]&#x2009;=&#x2009;0.671). A factor analysis revealed that items assessing melancholic features were most predictive of future depressive symptoms.<br><br>CONCLUSION: More complex machine learning approaches did not outperform regression in predicting future depressive symptoms. The integration of relevant multimodal predictors reveals which adolescent characteristics (e.g., melancholic features and physical anxiety) have a larger contribution to predicting short-term future depressive symptoms. Future studies are needed with larger sample sizes and longer follow-up periods to provide a more comprehensive test of such models.<br><br>CLINICAL TRIAL NUMBER: Not applicable.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12888-025-07665-8.},
}
@article {pmid41343618,
year = {2025},
author = {Athreya, GS and Gokhale, CS and Verma, P},
title = {Coexistence rules for small, antagonistically interacting microbial communities.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013763},
pmid = {41343618},
issn = {1553-7358},
mesh = {*Microbiota/physiology/drug effects ; Anti-Bacterial Agents/pharmacology/metabolism ; *Microbial Interactions/physiology ; *Microbial Consortia/physiology/drug effects ; Biodiversity ; Computational Biology ; *Models, Biological ; Computer Simulation ; },
abstract = {The coexistence of diverse microbial communities despite the common presence of antimicrobial weapons presents a fundamental puzzle in ecology. To address this issue, we investigate the role of antibiotic-mediated interactions in driving microbial diversity using methods from graph theory and theoretical ecology. Our exhaustive analysis of small interaction graphs involving antibiotic production, resistance, and degradation reveals that two factors together determine whether an interaction pattern can support coexistence or not: a certain producer-sensitive-degrader (PSD) motif is critical, and a form of cyclicity between the action of different antibiotics is necessary. Using individual-based simulations, we also explore the role of the PSD motif in spatially structured populations and demonstrate that community coexistence is robust over a wide range of antibiotic and degrader diffusivities. Our findings provide a deeper understanding of the interaction patterns that drive diversity in complex microbial communities. Specifically, we emphasize how antagonism does not preclude biodiversity. These results offer clear pathways for cultivating synthetic microbial consortia, enabling the design of more effective strategies for manipulating microbial communities.},
}
@article {pmid41343702,
year = {2025},
author = {Oba, T and Moriishi, C and Takano, K and Katahira, K and Kimura, K},
title = {Mobile-Based Ecological Momentary Intervention for Improving Physical Activity in Adults Without Regular Physical Activity: Pilot Randomized Controlled Trial.},
journal = {JMIR formative research},
volume = {9},
number = {},
pages = {e79360},
pmid = {41343702},
issn = {2561-326X},
mesh = {Humans ; Pilot Projects ; Female ; Male ; *Ecological Momentary Assessment ; *Exercise/psychology/physiology ; Adult ; Middle Aged ; Japan ; *Mobile Applications ; *Health Promotion/methods ; Fitness Trackers ; Health Behavior ; Heart Rate ; Feasibility Studies ; },
abstract = {BACKGROUND: The ecological momentary intervention (EMI) is one of the most promising digital-primarily mobile-interventions to enhance physical activity (PA) and other health behaviors. It is a combination of ecological momentary assessment (EMA), in which participants are prompted to indicate their momentary states and ongoing behaviors in daily life, and the just-in-time delivery of interventions tailored to the EMA responses. The EMI has typically been implemented in message-based interventions (eg, activity recommendations tailored to users' physical locations), but its efficacy and feasibility have not been sufficiently established because of the variability in design and implementation.<br><br>OBJECTIVE: This pilot, two-arm, parallel-group randomized controlled trial aimed to be an exemplar of EMI for improving PA and establishing efficacy and feasibility among adults without a habit of PA.<br><br>METHODS: A total of 40 participants (23 women; mean age 45.40, SD 10.50 years) were recruited from among community dwellers in northeast Japan and randomly allocated to the EMI or control group. Each participant wore an activity tracker to monitor their daily step count and heart rate (HR) for 4 weeks (fully automated). Simultaneously, they responded to EMA questions about the current weather, location, and social context 3 times during the daytime and an additional evening question about motivations for PA each day. Only the EMI group received messages tailored to their responses to EMA, recommending more active alternative behaviors suited to EMA-reported contexts.<br><br>RESULTS: Participants wore a Fitbit device for 90.3% (21.66/24 hours per day) of the study period (mean 90.3, SD 10.0), and no dropouts were observed. The EMI group showed no significant improvement in the self-reported amount of PA (P=.44), step count (P=.24), or motivation for PA (from P=.11 to P=.91) compared with the control group. However, the EMI group showed a significantly larger increase in the minutes of 40% HR reserve, a measure of moderate or high intensity of PA (mean 16.03, 95% CI 3.76-28.29; Cohen d=0.20-0.41; P=.02 for the follow-up weeks). The intervention was rated as marginally useful and satisfactory, and approximately half of the participants expressed a willingness to continue the intervention. The timing of the EMA prompting was considered inappropriate.<br><br>CONCLUSIONS: These findings suggest that the EMI with messages tailored to EMA-reported contexts was not effective in increasing the amount or motivation for PA but may increase the intensity as assessed by the HR. The intervention aimed to help individuals implement small but slightly more active behaviors in their daily routine, which may not accompany prominent body movements but may be reflected in the increased HR. Marginal feasibility indicates that the intervention has sufficient scope for improvement, particularly in terms of prompt timing.},
}
@article {pmid41344766,
year = {2026},
author = {Zhang, L and Zhang, Y and Huang, J and Zhou, R and Wu, C},
title = {A synthetic microbial community enhances flavor and safety in reduced-salt soy sauce fermentation: Multi-omics insights into microbial stabilization and metabolic regulation.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104974},
doi = {10.1016/j.fm.2025.104974},
pmid = {41344766},
issn = {1095-9998},
mesh = {Fermentation ; *Soy Foods/microbiology/analysis ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Sodium Chloride/metabolism/analysis ; *Microbial Consortia ; Flavoring Agents/metabolism ; Taste ; Food Microbiology ; *Microbiota ; Multiomics ; },
abstract = {Reducing sodium in soy sauce fermentation while preserving flavor and safety presents significant technical challenges. To address this, we constructed a synthetic microbial community (SynMC) comprising Tetragenococcus halophilus T10, Zygosaccharomyces rouxii QH-25, and Wickerhamiella versatilis CGMCC 3790 for reduced-salt fermentation (13 %NaCl). Multi-omics analysis revealed three coordinated improvements: First, microbial community stabilization through suppression of spoilage taxa (e.g., Millerozyma) and enrichment of functional genera (e.g., Wickerhamiella), reducing negative ecological correlations from 5.3 % to 1.7 % compared to the low-salinity control group. Second, metabolic restructuring enhanced characteristic aromas while reducing biogenic amines (BAs) to 21.98 mg/L (76 % lower than L group). Third, metatranscriptomics identified upregulated amino acid metabolism (238 % more BA-degrading enzymes) and carbohydrate utilization pathways. These synergistic effects indicate that strategic microbial consortia design can overcome the salt reduction challenge through targeted ecological and metabolic regulation, enabling industrial-scale production of superior, safer low-salt soy sauce.},
}
@article {pmid41345120,
year = {2025},
author = {Abad-Recio, IL and Rubel, V and Filker, S and Garate, L and Stoeck, T and Logares, R and Lanzén, A},
title = {The Basque Coast Estuarine Sediment Gene Catalogue.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1909},
pmid = {41345120},
issn = {2052-4463},
support = {Fi 2089/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STO 414/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Ecosystem ; *Estuaries ; Eukaryota/genetics ; *Geologic Sediments/microbiology ; Metagenomics ; Viruses/genetics ; Datasets as Topic ; },
abstract = {Estuaries are critical transition zones that link marine, riverine, and terrestrial ecosystems, including habitats like intertidal mudflats and tidal marshes. These ecosystems are biodiversity hotspots providing essential ecological functions such as nutrient cycling and pollutant removal. Despite their importance, there is a significant knowledge gap regarding the ecological functioning of these habitats and how they are impacted by anthropogenic pressures. From intertidal estuarine benthos along the Basque Coast 92 microbial metagenomic assemblies were retrieved that allowed us to reconstruct 390 medium plus 81 high quality MAGs, along with 108 million putative genes from bacteria, archaea, eukaryotes, and viruses. This unique dataset will enhance our understanding of ecosystem functioning, biodiversity, and be useful to reveal biogeochemical processes and the role of unculturable biomass.},
}
@article {pmid41345123,
year = {2025},
author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM},
title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1913},
pmid = {41345123},
issn = {2052-4463},
support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; },
mesh = {Ecosystem ; *Metagenome ; Microbiota ; Pacific Ocean ; *RNA, Transfer/genetics ; *Seawater/microbiology ; *Transcriptome ; Datasets as Topic ; },
abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.},
}
@article {pmid41345410,
year = {2025},
author = {Gómez-Suárez, M and Laeseke, P and Seebens, H},
title = {A global dataset of native and alien distributions of alien species.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1914},
pmid = {41345410},
issn = {2052-4463},
support = {521530235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 521530235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 521529463//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Introduced Species ; Animals ; },
abstract = {Biological invasions have been identified as a major threat to nature with far-reaching consequences also for human-wellbeing. Mitigating and preventing further impacts requires knowledge about the origins of alien species and their spread dynamics. While several new datasets have been published recently about alien species distributions, information about their native ranges is scarce and scattered. Here, we present a comprehensive dataset of the regions of origin and introduction of alien species worldwide. We accessed multiple global datasets of species distributions to compile, harmonize and integrate data of alien species distributions and their native ranges. Building on previous efforts, we advanced an existing workflow to allow full reproducibility and transparency in creating the dataset. The final dataset contains 427,956 records including alien distributions of 39,700 species and native distributions of 21,345 alien species in 289 regions worldwide. This dataset provides a solid foundation for analyses of alien species flows, the identification of new emerging alien species and the management of biological invasions through prioritizing major routes of spread.},
}
@article {pmid41345546,
year = {2025},
author = {Marko, &#x160; and Rusinko, A and Barka, M and Balogová, M and Rubáčová, L and Papežík, P},
title = {Snakes among citizens: distribution and ecology of the Aesculapian snake, Zamenis longissimus (Laurenti, 1768) in Bratislava revealed by citizen science.},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {136},
pmid = {41345546},
issn = {2730-7182},
mesh = {Animals ; *Animal Distribution ; Cities ; *Citizen Science ; *Colubridae ; Datasets as Topic ; *Ecosystem ; Slovakia ; *Social Media ; Humans ; },
abstract = {BACKGROUND: Urban environments are increasingly recognized as important habitats for wildlife, yet information on how reptiles use urban environments remains scarce. The Aesculapian snake (Zamenis longissimus), a non-venomous colubrid widespread in Central Europe, is considered a habitat generalist with a frequent association with human settlements. However, data on its occurrence and ecology in metropolitan areas are limited. To address this gap, we implemented a citizen science initiative in Bratislava, Slovakia, aiming to document the distribution and habitat use of the Aesculapian snake and to evaluate the potential and limitations of citizen science for reptile monitoring in urban environments.<br><br>RESULTS: Between April 2019 and October 2022, a citizen science initiative was implemented to monitor the distribution and ecology of the Aesculapian snake in Bratislava, Slovakia. The project relied primarily on social media, which proved to be the most effective channel for data collection, complemented by direct e-mail submissions. Altogether, volunteers provided 588 verified records of the focal species, alongside 184 misidentified observations of other native reptiles, most frequently Natrix spp. Spatial analyses showed that most observations of the Aesculapian snake in Bratislava were concentrated in natural and semi-natural areas at lower elevations below 300&#x2009;m a.s.l., with a few records above 500&#x2009;m. Within these areas, snakes were most often reported from built-up and forested land cover, while agricultural land yielded comparatively few sightings. Seasonal patterns indicated a pronounced peak in spring and early summer, while diurnal activity was dominated by midday and afternoon observations. Specifically, the number of reports declined with increasing urbanization intensity but was higher in more densely populated areas, reflecting both ecological patterns and the availability of observers.<br><br>CONCLUSION: This study delivers one of the most comprehensive datasets on the Aesculapian snake in an urban setting, highlighting its synanthropic behavior and frequent use of anthropogenic habitats. At the same time, the results underscore both the opportunities and inherent biases of citizen science, confirming its value as a complementary tool for monitoring reptile populations in metropolitan environments.},
}
@article {pmid41345722,
year = {2025},
author = {Bridgen, JRE and Jewell, C and Lewis, JM and Todd, S and Semple, MG and Feasey, N and Read, JM},
title = {Model-based methods for hospital infection prevention and control: potential and challenges.},
journal = {BMC global and public health},
volume = {3},
number = {1},
pages = {111},
pmid = {41345722},
issn = {2731-913X},
}
@article {pmid41346804,
year = {2025},
author = {Morucci, K and Ortiz Cam, L and Diaz, EW and Porras-Cotrina, G and Bustos, J and Verastegui, M and Gavidia, CM and Castillo-Neyra, R},
title = {GPS tracking of free-roaming dogs and human spillover risk of Echinococcus granulosus in highly endemic Peru.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1647590},
pmid = {41346804},
issn = {2297-1769},
support = {T32 AI070077/AI/NIAID NIH HHS/United States ; },
abstract = {INTRODUCTION: Cystic echinococcosis (CE), a neglected disease that results from infection with the larval stage of the Echinococcus granulosus sensu lato (s.l.) tapeworm, poses significant zoonotic risk to humans and is a persistent threat in developing agricultural communities around the world. While the prevalence of human CE in the central highlands of Peru has previously been estimated around 5-7%, true prevalence is likely higher given the protracted period of asymptomatic disease, reduced medical access of at-risk populations, increased contact between herders, livestock, and herding dogs, and poor understanding of local disease epidemiology. To beIer understand CE epidemiology in a highly endemic region of Peru, we studied the movement of free-roaming dogs in the community of Chanchayllo, Junin, Peru.<br><br>METHODS: We performed copro-ELISA to identify E. granulosus s.l. positive dogs, tracked the ranging behavior and calculated home ranges of 19 owned, free-roaming dogs to understand the movement of the definitive host of E. granulosus s.l. on the landscape. Specifically, we investigated the spatial association between E. granulosus-infected dog home ranges and proximity to their owners' houses and a local slaughterhouse.<br><br>RESULTS: Echinococcus granulosus s.l. infection prevalence was alarmingly high in our canine population, with 85% positivity (binomial exact 95% CI: 62.1-96.8%). All dog home ranges overlapped with their owners' households, and notably, even negative dog households overlapped with nearby positive dog home ranges.<br><br>DISCUSSION: These data suggest that widespread environmental contamination of E. granulosus s.l. egg-containing feces may be a significant driver of locally elevated disease prevalence in human populations. We use our findings to understand the local disease ecology of CE in free roaming dogs, assess pillover risk, and guide future intervention strategies aimed at reducing human cases. Our findings suggest that existing trategies delivering anthelmintic drugs to individual households have the potential to reduce spillover of E. granulosus s.l.},
}
@article {pmid41346809,
year = {2025},
author = {Castillo-Neyra, R and Díaz, EW and Bellotti, BR and Morucci, K and De la Puente-León, M and Ortiz-Cam, L and Levy, MZ},
title = {Cave dogs around major urban areas of Arequipa, Peru, threaten rabies elimination program.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1649737},
pmid = {41346809},
issn = {2297-1769},
support = {D43 TW012741/TW/FIC NIH HHS/United States ; K01 AI139284/AI/NIAID NIH HHS/United States ; R01 AI168291/AI/NIAID NIH HHS/United States ; T32 AI070077/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: In the city of Arequipa, Peru, the government has implemented control measures against dog rabies virus since the detection of its reintroduction in 2015. The city was previously considered free of animal reservoirs, except for free-roaming owned dogs, animals with identifiable owners but allowed to move unsupervised, and stray dogs, which include both abandoned and street-born dogs that roam freely while relying on human settlements for food, within its urban boundaries. However, multiple reports from peri-urban residents have suggested the presence of feral dogs, a population living independently of humans on the city's outskirts. We aim to document the presence and dietary patterns of feral dogs adjacent to the city margins.<br><br>METHODS: We conducted monthly field visits to four peri-urban localities in eastern Arequipa, an area where the presence of feral dogs had been previously reported. Dog caves were identified by tracking footprints and other field signs left by dogs, and their locations were georeferenced. Each cave was revisited monthly three times to record the presence of live and dead dogs, and puppies. Fecal samples collected around the caves were analyzed to assess dietary patterns.<br><br>RESULTS: We observed that feral dogs use caves for resting, hiding, and reproduction-some of which appear to be constructed by the dogs themselves. The high number of puppies and dead adult dogs indicates a high population turnover. Dietary analysis revealed that these dogs feed on local fauna, including birds, rodents, cats, sheep, and, notably, other dogs.<br><br>CONCLUSIONS: These unowned, cave-dwelling dogs are not reached by mass rabies vaccination or sterilization programs. Moreover, they exist outside the jurisdiction of health inspectors responsible for rabies surveillance, resulting in a lack of data on rabies infection in this subpopulation. Our findings highlight the need for integrated One Health strategies to address the potential challenges posed by feral dog populations in rabies elimination efforts.},
}
@article {pmid41348596,
year = {2025},
author = {Hernández-Velázquez, R and Ziemski, M and Bokulich, NA},
title = {ViromeXplore: integrative workflows for complete and reproducible virome characterization.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
pmid = {41348596},
issn = {1477-4054},
support = {22.00210//Swiss State Secretariat for Education, Research and Innovation/ ; //European Union nor European Research Executive Agency/ ; },
mesh = {*Virome ; *Workflow ; *Metagenomics/methods ; *Software ; High-Throughput Nucleotide Sequencing ; *Computational Biology/methods ; *Viruses/genetics/classification ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results ; },
abstract = {Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.},
}
@article {pmid41348921,
year = {2025},
author = {Ammar, M and Fogarty, L and Kandler, A},
title = {Memory, innovation and vertical learning.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013785},
pmid = {41348921},
issn = {1553-7358},
mesh = {Humans ; *Memory/physiology ; *Learning/physiology ; *Social Learning/physiology ; Computer Simulation ; Computational Biology ; Animals ; Cultural Evolution ; },
abstract = {One of the most controversial and actively debated questions about both human and non-human animal culture concerns its relationship with adaptation - under what circumstances might we expect culture, and the ability to learn socially from others, to be beneficial, and favored by natural selection? Existing theory posits that the benefit of social learning depends on the rate at which the environment changes, and recent work has shown that this relationship is mediated by how much information an individual can retain over time - by memory. Based on extensive ethnographic research, vertical learning-social learning from parent to offspring-appears to be an extremely salient and important type of social learning. Here we develop large-scale agent-based simulation models to investigate the evolutionary relationship between vertical social learning in particular and the memory and retention of cultural information. We show that the benefit of vertical learning depends on how quickly those information is forgotten and on the exact way in which individuals innovate. This work points to the importance of a complex interplay between the size of cultural repertoires, the benefits of cultural preservation, changing selective environments, and the mechanism of innovation - none of which can be fully understood in isolation.},
}
@article {pmid41348937,
year = {2025},
author = {Xu, X and Cai, Z and Jia, W and Cao, Y and Hao, Y and Zhou, X and Liang, A and Lin, Z and Zhuang, S and Zhang, Z and Han, L and Zhao, J and White, JC and Ma, C and Xing, B},
title = {Multiomics Insights into Nanoscale Boron Nitride Mediated Antioxidant Defense and Metabolic Reprogramming in Cucumber in Response to Fusarium Infection.},
journal = {ACS nano},
volume = {19},
number = {50},
pages = {42349-42364},
doi = {10.1021/acsnano.5c14128},
pmid = {41348937},
issn = {1936-086X},
mesh = {*Fusarium/drug effects ; *Antioxidants/metabolism/pharmacology/chemistry ; *Plant Diseases/microbiology ; *Boron Compounds/pharmacology/chemistry ; *Cucumis sativus/metabolism/microbiology/drug effects ; *Nanoparticles/chemistry ; Oxidative Stress/drug effects ; Metabolic Reprogramming ; Multiomics ; },
abstract = {Fusarium poses a significant threat to the global crop productivity and food security. This study evaluated the mechanisms of nanoscale boron nitride (nano-BN, 0-500 mg/kg) against Fusarium oxysporum in cucumber. Fusarium infection severely impaired plant growth with biomass declining by 60%. However, 50 mg/kg nano-BN treatment significantly increased shoot biomass by 64.9% compared to disease controls, restoring photosynthetic parameters to near-healthy levels. Nano-BN inhibited Fusarium proliferation by disrupting hyphal and spore structures and reduced mycotoxin production (beauvericin and enniatin) by over 63%. Metabolomic analysis demonstrates that nano-BN mitigated oxidative stress by enhancing glutathione metabolism, with significant increases in glutathione and ascorbic acid content by 166.67% and 478.78%, respectively. Importantly, the protein-protein interaction network shows that nano-BN counteracted Fusarium-induced suppression of ribosomal proteins and endoplasmic reticulum stress-related proteins, promoting protein synthesis and folding. The coexpression network identified sucrose and geshoidin as key metabolites linked to ribosomal and mitochondrial proteins, bridging metabolic resilience with enhanced disease resistance. Multiomics analysis suggests that nano-BN alleviated the Fusarium stress by regulating the phenylpropanoid biosynthesis and restoring the expression levels of key enzymes in carbohydrate metabolism. Overall, nano-BN effectively mitigates Fusarium stress by enhancing plant growth and modulating metabolic processes, offering a promising strategy for plant protection.},
}
@article {pmid41348994,
year = {2026},
author = {Tomarovsky, AA and Khan, R and Dudchenko, O and Beklemisheva, VR and Perelman, PL and Totikov, AA and Serdyukova, NA and Bulyonkova, TM and Pobedintseva, M and Abramov, AV and Weisz, D and Yakupova, A and Zhuk, A and Graphodatsky, AS and Powell, R and Aiden, EL and Koepfli, KP and Kliver, S},
title = {Novel chromosome-length genome assemblies of three distinct subspecies of pine marten, sable, and yellow-throated marten (genus Martes, family Mustelidae).},
journal = {The Journal of heredity},
volume = {117},
number = {3},
pages = {583-591},
doi = {10.1093/jhered/esaf101},
pmid = {41348994},
issn = {1465-7333},
support = {CF22-0680//Carlsbergfondet Research Infrastructure/ ; },
mesh = {Animals ; *Mustelidae/genetics/classification ; *Genome ; Karyotype ; },
abstract = {The genus Martes consists of medium-sized carnivores within the family Mustelidae that are commonly known as martens, many of which exhibit extensive geographic variation and taxonomic uncertainty. Here, we report chromosome-length genome assemblies for three subspecies, each representing a different marten species: the Tobol sable (Martes zibellina zibellina), the Ural pine marten (Martes martes uralensis), and the Far East yellow-throated marten (Martes flavigula aterrima). Using linked-read sequencing and Hi-C scaffolding, we generated assemblies with total lengths of 2.39 to 2.45 Gbp, N50 values of 137 to 145 Mbp, and high BUSCO scores (93.6% to 96.4%). We identified 19 chromosomal scaffolds for sable and pine marten, and 20 for yellow-throated marten, which agrees with the known karyotypes of these species (2n = 38 and 2n = 40, respectively). Annotation predicted ~ 20,000 protein-coding genes per genome, of which > 90% were assigned functional names. Repeats encompass 36.9% to 40.4% of the assemblies, with a prevalence of LINEs and SINEs, and are conservative across the genus. Synteny analysis of our generated and available marten genome assemblies revealed assembly artifacts in previously published assemblies, which we confirmed through investigation of Hi-C contact maps. Among other rearrangements, we verify a sable-specific inversion on chromosome 11 using the published cytogenetic data. Our assemblies broaden the genomic resources available for Martes, extending coverage to geographically distant and taxonomically significant subspecies. Together, they provide a robust framework for assessing intraspecific genetic diversity, identifying signatures of hybridization, and refining the complex taxonomy of the genus. Beyond conservation and evolutionary applications, these references will facilitate comparative genomics across Mustelidae and other carnivorans.},
}
@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 &amp; proteomics},
volume = {58},
number = {},
pages = {101708},
doi = {10.1016/j.cbd.2025.101708},
pmid = {41349461},
issn = {1878-0407},
mesh = {Male ; Animals ; *Spermatogenesis ; *Testis/growth &amp; development/metabolism ; *Catfishes/growth &amp; 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.},
}
@article {pmid41350118,
year = {2026},
author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.},
journal = {Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {55},
number = {3},
pages = {368-380},
pmid = {41350118},
issn = {1600-0714},
mesh = {Humans ; *Carcinoma, Squamous Cell/microbiology/pathology ; Male ; *Microbiota/genetics ; *Mouth Neoplasms/microbiology/pathology ; Female ; Middle Aged ; Aged ; Saliva/microbiology ; Case-Control Studies ; Adult ; *Mouth/microbiology ; DNA, Bacterial ; },
abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.<br><br>METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.<br><br>RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.<br><br>CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.},
}
@article {pmid41350530,
year = {2025},
author = {Mottl, O and Gaiser, F and Šímová, I and Flantua, SGA},
title = {VegVault dataset: linking global paleo-, and neo-vegetation data with functional traits and abiotic drivers.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1923},
pmid = {41350530},
issn = {2052-4463},
support = {GN23-06386I//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (Grant Agency of the Czech Republic)/ ; UNCE/24/SCI/006//Univerzita Karlova v Praze (Charles University)/ ; TMS2022STG03//Universitetet i Bergen (University of Bergen)/ ; },
mesh = {*Climate Change ; *Biodiversity ; *Ecosystem ; *Plants ; *Databases, Factual ; },
abstract = {Understanding the dynamics and persistence of biodiversity patterns over short (contemporary) and long (thousands of years) time scales is crucial for predicting ecosystem changes under global climate and land-use changes. A key challenge is integrating currently scattered ecological data to assess complex vegetation dynamics over time. Here, we present VegVault, an interdisciplinary SQLite database that uniquely integrates paleo- and neo-ecological plot-based vegetation data on a global and millennial scale, directly linking them with functional traits, soil, and climate information. VegVault currently comprises data from BIEN, sPlotOpen, TRY, Neotoma, CHELSA, and WoSIS, providing a comprehensive and ready-to-use resource for researchers across various fields to address questions about past and contemporary biodiversity patterns and their abiotic drivers. To further support the usability of the data, VegVault is complemented by the {vaultkeepr}
R package, enabling streamlined data access, extraction, and manipulation. This study introduces the structure, content, and diverse applications of VegVault, emphasizing its potential role in advancing ecological research to improve predictions of biodiversity responses to global climate change.},
}
@article {pmid41352621,
year = {2026},
author = {Kissane, ZM and Warren, KS and Yeap, L and Shephard, JM},
title = {Hazard identification and ecological risk assessment of pesticide exposure in wildlife using GPS telemetry: Case study on endangered Carnaby's Cockatoos.},
journal = {Environmental toxicology and pharmacology},
volume = {121},
number = {},
pages = {104894},
doi = {10.1016/j.etap.2025.104894},
pmid = {41352621},
issn = {1872-7077},
mesh = {Animals ; Risk Assessment ; Endangered Species ; *Pesticides/toxicity/analysis ; Telemetry ; Environmental Monitoring/methods ; Geographic Information Systems ; *Environmental Exposure/analysis ; Animals, Wild ; *Environmental Pollutants/analysis/toxicity ; },
abstract = {Wildlife toxicology faces increasing threats from pesticide use, yet the impacts on biodiversity remain unclear, as current toxicity thresholds often rely on laboratory data that do not reflect environmental exposure. Here we present a two-step methodology integrating ecotoxicology and movement ecology to investigate pesticide exposure in endangered Carnaby's cockatoos (Zanda latirostris). Using GPS telemetry and satellite tracking, this study identified pesticide exposure sites and quantified the likelihood and consequences of exposure. A total of 26 pesticides were detected in forage sources (agricultural seed), with 80 % of seed samples having one or more pesticides detected. The Maximum Residue Limit (MRL) was exceeded for multiple pesticides including imidacloprid, thiamethoxam, clothianidin, difenoconazole and metalaxyl. Results have highlighted the risks that granivorous birds face being exposed to insecticides, herbicides, and fungicides in agroecosystems. This methodology is broad in scope and applicable across species, providing the ecological realism missing in laboratory-based studies.},
}
@article {pmid41353493,
year = {2025},
author = {Gautam, A and Verma, P and Kushwaha, S and Dubey, S and Bhatt, D and Singh, A and Kalle, R},
title = {Three decades of remote sensing applications in avian ecological studies in India: A review and future directions in avian monitoring.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {1},
pages = {19},
pmid = {41353493},
issn = {1573-2959},
support = {NTA Ref. No. 200510046214//University Grants Commission/ ; },
mesh = {Animals ; *Birds ; India ; *Remote Sensing Technology ; *Environmental Monitoring/methods ; Ecosystem ; Conservation of Natural Resources ; Geographic Information Systems ; },
abstract = {Remote sensing technology enables broad-scale ecological studies, with birds indicating global changes and validating its data. Despite its global relevance, the integration of remote sensing in ornithological research in India remains limited and fragmented. We conducted extensive literature review on the remote sensing applications in ornithological studies in India from 1992 to 2022 to reorient ornithological research primarily focusing on the existing satellite data, telemetry and GIS tools. The objectives of the review are: (1) to provide an overview of remote-sensing data applications in avian ecological studies, (2) to report the spatiotemporal trends and patterns in the characteristics of remote sensing data (scale, resolution, data source) applied in the studies, and identify the region-specific approaches and (3) to identify the research gaps, improve the methods and propose priority research themes by outlining the future scope of its applications in avian ecology and the conservation efforts as an opportunity to strengthen avian research using remote sensing technology in rapidly changing landscapes. We systematically reviewed literature (N = 108) that related remotely sensed data to bird distribution, abundance assessment, and migration. Our review covered 132 bird species across 19 orders and 5 feeding guilds. Forest birds were more frequently studied than wetland birds, with nearly 50% of the studies focused on single species. Galliformes were the most represented while Falconiformes, Columbiformes, and Ciconiiformes were the least. Studies largely focused on habitat suitability using avian occurrence data (51%) while avian disease outbreak, genetics, and nest site data (each 2%) had least contribution. Our review suggests the need to bridge ecological knowledge gaps using remote sensing and GIS tools through interdisciplinary collaboration among ornithologists, remote sensing experts, and scientists from other allied fields as this can improve data-sharing policies and develop innovative user-friendly products for applications in avian research. Additionally, community participation through citizen science can generate valuable crowd-sourced data for bird conservation and ecosystem management.},
}
@article {pmid41360908,
year = {2025},
author = {Huang, Y and Han, X and Xia, C},
title = {Assessing the completeness and consistency of global-scale avian datasets.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1201},
pmid = {41360908},
issn = {2045-2322},
support = {32170491//National Natural Science Foundation of China/ ; },
mesh = {*Birds/physiology/classification ; Animals ; Ecosystem ; *Databases, Factual ; Biodiversity ; Ecology ; },
abstract = {The advancement of ecological research has increasingly focused on comparative methods and global-scale analyses. Birds are frequently selected for such studies for their widespread distribution and sensitivity to environmental changes. Given the need to integrate fragmented avian data, we aim to collect global-scale avian datasets and evaluate the completeness and consistency of them. We reviewed literature published in Springer Nature and American Association for the Advancement of Science (AAAS) from 2020 to 2024 and identified 90 articles with large-scale coverage and broad taxonomic representation. From these, we compiled 123 datasets covering environmental factors, avian traits, and ecosystem-level data. These were categorized into species-level and spatial data for completeness assessment, while consistency was evaluated across three modalities: species lists, nominal variables, and continuous variables. The database encompassed 12 distinct data types, including morphological, physiological, behavioural, and life-history traits, niche characteristics, evolutionary data, and environmental factors. Our assessment revealed that species distribution and abundance data were most frequently utilized in avian research worldwide. Both the species-level and spatial data exhibited high completeness. Continuous variables showed high consistency, whereas nominal variables and species lists exhibited moderate consistency with notable variability. Therefore, the supplementation of low-integrity data such as reproductive and behavioural datasets remains imperative. Systematic reconciliation between legacy and revised avian taxonomic inventories are critical for ensuring the consistency of data. We hope that the work can advance understanding of macroecology and providing guidance for global avian research.},
}
@article {pmid41365954,
year = {2025},
author = {González, AL and Merder, J and Andraczek, K and Brose, U and Filipiak, M and Harpole, WS and Hillebrand, H and Jackson, MC and Jochum, M and Leroux, SJ and Nessel, MP and Onstein, RE and Paseka, R and Perry, GLW and Peace, A and Rugenski, A and Sitters, J and Sperfeld, E and Striebel, M and Zandona, E and Mozsár, A and Bluhm, S and Doi, H and Eisenhauer, N and Farjalla, VF and Hood, J and Kratina, P and Lovelock, C and Moody, EK and Pollierer, ME and Potapov, A and Romero, GQ and Roussel, JM and Scheu, S and Scheunemann, N and Seeber, J and Steinwandter, M and Susanti, WI and Tiunov, A and Dézerald, O},
title = {Nitrogen deposition reveals global patterns in plant and animal stoichiometry.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10977},
pmid = {41365954},
issn = {2041-1723},
mesh = {*Nitrogen/metabolism/analysis ; Phosphorus/metabolism/analysis ; *Plants/metabolism/chemistry ; Ecosystem ; Animals ; Temperature ; },
abstract = {The elemental content of organisms links cellular biochemistry to ecological processes, from physiology to nutrient dynamics. While plant stoichiometry is thought to vary with climate and nutrient availability across latitudes, the consistency of these patterns across trophic groups and realms remains unclear. Using the StoichLife database, which includes nitrogen and phosphorus content data for 5443 species across 1390 sites, we examine how solar energy (temperature, radiation) and nutrients (nitrogen and phosphorus) influence stoichiometric variation. We find that plant stoichiometry in terrestrial and freshwater ecosystems is more strongly associated with environmental gradients, particularly nitrogen deposition, than animal stoichiometry. Contrary to expectations, temperature, radiation, and labile P show limited global effects. Latitudinal patterns in stoichiometry are more closely associated with species turnover rather than intraspecific variation. Given the strong links between stoichiometry and organismal performance, these findings underscore the need to predict the ecological consequences of anthropogenic disruption to global biogeochemical cycles.},
}
@article {pmid41366043,
year = {2026},
author = {Abraham, AJ and Hempson, GP and le Roux, E and Maré, C and Taylor, LL and Webster, AB and Duvall, ES and Prys-Jones, T and Coppock, J and Ridenour, C and de Jager, P and Augustine, D and Chapman, CA and Fashing, PJ and Harfoot, MBJ and Holdo, RM and Hopcraft, JGC and Johnson, C and van Langevelde, F and Malhi, Y and Morel, A and Nguyen, N and Owen-Smith, N and Potter, AB and Prins, HHT and Rothman, JM and Swedell, L and Svenning, JC and Thomson, ER and van der Plas, F and Veldhuis, MP and Pringle, RM and Clauss, M and Doughty, CE},
title = {Sodium constraints on megaherbivore communities in Africa.},
journal = {Nature ecology &amp; evolution},
volume = {10},
number = {1},
pages = {105-116},
pmid = {41366043},
issn = {2397-334X},
support = {16-HW16_2-0025//National Aeronautics and Space Administration (NASA)/ ; 18-SLSCVC18-0032//National Aeronautics and Space Administration (NASA)/ ; 101062339//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Herbivory ; Animals ; *Sodium/metabolism/analysis ; Africa South of the Sahara ; Feces/chemistry ; *Mammals/physiology ; *Plants/chemistry/metabolism ; Africa ; Population Density ; },
abstract = {Sodium (Na) is an essential nutrient for animals, but not for most plants. Consequently, herbivores may confront a mismatch between forage availability and metabolic requirement. Recent work suggests that larger-bodied mammals may be particularly susceptible to Na deficits, yet it is unknown whether Na availability constrains the density or distribution of large herbivores at broad scales. Here we show that plant-Na availability varies >1,000-fold across sub-Saharan Africa and helps explain continent-scale patterns of large-herbivore abundance. We combined field data with machine-learning approaches to generate high-resolution maps of plant Na, which revealed multi-scale gradients arising from sea-salt deposition, hydrology, soil chemistry and plant traits. Faecal Na concentration was positively correlated with modelled dietary Na, supporting the prediction that variation in plant Na is a major determinant of herbivore Na intake. Incorporating plant-Na availability improved model predictions of large-herbivore population density, especially for megaherbivore species, which are depressed in very-low-Na regions (<100 mg kg[-1]), consistent with Na limitation. Our study offers an explanation for the scarcity of megaherbivores in parts of Central and West Africa, which has major ecological ramifications given the strong influence of large herbivores on ecosystem functioning and the profound human-induced changes to Na availability in Africa and beyond.},
}
@article {pmid41367046,
year = {2025},
author = {Saputra, YA and Armawan, LVA and Lisa, M and Muharramah, DH and Pratiwi, LD},
title = {The Role of Hydrometeorological Factors in Leptospirosis Transmission in Central Java, Indonesia.},
journal = {Journal of preventive medicine and public health = Yebang Uihakhoe chi},
volume = {58},
number = {6},
pages = {553-562},
pmid = {41367046},
issn = {2233-4521},
mesh = {Indonesia/epidemiology ; *Leptospirosis/epidemiology/transmission ; Humans ; Geographic Information Systems ; Humidity ; Temperature ; Linear Models ; Rain ; },
abstract = {OBJECTIVES: This study investigates the relationship between hydrometeorological factors and leptospirosis cases in Central Java to elucidate disease spread patterns.<br><br>METHODS: An ecological study design was utilized, incorporating spatial elements by integrating geographic information systems (GIS) with statistical techniques. The analysis included data on temperature, humidity, rainfall, solar radiation, flooding, and monthly leptospirosis cases recorded from 2018 to 2022. Data sources comprised the Ministry of Health of the Republic of Indonesia, the Meteorology, Climatology, and Geophysics Agency, and the Central Java Provincial Water Resources Management Center. The study employed correlation tests, multiple linear regression, and spatial data visualization.<br><br>RESULTS: Correlation analysis indicated that monthly leptospirosis cases were significantly and positively correlated with minimum temperature (r=0.423; p=0.001), humidity (r=0.589; p<0.001), and rainfall (r=0.413; p=0.001). In contrast, maximum temperature (r=-0.355; p=0.005) and solar radiation (r=-0.431; p=0.001) showed significant negative correlations. Subsequent multiple linear regression showed that higher monthly leptospirosis was associated with higher humidity.<br><br>CONCLUSIONS: The findings offer essential insights for developing a comprehensive, science-based leptospirosis management strategy. A recommended approach is to establish a spatial monitoring system aimed at identifying high-risk areas, especially those with increased humidity and frequent flooding.},
}
@article {pmid41367904,
year = {2025},
author = {Pélabon, C and Agudelo-Cantero, GA and Araya Ajoy, YG and Bolstad, GH and Cheng, C and Galis, F and Guillaume, F and Haaland, TR and Hallgrímsson, B and Hansen, TF and Holstad, A and Houle, D and Hunt, G and Isaksen, A and Milocco, L and Mubalegh, N and Nuño de la Rosa, L and Orzack, SH and Porto, A and Reid, JM and Sztepanacz, JL and Undheim, EAB and Villegas, C and Voje, KL and Walling, C and Wright, J},
title = {Evolvability: progress and key questions.},
journal = {Bioscience},
volume = {75},
number = {12},
pages = {1042-1057},
pmid = {41367904},
issn = {0006-3568},
abstract = {Since the 1990s, evolutionary biologists have recognized the importance of explaining the ability of biological systems to evolve and how this ability itself evolves. This recognition of the need to explain evolvability emerged from an awareness that the kind and the amount of heritable variation available for natural selection require explanation. The concept of evolvability is now the focus of many research programs in diverse subdisciplines within evolutionary biology. In the present article, we first review and synthesise progress made in evolvability research. We then present key questions to set an agenda for future research on evolvability, identify challenges to answer these questions, and discuss opportunities to apply results from the evolvability research to conservation biology.},
}
@article {pmid41368214,
year = {2025},
author = {Lima, R and Barradas, G and Bermúdez I Badia, S},
title = {Music-induced physiological markers for detecting Alzheimer's disease using machine learning.},
journal = {Frontiers in aging neuroscience},
volume = {17},
number = {},
pages = {1701970},
pmid = {41368214},
issn = {1663-4365},
abstract = {INTRODUCTION: Alzheimer's disease (AD) is characterized by progressive cognitive and emotional decline, highlighting the need for novel, non-invasive biomarkers to aid in early detection, monitoring, and stage-specific interventions. This study investigates music-evoked physiological responses as potential biomarkers of AD and evaluates their translational value using machine learning (ML).<br><br>MATERIALS AND METHODS: A total of 36 AD patients, spanning different severity levels, listened to emotionally evocative musical excerpts while electrodermal activity and facial electromyography (corrugator and zygomaticus muscles) were recorded. Machine learning models were then trained on these signals to classify the presence and severity of AD and to detect residual emotion-specific physiological responses elicited by music.<br><br>RESULTS: Physiological reactivity to music declined with disease progression, with positive emotions eliciting more distinct responses than negative ones. The Random Forest classifier distinguished AD patients from healthy controls with 70.5% accuracy, while the Na&#xef;ve Bayes model predicted severity with 65.6% accuracy, demonstrating that ML models can detect subtle music-evoked physiological differences even in individuals with AD.<br><br>DISCUSSION: Music-evoked physiological signals reflect the hierarchical disruption of emotion-related neural circuits in AD and hold promise as complementary biomarkers for disease presence and stage. When combined with machine learning (ML), these measures provide a non-invasive, ecologically valid approach to support early detection, monitoring, and the development of stage-specific interventions.},
}
@article {pmid41368505,
year = {2025},
author = {Di Leo, D and Nilsson, E and Krinos, A and Pinhassi, J and Lundin, D},
title = {The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20328},
pmid = {41368505},
issn = {2167-8359},
mesh = {*Software ; Reproducibility of Results ; Workflow ; *Transcriptome ; *Computational Biology/methods ; *Molecular Sequence Annotation/methods ; *Metagenomics/methods ; },
abstract = {Metatranscriptomics-the sequencing of community RNA-has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.},
}
@article {pmid41369995,
year = {2025},
author = {Bouzemlal, H and Hentabli, M and Laidi, M and Laidani, Y and Kouider Amar, M and Ibrir, A and Zhang, J},
title = {Predicting adsorption capacities of pharmaceutical pollutants using chemoinformatics and machine learning techniques.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {1},
pages = {39},
pmid = {41369995},
issn = {1573-2983},
mesh = {Adsorption ; *Machine Learning ; *Water Pollutants, Chemical/chemistry ; *Cheminformatics ; Pharmaceutical Preparations/chemistry ; Neural Networks, Computer ; Support Vector Machine ; },
abstract = {Pharmaceutical pollutants are increasingly recognized as emerging contaminants in aquatic environments. Their persistence, bioactivity, and resistance to conventional treatment processes raise ecological and human health concerns, including the spread of antimicrobial resistance. Adsorption has emerged as a promising polishing step for their removal, but adsorption capacity (Qe, mg/g) varies widely depending on molecular structure and operational conditions, making predictive modeling essential. In this work, we developed machine learning models to predict adsorption capacities for Aspirin, Caffeine, Carbamazepine, Ketoprofen, Sulfamethoxazole, Nimesulide, and Paracetamol using chemoinformatics descriptors derived from SMILES strings and experimental inputs, including equilibrium concentration (Ce), initial concentration (C0), temperature, and contact time. Feature reduction with LassoCV and multicollinearity analysis yielded a compact, chemically interpretable descriptor set. Support Vector Regression (SVR), Extreme Gradient Boosting (XGB), and Artificial Neural Networks (ANN) were optimized with Optuna and evaluated using cross-validation. XGB delivered the best predictive performance (R2 = 0.997, RMSE = 2.62 mg/g), outperforming SVR and ANN. SHAP analysis highlighted the influence of charge-partitioned surface areas and nitro functionalities on adsorption outcomes. The best-performing model was deployed in a Streamlit application, enabling predictions of Qe from SMILES and experimental conditions with built-in applicability-domain checks.},
}
@article {pmid41370329,
year = {2025},
author = {Damsma, A and Cannon, J and Fink, LK and Doelling, KB and Grahn, JA and Honing, H and Kaplan, T and Large, EW and Bouwer, FL},
title = {Computational modeling of rhythmic expectations: Perspectives, pitfalls, and prospects.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013798},
pmid = {41370329},
issn = {1553-7358},
mesh = {Humans ; *Computer Simulation ; Computational Biology ; Music ; Learning/physiology ; *Periodicity ; },
abstract = {Rhythmic structure enables precise temporal expectations that are essential to human communication, including speech and music. Computational models have been developed to account for how humans perceive, produce, and learn rhythmic sequences. However, it is unclear how different types of models relate to each other and how they can be evaluated. In this review and perspective, we discuss how three major classes of models-entrainment, probabilistic, and timekeeper models-have been used to study rhythmic expectations. We critically assess each model class in terms of its level of explanation, the rhythmic behaviors it captures, its ability to account for learning and enculturation, and its ability to integrate other features, such as pitch. We show that entrainment, probabilistic, and timekeeper models differ substantially in the aspects of rhythmic expectations they can capture. To move the field forward, we propose that model comparison and integration are crucial. We identify key challenges to this effort, such as the varying nature of the input and output signals and divergent modeling goals. To address these challenges, we arrive at several practical recommendations: to equate input and output signals when comparing models, to consider several model outcomes beyond goodness-of-fit measures in model evaluation, to use model-integration efforts to inform theory building, and to make code and data openly accessible. Ultimately, understanding how models of rhythmic expectations relate, and how features in these models account for behavioral, neural, and cognitive aspects of rhythmic expectations, will deepen our understanding of a core aspect of human behavior.},
}
@article {pmid41373417,
year = {2025},
author = {Hu, Y and Jiang, G and Wang, J and He, H and Liu, L and Du, P and Li, H and Wang, F and Xie, Q},
title = {Genome-Wide Identification and Hormone-Induced Expression Analysis of the Anthocyanidin Reductase Gene Family in Sainfoin (Onobrychis viciifolia Scop.).},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
pmid = {41373417},
issn = {1422-0067},
support = {2022xjkkk0503//The third comprehensive scientific expedition project in Xinjiang/ ; 23CB008-01//Xinjiang Construction Corps Youth Science and Technology Innovation Talent Project/ ; 2024DA030//Xinjiang Construction Corps Science and Technology Plan Basic Research Project/ ; 2023AB070//Xinjiang Construction Corps Science and Technology Plan Key Areas of Science and Technology Research Plan./ ; },
mesh = {*Genome, Plant ; *Gene Expression Regulation, Plant/genetics ; *Anthocyanins/metabolism ; Oxylipins/chemistry ; Abscisic Acid/chemistry ; Cyclopentanes ; Gene Expression Profiling ; Protein Domains ; Amino Acid Motifs ; Plant Leaves ; Plant Stems ; Plant Roots ; Computational Biology ; *Hormones/chemistry ; *Fabaceae/enzymology ; Acetates ; },
abstract = {Sainfoin (Onobrychis viciifolia Scop.) is an important legume forage. Its anthocyanidin reductase (ANR) catalyzes the conversion of anthocyanins to epicatechins. This conversion reaction is not only a key step in the biosynthesis of proanthocyanidins (PAs) but also directly influences both forage quality and stress resistance. Here, we systematically identified 67 ANR gene family members in autotetraploid sainfoin for the first time. Using bioinformatics approaches, we analyzed gene structure, conserved domains, motifs, and cis-regulatory elements of the identified ANR genes. In this study, phylogenetic analysis revealed that the ANRs clustered into 11 distinct clades, with genes within the same clade predominantly originating from closely related species within the same family. Significant collinearity with Arabidopsis thaliana, Glycine max, Cicer arietinum, and Medicago truncatula further revealed the conserved evolutionary path of this gene family. RT-qPCR analysis showed differential expression patterns of OvANRs in root, stem, and leaf tissues. For instance, OvANR19 was significantly induced by abscisic acid (ABA) and methyl jasmonate (MeJA), with its expression upregulated by 79.7-fold and 3.8-fold in roots and by 16.2-fold and 31.3-fold in leaves. Furthermore, subcellular localization analysis confirmed that representative ANR proteins were localized in the cytoplasm. This study lays a foundation for molecular breeding aimed at enhancing stress resistance and forage quality in sainfoin.},
}
@article {pmid41373816,
year = {2025},
author = {Wang, F and Sun, X and Wang, K and Long, B and Li, F and Xie, D},
title = {Physiological and Multi-Omics Insights into Trichoderma harzianum Alleviating Aged Microplastic Stress in Nicotiana benthamiana.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
pmid = {41373816},
issn = {1422-0067},
support = {2022GDASZH-2022010110//'GDAS' Project of Science and Technology Development/ ; 0525149001//Innovation Capacity Building Project for Provincial Scientific Research Institutions/ ; 2024A1515030175//Guangdong Basic and Applied Basic Research/ ; },
mesh = {*Nicotiana/microbiology/drug effects/metabolism/genetics/growth &amp; development ; *Stress, Physiological/drug effects ; *Microplastics/toxicity ; *Hypocreales/physiology ; Reactive Oxygen Species/metabolism ; Transcriptome ; Gene Expression Regulation, Plant/drug effects ; *Trichoderma ; Multiomics ; },
abstract = {Microplastics derived from biodegradable PBAT film, widely used in agriculture, pose ecological and biological hazards. This study explores how Trichoderma harzianum T4 mitigates this microplastic-induced stress in Nicotiana benthamiana. Using five experimental setup-control (CK), low/high-dose aged microplastics (MP80/MP320), and their co-treatments with T. harzianum T4 (MP80+T4/MP320+T4), multi-omics analyses reveal the microplastic stress-alleviating mechanisms of T. harzianum T4. Aged microplastics significantly inhibit plant growth, promote reactive oxygen species (ROS) and malondialdehyde (MDA) accumulation, and disrupt metabolic homeostasis. Conversely, T. harzianum T4 activates the plant antioxidant defense system, reducing ROS/MDA levels and upregulating superoxide dismutase (SOD)/peroxidase (POD) activities, and promotes biomass. Transcriptomic analysis shows T. harzianum T4 reverses gene expression patterns disrupted by microplastics, particularly in DNA replication and pentose-glucuronic acid pathways. Metagenomic sequencing indicates T. harzianum T4 restores soil microbial diversity, increases the abundance of Bacteroidota and Myxococcota, downregulates antibiotic resistance genes (e.g., tetA5, MDR), and upregulates carbohydrate-active enzymes (CAZys), thereby enhancing carbon metabolism. In conclusion, T. harzianum T4 alleviates microplastic stress through a tripartite mechanism: activating plant stress-response gene networks, reshaping soil microbial communities, and modulating functional gene expression, offering a promising bioremediation strategy.},
}
@article {pmid41378881,
year = {2025},
author = {Blin, K and Loureiro, C and Louwen, NLL and Navarro-Muñoz, JC and Gerstmans, H and Robinson, SL and Rutz, A and Reitz, ZL and Doering, DT and van der Hooft, JJJ and Weber, T and Medema, MH and Zdouc, MM},
title = {Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
pmid = {41378881},
issn = {1477-4054},
support = {1229222&#xa0;N//Research Foundation-Flanders/ ; PZPGP2_209124/SNSF_/Swiss National Science Foundation/Switzerland ; NNF20CC003558//Novo Nordisk Foundation/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; KICH1.LWV04.21.013/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Computational Biology/methods ; *Databases, Genetic ; *Multigene Family ; Machine Learning ; *Data Curation/methods ; Genomics ; Biocuration ; },
abstract = {Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable comparative analysis, predictive modeling, and data integration across bioinformatics platforms. While professional biocuration is resource-intensive and usually limited to institutional settings, community-driven approaches can mobilize large-scale annotation of specialized datasets and are more resilient to disruptions in scientific funding. Here, we present a model for community-powered curation applied to the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Through a framework of workflows for metadata capture, annotation validation, and contributor coordination, the MIBiG 4.0 initiative recruited 267 scientists across 178 institutions from 33 countries, volunteering an estimated 4000 h of work. These efforts expanded the MIBiG repository by 22% and enhanced its usability in downstream molecular data analyses in comparative genomic analyses, natural product discovery, and machine learning applications. We provide strategies and actionable lessons for adopting this model, supporting the sustainability of curated bioinformatics resources central to nucleic acid research and related fields.},
}
@article {pmid41379974,
year = {2025},
author = {Edwards, SV and Fang, B and Khost, D and Kolyfetis, GE and Cheek, RG and DeRaad, DA and Chen, N and Fitzpatrick, JW and McCormack, JE and Funk, WC and Ghalambor, CK and Garrison, E and Guarracino, A and Li, H and Sackton, TB},
title = {Multispecies pangenomes reveal a pervasive influence of population size on structural variation.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6778},
pages = {eadw1931},
doi = {10.1126/science.adw1931},
pmid = {41379974},
issn = {1095-9203},
support = {R01 HG011485/HG/NHGRI NIH HHS/United States ; },
mesh = {*Population Density ; Animals ; *Genomic Structural Variation ; DNA Copy Number Variations ; *Evolution, Molecular ; Genome Size ; *Genome ; },
abstract = {Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs among three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 55-fold range in effective population size. We find rapid evolution of genome architecture, including ~100-megabase decreases in genome size driven by shifts in complex satellite landscapes. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with consistent evidence of adaptive fixation only in the largest population. Gene copy number variants exhibit an inverse relationship with population size, indicating strongly deleterious dynamics, with consequences for gene expression. Our long-read dataset and pangenome analysis demonstrate how population size shapes genome complexity.},
}
@article {pmid41385957,
year = {2026},
author = {Zhang, C and Wang, X and Wang, L and Li, P and Bao, Y and Zhang, Z and Jiang, Z and Feng, C and Chen, L},
title = {Multi-omics reveals gut microbiota-mediated environmental adaptation in Mallards and domesticated Shaoxing ducks.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106177},
pmid = {41385957},
issn = {1525-3171},
mesh = {Animals ; *Ducks/microbiology/physiology ; *Gastrointestinal Microbiome ; Domestication ; *Adaptation, Physiological ; Cecum/microbiology ; Ileum/microbiology ; *Metabolome ; Metabolomics ; Multiomics ; },
abstract = {Gut microbiota remodeling is a critical component of the domestication syndrome. However, the structural and functional consequences of domestication on gut microbiomes in ducks remain poorly understood. Understanding how domestication and associated ecological transitions influence gut microbial communities can shed light on host adaptation mechanisms. We performed integrated metagenomic and metabolomic analyses of the ileal and cecal microbiota from Mallards and Shaoxing ducks-two ecotypes of Anas platyrhynchos representing wild and domesticated lineages-to investigate microbial community structure, functional capacity, and host-microbe metabolic interactions. Principal coordinates analysis (PCoA) revealed distinct microbial stratification between intestinal compartments (ileum vs. cecum), with domestication-associated divergence observed primarily in the cecum. Metabolomic profiles were relatively stable across both segments and populations. Mallards harbored a more diverse and metabolically versatile gut microbiota, with significant enrichment in pathways related to carbohydrate, amino acid, and vitamin metabolism. The genus Gemmiger emerged as a key functional contributor, supporting branched-chain amino acid biosynthesis, coenzyme activation, and carbohydrate utilization, thus reflecting enhanced metabolic adaptability. In Shaoxing ducks, the gut microbiome was enriched in the glucagon signaling pathway and glucose-regulatory metabolites such as l-carnitine, myo-inositol, and quinate. Butyricicoccus sp017886875 was identified as a candidate taxon associated with glucose homeostasis. Additionally, immune-related pathways, including the NOD-like receptor signaling and antigen processing and presentation, were significantly enriched and linked to Anaerobiospirillum and Parabasalia, respectively. Co-enrichment of anti-inflammatory metabolites suggests the presence of a host-microbiota feedback mechanism that mitigates inflammation while maintaining immune readiness. These findings reveal that gut microbiota contribute to population-specific environmental adaptation in ducks, with distinct microbiome and functional traits associated with domestication history. The study highlights microbiota-mediated host adaptation as a key feature of domestication-related ecological transitions.},
}
@article {pmid41388108,
year = {2026},
author = {Yuan, H and Mancuso, CA and Johnson, K and Braasch, I and Krishnan, A},
title = {Computational strategies for cross-species knowledge transfer.},
journal = {Nature methods},
volume = {23},
number = {2},
pages = {312-327},
pmid = {41388108},
issn = {1548-7105},
support = {R35 GM128765/GM/NIGMS NIH HHS/United States ; R01 OD011116/OD/NIH HHS/United States ; R01OD011116//U.S. Department of Health &amp; Human Services | NIH | NIH Office of the Director (OD)/ ; R01 OD011116/CD/ODCDC CDC HHS/United States ; 1017799//Simons Foundation/ ; },
mesh = {Humans ; *Computational Biology/methods ; Animals ; Transcriptome ; Species Specificity ; Molecular Sequence Annotation ; Gene Regulatory Networks ; },
abstract = {Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling and drug testing. However, evolutionary divergence between humans and research organisms hinders effective knowledge transfer across species. Here, we review state-of-the-art methods for computationally transferring knowledge across species, primarily focusing on methods that use transcriptome data and/or molecular networks. Our Perspective addresses four key areas: (1) transferring disease and gene annotation knowledge across species, (2) identifying functionally equivalent molecular components, (3) inferring equivalent perturbed genes or gene sets and (4) identifying equivalent cell types. We conclude with an outlook on future directions and several key challenges that remain in cross-species knowledge transfer, including introducing the concept of 'agnology' to describe functional equivalence of biological entities, regardless of their evolutionary origins. This concept is becoming pervasive in integrative data-driven models in which evolutionary origins of functions can remain unresolved.},
}
@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/ ; },
mesh = {Humans ; *Asthma/prevention &amp; control/epidemiology/etiology ; *Hypersensitivity/prevention &amp; control/epidemiology ; Urban Population ; Environmental Exposure ; *Environment ; },
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 {pmid41389419,
year = {2026},
author = {Li, WC and Li, HM and Guo, ZW and Yan, P and Shen, Y and Chen, YP},
title = {A prior knowledge-enhanced Transformer model for data anomaly identification and processing in industrial park wastewater treatment plants.},
journal = {Water research},
volume = {290},
number = {},
pages = {125125},
doi = {10.1016/j.watres.2025.125125},
pmid = {41389419},
issn = {1879-2448},
mesh = {*Wastewater ; *Waste Disposal, Fluid ; China ; *Water Purification ; Industrial Waste ; Parks, Recreational ; },
abstract = {Accurate identification of anomalies and reconstruction of missing data are crucial for the intelligent operation of industrial park wastewater treatment plants (WWTPs). However, traditional statistical and model-based approaches often fall short in addressing anomalies characterized by complex spatio-temporal coupling within WWTP data. Accordingly, this study introduces a novel prior knowledge-enhanced Transformer (PK-T) model. The PK-T model leverages domain-specific knowledge from wastewater treatment within a deep learning architecture, which demonstrates superior performance in the high-precision identification and reconstruction of complex anomalies. The model was evaluated using one year of operational data from two industrial park WWTPs in China. Comparative analysis with conventional methods, including statistical, distance-based, and model-based approaches, reveals that PK-T significantly outperforms these approaches in both anomaly identification accuracy and data reconstruction precision. Remarkably, the model achieves reconstruction accuracies exceeding 90 % for critical water quality parameters. This research provides an innovative solution for robust data management and intelligent operation in industrial wastewater treatment, with considerable practical implications for enhancing the operational efficiency of WWTPs.},
}
@article {pmid41389554,
year = {2026},
author = {Yang, T and Zhan, Y and Sha, J and Zhao, J and Wang, C and Peng, T and Zhang, L},
title = {Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128418},
doi = {10.1016/j.micres.2025.128418},
pmid = {41389554},
issn = {1618-0623},
mesh = {*Rhizosphere ; *Angelica sinensis/microbiology/growth &amp; development/metabolism ; *Plant Growth Regulators/metabolism ; *Microbiota ; *Microalgae/metabolism/physiology ; Nitrogen/metabolism ; Soil Microbiology ; Coumaric Acids/metabolism ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Biomass ; Soil/chemistry ; Metagenomics ; Metabolomics ; Carbon/metabolism ; Chlorella vulgaris/metabolism ; Multiomics ; },
abstract = {Microalgae have recently been recognized as sustainable biofertilizers that improve soil fertility while enhancing crop performance. However, their roles in regulating medicinal plant growth and quality, as well as the underlying ecological mechanisms, remain poorly understood. In this study, we systematically assessed the effects of three representative microalgae-Anabaena cylindrica (AC), Phormidium tenue (PT), and Chlorella vulgaris (CV)-on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of Angelica sinensis. Field inoculation trials demonstrated that all three microalgae significantly promoted biomass accumulation and increased antioxidant capacity. AC and CV further enhanced the accumulation of ferulic acid and flavonoids, which are two key quality determinants. Microalgal inoculation significantly altered rhizosphere soil properties by increasing total organic carbon and alkali-hydrolyzable nitrogen, with AC uniquely elevating available phosphorus and iron. Metagenomic analysis revealed that AC and PT stimulated nitrification while suppressing denitrification, thereby reducing nitrogen loss and stabilizing the soil nitrogen pools. Distinct microbial taxa, including Rhodanobacter, Streptomyces, and Pseudomonas, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed A. sinensis phytohormone profiles in a species-specific manner. Partial least squares path modeling suggested that AC and CV promote ferulic acid biosynthesis through distinct mechanisms, with AC associated with reduced investment in C-mineralization processes and CV associated with lower salicylic acid levels, whereas PT enhances biomass accumulation mainly by stimulating N-cycle processes. Collectively, this study provides integrated evidence linking microalgae-mediated nutrient cycling, rhizosphere microbiome shifts and hormonal regulation to enhanced quality formation in A. sinensis.},
}
@article {pmid41391105,
year = {2026},
author = {Edwards, CJ and Smith, R and Lafit, G and Ward, T and Emsley, R and Rus-Calafell, M and Myin-Germeys, I and Peters, E and Bucci, S and Craig, TK and Haddock, G and Ball, H and Fornells-Ambrojo, M and Hardy, A and McLeod, H and Gumley, AI and McDonnell, J and Montague, A and Clancy, M and Huckvale, M and Garety, PA},
title = {The Impact of AVATAR Therapy on Voice Hearing in Everyday Life: ESM Outcomes of the AVATAR2 Trial.},
journal = {Schizophrenia bulletin},
volume = {52},
number = {1},
pages = {},
pmid = {41391105},
issn = {1745-1701},
support = {/WT_/Wellcome Trust/United Kingdom ; 215471/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Female ; Male ; Single-Blind Method ; Adult ; Middle Aged ; *Hallucinations/therapy ; *Ecological Momentary Assessment ; *Outcome Assessment, Health Care ; Follow-Up Studies ; Young Adult ; *Psychotherapy/methods ; Avatar ; },
abstract = {AVATAR therapy involves facilitated dialogs between a voice hearer and a digital embodiment of their distressing voice ("the avatar"). We conducted a multi-site single-blind randomized controlled trial to evaluate the efficacy of brief (AV-BRF) and extended (AV-EXT) forms of AVATAR therapy, compared with treatment as usual (TAU) alone (AVATAR2). This study reports the data from experience sampling method (ESM) assessments conducted at baseline, end of therapy (16 weeks), and follow-up (28 weeks). The research questions focused on whether those in the AV-BRF or AV-EXT arms experienced less voice-related distress, anxiety, and beliefs as measured by ESM, compared to TAU. Separate mixed-effects models were fitted for each research question. The final sample (n = 200) completed approximately 40% of questionnaires across all timepoints. Participants who received AV-EXT therapy, but not AV-BRF, reported reduced momentary voice-related distress at 16 (P = .022) and 28 weeks (p = .029). Appraisals of voice control were also reduced in the AV-EXT arm at 16 weeks when the voice was present (P = .002) or not (P = .008). Voice power appraisals were reduced (P < .035) in both arms when the voice was "not present but on my mind" at all timepoints. There were no changes in the frequency of voice hearing, appraisals of voice intent, or assertive responding. These findings from everyday life, reported for the first time, provide evidence of the impact on the primary AVATAR therapy treatment targets, including appraisals of voice power and control. The weight of evidence favors the AV-EXT protocol in the further development and implementation of AVATAR therapy.},
}
@article {pmid41396997,
year = {2025},
author = {Li, M and Cao, Y and Wu, W and Mo, Y and Wang, J and Geng, X and Xu, J and Fei, Y and Su, G and Hu, H and Li, K and Ni, J and Xu, ZF},
title = {EucaMOD: a comprehensive multi-omics database for functional genomics research and molecular breeding of fast-growing eucalyptus trees.},
journal = {The Plant journal : for cell and molecular biology},
volume = {124},
number = {5},
pages = {e70603},
pmid = {41396997},
issn = {1365-313X},
support = {JB22035001//Guangxi Key Research and Development Program/ ; AA23062055-2//Guangxi Science and Technology Major Program/ ; AD23026337//Guangxi Specific Project for Science and Technology Bases and Talents/ ; //Guangxi 'Bagui Young Talents' Special Fund/ ; },
mesh = {*Eucalyptus/genetics/growth &amp; development ; *Genomics ; *Databases, Genetic ; *Plant Breeding ; Genome, Plant/genetics ; Transcriptome/genetics ; Trees/genetics/growth &amp; development ; Multiomics ; },
abstract = {Eucalyptus, one of the most widely planted plantation tree species globally, is primarily found in tropical and subtropical regions and contributes significantly to economic and social benefits. With advances in sequencing technologies, there is an increasing demand for the systematic analysis of multi-omics data among Eucalyptus species to enhance genetic breeding efforts. Although several early genomic databases have been established for eucalyptus, they have not been updated in a timely manner and lack recent multi-omics data, rendering them insufficient for current research needs. To address this gap, we developed the eucalyptus multi-omics database (EucaMOD, http://eucalyptusggd.net/eucamod), a comprehensive resource for cross-omics studies. In this study, we functionally annotated 45 eucalyptus genomes and structurally annotated 15, conducting comparative genomics and pan-proteomics analyses across all genomes. Additionally, we analyzed eucalyptus transcriptome, epigenome, and variome data through standardized workflows, enabling the in-depth mining and reanalysis of multi-omics datasets. EucaMOD is the most comprehensive multi-omics database for eucalyptus to date and includes data from 45 genomes (39 species), 870 mRNA-seq samples, 17 miRNA-seq samples, 52 epigenomic datasets (histone modifications and transcription factor binding), and genetic variation data from 1219 samples. To support functional genomics and molecular breeding research, the database is organized into the following 11 modules: Home, Species, Genomics, Comparative genomics, Pan-proteomics, Transcriptomics, Epigenetics, Variomics, Tools, Download, and Help. EucaMOD also offers online analysis tools for data mining, providing free public services to aid eucalyptus gene function and genetic engineering studies.},
}
@article {pmid41397974,
year = {2025},
author = {Zheng, F and Yao, W and He, W and Zhang, W and Chen, Y and Chen, H and Zeng, Z and Liu, XL and Ding, S and Zheng, Y and Huang, L and Zhu, Y and Zhang, C},
title = {A comprehensive database for high-throughput identification of archaeal lipids using high-resolution mass spectrometry.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {588},
pmid = {41397974},
issn = {2041-1723},
support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42372354//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Archaea/chemistry/metabolism ; *Lipids/chemistry/analysis ; *Mass Spectrometry/methods ; *Lipidomics/methods ; Tandem Mass Spectrometry/methods ; *Databases, Factual ; *Membrane Lipids/chemistry ; },
abstract = {Archaeal membrane lipids are markedly distinct from those in bacteria and eukaryotes, serving as biomarkers for unraveling their ecological and biogeochemical roles. Recent advancements in high-resolution mass spectrometry-based lipidomic research facilitate detailed cellular-level characterizations of lipid compounds. However, the lack of a comprehensive and dedicated database severely limits large-scale, high-throughput investigations of archaeal lipids. We present ArchLips, a comprehensive database containing 219,348 in silico molecular structures and tandem mass spectra of 199,248 corresponding archaeal lipid compounds. ArchLips enables the automatic and accurate annotation of archaeal lipid compounds characterized by high-resolution mass spectrometry from both pure cultures and environmental samples, serving as a transformative tool for enhancing our understanding of archaeal diversity and its ecological and evolutionary significance within global ecosystems.},
}
@article {pmid41399279,
year = {2026},
author = {Culina, A},
title = {Co-BreeD: A milestone resource for studies on cooperative breeding.},
journal = {The Journal of animal ecology},
volume = {95},
number = {1},
pages = {17-20},
doi = {10.1111/1365-2656.70205},
pmid = {41399279},
issn = {1365-2656},
support = {HRZZ-IP-2022-10-2872//Hrvatska Zaklada za Znanost/ ; },
mesh = {Animals ; *Cooperative Behavior ; *Breeding ; *Databases, Factual ; *Birds/physiology ; *Mammals/physiology ; *Reproduction ; },
abstract = {Research Highlight: Ben Mocha, Y., Woith, M., Scemama de Gialluly, S., Bruscagnin, L., Kestel, N., Markman, S., Drobniak, S. M., Baglione, V., Boersma, J., Cousseau, L., Covas, R., Braga de Miranda, G. H., Dey, C. J., Doutrelant, C., Gula, R., Heinsohn, R., Keynan, O., Kingma, S. A., Leitão, A. V., … Griesser, M. (2025). An integrative, peer-reviewed open-source cooperative-breeding database (Co-BreeD). Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.70154. The Cooperative-Breeding Database (Co-BreeD) is an open, peer-reviewed resource that collects data on cooperative breeding across birds and mammals, including humans. As such, it serves as a valuable resource for studies on sociality and cooperation. Currently, Co-BreeD provides population-level data on nearly 40,000 breeding events from 316 species and is growing. The database allows for cooperative breeding to be treated as a continuous rather than binary trait, and at finer spatial and temporal scales, enabling detailed exploration of the ecological and evolutionary drivers of cooperation. This novel approach revealed that alloparental care, and hence cooperative breeding, is likely more widespread than previously recognised. The importance of curated, high-quality, and accessible data across ecology and evolution is becoming evident; Co-BreeD has great potential to contribute to such collaborative, reproducible, and robust research.},
}
@article {pmid41399480,
year = {2025},
author = {Bhat, R and Narayanan, P and Chanda, MM and Walsh, M},
title = {Parasitiformes (ticks) and Acariformes (mites) vectors and their vertebrate host diversity: A global scoping review.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101278},
pmid = {41399480},
issn = {2352-7714},
abstract = {BACKGROUND: While the infection ecology and epidemiology of some vector-borne pathogens have received extensive research focus, many tick- and mite-borne zoonoses, particularly in the global South, have been largely neglected. The current scoping review aims to understand the global state of knowledge for the infection ecology and epidemiology of tick- and mite-borne pathogens, contextualised by their maintenance community composition, in the landscapes in which these pathogens circulate.<br><br>METHODS: Online databases were searched with keyword combinations to gather evidence on the relationship between vertebrate host species diversity and the occurrence of tick- and mite-borne diseases. Information related to pathogen, vector species involved in transmission, geographic location, and ecological and epidemiological relationships between host species diversity and tick- and mite-borne disease was recorded.<br><br>RESULTS: A total of 5510 papers were initially selected for screening based on this search with a final total of 36 papers included in the review. The review found that the literature is highly skewed toward Lyme disease (29 out of 36 studies) and focused on the global North regions (32 out of 36 studies). A general lack of studies on mite-borne diseases globally was evident. Additionally, 42&#xa0;% of all studies reported evidence for the dilution effect whereby greater species richness in the maintenance community appeared to diminish pathogen transmission, while 31&#xa0;% of the studies identified both dilution and amplification effects in the disease systems.<br><br>CONCLUSIONS: While there has been an increase in studies on tick-borne diseases other than Lyme disease in the past decade, the current scoping review has identified an urgent need to study tick- and mite-borne diseases in the global South. The state of knowledge on these unique vector-pathogen systems with respect to relevant maintenance communities is sparse and requires targeted investigation in regions of the global South experiencing rapid habitat loss and subsequent changes in vertebrate species diversity.},
}
@article {pmid41403705,
year = {2025},
author = {Paccagnella, D and Bağcı, C and Gavriilidou, A and Ziemert, N},
title = {PanBGC: a pangenome-inspired framework for comparative analysis of biosynthetic gene clusters.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf225},
pmid = {41403705},
issn = {2730-6151},
abstract = {Bacterial secondary metabolites are a major source of therapeutics and play key roles in microbial ecology. These compounds are encoded by biosynthetic gene clusters (BGCs), which show extensive genetic diversity across microbial genomes. While recent advances have enabled clustering of BGCs into gene cluster families (GCFs), there is still a lack of frameworks for systematically analysing their internal diversity at a population scale. Here, we introduce "PanBGC", a pangenome-inspired framework that treats each GCF as a population of related BGCs. This enables classification of biosynthetic genes into core, accessory, and unique categories and provides openness metrics to quantify compositional diversity. Applied to over 250 000 BGCs from more than 35 000 genomes, PanBGC maps biosynthetic diversity of more than 80 000 GCFs. Our analysis reveals that gene composition reshuffling, rather than acquisition of new genes, is the dominant driver of diversity within GCFs, with most families exhibiting closed gene repertoires but high compositional variability. Additionally, transporter-related domains were commonly identified among core genes, reflecting the fundamental importance of compound export in BGC function. To facilitate exploration, we present PanBGC-DB (https://panbgc-db.cs.uni-tuebingen.de), an interactive web platform for comparative BGC analysis. PanBGC-DB offers gene- and domain-level visualizations, phylogenetic tools, openness metrics, and custom query integration. Together, PanBGC and PanBGC-DB provide a scalable framework for exploring BGCs at population resolution and for contextualizing newly discovered BGCs within the global landscape of secondary metabolism.},
}
@article {pmid41404704,
year = {2026},
author = {Saghaei, S and Siemers, M and Ossetek, KL and Richter, S and Edwards, RA and Roux, S and Zielezinski, A and Dutilh, BE and Marz, M and Cassman, NA},
title = {VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D912-D924},
pmid = {41404704},
issn = {1362-4962},
support = {//NFDI4Microbiota/ ; 460129525//Deutsche Forschungemeinschaft/ ; ZMII2-2524FSB62C//German Federal Ministry of Health/ ; 390713860//Germany's Excellence Strategy EXC 2051/ ; 101046203//Horizon Europe programme/ ; //PHI/ ; //Alexander von Humboldt Foundation/ ; //Federal Ministry of Education and Research/ ; DP220102915//Australian Research Council/ ; DP250103825//Australian Research Council/ ; FL250100019//Australian Research Council/ ; //U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; //Friedrich-Schiller-Universit&#xe4;t Jena/ ; 865694/ERC_/European Research Council/International ; },
mesh = {*Viruses/genetics/classification ; *Software ; *Computational Biology/methods ; Metadata ; Internet ; High-Throughput Nucleotide Sequencing ; *Databases, Genetic ; Data Curation ; Genome, Viral ; },
abstract = {High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.},
}
@article {pmid41405388,
year = {2026},
author = {Lahey, Z and Jones, T-KL and Simmons, AM and Andreason, SA},
title = {In silico detection and characterization of novel Picornavirales mined from publicly available insect RNA-seq data sets.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0170125},
pmid = {41405388},
issn = {2165-0497},
support = {//U.S. Department of Agriculture/ ; },
mesh = {Animals ; Genome, Viral ; Phylogeny ; *Picornaviridae/genetics/classification/isolation &amp; purification ; *Insecta/virology/genetics ; Computational Biology/methods ; RNA-Seq ; RNA, Viral/genetics ; Computer Simulation ; },
abstract = {Picornavirales is a hyperdiverse order of viruses that infect assorted hosts, including arthropods. Members of this group contain a positive-sense, single-stranded RNA genome with a polyadenylated tail. As such, they are often sequenced as "bycatch" in RNA-seq experiments targeting other organisms. We developed a simple-to-follow bioinformatic pipeline to assemble and annotate genomes of the order Picornavirales using publicly available insect metatranscriptome data sets. Using our pipeline, 40 novel viruses were discovered, including putative new members of the families Dicistroviridae, Iflaviridae, and Polycipiviridae. The hosts of the new picornaviruses include beetles (two families), crickets, parasitic wasps, sap-sucking hemipterans (members of all suborders), and thrips. We validated each virus as new in silico by performing a sequence similarity (BLAST) search of each virus against the NCBI non-redundant database and by phylogenetic reconstruction of the RNA-dependent RNA polymerase amino acid sequence from each novel virus and other members of the order Picornavirales. Three taxa classified as iflaviruses by the International Committee on Taxonomy of Viruses that infect Lepidoptera (butterflies and moths) render Iflaviridae paraphyletic, and their taxonomic status should be reevaluated. Two of the newly identified iflaviruses are dicistronic, the first genomes with this phenotype in the family Iflaviridae. A newly characterized psyllid iflavirus displays an inverted genome architecture and forms a clade with other psyllid-infecting iflaviruses that share this feature. We also detected and sequenced two of the novel iflaviruses, GnV2 and DcV1, in wild-captured Graminella nigrifrons and purchased Delphastus catalinae, demonstrating their presence in populations beyond those previously sequenced. Our pipeline provides an additional method by which novel viruses can be discovered, assembled, annotated, and submitted to nucleotide sequence archives.IMPORTANCEInsects are the most abundant group of animals on Earth and serve as reservoirs for myriad microscopic organisms, including viruses. Just a fraction of this viral diversity has been characterized despite some having considerable consequences to human and animal health, agricultural production, and overall ecological stability. In this study, we illustrate a bioinformatic viral discovery pipeline using single-stranded, positive-sense RNA viruses of the order Picornavirales as a case study. Picornaviruses are some of the 'dark taxa' of the virosphere that are ubiquitous in arthropods, including the vectors of serious plant diseases. Discoveries of these viruses have been accelerated by the advent of next-generation sequencing technologies, opening potential research avenues that could be exploited for pest control.},
}
@article {pmid41406178,
year = {2025},
author = {Somsen, ED and Septer, KM and Field, CJ and Patel, DR and Lowen, AC and Sutton, TC and Koelle, K},
title = {Quantifying viral pandemic potential from experimental transmission studies.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013808},
pmid = {41406178},
issn = {1553-7358},
support = {75N93021C00017/AI/NIAID NIH HHS/United States ; F31 AI186550/AI/NIAID NIH HHS/United States ; T32 AI138952/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Ferrets/virology ; Humans ; *Pandemics/statistics &amp; numerical data ; *Influenza, Human/transmission/epidemiology/virology ; Computational Biology ; Influenza A virus ; Risk Assessment ; Models, Biological ; *Orthomyxoviridae Infections/transmission/epidemiology/virology ; },
abstract = {In an effort to avert future pandemics, surveillance studies aim to identify animal viruses at high risk of spilling over into humans. These studies have revealed substantial diversity in identified viruses. However, the number of tools currently available to assess pandemic risk is limited. Methods currently in use include the characterization of candidate viruses using in vitro laboratory assays and experimental transmission studies in animal models. However, transmission experiments yield relatively low-resolution outcomes that are not immediately translatable to projections of viral dynamics at the level of a host population. To address this gap, we present an analytical framework to extend the use of measurements from experimental transmission studies to generate more quantitative risk assessments. Specifically, we use within-host viral titer data from index and contact animals to estimate parameters relevant to transmission between pairs of individuals. We then extend this model to estimate epidemiological parameters, such as reproduction numbers and generation intervals. We present our analytical framework in the context of two influenza A virus (IAV) ferret transmission experiments: one using influenza A/California/07/2009 (Cal/2009) and one using influenza A/Hong Kong/1/1968 (Hong Kong/1968). In a head-to-head comparison, we find that Cal/2009 has higher pandemic potential than Hong Kong/1968. Our results depend on several assumptions, including that within-host viral dynamics in humans and those in the model animal used (here, ferrets) share quantitative similarities and that viral transmissibility between model animals reflects viral transmissibility between humans. The methods we present to assess pandemic risk of viral isolates can be used to improve relative risk assessment of other emerging viruses of pandemic concern.},
}
@article {pmid41406850,
year = {2026},
author = {Suzuki, J and Kobayashi, Y and Fujino, Y and Tabuchi, T and Katori, Y},
title = {Prevalence and associated factors of self-reported olfactory dysfunction in Japan: Findings from a nationwide web-based cross-sectional survey.},
journal = {Auris, nasus, larynx},
volume = {53},
number = {1},
pages = {61-69},
doi = {10.1016/j.anl.2025.12.008},
pmid = {41406850},
issn = {1879-1476},
mesh = {Humans ; Male ; Female ; Japan/epidemiology ; Middle Aged ; Cross-Sectional Studies ; Prevalence ; Adult ; *Olfaction Disorders/epidemiology ; Aged ; Self Report ; *COVID-19/epidemiology ; Asthma/epidemiology ; Severity of Illness Index ; Risk Factors ; SARS-CoV-2 ; Chronic Disease ; Hypertension/epidemiology ; },
abstract = {OBJECTIVE: Olfactory dysfunction (OD) compromises safety and well-being in humans; however, large-scale Japanese data are lacking. We quantified the prevalence of subjective chronic OD (self-reported olfactory impairment persisting ≥3 months), identified associated health and occupational factors, and evaluated determinants for severity using data from a nationwide web-based survey in Japan.<br><br>METHODS: We analyzed data from the Japan coronavirus disease 2019 and Society Internet Survey 2023, a stratified, nationwide, cross-sectional survey of community-dwelling residents in Japan. From the initial 33,000 participants, we used the data of 25,569 participants (12,323 men, 13,246 women), after excluding those with implausible responses and missing data, to calculate prevalence. Inverse probability weighting was used to align the sample with the 2019 National Living Conditions Survey. Group differences concerning the presence and severity of OD were tested with &#x3c7;&#xb2; or Wilcoxon tests after excluding participants with additional missing data; independent associations were examined using weighted multivariable logistic regression analyses.<br><br>RESULTS: The weighted prevalence for chronic subjective OD was 1.3 % (95 % confidence interval [CI] 1.1-1.4); age-specific rates ranged from 0.6 % (40-49 years) to 2.1 % (60-69 years). Independent OD correlates included the factors current smoking (odds ratio [OR] 2.09, p = 0.016), homeworking (OR 2.75, p = 0.004), somatic symptoms (Somatic Symptom Scale-8 score &#x2265; 12; OR 2.66, p = 0.009), dysgeusia (OR 193.2, p < 0.001), current hypertension (OR 3.69, p = 0.005), current bronchial asthma (OR 6.09, p < 0.001), current allergic rhinitis (OR 1.97, p = 0.012), and moderate-severe presenteeism (Work Functioning Impairment Scale score &#x2265; 21; OR 3.04, p < 0.020). Being a woman was associated with lower OD severity (OR 0.34, p = 0.035, for moderate-severe vs mild), whereas having &#x2265; 1 day of sick absences in the previous month was associated with higher OD severity (OR 3.17, p = 0.044).<br><br>CONCLUSION: Subjective OD prevalence in Japan was 1.3 %. Presenteeism was associated with OD and absenteeism was associated with moderate-severe OD. Further studies on the relationship between OD and work productivity are warranted.},
}
@article {pmid41407116,
year = {2026},
author = {Dey, D and Lateef, HA and Leroux, A and Zipunnikov, V and Merikangas, K},
title = {Associations between daily outdoor temperature and subjective real-time ratings of emotional states and sleep in mood disorder subtypes.},
journal = {Journal of affective disorders},
volume = {397},
number = {},
pages = {120918},
doi = {10.1016/j.jad.2025.120918},
pmid = {41407116},
issn = {1573-2517},
mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; Aged ; Adolescent ; Aged, 80 and over ; *Temperature ; Child ; Ecological Momentary Assessment ; Young Adult ; *Mood Disorders/psychology ; *Sleep/physiology ; *Affect ; Seasons ; Sleep Quality ; *Emotions ; Bipolar Disorder/psychology ; },
abstract = {There is growing evidence for the influence of weather on mental health at both the aggregate level indices of mental health statistics of hospitalizations, morbidity, and mortality, and individual level dynamics of mood states. Most research on this topic has focused on light exposure and depressed mood as the sole indicators of seasonal fluctuations of mood disorders. This paper evaluates the association between daily maximum outdoor temperature (DMOT) and contemporaneously reported mood, energy, anxiousness, and sleep quality assessed with Ecological Momentary Assessment (EMA) in a community-based sample of 452 people, aged 11 to 85 years, comprising people with or without a history of mood disorders. After controlling for demographics, daily activity levels, and daytime cloud coverage as an index of light exposure, we found that higher DMOT was associated with better mood, increased energy, and better sleep quality among those with a history of mood disorders, particularly in the spring. These findings suggest that the dynamics of mood, energy, and sleep may underlie the aggregate population-level influences of temperature and correlated environmental influences on negative mental health outcomes, particularly among those with BD. Therefore, the conceptualization of risk and intervention for mood disorders should consider both the aggregate influences of temperature and light and associated environmental conditions, as well as individual-level sleep quality and energy as potential mechanisms for seasonal patterns of emotional states.},
}
@article {pmid41408523,
year = {2025},
author = {Wirth, M and Bischoff, S and Hering, R and Schulz, M and Mackowiak, M and Piedboeuf-Potyka, K and Brinks, R and Hoyer, A and Tönnies, T},
title = {Prevalence of type 2 diabetes from 2011 to 2023 by regional socioeconomic deprivation in Germany: an ecological study.},
journal = {BMC public health},
volume = {26},
number = {1},
pages = {258},
pmid = {41408523},
issn = {1471-2458},
abstract = {BACKGROUND: Type 2 diabetes prevalence is increasing globally and is unequally distributed across socioeconomic groups. In Germany, little is known about how these socioeconomic inequalities have developed over time. Therefore, we aimed to estimate the age- and sex-specific prevalence of type 2 diabetes in Germany from 2011 to 2023 and assess related temporal trends in socioeconomic inequality.<br><br>METHODS: We used nationwide claims data (N&#x2009;~&#x2009;70&#xa0;million persons per year) from the German statutory health insurance, aggregated at the county level and linked them to the German Index of Socioeconomic Deprivation (GISD), an area-based measure of deprivation based on education, occupation, and income. We identified prevalent type 2 diabetes cases using ICD-10 codes E11, E12, E13, and E14. Log-binomial regression was used to estimate prevalence ratios for the association between GISD quintiles and type 2 diabetes prevalence, with temporal trends assessed through the four-way interaction between age, sex, GISD, and calendar year.<br><br>RESULTS: Crude type 2 diabetes prevalence increased from 9.00% (95% confidence interval: 8.99&#x2013;9.01) in 2011 to 9.60% (9.59&#x2013;9.61) in 2023, while age-standardised prevalence showed a smaller increase, from 9.00 (8.99-9.00) in 2011 to 9.35% (9.34&#x2013;9.35) in 2023. A clear socioeconomic gradient emerged, with the highest prevalence of 11.80% (11.78&#x2013;11.82) in 2023 in the most deprived regions (quintile 5), compared to 8.00% (7.99&#x2013;8.01) in the least deprived regions (quintile 1). Prevalence was consistently higher in men than women, but the socioeconomic gradient was more pronounced among women (prevalence ratio 2023 women 1.29 (1.23&#x2013;1.35), men 1.22 (1.17&#x2013;1.26)).<br><br>CONCLUSIONS: Our findings highlight persistent socioeconomic disparities in type 2 diabetes prevalence, especially among women. Further research is needed to explore the mechanisms underlying these disparities and to evaluate targeted interventions for high-risk populations.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12889-025-25908-x.},
}
@article {pmid41408553,
year = {2025},
author = {Wyatt, S and Hobro, G and Seamer, P and Mohammed, MA and Spilsbury, P},
title = {Decomposing the effects of changes of population size, age-sex profile, health status and residual factors on growth in hospital activity in English hospitals: an ecological database study from 2011-2019.},
journal = {BMC health services research},
volume = {25},
number = {1},
pages = {1601},
pmid = {41408553},
issn = {1472-6963},
mesh = {Humans ; England ; Female ; Male ; Retrospective Studies ; *Health Status ; Adult ; Middle Aged ; *Population Density ; Aged ; State Medicine ; Databases, Factual ; Age Factors ; Sex Factors ; Adolescent ; Young Adult ; *Hospitalization/statistics &amp; numerical data/trends ; *Hospitals/statistics &amp; numerical data ; *Population Growth ; Infant ; },
abstract = {BACKGROUND: Hospitals are central to healthcare systems and understanding the drivers of hospital activity is critical for effective capacity planning, especially amid demographic shifts and fiscal pressure. In the English National Health Service (NHS), there are plans to construct 40 new hospitals. There is limited evidence on factors driving hospital activity. This study provides retrospective estimates of the effects of population growth (P), changes in the age-sex structure (S), shifts in age-specific health status (H), and residual factors (R) on hospital activity in England.<br><br>METHODS: Total annual growth is modelled as G&#x2009;=&#x2009;(1&#x2009;+&#x2009;P)(1&#x2009;+&#x2009;S)(1&#x2009;+&#x2009;H)(1&#x2009;+&#x2009;R)&#x2009;-&#x2009;1. Negative binomial regression models using hospital episode statistics from 2011 to 2019 were used to decompose total annual growth rates (G) into P,S,H and R by five points of delivery (listed below).<br><br>RESULTS: The annual growth rate for elective admissions was 2.29% (95% CI: 1.06% to 3.54%) which was made up of p&#x2009;=&#x2009;0.88% (-0.96% to 2.67%), S&#x2009;=&#x2009;0.69% (-0.62% to 2.18%), H&#x2009;=&#x2009;-0.03% (-0.23% to 0.17%) and R&#x2009;=&#x2009;0.73% (0.58% to 0.88%). The annual growth rate for non-elective admission was 2.69% (1.55% to 3.83%) which was made up of p&#x2009;=&#x2009;0.59% (-1.08% to 2.50%), S&#x2009;=&#x2009;0.25% (-1.17% to 1.61%), H&#x2009;=&#x2009;0.18% (-0.43% to 0.81%) and R&#x2009;=&#x2009;1.65% (1.13% to 2.17%). The annual growth rate for maternity admissions was -0.70% (-5.65% to 4.51%) which was made up of p&#x2009;=&#x2009;0.41% (-6.25% to 8.36%), S&#x2009;=&#x2009;-0.08% (-4.93% to 5.23%), H&#x2009;=&#x2009;0.00% (NA) and R&#x2009;=&#x2009;-1.02% (-1.61% to -0.43%). The annual growth rate for outpatient attendance was 4.51% (3.62% to 5.40%) which was made up of p&#x2009;=&#x2009;0.61% (-0.71% to 1.96%), S&#x2009;=&#x2009;0.46% (-0.63% to 1.56%), H&#x2009;=&#x2009;-0.02% (-0.43% to 0.38%) and R&#x2009;=&#x2009;3.41% (3.11% to 3.71%). The annual growth rate for emergency department attendance was 1.29% (0.71% to 1.88%) which was made up of p&#x2009;=&#x2009;0.27% (-0.56% to 1.09%), S&#x2009;=&#x2009;0.09% (-0.55% to 0.70%), H&#x2009;=&#x2009;0.09% (-0.21% to 0.39%) and R&#x2009;=&#x2009;0.84% (0.58% to 1.10%).<br><br>CONCLUSIONS: In general, growth in hospital activity was mostly driven by residual (R) factors, followed by population growth (P). Age-specific health status (H) had the lowest impact. These data may provide useful context for planning future hospital activity in England.},
}
@article {pmid41411345,
year = {2025},
author = {Fairbanks, EL and Baylis, M and Daly, JM and Tildesley, MJ},
title = {Quantifying vector diversion effects in zoonotic systems: A modelling framework for arbovirus transmission between reservoir and dead-end hosts.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013359},
pmid = {41411345},
issn = {1553-7358},
mesh = {Animals ; Humans ; *Mosquito Vectors/virology ; Culex/virology ; *Disease Reservoirs/virology ; *Models, Biological ; West Nile Fever/transmission ; *Zoonoses/transmission/virology ; West Nile virus ; Computational Biology ; Vector Borne Diseases/transmission ; *Arbovirus Infections/transmission ; },
abstract = {Vector-borne disease transmission involves complex interactions between vectors, reservoir hosts and dead-end hosts. We present a mathematical model for the vectorial capacity that incorporates multiple host types and their interactions, focusing specifically on West Nile virus transmission by Culex pipiens mosquitoes. Our model integrates climate-dependent parameters affecting vector biology with vector control interventions to predict transmission potential under various scenarios. We demonstrate how vector control interventions targeting one host type can significantly impact transmission dynamics across all host populations. By examining the effects of different vector control tool modes of action (repellency, preprandial killing, disarming and postprandial killing), we develop target product profiles that minimise unintended consequences of vector control. Notably, we identify the optimal intervention characteristics needed to prevent repellency on dead-end hosts from inadvertently increasing transmission among reservoir hosts. This research provides valuable insights for public health officials designing targeted vector control strategies and offers a flexible modelling framework that can be adapted to other vector-borne diseases with complex host dynamics.},
}
@article {pmid41411944,
year = {2026},
author = {Nour, HE and Garoub, MM},
title = {Heavy metal bioaccumulation and risk assessment in intertidal molluscan shells and sediments of Suez Bay.},
journal = {Marine pollution bulletin},
volume = {224},
number = {},
pages = {119141},
doi = {10.1016/j.marpolbul.2025.119141},
pmid = {41411944},
issn = {1879-3363},
mesh = {*Water Pollutants, Chemical/analysis/metabolism ; *Geologic Sediments/chemistry ; Animals ; *Metals, Heavy/analysis/metabolism ; Risk Assessment ; *Environmental Monitoring ; Bays/chemistry ; *Mollusca/metabolism/chemistry ; Bioaccumulation ; *Animal Shells/chemistry ; },
abstract = {This study investigated heavy metal (HM) concentrations in molluscan shells and associated sediments along the Suez Bay coast to assess bioaccumulation patterns, ecological and human health risks, and potential pollution sources. Bioaccumulation studies in this region remain scarce, making the present work a valuable contribution to addressing a critical knowledge gap. Three molluscan species (Cerithium ruppelli, Septifer bilocularis, and Modiolus auriculatus) were analyzed across five coastal sites. C. ruppelli accumulated higher levels of Pb, Co, and Cr, whereas S. bilocularis was more indicative of Cu and Cd enrichment. Bioaccumulation factors exhibited clear interspecific differences, with the shell-to-sediment ratios reflecting both localized metal exposure and the varying bioaccumulation capacities of each species. Sediment quality indices (Igeo, Cf, mCdeg, PLI, TRI) indicated a generally uncontaminated status; however, localized enrichment of Cd and Co was identified, requiring continuous monitoring. Human health risk assessment confirmed no immediate carcinogenic or non-carcinogenic risks, although potential hazards may arise from future increases in Ni and Cr. Overall, molluscan shells particularly S. bilocularis and C. ruppelli proved to be effective bioindicators, highlighting the need for continued biomonitoring and stricter regulation of industrial and urban discharges into Suez Bay.},
}
@article {pmid41413899,
year = {2025},
author = {Peng, M and Li, J and Xu, L and Chroumpi, T and Garrigues, S and Kun, RS and Meng, J and Aguilar-Pontes, MV and Lipzen, A and Ng, V and Clendinen, CS and Tolic, N and Baker, SE and Grigoriev, IV and de Vries, RP},
title = {Multi-Omics Analyses Reveal Divergent Molecular Mechanisms Underlying Plant Biomass Conversion by Five Fungi.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70201},
pmid = {41413899},
issn = {2045-8827},
support = {OCENW.XS23.2.218//NWO ENW-XS program/ ; OCENW.XS24.2.218//NWO ENW-XS program/ ; NGF.1609.241.001//NWO NGF-AiNedXS program/ ; NGF.1609.23.006//NWO NGF-AiNedXS program/ ; 202107720100//China Scholarship Council Scholarship/ ; 201907720027//Chinese Scholarship Council (CSC)/ ; //Dutch Research Council (NWO)/ ; //Ministry of Infrastructure and Water Management/ ; //Facilities Integrating Collaborations for User Science (FICUS)/ ; },
mesh = {*Biomass ; Lignin/metabolism ; *Ascomycota/metabolism/genetics/growth &amp; development ; Zea mays/metabolism/microbiology ; *Basidiomycota/metabolism/genetics/growth &amp; development ; Proteome/analysis ; Transcriptome ; Metabolome ; Gene Expression Profiling ; *Plants/metabolism/microbiology ; Multiomics ; },
abstract = {Fungal plant biomass conversion (FPBC) is of great importance to the global carbon cycle and has been increasingly applied for the production of biofuel and biochemicals from lignocellulose. However, the comprehensive understanding of relevant molecular mechanisms in different fungi remains challenging. Here, we comparatively analyzed the transcriptome, proteome and metabolome profile of four ascomycetes and one basidiomycete fungi during their growth on two common agricultural feedstocks (soybean hulls and corn stover). We revealed strong time-, substrate- and species-specific responses at multi-omics levels for the tested fungi, highlighting species-specific carbon utilization approaches and evolutionary adaptation to environmental niches. Notably, a remarkable expressional diversity of lignocellulose degrading enzymes, sugar transporter and metabolic genes, as well as industrially relevant metabolites were identified across different fungi and cultivation conditions. The findings improves our understanding of complex molecular networks underlying FPBC and fungal ecological roles, offering novel insights that can guide future genetic engineering of fungi for valorization of agriculture waste into value-added bioproducts.},
}
@article {pmid41415319,
year = {2025},
author = {Agboli, E and Zahouli, JZB and Sauer, FG and Sombie, A and Biré, YN and Adjobi, CN and Cadar, D and Horváth, B and Tomazatos, A and Schmidt-Chanasit, J and Lühken, R and Tóth, GE and Badolo, A and Jöst, H},
title = {Morphological and Genetic Heterogeneity in Aedes aegypti (Diptera: Culicidae) Populations Across Diverse Landscapes in West Africa.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72748},
pmid = {41415319},
issn = {2045-7758},
abstract = {Native to sub-Saharan Africa, Aedes aegypti (Linnaeus, 1762) has spread across the globe and is now one of the most significant vectors of arboviruses worldwide. However, data on the ranges of its populations remain sparse, and the genetic variability and ecological adaptability in West Africa are still poorly understood. In this study, we characterized the morphological and genetic diversity of Ae. aegypti across four landscape types (urban, peri-urban, rural, and sylvatic sites) in three West African countries (Burkina Faso, Côte d'Ivoire, and Ghana). The population exhibited significant variation in abdominal scaling patterns across countries and landscape types, with the sylvatic and urban populations in Burkina Faso displaying the highest proportions of white scales (> 50% white scales), while black scales predominated among those from Côte d'Ivoire and Ghana (> 80% black scales). Wing shape displayed limited differentiation between the countries, landscape types, and genetic clusters. Bayesian analysis indicated high gene flow among populations, with notable outliers observed in sylvatic sites from Burkina Faso and admixture patterns suggesting possible human-mediated dispersal. Additionally, two major mitochondrial lineages, clades A and B, were identified. Most samples were categorized under clade B, showing no evidence of clustering by country or landscape type. In contrast, clade A comprised primarily sylvatic specimens from Burkina Faso and a single urban individual from Côte d'Ivoire. These findings highlight the complex interplay of genetic, environmental, and ecological factors shaping the variations in Ae. aegypti populations in West Africa. They provide insights into the phenotypic and genetic diversity of Ae. aegypti, offering valuable implications for understanding arbovirus transmission dynamics and formulating targeted interventions against arboviral diseases.},
}
@article {pmid41419039,
year = {2026},
author = {Rozen-Rechels, D and Lemesle, P and Jouanneau, W and Sebastiano, M and Harris, SM and Blévin, P and Angelier, F and Gernigon, J and Lemesle, JC and Robin, F and Budzinski, H and Labadie, P and Bustamante, P and Chastel, O},
title = {How does habitat use influence PFAS contamination in wildlife? Combining stable isotopes and GPS tracking in three gull species.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {391},
number = {},
pages = {127556},
doi = {10.1016/j.envpol.2025.127556},
pmid = {41419039},
issn = {1873-6424},
mesh = {Animals ; *Charadriiformes/metabolism ; *Fluorocarbons/metabolism/blood ; *Ecosystem ; *Environmental Monitoring/methods ; France ; Geographic Information Systems ; Male ; *Environmental Pollutants/metabolism/blood ; Female ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; Food Chain ; },
abstract = {Per- and polyfluoroalkyl substances (PFAS) are toxic and persistent compounds widely distributed in the environment and accumulate in top predators, including seabirds. Because of the biomagnification potentials of some PFAS, diet is thought to be a key exposure route for PFAS. However, other factors such as habitat use, may mask interspecific differences in PFAS exposure expected from trophic structure. Among seabirds, gulls are generalists that forage in both terrestrial and marine habitats, making them relevant models to concurrently investigate the influence of foraging habitats and trophic position on PFAS exposure. We combined plasma PFAS concentrations with GPS tracking and stable isotopes to define foraging habitats (δ[13]C; δ[34]S; GPS) and trophic positions (δ[15]N) in three sympatric gull species breeding in France (Isle of Ré). In herring gulls (Larus argentatus), long-chain perfluoroalkyl carboxylic acids (PFCAs) were positively correlated with high trophic resources from marine habitats. We found compound- and sex-dependent relationships between PFAS concentrations and stable isotope values in lesser black-backed gulls (Larus fuscus), while no association was found with habitat use. No association was found between PFAS levels and stable isotopes in great black-backed gulls (Larus marinus). Our study suggests that coastal habitat could be a source of PFCA contamination and highlights that the influence of habitat use on gull exposure to PFAS varied depending on species, sex, and compounds.},
}
@article {pmid41420859,
year = {2026},
author = {Beghini, F and Brito, IL and Gerstein, M and Christakis, NA},
title = {Characterization of gut microbiomes in rural Honduras reveals uncharacterized species and associations with human genetic variation.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116724},
doi = {10.1016/j.celrep.2025.116724},
pmid = {41420859},
issn = {2211-1247},
mesh = {Humans ; Honduras ; *Gastrointestinal Microbiome/genetics ; *Genetic Variation ; Rural Population ; Male ; Female ; COVID-19/virology/microbiology ; Adult ; Metagenomics ; Middle Aged ; SARS-CoV-2 ; Metagenome ; },
abstract = {The gut microbiome is integral to human health, yet research data to date have emphasized industrialized populations. Here, we performed large-scale shotgun metagenomic sequencing on 1,893 individuals from rural Honduras, providing the most comprehensive microbiome dataset from Central America. We identify a distinct microbial composition enriched in Prevotella species. Longitudinal analysis in 301 individuals reveals microbiome instability, with shifts in taxonomic diversity and metabolic potential, including changes associated with severe acute respiratory syndrome coronavirus 2 infection. Additionally, we characterize the gut virome and eukaryotic microbiome, identifying uncharacterized viral taxa and a high prevalence of Blastocystis species in individuals with greater microbial diversity. Finally, by integrating host genomic data, we uncover significant host-microbiome associations, highlighting the influence of human genetic variation on microbial composition. These findings expand our understanding of microbiome diversity in non-industrialized populations, underscoring the need for global microbiome research.},
}
@article {pmid41421202,
year = {2026},
author = {Webster, AB and Bennett, NC and Clauss, M and Ganswindt, A and Abraham, AJ},
title = {Soil ingestion: An important contamination pathway for toxic element exposure in wild herbivores.},
journal = {The Science of the total environment},
volume = {1012},
number = {},
pages = {181193},
doi = {10.1016/j.scitotenv.2025.181193},
pmid = {41421202},
issn = {1879-1026},
mesh = {Animals ; *Soil Pollutants/analysis/metabolism ; *Herbivory ; *Environmental Monitoring ; Soil/chemistry ; Animals, Wild ; },
abstract = {Human activities have increased pollution and toxic element concentrations in soils across the Earth's surface. These activities could have profound implications for wildlife that directly or incidentally ingest soil during foraging, and for humans that consume animals as a primary source of protein. To date, levels of soil ingestion in large herbivores and species-specific vulnerability to toxic element exposure via this pathway have not yet been assessed. Here, we tested the hypothesis that animals feeding closer to the ground ingest more soil than their browsing counterparts. Across a community of 16 African herbivore species, we found that soil ingestion was highest in grazing (blue wildebeest, white rhino and buffalo) and fossorial (warthog and porcupine) animals. This translated to 20-60 % higher total element intake for chromium, cobalt, tin, lead, vanadium and arsenic in these groups. Faecal and fur concentrations were similarly elevated in these species, highlighting that the toxic elements ingested from soil are assimilated into body tissues with potential repercussions for animal and human health. In ungulates, soil ingestion rates align with species-level hypsodonty (height of the tooth crown). We propose that hypsodonty can be used as a proxy for identifying species-specific vulnerability to toxic-element exposure at broad scales. The non-invasive framework developed here, may be applied to monitoring wild herbivore exposure to toxic elements and may be particularly relevant for ongoing conservation and rewilding efforts in areas with high levels of anthropogenic pollution.},
}
@article {pmid41422551,
year = {2025},
author = {Almeida-Filho, N and Ayres, JRCM},
title = {[Intersubjectivity and modes of care in health: eco-ethno-social sensitivity and critical technological competence for quality-equity in digital health].},
journal = {Salud colectiva},
volume = {21},
number = {},
pages = {e5763},
pmid = {41422551},
issn = {1851-8265},
mesh = {Humans ; *Delivery of Health Care/organization &amp; administration ; *Digital Technology ; *Quality of Health Care ; Digital Health ; },
abstract = {In this essay, we propose that Mendes Gonçalves' theory of the labor process in health can contribute to a critical theory of digital health capable of deconstructing technological alienation within digital transformation processes in the health sector. First, we identify modes of care and models of technological organization of healthcare delivery. Second, we analyze the collective-informational mode of care oriented toward sociotechnical health networks, highlighting collaborative practices rooted in territories and local realities. Third, we propose a theoretical platform for understanding digital transformation in health, based on the articulation of the following concepts: sociotechnical appropriation, metapresence, critical technological competence, quality-equity, and eco-ethno-social sensitivity. Finally, we outline the epistemological and theoretical foundations necessary for a "digital epistemodiversity," understood as an ecology of knowledges in which technical objects, sociotechnical systems, human agents, and transhuman beings may coexist, interact, and produce systemic changes in the health field, with the protagonism of healthcare workers and broad popular participation.},
}
@article {pmid41423362,
year = {2026},
author = {Yang, B and Molton, I and Humbert, A and Gregg, E and Iribarren, S and Hurvitz, P and Lee, D},
title = {Is doing more always better? A mixed methods study examining the relationship between subjective and objective aspects of community participation among people with multiple sclerosis.},
journal = {Disability and health journal},
volume = {19},
number = {2},
pages = {102020},
pmid = {41423362},
issn = {1876-7583},
support = {R01 NR016942/NR/NINR NIH HHS/United States ; },
mesh = {Humans ; *Multiple Sclerosis/psychology ; Female ; Male ; Middle Aged ; Adult ; *Community Participation ; Focus Groups ; *Persons with Disabilities/psychology ; *Social Participation ; *Personal Satisfaction ; Aged ; Activities of Daily Living ; },
abstract = {BACKGROUND: Community participation is an important health outcome among people with multiple sclerosis (PwMS) and includes subjective (e.g., satisfaction) and objective aspects (e.g., frequency). Conceptual literature emphasizes the need for measuring both types of aspects to fully understand participation, yet empirical evidence remains limited.<br><br>OBJECTIVE: To examine the relationship between subjective and objective aspects of community participation and their associations with person-related and environmental factors.<br><br>METHODS: A mixed methods design was used. Correlation analyses of previously collected self-reported and GPS-based data from 100 PwMS assessed statistical associations between subjective and objective participation. Four focus groups were conducted with 24 PwMS discussing the relationship between participation satisfaction and performance. Qualitative data were analyzed using content analysis.<br><br>RESULTS: Moderate to strong correlations (.4-.78, p&#xa0;<&#xa0;0.001) were found within objective (trip frequency, distance, duration, and activity space) and subjective participation measures (perceived ability and satisfaction). However, associations between subjective and objective aspects were mostly weak (.2-.32, p&#xa0;<&#xa0;0.05). Person-related and environmental factors showed varying correlations, with generally stronger associations for subjective participation measures (.17 to -.57, p&#xa0;<&#xa0;0.01) than objective measures (.16-.36, p&#xa0;<&#xa0;0.05). Aligned with quantitative results, qualitative themes revealed that greater participation quantity may facilitate satisfaction, but frequent and extensive participation is not necessary to reach satisfaction.<br><br>CONCLUSIONS: This study provides integrated quantitative and qualitative evidence that subjective and objective aspects of participation are related but distinct. Attention must be paid to the divergence between these aspects to address real-world barriers.},
}
@article {pmid41425596,
year = {2025},
author = {Yu, R and Hasan, A and Ibrahim, M and Alonazi, WB and Bin, L},
title = {An integrated immunoinformatic approach to design a novel multiepitope chimeric vaccine against Mycoplasma phocimorsus as a causal agent of bloodstream infections.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1719398},
pmid = {41425596},
issn = {1664-3224},
mesh = {*Bacterial Vaccines/immunology/genetics ; *Mycoplasma Infections/immunology/prevention &amp; control/microbiology ; Humans ; *Mycoplasma/immunology ; Computational Biology/methods ; Epitopes, B-Lymphocyte/immunology ; Animals ; Epitopes/immunology ; Proteomics/methods ; Vaccine Development ; *Sepsis/immunology/prevention &amp; control/microbiology ; },
abstract = {INTRODUCTION: Mycoplasma phocimorsus is increasingly recognized as an emerging human pathogen, despite its primary association with marine mammals. It has recently been identified as a causative agent of bloodstream infections and sepsis, a major cause of mortality among hospitalized patients. To date, no approved vaccine is available against M. phocimorsus, underscoring the urgent need for preventive strategies.<br><br>METHODS: The current study was aimed at employing immunoinformatic approaches to design a vaccine based on multiple epitopes derived from the six core proteomic datasets of representative M. phocimorsus strains.<br><br>RESULTS: By subtractive genomics, we retrieved 3,576 nonredundant proteins from M. phocimorsus proteomes following only one putative immunoglobulin-blocking virulence outer membrane protein conserved in six strains. The epitopes derived from the putative immunoglobulin-blocking virulence protein exhibited promising features such as strong binding affinity, lack of allergenicity, nontoxic properties, high antigenicity scores, and excellent solubility. Moreover, these epitopes include nine linear B cell epitopes, eight MHC class I epitopes, and five MHC class II epitopes. In addition, adjuvants and linker molecules were successfully merged into a chimeric vaccine with significant immunogenicity and stimulation of both adaptive and innate immune responses. The promising potential of the selected vaccine candidates was further validated through their favorable physico-chemical characteristics, strong interaction with TLR-4, and stable performance in molecular dynamics simulations.<br><br>DISCUSSION: These results suggest that the putative immunoglobulin-blocking outer membrane virulence protein could effectively participate in activating the primary innate immune response, thereby serving as a strong foundation for subsequent adaptive immune activation. The proposed vaccine provides substantial basis for developing effective preventive and therapeutic measures against the zoonotic M. phocimorsus, whose association with sepsis, soft tissue, and respiratory infections, particularly in immunocompromised individuals emphasizes the crucial need for vaccine development.},
}
@article {pmid41425965,
year = {2025},
author = {Lin, Y and Chen, S and Che, J and Sun, M and Wang, Y},
title = {Multi-omics approaches for image classification in disease diagnosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616189},
pmid = {41425965},
issn = {2235-2988},
mesh = {Humans ; *Genomics/methods ; *Computational Biology/methods ; *Proteomics/methods ; *Metabolomics/methods ; Multiomics ; },
abstract = {INTRODUCTION: The integration of multi-omics data for disease diagnosis holds transformative potential in the field of computational biology, especially when applied to the intricate and dynamic interactions between microbial communities and their human hosts.<br><br>METHODS: This integrative approach enables to capture diverse biological signals across genomic, transcriptomic, proteomic, and metabolomic layers, providing a more comprehensive understanding of disease mechanisms. In alignment with emerging priorities in disease microbiology, our study addresses a critical and timely need for interpretable, scalable, and biologically robust computational models that can extract clinically meaningful diagnostic insights from inherently high-dimensional, heterogeneous, and often incomplete biological datasets.<br><br>RESULTS AND DISCUSSION: Traditional image classification approaches in disease contexts-such as those relying solely on histopathological features or genomic imaging-tend to overlook the broader ecological and systemic dimensions that are essential for decoding the mechanisms of microbial pathogenesis. These single-modal methods often suffer from significant limitations, including reduced scalability to diverse clinical settings, poor generalizability across patient populations, and an inability to handle partially observed or biologically variable data. Such constraints diminish their effectiveness in precision diagnostics, disease subtyping, and therapeutic decision-making. By contrast, our approach emphasizes multi-modal integration and model interpretability, aiming to overcome these limitations and advance the development of next-generation diagnostic tools that are both clinically actionable and biologically grounded.},
}
@article {pmid41427113,
year = {2025},
author = {Garai, S and Vo, S and Blank, L and Xu, F and Chen, J and Duong-Tran, D and Zhao, Y and Brown, BC and Shen, L},
title = {H-VIP: quantifying regional topological contributions of the brain network to cognition.},
journal = {Frontiers in radiology},
volume = {5},
number = {},
pages = {1686780},
pmid = {41427113},
issn = {2673-8740},
support = {R01 AG068191/AG/NIA NIH HHS/United States ; R01 EB034720/EB/NIBIB NIH HHS/United States ; RF1 AG081413/AG/NIA NIH HHS/United States ; },
abstract = {INTRODUCTION: Understanding the role of various brain regions of interest (ROIs) in various cognitive functions or tasks, across healthy or neurodegenerative conditions and multiple degrees of separation, remains a key challenge in neuroscience. Conventional network measures can only capture localized or quasi-localized features of brain ROIs. Topological data analysis (TDA), particularly persistent homology, provides a threshold-free, mathematically rigorous framework for identifying topologically salient features in complex networks. In this paper, we introduce a new metric, the Homological Vertex Importance Profile (H-VIP), designed to assess the relevance of vertices that participate in persistent topological structures (e.g., connected components, cycles or cavities) in brain networks. The H-VIP quantifies the topological features of the network at the ROI (node) level by compressing its higher-order connectivity profile using homological constructs.<br><br>METHODS: Leveraging homological constructs of brain connectomes, we extend two of our previously defined network-level measures-average persistence and persistence entropy-to an ROI-level measure, i.e., the H-VIP. We then applied the H-VIP to two independent datasets: structural connectomes from the Human Connectome Project and functional connectomes from the Alzheimer's Disease Neuroimaging Initiative. Persistent homology was computed for each network, and H-VIP scores were derived to evaluate vertex-level contributions. Finally, H-VIP scores were used for the prediction of multiple cognitive measures.<br><br>RESULTS: In both anatomical and functional brain networks, H-VIP values demonstrate predictive power for various cognitive measures. Notably, the connectivity of the frontal lobe exhibited stronger correlations with cognitive performance than the whole-brain network.<br><br>DISCUSSION: H-VIP offers a robust and interpretable means to locate, quantify, and visualize region-specific contributions to network's topological, higher-order landscape. Its ability to detect potentially impaired connectivity at the individual level suggests possible applications in personalized medicine for neurological diseases and disorders. Beyond brain connectomics, the H-VIP can be used for other types of complex networks where topological features are of importance, such as financial, social, or ecological networks.},
}
@article {pmid41427890,
year = {2026},
author = {Martin, SLF and La Torre, R and Danneels, B and Tooming-Klunderud, A and Skage, M and Kollias, S and Tørresen, OK and Anbaran, MF and Stur, E and Jakobsen, KS and Martin, MD and Ekrem, T},
title = {Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids.},
journal = {GigaScience},
volume = {15},
number = {},
pages = {},
pmid = {41427890},
issn = {2047-217X},
support = {326819//Research Council of Norway/ ; 270068//Research Council of Norway/ ; //University of Bergen/ ; //University of Oslo/ ; //Norwegian University of Life Sciences/ ; },
mesh = {Animals ; *Chironomidae/genetics/physiology/classification ; Altitude ; Phylogeny ; Cold Temperature ; *Haplotypes ; *Adaptation, Physiological/genetics ; *Genome, Insect ; Arctic Regions ; *Acclimatization/genetics ; Genomics/methods ; },
abstract = {BACKGROUND: Arctic and alpine insects experience extreme environmental stressors, yet the genomic basis of their adaptation is poorly understood. Diamesa midges (Diptera: Chironomidae) are cold-adapted insects inhabiting glacial and high-altitude freshwater ecosystems, but no chromosome-level genomes have been available to date.<br><br>FINDINGS: We present the first haplotype-resolved, chromosome-level genomes for four Diamesa species (Diamesa hyperborea, Diamesa lindrothi, Diamesa serratosioi, and Diamesa tonsa), assembled using PacBio HiFi sequencing and Hi-C scaffolding. The assemblies show high completeness and k-mer representation. Phylogenomic analyses place Diamesinae as sister to other Chironomidae except Podonominae, and comparisons suggest introgression between the distinct species D. hyperborea and D. tonsa. Comparative genomic analyses across 20 Diptera species identified significant gene family contractions in Diamesa related to oxygen transport and metabolism, consistent with adaptation to high-altitude, low-oxygen environments. Expansions were observed in histone-related and Toll-like receptor gene families, suggesting roles in chromatin remodeling and immune regulation under cold stress. A glucose dehydrogenase gene family was significantly expanded across all cold-adapted species studied, implicating it in cryoprotectant synthesis and oxidative stress mitigation. Diamesa exhibited the largest gene family contraction at any phylogenetic node, with limited overlap in expansions with other cold-adapted Diptera, indicating lineage-specific adaptation.<br><br>CONCLUSIONS: Our findings support the hypothesis that genome size condensation and selective gene family changes underpin survival in cold environments. These new genome assemblies provide a valuable resource for studying adaptation, speciation, and conservation in cold-specialist insects. Future integration of gene expression and population genomics will further clarify the evolutionary resilience of Diamesa in a warming world.},
}
@article {pmid41429884,
year = {2025},
author = {Song, W and Hu, Q and Liu, S and Hou, Y},
title = {Decadal spatiotemporal dynamics of surface water bodies in Zhengzhou, China: remote sensing monitoring and analysis of driving factors.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {45089},
pmid = {41429884},
issn = {2045-2322},
abstract = {Water is essential for life, human activities, and ecological balance. Understanding the spatiotemporal dynamics of urban water bodies is critical for sustainable water management, especially in fast-growing cities like Zhengzhou. This study investigates the evolution of water bodies in Zhengzhou from 2014 to 2023, using multi-seasonal Landsat 8 imagery and GIS analysis. Three water extraction methods-thresholding, random forest (RF), and a hybrid RF model incorporating spectral indices (NDWI, MNDWI, EWI) and GLCM-based texture features-were evaluated. The hybrid RF approach demonstrated the highest classification accuracy and was applied to generate seasonal water body maps for the target years. The results show a general increase in surface water area, with seasonal peaks in July–September, and spatial expansion mainly in the northern and northeastern regions. These changes are driven by both natural (e.g., precipitation) and anthropogenic (e.g., urban development, artificial lake construction) factors. Compared to previous studies, this research offers three key innovations: (1) a decade-long, seasonal-scale analysis of water dynamics; (2) a robust multi-feature classification framework for complex urban settings; and (3) an integrated interpretation of natural and human influences. The findings provide valuable references for water resource planning and urban ecological restoration, and the methods used may be transferable to similar inland cities under monsoon climates.},
}
@article {pmid41432067,
year = {2025},
author = {Banse, SA and Sedore, CA and Coleman-Hulbert, A and Johnson, E and Onken, B and Hall, D and Segerdell, E and Jackson, EG and Song, Y and Osman, HC and Xue, J and Basttistoni, E and Guo, S and Foulger, A and Achanta, M and Sheikh, M and Fitzgibbon, T and Willis, JH and Woodruff, GC and Driscoll, M and Lithgow, G and Phillips, PC},
title = {Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically diverse Caenorhabditis nematodes.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {41432067},
issn = {2050-084X},
support = {AG045844/NH/NIH HHS/United States ; AG045864/NH/NIH HHS/United States ; U01 AG045829/AG/NIA NIH HHS/United States ; U01 AG045864/AG/NIA NIH HHS/United States ; U24 AG056052/AG/NIA NIH HHS/United States ; AG045829/NH/NIH HHS/United States ; AG056052/NH/NIH HHS/United States ; U01 AG045844/AG/NIA NIH HHS/United States ; P40 OD010440/OD/NIH HHS/United States ; },
mesh = {Animals ; *Longevity/drug effects/genetics ; *Tretinoin/metabolism/pharmacology ; *Caenorhabditis elegans/genetics/drug effects/physiology ; Signal Transduction/drug effects ; Caenorhabditis elegans Proteins/metabolism/genetics ; Computational Biology ; },
abstract = {Discovery of new compounds that ameliorate the negative health impacts of aging promises to be of tremendous benefit across a number of age-based comorbidities. One method to prioritize a testable subset of the nearly infinite universe of potential compounds is to use computational prediction of their likely anti-aging capacity. Here, we present a survey of longevity effects for 16 compounds suggested by a previously published computational prediction set, capitalizing upon the comprehensive, multi-species approach utilized by the Caenorhabditis Intervention Testing Program. While 11 compounds (aldosterone, arecoline, bortezomib, dasatinib, decitabine, dexamethasone, erlotinib, everolimus, gefitinib, temsirolimus, and thalidomide) either had no effect on median lifespan or were toxic, 5 compounds (all-trans retinoic acid, berberine, fisetin, propranolol, and ritonavir) extended lifespan in Caenorhabditis elegans. These computer predictions yield a remarkable positive hit rate of 30%. Deeper genetic characterization of the longevity effects of one of the most efficacious compounds, the endogenous signaling ligand all-trans retinoic acid (atRA, designated tretinoin in medical products), demonstrated a requirement for the regulatory kinases AKT-1 and AKT-2. While the canonical Akt-target FOXO/DAF-16 was largely dispensable, other conserved Akt-targets (Nrf2/SKN-1 and HSF1/HSF-1), as well as the conserved catalytic subunit of AMPK AAK-2, were all necessary for longevity extension by atRA. Our results highlight the potential of combining computational prediction of longevity interventions with the power of nematode functional genetics and underscore that the manipulation of a conserved metabolic regulatory circuit by co-opting endogenous signaling molecules is a powerful approach for discovering aging interventions.},
}
@article {pmid41432418,
year = {2026},
author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R},
title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.},
journal = {Journal of bacteriology},
volume = {208},
number = {1},
pages = {e0037425},
pmid = {41432418},
issn = {1098-5530},
support = {R01 AI187174/AI/NIAID NIH HHS/United States ; R01 AI143638/AI/NIAID NIH HHS/United States ; R01-AI188648/NH/NIH HHS/United States ; K22-AI7220/NH/NIH HHS/United States ; R01-AI143638/NH/NIH HHS/United States ; R01 AI188648/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; U19-AI174998/NH/NIH HHS/United States ; R01-AI187174/NH/NIH HHS/United States ; R35-GM138369/NH/NIH HHS/United States ; },
mesh = {*Enterococcus faecalis/physiology/genetics ; *Clostridioides difficile/genetics/growth &amp; development/physiology ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Phenotype ; *Microbial Interactions ; Gastrointestinal Microbiome ; Signal Transduction ; },
abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase-variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes, including colony morphology, cell elongation, and cell chaining in C. difficile. Here, we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state, leading to chaining and a rough colony morphology. This phenomenon is most pronounced with E. faecalis, as other enterococcal species and select Gram-negative enteric bacteria do not show a similar effect. These results suggest that the composition of the polymicrobial environment in the gut is critical to influencing C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.IMPORTANCEClostridioides difficile is an enteric pathogen with critical implications for public health. The microbial ecosystem in which C. difficile resides shapes the behavior and fitness of C. difficile; however, the mechanisms underlying these interactions are not well defined. Here, we demonstrate that Enterococcus faecalis, an opportunistic pathogen known to co-colonize the gut with C. difficile, influences phase variation and downstream growth phenotypes in C. difficile. This phenomenon represents a new paradigm by which co-residing bacteria can modulate phase variation dynamics in C. difficile or other enteric pathogens. Understanding factors that influence C. difficile behavior may elucidate new therapeutic strategies, especially in complex polymicrobial infections.},
}
@article {pmid41432923,
year = {2025},
author = {Pu, SY and Lu, JS and Tao, XL and Li, ZF and Wang, YN and Zhang, HM and Lu, X},
title = {The Odonata of China: a data-driven, open-access resource for biodiversity research and conservation.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
pmid = {41432923},
issn = {1758-0463},
support = {202401BC070017//Yunnan Fundamental Research Projects/ ; //Yunnan Revitalization Talent Support Program Yunling Scholar Project (Xuemei Lu)/ ; XDA0460405//Chinese Academy of Sciences/ ; 202505AT350003//Chinese Academy of Sciences/ ; 202405AS350022//Chinese Academy of Sciences/ ; 202305AD160021//Yunnan Technology Innovation Talent Program/ ; },
mesh = {China ; *Biodiversity ; Animals ; *Conservation of Natural Resources ; *Odonata/genetics/classification ; *Databases, Factual ; Phylogeny ; },
abstract = {Odonata (dragonflies and damselflies) are among the most ancient winged insects, with over 900 species recorded in China, representing the highest global diversity. However, the lack of a centralized database integrating morphological, ecological, and multiomics data has hindered large-scale research and conservation efforts. We present Odonata of China (http://dragonflies.kiz.ac.cn), a comprehensive database compiling taxonomic, biogeographic, phenotypic, and multiomics data for 820 species across 3 suborders, 22 families, and 172 genera. The database features advanced search modules (direct, phylogenetic, and map-based), genomic and transcriptomic data for 20 representative families, and high-resolution images. The platform is constructed based on mainstream open-source technologies, ensuring scalability and reproducibility. Odonata of China provides a critical resource for evolutionary biology, conservation, and ecological studies. By integrating heterogeneous data types and leveraging modern technologies, this database bridges a significant gap in invertebrate biodiversity informatics and supports global initiatives to monitor insect declines.},
}
@article {pmid41435586,
year = {2025},
author = {Zeng, T and Du, H and Wu, R},
title = {The chemical structures, and biological activities of marine terpenoids: a review and perspective from cheminformatics.},
journal = {Chinese journal of natural medicines},
volume = {23},
number = {12},
pages = {100006},
doi = {10.1016/j.cjnm.2025.100006},
pmid = {41435586},
issn = {1875-5364},
mesh = {*Terpenes/chemistry/pharmacology ; *Aquatic Organisms/chemistry ; *Biological Products/chemistry/pharmacology ; *Cheminformatics ; Humans ; Animals ; Molecular Structure ; Anti-Inflammatory Agents/chemistry/pharmacology ; Antineoplastic Agents/chemistry/pharmacology ; },
abstract = {Marine terpenoids are a structurally diverse class of natural products produced by marine organisms, characterized by unique molecular architectures and notable biological activities. They play essential roles in ecological interactions and chemical defense, while also exhibiting promising therapeutic properties, including anti-inflammatory and anti-tumor effects. In this review, we compile 13 132 reported marine terpenoids, of which 2066 have documented biological activities, and provide a concise summary of their organismal origins, molecular scaffolds, and associated activities. Cheminformatics approaches are further applied to compare the chemical space of marine versus terrestrial terpenoids, highlighting their structural distinctiveness. Finally, we discuss promising directions for the discovery, utilization, and synthesis of marine terpenoids, with the goal of promoting comprehensive and sustainable exploration of these valuable marine resources.},
}
@article {pmid41436485,
year = {2025},
author = {Sardeshpande, M and Bangira, T and Azong Cho, M and Matongera, TN and Mabhaudhi, T},
title = {Exploring the social-ecological potential for indigenous agroforestry in peri-urban areas: a participatory mapping approach.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44344},
pmid = {41436485},
issn = {2045-2322},
support = {/WT_/Wellcome Trust/United Kingdom ; 205200/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Forestry/methods ; Humans ; South Africa ; Geographic Information Systems ; *Agriculture/methods ; Conservation of Natural Resources ; Socioeconomic Factors ; },
abstract = {Peri-urban agroforestry can provide affordable, fresh, and nutritious food and a departure from conventional forms of cropping. Indigenous foods are well-adapted to local conditions, and may hold cultural and economic value for peri-urban residents. Social, ecological, and economic variables influence the feasibility of indigenous agroforestry in peri-urban areas. This study uses participatory mapping and geographic information systems (GIS) to assess these variables and to map suitable spaces and species for peri-urban indigenous agroforestry at three peri-urban sites in Durban, South Africa. We find that: land tenure, livelihood opportunities, and indigenous food perceptions factor into socioeconomic preferences; topography and soil quality influence ecological feasibility; access to water and roads influences perceived economic viability. Although GIS techniques can identify land suitability, participatory mapping adds local fine-scale context to enhance decision-making. Based on the social-ecological conditions at the three sites, we suggest specific configurations of locally adapted foods and farm designs for peri-urban agroforestry. Our study demonstrates how agroforestry is more feasible in places where basic living conditions are fulfilled, and how co-design can improve recognition of local needs, accessibility to services, and balancing urban green equity.},
}
@article {pmid41438403,
year = {2025},
author = {Khaleghi, P and Cakir, D and Hamidoğlu, A and Gul, OM and Kadry, S},
title = {Interpretable deep learning for depression detection in neurological patients using EEG signals.},
journal = {MethodsX},
volume = {15},
number = {},
pages = {103736},
pmid = {41438403},
issn = {2215-0161},
abstract = {Depression affects over 280 million people worldwide, with neurological patients particularly prone to medication-induced episodes. Conventional diagnostic approaches rely on subjective evaluations, limiting reproducibility and consistency in clinical settings. This study proposes an interpretable deep learning framework for objective depression detection using EEG signals. We hypothesize that combining EEG-based features with explainable artificial intelligence can provide both high accuracy and transparency in diagnosis. The model was trained on EEG data from 232 neurological patients, achieving 98 % classification accuracy. Interpretability was enhanced through SHAP (SHapley Additive exPlanations) analysis, which identified clinically meaningful EEG biomarkers such as the delta/alpha ratio and theta band power. This paper highlights the following contributions: Integration of EEG features with a lightweight deep learning model for depression detection High diagnostic accuracy achieved while maintaining interpretability for clinicians An objective tool that is compatible with existing EEG infrastructure, supporting clinical adoption These results show that our framework bridges predictive performance with interpretability, offering a transparent and scalable EEG-based diagnostic tool. We conclude that this approach can complement clinical decision-making, reducing dependence on subjective evaluation and enabling more consistent, data-driven mental health care.},
}
@article {pmid41442946,
year = {2026},
author = {Huang, XL and Xiong, YX and Yu, S and Chen, XW and Li, DW and Ou, LJ},
title = {Construction of a coccolithophore database platform for ecological and molecular applications.},
journal = {Water research},
volume = {291},
number = {},
pages = {125107},
doi = {10.1016/j.watres.2025.125107},
pmid = {41442946},
issn = {1879-2448},
mesh = {*Haptophyta/genetics ; *Databases, Factual ; China ; Microalgae ; },
abstract = {Coccolithophores play a critical role in marine carbon cycling and biogeochemical processes, yet their ecological distribution and in situ abundance remain understood. This study introduces an open-access coccolithophore database, integrating global occurrence records of Gephyrocapsa huxleyi and Chrysotila spp. from multiple microalgal datasets. The platform integrates taxonomic, distributional, and ecological information of coccolithophores, offering BLAST-based sequence analysis and user data submission features to enhance ecological monitoring and functional studies. To evaluate the database's utility and quantify field abundance, we developed and validated species-specific qPCR primers, demonstrating high specificity and efficiency. Application in Daya Bay, China, revealed G. huxleyi as dominant in offshore and central regions, while C. dentata showed lower abundance, confined to nearshore areas. QPCR-based estimates aligned closely with microscopy-based counts (R[2] > 0.89), affirming method reliability. This study provides a robust digital framework and molecular tools, advancing systematic monitoring of coccolithophore communities and their contributions to oceanic carbon cycling.},
}
@article {pmid41443507,
year = {2026},
author = {Zhou, M and Tian, H and Ma, M},
title = {Multi-omics analysis of gibberellin-induced internode elongation in Apocynum pictum Schrenk and preliminary investigation into the potential role of WRKY40.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {364},
number = {},
pages = {112957},
doi = {10.1016/j.plantsci.2025.112957},
pmid = {41443507},
issn = {1873-2259},
mesh = {*Gibberellins/metabolism/pharmacology ; *Plant Growth Regulators/metabolism ; Gene Expression Regulation, Plant ; *Transcription Factors/metabolism/genetics ; *Plant Proteins/metabolism/genetics ; Indoleacetic Acids/metabolism ; Gene Expression Profiling ; Transcriptome ; Cell Wall/metabolism ; Cytokinins/metabolism ; Gene Regulatory Networks ; Signal Transduction ; Multiomics ; },
abstract = {This study aimed to elucidate the molecular mechanisms underlying gibberellin (GA3)-induced internode elongation in Apocynum pictum Schrenk. Through exogenous GA3 application, transcriptome sequencing, phytohormone profiling, and weighted gene co-expression network analysis (WGCNA), we proposed an innovative three-tier regulatory framework encompassing "signal perception, network transduction, and coordinated response." The results demonstrated that exogenous GA3 significantly promoted plant height and internode elongation by enhancing cell length rather than increasing cell number. Transcriptomic analysis identified 4321 differentially expressed genes, with KEGG and GO enrichment analyses revealing their significant involvement in plant metabolism, signal transduction, and cell wall organization processes. Hormonal profiling indicated that GA3 dynamically regulated the metabolism and signaling pathways of multiple phytohormones, including auxin and cytokinin, by suppressing cytokinin biosynthesis and delaying auxin activation, thereby reprogramming hormonal homeostasis to drive cell elongation. WGCNA further identified a WRKY40-centered transcriptional regulatory network, which is postulated to mediate GA3 responses, potentially by coordinating the expression of genes involved in auxin biosynthesis and cell wall remodeling genes while coordinating cross-talk among multiple hormone pathways. Concurrently, GA3 optimized cell wall composition by upregulating lignin biosynthesis genes and repressing cellulose hydrolase genes. Additionally, it modulated the stability of key proteins through genes associated with protein turnover, collectively facilitating internode elongation. This study unveils a systematic regulatory mechanism governing GA3-induced internode elongation in A. pictum, providing theoretical insights into phytohormone-mediated growth regulation and potential targets for crop architecture improvement.},
}
@article {pmid41443831,
year = {2026},
author = {Okuda, N and Nakamura, K and Watanabe, M and Kamide, K and Yoshita, K and Torii, S and Miura, K and Higashiyama, A and Tanno, K and Yonekura, Y and Nagahata, T and Kuribayashi, T and Okayama, A},
title = {Factors Affecting Body Weight/Waist Circumference Changes after Specific Health Guidance for Obese People with CVD Risk Factors in Japan.},
journal = {Journal of atherosclerosis and thrombosis},
volume = {33},
number = {5},
pages = {589-606},
pmid = {41443831},
issn = {1880-3873},
mesh = {Humans ; Male ; Female ; Middle Aged ; *Obesity/complications/epidemiology ; *Waist Circumference ; Adult ; Japan/epidemiology ; *Body Weight ; *Cardiovascular Diseases/etiology/epidemiology/prevention &amp; control ; Body Mass Index ; Risk Factors ; Heart Disease Risk Factors ; Follow-Up Studies ; },
abstract = {AIM: Specific Health Checkups (SHCs) and Specific Health Guidance (SHG) were launched in 2008, but the factors related to their effectiveness have not been clarified. We examined the mean reduction in body weight (BW) and waist circumference (WC) of participants eligible for active support under SHG. Body size was considered, as well as the number of support points given during SHG, which indicates the amount of support they received.<br><br>METHODS: A dataset of participants (aged 40-64) who were eligible for SHG and had SHC results collected between 2011 and 2012 was analyzed (n = 76,565). The mean changes in BW and WC between 2011 and 2012 were compared among participants based on their participation status (did not participate, dropped out, finished) and the number of support points for those who finished. Participants were also stratified by sex and BMI (kg/m[2]): normal weight, overweight, and obese.<br><br>RESULTS: The mean BW change (95% CI) for those who did not participate and finished SHG was -0.45 kg (-0.47, -0.43) and -1.32 kg (-1.39, -1.25) in men, and -0.66 kg (-0.72, -0.60) and -1.68 kg (-1.87, -1.49) in women, respectively. Higher support points and larger body sizes correlated with greater reductions in BW in men (P&#xff1c;0.001), but the associations were not significant in women. The reduction in WC was greater in women with normal weight than in obese women.<br><br>CONCLUSION: Sex differences were observed in the association between BW/WC reduction and body size or the amount of support given during SHG.},
}
@article {pmid41446515,
year = {2025},
author = {Mehrotra, S and Duggal, C and Rustagi, N and Ransing, RS and Indu, PS and Chakraborty, S and Mene, T and Sharma, P and Prasad, D and Prinja, S and Verma, P and Dhamija, RK and Kataria, K and Munivenkatappa, M and Suthar, N and Anilkumar, TV and Dahiya, N and Grover, A},
title = {Multistate study on suicide risk reduction and improving mental well-being among school and college students in India - an implementation research study protocol.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1708246},
pmid = {41446515},
issn = {2296-2565},
mesh = {Adolescent ; Female ; Humans ; Male ; Young Adult ; India ; *Mental Health ; Research Design ; *Risk Reduction Behavior ; Schools ; *Students/psychology/statistics &amp; numerical data ; Suicide/psychology ; *Suicide Prevention ; Universities ; },
abstract = {UNLABELLED: Suicide remains a crucial public health concern in India, especially among students and young adults. The growing academic pressure, social stigma, and lack of accessible mental health services contribute to the growing crisis and suicide rates in India. The study aims to develop an implementation model for educational institutions for reducing risk of suicide behavior (perceived stress and depressive symptoms) and enhance help-seeking behavior. This multi-sectoral implementation model is grounded in the WHO's recommendation for youth suicide prevention and UMMEED guidelines. The study will adopt a concurrent mixed methods design, incorporating both quantitative and qualitative aspects that would be captured simultaneously. A formative research phase will be initially conducted before taking on the main study and it will be guided by the Updated Consolidated Framework for Implementation Research (CFIR). Additionally, the evaluation of the implementation process will be structured using the RE-AIM framework. The study participants will be school and pre-university students, and college students The expected outcome will be achieving reduction of suicide risk behaviors among school and college students in selected districts. The key barriers and facilitators identified through this implementation research will inform recommendations for the potential nation-wide scale up of strategies aimed suicide prevention strategies at educational institutes.<br><br>CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, CTRI/2024/08/072027.},
}
@article {pmid41450553,
year = {2025},
author = {Hao, W and Shan, YF and Kimura, T and Ukawa, S and Ohira, H and Okabayashi, S and Wakai, K and Ando, M and Tamakoshi, A},
title = {Effect modification by dietary patterns in the relationship between slow gait and incident depressive symptoms: a 6-year cohort study of older Japanese adults (NISSIN Project).},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1698581},
pmid = {41450553},
issn = {2296-861X},
abstract = {INTRODUCTION: Slower gait speed is a well-established predictor of late-life depressive symptoms. Previous research suggests that diet can influence biological processes implicated in both gait decline and depression and may therefore serve as an effect modifier in their association. This study aimed to examine whether adherence to healthy dietary patterns modifies the relationship between gait speed and incident depressive symptoms in older adults.<br><br>METHODS: In this longitudinal observational cohort study, we analyzed data from 1,887 depression-free, community-dwelling adults aged 64-65 years, obtained from the New Integrated Suburban Seniority Investigation (NISSIN) Project in Japan. Gait speed was self-rated at baseline as fast, normal, or slow. Dietary intake was assessed using a validated food frequency questionnaire (FFQ), and principal component analysis was performed to identify three dietary patterns: vegetables, Fat and Meat, and Bread and Egg. Incident depressive symptoms were defined as having a 15-item Geriatric Depression Scale (GDS-15) score of &#x2265;6 after a 6-year follow-up. Modified Poisson regression was used to estimate relative risks (RRs), and interactions were assessed on multiplicative and additive scales.<br><br>RESULTS: After 6 years, 12.5% of the participants developed depressive symptoms. Slow gait speed was significantly associated with a higher risk of depression (RR: 2.7; 95% CI: 1.6-4.6), while no dietary pattern was independently associated with depressive symptoms. This risk tended to be lower among slow walkers with higher adherence to a vegetable or Bread and Egg dietary pattern, although the interactions were not statistically significant. A significant negative interaction was found between slow gait and low adherence to a Fat and Meat diet on both additive (RERI = -2.5; 95% CI: -4.1 to -0.8) and multiplicative scales (Ratio of RRs: 0.3; 95% CI: 0.2-0.3).<br><br>DISCUSSION: Dietary patterns may influence the link between slow gait and depression in older adults. Notably, reduced adherence to Fat and Meat diets was associated with a lower overall risk. These findings support dietary improvement as a scalable mental health strategy for physically vulnerable older adults.},
}
@article {pmid41452932,
year = {2025},
author = {Giral Martínez, J and Barbier, M and De Monte, S},
title = {Interplay of structured and random interactions in complex ecosystems dynamics.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013786},
pmid = {41452932},
issn = {1553-7358},
mesh = {*Ecosystem ; *Models, Biological ; Computational Biology ; Population Dynamics ; Computer Simulation ; Animals ; },
abstract = {Minimal models for complex ecosystems often assume random interactions, whose statistics suffice to predict dynamical and macroecological patterns. However, ecological networks commonly possess a variety of properties, such as hierarchies or functional groups, that structure species interactions. Here, we ask how conclusions from random interaction models are altered by the presence of such community-level network structures. We consider a Lotka-Volterra model where pairwise species interactions combine structure and randomness, and study macroscopic community-level observables, abundance distributions and dynamical regimes. Randomness and structure combine in a surprisingly yet deceptively straightforward way: contributions from each component to community patterns are largely independent. Yet, their interplay has non-trivial consequences, notably out of equilibrium. We conclude that whether interaction structure matters depends on the pattern: when breaking species equivalence, static patterns of species presence and abundance predicted from random interaction models are less robust than the qualitative nature of dynamical regimes.},
}
@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 &amp; development ; *Seeds/metabolism/growth &amp; 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.},
}
@article {pmid41455448,
year = {2026},
author = {Nosair, AM and Samra, RE and Hassan, R and Gemail, K},
title = {Groundwater sustainability challenges in urban deltas: A DRASTIC-GIS and hydrogeophysical approach for assessing the Nile Delta aquifer for sustainable management.},
journal = {Journal of contaminant hydrology},
volume = {277},
number = {},
pages = {104823},
doi = {10.1016/j.jconhyd.2025.104823},
pmid = {41455448},
issn = {1873-6009},
mesh = {*Groundwater/chemistry/analysis ; Geographic Information Systems ; *Environmental Monitoring/methods ; Egypt ; Water Pollutants, Chemical/analysis ; *Conservation of Water Resources ; Cities ; *Conservation of Natural Resources ; Models, Theoretical ; Rivers ; Hydrology ; },
abstract = {Groundwater sustainability in densely populated deltas, such as Egypt's Nile Delta, faces growing threats from wastewater contamination, climate change, and unregulated urban development. This study employs a multidisciplinary approach, combining hydrochemical analysis, GIS-based DRASTIC modeling, and 1D/2D hydrogeophysical resistivity surveys to evaluate aquifer vulnerability in the southeastern Nile Delta. A significant innovation in this research is the integration of DC resistivity measurements with the DRASTIC index, which improves the identification of high-risk zones. Furthermore, anthropogenic impacts were incorporated as an additional layer in the vulnerability modeling, guided by a sensitivity analysis of the controlling parameters. The results indicate two major threats to the Quaternary aquifer. First, the southern and eastern regions are highly vulnerable due to the lack of protective clay layers and detrimental land-use practices, such as wastewater irrigation and urban growth. Second, hydraulic connectivity between the freshwater Quaternary and brackish Miocene aquifer exacerbates salinization and pollutant migration from intensive pumping. Validation using hydrogeophysical data reveals a strong correlation with the DRASTIC model, highlighting areas with significant groundwater degradation, including high total dissolved solids (TDS) levels (>6470 ppm) and nitrate concentrations (>102 mg/L). In contrast, northwestern areas with thick clay caps (exceeding 9 m) exhibit greater resilience. These findings highlight the critical role of land-use practices and aquifer connectivity in urban groundwater management. The study recommends strategies such as optimal extraction zone mapping, IoT monitoring, and drainage lining to minimize contamination, offering a scalable model for sustainable groundwater management in water-stressed deltaic regions.},
}
@article {pmid41455740,
year = {2025},
author = {Deb, N and Rahman, T and Moniruzzaman, M and Bin Obadi, AS and Jizat, NM and Al-Bawri, SS and Rahman, AAM},
title = {Integrating feature selection and explainable CNN for identification and classification of pests and beneficial insects.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {2721},
pmid = {41455740},
issn = {2045-2322},
mesh = {Animals ; *Neural Networks, Computer ; *Insecta/classification ; Crops, Agricultural/parasitology ; Aphids/classification ; Coleoptera/classification ; },
abstract = {Reliable identification of agricultural pests and beneficial insects is crucial for sustainable crop protection and ecological balance, yet most vision-based models remain black boxes and require high-dimensional features. This paper proposes an explainable hybrid insect-classification framework that combines convolutional neural network (CNN) feature extraction with a dual-XAI feature selection strategy. SHapley Additive exPlanations (SHAP) and Permutation Feature Importance (PFI) are applied in parallel to rank handcrafted and CNN-derived features, and their intersection yields a compact, biologically meaningful subset for final classification. The selected features are evaluated using lightweight classifiers and a hybrid ensemble, enabling accurate inference under field variability. Experiments on a curated, balanced dataset of four classes (Colorado potato beetle, green peach aphid, seven-spot ladybird, and healthy leaves) collected under diverse lighting and background conditions achieve 96.7% overall accuracy, with precision, recall, and F1-scores all above 96%. Importantly, performance remains stable when reducing dimensionality, retaining ≥90% accuracy using only the top 11 hybrid-selected features. These results demonstrate that integrating SHAP and PFI improves both robustness and interpretability, supporting practical deployment for automated pest monitoring and precision agriculture.},
}
@article {pmid41456016,
year = {2025},
author = {Guo, W and Chen, Y and Fan, H and Huang, X and Chen, X and Xiao, Y and Zhang, C and Zhou, W and Wei, F},
title = {Pygmy sperm whale multi-omics data reveal hypoxia adaptations in deep-diving cetaceans.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {20},
pmid = {41456016},
issn = {1741-7007},
mesh = {Animals ; *Adaptation, Physiological/genetics ; *Hypoxia/genetics ; Genome ; *Whales/physiology/genetics ; Multiomics ; },
abstract = {BACKGROUND: Deep-diving cetaceans tolerate acute hypoxia better than their terrestrial ancestors and shallow-diving counterparts. However, our poor understanding of how genetic factors, cellular functions, and physiological characteristics combine to drive hypoxia adaptation in deep-diving cetaceans remains a critical gap.<br><br>RESULTS: Here, we studied the genetic basis for this ability by creating a de&#xa0;novo genome assembly for the pygmy sperm whale (Kogia breviceps) and comparatively analyzing genomes from 12 cetacean species, including 2 other deep-diving cetaceans. We also sequenced and compared single-nucleus RNA data from the muscle and heart of the pygmy sperm whale and its terrestrial relative Bos taurus. We found that genetic and cellular changes in the HIF-1 pathway, electron transport chain, glucose and fatty acid catabolism, and heart rate may contribute to hypoxia tolerance in deep-diving cetaceans. Key adaptations include rapid evolution of glycolysis-related genes (PYGM and ENO3), differential expression of HIF-1 pathway genes like ARNT, and accelerated conserved noncoding elements in genes such as ATP5F1E (ATP synthase) and DMD (dystrophin). We found an increase in myocytes and type II cardiomyocytes in the pygmy sperm whale's muscle and heart tissues, which may support energy metabolism and homeostasis during deep dives.<br><br>CONCLUSIONS: These findings suggest deep-diving cetaceans have unique genetic and cellular adaptations to cope with hypoxia, offering insights into how mammals handle low oxygen levels at the cellular level.},
}
@article {pmid41458310,
year = {2025},
author = {Feiner, N and Uller, T and Abalos, J and Slimani, T and S'Khifa, A and Meier, J and , and , and , and , },
title = {The genome sequence of the Andalusian wall lizard, Podarcis vaucheri (Boulenger, 1905).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {265},
pmid = {41458310},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Podarcis vaucheri (Andalusian wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1,614.91 megabases and 1,510.74 megabases. Most of haplotype 1 (98.26%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex chromosomes. Most of haplotype 2 (98.63%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.24 kilobases.},
}
@article {pmid41458448,
year = {2025},
author = {Lin, S and Zhang, M and Feng, L and Lu, M and Liu, X},
title = {Spatio-temporal evolution and influencing factors of cultural heritage embedded cultural tourism efficiency.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1690535},
pmid = {41458448},
issn = {2296-2565},
mesh = {Humans ; China ; *Tourism ; *Spatio-Temporal Analysis ; },
abstract = {Enhancing the efficiency of cultural tourism serves as a critical catalyst for the synergistic development of culture and the economy. However, existing research has primarily focused on the content of the cultural tourism industry and its coupling coordination relationships, while comparatively little attention has been given to incorporating key resources-such as cultural heritage-into analytical frameworks access efficiency and underlying impact mechanisms. This study introduces an innovative perspective that embeds cultural heritage within the evaluation process. To address the issue of intertemporal and regional comparability, the Super SBM-DEA model is employed to measure the efficiency of cultural heritage embedded cultural tourism (CHECTE) across 30 Chinese provinces from 2012 to 2022 and identifies its driving factors through Tobit regression. The findings demonstrate that average efficiency exhibits a "declining-rising-declining" pattern over the observed period. Specifically, efficiency decreased to 0.5829 in 2015, reached a peak of 0.8511 in 2019, and then experienced a subsequently decline. During periods of decline, efficient areas contract toward the central and western regions, whereas during periods of improvements, these areas expand into the southwest and southeast. This spatial dynamic reveals a notable departure from traditional regional economic gradients. The central region attained a higher average efficiency of 0.7499 compared to the eastern region of 0.5746, suggesting that the central region derives greater benefits from cultural heritage resources than its eastern counterpart. Tobit regression results reveal that transportation conditions, informatization level, policy environment, higher education, and technological innovation are the key driving factors, with significant regional differences. The eastern region is primarily driven by technological innovation and consumption demand, the central region by the policy environment and informatization, and the western region by transportation conditions and higher education. This study offers theoretical and practical guidance for resource allocation and region-specific cultural tourism policies.},
}
@article {pmid41459590,
year = {2025},
author = {Holmqvist, S and Shou, H and Halberstadter, K and Kaplan, M and Chaturvedi, R and Rhodes, E and Giovannetti, T},
title = {Bidirectional associations of daily mood and subjective cognition in older adults using Ecological Momentary Assessment.},
journal = {Aging &amp; mental health},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/13607863.2025.2606875},
pmid = {41459590},
issn = {1364-6915},
abstract = {OBJECTIVES: Depressive symptoms and subjective cognition are linked in older adults, but traditional measures have numerous limitations that may be addressed by ecological momentary assessment (EMA). This study examined whether baseline depressive and cognitive measures correspond to daily EMA ratings and evaluated concurrent and lagged relations between mood and subjective cognition.<br><br>METHOD: Fifty-five community-dwelling older adults (31% Black/African American; 44 cognitively healthy, 11 mild cognitive impairment) completed a four-week daily EMA survey assessing mood and subjective cognition. Baseline measures included a global cognitive composite and self-reported depressive symptoms, functional independence, and cognitive decline. Cumulative link mixed models examined associations between baseline and EMA measures and concurrent and lagged EMA relations.<br><br>RESULTS: EMA mood correlated with baseline depressive symptoms, while EMA subjective cognition was most strongly associated with functional independence rather than objective cognition or self-reported cognitive decline. EMA mood and cognition were reciprocally associated concurrently. In lagged models, worse EMA subjective cognition predicted worse next-day mood, whereas the reverse association was not statistically significant. Lagged effects were attenuated after accounting for temporal trends and prior-day EMA values.<br><br>CONCLUSION: EMA provides low-burden insights into mood and subjective cognition, supporting its utility for naturalistic assessment in older adults.},
}
@article {pmid41460880,
year = {2025},
author = {Langmüller, AM and Chandrasekher, KA and Haller, BC and Champer, SE and Murdock, CC and Messer, PW},
title = {Gaussian process emulation for exploring complex infectious disease models.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013849},
pmid = {41460880},
issn = {1553-7358},
support = {R35 GM152242/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Normal Distribution ; Dengue/epidemiology ; *Communicable Diseases/epidemiology ; *Epidemiological Models ; Computational Biology ; Disease Outbreaks/statistics &amp; numerical data ; Colombia/epidemiology ; Computer Simulation ; Epidemics/statistics &amp; numerical data ; Seasons ; Models, Statistical ; },
abstract = {Epidemiological models that aim for a high degree of biological realism by simulating every individual in a population are unavoidably complex, with many free parameters, which makes systematic explorations of their dynamics computationally challenging. In this study, we demonstrate how Gaussian Process emulation can overcome this challenge. To simulate disease dynamics, we developed an abstract individual-based model that is loosely inspired by dengue, incorporating some key features shaping dengue epidemics such as social structure, human movement, and seasonality. We focused on three epidemiological metrics derived from the individual-based model outcomes - outbreak probability, maximum incidence, and epidemic duration - and trained three Gaussian Process surrogate models to approximate these metrics. The GP surrogate models enabled the rapid prediction of these epidemiological metrics at any point in the eight-dimensional parameter space of the original model. Our analysis revealed that average infectivity and average human mobility are key drivers of these epidemiological metrics, while the seasonal timing of the first infection can influence the course of the epidemic outbreak. We used a dataset comprising more than 1,000 dengue epidemics observed over 12 years in Colombia to calibrate our Gaussian Process model and evaluated its predictive power. The calibrated Gaussian Process model identified a subset of municipalities with consistently higher average infectivity estimates; the notable overlap between these municipalities and previously reported dengue disease clusters suggests that statistical emulation can facilitate empirical data analysis. Overall, this work underscores the potential of Gaussian Process emulation to enable the use of more complex individual-based models in epidemiology, allowing a higher degree of realism and accuracy that should increase our ability to control diseases of public health concern.},
}
@article {pmid41461568,
year = {2026},
author = {Liu, Y and Luo, Z and Xiao, Y and Li, Y and Liu, M and Shi, Y and Li, Z and Lei, W and Li, C and Jin, LN and Yan, W},
title = {Microplastics in Motion: How Earthworm Guts Become Microbial Gateways through Plastic Surface Dynamics.},
journal = {Environmental science &amp; technology},
volume = {60},
number = {1},
pages = {338-349},
doi = {10.1021/acs.est.5c15257},
pmid = {41461568},
issn = {1520-5851},
mesh = {Animals ; *Oligochaeta ; *Microplastics ; Plastics ; Polystyrenes ; },
abstract = {Microplastics (MPs) pollution in terrestrial ecosystems poses significant ecological risks, particularly as carriers of microbial communities and potential pathogens. However, the mechanisms by which MPs interact with microbes during transit through soil animal digestive systems remain poorly understood. This study investigated the interactions between poly(ethylene terephthalate) (PET) and polystyrene (PS) MPs and gut-derived microbes using a biomimetic earthworm gut model. PET and PS MPs exhibited distinct microbial colonization patterns, driven by their physicochemical properties. PET MPs, with rougher surfaces, preferentially adsorbed cocci such as Paraclostridium, fostering high-density but low-activity bacterial populations. Conversely, PS MPs, with smoother surfaces, enriched bacilli such as Raoultella, supporting low-density but high-activity bacterial communities. PET MPs facilitated rapid bacterial proliferation but lacked long-term stability, whereas PS MPs created persistent microenvironments that increased the ecological risk of pathogen retention and spread. The oxidative degradation of MPs during gut transit enhanced bacterial adhesion by forming reactive surface functionalities. MPs significantly altered microbial diversity and served as selective vectors for microbial dissemination into soil ecosystems, disrupting the microbial dynamics. These findings underscore the dual role of MPs as microbial scaffolds and ecological disruptors, providing critical insights into their ecological impacts and guiding strategies to mitigate MP contamination and pathogenic risks.},
}
@article {pmid41464285,
year = {2025},
author = {Alkattan, A and Norful, AA and Pan, CX and August, P and Crupi, RS and Schwartz, JE and Miele, A and Brondolo, E},
title = {Monitoring Redeployment-Associated Burnout in Healthcare Workers: A Real-Time Approach Using Ecological Momentary Assessment.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {24},
pages = {},
pmid = {41464285},
issn = {2227-9032},
support = {1K08MH130652-01/NH/NIH HHS/United States ; },
abstract = {Background/Objectives: Ecological momentary assessment (EMA) is a methodology that offers a real-time approach to monitoring clinician well-being, but its utility during high-intensity operational periods remains underexplored. This study examines the feasibility and performance of an EMA-based system for tracking clinical responsibilities and burnout among healthcare workers during the first year of the COVID-19 pandemic. Methods: Utilizing an intensive longitudinal design, 398 healthcare workers, including physicians, physician assistants, nurses, and trainees, completed brief EMA surveys every five days from April 2020 to March 2021. Burnout was assessed with a validated single-item measure and analyzed in relation to redeployment status and hospital caseloads. Results: The EMA approach successfully captured meaningful temporal fluctuations in burnout. Redeployment was associated with higher burnout levels (b = 0.125; p = 0.01), and rising caseloads amplified this effect (interaction b = 0.169; p = 0.001). Nurses showed the strongest caseload-related increases in burnout (b = 0.359; p < 0.001). These patterns persisted even after individuals returned to their usual roles. Conclusions: This study demonstrates that EMA is a scalable and sensitive approach for continuous burnout surveillance, capable of detecting role-specific and context-dependent stress responses in real time. EMA-based monitoring can support early identification of at-risk groups, guide staffing and redeployment decisions, and inform timely organizational interventions during crises and other periods of operational strain.},
}
@article {pmid41464893,
year = {2025},
author = {Yan, R and Chen, Z and Zhou, S and Niu, G and Li, Y and Liu, Z and Wang, J and Wu, X and Luo, Q and Zhou, Y and Jin, Y and Liu, K and Yuan, W and Xu, J and Xu, F},
title = {ForestFoodKG: A Structured Dataset and Knowledge Graph for Forest Food Taxonomy and Nutrition.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {24},
pages = {},
pmid = {41464893},
issn = {2304-8158},
abstract = {Forest foods play a vital role in enhancing dietary diversity, human health, and the sustainable use of forest ecosystems. However, structured and machine-readable resources that systematically describe their taxonomic and nutritional attributes remain scarce. To fill this gap, we introduce ForestFoodKG, a comprehensive resource that integrates taxonomic hierarchy and nutritional composition of 1191 forest food items. The resource consists of two components-(i) the ForestFoodKG dataset, containing standardized taxonomic and nutritional records across seven biological levels, and (ii) the ForestFoodKG Knowledge Graph (ForestFoodKG-KG), which semantically links forest food entities using named entity recognition and relation extraction. The constructed graph comprises 4492 entities and 14,130 semantic relations, providing a structured foundation for intelligent querying, nutrition analytics, and ecological informatics. All data were manually verified and made publicly available in CSV format on GitHub. ForestFoodKG serves as the first structured knowledge base for forest foods, promoting data-driven research in nutrition science, sustainable forestry, and knowledge-based decision-making.},
}
@article {pmid41467398,
year = {2026},
author = {Sugimoto, N and Matsugaki, R and Cooray, U and Kuhara, S and Onoue, T and Saeki, S and Muramatsu, K and Fushimi, K and Matsuda, S and Murakami, M and Ikeda, T},
title = {Safety of Early Rehabilitation for Acute Heart Failure Using Japanese Medical Claims.},
journal = {Journal of the American Heart Association},
volume = {15},
number = {1},
pages = {e045953},
pmid = {41467398},
issn = {2047-9980},
mesh = {Humans ; *Heart Failure/rehabilitation/mortality/physiopathology ; Japan/epidemiology ; Male ; Female ; Aged ; Middle Aged ; Acute Disease ; Time Factors ; Aged, 80 and over ; Incidence ; *Cardiac Rehabilitation/methods/adverse effects ; Retrospective Studies ; Treatment Outcome ; East Asian People ; },
abstract = {BACKGROUND: The safety of initiating early physical rehabilitation therapy and its optimal load in patients with acute decompensated heart failure (ADHF) remain unclear. This study evaluated the safe timing and load of early rehabilitation therapy for patients with ADHF.<br><br>METHODS: In this cohort study using nationwide medical claims data from Japan, we included patients aged &#x2265;18&#x2009;years who were admitted for ADHF and received in-hospital rehabilitation therapy for at least 2&#x2009;days within the first 4&#x2009;days of admission between 2016 and 2020. Nine hypothetical treatment regimens within the first 7&#x2009;days of admission, varying in timing, duration, and load were used as exposures. The outcome was the cumulative incidence of adverse events (eg, death) within 30&#x2009;days after admission. A per-protocol analysis was conducted using a target trial emulation framework with a sequential doubly robust estimator.<br><br>RESULTS: Altogether, 10&#x2009;179 patients with ADHF were enrolled, with 752 developing adverse events (incidence 7.39%). The lowest incidence rate (4.13%) was observed in the regimen where therapy was initiated on the first day of admission with 20&#x2009;minutes of therapy, continuing for up to 7&#x2009;days (95% CI, 3.30-4.95). Conversely, the highest incidence rate was observed in the regimen where therapy was initiated on the third day of admission with 40&#x2009;minutes of therapy, continuing for up to 7&#x2009;days (8.67% [95% CI, 8.22-9.13]).<br><br>CONCLUSIONS: Very early, low-load rehabilitation therapy for patients with ADHF may reduce the risk of adverse events. These findings suggest important implications in the implementation of early rehabilitation.},
}
@article {pmid41468766,
year = {2026},
author = {Zheng, J and Sun, Z and Guo, R and Wang, R and Jin, D and Hu, J and Xing, X and Tong, M and Wang, P},
title = {High-throughput and rapid classification on harmful algal bloom species based on mega image database and artificial intelligence.},
journal = {Marine pollution bulletin},
volume = {224},
number = {},
pages = {119170},
doi = {10.1016/j.marpolbul.2025.119170},
pmid = {41468766},
issn = {1879-3363},
mesh = {*Microalgae/classification ; *Harmful Algal Bloom ; *Artificial Intelligence ; *Environmental Monitoring/methods ; Databases, Factual ; Ecosystem ; },
abstract = {Microalgae are essential components of marine ecosystems and have significant industrial applications. However, their rapid identification, especially HAB species, poses a challenge. This study constructed a comprehensive microalgae image database and developed AI-based classification algorithms to improve identification accuracy. Using DenseNet, EfficientNet, and ViT models, we achieved high classification performance, with ViT showing the best results. The study highlighted the importance of dataset size and diversity in enhancing model performance. Additionally, the trained model was applied to analyze field-collected samples, and the results were compared with those obtained from microscopic examination and metabarcoding analyses. The application of AI technology in microalgae classification provides a reliable basis for early warning and rapid response to HABs, reducing ecological and economic losses. Our findings demonstrate the potential of AI in enhancing the speed and accuracy of microalgae identification, contributing to better management and protection of marine ecosystems.},
}
@article {pmid41468864,
year = {2025},
author = {Cho, YJ and Kim, KH and Suh, DW and Baek, IS and Phee, JH and Yu, JY and Kim, KM and Park, YR},
title = {Shadow-Induced Forgetting in a Game-Based Paradigm on Nonclinical Adults and Its Effects on Consciousness, Emotional Valence, and Temporal Dynamics: Crossover Study.},
journal = {JMIR serious games},
volume = {13},
number = {},
pages = {e76946},
pmid = {41468864},
issn = {2291-9279},
abstract = {BACKGROUND: Memory suppression transiently disrupts hippocampal activity, leading to suppression-induced forgetting, especially for negative stimuli. However, traditional paradigms such as Think/No-Think rely on explicit control and lack ecological validity. This study introduces a game-based task that implicitly elicits suppression through reversed motor mappings, providing a naturalistic approach to studying memory inhibition.<br><br>OBJECTIVE: This study aims to examine how shadow-induced forgetting (ShIF) varies across short-term and long-term intervals (0 hours, 24 hours, and 72 hours), under conscious versus unconscious exposure, and between positive and negative emotional stimuli.<br><br>METHODS: This single-center, within-subjects experimental study involved 56 university students (mean age 23.37, SD 1.84 years) and was conducted between December 1, 2023, and March 1, 2024. Participants learned 36 cue-target image pairs varying in emotional valence (positive and negative). They underwent a game-based paradigm where habitual motor responses were disrupted through reversed key mappings to induce an amnesic shadow. During gameplay, selected cues were presented either consciously or unconsciously, while others served as controls. Memory performance was assessed using Metric for Evaluation of Translation with Explicit Ordering scores (semantic similarity) immediately after intervention (0 hour) and again at 24 hours and 72 hours. Electroencephalography was recorded in a subset of 40 participants to examine neural correlates of memory suppression.<br><br>RESULTS: ShIF effects were short-term, conscious-dependent, and selective for negative memories. A significant interaction between exposure condition and time (F&#x2083;.&#x2086;&#x2082;,&#x2081;&#x2089;&#x2089;.&#x2083;&#x2083;=2.7, P=.04, &#x3b7;&#xb2;p=0.05, 95% CI 0.00-1.00) indicated that the effect varied across time points. Specifically, a significant ShIF effect emerged immediately after the intervention (0 hour) in the conscious condition (t&#x2085;&#x2085;=-2.86, P=.02, d=0.38) but was absent in the unconscious condition and dissipated by 72 hours. Robust main effects of time (F&#x2082;,&#x2081;&#x2080;&#x2089;.&#x2089;&#x2089;=102.91, P<.001, &#x3b7;&#xb2;p=0.65, 95% CI 0.57-1.00) and emotional valence (F&#x2081;,&#x2085;&#x2085;=42.43, P<.001, &#x3b7;&#xb2;p=0.44, 95% CI 0.27-1.00) showed that overall recall declined over time and was consistently lower for negative images. Electroencephalography analyses revealed enhanced right frontal beta (FC6, F4, and F8: P<.001) and posterior gamma (O1: P<.001, O2: P<.001, and P8: P=.002) activity during suppression of negative cues, reflecting neural inhibition processes underlying ShIF.<br><br>CONCLUSIONS: ShIF occurs primarily for consciously processed negative memories and diminishes over several days, highlighting the temporal and emotional boundaries of intentional forgetting. This study introduces a game-based approach that extends traditional suppression paradigms and offers an ecologically valid framework for investigating memory control. Importantly, we demonstrate that suppression can be induced through a game-based paradigm. By examining emotional valence, exposure condition, and temporal dynamics, we extend previous work focused only on transient effects and clarify the potential for practical implementation in digital therapeutic applications such as posttraumatic stress disorder treatment.},
}
@article {pmid41472087,
year = {2025},
author = {Schalli, M and Inwinkl, SM and Platzer, S and Baumert, R and Reinthaler, FF and Ofner-Kopeinig, P and Haas, D},
title = {Correction: Schalli et al. Cefsulodin and Vancomycin: A Supplement for Chromogenic Coliform Agar for Detection of Escherichia coli and Coliform Bacteria from Different Water Sources. Microorganisms 2022, 10, 2499.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472087},
issn = {2076-2607},
abstract = {In the original publication [...].},
}
@article {pmid41472845,
year = {2025},
author = {Zhu, Z and Zhang, L and Yao, X and Zeng, M and Wang, Y and Luo, H and Zhou, Y and Zhang, T and Xun, J and Bai, D and Yang, H and Xu, S and Zhou, Y and Gao, Y and Xu, J and Han, W and Shen, Z and Zhang, B and Ma, T and Wan, XL and Ma, C and Hui, F and Bai, H and Bai, L and Bai, Q and Bao, Q and Cao, G and Cao, P and Cao, Q and Chen, H and Chen, J and Chen, J and Chen, L and Chen, T and Chen, Y and Cui, H and Dai, S and Dai, XJ and Dai, X and Dang, Y and Deng, L and Deng, Y and Ding, X and Dong, B and Dong, L and Dou, S and Du, H and Fang, Z and Feng, X and Fu, M and Gao, Y and Gong, W and Guo, X and Han, W and Hao, Z and He, ZG and Hu, H and Hu, H and Hu, X and Huang, L and Huang, X and Huang, X and Hui, H and Jia, D and Jiang, A and Jiang, D and Jiang, K and Jiang, D and Jin, Y and Lai, K and Li, C and Li, F and Li, F and Li, J and Li, J and Li, J and Li, K and Li, L and Li, M and Li, P and Li, P and Li, R and Li, S and Li, S and Li, W and Li, W and Li, X and Li, X and Li, X and Liang, Q and Liao, X and Liu, B and Liu, C and Liu, C and Liu, D and Liu, F and Liu, J and Liu, J and Liu, S and Liu, T and Liu, W and Liu, Y and Liu, Y and Liu, Y and Liu, Y and Liu, Y and Liu, Z and Liu, Z and Lu, X and Luo, X and Ma, G and Meng, J and Meng, Y and Miao, R and Miao, L and Ni, Y and Niu, D and Niu, T and Pan, H and Qin, G and Qiu, T and Qiu, Y and Qu, H and Qu, L and Ren, N and Sun, Q and Shang, R and She, P and Shen, X and Shi, B and Shu, Y and Song, J and Song, W and Su, Q and Sun, Q and Sun, Y and Sun, Z and Tang, B and Tang, D and Tang, H and Tao, Y and Teng, T and Tu, Y and Wang, C and Wang, H and Wang, Y and Wang, C and Wang, D and Wang, G and Wang, J and Wang, K and Wang, M and Wang, S and Wang, S and Wang, X and Wang, XC and Wang, Y and Wang, J and Wang, Z and Wang, W and Wei, Y and Xu, W and Wu, F and Wu, J and Wu, S and Xiao, J and Xiao, W and Xiao, Y and Xiong, X and Xiong, X and Xu, F and Xu, J and Xu, W and Xu, J and Xu, Y and Yan, J and Yao, L and Yang, J and Yang, L and Yang, X and Yin, N and You, H and You, M and Yu, T and Yu, Y and Yu, R and Yuan, S and Yue, C and Zeng, X and Zha, A and Zhai, L and Zhang, C and Zhang, D and Zhang, H and Zhang, H and Zhang, H and Zhang, J and Zhang, J and Zhang, L and Zhang, Q and Zhang, X and Zhang, X and Zhang, X and Zhang, Y and Zhang, Y and Zhang, Z and Zhao, J and Zhao, J and Zhao, K and Zhao, M and Zhao, Y and Zhao, Y and Zhong, J and Zhong, L and Zhong, X and Zhou, D and Zhou, W and Zhou, W and Zhou, Y and Zhou, Z and Zhu, S and Liu, SJ and Feng, S and Jin, S and Xiao, C and Wang, Z and Luo, P and Chen, T and Chen, G and Liu, YX},
title = {iMeta Conference 2025: Creating high-impact international journals.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70086},
pmid = {41472845},
issn = {2770-596X},
abstract = {The iMeta Conference 2025, part of the iMeta Conference series, themed "Creating High-Impact International Journals," held at the Huangjiahu Campus of Hubei University of Chinese Medicine from August 23rd to 25th, 2025, and focused on frontier topics such as microbiology, medicine, traditional Chinese medicine, botany, and research career development. The event aimed to support the development of researchers and strengthen the impact of academic journals. Through invited reports, thematic seminars, and poster presentations, the conference highlighted hot topics including multi-omics technologies, microbe-host interactions, AI-assisted research, live biotherapeutic products, and the modernization of traditional Chinese medicine. The event demonstrated the innovative momentum of interdisciplinary integration and technological convergence, providing an international platform for academic exchange and laying a foundation for building an innovative scientific research ecosystem and enhancing the global influence of Chinese academic journals.},
}
@article {pmid41474351,
year = {2026},
author = {Beumer, LT and Hertel, AG and Royauté, R and Tucker, MA and Albrecht, J and Beltran, RS and Cagnacci, F and Davidson, SC and Dejid, N and Kays, R and Kölzsch, A and Lohr, A and Neuschulz, EL and Safi, K and Scharf, AK and Schleuning, M and Wikelski, M and Mueller, T},
title = {MoveTraits-A Database for Integrating Animal Behaviour Into Trait-Based Ecology.},
journal = {Ecology letters},
volume = {29},
number = {1},
pages = {e70297},
pmid = {41474351},
issn = {1461-0248},
support = {//Hessian Ministry of Science and Research, Arts and Culture, Germany/ ; 80NSSC21K1182//NASA's Ecological Forecasting Program/ ; 101086640//HORIZON EUROPE Research and Innovation Programme/ ; 01LC2320A//German Federal Ministry for Research, Technology and Aeronautics/ ; HE 8857/1-1//Deutsche Forschungsgemeinschaft/ ; NE1863/2-2//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Databases, Factual ; *Birds/physiology ; *Behavior, Animal ; *Ecology/methods ; *Mammals/physiology ; Ecosystem ; Biodiversity ; },
abstract = {Trait-based approaches are key to understanding eco-evolutionary processes but rarely account for animal behaviour despite its central role in ecosystem dynamics. We propose integrating behaviour into trait-based ecology through movement traits-standardised and comparable measures of animal movement derived from biologging data, such as daily displacements or range sizes. Accounting for animal behaviour will advance trait-based research on species interactions, community structure and ecosystem functioning. Importantly, movement traits allow for quantification of behavioural reaction norms, offering insights into species' acclimation and adaptive capacity to environmental change. We outline a vision for a 'living' global movement trait database that enhances trait data curation by (1) continuously growing alongside shared biologging data, (2) calculating traits directly from individual-level data using standardised, consistent methodology and (3) providing information on multi-level (species, individual, within-individual) trait variation. We present a proof-of-concept 'MoveTraits' database with 52 mammal and 97 bird species, demonstrating calculation workflows for 5 traits across multiple timescales. Movement traits have significant potential to improve trait-based global change predictions and contribute to global biodiversity assessments as Essential Biodiversity Variables. By making animal movement data more accessible and interpretable, this database could bridge the gap between movement ecology and biodiversity policy, facilitating evidence-based conservation.},
}
@article {pmid41474484,
year = {2025},
author = {Kinkpe, L and Solomon, AI and Niu, Y and Goswami, N and Ikele, CM and Hu, D and Abdessan, R and Zhigang, H and Xia, W},
title = {A guide to network analysis, multi-omics integration, and applications in livestock microbiome research.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {1},
pages = {17},
pmid = {41474484},
issn = {1573-0972},
support = {2023YFD1300300//National Key Research and Development Program of China/ ; (CARS-42-2)//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; *Livestock/microbiology ; *Gastrointestinal Microbiome ; *Genomics/methods ; *Microbiota ; Computational Biology/methods ; Machine Learning ; Multiomics ; },
abstract = {The function of the livestock gut microbiome in driving animal growth, health, and methane emissions is controlled by networks of interactions among microbes. A major challenge is to move beyond simply listing microbial members to understanding these interaction networks, which determine how the community functions as a whole. This review synthesizes how network analysis, combined with multi-omics data, can meet this challenge. We focus on the critical task of identifying keystone species, the disproportionately influential microbes that direct processes like fiber digestion and immune function, yet are often missed by standard surveys. We evaluate a progression of methods, from identifying correlated species to building models that integrate genomic, metabolic, and host data. This integration is key to separating true ecological relationships from statistical noise and to linking microbial presence to function. We highlight how computational techniques like metabolic modeling and machine learning are turning networks into predictive tools. Finally, we outline the path forward: field-ready studies that track microbiomes over time, the development of livestock-specific metabolic models, and analytical standards that will allow research to translate into practical strategies. The goal is to provide a framework for using network science to actively manage the microbiome, enhancing sustainable livestock production.},
}
@article {pmid41475540,
year = {2026},
author = {Han, M and Sang, R and Mao, R and Pan, M and Guo, Y and Chen, Z and Yan, X},
title = {Integrated multi-omics reveals the interactive mechanisms of antioxidant defense, energy metabolism, and programmed cell death in cadmium tolerance of Elymus nutans Griseb.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {364},
number = {},
pages = {112969},
doi = {10.1016/j.plantsci.2025.112969},
pmid = {41475540},
issn = {1873-2259},
mesh = {*Cadmium/toxicity/metabolism ; *Antioxidants/metabolism ; *Energy Metabolism/drug effects ; *Apoptosis/drug effects ; *Soil Pollutants/toxicity ; Photosynthesis/drug effects ; Biodegradation, Environmental ; Transcriptome ; Metabolomics ; Gene Expression Regulation, Plant ; Multiomics ; },
abstract = {Cadmium (Cd), a non-essential toxic heavy metal, presents severe threats to agricultural productivity, plant development, and human health through food chain contamination. Although Elymus nutans Griseb. (E. nutans) exhibits substantial potential for phytoremediation of Cd-contaminated soils, its molecular Cd-tolerance mechanisms remain poorly characterized. This study employed integrated morphological, physiological, ultrastructural, transcriptomic, and metabolomic analyses to systematically investigate Cd stress responses in E. nutans. Results demonstrated that Cd stress significantly inhibited growth and photosynthesis, activated antioxidant system, and induced lipid peroxidation in E. nutans seedlings. Notably, cellular ultrastructural damage coincided with disrupted energy metabolism and substantial accumulation of reactive oxygen species (ROS), which ultimately triggered programmed cell death (PCD). Transcriptomic analysis revealed differentially expressed genes (DEGs) enriched in Plant hormone signal transduction and Carbon metabolism pathways. Metabolomic profiling identified 128 differentially expressed metabolites (DEMs) associated with ABC transporters and Isoquinoline alkaloid biosynthesis. Integrated multi-omics analysis demonstrated that glutathione metabolism and photosynthetic carbon fixation pathways regulate E. nutans response to Cd by modulating photosynthesis, antioxidant defense, and energy metabolism. This study reveals phytoremediation mechanisms of E. nutans under Cd stress, offering a scientific foundation for restoring soil health and ecological functions in high-altitude contaminated areas through sustainable soil management strategies.},
}
@article {pmid41475601,
year = {2026},
author = {Tang, J and Liu, Y and Zhang, Q and Zhang, H and Ni, BJ and Lv, W},
title = {Multi-omics dissection of yeast-centric fungal-bacterial synergies in food-processing wastewater: insights from four full-scale treatment plants.},
journal = {Bioresource technology},
volume = {443},
number = {},
pages = {133911},
doi = {10.1016/j.biortech.2025.133911},
pmid = {41475601},
issn = {1873-2976},
mesh = {*Wastewater/microbiology ; *Bacteria/genetics/metabolism ; *Food Handling ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Fungi/genetics/metabolism ; *Yeasts/genetics/metabolism ; *Food-Processing Industry ; Multiomics ; },
abstract = {Fungal presence and ecological roles in activated sludge at municipal wastewater treatment plants are increasingly recognized, yet their diversity and functional contributions-especially of yeasts-in treating food-processing wastewater remain underexplored. High-throughput ITS and 16S rRNA sequencing and shotgun metagenomics, together with FUNGuild, were used to analyze microbial community structure, functional microorganisms, co-occurrence patterns, interkingdom interactions, functional pathways, and the distributions of degradation enzymes and functional genes for characteristic pollutants among four full-scale food-processing plants (seafood, pastry, orange-canning, and vegetable-oil refining). Community diversity and structural differences shaped by wastewater types, associated with metabolic traits and enzyme-secretion. Saccharomycetes emerged as the dominant fungal class; bacteria displayed more even class-level and genus-level distributions than fungi across plants, combining LEfSe (LDA > 4, p < 0.05) to reveal plant-specific environmental-driven taxa, mainly included members of Saccharomycetales among fungi. Module-based co-occurrence networks indicated symbiotic interactions among yeasts; predominant cooperation of fungal-bacterial interaction network, in which yeasts exhibited the highest degree among fungi; strong correlations between Saccharomycetales and functional genes. Metabolism was the most abundant functional pathway. "Undefined Saprotroph" was the most widespread fungal functional guild. We annotated 86 degradation enzymes and 150 functional genes targeting eight pollutant categories (proteins, lipids, starch, pectin, lignin, cellulose, hemicellulose, chitosan), elucidating plant-specific distributions and enzymatic synergies. These multi-plant comparisons disentangle conserved from plant-specific features of catabolism. Overall, this study elucidates microbial diversity, interactions, and functional potential in food-processing wastewater treatment, reveals yeasts as keystone microbes for pollutant degradation, and provides actionable insights for treatment strategies and process optimization.},
}
@article {pmid41476124,
year = {2025},
author = {Abdou, ANA and Hamed, M and Hassan, AMM and Khaled, MA},
title = {Assessment of industrial pollution and water quality in the Nile River using GIS-based indices at Aswan, Egypt.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {3731},
pmid = {41476124},
issn = {2045-2322},
mesh = {Egypt ; *Rivers/chemistry ; *Water Quality ; *Geographic Information Systems ; *Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; *Water Pollution/analysis ; Ecosystem ; *Industrial Waste/analysis ; },
abstract = {Industrial pollution represents a critical threat to freshwater ecosystems, particularly in regions where rivers serve multiple socio-economic functions. The Nile River in Aswan Governorate, southern Egypt, is a vital source of drinking water, irrigation, fisheries, and tourism, yet it is increasingly exposed to untreated industrial effluents. This study assessed the spatial extent and intensity of such pollution using geographic information system (GIS)-based spatial interpolation alongside two comprehensive indices: the weighted arithmetic water quality index (WAWQI) and the canadian water quality index (CWQI). Findings revealed distinct pollution hotspots near major industrial discharge areas, where water quality was classified as poor to very poor (WAWQI: 52.6-127.4; CWQI: 74.2-68.3). In contrast, upstream and downstream zones more distant from effluent sources exhibited good water quality (WAWQI: 24.5-38.1; CWQI: 93.69-85.52). The most degraded sites were characterized by elevated concentrations of chemical oxygen demand (13.1-59.6 mg/L), biochemical oxygen demand (7.67-36.5 mg/L), total suspended solids (4.67-13.1 mg/L), turbidity (6.01-17.1 NTU), total nitrogen (1.13-3.35 mg/L), and phenol (8.01-10.10 µg/L). These results highlight the ecological vulnerability of the Nile River in Aswan to industrial activities, with direct implications for ecosystem health and resource sustainability. They also underscore the limitations of relying solely on traditional water quality monitoring without spatial analysis, as GIS-based interpolation proved critical in detecting pollution gradients beyond sampling sites. The study supports the enforcement of Egypt's Law 48/1982 on water protection and contributes to global sustainable development goals, particularly SDG 6 (Clean Water and Sanitation), SDG 12 (Responsible Consumption and Production), and SDG 14 (Life Below Water).},
}
@article {pmid41476368,
year = {2026},
author = {Hong, C and Cheng, W and Li, Z and Deng, J and Li, Y and Zang, Y and Gao, H},
title = {UniSplicer: A deep-learning framework for accurate splice-site prediction and splice-altering mutation detection across diverse taxa.},
journal = {Plant communications},
volume = {7},
number = {5},
pages = {101686},
pmid = {41476368},
issn = {2590-3462},
mesh = {*Deep Learning ; *RNA Splice Sites/genetics ; *RNA Splicing/genetics ; *Mutation ; Arabidopsis/genetics ; Introns/genetics ; *Computational Biology/methods ; },
abstract = {RNA splicing removes non-coding introns from pre-mRNA to generate mature mRNA in eukaryotes, and accurate identification of splice sites is essential for understanding gene structure and regulation. Traditional gene annotation and splice-site prediction rely heavily on high-quality genome assemblies, extensive functional characterization, and substantial computational and experimental resources, limiting their applicability to many non-model species. Here, we present UniSplicer, a deep-learning-based training framework capable of generating accurate intron splice-site prediction models for diverse species using relatively limited transcriptomic data. UniSplicer-based models (http://www.unisplicer.com) consistently outperform existing prediction tools across a wide range of taxa, including plants, fungi, and metazoans. UniSplicer prediction scores serve as reliable indicators of mutational effects across multiple types of splice mutants. Moreover, application of the UniSplicer Arabidopsis thaliana model identified genes in natural ecotypes that exhibit aberrant splicing due to sequence variation near splice sites, suggesting potential roles in environmental adaptation. Collectively, UniSplicer-based models achieve high predictive accuracy and provide insight into how sequence variation drives splicing alterations across large genomic datasets.},
}
@article {pmid41480146,
year = {2025},
author = {Formenti, G and Jain, N and Medico, JA and Sollitto, M and Antipov, D and Barcellos, S and Biegler, M and Borges, I and Chang, JK and Chen, Y and Cheng, H and Conceição, H and Davenport, M and De Oliveira, L and Duarte, E and Durham, G and Fenn, J and Forde, N and Galante, PA and Gerhardt, K and Giani, AM and Giunta, S and Kim, J and Komissarov, A and Koo, B and Koren, S and Larkin, D and Lee, C and Li, H and Makova, K and Masterson, P and Murphy, T and McCaffrey, K and Mercuri, RLV and Na, Y and O'Connell, MJ and Ou, S and Phillippy, A and Popova, M and Rhie, A and Ruiz-Ruano, FJ and Secomandi, S and Smeds, L and Suh, A and Tilley, T and Vontzou, N and Waters, PD and Balacco, J and Jarvis, ED},
title = {The complete genome of a songbird.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41480146},
issn = {2692-8205},
support = {K99 HG014014/HG/NHGRI NIH HHS/United States ; },
abstract = {Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch (Taeniopygia guttata), a model organism for neuroscience and evolutionary genomics. Combining multiple sequencing strategies resulted in closing nearly all gaps, adding ~90 Mbp of previously missing sequence (7.8%). This includes T2T assemblies for all microchromosomes, including dot chromosomes, and the previously almost entirely missing chr16. The T2T genome is comprehensively annotated for genes, repeats, structural variants, and long-read methylation calls. Complete centromeric structures were assembled and annotated along with kinetochore binding sites. Relative to the previous high-quality reference of the Vertebrate Genomes Project, 2,778 (8.51%) previously unassembled or unannotated genes were identified, of which 9% overlap with segmental duplications. This first complete genome of a songbird, now the new public reference, illuminates avian genome architecture and function.},
}
@article {pmid41480951,
year = {2026},
author = {Zhang, S and Jiao, Z and Liu, Z and Peng, Z and Cui, L and Hu, Z and Jiao, Z and Yuan, Q and Qiu, Z and Yan, C},
title = {Multiomics Analysis Revealed the Role of LsBBX22-LsHY5a/b Module in Promoting UV-B-Mediated Anthocyanin Accumulation in Lettuce.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {1},
pages = {1788-1803},
doi = {10.1021/acs.jafc.5c08530},
pmid = {41480951},
issn = {1520-5118},
mesh = {*Anthocyanins/biosynthesis/metabolism ; *Lactuca/metabolism/genetics/radiation effects ; Ultraviolet Rays ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant/radiation effects ; *Transcription Factors/metabolism/genetics ; Multiomics ; },
abstract = {Ultraviolet-B (UV-B) radiation profoundly affects plant photomorphogenesis and secondary metabolism, yet its regulatory role in lettuce (Lactuca sativa) remains poorly understood. We conducted metabolome and transcriptome analyses to reveal the molecular basis of UV-B adaptation in highland-grown lettuce. Flavonoid accumulation was enhanced as a key adaptive strategy for UV-B acclimation. The key UV-B signaling components LsHY5a/b showed positive correlations with ten LsBBXs and flavonoid/anthocyanin-related genes. UV-B treatment rapidly induced the transcription of LsHY5a/b and LsBBX22-1. LsBBX22-1 physically interacted with LsHY5a/b. While LsBBX22-1 activated the expression of anthocyanin-related genes, it could not bind directly to their promoters. By contrast, LsHY5a/b directly bound to the promoters of LsCHS1, LsCHI3, and LsF3H. Thus, LsBBX22 and LsHY5a/b acted synergistically to regulate UV-B-induced anthocyanin biosynthesis. This study clarified the molecular mechanism of the LsBBX22-1-LsHY5a/b module in promoting UV-B-induced anthocyanin accumulation in lettuce, providing a theoretical basis for cultivating high-quality vegetables in highland regions.},
}
@article {pmid41482560,
year = {2026},
author = {Chakaroun, RM and Pradhan, M and Björnson, E and Arvidsson, D and Fridolfsson, J and Gummesson, A and Schoeler, M and Mitteregger, M and Smith, GJ and Larsson, I and Börjesson, M and Blüher, M and Uhlén, M and Stumvoll, M and Bergström, G and Tremaroli, V and Bäckhed, F},
title = {Multi-omic definition of metabolic obesity through adipose tissue-microbiome interactions.},
journal = {Nature medicine},
volume = {32},
number = {1},
pages = {113-125},
pmid = {41482560},
issn = {1546-170X},
support = {2017.0026//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2017.0026//Diabetesfonden (Stiftelsen Svenska Diabetesf&#xf6;rbundets Forskningsfond)/ ; 20210366//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 20240882//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; NNF15OC0016798//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21OC0070298//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF24OC0092455//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 17CVD01//Fondation Leducq/ ; ERC-2022-ADG 101096705//Fondation Leducq/ ; 2019-01599//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; EXC3105/1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Humans ; *Obesity/metabolism/microbiology ; *Adipose Tissue/metabolism/microbiology ; Male ; Body Mass Index ; Female ; Middle Aged ; *Microbiota/physiology ; Adult ; Metabolome ; Insulin Resistance ; Metabolomics/methods ; Adiposity ; Multiomics ; },
abstract = {Obesity's metabolic heterogeneity is not fully captured by body mass index (BMI). Here we show that deep multi-omics phenotyping of 1,408 individuals defines a metabolome-informed obesity metric (metBMI) that captures adipose tissue-related dysfunction across organ systems. In an external cohort (n = 466), metBMI explained 52% of BMI variance and more accurately reflected adiposity than other omics models. Individuals with higher-than-expected metBMI had 2-5-fold higher odds of fatty liver disease, diabetes, severe visceral fat accumulation and attenuation, insulin resistance, hyperinsulinemia and inflammation and, in bariatric surgery (n = 75), achieved 30% less weight loss. This obesogenic signature aligned with reduced microbiome richness, altered ecology and functional potential. A 66-metabolite panel retained 38.6% explanatory power, with 90% covarying with the microbiome. Mediation analysis revealed a bidirectional, metabolite-centered host-microbiome axis, mediated by lipids, amino acids and diet-derived metabolites. These findings define an adipose-linked, microbiome-connected metabolic signature that outperforms BMI in stratifying cardiometabolic risk and guiding precision interventions.},
}
@article {pmid41483326,
year = {2026},
author = {Liu, Z and Liu, W and Wang, S and Wang, X and Zhu, J and Wang, D and Dong, C and Cheng, G and Mei, Y and Qi, X},
title = {Divergent occupational heat stress strategies required for Northern and Southern China under climate change.},
journal = {International journal of biometeorology},
volume = {70},
number = {1},
pages = {6},
pmid = {41483326},
issn = {1432-1254},
support = {2025A04J5097//Guangzhou Basic and Applied Basic Research Foundation/ ; 42301021//National Natural Science Foundation of China/ ; },
mesh = {*Climate Change ; China/epidemiology ; *Heat Stress Disorders/epidemiology/economics/prevention &amp; control ; Humans ; Hot Temperature ; Climate Models ; *Occupational Exposure ; },
abstract = {Observable climate change has led to an increase in compound heat events, thereby amplifying the economic impacts of labor heat stress and necessitating intervention strategies. Current research lacks high-resolution precision in projecting future heat stress and quantifying adaptation strategies, which is particularly critical for China given its spatial disparities in climate, workforce distribution, and economic development. This study integrates high-resolution CMIP6 climate models, a Wet-bulb Globe Temperature (WBGT) algorithm, and localized Exposure-response Functions (ERFs) to project heat-induced labor productivity loss across China under the SSP5-8.5 scenario. It systematically analyzes and quantitatively compares the effectiveness of two adaptation strategies (shading and work schedule adjustments) while estimating direct economic losses in outdoor heavy labor industries. This study precisely identifies the thermal stress hotspots categorized as primary (South China: loss rate > 11%, increment 5-7%), secondary (middle-lower Yangtze River: 7-11% loss, 3-5% increment), and tertiary hotspots (Yangtze River Delta &amp; North China Plain: 6-9% loss, 2-4% increment) based on productivity loss magnitudes. Our findings also reveal that optimal strategies diverge north-south along the 33°N: shading dominates in the south and schedule adjustments in the north due to distinct heat patterns, though future climate trends may reduce the efficacy of time shift adjustments nationwide. Additionally, economic loss estimation reveals surging heat-induced losses in agriculture and construction over two decades (annual growth rates of 11.16% and 20.69%, respectively), with combined strategies potentially reducing direct losses by 65-70% in hotspot provinces. These findings enable province- and industry-specific intervention designs considering regional climate variations and strategy effectiveness.},
}
@article {pmid41484280,
year = {2026},
author = {Lancaster, T and Tut, G and Sylla, P and Bone, D and Bentley, C and Spalkova, E and Jadir, A and Bruton, R and Spencer, K and Mallick, S and Elzaidi, A and Plass, S and Kaur, N and Butler, M and Hulme, S and Dowell, AC and Krutikov, M and Stirrup, O and Azmi, B and Hayward, A and Copas, A and Shallcross, L and Moss, P},
title = {Endemic penetrance of SARS-CoV-2 has impacted marginally on immunity to spike protein of human coronaviruses.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {196},
pmid = {41484280},
issn = {2399-3642},
support = {1400035//RCUK | Medical Research Council (MRC)/ ; National Core Study 1644507//RCUK | MRC | Medical Research Foundation/ ; },
mesh = {Humans ; *Spike Glycoprotein, Coronavirus/immunology ; *SARS-CoV-2/immunology ; *COVID-19/immunology/epidemiology ; Antibodies, Viral/immunology/blood ; Cross Reactions ; Pandemics ; Adaptive Immunity ; Coronavirus OC43, Human/immunology ; Coronavirus 229E, Human/immunology ; Antibodies, Neutralizing/immunology ; *Coronavirus Infections/immunology/virology/prevention &amp; control/epidemiology ; Female ; T-Lymphocytes/immunology ; COVID-19 Vaccines/immunology ; Adult ; Male ; },
abstract = {SARS-CoV-2 has emerged as the 5th endemic coronavirus and immunological cross protection between coronaviruses will influence their infectivity and clinical impact. We determined adaptive immunity against the spike protein of each human coronavirus during the course of the COVID-19 pandemic. A characteristic pattern of HCoV immunodominance, dominated by OC43 and 229E, was apparent prior to SARS-CoV-2 and was largely unaffected by SARS-CoV-2 infection, which itself elicited moderate antibody titre. Vaccination or hybrid immunity elicited supraphysiological levels of coronavirus-specific antibodies, only a proportion of which was cross-reactive with SARS-CoV-2 spike indicating substantial backboosting of HCoV-specific responses. SARS-CoV-2 vaccination focused antibody responses against the S1 domain of SARS-CoV-2 spike whilst T cell responses recognised peptides equivalently across S1 and S2. Coronavirus-specific T cells exhibited strong production of IFN-γ, IL-2 and CXCL8. In summary, the entry of SARS-CoV-2 into its ecological niche has impacted marginally on relative immunity against other human coronaviruses although vaccination provides a modest antibody increment which is unlikely to be maintained. Further, although SARS-CoV-2 vaccination elicits spike-specific adaptive immune responses that are focused against the S1 domain, thereby favouring neutralising antibodies, the natural history of HCoV immunity indicates that adaptive responses may transition towards S2 recognition across the life course.},
}
@article {pmid41488255,
year = {2025},
author = {Li, R and Li, J and , and , and , and , and Blaxter, ML},
title = {The genome sequence of the Atlantic Strawberry Cockle, Americardia media (Linnaeus, 1758) (Cardiida: Cardiidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {630},
pmid = {41488255},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual Americardia media (Atlantic Strawberry Cockle; Mollusca; Bivalvia; Cardiida; Cardiidae). The assembly contains two haplotypes with total lengths of 1 299.87 megabases and 1 284.99 megabases. Most of haplotype 1 (99.42%) is scaffolded into 19 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 47.2 kilobases.},
}
@article {pmid41488433,
year = {2025},
author = {LE, HA and Potter, V and Choube, A and Lakshminarayanan, R and Mishra, V and Intille, S},
title = {A Context-Assisted, Semi-Automated Activity Recall Interface Allowing Uncertainty.},
journal = {Proceedings of the ACM on interactive, mobile, wearable and ubiquitous technologies},
volume = {9},
number = {4},
pages = {},
pmid = {41488433},
issn = {2474-9567},
support = {P30 DA029926/DA/NIDA NIH HHS/United States ; R01 CA252966/CA/NCI NIH HHS/United States ; },
abstract = {Measuring activities and postures is an important area of research in ubiquitous computing, human-computer interaction, and personal health informatics. One approach that researchers use to collect large amounts of labeled data to develop models for activity recognition and measurement is asking participants to self-report their daily activities. Although participants can typically recall their sequence of daily activities, remembering the precise start and end times of each activity is significantly more challenging. ACAI is a novel, context-assisted ACtivity Annotation Interface that enables participants to efficiently label their activities by accepting or adjusting system-generated activity suggestions while explicitly expressing uncertainty about temporal boundaries. We evaluated ACAI using two complementary studies: a usability study with 11 participants and a two-week, free-living study with 14 participants. We compared our activity annotation system with the current gold-standard methods for activity recall in health sciences research: 24PAR and its computerized version, ACT24. Our system reduced annotation time and perceived effort while significantly improving data validity and fidelity compared to both standard human-supervised and unsupervised activity recall approaches. We discuss the limitations of our design and implications for developing adaptive, human-in-the-loop activity recognition systems used to collect self-report data on activity.},
}
@article {pmid41488783,
year = {2026},
author = {Luongo, G and Dell'Anno, A and Tangherlini, M and Corinaldesi, C and A Ruhl, H and Danovaro, R},
title = {Major changes in micro-eukaryotic biodiversity of the abyssal ecosystem of the NE Atlantic: A comparison between 1996 and 2018.},
journal = {iScience},
volume = {29},
number = {1},
pages = {114266},
pmid = {41488783},
issn = {2589-0042},
abstract = {Time-separated snapshots of deep-sea regions can provide crucial insights into how fluctuations in environmental changes and food supply shape microbial communities. Here, we compared molecular and environmental data collected in 1996 and 2018 at 4,800-m depth in the northeast (NE) Atlantic Ocean. We report lower values of primary production (-66%) associated with lower concentrations of sedimentary labile organic matter (-12%). Metabarcoding analyses revealed a significant decrease in the Chlorophyta taxa, only partly compensated by the increase in Dinoflagellate taxa, consistent with patterns observed in NE Atlantic Ocean phytoplankton. Benthic prokaryotic assemblages showed a limited response to such changes, whilst micro-eukaryotic assemblages changed significantly even at subdivision level. Overall, data reported here suggest that the Porcupine abyssal plain may undergo significant variations in terms of quantity and quality of biopolymeric carbon and that such changes caused a shift in micro-eukaryotic biodiversity, with potentially relevant effects also on the deep-sea ecosystem functioning.},
}
@article {pmid41491008,
year = {2026},
author = {Ajene, IJ and Tanga, CM and Akutse, KS and Karanu, SW and Khamis, FM},
title = {Multi-omics comparison of two emerging storage pests (Necrobia rufipes and Tribolium castaneum) of dried black soldier fly larvae product.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {4747},
pmid = {41491008},
issn = {2045-2322},
support = {ProteinAfrica: LS/2020/154//Australian Centre for International Agricultural Research/ ; WAVE-IN: 2021 FOD 030//Rockefeller Foundation/ ; G-2204-02144//IKEA Foundation/ ; NESTLER Project: 101060762 and INNOECOFOOD project: 101136739//European Commission/ ; },
mesh = {Animals ; Larva/microbiology/genetics ; Gastrointestinal Microbiome ; *Tribolium/microbiology/genetics ; Genome, Mitochondrial ; Bacteria/genetics/classification ; Multiomics ; },
abstract = {The black soldier fly (BSF) larvae is a rich and promising source of alternative protein that continues to increasingly gain global traction as a functional ingredient for sustainable livestock and fish production. The key setback to postharvest processing of stored BSF larvae (BSFL) products is the significant damage caused by two notable storage pests (Tribolium castaneum and Necrobia rufipes). Here, we present a comparative analysis of the complete mitochondrial genomes and gut microbiome profiles of T. castaneum and N. rufipes. The study mitogenomes were similar in size and structure to other coleopteran mitogenomes. The gut microbiome profiles of the two pests showed a high abundance of bacteria in the Proteobacteria and Firmicutes phyla. However, T. castaneum had 78% more phyla represented within its microbiome than N. rufipes. The most abundant genera in T. castaneum were Staphylococcus and Streptococcus, while in N. rufipes, the dominant genera were Klebsiella and Synechococcus. We also identified the presence of potentially clinically harmful microbial genera (Stenotrophomonas maltophilia) in the gut of T. castaneum and N. rufipes in relatively high abundance. These results provide insight into potential harmful associations in the gut of the storage pest, picked from contaminated, poorly processed BSFL products.},
}
@article {pmid41491638,
year = {2026},
author = {Wang, Y and Zhao, J and He, X and Yang, D and Jin, Y and Wu, R},
title = {A Computational Ecological Genetic Model of Phenotypic Plasticity in Species Interactions.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70095},
pmid = {41491638},
issn = {1755-0998},
support = {SIMIS-ID-2024-WN//Interdisciplinary Project at Shanghai Institute for Mathematics and Interdisciplinary Sciences/ ; 31971398//National Natural Science Foundation of China/ ; },
mesh = {Phenotype ; *Escherichia coli/genetics/physiology/growth &amp; development ; *Staphylococcus aureus/genetics/physiology/growth &amp; development ; *Models, Genetic ; *Computational Biology/methods ; Genotype ; *Microbial Interactions ; Epistasis, Genetic ; },
abstract = {Multiple species respond to each other in their co-existing communities. Such reciprocal phenotypic plasticity can shape the behaviour and evolution of ecological communities, but its genetic architecture remains elusive. We address this issue by developing a computational mapping model that combines community ecology and quantitative genetics into a unifying context. Culturing a pair of genotypes from two species in a socially isolated environment (monoculture) and a socialised environment (co-culture) allows for the quantitative estimation of reciprocal phenotypic plasticity, that is, the difference between trait values of one (defensive) species expressed in the monoculture and the co-culture with the other (offensive) species. Classic quantitative genetic theory is implemented to map genetic variants for reciprocal phenotypic plasticity, including defensive loci derived from the defensive species and offensive loci from the offensive species, and estimate the direct effects of the defensive loci, the indirect effects of the offensive loci and horizontal epistasis due to interactions between the two genomes. We design an ecological genetic experiment of monocultures and co-cultures using 100 pairs of genotyped Escherichia coli and Staphylococcus aureus strains, from which the model identifies the existence of defensive and offensive loci, despite a remarkable asymmetry between the two bacterial species. We find that horizontal epistasis between defensive and offensive loci plays a sizable role in mediating reciprocal phenotypic plasticity. The biological functions of these identified loci are annotated via GO analysis. Our model could produce unique results that shed light on the genetic mechanisms of interspecies interactions and their adaptation in ecological communities.},
}
@article {pmid41492055,
year = {2026},
author = {Marinucci, M and Schaefer, CD and Dupont, PL and Manley, D and Taylor, LK and McKeown, S},
title = {Desegregating spaces: The interplay between ecological intergroup contact and GPS-traced spatial segregation among youth in two UK cities.},
journal = {The British journal of social psychology},
volume = {65},
number = {1},
pages = {e70043},
pmid = {41492055},
issn = {2044-8309},
support = {//Economic and Social Research Council/ ; },
mesh = {Humans ; Adolescent ; Male ; Female ; Geographic Information Systems ; United Kingdom ; *Social Segregation/psychology ; Cities ; Ecological Momentary Assessment ; Ethnicity/psychology ; *Group Processes ; *Interpersonal Relations ; },
abstract = {Recent advances in intergroup contact research have drawn on methods from human geography to investigate how segregation shapes, and is shaped by, everyday intergroup experiences. Emerging findings suggest that the phenomena might be reciprocally intertwined, but empirical evidence is limited and mixed. This research tested the reciprocal relationship between everyday intergroup contact and segregation using ecological momentary assessment and GPS-GIS tracking in two segregated UK cities with youths aged 15-17. Study 1 (Belfast; nparticipants = 15; ninteractions = 115; nGPS-point = 633) focused on Catholics-Protestants divisions, and Study 2 (Bradford; nparticipants = 30; ninteractions = 334; nGPS-point = 2868) addressed ethnic segregation among Asian, White, and Black communities. In both studies, youths reported on social interactions throughout 6 days, while their urban mobility in outgroup spaces was tracked. In Belfast, more mixed districts predicted higher anxiety during intergroup interactions, yet, positive intergroup contact was followed by increased visits to outgroup spaces. In Bradford, mixed districts increased the likelihood (but not the quality) of intergroup contact, while the link between positive contact and subsequent outgroup space use was replicated. The findings highlight a virtuous cycle depending on contextual norms by which positive contact and desegregation practices might reinforce each other, arguably demonstrating the potential of intergroup contact for levelling urban divisions.},
}
@article {pmid41494263,
year = {2026},
author = {Mummidivarapu, SK and Rehana, S},
title = {Spatiotemporal risk assessment of river water quality for tropical river systems using hydrological dynamics, anthropogenic influences, and ecological health index.},
journal = {The Science of the total environment},
volume = {1013},
number = {},
pages = {181329},
doi = {10.1016/j.scitotenv.2025.181329},
pmid = {41494263},
issn = {1879-1026},
mesh = {*Rivers/chemistry ; Risk Assessment ; *Environmental Monitoring/methods ; *Water Quality ; Hydrology ; Anthropogenic Effects ; Tropical Climate ; Water Pollutants, Chemical/analysis ; Monte Carlo Method ; },
abstract = {Sustainable management of River Water Quality (RWQ) in tropical river systems requires an approach that addresses both spatial and temporal risks associated with hydrological dynamics, anthropogenic influences, and ecological health. This study develops an uncertainty-aware spatiotemporal risk assessment approach integrating upstream hydrological dynamics (SWAT), operational variability with Environmental Flow (Eflow), water quality simulations (QUAL2K), and probabilistic Water Quality Index (WQI) calculations. Block-Bootstrap ensembles and Monte Carlo techniques are used to quantify uncertainty propagation and construct confidence intervals within the model chain. The monthly WQI estimates under the different Eflow and pollution control scenarios are used to assess the spatial risk variability of the river system. Temporal risk was assessed with WQI using various probabilistic measures, including mean, variance, loss probability, entropy, mean excess loss, and value at risk. A unified risk ranking was developed by using Borda and Copeland aggregation techniques. Categorised spatial risk maps were created using GIS by integrating Eflows and ecological index. The results revealed significant seasonal variations in water quality, with April, March, and May identified as high-risk months due to increased pollution levels. The monthly WQI-mean in the Monte Carlo analysis (1000 iterations), as per the severity of the risk, April, March, and May months are identified as the riskiest months. Spatial risk mapping revealed distinct high-risk zones and highlighted the necessity of pollution treatment level of 25-50 % to reduce ecological risk under optimal Eflow regimes. This comprehensive framework underscores the need for both flow regulation and pollution management to protect river ecosystems, providing actionable insights for effective river health protection.},
}
@article {pmid41495476,
year = {2026},
author = {Green, A and Ontiveros-Palacios, N and Jandalala, I and Panni, S and Wood, V and Antonazzo, G and Attrill, H and Bateman, A and Sweeney, B},
title = {GOFlowLLM-curating miRNA literature with large language models and flowcharts.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {1},
pages = {},
pmid = {41495476},
issn = {1367-4811},
support = {UKRI746:24BBR//United Kingdom Research and Innovation (UKRI) Biotechnology and Biological Sciences Research Council/ ; //European Union's Horizon 2020 Marie Sk&#x142;odowska-Curie Actions/ ; 310300/Z/24/Z &amp; 218236/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; MR/W024233/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //European Molecular Biology Laboratory/ ; },
mesh = {*MicroRNAs/genetics ; *Software ; Gene Ontology ; *Data Curation/methods ; Humans ; *Computational Biology/methods ; Molecular Sequence Annotation/methods ; Large Language Models ; },
abstract = {MOTIVATION: The exponential growth of non-coding RNA research-with over 230 000 papers published since 2000-has created an urgent knowledge management crisis in molecular biology. Despite their crucial regulatory roles, microRNAs (miRNAs) face a significant curation bottleneck, with only 1400 articles manually curated to the Gene Ontology (GO) knowledgebase over a decade. This highlights the critical need for automated systems that can accelerate biocuration while maintaining high-quality standards.<br><br>RESULTS: We present GOFlowLLM, an automated curation pipeline powered by reasoning-enabled Large Language Models (LLMs) that follows established GO curation flowcharts to extract and structure miRNA-mediated gene silencing data at scale. When evaluated on existing curation, GOFlowLLM selects the correct GO term in 90% of cases, with curators agreeing with 95% of the system's reasoning steps and 90% of the evidence selected. Applied to 6996 previously uncurated articles using the Qwen QwQ-32B model, our system identified 2538 new candidate GO annotations on 1785 articles in just 58&#x2009;hours-potentially doubling the available miRNA GO curation. Manual review shows curators agreed with the selected term in 87% of cases, the model's reasoning in 92% of cases, and the extracted evidence in 93%. The integration of reasoning traces provides transparent justification for annotations that can be reviewed by human curators, addressing a key challenge in adopting AI for scientific curation.<br><br>GOFlowLLM is implemented as an automated pipeline that follows expert-designed reasoning frameworks to maintain curation quality. The system is available on GitHub: https://github.com/RNAcentral/GO_Flow_LLM.},
}
@article {pmid41495641,
year = {2026},
author = {Khan, N and Das, A and Kumar, R and Jonnalagadda, M},
title = {Comparative evolutionary and structural bioinformatic analysis of the human N-Acetyltransferase-2 (NAT2) gene with different mammalian and avian taxa.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {143},
pmid = {41495641},
issn = {1471-2164},
mesh = {*Arylamine N-Acetyltransferase/genetics/chemistry/metabolism ; Humans ; Animals ; *Evolution, Molecular ; Phylogeny ; *Computational Biology/methods ; *Birds/genetics/classification ; *Mammals/genetics/classification ; Molecular Docking Simulation ; Folic Acid/metabolism ; CpG Islands ; },
abstract = {Effective metabolization of exogenous compounds in humans is a key for health and drug efficacy albeit a complex process determined by one's genetic background. The enzyme, N-Acetyltransferase-2 (NAT2), which metabolizes different xenobiotic compounds (including folate) and various therapeutic drugs, is encoded by the NAT2 gene. Based on acetylation capacity, an individual is either a fast or slow acetylator. Although the apportionment of NAT2 gene and its acetylator types are widely documented in human populations, the evolutionary genetic affinities and functional background of NAT2 variations with closely-related taxa are not well understood. Herein, we have analyzed 60 NAT2 gene coding sequences (873 bp) representing 59 different taxa belonging to mammalian and avian taxa and two most prevalent human NAT2 alleles ((NAT2*4 and NAT2*6A) to document the phylogenetics relationship among taxa; to characterize DNA methylation patterns in this gene and to evaluate species specific binding efficiency to folate using molecular docking approach. Phylogenetic analysis showed 3 broad clades representing where humans and other primates were found to be closely related. The CpG analysis revealed a one conserved region of same length (total 200 bp) across taxa as well as variable short regions of differing lengths (ranging from minimum 50 to maximum 100 bp length sequences) in some taxa. Molecular docking showed variable binding affinities of NAT2 protein models with human slow acetylator allele (NAT2*6A) showing highest binding affinity to folate, indicative of adaptive response to folate bioavailability. Through our analysis we highlight the evolutionary conservation and functional divergence in NAT2 gene across Mammals and Aves likely to be driven by ecological and dietary factors. Our findings provide new insights into evolutionary adaptations to processing folate across various taxa, which may be significant in studies focusing on evolutionary genetics of drug metabolism.},
}
@article {pmid41497383,
year = {2025},
author = {Hostens, M and Franceschini, S and van Leerdam, M and Yang, H and Pokharel, S and Liu, E and Niu, P and Zhang, H and Noor, S and Hermans, K and Salamone, M and Sharma, S},
title = {The future of big data and artificial intelligence on dairy farms: A proposed dairy data ecosystem.},
journal = {JDS communications},
volume = {6},
number = {Suppl 1},
pages = {S9-S14},
pmid = {41497383},
issn = {2666-9102},
abstract = {The dairy sector should overcome challenges in productivity, sustainability, and data management by adopting intelligent, scalable, and privacy-preserving technological solutions. Adopting data and artificial intelligence (AI) technologies is essential to ensure efficient operations and informed decision making and to keep a competitive market advantage. This paper proposes an integrated, multimodal AI framework to support data-intensive dairy farm operations by leveraging big data principles and advancing them through AI technologies. The proposed architecture incorporates edge computing, autonomous AI agents, and federated learning to enable real-time, privacy-preserving analytics at the farm level and promote knowledge sharing and refinement through research farms and cloud collaboration. Farms collect heterogeneous data, which can be transformed into embeddings for both local inference and cloud analysis. These embeddings form the input of AI agents that support health monitoring, risk prediction, operational optimization, and decision making. Privacy is preserved by sharing only model weights or anonymized data externally. The edge layer handles time-sensitive tasks and communicates with a centralized enterprise cloud hosting global models and distributing updates. A research and development cloud linked to research farms ensures model testing and validation. The entire system is orchestrated by autonomous AI agents that manage data, choose models, and interact with stakeholders, and human oversight ensures safe decisions, as illustrated in the practical use case of mastitis management. This architecture could support data integrity, scalability, and real-time personalization, along with opening up space for partnerships between farms, research institutions, and regulatory bodies to promote secure, cross-sector innovation.},
}
@article {pmid41499681,
year = {2026},
author = {Astill Wright, L and Shajan, G and Purewal, D and Stone, J and Majid, M and Guo, B and Morriss, R},
title = {Mood Monitoring, Mood Tracking, and Ambulatory Assessment Interventions in Depression and Bipolar Disorder: Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {JMIR mental health},
volume = {13},
number = {},
pages = {e84020},
pmid = {41499681},
issn = {2368-7959},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Bipolar Disorder/therapy/diagnosis/psychology ; Randomized Controlled Trials as Topic ; *Affect ; *Monitoring, Ambulatory/methods ; *Depressive Disorder/therapy/diagnosis ; *Depression/diagnosis/therapy ; },
abstract = {BACKGROUND: Mood monitoring is widely used by people with depression and bipolar disorder (BD) to prevent relapse and improve insight into their condition, but it is unclear if these interventions have an impact on symptoms and for whom. As the capacity for passive mood monitoring increases, it is vital to improve our understanding of frequent mood assessment.<br><br>OBJECTIVE: This systematic review and meta-analysis assessed the effect of mood monitoring interventions in people with depression and BD to decrease relapse risk and symptoms of depression and mania.<br><br>METHODS: We conducted a systematic review and meta-analysis (PROSPERO, International Prospective Register of Systematic Reviews: CRD42023396473) and reported results according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines. Randomized controlled trials with clinically important follow-up periods were identified via multiple database searches and rated for risk of bias using the Cochrane Risk of Bias tool. The primary outcomes were symptoms of depression and mania. Available data were pooled to calculate standardized mean differences (SMDs) for the primary outcomes: severity of depression, bipolar depression, and mania/hypomania.<br><br>RESULTS: We included 8 trials of 1230 participants and 6 different mood monitoring protocols. In BD, meta-analysis found a small but not statistically significant effect of mood monitoring interventions on decreasing mania symptoms (6 comparisons, n=873; SMD 0.16, 95% CI-0.34 to 0.01; P=.06) and no effect on bipolar depression (6 comparisons, n=873; SMD -0.08, 95% CI -0.31 to 0.15; P=.02). In depression, we found a small effect in decreasing symptoms of depression of borderline statistical significance at 12 months (2 comparisons, n=262; SMD -0.25, 95% CI -0.49 to 0.00; P=.05) but not at 6 months (2 comparisons, n=268; SMD -0.21, 95% CI -0.54 to 0.12; P=.21). There was an absence of evidence on the effect of mood monitoring on decreased relapse rates or readmission rates. Studies had a low risk of bias. There was no evidence on mood monitoring through ecological momentary assessment.<br><br>CONCLUSIONS: Overall mood monitoring interventions do not increase or decrease mood symptoms in people with BD, nor is there robust evidence of such effects in people with unipolar depression. Further research is merited on different forms of mood monitoring and to determine under what circumstances mood monitoring might have beneficial or adverse effects. These results initially suggest that ambulatory assessment does not induce large placebo effects or significantly negatively or positively affect mood, and thus that mood monitoring may be an appropriate outcome measure for research or for clinical practice.},
}
@article {pmid41501044,
year = {2026},
author = {von Borries, K and Beckwith, KV and Goodman, JM and Chiu, WA and Jolliet, O and Fantke, P},
title = {Uncertainty-aware machine learning to predict non-cancer human toxicity for the global chemicals market.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {647},
pmid = {41501044},
issn = {2041-1723},
support = {P30 ES029067/ES/NIEHS NIH HHS/United States ; P42 ES027704/ES/NIEHS NIH HHS/United States ; DIA 2018/11//Stiftelsen f&#xf6;r Milj&#xf6;strategisk Forskning (Swedish Foundation for Strategic Environmental Research)/ ; EP/S024220/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; },
mesh = {Humans ; *Machine Learning ; Uncertainty ; Predictive Learning Models ; Prediction Algorithms ; },
abstract = {Humans are exposed to thousands of chemicals, yet limited toxicity data hinder effective management of their impacts on human health. High-performing machine learning models hold potential for addressing this gap, but their uncharacterized prediction performance across the wider range of chemicals undermines confidence in their results. We develop uncertainty-aware models to predict reproductive/developmental and general non-cancer human toxicity effect doses. Our well-calibrated models provide uncertainty estimates aligned with observed prediction errors and chemical familiarity. We predict toxicity with 95% confidence intervals for >100,000 globally marketed chemicals and identify toxicity and uncertainty hotspots. These results can be applied to inform decisions aimed at reducing potential human health impacts and guide targeted data generation and modeling efforts to reduce prediction uncertainty. Here, we show that enhancing transparency in prediction uncertainty provides key insights for building confidence in toxicity predictions, supporting the sound integration of machine learning-based predictions in chemical assessments.},
}
@article {pmid41502538,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Drinker, Euthrix potatoria (Linnaeus, 1758) (Lepidoptera: Lasiocampidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {534},
pmid = {41502538},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Euthrix potatoria (Drinker; Arthropoda; Insecta; Lepidoptera; Lasiocampidae). The assembly contains two haplotypes with total lengths of 487.86 megabases and 466.06 megabases. Most of haplotype 1 (99.97%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.43 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 {pmid41502542,
year = {2025},
author = {Crowley, LM and Hutchinson, F and Boyes, D and , and , and , and , and , and , },
title = {The genome sequence of the Barred Hook-tip, Watsonalla cultraria (Fabricius, 1775) (Lepidoptera: Drepanidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {618},
pmid = {41502542},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from a male specimen of Watsonalla cultraria (Barred Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence has a total length of 319.38 megabases. Most of the assembly (99.94%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Gene annotation of this assembly on Ensembl identified 16 011 protein-coding genes. The mitochondrial genome has also been assembled, with a length of 15.21 kilobases.},
}
@article {pmid41502546,
year = {2025},
author = {Boyes, D and Hutchinson, F and Crowley, LM and , and , and , and , and , and , and , },
title = {The genome sequence of the Red-barred Tortrix moth, Ditula angustiorana (Haworth, 1811).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {202},
pmid = {41502546},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Ditula angustiorana (Red-barred Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 468.36 megabases. Most of the assembly (99.83%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.19 kilobases.},
}
@article {pmid41503483,
year = {2026},
author = {Castillo-Neyra, R and Ortiz-Cam, L and Díaz, EW and Cañari-Casaño, JL and Recuenco, SE and Paz-Soldán, VA},
title = {The return of human rabies: A foretold case in Latin America Through the Lens of One Health.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {41503483},
support = {R01 AI168291/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: Despite ongoing rabies control efforts in Arequipa, Peru-including mass dog vaccination campaigns and reactive ring interventions-the region has failed to reduce the number of rabid dogs, leading to the first reported human dog-mediated rabies case after 8 years. The gaps in the rabies control program and the complex dynamics among stakeholders are unknown.<br><br>OBJECTIVE: To integrate epidemiologic, socio-ecological, and policy data to identify the factors contributing to the 2023 human rabies case and propose strategies to make this a 'never event'.<br><br>METHODS: We used stakeholder mapping and field quantitative and qualitative data to identify the roles and connections of key actors in rabies control, identifying gaps in their functions. We then applied the Swiss Cheese model to characterize the defense layers against dog-mediated rabies, highlighting critical vulnerabilities across these protective barriers.<br><br>CONCLUSIONS: We identified multiple breaches in the defense against dog-mediated human rabies. Weak surveillance, insufficient dog vaccination, and inadequate management of free-roaming and feral dogs, coupled with bureaucratic inefficiencies, were key gaps. Outbreak responses were delayed and insufficient, and access to post-exposure prophylaxis (PEP) remained limited. Communication breakdowns exacerbated the problem. Systemic issues, such as outdated public health policies, insufficient training of health professionals, and fragmented efforts, further hindered timely exposure response. Dog ecology and demographic factors also contributed to dog rabies spread. These failures in policy, response, capacity, and external factors led to the 2023 human rabies case. Despite awareness of these challenges, the contributing conditions remain unchanged. Eliminating dog-mediated human rabies by 2030 will require targeted interventions, including enhanced surveillance, context-specific policy reforms, stronger community and institutional collaboration, and better management of free-roaming dogs.},
}
@article {pmid41506426,
year = {2026},
author = {Geng, Y and Guo, W and Li, Q and Zhang, F and Zhong, A and Hu, Z},
title = {Driving mechanisms of vegetation carbon sink distribution based on explainable machine learning and evaluation of carbon sequestration in open-pit mines.},
journal = {Environmental research},
volume = {293},
number = {},
pages = {123715},
doi = {10.1016/j.envres.2026.123715},
pmid = {41506426},
issn = {1096-0953},
mesh = {*Carbon Sequestration ; China ; *Mining ; *Machine Learning ; *Environmental Monitoring ; Bayes Theorem ; Boosting Machine Learning Algorithms ; Ecosystem ; Rivers ; },
abstract = {Vegetation carbon sequestration plays a crucial role in mitigating global warming and maintaining regional carbon balance. The Yellow River Basin (YRB) is a key region for energy development and ecological conservation in China, yet the driving mechanisms underlying the spatial distribution of vegetation carbon sequestration and the carbon sequestration capacity of open-pit mines have not been systematically evaluated. Based on multi-source datasets, this study first employs the Sen's slope estimator combined with the Mann-Kendall trend test model to identify the temporal trends of vegetation carbon sequestration. It then applies a Bayesian-optimized Bayesian-optimized Extreme Gradient Boosting model integrated with Shapley Additive Explanations model to uncover the driving mechanisms of climate, soil, and human activities on its spatial distribution. Finally, a buffer zone comparison method is used to quantify the carbon sequestration potential of open-pit mines. The main conclusions are as follows: (1) Over the 24-year period, Net Ecosystem Productivity (NEP) in the YRB has shown a continuous increase, reaching 159.69 gC·m[-2] in 2024, which is five times the level in 2001. The most significant growth occurred in the middle and upper reaches, while the endorheic region exhibited limited improvement, with some areas even functioning as carbon sources. (2) Among the driving factors of NEP distribution in the YRB, precipitation, solar radiation, and soil organic carbon are the dominant contributors, accounting for more than 58 % in total. (3) The NEP of different types of open-pit mines varies substantially. Active mines function overall as carbon sources (-17.93 Gg), whereas stable and revegetated mines act as carbon sinks. The total carbon sequestration potential of all open-pit mines is 93.57 Gg, representing approximately 89 % of the current carbon sequestration level. This study provides a quantitative foundation for enhancing carbon sequestration, evaluating ecological restoration, and supporting the implementation of the "dual-carbon" strategy in the YRB.},
}
@article {pmid41507331,
year = {2026},
author = {Zhang, K and Zhang, LY and Qin, X and Zhang, YW and Xie, WJ and Wan, RD and Fang, YG and Yang, QE},
title = {Integrated multiomics analysis reveals the molecular features and crucial regulators of hair follicles in yak (Bos grunniens).},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {190},
pmid = {41507331},
issn = {2399-3642},
support = {U22A20447//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Cattle/genetics ; *Hair Follicle/metabolism/cytology ; Multiomics ; Wnt Signaling Pathway ; Gene Expression Profiling ; },
abstract = {Yak is a unique bovine species that adapts to the extreme climate of the Qinghai-Tibet Plateau in part owing to its dense skin coat. Despite its essential role in cold adaptation, the genetic basis of hair follicle structure and growth has not been extensively studied in this iconic animal. In the present study, we construct a single-cell atlas of hair follicle (HF) cells from yak and taurine cattle and examine differences in their cellular composition and gene expression. Among the 14 cell types identified in HFs, the dermal papilla (DP) displays the most dramatic differences between cattle and yak. Detailed analysis reveals that the genes in the WNT signaling pathway are differentially expressed in the dermal papilla (DP) cells of yak. Using primary cultures of DP cells, we reveal that the inhibition or activation of WNT/β-Catenin dramatically alters cell cycle progression and autophagy. In complimentary with the ATAC-seq data, we show that SOX4 is directly associated with the promoters of WNT1 and WNT3A. Interestingly, increased autophagy regulates the expression of SOX4/WNT/β-Catenin to promote the proliferation of DP cells in yak. Together, these results reveal the molecular signature of coat adaptation at the single-cell transcription level and provide a new understanding of animal adaptation to extreme environments.},
}
@article {pmid41512112,
year = {2026},
author = {Shimmura, T and Kurachi, T and Matsuda, Y and Rafati, N and Shimura, K and Goto, T and Kawakami, SI and Maeda, R and Yamada, Y and Pettersson, ME and Nakamura, Y and Higashiura, Y and Shimura, NN and Bendesky, A and Tsudzuki, M and Andersson, L},
title = {Genomic and neurobiological bases of variation in fighting strategies in gamecocks.},
journal = {Molecular biology and evolution},
volume = {43},
number = {1},
pages = {},
pmid = {41512112},
issn = {1537-1719},
support = {18K19266//JSPS KAKENHI/ ; 19H03102//JSPS KAKENHI/ ; 21H00339//JSPS KAKENHI/ ; 21K19185//JSPS KAKENHI/ ; 24H00541//JSPS KAKENHI/ ; //MEXT/ ; JPMJFR211D//JST FOREST Program/ ; //TUAT TAMAGO/ ; //Kieikai Research Foundation/ ; },
mesh = {Animals ; *Aggression/physiology ; *Chickens/genetics/physiology ; Male ; *Behavior, Animal ; Brain/metabolism ; },
abstract = {Aggression is an essential animal behavior for survival, particularly in situations where fighting cannot be avoided. In such situations, the choice of fighting strategy (eg biting, charging, or defending) is critical. Although the molecular bases of fighting and aggressiveness have been previously studied, how genetic, transcriptional, and neurobiological mechanisms contribute to the choice of fighting strategy remains largely unknown. Here, we use two subpopulations of chickens bred for cockfighting that show markedly different fighting strategies: offensive and defensive attack. A genome-wide screen comparing individuals from the two subpopulations indicated a polygenic background and we identified 15 candidate genes, five of which are implicated in neuronal development. Among these, the transcription factor gene FOXP1 was notable. FOXP1 is essential for neuronal development in the brain and has been implicated in the regulation of motor circuits. Transcriptomic analysis of the diencephalon also revealed differential expressions of genes involved in neurodevelopment, as well as in the synthesis and release of neurotransmitters. RNA-sequencing and immunohistochemistry suggested that activation of the indirect pathway of the brain motor circuit promotes the defensive fighting strategy. This was further supported by behavioral pharmacological experiments targeting dopaminergic signaling. Taken together, our results indicate that genomic variation and altered expression of neurodevelopment-related genes underlie differences in fighting strategies, and that the neuroendocrine changes in brain circuits further modulate these behavioral outcomes.},
}
@article {pmid41512284,
year = {2026},
author = {Nemoto, Y and Okawara, M and Nishizawa, N and Mori, M and Takenaka, M and Kuroda, K and Fujino, Y and Matsuda, S and Fushimi, K and Tanaka, F},
title = {Robotic Versus Video-Assisted Thoracoscopic Lobectomy/Segmentectomy: Multilevel Analysis in Japan.},
journal = {Interdisciplinary cardiovascular and thoracic surgery},
volume = {41},
number = {1},
pages = {},
pmid = {41512284},
issn = {2753-670X},
mesh = {Humans ; *Thoracic Surgery, Video-Assisted/adverse effects/mortality ; Japan ; *Pneumonectomy/methods/adverse effects/mortality ; *Robotic Surgical Procedures/adverse effects/mortality ; Female ; Retrospective Studies ; *Lung Neoplasms/surgery/mortality/pathology ; Male ; Aged ; Middle Aged ; Postoperative Complications/epidemiology ; Treatment Outcome ; },
abstract = {OBJECTIVES: Large-scale comparative data on the perioperative safety of robotic-assisted thoracoscopic surgery and video-assisted thoracoscopic surgery in Asia are limited. We compared the perioperative outcomes of these 2 approaches for lung cancer.<br><br>METHODS: This retrospective study used data from the Diagnostic Procedure Combination database in Japan. We included 47&#xa0;541 patients who underwent lobectomy or segmentectomy for lung cancer from 2018 to 2021 and performed multivariable analyses.<br><br>RESULTS: Among 47&#xa0;541 patients, 2835 underwent robotic-assisted thoracoscopic surgery. Perioperative mortality did not differ significantly between groups (incidence rate ratio, 1.71; 95% CI, 0.88-3.33). Robotic-assisted surgery was associated with longer anaesthesia time and a higher incidence of mechanical ventilation postoperatively (incidence rate ratio, 1.96; 95% CI, 1.36-2.81), although the absolute difference was small (Marginal risk difference, +0.52 percentage points; 95% CI, +0.14 to +0.91). No significant differences were observed in other major complications, reoperation, or hospital stay.<br><br>CONCLUSIONS: In this large, real-world Japanese cohort including the early experience with robotic surgery, overall perioperative safety was comparable between robotic-assisted and video-assisted thoracoscopic surgery, although a statistically significant but small absolute increase in postoperative ventilation was observed with the robotic approach. This association remained robust across a series of sensitivity analyses. However, it is likely influenced by unmeasured confounding. Future prospective studies should investigate specific procedural factors, including anaesthetic management and patient selection, to optimize outcomes.},
}
@article {pmid41512299,
year = {2026},
author = {Beavan, AJS and Domingo-Sananes, MR and McInerney, JO},
title = {PanForest: predicting genes in genomes using random forests.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {1},
pages = {},
pmid = {41512299},
issn = {1367-4811},
support = {108290//Leverhulme Trust Research Fellowship/ ; },
mesh = {*Software ; Random Forest ; *Genomics/methods ; Escherichia coli/genetics ; *Genome, Bacterial ; *Computational Biology/methods ; Prediction Algorithms ; },
abstract = {MOTIVATION: The presence or absence of some genes in a genome can influence whether other genes are likely to be present or absent. Understanding these gene co-occurrence and avoidance patterns reveals fundamental principles of genome organization, with applications ranging from evolutionary reconstruction to rational design of synthetic genomes.<br><br>RESULTS: PanForest, presented here, uses random forest classifiers to predict the presence and absence of genes in genomes from the set of other genes present. Performance statistics output by PanForest reveal how predictable each gene's presence or absence is, based on the presence or absence of other genes in the genome. Further, PanForest produces statistics indicating the importance of each gene in predicting the presence or absence of each other gene. The PanForest software can run serially or in parallel, thereby facilitating the analysis of pangenomes at Network of Life scale.A pangenome of 12&#xa0;741 accessory genes in 1000 Escherichia coli genomes was analysed in around 5&#x2009;h using eight processors. To demonstrate PanForest's utility, we present a case study and show that certain genes associated with resistance to antimicrobial drugs reliably predict the presence or absence of other genes associated with resistance to the same drug. Further, we highlight several associations between those genes and others not known to be associated with antimicrobial resistance (AMR), or associated with resistance to other drugs. We envisage PanForest's use in studies from multiple disciplines concerning the dynamics of gene distributions in pangenomes ranging from biomedical science and synthetic biology to molecular ecology.<br><br>The software if freely available with a full manual and can be found with at www.github.com/alanbeavan/PanForest DOI: https://doi.org/10.5281/zenodo.17865482.},
}
@article {pmid41513569,
year = {2026},
author = {Narita, M and Matsugaki, R and Muramatsu, K and Fushimi, K and Matsuda, S},
title = {Corrigendum to "Obesity and risk of post-operative pneumonia among older adult patients with hip fracture: An obesity paradox" [Clin Nutr ESPEN 68 (2025) 342-347].},
journal = {Clinical nutrition ESPEN},
volume = {72},
number = {},
pages = {102904},
doi = {10.1016/j.clnesp.2025.102904},
pmid = {41513569},
issn = {2405-4577},
}
@article {pmid41513661,
year = {2026},
author = {Meyer, AR and Tan, JP and Mihaila, MP and Neugebauer, M and Nyström, L and Bokulich, NA},
title = {Shipped and shifted: modeling collection-induced bias in microbiome multi-omics using a tractable fermentation system.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {43},
pmid = {41513661},
issn = {2055-5008},
support = {101060247//HORIZON EUROPE European Research Council/ ; 22.00210//Swiss State Secretariat for Education, Research and Innovation (SERI)/ ; },
mesh = {Multiomics ; Fermentation ; *Microbiota ; Temperature ; Metabolome ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fungi/classification/genetics/metabolism ; *Specimen Handling/methods ; Metabolomics/methods ; },
abstract = {Large-scale, decentralized microbiome sampling surveys and citizen science initiatives often require periods of storage at ambient temperature, potentially altering sample composition during collection and transport. We developed a generalizable framework to quantify and model these biases using sourdough as a tractable fermentation system, with samples subjected to controlled storage conditions (4 °C, 17 °C, 30 °C, regularly sampled up to 28 days). Machine-learning models paired with multi-omics profiling-including microbiome, targeted and untargeted metabolome profiling, and cultivation-revealed temperature-dependent shifts in bacterial community structure and metabolic profiles, while fungal communities remained stable. Storage induced ecological restructuring, marked by reduced network modularity and increased centrality of dominant taxa at higher temperatures. Notably, storage duration and temperature were strongly encoded in the multi-omics data, with temperature exerting a more pronounced influence than time. 24 of the top 25 predictors of storage condition were metabolites, underscoring functional layers as both sensitive to and informative of environmental exposure. These findings demonstrate that even short-term ambient storage (<2 days) can substantially reshape microbiome, metabolome, and biochemical profiles, posing risks to data comparability in decentralized studies and emphasizing the need to recognize and address such biases. Critically, the high predictability of storage history offers a path toward bias detection and correction- particularly when standardized collection protocols are infeasible, as is common in decentralized sampling contexts. Our approach enables robust quantification and modeling of such storage effects across multi-omics datasets, unlocking more accurate interpretation of large-scale microbiome surveys.},
}
@article {pmid41514910,
year = {2025},
author = {Abdullah, NI and Elias, N' and Ohte, N and Vincenot, CE},
title = {Bat Community Response to Insect Abundance in Relation to Rice Phenology in Peninsular Malaysia.},
journal = {Biology},
volume = {15},
number = {1},
pages = {},
pmid = {41514910},
issn = {2079-7737},
support = {SS2011//Bat Conservation International/ ; ABDUMALA1220-00//Idea Wild/ ; RG-07012020/02//The Habitat Foundation/ ; },
abstract = {Bats provide essential ecosystem services, particularly in regulating insect populations within agricultural landscapes. However, research on bat-insect interactions in Malaysian rice fields remains limited. This study examined bat diversity and insect abundance in the rice field area of Gunung Keriang, Kedah, using two harp traps, two mist nets and a light trap at three selected sites. A total of 2499 bats representing 27 species were captured, alongside 161,539 insects from 11 orders. Rhinolophus pusillus was the dominant bat species across all seasons. During the dry season, Chilo polychrysus (stem borer) was the dominant insect pest, whereas Nilaparvata lugens (brown planthopper) prevailed during the wet season. Insects from the order Coleoptera, dominant in the dry season, are likely consumed by larger bat species with stronger bite forces. Bat foraging activity peaked concurrently with insect emergence, corresponding to periods of high food availability. Statistical analysis revealed significant associations between bat activity, temperature, and rainfall, but not insect abundance. These findings underscore the ecological importance of bats as natural pest regulators in rice field ecosystems and highlight their potential role in promoting sustainable, ecosystem-based agricultural management.},
}
@article {pmid41515900,
year = {2025},
author = {Wu, J and Zhou, L and Qiu, D and Wei, T and Xie, C and Chen, E and Lin, M and Fan, Y},
title = {Integrating Bioinformatics and Experimental Validation Identifies SCD as a Ferroptosis-Related Immune Regulator and Therapeutic Target in Crohn's Disease.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41515900},
issn = {1422-0067},
support = {2025J011410//the Natural Science Foundation of Fujian Province/ ; 2025J08298//the Natural Science Foundation of Fujian Province/ ; },
mesh = {*Crohn Disease/genetics/immunology/pathology/metabolism ; *Ferroptosis/genetics/immunology ; Humans ; Animals ; *Computational Biology/methods ; Mice ; Gene Expression Profiling ; Gene Expression Regulation ; },
abstract = {This study investigates the role of ferroptosis-related genes (FRGs) in the intestinal inflammation of Crohn's disease (CD). Through integrated bioinformatics and experimental validation, we identified differentially expressed genes from RNA-seq data and intersected them with known FRGs to obtain ferroptosis-related differentially expressed genes (FEDGs). Functional enrichment and immune infiltration analyses were performed, and seven hub FEDGs were selected using machine learning. A diagnostic model based on these genes showed strong predictive ability. Immune analysis revealed significant associations with macrophages, neutrophils, dendritic cells, and CD4+ T cells. Protein expression of key hub genes was validated in clinical CD samples and a DSS-induced colitis model. Importantly, localized inhibition of SCD alleviated disease severity in experimental colitis. These findings highlight the involvement of ferroptosis in CD immune dysregulation and propose SCD as a potential therapeutic target.},
}
@article {pmid41516498,
year = {2025},
author = {Výbošťok, J and Chudá, J and Tomčík, D and Gretsch, D and Tomaštík, J and Pełka, M and Bedkowski, J and Skladan, M and Mokroš, M},
title = {An Open and Novel Low-Cost Terrestrial Laser Scanner Prototype for Forest Monitoring.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {1},
pages = {},
pmid = {41516498},
issn = {1424-8220},
support = {09I03-03-V04-00341.//Recovery and Resilience Plan for Slovakia/ ; VEGA 1/0604/24//Ministry of Education of Slovak Republic/ ; VV-MVP-24-0412//Slovak Research and Development Agency/ ; },
abstract = {Accurate and efficient forest inventory methods are crucial for monitoring forest ecosystems, assessing carbon stocks, and supporting sustainable forest management. Traditional field-based techniques, which rely on manual measurements such as diameter at breast height (DBH) and tree height (TH), remain labour-intensive and time-consuming. In this study, we introduce and validate a fully open-source, low-cost terrestrial laser scanning system (LCA-TLS) built from commercially available components and based on the Livox Avia sensor. With a total cost of €2050, the system responds to recent technological developments that have significantly reduced hardware expenses while retaining high data quality. This trend has created new opportunities for broadening access to high-resolution 3D data in ecological research. The performance of the LCA-TLS was assessed under controlled and field conditions and benchmarked against three reference devices: the RIEGL VZ-1000 terrestrial laser scanner, the Stonex X120GO handheld mobile laser scanner, and the iPhone 15 Pro Max structured-light device. The LCA-TLS achieved high accuracy for estimating DBH (RMSE: 1.50 cm) and TH (RMSE: 0.99 m), outperforming the iPhone and yielding results statistically comparable to the Stonex X120GO (DBH RMSE: 1.32 cm; p > 0.05), despite the latter being roughly ten times more expensive. While the RIEGL system produced the most accurate measurements, its cost exceeded that of the LCA-TLS by a factor of about 30. The hardware design, control software, and processing workflow of the LCA-TLS are fully open-source, allowing users worldwide to build, modify, and apply the system with minimal resources. The proposed solution thus represents a practical, cost-effective, and accessible alternative for 3D forest inventory and LiDAR-based ecosystem monitoring.},
}
@article {pmid41518802,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG},
title = {Multi-omics assessment of synthetic microbiome-mediated remediation of cyclotetramethylene tetranitroamine (HMX) contaminated water.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141026},
doi = {10.1016/j.jhazmat.2026.141026},
pmid = {41518802},
issn = {1873-3336},
mesh = {*Water Pollutants, Chemical/metabolism ; *Microbiota ; Biodegradation, Environmental ; Multiomics ; Bacteria/metabolism ; *Aniline Compounds/metabolism ; Triazines ; },
abstract = {Cyclotetramethylene tetranitroamine (HMX) is a typical high-energy nitramine pollutant with an environmental persistence and toxic effects that pose serious ecological risks. In this study, a synthetic microbiome with complementary functions is built that enables the integration of multigroup technology to conduct a systematic analysis of the mechanism of remediation of HMX-contaminated water bodies. Four core bacterial strains (Bacillus altitudinis, B. cereus, B. subtilis, and Pseudomonas stutzeri) were directionally domesticated and screened from HMX-contaminated water. Through functional verification, they were confirmed to express key enzymes NfsA, YdhA, FdhA, and NirS, respectively, to form a complete HMX deep degradation-level connection path. The synthetic microbiome achieved 100 % removal of HMX and its intermediates within 60 days, and isotope tracing (δ[15]N enrichment +2.7 ‰) confirmed its complete mineralization ability. Multiomic analysis showed that the restoration process is accompanied by a systematic reshaping of the water microecology and chemical environment, so that the microbial community structure is optimized and the synthetic microbiome is successfully colonized and becomes the core node. Meanwhile, the energy metabolic network (glycolysis, TCA cycle, oxidative phosphorylation) is significantly enhanced; metagenomic data also revealed reduced viral abundance. Ionomics revealed that key nutrient elements, such as P and S, are efficiently assimilated and utilized. These findings identify an efficient HMX bioremediation strategy that utilizes the multiple dimensions of "community structure-metabolic function-environmental effects" through a multigroup integration framework. More importantly, this study provides a theoretical basis and practical paradigm for the rational design of functional microbial communities.},
}
@article {pmid41520592,
year = {2026},
author = {Chen, H and Liu, Y and Wang, G and Fan, W and Rong, G and Wang, H},
title = {Multi-omics and stable isotopic reveal coordinated carbon-nitrogen metabolic reprogramming sustaining diatom cellular homeostasis under CO2 limitation.},
journal = {Marine environmental research},
volume = {215},
number = {},
pages = {107843},
doi = {10.1016/j.marenvres.2026.107843},
pmid = {41520592},
issn = {1879-0291},
mesh = {*Diatoms/physiology/metabolism ; *Carbon Dioxide/metabolism ; *Nitrogen/metabolism ; *Carbon/metabolism ; Multiomics ; Homeostasis ; Metabolic Reprogramming ; Metabolomics ; Eutrophication ; Carbon Isotopes ; },
abstract = {Algal blooms frequently trigger CO2 limitation, under which diatoms not only survive but dominate. However, the cellular metabolic adaptations underlying this ecological phenomenon remain poorly understood. This study systematically investigated the coordinated carbon-nitrogen metabolic response of the typical diatom Skeletonema costatum (S. costatum) to CO2 limitation (300 ppm, 100 ppm) via stable isotope and multi-omics analysis. CO2 limitation triggered the carbon concentrating mechanism (CCM) and attenuated nitrogen isotope fractionation, redirecting carbon flux towards amino acid biosynthesis rather than fatty acid biopathway. Integrated transcriptomic and metabolomic profiling revealed that carbon fixation and the tricarboxylic acid (TCA) cycle were activated, while fatty acid synthesis was inhibited. This redirected carbon skeletons from acetyl-CoA into the TCA cycle to support amino acid production. Concurrent upregulation of nitrogen assimilation genes, particularly those involved in glutamine/glutamate synthesis, facilitated ammonium incorporation. The alanine-aspartate-glutamate pathway served as a central hub, integrating carbon skeletons and amino groups to drive amino acid synthesis and maintain cellular homeostasis. These findings systematically delineate the metabolic reprogramming that enables diatoms to adapt to CO2 limitation, providing key insights into their dominance during algal blooms.},
}
@article {pmid41523158,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Light Arches, Apamea lithoxylaea (Denis &amp; Schiffermüller), 1775 (Lepidoptera: Noctuidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {508},
pmid = {41523158},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Apamea lithoxylaea (Light Arches; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 577.73 megabases and 521.26 megabases. Most of haplotype 1 (98.15%) is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.43 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 {pmid41525251,
year = {2026},
author = {Palenova, E and Veraverbeke, S and Drobyshev, I and Kontos, T and Ebert, K},
title = {Prioritizing areas for post-fire restoration in Greece using mixed-methods spatial analysis.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0339998},
pmid = {41525251},
issn = {1932-6203},
mesh = {Greece ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Spatial Analysis ; *Wildfires/prevention &amp; control ; Ecosystem ; Climate Change ; *Fires ; },
abstract = {The Mediterranean region will likely face an increase in the frequency and intensity of wildfires due to climate change. Despite being fire-prone, Greece lacks a developed standardized system for identifying and prioritizing burned areas in relation to their restoration needs. Prioritization of areas for post-fire restoration efforts using Geographic Information System and Remote Sensing is a powerful decision-making tool, which, however, can be insufficient in effectively integrating socio-ecological criteria and perspectives from multiple stakeholders. Combining qualitative methods such as interviews with remotely sensed data can enhance the understanding of nuances in a local context. We designed an approach to identify high-priority areas for post-fire vegetation restoration. The identification was based on stakeholder interviews and the subsequent integration of their responses with subsequent multi-criteria overlay analysis. We selected criteria to rank the areas by interviewing 15 stakeholders working on post-fire issues. The expert interviews revealed the key characteristics respondents consider essential for prioritizing burned areas for restoration. Areas covering 77.25 km[2] were selected for restoration depending on the fire history, slope, and designation as part of the protected areas. Outcomes of the analysis helped to highlight three locations that potentially need special attention, with the total area of 31 km[2]. We propose a prioritization system that is flexible, scalable, and can help government agencies, local foresters, private consultancies, and NGOs plan restoration actions and optimize the effectiveness of restoration programs in various ecosystems.},
}
@article {pmid41525285,
year = {2026},
author = {Ramirez-Gil, JG and López-Hernández, F and Conejo-Rodriguez, DF and Henao-Rojas, JC and Quiroga-Benavides, KE and Cortés, AJ and Chacón-Sánchez, MI},
title = {GermVersity: A free and user-friendly interface to enhance the visualization and analysis of genebank data.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0340826},
pmid = {41525285},
issn = {1932-6203},
mesh = {*User-Computer Interface ; Genetic Variation ; Polymorphism, Single Nucleotide ; *Databases, Genetic ; *Software ; *Seed Bank ; Phenotype ; Fabaceae/genetics ; },
abstract = {Genebanks are crucial for food security and industrial applications. However, their heterogeneous nature hinders effective utilization. To address this, the GermVersity platform was developed to integrate conventional, artificial intelligence, and data science approaches to the transversal analysis of data associated with genebank accessions. GermVersity aids in the classification and prioritization of germplasm diversity, facilitating the conservation and utilization of valuable genetic resources in agriculture. The GermVersity proposal is focused on developing a user-friendly application to visualize, analyze and interpret analysis-ready data from genebanks. The application's case study uses data from the bean genebank at Bioversity International - CIAT but can be adapted for other genebanks and broader collections. GermVersity is divided into three modules. The first module analyzes genetic diversity using phenotypic and SNP data. In this module users can prioritize morphological descriptors for efficient classification of accessions, define genetic clusters or populations, calculate basic diversity statistics per locus and per population, and estimate genetic divergence among clusters or populations. The second module implements spatial distribution modeling, allowing users to understand ecological diversity across the geographical distribution range of a set of accessions. The third module characterizes the genomic architecture of phenotypic trait variation and adaptation to ecological niches using genome-wide association implemented in prediction integrated tools (GAPIT) and Latent Factor Mixed Model (LFMM) analysis. The GermVersity platform was built using Shiny-Golem and is hosted on GitHub for free use. To access it, users can install the library and run the application through specific commands in R. Responsible use of algorithms is recommended, along with the inspection of results for biological coherence. Ultimately, GermVersity offers an integrated analytical pipeline to leverage genebank diversity as part of pre-breeding efforts.},
}
@article {pmid41525703,
year = {2026},
author = {Astill Wright, L and Roe, J and Guo, B and Morriss, R},
title = {Dropout, Attrition, Adherence, and Compliance in Mood Monitoring and Ambulatory Assessment Studies for Depression and Bipolar Disorder: Systematic Review and Meta-Analysis.},
journal = {JMIR mental health},
volume = {13},
number = {},
pages = {e83765},
pmid = {41525703},
issn = {2368-7959},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Affect ; *Bipolar Disorder/diagnosis ; *Depressive Disorder/diagnosis ; *Monitoring, Ambulatory/statistics &amp; numerical data ; *Patient Compliance/statistics &amp; numerical data ; *Patient Dropouts/statistics &amp; numerical data ; },
abstract = {BACKGROUND: Ambulatory assessment and mood monitoring are different methods that can use novel technology to deliver a more efficient, flexible, and usable method of clinical outcome assessment compared with established measures of behavior and mood. Concerns have been raised around attrition in and adherence to these new protocols, particularly over the medium to long term by people with mood disorders.<br><br>OBJECTIVE: This systematic review and meta-analysis assessed attrition from and adherence to active and passive ambulatory assessment and mood monitoring protocols by people with bipolar disorder and depression over the medium and long term.<br><br>METHODS: Randomized controlled trials and nonrandomized studies were identified and rated for risk of bias. Adherence and attrition data were pooled to calculate effect sizes. We analyzed specific factors that we hypothesized a priori could affect the prevalences of attrition and adherence by means of subgroup meta-analysis or metaregression modeling.<br><br>RESULTS: We evaluated 77 mood tracking or ambulatory assessment studies including 17,123 participants. Pooled adherence was 0.64% (95% CI 0.59%-0.70%; P<.001), and pooled attrition was 0.28% (95% CI 0.22%-0.34%; P<.001). Three factors had a statistically significant subgroup difference for adherence: The presence of financial incentives increased adherence, and the presence of mood monitoring reminders and a higher study risk of bias decreased adherence. Four factors had a statistically significant subgroup difference for attrition: Digital mood monitoring decreased attrition versus analogue studies, but mood monitoring reminders, mood monitoring versus other protocols, and a high risk of study bias increased attrition. These analyses, however, were vulnerable to confounding by study design and protocol design. Attrition rates were not reported by 17 studies (17/77, 22%), and 20 studies (20/77, 26%) did not report adherence rates. Most studies had a low-to-moderate risk of bias, but heterogeneity was very high. Only 16 studies reported adherence systematically.<br><br>CONCLUSIONS: Reporting of attrition and adherence to ambulatory assessments was not systematic nor universal, and until it is, analyses are unlikely to demonstrate clear conclusions. We found very high heterogeneity and evidence of publication bias, and this limited the certainty of our conclusions. Financial incentives may increase adherence, and attrition may be lower in digital than analogue studies of mood monitoring. There was no statistically significant difference in adherence and attrition between studies of passive and active ambulatory assessments. Reminders of mood monitoring increased attrition and decreased adherence, but the results may be confounded by longer length of follow-up versus other studies.},
}
@article {pmid41529073,
year = {2026},
author = {Vessman, B and Guridi-Fernández, P and Arias-Sánchez, FI and Mitri, S},
title = {Novel artificial selection method improves function of simulated microbial communities.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013863},
pmid = {41529073},
issn = {1553-7358},
mesh = {Computer Simulation ; *Models, Biological ; *Selection, Genetic ; Computational Biology ; *Microbiota/physiology/genetics ; },
abstract = {There is increasing interest in artificially selecting or breeding microbial communities, but experiments have reported modest success. Here, we develop computational models to simulate two previously known selection methods and compare them to a new "disassembly" method. We evaluate all three methods in their ability to find a community that could efficiently degrade toxins, whereby investment into degradation results in slower growth. Our disassembly method relies on repeatedly competing different communities of known species combinations against one another, while regularly shuffling around their species combinations. This approach allows many species combinations to be explored, thereby maintaining enough between-community diversity for selection to act on, and resulting in communities with high performance. Nevertheless, selection at the community level in our simulations did not counteract selection at the individual level, nor the communities' ecological dynamics. Species in our model evolved to invest less into community function and more into growth, but increased growth compensated for reduced investment, such that overall community performance was barely affected by within-species evolution. Within-community ecological dynamics were more of a challenge, as we could control them during the selection process, but community composition and function dropped in the longer term. Our work shows that the strength of disassembly lies mainly in its ability to explore different species combinations, and helps to propose alternative designs for community selection experiments.},
}
@article {pmid41531076,
year = {2026},
author = {Liu, PD and Huang, L and Meng, F and Zhao, HH and Liu, JT},
title = {[Multi-scenario Prediction and Ecological Security Pattern Construction Based on InVEST-PLUS Model: A Case Study of Liaoning Province].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {1},
pages = {467-480},
doi = {10.13227/j.hjkx.202412160},
pmid = {41531076},
issn = {0250-3301},
abstract = {Taking policy factors into account in constructing an ecological security pattern is of great significance in helping to realize the ecological civilization strategy. Taking Liaoning Province as an example， the study adopts a research framework of "core-regional-strip-multi-point" based on five land use data sets from 2000 to 2020 and couples the InVEST-PLUS model to predict the land use and carbon storage in the SN， SW， CLD， and SE scenarios for the year 2030. The study then combines the MSPA and MCR models to construct an ecological security pattern and proposes new ideas for ecological construction. The results showed that： ① The land use prediction results indicated that land use was mainly composed of farmland and forests. The farmland area decreased slowly， and the forest area increased continuously from 2000 to 2030. ② The spatial distribution of carbon storage was mainly in the east， and the eastern region was a key protected forest area. The trend of carbon storage in the eastern region was relatively stable， while the carbon storage in the western region continued to increase. ③ The ecological security network structure in the SE scenario was complex and highly connected， identifying 30 ecological source areas， 97 discontinuities， 56 ecological corridors with a total length of 211 km， and a northeastern-southeastern strip-shaped extension pattern with dense networks in the middle and western regions and sparse networks in the eastern coastal areas. ④ Comparing the structure and connectivity of the ecological security network in different scenarios， the study selected the SE scenario and proposed the "one core， three regions， three belts， and multiple points" ecological security pattern construction strategy. It also proposed ecological management policy recommendations to promote sustainable development in Liaoning Province.},
}
@article {pmid41532084,
year = {2026},
author = {Carvalho, PC and Voltolini, GB and Goedert, A and Chiaratti, VKC and Cantarelli, EH and Francisco, JC and Almeida, TB and Burigo, IP},
title = {Hospitalizations due to Alzheimer's disease in Brazil during the COVID-19 pandemic: an update on frequency, mortality, and costs.},
journal = {Dementia &amp; neuropsychologia},
volume = {20},
number = {},
pages = {e20250322},
pmid = {41532084},
issn = {1980-5764},
abstract = {UNLABELLED: Hospitalizations related to Alzheimer's disease (AD) impose a growing burden on health systems, but recent, nationally representative estimates for Brazil are limited.<br><br>OBJECTIVE: To describe the epidemiological profile of hospital admissions due to AD in Brazil from 2018 to 2024.<br><br>METHODS: Ecological time-series study using the Hospital Information System of the Brazilian Unified Health System (SIH/SUS), accessed via the Department of Informatics of the SUS (DATASUS). We included all regions and states from January 2018 to December 2024. Admissions were identified by the International Classification of Diseases, 10[th] Revision (ICD-10) codes G30.0-G30.9 and F00.0-F00.9. Variables comprised sex, age group, race/color, admission type (urgent/elective), in-hospital mortality, length of stay, and hospital costs. Temporal trends were evaluated with linear regression.<br><br>RESULTS: From 2018 to 2024, 11,212 AD-related hospitalizations were recorded; 79.4% were urgent. The Southeast had the highest absolute number (47.8%), followed by the South (25.1%), Northeast (17.2%), Midwest (6.5%), and North (3.4%). Females accounted for 65% of admissions and 64.7% of in-hospital deaths. Older adults, especially those &#x2265;80 years, represented most hospitalizations (59.3%) and deaths (69.7%). Total hospital expenditures exceeded R$ 14 million, with the Southeast concentrating >60% of national costs. No significant linear trend was detected in annual rates.<br><br>CONCLUSION: Urgent admissions comprised the majority of AD hospitalizations nationwide, with the Southeast presenting the highest numbers. The predominance of older female patients and high in-hospital mortality underscore the need for targeted clinical and public health strategies. Rising expenditures reinforce investment in health infrastructure and long-term dementia-care policies in Brazil.},
}
@article {pmid41534287,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG},
title = {Multi-omic analysis reveals the microecological mechanism of organic arsenic toxicity in a Japanese abandoned chemical weapons site and targeted bioremediation strategies.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141101},
doi = {10.1016/j.jhazmat.2026.141101},
pmid = {41534287},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; *Arsenicals/metabolism ; Multiomics ; Bacillus subtilis/metabolism/genetics/drug effects ; *Water Pollutants, Chemical/toxicity/metabolism ; Japan ; Hazardous Waste Sites ; *Chemical Warfare Agents/toxicity/metabolism ; },
abstract = {Diphenylarsonic acid (DPAA) and phenylarsonic acid (PAA), persistent degradation products of Japanese abandoned chemical weapons (JACWs), threaten aquatic ecosystems. However, their microecological toxicity mechanisms and effective remediation strategies remain poorly understood. Here, we constructed 60-day freshwater microcosms to systematically reveal the toxic effects of DPAA and PAA using integrated multi-omics. We found that both pollutants exhibited extreme persistence (> 98 % residue) and triggered a microbial energy crisis by specifically disrupting the oxidative phosphorylation pathway, with up to 46 genes in the NADH dehydrogenase complex significantly downregulated. Multi-omics integration identified cysteine and methionine metabolism as the central hub of metabolic network disturbance, impairing sulfur cycling and methyl donor supply. Furthermore, pollutant stress activated the viral community and increased antibiotic resistance gene abundance, revealing latent ecological risks. Crucially, guided by these mechanistic insights, we successfully screened a Bacillus subtilis strain from the stressed environment and immobilized it on bamboo biochar to create a novel composite remediation agent. This agent achieved complete mineralization of DPAA and PAA within 5 days, a process associated with the significant upregulation of nine key dioxygenases. Our study not only deciphers the microecological toxicity mechanisms of JACW-related organic arsenicals but also demonstrates a mechanism-informed strategy for developing effective in situ bioremediation.},
}
@article {pmid41535740,
year = {2026},
author = {Ualiyeva, D and Guo, X and Dujsebayeva, T and Chirikova, M and Ananjeva, NB and Kryukov, K and Zeng, X},
title = {Mitochondrial genomic variations shed light on the phylogeny and biogeography of the Phrynocephalus guttatus species group (Reptilia: Agamidae) in arid Central Asia.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {176},
pmid = {41535740},
issn = {1471-2164},
support = {180GJHZ2024036MI//Central Asia Drug Discovery and Development Centre of Chinese Academy of Sciences/ ; 32470466//National Natural Science Foundation of China/ ; BR21882199//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; 125012800908-0//Zoological Institute RAS/ ; },
abstract = {BACKGROUND: The lizard genus Phrynocephalus is an emerging model for studying mitochondrial genome evolution. Within this genus, the P. guttatus species-group represents a taxonomically and ecologically diverse clade whose evolutionary relationships remain poorly resolved. Previous studies based on morphology and partial molecular data have been unable to fully clarify relationships within this rapidly radiated group. Complete mitochondrial genomes provide a solid basement to clarify phylogenetic relationships and assess the role of genomic structural variation in diversification.<br><br>RESULTS: We sequenced and assembled the complete mitochondrial genomes from multiple representatives of the&#xa0;P. guttatus&#xa0;complex across Central Asia and performed comprehensive analyses including annotation, phylogenetic reconstruction, molecular dating, and biogeography assessment. Mitogenomic data resolved phylogenetic relationships with strong support and revealed pronounced structural dynamism, including lineage-specific tRNA duplications and rearrangements. Eastern lineages (P. melanurus 1 and 2, P. kuschakewitschii) differed from western taxa (P. g. kalmykus, P. g. guttatus) in tRNA composition, control region numbers, and rearrangement patterns. Eastern species exhibited duplication of tRNA-Phe and up to three control regions. Novel rearrangement types (F-, G-, and H-types) expand existing mitogenomic classification schemes. Divergence time analyses placed the initial radiation in the Late Miocene &#x2012; Pliocene (~&#x2009;3.13 Mya), with a major eastern diversification between 2.72 and 0.31 Mya, correlating with intense aridification of Central Asia. Ancestral range reconstruction indicated an origin in the Dzungar Basin, followed by dispersal and vicariance events driven by climatic and orographic changes.<br><br>CONCLUSIONS: Our study establishes a robust mitogenome-based phylogenetic framework for the P. guttatus complex and demonstrates that its diversification was shaped by Neogene environmental dynamics and intrinsic mitochondrial genome rearrangements. The discovery of lineage-specific structural changes highlight the evolutionary significance plasticity in desert lizards adaptation.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12529-w.},
}
@article {pmid41538474,
year = {2026},
author = {Chami, AM and Zózimo, TRS and Matosinho, CGR and Silva-Filho, ALD and Carvalho, MRS and Braga, LDC},
title = {Characterization of a novel MSH2 variant in Lynch syndrome: clinical data and complementary bioinformatics assessment.},
journal = {Einstein (Sao Paulo, Brazil)},
volume = {24},
number = {},
pages = {eAO0757},
pmid = {41538474},
issn = {2317-6385},
mesh = {Humans ; *MutS Homolog 2 Protein/genetics ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/pathology ; Female ; Computational Biology ; Middle Aged ; Pedigree ; Germ-Line Mutation/genetics ; Immunohistochemistry ; Phenotype ; Male ; },
abstract = {OBJECTIVE: To describe the clinical characteristics and perform a multi-step bioinformatics evaluation of the pathogenicity of NM_000251.3(MSH2):c.1894_1898del (p.Ile633Lysfs*9), an MSH2 germline variant detected in a family with Lynch syndrome.<br><br>METHODS: Clinical evaluation included description of phenotype, family history, and immunohistochemical characterization of the proband's tumors. For pathogenicity classification according to the American College of Genetics and Genomics/Association for Molecular Pathology (ACMG/APA) criteria, bioinformatics analyses included: (i) literature and database screening, searching for the variant allele frequency, case reports, or functional studies, including ClinVar, VarSome, Ensembl, PubMed, EVA, and ABraOM; (ii) prediction of variant impacts using ExPASy Translate, Pfam, and Modeller 9.24; and, (iii) mechanisms that could mitigate the effects of the variant included alternative splicing and exon skipping (UniProt and GTex) and nonsense-mediated decay (NMD; MutationTaster2021).<br><br>RESULTS: The proband, a 55-year-old female, was diagnosed with two metachronous colorectal cancers. Immunohistochemical analysis showed loss of expression (MSH2 in one tumor, and MSH2 and MSH6 in the other). Seven deceased family members were diagnosed with cancer (four colorectal, one uterine, and two unspecified). This variant caused a stop codon in MSH2 exon 12 of 16. When translated, the protein loses 294 C-terminal residues, which may prompt protein degradation. If the mutated protein escapes degradation, dimerization and DNA-binding domains will be present. Therefore, negative dominance effects were possible. No isoforms ending in exon 12 have been identified in the literature or in RNA splicing databases. A stop codon before the last exon-exon boundary indicated the occurrence of NMD.<br><br>CONCLUSION: No evidence of protein-rescuing mechanisms was found, supporting the classification of this variant as likely pathogenic/pathogenic.},
}
@article {pmid41538792,
year = {2026},
author = {Kurilla, A and Čavojská, N and Ikegwuonu, T and Nemčíková, M and Schulte-Strathaus, JC and Uyttebroek, L and Beames, JR and Breznoščáková, D and Dančík, D and Hajdúk, M and Heretik, A and Izáková, &#x13d; and Katreniaková, Z and Myin-Germeys, I and Pečeňák, J and Reininghaus, U and Schick, A and Wolters, M},
title = {Preferences for an Experience Sampling Method-Based Tool as an Adjunct to Usual Treatment in Patients With Problem Substance Use: Qualitative Study.},
journal = {JMIR formative research},
volume = {10},
number = {},
pages = {e79510},
pmid = {41538792},
issn = {2561-326X},
mesh = {Humans ; Female ; Male ; *Substance-Related Disorders/therapy/psychology ; Adult ; Qualitative Research ; Middle Aged ; Adolescent ; *Patient Preference/psychology ; Young Adult ; Europe ; *Ecological Momentary Assessment ; },
abstract = {BACKGROUND: Mobile health tools that use the Experience Sampling Method (ESM) appear to be a promising tool to streamline and improve the treatment of substance use disorders. However, patient involvement in the development of these tools is uncommon, and research on the preferences of people being treated for substance use disorders has been scarce. In the scope of the European Union IMMERSE (Implementing Mobile Mental health Recording Strategy for Europe) consortium, an ESM-based tool for Digital Mobile Mental Health (DMMH) was first codeveloped and later tested in 4 European countries.<br><br>OBJECTIVE: This study aimed to achieve an understanding of preferences for features of DMMH among mental health service users with problem substance use.<br><br>METHODS: In 4 European countries, service users were recruited for a semistructured&#xa0;qualitative interview, which started with the presentation of a prototype of the DMMH. Data analysis was performed through directed qualitative content analysis.<br><br>RESULTS: The analytical sample consisted of 12 (5 female, 6 male, and 1 nonbinary person) participants with problem substance use aged 18-50 years. There were 4 participants from Slovakia, 3 from Belgium, 4 from Germany, and 1 from Scotland. Patient preferences were classified into 7 categories: notifications, questions, user interface, functionality changes, visualizations, sharing data with clinicians, and sharing data with others. The proposed intensive notification schedule was deemed acceptable by service users as long as the questionnaire is short. Participants expressed a preference for open-text response options, Ecological Momentary Interventions, and options for individual customization of several elements of the tool. Data visualization was considered an important aid for communication with clinicians, with whom all participants wanted to share data obtained with DMMH. The possibility of sharing data with other people depended on the quality of the relationship with them.<br><br>CONCLUSIONS: In the development of ESM-based mobile health tools for people with problem substance use, their preferences for content, functionality, and appearance of the tools should be considered so they match patients' treatment needs.},
}
@article {pmid41539503,
year = {2026},
author = {Li, S and Liu, J and Li, J and Han, M and Zhang, X and Wu, Z and Hu, S and Jin, H and Hua, K and Tu, K},
title = {Eco-friendly chitosan-based hydrogel for coal dust suppression via salting-out effect.},
journal = {International journal of biological macromolecules},
volume = {341},
number = {Pt 1},
pages = {150171},
doi = {10.1016/j.ijbiomac.2026.150171},
pmid = {41539503},
issn = {1879-0003},
mesh = {*Chitosan/chemistry ; *Coal ; *Dust/prevention &amp; control ; *Hydrogels/chemistry ; Coal Mining ; Adsorption ; Hydrogen-Ion Concentration ; },
abstract = {Coal mining-related dust pollution poses significant threats to ecological integrity, occupational health, and industrial sustainability. Conventional dust suppressants, however, suffer from inherent limitations such as inadequate capture efficiency, poor water retention, and a tendency to cause secondary pollution. To overcome these challenges, this study developed a novel bio-based chitosan hydrogel dust suppressant using highly deacetylated chitosan and sodium citrate via an innovative salting-out method. By acting as both a salting-out agent and a pH regulator, sodium citrate enhances the binding affinity with coal dust to improve suppression performance. Its dust suppression primarily occurs through synergistic mechanisms including electrostatic adsorption, moisture retention/locking, and physical coverage. After 72 h, the hydrogel dust suppressant maintained a water retention rate close to 75%. Its wind erosion resistance rate remained at approximately 99% within 3-7 days, and its degradation rate reached about 96% within 25 days. Notably, compared to conventional materials, this formulation exhibits excellent biodegradability, with its carbon-containing degradation products providing nutrients for plant growth. This green multifunctional system avoids complex preparation processes, integrating high-efficiency dust suppression, environmental safety, and ecological compatibility. It demonstrates significant application potential in sustainable mining practices.},
}
@article {pmid41539810,
year = {2026},
author = {Liu, Y and Guo, Y and Mu, H and Aaqil, M and Zhang, F and Zheng, J and Sheng, J and Tian, Y and Zhao, C},
title = {Microbial succession-potential influence mechanism on flavor modulation in spontaneously fermented Moringa oleifera leaves: An integrative multi-omics approach.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118184},
doi = {10.1016/j.foodres.2025.118184},
pmid = {41539810},
issn = {1873-7145},
mesh = {*Moringa oleifera/microbiology/chemistry ; *Fermentation ; Gas Chromatography-Mass Spectrometry ; *Plant Leaves/microbiology/chemistry ; *Taste ; Odorants/analysis ; Multiomics ; Amino Acids/analysis ; Volatile Organic Compounds/analysis ; *Food Microbiology ; *Microbiota ; *Bacteria/metabolism/classification ; *Fermented Foods/microbiology ; Food, Processed ; },
abstract = {In this study, the relationship between flavor composition and microbial succession in Moringa oleifera pickles (MOPs) at different stages of spontaneous fermentation was systematically investigated. The results demonstrated a significant increase in the content of organic acids and amino acids during fermentation including malonic acid, citric acid, valine (Val), and asparagine (Asn). These compounds not only enhanced the overall flavor profile but also provided favorable nutritional conditions that supported microbial succession. Furthermore, an integrated aroma network was established through the combined application of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-MS identified key aroma-active compounds such as ethyl caproate (fruity note), 3-hexenal (green, grassy note), and 2-phenylethanol (floral, rosy note). Complementarily, GC-IMS confirmed that esters, alcohols, and terpenes were the major contributors to fruit-like, mushroom-like, and fresh herbal aromas, indicating their critical role as flavor-modulating compounds throughout fermentation. Metagenomic analysis revealed Corynebacterium, Escherichia, Pseudomonas, Xanthomonas, and Pantoea as the dominant microbial genera involved in fermentation. These microbes primarily participated in amino acid, carbohydrate, and nucleotide metabolism and exhibited a close association with the formation of key flavor compounds. The strong influence of microbial succession on flavor evolution is likely driven by the observed correlations between microbial taxa and volatile organic compounds (VOCs). These correlations may stem from a series of complex ecological and metabolic interactions, including substrate competition, niche adaptation, and upstream-downstream dependencies within microbial metabolic networks. This study provides a theoretical foundation for the quality control of MOPs and the mitigation of potential pathogenic microorganisms, thereby supporting its application in enhancing product quality and consumer sensory satisfaction in the pickle industry.},
}
@article {pmid41545385,
year = {2026},
author = {Verbiest, WWM and Hicter, P and Beeckman, H and Wallenus, D and Ilondea, BA and Bastin, JF and Bauters, M and Chave, J and De Blaere, R and de Hauleville, T and De Mil, T and de Ridder, M and De Troyer, C and Ewango, CEN and Fayolle, A and Gorel, A and Fischer, FJ and Kaçamak, B and Kimbuluma, C and Luambua, NK and Laurent, F and Liévens, K and Makana, JR and Malaisse, F and Wasukundi, M and Monnoye, M and Ngomanda, A and Ambounda, FRO and Toirambe, B and Otepa, C and Van Acker, J and Van den Abbeele, B and Van den Bulcke, J and Van Houtte Alonso, B and Wankana, T and Djiofack, BY and Hubau, W},
title = {The Tervuren xylarium Wood Density Database (TWDD).},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {243},
pmid = {41545385},
issn = {2052-4463},
support = {EOS O.0026.22//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; EOS O.0026.22//Fonds De La Recherche Scientifique - FNRS (Belgian National Fund for Scientific Research)/ ; PilotMAB//Belgisch Ontwikkelingsagentschap (Belgian Development Agency)/ ; },
mesh = {*Wood ; Forests ; *Databases, Factual ; Biomass ; Africa ; Trees ; },
abstract = {Wood density is a key plant property, indispensable for estimating forest biomass. Yet, despite tropical regions' substantial contributions to global tree diversity and carbon cycling, they remain underrepresented in wood density datasets such as the CIRAD and Global Wood Density Database (GWDD). To address this gap, we present the 'Tervuren xylarium Wood Density Database' (TWDD), containing 13,332 samples from 2,994 species, 1,022 genera, and 156 plant families across six continents (72% from Africa). TWDD offers direct measurements of oven-dry (oven-dry mass/oven-dry volume, all samples), air-dry (air-dry mass/air-dry volume, 6,408 samples), green (green mass/green volume, 1,657 samples), and basic wood density (oven-dry mass/green volume, 1,686 samples). Basic density was estimated for the remaining 11,646 samples via conversion from oven-dry density. TWDD closes a substantial wood density data gap, especially in Africa, adding 1,164 new species, 160 new genera, and 8 new plant families not included in GWDD or CIRAD datasets. The TWDD provides a critical resource for advancing research on forest community dynamics, ecosystem functioning, carbon cycling, and trait-based ecology worldwide.},
}
@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.},
}
@article {pmid41547987,
year = {2026},
author = {Ding, S and Zhou, F and Yang, S and Li, Y and Ma, Y and Qiu, Y},
title = {Chromosome-level genome assembly of a Chinese evergreen sweetgum (Liquidambar gracilipes, Altingiaceae).},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {66},
pmid = {41547987},
issn = {2052-4463},
support = {32300202//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {China ; *Chromosomes, Plant ; *Genome, Plant ; Molecular Sequence Annotation ; Datasets as Topic ; },
abstract = {Liquidambar gracilipes, an evergreen species endemic to China and a member of the Altingiaceae family, is morphologically distinguished by its unlobed leaves and represents an ecologically and economically valuable resource. Prized for its ornamental beauty, valuable timber, and medicinal properties, this species is a key component of subtropical evergreen broad-leaved forests in East China. To improve our understanding of its evolutionary and functional genomics, we performed a de novo genome assembly of L. gracilipes by integrating PacBio HiFi long reads, Illumina short reads, and Hi-C data. A high-quality chromosome-level genome assembly was obtained with a genome size of approximately 715.54 Mb and contig N50 of 18.61 Mb, of which 96.87% was anchored to 16 pseudo-chromosomes with a scaffold N50 of 42.40 Mb. Genome annotation identified 24,809 protein-coding genes (97.02% functionally annotated) and revealed a repetitive sequence content of 59.72%. BUSCO analysis against the embryophyte dataset indicated a high level of completeness, with a score of 98.70%. The high-quality genome assembly of L. gracilipes provides a valuable genetic resource for molecular breeding of sweetgums and lays the foundation for future in-depth evolutionary and functional genomics studies of this species.},
}
@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 &amp; proteomics},
volume = {58},
number = {},
pages = {101750},
doi = {10.1016/j.cbd.2026.101750},
pmid = {41548390},
issn = {1878-0407},
mesh = {Animals ; *Brachyura/genetics/metabolism/growth &amp; development ; RNA, Competitive Endogenous ; Multiomics ; *Gene Regulatory Networks ; *Body Size/genetics ; Transcriptome ; *Metabolome ; Metabolomics ; },
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.},
}
@article {pmid41548666,
year = {2026},
author = {van Kessel, SAM and Schoffelen, AF and van Son, KHS and Notermans, DW and Severin, JA and Bakhshi-Raiez, F and Velthuis, F and Schipper, M and Dongelmans, D and Verbon, A and Wielders, CCH and , and , },
title = {Water-free care in Dutch intensive care unit patient rooms: impact on Gram-negative bacteria detections in routine patient care.},
journal = {The Journal of hospital infection},
volume = {170},
number = {},
pages = {9-16},
doi = {10.1016/j.jhin.2025.12.013},
pmid = {41548666},
issn = {1532-2939},
mesh = {*Intensive Care Units/statistics &amp; numerical data ; Humans ; Netherlands/epidemiology ; *Gram-Negative Bacteria/isolation &amp; purification/classification ; Retrospective Studies ; *Cross Infection/prevention &amp; control/epidemiology/microbiology ; *Patients' Rooms ; *Gram-Negative Bacterial Infections/epidemiology/prevention &amp; control/microbiology ; Incidence ; },
abstract = {BACKGROUND: Patients in intensive care units (ICUs) are at an increased risk of healthcare-associated infections with Gram-negative bacteria (GNB), for which sinks in patient rooms are known reservoirs. We investigated the association between water-free care practices and the incidence of GNB detections in Dutch ICUs in non-outbreak settings.<br><br>METHODS: We performed a retrospective ecological study (2018-2022) using data from the Infectious diseases Surveillance Information System-Antibiotic Resistance (ISIS-AR), the National Intensive Care Evaluation registry and a questionnaire on water-free care. Detections (colonisation and infections) of seven bacteria groups (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter spp., all Enterobacterales, extended-spectrum beta-lactamase-producing Enterobacterales [ESBL-E] and carbapenemase-producing Enterobacterales) were analysed at ICU-year level. Incidence rate ratios (IRRs) were calculated for water-free vs. non-water-free ICUs, adjusted for ICU and patient characteristics.<br><br>FINDINGS: Data from 37 ICUs were analysed, 22 ICU-years in the water-free group and 131 in the non-water-free group. Water-free ICUs were larger, with more surgery admissions and mechanically ventilated patients. For all bacteria, adjusted IRRs were close to 1 with broad 95% confidence intervals (CIs), ranging from 0.82 (95% CI: 0.44-1.52) for ESBL-E to 1.39 (95% CI: 0.69-2.84) for Acinetobacter spp. Sensitivity analyses showed similar results.<br><br>CONCLUSION: Although positive effects of water-free care on GNB detection rates have been described in single ICUs, these findings were not reflected in this Dutch multi-centre study. Possible explanations are low infection prevalence, high prevention standards, widespread usage of selective decontamination and insufficient power to detect small differences. Evidence for benefits of water-free care in non-outbreak settings remains limited, highlighting the importance of future research in different ICU settings.},
}
@article {pmid41550075,
year = {2026},
author = {Patron-Rivero, C and Yañez-Arenas, C and Ruane, S and Chiappa-Carrara, X and Rojas-Soto, OR},
title = {A comprehensive morphological database of hognose Porthidium pitvipers (Viperidae: Crotalinae).},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {41550075},
issn = {1758-0463},
support = {1010703//Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; //Programa de Apoyo a los Estudios de Posgrado/ ; //Secretar&#xed;a de Investigaci&#xf3;n, Innovaci&#xf3;n y Educaci&#xf3;n Superior/ ; },
mesh = {Animals ; *Viperidae/anatomy &amp; histology/classification ; *Databases, Factual ; },
abstract = {Generating and sharing primary biological data is essential to support reproducible research, stimulate new hypotheses, and advance our understanding of biodiversity. Here, we present a comprehensive database of morphological traits for snakes of the genus Porthidium (Viperidae: Crotalinae). This database includes linear measurements, pholidosis (scale counts), and head shape data from preserved specimens across five different herpetological collections. These data comprise 13 morphological traits, 8 scale counts, and 55 landmarks collected from 484 individuals across 9 species. The specimens represent both juvenile and adult stages. All data were collected using standardized protocols to ensure comparability across individuals and species. The dataset is a valuable resource for studies in systematics, morphological evolution, ecological adaptation, and ontogeny, as well as facilitating reproducibility and reuse in the fields of evolutionary biology, herpetology, and comparative morphology.},
}
@article {pmid41550274,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Barred Straw, Gandaritis pyraliata (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {435},
pmid = {41550274},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Gandaritis pyraliata (the Barred Straw; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 295.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.74 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,805 protein coding genes.},
}
@article {pmid41551931,
year = {2026},
author = {Mak, L and Tierney, B and Wei, W and Ronkowski, C and Toscan, RB and Turhan, B and Toomey, M and Andrade-Martínez, JS and Fu, C and Lucaci, AG and Solano, AHB and Setubal, JC and Henriksen, JR and Zimmerman, S and Kopbayeva, M and Noyvert, A and Iwan, Z and Kar, S and Nakazawa, N and Meleshko, D and Horyslavets, D and Kantsypa, V and Frolova, A and Kahles, A and Danko, D and Elhaik, E and Labaj, P and Mangul, S and , and Mason, CE and Hajirasouliha, I},
title = {CAMP: a modular metagenomics analysis system for integrated multistep data exploration.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {1},
pages = {lqaf172},
pmid = {41551931},
issn = {2631-9268},
support = {R01 AI151059/AI/NIAID NIH HHS/United States ; R35 GM138152/GM/NIGMS NIH HHS/United States ; T32 GM083937/GM/NIGMS NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; *Software ; *Computational Biology/methods ; Workflow ; },
abstract = {Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architecture. Each module can run independently or in sequence to produce target data formats (e.g. short-read preprocessing alone or followed by de novo assembly), and provides output summary statistics reports and Jupyter notebook-based visualizations. We applied CAMP to a set of 10 metagenomics samples, demonstrating how a modular analysis system with built-in data visualization facilitates rich seamless communication between outputs from different analytical purposes. The CAMP ecosystem (module template and analysis modules) can be found at https://github.com/Meta-CAMP.},
}
@article {pmid41556837,
year = {2026},
author = {McConnell, RD and Jarrett, C and Ferreira, DF and Powell, LL and Quiñones, ALS and Dominoni, DM and Welch, AJ},
title = {Dietary DNA Metabarcoding From Animal Fecal Samples.},
journal = {Current protocols},
volume = {6},
number = {1},
pages = {e70226},
pmid = {41556837},
issn = {2691-1299},
mesh = {*Feces/chemistry ; Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA/genetics ; *Diet ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; },
abstract = {Fecal DNA metabarcoding is a powerful tool for examining animal diets with unprecedented resolution, offering insights into ecological patterns shaped by trophic interactions. As a result, dietary metabarcoding has become widely applied across ecology, evolution, behavior, and conservation. This article provides a practical guide to the key steps involved in metabarcoding animal fecal samples, from field collection and storage through to laboratory processes, such as DNA extraction, PCR amplification, and sequencing library preparation. It also outlines a bioinformatics workflow using the open-source QIIME2 platform to filter, error-correct, and assign taxonomy to dietary DNA sequences. We present key considerations for study design, highlighting potential caveats and limitations to enable researchers to make informed methodological choices. In addition, we offer guidance on the statistical analysis of diet data, including generalized linear models, multivariate analyses, and network analyses. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Metabarcoding library preparation of animal fecal dietary DNA for Illumina MiSeq sequencing Support Protocol 1: Making a SpeedBeads solution Support Protocol 2: Calibrating the SpeedBeads solution Basic Protocol 2: QIIME2 bioinformatics workflow for metabarcoded dietary DNA.},
}
@article {pmid41557733,
year = {2026},
author = {Smith, C and Kasoar, M and Perkins, O and Millington, JDA and Mistry, J},
title = {Small-scale livelihood and cultural fire: Global spatiotemporal characteristics, and gaps in data.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0339561},
pmid = {41557733},
issn = {1932-6203},
mesh = {Humans ; *Fires ; Ecosystem ; Spatio-Temporal Analysis ; Databases, Factual ; *Conservation of Natural Resources ; Agriculture ; *Wildfires ; },
abstract = {Human fire use is a key activity and process in many landscapes and ecosystems around the world, varying spatiotemporally depending on social, economic, and ecological factors. Recently, initiatives have begun to synthesise data on global fire use from across multiple disciplines and disparate sources into coherent databases. Here, we draw on information from one of these databases, the Livelihood Fire Database, which collates data on fire use practices worldwide from case studies in the literature. We examine data from 345 case study locations spanning 69 countries regarding return interval, area burned, and seasonality of anthropogenic fires set to meet small-scale rural livelihood objectives and/or for cultural reasons. We distinguish patterns in the spatiotemporal nature of fires associated with different fire-use purposes, such as clearing vegetation for agriculture, maintaining pasture for livestock, promoting certain plant species for gathering, or driving game when hunting. For many fire uses, especially those related to hunting, gathering, human wellbeing, and social signalling, there are very limited quantitative data available, but it is possible to draw qualitative insights from case studies. Case studies demonstrate that environmental and social conditions drive variation in fire use for the same purpose, reiterating that assumptions of uniform drivers of anthropogenic fire may be misleading. Nonetheless where quantitative data are available, we find some correspondence between the spatiotemporal nature of fires and fire-use purpose, suggesting that distinguishing between different fire-use purposes may be useful to understand and to better model their likely timing, size, and frequency relative to climate and other drivers. We recommend examples where the diagnosis of these broad relationships between fire-use purpose and fire properties could enable improved representation of anthropogenic fire in global land surface models, and aid interpretation of remote sensing data. Many of the smaller fires now being revealed in global burned area data by new fine-scale remote sensing products are likely human-set; continued collection, collation, and analyses of case study data on human fire use globally will be essential to help interpret this improved detection of small fires, and to ensure appropriate representation of the underlying drivers of human activity when modelling fire regimes.},
}
@article {pmid41559770,
year = {2026},
author = {Novak, M and Foust, P and Hennessey, S and Tanis, BP and Coblentz, KE and Wolf, C and Segui, LM and Henderson, JS and Ingeman, KE and Falke, LP and Layden, TJ and Gradison, DJ and Randell, Z and Harris, CL and Lester, S and Naito, KA and Nakata, T and Nichols, G and Postma, BC and Alves, R and Jarman, CN and Kalytiak-Davis, AR and Martin, A and Pajiah, TJ and Pinos-Sánchez, A and Preston, DL},
title = {FracFeed: Global database of the fraction of feeding predators.},
journal = {Ecology},
volume = {107},
number = {1},
pages = {e70296},
doi = {10.1002/ecy.70296},
pmid = {41559770},
issn = {1939-9170},
support = {DEB-1353827//Division of Environmental Biology/ ; },
mesh = {Animals ; *Predatory Behavior/physiology ; *Databases, Factual ; *Feeding Behavior/physiology ; *Diet ; *Vertebrates/physiology ; *Food Chain ; *Invertebrates/physiology ; Gastrointestinal Contents ; },
abstract = {The proportion of individuals that are found to have empty stomachs during a survey of a predator population's diet has been used as an indicator of the average individual's state of energy balance and of the degree to which its feeding rate (i.e., its functional response) is saturated with respect to prey availability. As such, the proportion of empty stomachs provides insights into the effects of prey on predators and vice versa, although it is typically unreported in deference to descriptions of the contents of the non-empty stomachs. The FracFeed database is an ongoing compilation of the proportions of empty and non-empty stomachs (for gut content surveys) and of feeding and not feeding individuals (for direct observation surveys) reported in publications of predator diet surveys. FracFeed contains data from 4920 diet surveys on 1507 taxa (>4.3 million individuals) spanning cnidarians, ctenophores, chaetognaths, birds, annelids, amphibians, arthropods, mammals, mollusks, reptiles, echinoderms, and fishes that were surveyed in terrestrial, marine, and freshwater ecosystems across the globe over more than 135 years (1887-2023). For most surveys, covariate data include information on the spatial and temporal extent of the diet survey, its central geographical coordinates, the method by which the survey was performed (lethal gut contents, lavage, or direct observation), as well as each predator's standardized taxonomic name and identifier in the Open Tree of Life, its body mass (compiled mostly from independent compilations and additional publications), and its apparent diet's taxonomic richness and resolution. We appeal to more researchers who perform diet surveys to report on the number of empty stomachs they find and encourage additional contributions to the database-particularly from underrepresented geographic regions (e.g., North and Central Asia, North and Central Africa)-to help grow its scope and utility. The database is provided under a CC-BY-NC-S4 4.0 license. Users are requested to cite this data paper when using the data.},
}
@article {pmid41559958,
year = {2026},
author = {Lin, Y and Liu, Y and Tan, Y and Wu, N and Wang, L and Chen, J and Sun, X and Dong, X and Chen, B and Pan, Z and Wang, W and Lin, C},
title = {Source apportionment and ecological risks of trace metals in multiple media in a typical Chinese industrialized bay on the basis of SOM, PMF and GIS methods.},
journal = {Marine pollution bulletin},
volume = {223},
number = {},
pages = {119039},
doi = {10.1016/j.marpolbul.2025.119039},
pmid = {41559958},
issn = {1879-3363},
mesh = {*Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; China ; Bays/chemistry ; Geologic Sediments/chemistry ; Geographic Information Systems ; Seawater/chemistry ; *Trace Elements/analysis ; Risk Assessment ; *Metals, Heavy/analysis ; },
abstract = {The concentrations and risks of trace metals (TMs) in different media of aquatic systems are gradually increasing, driven by increasingly frequent anthropogenic activities. This research aimed to examine the distribution and bioaccumulation patterns of TMs in various environmental media via the analysis of samples from a typical petrochemical industrial bay in southern China. In addition, the ecological risks and anthropogenic sources of these elements were assessed. The results indicated that the levels of Zn and Hg were highest and lowest, respectively, in surface seawater, sediment, and seafood, with other TMs varying in content between those of these two trace metals. The integrated pollution index (IPI) values for TMs in seawater ranged from 1.13 to 3.16, remaining at a minimal contamination level. After multiple pollution assessment methods, were comprehensively applied, Cd and Hg were highlighted as key contributors to significant pollutant buildup and elevated ecological risks in sediments. Based on the combined use of geographic information system (GIS), self-organizing map (SOM), and positive matrix factorization (PMF) methods, the sources and contributions of TMs were analysed. The results revealed that fossil fuel combustion (24.3 %), natural geological processes (48.0 %), and aquaculture practices (27.7 %) were the primary sources of TM accumulation in sediments. This study provides important data for reducing TM pollution in typical petrochemical industry bays, enhancing ecological safety, and assessing the risks of potentially toxic elements in seafood to human health.},
}
@article {pmid41561390,
year = {2026},
author = {Fehrenbach, A and Mitrofanov, A and Backofen, R and Baumdicker, F},
title = {The complexity of multiple CRISPR arrays in strains with (co-occurring) CRISPR systems.},
journal = {microLife},
volume = {7},
number = {},
pages = {uqaf042},
pmid = {41561390},
issn = {2633-6693},
abstract = {CRISPR and their associated Cas proteins provide adaptive immunity in prokaryotes, protecting against invading genetic elements. These systems are categorized into types and are highly diverse. Genomes often harbor multiple CRISPR arrays varying in length and distance from Cas loci. However, the ecological roles of multiple CRISPR arrays and their interactions with multiple Cas loci remain poorly understood. We present a comprehensive analysis of CRISPR systems that uncovers variation between diverse Cas types regarding the occurrence of multiple arrays, the distribution of their lengths and positions relative to Cas loci, and the diversity of their repeat sequences. Some types tend to occur as the sole Cas locus present in the genome, but typically have two or more associated arrays, especially for types I-E and I-F. Multiple Cas types are also common, with some systems showing a preference for specific co-occurrence. Distinct array distributions and orientations around Cas loci indicate substantial differences in functionality and transcriptional behavior among Cas types. Our analysis suggests that arrays with identical repeats in the same genome acquire new spacers at comparable rates, irrespective of their proximity to the Cas locus. Furthermore, repeat similarities indicate that arrays of systems that often co-occur with other systems tend to have more diverse repeats than those mostly appearing alongside solitary systems. Our results indicate that co-occurring Cas-type pairs might not only collaborate in spacer acquisition but also maintain independent and complementary functions and that CRISPR systems distribute their defensive spacer repertoire equally across multiple CRISPR arrays.},
}
@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.},
}
@article {pmid41566104,
year = {2026},
author = {Sau, D and Tudu, GC and Hazra, T and Shiuly, A},
title = {Evaluation of microplastic pollution in urban lentic ecosystem using remote sensing, GIS, and Support Vector Machine (SVM): relevance for environmental and ecological risk.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {2},
pages = {160},
pmid = {41566104},
issn = {1573-2959},
mesh = {*Microplastics/analysis ; *Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; Remote Sensing Technology ; India ; Support Vector Machine ; Geographic Information Systems ; Ecosystem ; Lakes/chemistry ; Risk Assessment ; },
abstract = {Plastic waste is a major source of microplastic (MP) pollution, posing adverse environmental and public health risks. This study assessed MP abundance in 24 urban ponds and lakes within the Kolkata Municipal Corporation, India, during the post- and pre-monsoon seasons of 2022-2023. Results showed that MP concentrations were significantly higher in the post-monsoon season (20 ± 3.46 items L[-][1]; ANOVA, p < 0.05), with red, white, and black particles being the most prevalent. MPs prevalently ranged between 500 and 1000 µm with fibers constituting 58-59% of the total MPs. Fourier-transform infrared (FTIR) analysis identified polyethylene (PE) as the dominant polymer. MP abundance showed negative correlations with dissolved oxygen and turbidity, and positive associations with pH, TDS, BOD5, and total coliform counts. A Support Vector Machine (SVM) model was developed for morphology-based MP classification, achieving an accuracy of 89%. Additionally, remote sensing and GIS techniques were used to develop index-based models for water-body identification and MP quantification (items L[-][1]) using spectral data from Sentinel-2 imagery. These models demonstrated high validation accuracy of 98.01% and 92.60%, respectively. Metal analysis of sediment and MPs of water detected chromium, suggesting possible MP-metal interactions within sediments. Although the Pollution Load Index (PLI) indicated relatively low contamination levels, the Polymer Hazard Index (PHI) exceeded 1000, indicating substantial ecological risk. Future studies should focus on long-term monitoring, socio-economic and health impact assessments and development of effective mitigation strategies particularly addressing plastic-waste derived-MPS.},
}
@article {pmid41572218,
year = {2026},
author = {Liang, Y and Ma, S and Chen, X and Su, Y and Zhong, D and Yan, H and Chen, Y and Wang, M and Leng, Z and Huang, X},
title = {Integrative multi-omics reveal a CD4[+] T cell-derived six-gene signature linking the immune-stromal ecosystem to prognosis and immunotherapy selection in pancreatic cancer.},
journal = {BMC cancer},
volume = {26},
number = {1},
pages = {262},
pmid = {41572218},
issn = {1471-2407},
support = {2024YFHZ0358//Research Project of Science and Technology Department of Sichuan Province/ ; 2024ZD0525500/2024ZD0525506//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; },
mesh = {Humans ; *CD4-Positive T-Lymphocytes/immunology/metabolism ; *Pancreatic Neoplasms/genetics/immunology/therapy/mortality/pathology ; *Tumor Microenvironment/immunology/genetics ; Prognosis ; *Immunotherapy/methods ; *Biomarkers, Tumor/genetics ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic ; Single-Cell Analysis ; Transcriptome ; Gene Expression Profiling ; Stromal Cells/immunology ; Male ; Multiomics ; },
abstract = {BACKGROUND: Pancreatic cancer (PC) exhibits dismal outcomes and an immune-excluded microenvironment that blunts immunotherapy. Robust, immune-anchored biomarkers are needed to stratify risk and inform treatment design.<br><br>METHODS: We integrated The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) dataset and validated findings in Gene Expression Omnibus (GEO) dataset (GSE57495). Immune infiltration, survival modeling, pathway activity, tumor microenvironment, and immunotherapy responses were analyzed. Single-cell RNA sequencing (GSE212966) informed CD4&#x207a; T-cell differentially expressed genes (DEGs), pseudotime, and intercellular communication (CellChat). Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot in H6C7, CAPAN-1, and PANC-1 cell lines were performed.<br><br>RESULTS: Among 28 immune subsets, CD4&#x207a; T-cell populations most strongly associated with overall survival (OS). A six-gene signature (KLF3, EZR, SMDT1, JPT1, ISG15, MT1X) derived from 111 CD4&#x207a; T-cell DEGs successfully stratified OS with time-dependent AUCs ranging from 0.637 to 0.838 across the training and validation cohorts. The high-risk group showed significantly poorer OS, higher stromal scores, broad checkpoint upregulation, and greater immune exclusion (P&#x2009;<&#x2009;0.05), indicating an immune-stromal ecosystem favoring tolerance. Single-cell RNA sequencing localized model genes to fibroblasts, ductal cells, and CD4&#x207a; T cells subsets. CellChat revealed globally intensified crosstalk in PC and strengthened CD4&#x207a; T-cell interactions with myeloid and stromal compartments. Western blot and qRT-PCR results confirmed up-expression of all model gene except SMDT1 in PC cell lines.<br><br>CONCLUSIONS: CD4&#x207a; T-cell subsets serve as central determinant of the immune landscape and clinical outcome in PC. The CD4&#x207a; T cell-anchored six-gene signature enables risk stratification, links immune contexture to stromal ecology, and motivates biomarker-guided trials and rational combinations that alleviate immunosuppression while targeting metabolic-stress pathways.},
}
@article {pmid41573256,
year = {2025},
author = {Manzano-Marín, A and Böhne, A and Monteiro, R and Marcussen, T and Struck, TH and Oomen, RA and , and , and , and Howard, C and Howe, K and Blaxter, M and McCarthy, S and Wood, JMD and Martin, F and Lazar, A and Haggerty, L and Bortoluzzi, C},
title = {ERGA-BGE reference genome of Hirudo verbana, a once neglected freshwater haematophagous European medicinal leech.},
journal = {Open research Europe},
volume = {5},
number = {},
pages = {395},
pmid = {41573256},
issn = {2732-5121},
abstract = {Hirudo verbana Carena, 1820, commonly known as the southern medicinal leech, is one of several European medicinal leeches, whose full diversity has just recently started to be uncovered. Historically, it has been widely used as a medicinal leech and for centuries it was treated erroneously under the specific name of Hirudo medicinalis L. 1758. Recent molecular and taxonomic analyses have revealed subspecific diversity within the morphospecies H. verbana. Hirudo verbana is a blood-feeding species sucking blood from amphibians, fish, and mammals. It occupies freshwater habitats, typically shallow ponds and lakes. Studies show that this leech species has a "naturally limited microbiome", suggesting it may serve as a powerful model system for the study of gut microbiota. We expect this chromosome-level assembly of H. verbana to serve as a high-quality genomic resource for this most famous leech genus and to serve as a foundation to the study of the diversification and biodiversity of European medicinal leeches, as well as their gut-associated symbionts. The genome of H. verbana was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the primary haplotype was assembled into 14 contiguous chromosomal pseudomolecules, including the mitogenome. This chromosome-level assembly encompasses 0.18 Gb, composed of 277 contigs and 27 scaffolds, with contig and scaffold N50 values of 1.3 Mb and 13.4 Mb, respectively.},
}
@article {pmid41574452,
year = {2026},
author = {Templ, B and Scheifinger, H and Ostovary, I and Ungersböck, M and Ressl, H},
title = {PEP725: 15 years of driving European and global phenology science.},
journal = {The New phytologist},
volume = {250},
number = {2},
pages = {717-734},
pmid = {41574452},
issn = {1469-8137},
support = {CRSII5_201792//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {Europe ; Seasons ; Climate Change ; *Databases, Factual ; *Internationality ; *Plants ; Ecosystem ; *Plant Development ; },
abstract = {Phenology - the timing of seasonal biological events - is a sensitive indicator of climate change and ecosystem dynamics. Long-term, broad-scale phenological data are crucial for understanding and predicting plant responses to environmental change. However, until the mid-2000s, European phenological observations were scattered across national networks, limiting large-scale analyses. In response, the Pan European Phenology (PEP725) database was established 15 years ago as an open-access, reference-grade infrastructure for plant phenology data. PEP725 unifies observations from over 30 countries, compiled from 1868 through the present, with all records standardized to a common protocol. The database now contains more than 13 million phenological records for c. 265 plant species across 46 phenophases, making it the world's largest repository of ground-based plant phenology data. We highlight key scientific insights and cross-sector applications enabled by the dataset, and share technical lessons learned. Looking ahead, we outline a roadmap for PEP725's evolution - including new data contributions, technological upgrades, global integration, and community engagement - to ensure it remains a vibrant, open community resource driving phenology science forward. We invite the plant science community to utilize, contribute to, and further cocreate this phenological data platform.},
}
@article {pmid41575069,
year = {2026},
author = {Zupunski, L and Yaumenenka, A and Veyalkin, I and Minenko, V and Moiseyev, P and Schüz, J and Kukhta, T and Trofimik, S and Harbron, R and Drozdovitch, V and Ostroumova, E},
title = {Lymphoma, multiple myeloma and leukaemia incidence in regions of Belarus most heavily contaminated by the Chernobyl accident.},
journal = {International journal of cancer},
volume = {158},
number = {12},
pages = {3161-3172},
pmid = {41575069},
issn = {1097-0215},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Humans ; *Chernobyl Nuclear Accident ; Republic of Belarus/epidemiology ; *Multiple Myeloma/epidemiology/etiology ; Male ; Female ; Incidence ; Middle Aged ; Adult ; Aged ; Aged, 80 and over ; *Lymphoma/epidemiology/etiology ; Young Adult ; Adolescent ; Child ; Infant ; Registries ; Child, Preschool ; *Leukemia/epidemiology/etiology ; *Neoplasms, Radiation-Induced/epidemiology ; *Radiation Exposure/adverse effects ; },
abstract = {There is little information on non-thyroid cancer risks, including haematological malignancies (HM), among the residents of most contaminated regions after the Chernobyl (Chornobyl) nuclear power plant accident. We studied the incidence of lymphoma, multiple myeloma and leukaemia in relation to the raion-average age-specific cumulative absorbed red bone marrow (RBM) dose among the residents of Gomel and Mogilev oblasts in Belarus, which were highly contaminated. The follow-up period was 40 years (1978-2018). HM cases and population size data were received from the Belarusian national cancer registry and the state department of statistics. Our ecological study included 7328 lymphoma, 9476 leukaemia and 2003 multiple myeloma incident cases and 90.8 million person-years in people who were born before the accident and have attained age <80 years old. The mean (median) RBM dose accumulated by December 31, 2018 was 14.2 (6.4) mGy. We found no evidence of increased risks of Hodgkin and non-Hodgkin lymphoma, multiple myeloma or total leukaemia associated with two-year lagged raion-average cumulative RBM dose after adjustment for sex, attained age, urban/rural status and calendar period effects. There was a suggestion of an elevated relative risk of myeloid leukaemia per 100 mGy after exclusion of Gomel and Mogilev cities. Little evidence was found on interaction between selected factors, except sex, and RBM dose for each study outcome. Studies with individually reconstructed cumulative absorbed RBM doses are warranted to provide more insight on dose-effect relationships between HM risk, specifically leukaemia, and protracted environmental exposure at a low dose range.},
}
@article {pmid41575653,
year = {2026},
author = {Astill Wright, L and Bakstein, E and Saunders, K and Guo, B and Morriss, R},
title = {Performance of active and passive ambulatory assessment measures and mood monitoring in bipolar disorder: a systematic review.},
journal = {International journal of bipolar disorders},
volume = {14},
number = {1},
pages = {4},
pmid = {41575653},
issn = {2194-7511},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {BACKGROUND: Ambulatory assessment uses digital technology to capture real-time data on mood, mental state and behaviour. It has the potential to enhance traditional clinical outcome measures, but the practical application of these tools fundamentally depends on their performance.<br><br>AIMS: This systematic review aimed to assess the performance of active and passive ambulatory assessment and mood monitoring outcome measures in non-randomised and randomised studies in bipolar disorder over 3&#xa0;months or longer. We aimed to evaluate their performance against established clinical measures and through inter-ambulatory assessment comparisons.<br><br>METHODS: Systematic review (PROSPERO: CRD42023396473) of performance of mood monitoring and ambulatory assessment protocols in RCTs and non-randomised studies in bipolar disorder. Identified studies were assessed for risk of bias. Due to the very high heterogeneity in included studies and performance metrics we were not able to aggregate the data via meta-analysis.<br><br>RESULTS: The review included 42 studies with a combined sample of 7,813 participants. We included 28 distinct ambulatory assessment protocols which reported 487 different smartphone-based performance metrics. The considerable variability and inconsistency across these metrics limited our ability to make definitive comparisons of performance. Overall, some active ambulatory assessment approaches showed good performance when compared with established clinical measures. There was a paucity of data examining the performance of passive ambulatory assessment measures. Most studies were rated as having low to moderate risk of bias.<br><br>CONCLUSIONS: While ambulatory assessment holds significant promise, current evidence fails to establish the validity and reliability of passive ambulatory assessment to measure mood. The substantial methodological variation-particularly in how performance metrics are defined and reported-limits meaningful comparison and replication. Greater consistency in ambulatory assessment design and reporting standards is essential to support reliable evaluation and broader adoption of these behavioural assessment tools.},
}
@article {pmid41578325,
year = {2026},
author = {Lim, KO and Kummerfeld, E and Anderson, LM and Wonderlich, SA and Engel, S and Crosby, RD and Peterson, CB},
title = {Personal causal modeling of affect and eating behaviors in bulimia nervosa: implications for personalized treatment.},
journal = {Journal of eating disorders},
volume = {14},
number = {1},
pages = {52},
pmid = {41578325},
issn = {2050-2974},
support = {K23MH123910/NH/NIH HHS/United States ; R01MH059674/NH/NIH HHS/United States ; R34MH099040/NH/NIH HHS/United States ; K23MH123910/NH/NIH HHS/United States ; R01MH059674/NH/NIH HHS/United States ; R34MH099040/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Affect regulation models suggest high negative and low positive affect may drive binge eating and purging in bulimia nervosa (BN). While ecological momentary assessment (EMA) studies often support these theories, inconsistent outcomes in affect-targeted interventions suggest causal relations vary across individuals. This study applied causal discovery analysis (CDA) to EMA data to characterize such heterogeneity in person-specific causal models for BN.<br><br>METHODS: EMA data from 118 adult women with BN, collected over 14 days, assessed momentary negative affect, positive affect, binge eating, and self-induced vomiting. Using the Greedy Fast Causal Inference algorithm, we derived individual causal models and estimated effect sizes via structural equation modeling. Heterogeneity was evaluated by the proportion of participants with affect as a causal factor for BN behaviors.<br><br>RESULTS: Causal patterns were highly heterogeneous. Elevated negative affect was causal for binge eating in 16.9% of participants, vomiting in 18.6%, and either behavior in 27.1%. Low positive affect was causal for binge eating in 8.5%, vomiting in 11.0%, and either behavior in 15.3%. Behavior-behavior causality was also common: vomiting caused binge eating in 26.3% of participants, and binge eating caused vomiting in 22.0%.<br><br>CONCLUSIONS: CDA revealed marked heterogeneity in causal factors underlying BN behaviors, with some models showing affect-driven behaviors and others indicating behavior-driven patterns. Ultimately, this work indicates that the link between momentary affect and BN behaviors is highly individualized, underscoring the need for precision-targeted interventions rather than one-size-fits-all treatments.},
}
@article {pmid41578851,
year = {2026},
author = {Peltier, DMP and Malone, SC and McIntire, CD and Thompson, RA and Pinzon-Navarro, S and Pereverzeva, KA and Richardson, AD and McDowell, NG and Adams, HD and Carbone, MS and Pockman, WT and Trowbridge, AM},
title = {Resin-based defenses in Pinus edulis are only reduced after long-term drought.},
journal = {Tree physiology},
volume = {46},
number = {2},
pages = {},
doi = {10.1093/treephys/tpag004},
pmid = {41578851},
issn = {1758-4469},
support = {1019284//US Department of Agriculture, National Institute of Food and Agriculture, McIntire Stennis/ ; 1-842493//NSF GRFP/ ; 1936205//NSF-IOS/ ; 1755345//NSF-IOS/ ; 1755346//NSF-IOS/ ; },
mesh = {*Pinus/physiology/metabolism ; *Droughts ; *Resins, Plant/metabolism ; Animals ; Phenols/metabolism ; },
abstract = {Constrained carbon allocation toward secondary metabolites involved in chemical defense is a common explanation for widespread drought-related beetle-kill in conifers-we challenge the generality of this explanation. While monitoring drought stress (ψpd), we tracked both carbon reserves (non-structural carbohydrates) and chemical defenses (terpenes, phenolics, resin flow) in mature Pinus edulis Englem. trees experiencing either short-term (3-year) or a 'legacy' long-term (13-year) throughfall exclusion treatments, plus a control. We also quantified the Δ14C-age of resin to measure past allocation to current defense. While 72% of trees in short-term throughfall exclusion plots died (attacked by bark beetles, Ips confusus LeConte), mortality patterns were unrelated to throughfall exclusion intensity and all 'legacy' trees survived. We thus assessed trees in four survivorship categories: control, 'legacy', surviving, and dying trees. We found concentrations of certain defense compounds (leaf phenolics, twig monoterpenes) increased with drought stress, particularly in dying trees. In the main stem, dying trees exhibited similar terpene concentrations (94%) and phenolic concentrations (139%) relative to control trees. Compared with control trees, only 'legacy' trees had reduced stem terpenes (-49%, P < 0.05) after a decade of drought. Δ14C-age of resin could be up to 10.2 ± 0.5 years old, where the oldest resin was exuded from trees with low sugar concentrations and more negative Ψpd. Our results suggest that drought imposes a weak constraint on carbon allocation to resin-based defense. Instead, we primarily found evidence of increased concentrations of terpene and phenolic compounds under drought, even in dying trees, and only observed reductions in resin-based defenses after 10+ years of drought. Δ14C-ages demonstrate limited resin turnover and/or synthesis of resin from old reserves, suggesting that long-term drought is required to reduce resin-based defenses. Persistent allocation coupled with past investments appears to preserve or enhance concentrations of resin-based defenses even under lethal drought stress in P. edulis.},
}
@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.},
}
@article {pmid41587566,
year = {2026},
author = {Liu, Y and Zhang, Z and Chen, X and Liu, G and Li, D and Li, J and Song, Y and Duan, J and Sun, K and Feng, Y},
title = {Multi-objective decision model for wastewater treatment technology selection based on machine learning.},
journal = {Bioresource technology},
volume = {446},
number = {},
pages = {134087},
doi = {10.1016/j.biortech.2026.134087},
pmid = {41587566},
issn = {1873-2976},
mesh = {*Machine Learning ; *Wastewater/chemistry ; *Water Purification/methods ; Bioreactors ; Monte Carlo Method ; *Decision Support Techniques ; },
abstract = {This study integrated life cycle assessment (LCA), machine learning (ML), and analytic hierarchy process (AHP) to optimize wastewater treatment technology selection in the upper Yellow River Basin-a region constrained by limited carrying capacity and ecological fragility. LCA results from a representative city in Gansu Province identified anaerobic-anoxic-oxic combined with sequencing batch reactor (AAO + SBR) as the configuration with the lowest environmental footprint. Monte Carlo simulations were employed to augment the dataset, ensuring statistical reliability. In a comparative analysis, the XGBoost outperformed random forest (RF) and support vector machine (SVM), reducing mean squared error (MSE) by 1.4-3.1%. Ultimately, the integrated AHP-ML model confirmed AAO + SBR and AAO with membrane bioreactor (AAO + MBR) as the optimal technologies under current condition. The data-driven intelligent model constructed in this study, reconciling treatment efficiency with ecological sustainability, provided precise guidance for low-carbon wastewater governance in the Yellow River Basin and similar ecologically fragile regions.},
}
@article {pmid41588471,
year = {2026},
author = {Sulaiman, N and Sõukand, R and Ullah, I and Pieroni, A},
title = {Searching for a ghost?! The vain ethnobotany of foraging in three coastal Mediterranean areas.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {22},
number = {1},
pages = {15},
pmid = {41588471},
issn = {1746-4269},
support = {Horizon ID 101159928//ETHCSTWIN/ ; },
mesh = {*Ethnobotany ; Humans ; Knowledge ; France ; Mediterranean Region ; Vegetables ; Malta ; },
abstract = {This paper explores the erosion of foraging-related ethnobotanical knowledge in three coastal Mediterranean areas: Gozo Island (Malta), Kasos Island (Greece), and the Castagniccia region of Corsica Island (France). Based on recent ethnobotanical fieldwork between the summer of 2023 and the spring of 2025 in the three study areas, we document the few remaining wild vegetable uses in each region and contextualise the absence of robust LEK linked to plant foraging within broader socio-environmental changes. Our findings show that land abandonment, mass migration, desertification, and the rise of seasonal tourism have contributed to the disintegration of Local Ecological Knowledge (LEK). These forces have severed communities from everyday land-based practices, transforming vibrant ethnobotanical traditions into fragmented memories. We argue that LEK, particularly foraging knowledge, cannot survive in the absence of continuous interaction with the landscape, and that the revival of such practices requires more than nostalgic return, demanding a reconnection with local agro-ecological systems.},
}
@article {pmid41588622,
year = {2026},
author = {Hessl, AE and Richardson, AD and Filwett, R and Andreu-Hayles, L and Walker, M and Oelkers, R and Robison, AS and Leshyk, VO and Carbone, MS},
title = {Carbon uptake, storage, and allocation patterns contribute to blurring of annual [14]C signals in tree rings.},
journal = {The New phytologist},
volume = {250},
number = {6},
pages = {3584-3600},
doi = {10.1111/nph.70868},
pmid = {41588622},
issn = {1469-8137},
support = {2411569//NSF Solar Terrestrial/ ; 2411571//NSF Solar Terrestrial/ ; 2136524//NSF GRF/ ; 1832210//NSF LTER/ ; 2224545//NSF LTER/ ; PID2021-126411OB-I00//MICIU/AEI/10.13039/501100011033/ ; },
mesh = {*Trees/metabolism/anatomy &amp; histology ; *Carbon/metabolism ; *Carbon Radioisotopes/metabolism ; Wood/metabolism ; Photosynthesis ; },
abstract = {Tree rings are considered the gold standard for observing variation in past atmospheric radiocarbon ([14]C), yet little attention has been paid to whether different trees record tropospheric [14]C evenly. The discovery of Miyake events, rapid increases in [14]C production occurring in past millennia, has led to repeated measurements of [14]C in tree rings across species and locations. These records demonstrate remarkable synchrony, yet significant variability between samples remains, limiting reliable use of tree rings as a precise indicator of the timing and scale of past [14]C production. Understanding how trees and species record tropospheric [14]C would improve reconstructions of past [14]C production events, refine geochronological control, and because of the pulse-like nature of past [14]C production events, shed light on a fundamental question in tree physiology and dendrochronology: what is the lag time between photosynthesis, storage, and allocation to wood and how might this lag blur isotopic signals in tree rings? Here, we evaluate the implicit assumption that all trees record tropospheric [14]C evenly by focusing on the path carbon takes within trees including: phenology of carbon uptake and wood formation, storage and use of nonstructural carbohydrates, and how these factors interact to affect the tropospheric [14]C signal in wood.},
}
@article {pmid41588693,
year = {2026},
author = {Bhattacharya, D and Nandi, S and Chille, EE and Arroyo, M and Stephens, TG},
title = {The Host Coral Bleaching Response Viewed Through the Lens of Multi-Omics: Multi-Omics Provides the Tools to Understand the Complex Molecular Basis of Coral Bleaching, Which Can Aid Conservation Efforts.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {48},
number = {1},
pages = {e70110},
pmid = {41588693},
issn = {1521-1878},
support = {23-7825575//Catalyst Science Fund, Revive &amp; Restore, and the National Philanthropic Trust/ ; 2128073//National Science Foundation/ ; NJ01180//USDA National Institute of Food and Agriculture Hatch Formula/ ; },
mesh = {Animals ; *Anthozoa/genetics/physiology ; Symbiosis ; *Coral Bleaching ; Genomics/methods ; Coral Reefs ; Conservation of Natural Resources ; Climate Change ; Oxidative Stress ; Heat-Shock Response ; Multiomics ; },
abstract = {We review recent multi-omics analyses of the coral heat stress response to explore the generality of the Oxidative Theory of Coral Bleaching (OTCB), which posits that algal symbiont release is the final act of defense by the coral host to survive alga-derived oxidative stress. The OTCB is particularly relevant given that ocean warming, which is accelerating under climate change, has proven devastating for corals, leading to the bleaching phenotype and widespread reef loss. Multi-omics results, in combination with other data, such as genome-wide association studies, support the idea that coral bleaching is a multifactorial response that reflects a wide array of causes and effects and is population-specific under most conditions, with coral ploidy and genotype being critical to bleaching sensitivity. This perspective leverages the location, algal and prokaryotic microbiome, and host genotype-specific aspects of coral resilience to promote a new "personal genomics" approach to coral conservation, analogous to that used in human health.},
}
@article {pmid41591842,
year = {2026},
author = {Islam, H and Sharma, A and Blair, J and Lopatkin, AJ},
title = {PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis.},
journal = {Nucleic acids research},
volume = {54},
number = {3},
pages = {},
pmid = {41591842},
issn = {1362-4962},
support = {//Edward Mallinckrodt Jr. Foundation/ ; R35 GM150871/GM/NIGMS NIH HHS/United States ; 1R35GM150871-01/NH/NIH HHS/United States ; 2440082//National Science Foundation/ ; //Pew Charitable Trusts Foundation/ ; },
mesh = {*Plasmids/genetics ; *Molecular Sequence Annotation/methods ; *Databases, Genetic ; Genome, Bacterial ; Software ; DNA Transposable Elements ; Genes, Bacterial ; Bacteria/genetics ; },
abstract = {Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse microbial populations, yet annotating them remains challenging due to their highly mosaic genetic architectures and inconsistent gene naming conventions that complicate functional predictions and comparative analyses. To address this, we developed PlasAnn, a database designed specifically for genes encoded on natural plasmids, paired with a dedicated annotation pipeline (available via Bioconda or through the URL https://plasann.rochester.edu/). The curated database provides highly accurate, plasmid-type-specific gene names with standardized functional annotations, enabling direct comparison across plasmids without manual curation or specialized expertise, while the integrated annotation tool incorporates other common plasmid features for a fast, one-stop solution that outperforms broad prokaryotic genome annotation pipelines in both accuracy and efficiency. We demonstrate PlasAnn's utility by showing that plasmid accessory genes from different groups often share conserved repertoires, suggesting dynamic, modular networks of interconnected genes, and by revealing that plasmid-encoded transposable elements frequently carry genes related to bacterial adaptation beyond antibiotic resistance, including metabolism, virulence, and stress responses, emphasizing their broader contributions to fitness and adaptability. These insights, not captured by current field-standard tools, highlight how PlasAnn improves plasmid annotation and advances our understanding of plasmid biology, microbial ecology, and evolution.},
}
@article {pmid41591867,
year = {2026},
author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C},
title = {Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70215},
doi = {10.1002/mbo3.70215},
pmid = {41591867},
issn = {2045-8827},
support = {//European Union, NextGeneration EU, PNRR-M4C2- I1.1, PRIN 2022 - Project Code 20229LEB99 - CUP Code D53D23014150006/ ; T5-AN-11//Piano di Sviluppo e Coesione of the Italian Ministry of Health 2014-2020/ ; },
mesh = {*Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; *Databases, Genetic ; Microbiota/genetics ; Environmental Pollutants/metabolism ; Metagenome ; Metagenomics ; },
abstract = {Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.},
}
@article {pmid41592132,
year = {2026},
author = {Rathod, DR and Silverman, JD},
title = {PCR bias impacts microbiome ecological analyses.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013908},
pmid = {41592132},
issn = {1553-7358},
support = {R01 GM148972/GM/NIGMS NIH HHS/United States ; T32 GM145449/GM/NIGMS NIH HHS/United States ; },
mesh = {*Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Polymerase Chain Reaction/methods ; Computational Biology ; Bias ; Biodiversity ; },
abstract = {Polymerase Chain Reaction (PCR) is a critical step in amplicon-based microbial community profiling, allowing the selective amplification of marker genes such as 16S rRNA from environmental or host-associated samples. Despite its widespread use, PCR is known to introduce amplification bias, where some DNA sequences are preferentially amplified over others due to factors such as primer-template mismatches, sequence GC content, and secondary structures. Although these biases are known to affect transcript abundance, their implications for ecological metrics remain poorly understood. In this study, we conduct a comprehensive evaluation of how PCR-bias influences both within-samples (α-diversity) and between-sample (β-diversity) analyses. We show that perturbation-invariant diversity measures remain unaffected by PCR bias, but widely used metrics such as Shannon diversity and Weighted-Unifrac are sensitive. To address this, we provide theoretical and empirical insight into how PCR-induced bias varies across ecological analyses and community structures, and we offer practical guidance on when bias-correction methods should be applied. Our findings highlight the importance of selecting appropriate diversity metrics for PCR-based microbial ecology workflows and offer guidance for improving the reliability of diversity analyses.},
}
@article {pmid41593110,
year = {2026},
author = {Syverson, VJP and Goring, SJ and Cullen, N and Jarzyna, MA and Bellvé, AM and Martindale, A and Blois, JL},
title = {Updated chronologies for North American small mammal fossil localities in the Neotoma Paleoecology Database.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {173},
pmid = {41593110},
issn = {2052-4463},
support = {EAR-2410961//National Science Foundation (NSF)/ ; EAR-2149419//National Science Foundation (NSF)/ ; EAR-2149416//National Science Foundation (NSF)/ ; EAR-1948579//National Science Foundation (NSF)/ ; EAR-2410965//National Science Foundation (NSF)/ ; },
mesh = {*Fossils ; Animals ; *Mammals ; Paleontology ; North America ; Radiometric Dating ; Databases, Factual ; },
abstract = {Community paleoecology is a powerful approach for analyzing ecological communities during long-term climate shifts like the Pleistocene-Holocene transition, but it depends on accurate estimates of species co-occurrences. The Neotoma Paleoecology Database is an open paleodata resource that stores assemblage-level taxonomic, spatial, and temporal information for Quaternary fossil localities. However, its age estimates for many vertebrate fossil localities are based on uncalibrated radiocarbon dates, hindering comparisons with other paleoenvironmental proxies. In order to provide consistent and updated age inferences suitable for broad-scale paleoecological studies, we have reassessed the radiocarbon chronologies for all 14C-dated North American small mammal collections in Neotoma. Here we present the resulting database update, including 2074 radiocarbon dates newly added to Neotoma and new calibrated radiocarbon chronologies for 1553 fossil collections. The new chronologies cover more sites and include more dates than the chronologies previously available in Neotoma. They also provide fossil assemblage age estimates in calendar years, facilitating integration with other data sources. We anticipate that these updates will be useful for various applications in community paleoecology.},
}
@article {pmid41593363,
year = {2026},
author = {Sorensen, PO and Karaoz, U and Beller, HR and Bill, M and Bouskill, NJ and Banfied, JF and Chu, RK and Hoyt, DW and Eder, E and Eloe-Fadrosh, E and Sharrar, A and Tfaily, MM and Toyoda, J and Tolic, N and Wang, S and Wong, AR and Williams, KH and Zhong, Y and Brodie, EL},
title = {Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt.},
journal = {Nature microbiology},
volume = {11},
number = {2},
pages = {359-374},
pmid = {41593363},
issn = {2058-5276},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DBI-1315705//National Science Foundation (NSF)/ ; },
mesh = {*Bacteria/metabolism ; Biomass ; Bradyrhizobium/metabolism ; Climate Change ; Metagenome ; Microbiota ; Nitrogen/metabolism ; *Nitrogen Compounds/metabolism ; *Nitrogen Cycle ; *Seasons ; *Snow ; *Soil Microbiology ; Ecosystem ; Multiomics ; },
abstract = {Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.},
}
@article {pmid41593685,
year = {2026},
author = {Naserrudin, NA and Rahman, AB and Manah, AM and Donnie, EM and Jamaji, L and Lin, PYP and Miller, A and Krishnan, M and Hassan, MR},
title = {What does monkey malaria mean to you? A participatory photovoice study in rural Malaysian Borneo.},
journal = {Malaria journal},
volume = {25},
number = {1},
pages = {105},
pmid = {41593685},
issn = {1475-2875},
mesh = {Adult ; Middle Aged ; Humans ; *Malaria/psychology/epidemiology/prevention &amp; control ; *Rural Population/statistics &amp; numerical data ; Young Adult ; Male ; *Plasmodium knowlesi/physiology ; Animals ; Female ; Adolescent ; Photography ; Borneo/epidemiology ; *Zoonoses ; Malaysia ; Focus Groups ; },
abstract = {BACKGROUND: Zoonotic (monkey) malaria, caused by Plasmodium knowlesi, is an escalating concern in Sabah, Malaysia, where humans, macaques and mosquito vectors share overlapping ecosystems. Conventional research methods often overlook how affected communities perceive and respond to this risk within their cultural and environmental contexts. This study uses photovoice, a participatory visual method to explore the question 'What does monkey malaria mean to you? and to elevate community voices in guiding locally relevant disease prevention strategies.<br><br>METHODS: From January to May 2024, twenty participants aged 18 to 62 from three rural Sabah villages captured photographs over a 20-day period using their smartphones to document their experiences and perceptions on monkey malaria. Follow-up focus group discussions (FGDs) enabled participants to collectively reflect on and interpret their images. Reflexive thematic analysis was applied to the visual and verbal data and findings. Digital tools supported coordination and data management without replacing the participant-researcher engagement.<br><br>RESULTS: Five interrelated themes were generated: (1) monkey malaria as an embedded, everyday risk, (2) community resilience manifested through locally derived practices, (3) structural and socio-ecological challenges shaping exposure, (4) the interface of human, wildlife, and environmental health, (5) cultural knowledge and blended practices for coping with malaria risk. Participants articulated how landscape features, economic dependence on forested and plantation areas, and daily routines collectively structure risk, reflecting a dynamic 'landscape of risk'. They also expressed aspirations for collaborative and culturally appropriate strategies.<br><br>CONCLUSION: Using photovoice, participants described how malaria risk is part of their everyday lives, the coping strategies they use and the social and environmental conditions that influence their understanding. By prioritising community voices, the findings show that effective malaria control should go beyond strictly biomedical models to include local priorities, cultural practices and lived experience. Photovoice generated deep insights grounded in the community context and encouraged meaningful participation, providing useful guidance for designing intervention strategies that are culturally appropriate and more sustainable.},
}
@article {pmid41593706,
year = {2026},
author = {Gothe, S and Jagtap, S and Böhmer, P and Reuter, M and Frank, S and Sreenu, VB and Bell-Sakyi, L and Merits, A and Altinli, M and Schnettler, E},
title = {Characterization of Culex pipiens cell lines: virus infection and RNAi response.},
journal = {Parasites &amp; vectors},
volume = {19},
number = {1},
pages = {},
pmid = {41593706},
issn = {1756-3305},
support = {Culifo3//BMLE/ ; TTU 01.708//Deutsches Zentrum f&#xfc;r Infektionsforschung/ ; TTU 01.701 and TTU 01.708//Deutsches Zentrum f&#xfc;r Infektionsforschung/ ; 500072465//Deutsche Forschungsgemeinschaft/ ; 497659464//Deutsche Forschungsgemeinschaft/ ; GSO KT/24//Klaus Tschira Stiftung/ ; BB/P024270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 223743/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Culex/virology/cytology ; Cell Line/virology ; *RNA Interference ; *Mosquito Vectors/virology ; Virus Replication ; *Arboviruses/physiology/genetics ; },
abstract = {BACKGROUND: Arboviruses transmitted by mosquitoes pose a global health threat, causing diseases ranging from mild fevers to severe encephalitis and hemorrhagic fevers. Despite their growing impact, arbovirus research is hindered by biosafety constraints and the need of specialized BSL-3 insectariums. To circumvent these challenges, mosquito-derived cell lines have become indispensable tools for investigating virus-vector interactions. However, most available cell lines originate from Aedes and Anopheles spp., creating a critical research gap for other key vectors such as Culex spp. Although a few cell lines were previously established, they did not represent primary transmitters of West Nile virus (WNV) and other emerging arboviruses in Europe, such as Culex pipiens.<br><br>METHODS: To address this gap, the current study aimed to characterize two recently established Culex pipiens cell lines: CPE/LULS50 (Culex pipiens pipiens &amp; molestus) and CPL/LULS56 (Culex pipiens molestus) in more detail including testing their virus susceptibility, antiviral RNAi response, and possible presence of insect-specific viruses.<br><br>RESULTS: The replication of arboviruses from three clinically relevant families (Flaviviridae, Peribunyaviridae, and Togaviridae), as well as insect-specific viruses, was observed in both CPE/LULS50 and CPL/LULS56 cell lines. Furthermore, small RNA profiling revealed production of virus-specific small interfering RNA (siRNA) in both cell lines for all tested viruses. Interestingly, virus-specific PIWI-interacting RNA (piRNA) was only detected for the Peribunyaviridae.<br><br>CONCLUSIONS: The current study demonstrates that the CPE/LULS50 and CPL/LULS56 cell lines are suitable candidates to facilitate research into Culex-specific virus-vector interactions, ultimately contributing to mitigation of the impact of Culex-borne arboviruses on public health.},
}
@article {pmid41595397,
year = {2026},
author = {Jean-Baptiste, CO},
title = {A Prevention-Focused Geospatial Epidemiology Framework for Identifying Multilevel Vulnerability Across Diverse Settings.},
journal = {Healthcare (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
pmid = {41595397},
issn = {2227-9032},
abstract = {Background/Objectives: Geographic Information Systems (GIS) offer essential capabilities for identifying spatial concentrations of vulnerability and strengthening context-aware prevention strategies. This manuscript describes a geospatial architecture designed to generate anticipatory, place-based risk identification applicable across diverse community and institutional environments. Interpersonal Violence (IPV), one of several preventable harms that benefit from this spatially informed analysis, remains a critical public health challenge shaped by structural, ecological, and situational factors. Methods: The conceptual framework presented integrates de-identified surveillance data, ecological indicators, environmental and temporal dynamics into a unified spatial epidemiological model. Multilevel data layers are geocoded, spatially matched, and analyzed using clustering (e.g., Getis-Ord Gi*), spatial dependence metrics (e.g., Moran's I), and contextual modeling to support anticipatory identification of elevated vulnerability. Framework Outputs: The model is designed to identify spatial clustering, mobility-linked risk patterns, and emerging escalation zones using neighborhood disadvantage, built-environment factors, and situational markers. Outputs are intended to support both clinical decision-making (e.g., geocoded trauma screening, and context-aware discharge planning), and community-level prevention (e.g., targeted environmental interventions and cross-sector resource coordination). Conclusions: This framework synthesizes behavioral theory, spatial epidemiology, and prevention science into an integrative architecture for coordinated public health response. As a conceptual foundation for future empirical research, it advances the development of more dynamic, spatially informed, and equity-focused prevention systems.},
}
@article {pmid41595990,
year = {2026},
author = {Ha, S and Lee, T and Seo, H and Yoon, S and Lee, H},
title = {A Selective RAG-Enhanced Hybrid ML-LLM Framework for Efficient and Explainable Fatigue Prediction Using Wearable Sensor Data.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {13},
number = {1},
pages = {},
pmid = {41595990},
issn = {2306-5354},
support = {RS-2024-00457381//National Research Foundation of Korea/ ; RS-2024-00440371//National Research Foundation of Korea/ ; },
abstract = {Fatigue is a multifactorial phenomenon affecting both physical and psychological performance, particularly in high-stress occupations. Although wearable sensors enable continuous monitoring, conventional machine-learning (ML) models can produce unstable, weakly calibrated, and opaque predictions in real-world settings. To improve reliability and interpretability, we developed a selective Retrieval-Augmented Generation (RAG)-enhanced hybrid ML-LLM framework that integrates the efficiency of ML with the reasoning capability of large language models (LLMs). Using wearable and ecological momentary assessment data from 297 emergency responders (9543 seven-day windows), logistic regression, XGBoost, and LSTM models were trained to classify fatigue levels dichotomized by the median of daily tiredness scores. The LLM was selectively activated only for borderline ML outputs (0.45 ≤ p ≤ 0.55), using symbolic rules and retrieved analog examples. In the uncertainty region, performance improved from 0.556/0.684/0.635/0.659 to 0.617/0.703/0.748/0.725 (accuracy/precision/recall/F1). On the full test set, performance similarly improved from 0.707/0.739/0.918/0.819 to 0.718/0.741/0.937/0.827, with gains confirmed by McNemar's paired comparison test (p < 0.05). SHAP-based ML interpretation and LLM reasoning analyses independently identified short-term sleep duration and heart-rate variability as dominant predictors, providing transparent explanations for model behavior. This framework enhances classification robustness, interpretability, and efficiency, offering a scalable solution for real-world fatigue monitoring.},
}
@article {pmid41596699,
year = {2026},
author = {Wang, R and Gu, C and Li, H and Wang, L and Sun, R and Fu, K and Shi, W and Wan, X},
title = {Multi-Omics Profiling of the Hepatopancreas of Ridgetail White Prawn Exopalaemon carinicauda Under Sulfate Stress.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
pmid = {41596699},
issn = {1422-0067},
support = {JC2023085//The Nantong City Natural Science Foundation Project/ ; },
mesh = {Animals ; *Palaemonidae/metabolism/genetics/drug effects ; *Hepatopancreas/metabolism/drug effects/ultrastructure ; *Sulfates/toxicity ; Proteomics/methods ; *Stress, Physiological ; Transcriptome ; Multiomics ; },
abstract = {With intensifying global climate change and human activities, and with regional topography interactions, soil and water salinization has intensified, posing major ecological and environmental challenges worldwide. Here, we integrated histology, transmission electron microscopy, RNA sequencing (RNA-seq) and data-independent acquisition (DIA)-based proteomics to profile hepatopancreas responses of Exopalaemon carinicauda during acute sulfate stress (≤48 h). Sulfate exposure disrupted tubular architecture and organelle integrity, consistent with early cellular injury. Multi-omics analyses revealed metabolic reprogramming marked by suppressed glycolysis (e.g., HK2, ENO) and enhanced oxidative phosphorylation (e.g., ATP5F1B), together with activation of calcium signaling (e.g., SLC8A1, ADCY9) and reinforcement of antioxidant/one-carbon and glucose-branch pathways (e.g., SHMT2, PGAM2). These coordinated transcript-protein changes indicate a shift from rapid cytosolic ATP supply to mitochondrial ATP production while buffering Ca[2+] overload and reactive oxygen species. Collectively, our results delineate the physiological and molecular adjustments that enable E. carinicauda to cope with sulfate conditions and provide mechanistic targets for selective breeding and water-quality management in saline-alkaline aquaculture.},
}
@article {pmid41597231,
year = {2026},
author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y},
title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
pmid = {41597231},
issn = {2073-4409},
support = {2024YFD2401102//National Key R&amp;D ProgramNational Key R&amp;D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; },
mesh = {Animals ; *Carps/virology/microbiology ; *Fish Diseases/virology/microbiology/genetics ; *Intestinal Mucosa/virology/pathology/microbiology ; Gastrointestinal Microbiome ; Metagenomics ; Transcriptome ; Multiomics ; },
abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.},
}
@article {pmid41597405,
year = {2026},
author = {Sekulic, M and Stepovic, M and Sorak, M and Mijailovic, S and Rajkovic Pavlovic, Z and Vulovic, M and Radmanovic, O and Radmanovic, B and Vuckovic Filipovic, J and Gavrilovic, J and Jovanovic, B and Spasic, B and Folic, N and Rosic, V and Dragicevic, T and Markovic, V},
title = {Elevated Blood Pressure and Risk Factors in 19-Year-Olds in Serbia: A Cross-Sectional Study.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {1},
pages = {},
pmid = {41597405},
issn = {1648-9144},
mesh = {Humans ; Male ; Serbia/epidemiology ; Cross-Sectional Studies ; Female ; *Hypertension/epidemiology ; Risk Factors ; Young Adult ; Logistic Models ; Surveys and Questionnaires ; Feeding Behavior ; Blood Pressure/physiology ; Adult ; Prevalence ; },
abstract = {Background and Objectives: Hypertension in young adulthood is increasingly recognized as a precursor to future cardiovascular disease. Early identification of modifiable risk factors, such as dietary habits, lifestyle behaviors, and psychological indicators, is critical for prevention. This study aimed to examine the elevated clinic blood pressure and associated factors in 19-year-old individuals in Serbia. Materials and Methods: A cross-sectional study was conducted using data from the 2019 Fourth National Health Survey. A total of 212 participants underwent blood pressure measurement, anthropometric assessment, and completed standardized questionnaires on diet, physical activity, depressive symptoms, and sociodemographic characteristics. Blood pressure was classified according to ESC/ESH guidelines. Associations with elevated blood pressure were assessed using chi-square tests and multivariate logistic regression. Results: Most participants had optimal or normal blood pressure, while 18.9% had elevated blood pressure, including high-normal and Grade I-II hypertension. Elevated blood pressure was more prevalent among males and was associated with depressive symptoms. Nutrition status was significantly associated with elevated blood pressure, and some dietary habits like consumption of pure fruit or vegetable juices and the intake of processed meat products. Other socioeconomic factors, eating habits and physical activity were not significantly correlated. In multivariate logistic regression, elevated arterial blood pressure was significantly associated with consuming pure fruit or vegetable juices less than once per week (OR = 3.239; 95% CI: 1.413-7.427) and with consuming processed meat products several times per week in comparison to the daily consumption (OR = 0.325; 95% CI: 0.130-0.812), while no other variables remained statistically significant. Conclusions: Clinically elevated arterial blood pressure is present in a substantial proportion of 19-year-olds. Early lifestyle interventions targeting nutrition and psychological health may prevent progression to hypertension and reduce long-term cardiovascular risk.},
}
@article {pmid41597522,
year = {2025},
author = {Tamahara, T and Kouketsu, A and Fukase, S and Sripodok, P and Saito, T and Ito, A and Li, B and Kumada, K and Shimada, M and Iikubo, M and Shimizu, R and Yamauchi, K and Sugiura, T},
title = {Ecological and Functional Landscape of the Oral Microbiome: A Multi-Site Analysis of Saliva, Dental Plaque and Tongue Coating.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
pmid = {41597522},
issn = {2076-2607},
support = {JP24K1310 and JP22K17150//JSPS KAKENHI/ ; },
abstract = {The oral cavity contains several microbial niches, including saliva, dental plaque and tongue coating, each shaped by distinct local environments and host factors. This study compared the ecological and functional characteristics of the microbiomes of these three oral sites within the same individuals and examined host conditions associated with their variation. Saliva, supragingival plaque and tongue coating samples were collected simultaneously from 31 adults without clinical oral lesions. The bacterial 16S rRNA gene (V3-V4 region) was sequenced using the Illumina MiSeq platform, and analyses included α and β diversity, Mantel correlations, differential abundance tests, network analysis and functional prediction. The three sites displayed a clear ecological gradient. Saliva and tongue coating were taxonomically similar but were influenced by different host factors, whereas plaque maintained a distinct, biofilm-like structure with limited systemic influence. Functional divergence was most pronounced on the tongue coating despite its taxonomic similarity to saliva, whereas functional differences between saliva and plaque were modest despite larger taxonomic separation. These findings indicate that microbial composition and function vary independently across oral niches and support the need for multi-site sampling to more accurately characterize oral microbial ecology.},
}
@article {pmid41599943,
year = {2026},
author = {Rocha, HR and Ribeiro, P and Rodrigues, PM and Gomes, AM and Pintado, M and Coelho, MC},
title = {Bioinformatic Insights into the Carotenoids' Role in Gut Microbiota Dynamics.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
pmid = {41599943},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Carotenoids/pharmacology/chemistry ; *Computational Biology ; Humans ; Fermentation ; Lycopene/pharmacology ; Lutein/pharmacology ; Bacteria/drug effects/genetics/classification ; beta Carotene/pharmacology ; },
abstract = {Background/Objectives: Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. Methods: Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. Results: β-carotene and lycopene promoted acid-tolerant taxa such as Escherichia-Shigella, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including Bifidobacterium and Bacteroides and promoting structured ecological trajectories. Conclusions: These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.},
}
@article {pmid41600098,
year = {2026},
author = {Tajti, K and Farkas, A and Farkas, M and Bíró, T and Ördög, V and Maróti, G},
title = {Synergistic Plant Biostimulatory Effects of an Inter-Kingdom Interaction: Chlorella sp. and Kocuria rhizophila Algal-Bacterial Co-Culture for Sustainable Crop Production.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41600098},
issn = {2223-7747},
abstract = {Plant biostimulatory effects of the green alga Chlorella sp. MACC-360, the Kocuria rhizophila FSP120 bacterial strain, and the combined inter-kingdom co-culture of the alga and bacterium were investigated using Solanum lycopersicum as a model plant grown under controlled greenhouse conditions. The application of algal-bacterial co-cultures using the soil drench method significantly improved plant growth parameters, vegetative biomass yield, fruit yield, and photosynthetic performance of the tomato plants. The combined treatment resulted in a 43.7% increase in mean fruit yield, while individual applications of K. rhizophila FSP120 and Chlorella sp. MACC-360 enhanced yields by 30.85% and 19.44%, respectively. Although total yield increases did not reach statistical significance due to high intra-group variability, the treatment's efficacy was statistically confirmed through key yield parameters including significantly higher fruit weight and fruit diameter (p < 0.05). The enhanced specific biostimulatory effects of the combined treatment could be at least partly attributed to the increased level of algal extracellular polymeric substances (EPS), which was a specific effect of algal co-cultivation with a Kocuria rhizophila bacterium. Detailed analysis of plant phenotypic alterations, biomass yield, fruit and flowering parameters, as well as microbial community analysis of the rhizosphere, were conducted and compared among the various treatments. Our results indicate that an appropriately chosen combination and application of biostimulatory microbes can significantly enhance crop production, which might contribute to more sustainable agriculture.},
}
@article {pmid41604932,
year = {2026},
author = {Mei, X and Zhu, T and Zhong, B and Wu, WM and Li, N and Wang, Y and Liu, X and Liu, R and Abdul, R and Yi, S and He, Y},
title = {Artificial intelligence in microplastics domain: Current progress, challenges, and sustainable prospects.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141233},
doi = {10.1016/j.jhazmat.2026.141233},
pmid = {41604932},
issn = {1873-3336},
abstract = {Microplastics (MPs) have emerged as pervasive and persistent global environmental contaminants. However, the current inability to robustly analyze these particles hinders a deeper mechanistic understanding of their environmental behavior and ecological consequences. Artificial Intelligence (AI), with its computational power and data processing capabilities, is revolutionizing the analysis of MPs and transforming methodological paradigms. This critical review summarizes key challenges in the field, including persistent methodological limitations in characterization techniques and the interpretation of environmental behavior. We also critically examine emerging applications of AI in MPs domain. We explore the reliability and generalizability of these AI-driven approaches, highlighting that while data accessibility and computational resources pose core operational challenges, the environmental costs and ethical dilemmas of AI also demand scrutiny. Finally, we envision a paradigm shift towards an eco-conscious AI that harmonizes ecological accountability with computational efficiency. Fostering this transition through interdisciplinary collaboration is crucial for guiding MPs research toward a future that is sustainable across environmental, economic, and social consideration.},
}
@article {pmid41610226,
year = {2026},
author = {Schakowski, A and Deffner, D and Kortet, R and Niemelä, PT and Kavelaars, MM and Monk, CT and Pykälä, M and Kurvers, RHJM},
title = {High-precision tracking of human foragers reveals adaptive social information use in the wild.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6784},
pages = {eady1055},
doi = {10.1126/science.ady1055},
pmid = {41610226},
issn = {1095-9203},
mesh = {Humans ; Geographic Information Systems ; *Social Behavior ; Cognition ; *Decision Making ; *Feeding Behavior ; Video Recording ; },
abstract = {Foraging complexity and competitive social challenges are considered key drivers of human cognition. Yet, the decision-making mechanisms that underlie social foraging in the real world remain unknown. Integrating high-precision Global Positioning System (GPS) tracking and video footage from large-scale foraging competitions with cognitive-computational modeling and agent-based simulations, we show how foragers integrate personal, social, and ecological information to guide spatial search and patch-leaving decisions. We show how the social context emerges as a key driver of foraging dynamics. Foragers adaptively rely on social information to locate resources when unsuccessful and extend giving-up times in the presence of others, which results in increased area-restricted search at high social densities. These findings demonstrate the importance of sociality for human foraging decisions and provide a template for harnessing high-resolution tracking data to study real-world cognition.},
}
@article {pmid41610512,
year = {2026},
author = {Lopez-Rodriguez, D and Guerrero-Limón, G and Chèvre, N},
title = {A chemical space model for the exploration of eco-toxicological data.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110096},
doi = {10.1016/j.envint.2026.110096},
pmid = {41610512},
issn = {1873-6750},
mesh = {Animals ; Daphnia/drug effects ; *Ecotoxicology/methods ; Risk Assessment ; *Models, Chemical ; Databases, Factual ; Hazardous Substances/toxicity ; },
abstract = {With over 350,000 chemicals and mixtures currently registered for production and use worldwide, around 83% of authorized chemicals lack adequate toxicity data, leaving the majority of chemicals poorly characterized. International agencies urge scientists to develop screening methods to explore, identify, and predict chemical hazards, supporting the prioritization of chemical risk assessment. Here, Tree Manifold Approximation and Projection (TMAP) were applied, with the aim of reducing the dimensionality of large toxicological dataset, providing the foundations to data imputation methods allowing to get an understanding of chemical modes of action. Specifically, TMAP was implemented using MHFP6 fingerprints and the NORMAN SusDat database, which contains over 100,000 compounds. To ensure that the TMAP layout preserves chemical structural similarity, a quantitative parameter optimization procedure was developed. The defined optimal parameter set allowed us to define the embeddings that preserves the most structural similarity among nearest connected neighbors, with similarity progressively decreasing as the distance between nodes increases. Leveraging this approach, a graph-based spatial imputation function was generated to obtain insights into the potential ecotoxicity mechanisms of data poor chemicals using physicochemical properties and CTD toxicogenomic data. The relevance and meaningfulness of TMAP chemical space was explored for Daphnia magna, Pimephales promelas and Algae. Chemical classes known to be structurally similar were found to be grouped together in the TMAP chemical space, while heterogeneous classes were found to be sparse. Data imputation allowed for the identification of known and potential chemical mechanisms of action. Indeed, acetylcholinesterase and transthyretin were confirmed as major mechanisms of action of organothiophosphate and brominated flame retardant toxicity in Daphnia magna and Pimephales promelas, respectively. Overall, transdisciplinary toxicological databases combined with TMAP, stand out as a computationally efficient and suitable method to explore and analyze large datasets, allowing for the inference of associations between chemical structures and chemical hazard identification and other potential applications of this hypotheses-generating tool.},
}
@article {pmid41610663,
year = {2026},
author = {Lu, W and Du, Q and Shang, Y and Du, Y and Zhang, Z and Jin, H and Zhang, W and Li, L},
title = {Multi-omics insights into Alizarin red S-induced alterations in redox balance, immune function and metabolism in juvenile silver carp (Hypophthalmichthys molitrix).},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141270},
doi = {10.1016/j.jhazmat.2026.141270},
pmid = {41610663},
issn = {1873-3336},
mesh = {Animals ; *Anthraquinones/toxicity ; *Water Pollutants, Chemical/toxicity ; *Carps/metabolism/immunology/genetics ; Oxidation-Reduction ; Gills/drug effects/metabolism/pathology ; Transcriptome/drug effects ; Oxidative Stress/drug effects ; Metabolomics ; Metabolome/drug effects ; Multiomics ; },
abstract = {Alizarin red S (ARS), a widely used anthraquinone dye in industrial processes, has emerged as a potential environmental contaminant with poorly understood ecotoxicological impacts on aquatic organisms. In this study, juvenile silver carp (Hypophthalmichthys molitrix) were exposed to graded concentrations of ARS (0, 100, 125, and 150 mg/L) for 96 h, revealing clear dose-dependent toxicity characterized by reduced survival and progressive histopathological damage in pelvic fins, opercula, and otoliths. Integrated multi-omics analyses of gill tissues demonstrated that high-dose ARS exposure profoundly disrupts physiological homeostasis. Transcriptomic profiling revealed concentration-dependent dysregulation of genes involved in xenobiotic metabolism, oxidative stress, immune response, and metabolic pathways. Notably, exposure to 150 mg/L ARS significantly perturbed signaling pathways associated with immune dysregulation and cellular stress responses. Metabolomic analysis identified 478 differentially abundant metabolites, with pathway enrichment indicating disruption of lipid and amino acid metabolism, particularly glutathione and arginine metabolism. Integrated transcriptome-metabolome analysis further highlighted coordinated alterations in critical pathways including glutathione metabolism, antigen processing and presentation, phagosome, and cytochrome P450-mediated drug metabolism, suggesting a transition from antioxidant defense to systemic immune and metabolic dysfunction under high-dose exposure. Functionally, the activities of catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px), along with glutathione (GSH) content, peaked at 100 mg/L ARS. Critically, malondialdehyde (MDA) content decreased significantly with increasing ARS concentration, attaining a minimum at 150 mg/L ARS. Collectively, these findings define a critical threshold for toxicological transition, provide crucial insights into the ecological hazards posed by anthraquinone dyes and underscore the necessity for stringent regulatory control of ARS emissions into aquatic ecosystems.},
}
@article {pmid41610871,
year = {2026},
author = {Weiskopf, SR and Morelli, TL and Mozelewski, TG and Shiklomanov, AN and Lerman, SB},
title = {Restoration based on cost-benefit optimization: A grasslands pilot study.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {36},
number = {1},
pages = {e70174},
pmid = {41610871},
issn = {1939-5582},
mesh = {*Grassland ; *Conservation of Natural Resources/economics/methods ; Animals ; Pilot Projects ; Cost-Benefit Analysis ; *Environmental Restoration and Remediation/economics/methods ; Kansas ; Biodiversity ; },
abstract = {Ecological restoration is essential to meeting global biodiversity conservation goals. Given limited conservation budgets, deciding where to restore habitat is a key challenge for the coming decade. We developed a spatially explicit framework to optimize ecological restoration site selection by integrating land use history, species distributions, and economic costs. The framework includes the following steps: identify potential restoration area based on relevant environmental measures like land use; identify species of interest; calculate restoration benefits by modeling habitat and climate suitability and estimating reduced extinction risk associated with restoring a particular land parcel based on a modified species-area relationship; aggregate benefits across species; and compare to parcel-level land acquisition costs. We applied linear programming to maximize conservation benefit/restoration cost ratios to identify optimized restoration sites. We illustrate this approach using a case study for highly threatened grassland ecosystems in the Great Plains region of Kansas, USA. We selected five grassland animal species (greater prairie chickens [Tympanuchus cupido], lesser prairie chickens [Tympanuchus pallidicinctus], swift fox [Vulpes velox], pronghorn [Antilocapra americana], and regal fritillary [Speyeria idalia]) as indicators of restoration benefit across taxa. For the indicator species that we chose, shortgrass and mixed-grass prairies had the highest conservation benefit to cost ratio. Setting a minimum restoration threshold for each habitat type allowed us to identify high-priority tallgrass prairie sites. Despite increasing interest in ecological restoration, optimizing restoration site selection is challenging because one must consider habitat features that do not currently exist. The modeling approach described here is flexible and can be updated for different ecosystems, species, and conservation priorities. We outline potential alterations that can be made in future analyses, depending on desired restoration goals.},
}
@article {pmid41611716,
year = {2026},
author = {Xue, M and Yang, X and Chen, X and Ciais, P and Zhou, L and Reich, PB and Xiao, J and Li, X and Xiao, X and Green, JK and Chen, JM and Liu, J and Shang, J and Luo, X and Tian, J and Liu, H and Zhu, P and Yan, K and Fu, X and Han, L and Yuan, W and Wu, C},
title = {Pantropical moist forests are converging towards a middle leaf longevity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41611716},
issn = {2041-1723},
mesh = {*Plant Leaves/physiology ; Climate Change ; *Forests ; Temperature ; *Trees/physiology ; Ecosystem ; Photosynthesis ; Tropical Climate ; },
abstract = {Leaf longevity is a fundamental plant trait that largely explains ecosystem functional dynamics in global pantropical moist forests. However, the signs, magnitudes, and mechanisms of the spatiotemporal variations in leaf longevity with ongoing climate change are still lacking. Using both ground measurements and gridded leaf age-dependent leaf area index data, we map the continental-scale variability of annual mean leaf longevity across pantropical moist forests over 2001-2023. We find a biome-dependent and converging trend in leaf longevity under climate change. In Amazon and tropical Asia with long leaf longevity (> ~1.8 years), leaf longevity decreases due to rising temperature and intensified atmospheric dryness. In contrast, an increasing trend is observed in Congo and subtropical Asia where forests have short leaf longevity (<~1.8 years). These responses cause a convergence of pantropical short and long leaf longevity into a middle longevity range, with maximization of plant functional traits, photosynthesis, and species evenness, which are expected to better resist climate variability. Our study provides emerging evidence for large-scale structural and functional adaptions across pantropical moist forests and is helpful for predicting climate-driven risks to ecosystem stability.},
}
@article {pmid41617719,
year = {2026},
author = {Li, T and Zhang, J and Guo, J and Sun, B and Han, Y and Xu, H and Weng, Y and Cao, Q and Li, M and Zhao, G and Liu, L and Gao, X and Dai, L and Wang, D and Cao, Y},
title = {Engineered internal architecture of core-shell lipid nanoparticles promotes efficient mRNA endosomal release.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41617719},
issn = {2041-1723},
mesh = {*RNA, Messenger/metabolism/genetics/administration &amp; dosage/chemistry ; Gold/chemistry ; *Endosomes/metabolism ; Humans ; *Metal Nanoparticles/chemistry ; Animals ; Mice ; Female ; *Nanoparticles/chemistry ; *Lipids/chemistry ; SARS-CoV-2/immunology ; COVID-19/prevention &amp; control/immunology ; Cell Line, Tumor ; Hydrogen-Ion Concentration ; Triple Negative Breast Neoplasms/therapy ; Liposomes ; },
abstract = {Messenger RNA (mRNA) therapeutics rely on lipid nanoparticles (LNPs) for delivery, yet inefficient endosomal escape remains a major bottleneck, with only a small fraction of internalized cargo reaching the cytoplasm. Conventional LNPs encapsulate mRNA in amorphous lipid cores, where partial charge neutralization and lack of structural order limit protonation-driven membrane disruption. Here, we present an architectural strategy that engineers LNP internal structure using ionizable lipid-coated gold nanoparticles (IC-AuNPs) as rigid, pH-responsive cores. The Au cores template the formation of radially ordered core-shell architectures that stabilize particles at physiological pH while amplifying charge segregation and curvature stress under acidic endosomal conditions. As a result, Au-LNPs achieve a twofold increase in endosomal escape and ~100-fold greater cytoplasmic mRNA diffusion compared to conventional LNPs. Functionally, Au-LNPs enhance mRNA expression in vitro, increases in vivo protein production up to sevenfold, boost antibody responses to SARS-CoV-2 vaccines, and improve therapeutic efficacy in a triple-negative breast cancer model.},
}
@article {pmid41617738,
year = {2026},
author = {Sentil, A and Miličić, M and Benrezkallah, J and Ačanski, J and Andrić, A and Aubert, M and Bartomeus, I and Biella, P and Boustani, M and Carstensen, LB and Bogusch, P and Bot, S and Brau, T and Budrys, E and Salazar, LC and Cappellari, A and Carion, F and Castro, S and Cavaillès, S and Cerretti, P and Dathe, HH and De Groot, M and De Tandt, B and Devalez, J and Devorsine, R and Díaz-Calafat, J and Đorđević, A and Dormal, A and Dufrêne, E and Dussaix, C and Fedorova Zaytseva, LA and Fiordaliso, W and Flaminio, S and Földesi, R and Forgeois, V and Gadoum, S and Garrin, M and Gaspar, H and Gazzea, E and Geppert, C and Gérard, M and Geslin, B and Ghisbain, G and Gibernau, M and Grković, A and Heimburg, H and Herinckx, A and Demeter, I and Janković Milosavljević, M and Janssen, K and Kasparek, M and Kierat, J and Kleijn, D and Kuhlmann, M and Lair, X and Lemaire, S and Lenzi, L and Likov, L and Litman, J and Lopes, SB and Loureiro, J and Maarten, J and Maestracci, PY and Marini, L and Maritano, U and Mei, M and Mignot, M and Stojnić, SM and Nedeljković, Z and Ockermueller, E and Ortiz-Sanchez, FJ and Patiny, S and Paukkunen, J and Pennards, G and Perrard, A and Petanidou, T and Popov, G and Popov, S and Potts, SG and Prokhorov, A and Pruner, S and Radchenko, V and Radenković, S and Rasmont, P and Reverté, S and Ricarte, A and Rojo, S and Romig, T and Rosa, P and Ruiz, C and Sagot, P and Santerre, R and Scheper, J and Selis, M and Sgolastra, F and Shparyk, V and Siopa, C and Skendžic, T and Smit, J and Sommaggio, D and Soon, V and Ssymank, A and Ståhls, G and Stavrinides, M and Steffan-Dewenter, I and Straka, J and Thulier, J and Tot, T and Tourbez, C and van Steenis, J and van Steenis, W and Varnava, A and Veselić, S and Vesnic, A and Vray, S and Williams, P and Wood, TJ and Zimmermann, D and Żmuda, A and Vujić, A and Michez, D and de Manincor, N},
title = {Synthesised database of wild bee and hoverfly records in Europe.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {227},
pmid = {41617738},
issn = {2052-4463},
mesh = {Animals ; Bees ; Europe ; *Diptera ; Pollination ; Databases, Factual ; },
abstract = {Wild bees (Hymenoptera: Anthophila) and hoverflies (Diptera: Syrphidae), the two major groups of insect pollinators, are undergoing alarming declines worldwide, including Europe. The lack of accessible and verified spatial and temporal occurrence records currently challenges efforts to understand and mitigate this decline. Here, we compiled datasets from diverse sources, including taxonomists, national experts, public repositories, museum collections, published literature, verified open-access platforms, and aggregated datasets from previous European projects. The collected data were standardised, cleaned and validated by taxonomists and national experts. This collective effort resulted in two databases comprising more than 4.34 million and 1.04 million records for wild bees and hoverflies, respectively. The databases cover 97% of the European bee fauna (2,083 species out of 2,138 recorded in Europe) and 97% of the European hoverfly fauna (886 species out of 913 recorded in Europe). These standardised databases constitute essential resources for future assessments of status and trends, habitat associations, and other research and conservation initiatives to protect and understand wild pollinators on the European continent.},
}
@article {pmid41617863,
year = {2026},
author = {Sharma, A and Singh, AP and Rallapalli, S},
title = {Adaptive Basin Management under Determinate and Indeterminate Sustainability Factors.},
journal = {Environmental management},
volume = {76},
number = {3},
pages = {69},
pmid = {41617863},
issn = {1432-1009},
mesh = {*Conservation of Natural Resources/methods ; *Rivers ; Climate Change ; Fuzzy Logic ; Decision Support Techniques ; },
abstract = {Adaptive river basin management is uncertain and complex, as it requires assessing the combined effects of climate change and human activities. Conventional strength-weakness-opportunities and threat (SWOT) decision analysis failed to quantify the indeterminacy concerning factors in adaptive management. To address these limitations, this study introduces a hybrid decision-support system that combines interval valued fuzzy hybrid SWOT (IVFH-SWOT) analysis with fuzzy evaluation of resilience metrics (FERM). To demonstrate its effectiveness, the study evaluated 11 strategic options across four aspects of adaptive sustainability: ecological balance, hydrological-geomorphological integrity, socio-economic and energy potential, and catastrophe resilience. The derived strategies were prioritized based on the multi-stakeholder analysis performed on the data gathered about these four aspects. The findings underscore dam operations regulations (score: 0.7561), treatment of wastewater infrastructure (0.7226), and development of hydropower (0.7122) as the most efficacious strategies. These findings illustrate the trade-offs between resilience performance and sustainability under indeterminate conditions. The proposed framework offers a robust, transferable tool for practitioners and policymakers for adaptive sustainable river basin management.},
}
@article {pmid41618863,
year = {2026},
author = {Mehr, S and Castoe, T and Daly, M and Jungo, F and Kirchhoff, KN and Koludarov, I and Mackessy, SP and Macrander, J and Naidu, P and Modica, MV and Sanchez, EE and Zancolli, G and Holford, M},
title = {A Proposed Unified, Scalable Platform for Integrative Research on Venomous Species.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf153},
pmid = {41618863},
issn = {2047-217X},
abstract = {Venomous animal research is hampered by fragmented, specialized, and non-interoperable databases (isolated genomic, proteomic, and ecological data). Despite the immense promise of venomous organisms to yield novel bioactive compounds for pharmacological and evolutionary applications, the informatics landscape for such taxa has remained patchy, lacking macro-scale integration across species. We present VenomsBase, an integrated, modular resource that synthesizes multi-omics data, ecological metadata, and functional annotations for venom-bearing organisms. Following the FAIR guidelines, VenomsBase combines an ontology-driven architecture with big-data cloud workflows for sequence integration, motif clustering, 3D display, and linking ecological metadata. Standardized tools and training modules facilitate worldwide access to resources for both researchers in developed countries and in resource-limited areas. Its plug-and-play design allows for integration of additional analytical modules and extension to other species. One can also examine evolutionary trends and connect venom chemistry to ecological niches. VenomsBase would (i) accelerate the pace of venom discovery, whether for therapeutic purposes or evolutionary significance, by providing validated, cross-referenced data sets and community-driven curation, and (ii) foster an open, just, and innovation-ready venom research ecosystem.},
}
@article {pmid41619592,
year = {2026},
author = {Nguyen, HT and Wijaya, J and Kim, J and Lee, JE and Yoon, JK and Oh, S},
title = {Predictive monitoring, identification, and control of Microcystis blooms in a drinking water source basin: An integrative artificial intelligence and bioinformatics approach.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141288},
doi = {10.1016/j.jhazmat.2026.141288},
pmid = {41619592},
issn = {1873-3336},
mesh = {*Microcystis/genetics/isolation &amp; purification/growth &amp; development ; *Artificial Intelligence ; *Harmful Algal Bloom ; Computational Biology ; *Drinking Water/microbiology ; *Environmental Monitoring/methods ; Water Supply ; Water Purification ; },
abstract = {Harmful algal blooms (HABs) pose serious challenges for drinking water utilities; however, conventional monitoring in drinking water source basins remains largely reactive. To address this, we present an integrative framework that combines artificial intelligence (AI) forecasting with strain-resolved bioinformatic diagnostics to enable proactive monitoring of bloom-causing HAB in drinking water source. The AI model employed environmental input features and was optimized, which achieved high predictive accuracy (up to 0.9 R[2]) with early warning capabilities (1 week lead time). Explainable AI pinpointed organic and nitrogen compounds as top predictors for HAB events. Phylogenomic analysis using short- and long-read sequencing elucidated the population structure, toxicological traits, and ecological adaptation of the bloom-causing Microcystis population (NRERC-214). Field surveys with bioinformatic analysis at a full-scale drinking water treatment plant found complete removal of Microcystis. The relative strengths and weaknesses of the individual units in removing Microcystis in the plant was validated with the phenotypic/genotypic features of Microcystis bioinformatically determined in this study. Overall, this study suggested the integration of a predictive surveillance and diagnosis framework into a source water management scheme, supporting a paradigm shift from reactive post-event management to proactive, risk-based control for drinking water.},
}
@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.},
}
@article {pmid41621727,
year = {2026},
author = {De Luca, D},
title = {FastqOrienter: A Python utility for the automated orientation and quality diagnostics of paired-end Illumina metabarcoding reads.},
journal = {Journal of microbiological methods},
volume = {242},
number = {},
pages = {107413},
doi = {10.1016/j.mimet.2026.107413},
pmid = {41621727},
issn = {1872-8359},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Software ; *Sequence Analysis, DNA/methods ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; },
abstract = {FastqOrienter is a Python tool that corrects inconsistent read orientations in Illumina paired-end metabarcoding reads using a primer-aware logic and IUPAC-compliant matching. In addition, it provides detailed diagnostics and actionable insights for discarded reads. It ensures data integrity for downstream pipelines like DADA2 and QIIME 2.},
}
@article {pmid41623561,
year = {2026},
author = {Xiao, S and Adams, JM and Li, S and Slik, F and Griffith, DM and Quaresma, A and Sultana, A and Rozak, AH and Muñoz, AA and Marshall, AR and Gabriel, A and Dar, AA and Mansor, A and Narayanan, A and Herault, B and Joly, CA and Piotto, D and Harris, DJ and Drake, DR and Sheil, D and Rocha, DSB and de Oliveira, EL and Nurtjahya, E and van den Berg, E and Webb, EL and Ibrahim, FH and Saiter, FZ and Wittmann, F and Ardila, FM and Durigan, G and Shukla, G and Ibarra-Manríquez, G and Nagamasu, H and Theilade, I and Zo-Bi, IC and Huamantupa-Chuquimaco, I and Rangel-Ch, JO and Grogan, J and Dar, JA and Schöngart, J and Herbohn, J and Poulsen, JR and Williams, JN and Lovett, J and De Alban, JD and Lozada, JR and Pinto, JRR and Guevara-Andino, JE and Cristóbal-Azkarate, J and Homeier, J and Böhning-Gaese, K and Hakeem, KR and Feeley, K and Tomlinson, KW and Rasingam, L and Demarchi, LO and Laumonier, Y and Alves, LF and Montenegro, LT and Satdichanh, M and Macía, MJ and Tabarelli, M and Suganuma, MS and Ríos Paredes, MA and Fernandez Piedade, MT and Schulze, M and van de Bult, M and Bastian, ML and Khan, ML and Hussain, MS and Kessler, M and Lawes, MJ and Munguía-Rosas, MA and Parthasarathy, N and Seuaturian, N and Kanda, NB and Jagadeesan, N and Pitman, N and Onrizal, O and Vetaas, OR and Munishi, P and Chhang, P and Bispo, PDC and Zakaria, R and Sukri, RS and Muthu, R and Prasad, RC and V S, R and Harrison, RD and Veridiano, RK and Steinmetz, R and Chazdon, RL and Tumaneng, R and Gonçalves Rolim, S and Garkoti, SC and Báez, S and Wich, S and Mukul, SA and Joseph, S and Vieira, SA and Muthuramkumar, S and Sundarapandian, S and Chakravarty, S and Kothandaraman, S and Wendt, T and Metzker, T and Whitfeld, T and Su, T and Van Andel, TR and Hans, V and Arroyo-Rodríguez, V and Chutipong, W and Laurance, WF and Carrero, YA and Zhou, Z},
title = {Analogous environments across the tropics have similar levels of tree species alpha diversity.},
journal = {National science review},
volume = {13},
number = {2},
pages = {nwaf465},
pmid = {41623561},
issn = {2053-714X},
abstract = {Different regions of the tropics vary in overall tree species diversity, with the tropical Americas exhibiting strikingly higher regional tree species richness than Africa and Southeast Asia. We investigated whether these differences also occur at the local scale and whether the environmental conditions associated with tree species richness are consistent across tropical regions despite highly dissimilar species pools. A spatial random forest model was trained by using a network of 429 1-hectare plots across the tropics, together with 24 environmental variables, to predict plot-level tree α diversity. A combination of climatic, soil and topographical variables explained ∼86% of the variation in richness. Despite differences in regional species pools and the potentially disruptive effects of different geological, climatic and evolutionary histories, the relationship between environmental variables and local-scale tree species richness is closely similar across different continents. Our findings imply a pervasive role of niche-based mechanisms in structuring local tree species richness, regardless of the regional species assemblages. This pantropical convergence in the richness-environment relationship poses a challenge for ecology to explain.},
}
@article {pmid41625303,
year = {2023},
author = {Lohse, K and Vila, R and Hayward, A and Laetsch, DR and Toro-Delgado, E and , and , and , and , },
title = {The genome sequence of the Silver-spotted Skipper, Hesperia comma (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {457},
pmid = {41625303},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Hesperia comma (the Silver-spotted Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 525.3 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,725 protein coding genes.},
}
@article {pmid41626904,
year = {2025},
author = {Lagisz, M and Yang, Y and Young, S and Nakagawa, S},
title = {A practical guide to evaluating sensitivity of literature search strings for systematic reviews using relative recall.},
journal = {Research synthesis methods},
volume = {16},
number = {1},
pages = {1-14},
pmid = {41626904},
issn = {1759-2887},
support = {//Australian Research Council/ ; },
mesh = {Humans ; *Information Storage and Retrieval/methods ; *Review Literature as Topic ; Reproducibility of Results ; Algorithms ; Databases, Bibliographic ; Research Design ; Benchmarking ; Sensitivity and Specificity ; *Systematic Reviews as Topic ; Mental Recall ; },
abstract = {Systematic searches of published literature are a vital component of systematic reviews. When search strings are not "sensitive," they may miss many relevant studies limiting, or even biasing, the range of evidence available for synthesis. Concerningly, conducting and reporting evaluations (validations) of the sensitivity of the used search strings is rare, according to our survey of published systematic reviews and protocols. Potential reasons may involve a lack of familiarity or inaccessibility of complex sensitivity evaluation approaches. We first clarify the main concepts and principles of search string evaluation. We then present a simple procedure for estimating a relative recall of a search string. It is based on a pre-defined set of "benchmark" publications. The relative recall, that is, the sensitivity of the search string, is the retrieval overlap between the evaluated search string and a search string that captures only the benchmark publications. If there is little overlap (i.e., low recall or sensitivity), the evaluated search string should be improved to ensure that most of the relevant literature can be captured. The presented benchmarking approach can be applied to one or more online databases or search platforms. It is illustrated by five accessible, hands-on tutorials for commonly used online literature sources. Overall, our work provides an assessment of the current state of search string evaluations in published systematic reviews and protocols. It also paves the way to improve evaluation and reporting practices to make evidence synthesis more transparent and robust.},
}
@article {pmid41628277,
year = {2026},
author = {Marrec, L and Lehtinen, S},
title = {Cluster dispersal shapes microbial diversity during community assembly.},
journal = {PLoS computational biology},
volume = {22},
number = {2},
pages = {e1013918},
pmid = {41628277},
issn = {1553-7358},
mesh = {*Microbiota/physiology ; *Biodiversity ; *Models, Biological ; Computational Biology ; Cluster Analysis ; },
abstract = {Identifying the drivers of diversity remains a central challenge in microbial ecology. In microbiota, within-community diversity is often linked to host health, which makes it all the more important to understand. Since many communities assemble de novo, microbial dispersal plays a critical role in shaping community structure during the early stages of assembly. While theoretical models typically assume microbes disperse individually, this overlooks cases where microbes disperse in clusters, such as, for example, during host feeding. Here, we investigate how cluster dispersal impacts species richness, between-community dissimilarity, and species abundance in the initial steps of microbial community assembly. We developed a model in which microbes disperse from a pool into communities as clusters and then replicate locally. Using both analytical and numerical approaches, we show that cluster dispersal promotes community homogenization by increasing within-community richness and reducing dissimilarity across communities, even at low dispersal rates. Moreover, it modulates the influence of local selection on microbial community assembly and, consequently, on species abundance. Our results demonstrate that cluster dispersal has distinct effects from simply increasing the dispersal rate. This work reveals new evidence for the role of cluster dispersal in the early dynamics of microbial community assembly.},
}
@article {pmid41628813,
year = {2026},
author = {Gasser, RB},
title = {Biotechnology advances and the parasitology paradigm: From genomes to multi-omics and translation.},
journal = {Biotechnology advances},
volume = {89},
number = {},
pages = {108813},
doi = {10.1016/j.biotechadv.2026.108813},
pmid = {41628813},
issn = {1873-1899},
mesh = {*Biotechnology ; Humans ; *Genomics ; Animals ; *Parasitology ; Proteomics ; *Parasitic Diseases/genetics/parasitology ; Metabolomics ; *Genome ; Host-Parasite Interactions ; Multiomics ; },
abstract = {Parasitic diseases impose a substantial and often underestimated burden on human and animal health, food security and economic development. Over recent decades, advances in biotechnology have expanded parasitology into a genomics-enabled field. Early progress stemmed from the use of molecular markers, PCR and immunological assays, followed by draft genomes generated through high-throughput sequencing and bioinformatics. The advent of long-read sequencing and chromosome conformation capture (Hi-C) mapping technologies subsequently enabled chromosome-scale assemblies, providing robust frameworks for comparative analyses across parasitic taxa. Building on this progress, multi-omics platforms - including transcriptomics, proteomics, lipidomics and metabolomics - have been applied to characterise developmental trajectories, host-parasite interactions and parasite-specific pathways, and the integration of these datasets is facilitating the construction of systems-level models linking genetic variation to phenotype and disease processes. More recently, artificial intelligence (AI), including machine learning, has been applied to predict essential genes, accelerate structure-based drug discovery, guide reverse vaccinology and integrate heterogeneous datasets, thereby establishing new approaches for genome-guided identification of diagnostic markers and candidate vaccine and therapeutic targets. Importantly, perspectives within the discipline have emphasised that taxonomy, ecology and field parasitology remain critical for contextualising molecular findings. The future of molecular parasitology will depend on integrating breadth with depth; genomic and multi-omics resources should align with the FAIR (findable, accessible, interoperable and reusable) principles and be embedded within a One Health framework, enabling fundamental discoveries to translate into improved diagnostics, novel therapeutics and sustainable strategies for parasite control.},
}
@article {pmid41629371,
year = {2026},
author = {Xiao, L and Xiang, J and Liu, X and Zhao, L and Li, Y and Chen, S},
title = {Unveiling scale effects in human settlement environment suitability through a novel multi-factor weighting approach.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6952},
pmid = {41629371},
issn = {2045-2322},
support = {24C0383//Scientific Research Project of Hunan Provincial Department of Education of China/ ; 2026JJ90040//the Industry-Education Integration Project of the Ministry of Education of China/ ; },
mesh = {Humans ; China ; *Rural Population ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Spatial Analysis ; Sustainable Development ; Environment ; },
abstract = {Rural human settlement environment suitability is a key indicator for guiding land-use planning and promoting sustainable rural revitalization. This study develops a refined framework for evaluating the natural suitability of rural human settlement environments in central Hunan, China, using GIS-based spatial analysis. We propose an enhanced factor-weighting method that integrates normalized information entropy (NIE) and the coefficient of variation (CV) into a Pearson correlation coefficient (PCC)-driven approach, thereby improving the objectivity and sensitivity of weight determination. Comparative experiments demonstrate that this hybrid method captures the relative influence of natural factors more accurately than traditional PCC-based techniques. Results reveal a pronounced scale effect: as the spatial analysis scale decreases, disparities in factor weights become more evident. The spatial distribution of suitability exhibits a distinct east-high, west-low gradient, reflecting strong spatial heterogeneity across the region. Among all factors, terrain relief emerges as the dominant driver of suitability variations. Based on the calculated suitability index, the study delineates five functional zones and formulates corresponding development strategies tailored to local conditions. These findings offer a scientific basis for optimizing rural spatial planning and promoting sustainable development in central Hunan and similar regions. Beyond the case region, the framework provides a transferable approach for evaluating natural suitability in other mountainous rural areas. It also offers practical guidance for policymakers seeking to balance ecological protection with sustainable land-use development.},
}
@article {pmid41629448,
year = {2026},
author = {Tschimmel, D and Saeed, M and Milani, M and Waldherr, S and Hucho, T},
title = {Computational epitope heterogeneity analysis in immunostainings from antibody-dilution series.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {238},
pmid = {41629448},
issn = {2399-3642},
support = {459759629//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Epitopes/immunology/chemistry ; Humans ; *Antibodies/immunology ; *Fluorescent Antibody Technique/methods ; *Computational Biology/methods ; Animals ; },
abstract = {Antibodies are widely used in life sciences and medical therapy. Broadly applicable methods to determine epitope heterogeneity in immunostaining systems are missing. Here, we present a simple-to-use approach to characterize and quantify antibody binding properties that constitute the staining directly in the system of choice. We determine an epitope heterogeneity on the basis of a computational analysis of antibody-dilution immunofluorescence stainings. This allows us to choose signal-specificity maximizing dilutions and to improve signal quantification. Furthermore, the computational analysis provides approaches to obtain a single-channel antibody multiplexing. Our approach could help improving immunostainings in many laboratories by guiding the choice of antibody dilution, by increasing the possibility of antibody-multiplexing in the same color-channel and by allowing for the analysis of binding targets of multi-specific antibodies.},
}
@article {pmid41629941,
year = {2026},
author = {Aziz, MA and Malik, A and Hasan, M and Abidullah, S and Ullah, A and Ullah, Z and Abbasi, AM and Pieroni, A},
title = {Displacement threatens local knowledge: plant foraging in a cross-cultural context in the Gomal area, NW Pakistan.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {22},
number = {1},
pages = {12},
pmid = {41629941},
issn = {1746-4269},
mesh = {Pakistan ; Humans ; *Plants, Edible ; *Ethnobotany ; *Knowledge ; Female ; Male ; Cross-Cultural Comparison ; Adult ; Middle Aged ; Ethnicity ; },
abstract = {In the context of human displacement, it is essential to study how local knowledge is reshaped, eroded, or transformed. This study sheds light on how wild plant reports are articulated after migration, retained, and kept; the research explores specifically the ethnobotanical knowledge linked to wild food plants of five ethnic communities, namely the Bettani, Ormur, Mehsud, and Miani populations living in the Gomal area of NW Pakistan, of which three are displaced communities. The study aims to record the knowledge of wild food plants and their use among generations in these communities. To better determine the impact of displacement, we have analysed the data along two trajectories: (a) cross-geographically comparing the recorded wild food plant reports with the available published literature in NW Pakistan and (b) conducting a cross-cultural comparison of the local plant knowledge among the considered groups (displaced ones: Mehsud, Ormur, and Powanda; autochthonous: Bettani and Miani) residing in the Gomal area. Via semi-structured interviews with a hundred study participants (twenty for each ethic group), the study revealed the use of 69 wild food taxa, showing a remarkable diversity of food uses, with Ormur and Powanda exhibiting several idiosyncratic reports. The research highlights that displacement may have disrupted potential pathways of knowledge transmission among the Mehsud, Ormur, and Powanda; however, local plant knowledge about their past environment remains part of the collective memory of these communities. Moreover, post-migration exposure to a new ecological system has become a challenge for the newcomers, necessitating adaptation to rearticulate their relationship with nature and plants. The broken paths have a profound impact on plant knowledge transmission to youngsters, as social structures and gatherings have been significantly altered or disrupted; these were the primary means of interaction between youngsters and their elders. The exposure to urbanisation compounds the issue of displacement, and the erosion of knowledge systems has come at the expense of hands-on experiences among the selected groups. Notably, the local plant nomenclature of Ormur is also highly threatened. We advocate incorporating local plant knowledge into local educational curricula, which may be crucial for the sustainability of natural knowledge and have profound impacts on mitigating the effects of socioecological change.},
}
@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.<br><br>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.<br><br>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.},
}
@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 F&#xf6;rderung 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.<br><br>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.<br><br>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.},
}
@article {pmid41635465,
year = {2026},
author = {Bell, KM and Alfikri, Z and Anderst, W and Clark, WW and Cook, HA and Darwin, J and Dicianno, BE and Greco, CM and Hoydick, J and Jakicic, JM and McKernan, GP and Parmanto, B and Patterson, CG and Piva, SR and Roos, RE and Schneider, MJ and Sundaram, M and Vo, NV and Zhou, L and Sowa, GA},
title = {In-Field Ecological Momentary Assessment From Wearable Motion Sensors and Self-Report in a Chronic Low Back Pain Cohort.},
journal = {JOR spine},
volume = {9},
number = {1},
pages = {e70156},
pmid = {41635465},
issn = {2572-1143},
support = {U19 AR076725/AR/NIAMS NIH HHS/United States ; },
abstract = {BACKGROUND: Chronic low back pain (cLBP) is a prevalent and debilitating condition. Gaining insight into the daily experiences of those with cLBP is crucial for developing effective management. Pain and activity are typically assessed at a single time point and often rely on retrospective self-reports, which can be prone to recall bias and may not reflect the day-to-day variability of these experiences. As a part of the University of Pittsburgh LB[3]P Mechanistic Research Center, this study used ecological momentary assessment (EMA) and wearable devices to collect real-time data in a large cohort of adults with cLBP. The primary aims were to collect and characterize pain and activity profiles of individuals with cLBP.<br><br>METHODS: This study enrolled 1007 adults with cLBP who met the National Institutes of Health defined criteria. Over 7&#x2009;days, participants were assessed in their own environment. EMA was gathered in real-time via a custom mobile app, prompting participants three times daily to provide their perceptions of current pain intensity (0-10), pain interference (0-10), and activity level (very light to vigorous). Time of falling asleep and waking was also reported. Participants wore ActiGraph GT9X devices on their wrist and waist. A custom back sensor was also adhered to the skin over the lumbar (L5) segment. Activity counts, wear time, and step counts were calculated, utilizing algorithms provided by ActiGraph. Sensor data were filtered to include at least 4&#x2009;days of 10 or more hours each. Activity counts were categorized into sedentary, light, and moderate-to-very-vigorous based on Freedson Adult cutpoints.<br><br>RESULTS: Out of 1007 participants, 989 submitted EMA data (58.8&#x2009;&#xb1;&#x2009;16.5&#x2009;years old; 40% male and 60% female; mean pain intensity at enrollment of 5.4 (SD 2.1) and a median of 5 (interquartile range [IQR] 3) on a 0-10 scale; mean PROMIS Pain Interference T-score at enrollment of 60.5 (SD 7.5) and a median of 61.2 (IQR 9.6)). The median reported pain intensity level from the EMA was 1 (IQR&#x2009;=&#x2009;3), while pain interference was 3 (IQR&#x2009;=&#x2009;3). More than half of the participants reported a median pain intensity of either 0 or 1 (54.0%) and a median pain interference between 0 and 3 (57.4%). Most participants self-reported their activity levels as moderate (36%) or light (33%). Based on pain ratings during each day, most participants had their pain intensity (30%) and pain interference (40%) peaking in the evening. ActiGraph data from 884 wrist-worn and 785 waist-worn devices were analyzed. Wrist data showed a median of 1&#x2009;765&#x2009;325 (IQR 796&#x2009;995) activity counts/day and 9575 (IQR 4228) steps/day. Waist data showed 358&#x2009;390 (IQR 223&#x2009;758) activity counts/day and 4114 (IQR 3146) steps/day. The percentage of daily sedentary activity was 47.3% for wrist and 72.8% for waist. The back sensor data from 586 participants showed a median of 340&#x2009;345 (IQR&#x2009;=&#x2009;223&#x2009;399) activity counts/day and a median of 3695 (IQR&#x2009;=&#x2009;2743) steps/day. The percentage of time spent in daily sedentary activity was 82.6%. Both ActiGraph devices and the back sensor indicated that the majority of the time was spent in sedentary activity level, which is lower than the activity level reported in the EMA.<br><br>CONCLUSIONS: Despite having cLBP with self-reported moderate pain levels, participants generally reported periods of relatively low levels of pain intensity and interference in their EMA. In addition, their EMA-reported activity levels differed from the sensor data. Participants self-reported higher levels of activity compared to the activity levels calculated by the wearable sensors. This suggests that participants overestimated their activity levels on EMA, or that the activity level cut-points may need to be re-evaluated for the cLBP population. Additionally, sensors placed on different body locations showed varying activity and step counts. The activity counts calculated from the waist ActiGraph and the back sensor from this cohort were lower than the average activity counts in the US adult population. Further research is needed to better quantify these differences for people with cLBP to develop a more comprehensive understanding of the pain experience.},
}
@article {pmid41638375,
year = {2026},
author = {Liu, Y and Wang, C and Wang, C and Fu, L and Zhang, Y and Gao, Z and Yang, Z and Meng, F},
title = {High-concentration polyethylene and polystyrene microplastics co-exposure shorten insect lifespan and impose ecological risk: Multi-omics evidence from Drosophila melanogaster.},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {303},
number = {},
pages = {110474},
doi = {10.1016/j.cbpc.2026.110474},
pmid = {41638375},
issn = {1532-0456},
mesh = {Animals ; *Drosophila melanogaster/drug effects/metabolism/genetics/physiology ; *Longevity/drug effects ; *Microplastics/toxicity ; *Polyethylene/toxicity ; *Polystyrenes/toxicity ; Metabolomics ; Transcriptome/drug effects ; Risk Assessment ; *Environmental Pollutants/toxicity ; Multiomics ; },
abstract = {Microplastics (MPs) are pervasive environmental pollutants, accumulating in ecosystems and posing a long-term exposure risk to both the entire ecosystem and human health. However, the combined impact of such high doses on insect longevity and the consequent ecological consequences remain understudied. Here we used Drosophila melanogaster as a model to quantify lifespan shortening under environmentally realistic and extreme concentrations of Polyethylene (PE) and Polystyrene (PS) co-exposures and to unravel the molecular bases of the observed toxicity. Furthermore, we delved into the underlying mechanism through metabolomics and transcriptomics analysis. Our results demonstrated PE and PS MPs co-exposure with greatly high concentrations significantly reduced the lifespan of Drosophila and influenced age-related phenotypes such as climbing ability, intestinal barrier and hunger resistance. We found that differential metabolites were engaged in various metabolic pathways, including ABC transporters, alanine, aspartate and glutamate metabolism. Differentially expressed genes (DEGs) were closely related to Toll and Imd signaling pathway and Longevity regulating pathway. Gram-level PE and PS co-exposure triggers immune-metabolic crosstalk failure and represents a realistic terrestrial risk factor for insect longevity. Our data highlight the urgent need to include high-dose microplastic mixtures in terrestrial ecotoxicological risk assessments and biodiversity conservation strategies. SYNOPSIS: Co-exposure to PE and PS MPs with high concentrations induces changes in gene expression and metabolites associated with immune system and energy metabolism in Drosophila, thereby affecting their lifespan.},
}
@article {pmid41638723,
year = {2026},
author = {Holzer, KJ and Alaverdyan, H and Xu, Z and Frumkin, MR and Frey, KA and Gregory, SH and Rodebaugh, TL and Lu, C and King, CR and Head, D and Kannampallil, T and Haroutounian, S},
title = {Protocol for Personalised Prediction of Persistent Postsurgical Pain.},
journal = {BMJ open},
volume = {16},
number = {2},
pages = {e107055},
pmid = {41638723},
issn = {2044-6055},
mesh = {Humans ; *Postoperative Pain/diagnosis/psychology ; Adult ; Prospective Studies ; Middle Aged ; Aged ; Female ; Adolescent ; Young Adult ; Male ; Pain Measurement ; Ecological Momentary Assessment ; *Precision Medicine ; Quality of Life ; Machine Learning ; Analgesics, Opioid/therapeutic use ; },
abstract = {INTRODUCTION: Persistent postsurgical pain (PPSP) affects up to 15% of patients after major surgery, impairing physical function, quality of life and increasing risk for long-term opioid use. Current PPSP prediction models rely on static or retrospective data and fail to incorporate dynamic perioperative factors. The Personalised Prediction of Persistent Postsurgical Pain (P5) study aims to develop individualised, multimodal prediction models by integrating preoperative behavioural, psychophysical and neurocognitive assessments and high-frequency symptom monitoring.<br><br>METHODS AND ANALYSIS: P5 is a prospective, single-centre cohort study enrolling 2500 adults aged 18-75 undergoing major surgery at a tertiary academic hospital. Participants complete baseline surveys, cognitive testing and quantitative sensory testing preoperatively. Ecological momentary assessments (EMAs) are collected via smartphone three times per day through 30 days postoperatively, capturing pain, mood, catastrophising and medication use. Participants are assessed on postoperative day 1 and complete online surveys at 3 and 6 months, evaluating pain persistence, interference, neuropathic symptoms and related outcomes. Clinical and perioperative data are extracted from the electronic health record. The primary outcome is PPSP at 3 months. Predictive models will be developed using supervised machine learning and dynamic structural equation modelling to extract latent features from EMA data. Model performance will be assessed using area under the receiver operating characteristic curve, area under the precision-recall curve and SHapley Additive exPlanations for interpretability.<br><br>ETHICS AND DISSEMINATION: This study has received ethics approval from the Washington University School of Medicine Institutional Review Board #202101123. Informed consent is required. Results will be submitted for publication in peer-reviewed journals and presented at research conferences.<br><br>TRIAL REGISTRATION NUMBER: NCT04864275.},
}
@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, M&#xc1; 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.},
}
@article {pmid41639126,
year = {2026},
author = {Molino, RJEJ and Van Weerd, M and Torreno, VPM and Rellin, KFB and Mondragon, MV and Parungao, L and Manila-Fajardo, AC and Santos, DMC and Junio, HA},
title = {Multi-omics and palynology of selected Philippine forest honey.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5359},
pmid = {41639126},
issn = {2045-2322},
support = {ORG 2021-0013//Forest Foundation Philippines/ ; },
mesh = {*Honey/analysis ; Philippines ; *Forests ; *Metabolomics/methods ; Bees ; Mass Spectrometry ; Animals ; Chromatography, Liquid ; Multiomics ; },
abstract = {The Sierra Madre Mountains, which happen to be the longest mountain range in the Philippines, is home to lush floral and faunal species as well as forest-based indigenous communities actively involved in preserving local biodiversity. With active reforestation efforts ongoing for decades, the locals are further encouraged to continue their long-standing practice of honey gathering as a form of cultural manifestation and as an important source of livelihood. To further inspire ongoing conservation efforts, we aim to show that the small molecule diversity in Sierra Madre forest honey reflects the local floral composition and is reflective of the positive impact of previous reforestation initiatives. In order to do this, liquid chromatography-mass spectrometry (LC-MS) based metabolomics was used to profile and compare metabolite diversity in honey produced by Apis cerana, Apis breviligula Maa. and Tetragonula biroi (Friese) honey from Palaui Island and Laiban in Northern and Southern Sierra Madre, respectively. Surprisingly, the Philippine National Tree and unfortunately endangered Pterocarpus indicus Willd (loc. Narra) proved to be important, especially in Palaui Island where honey from A. cerana is close to being monofloral. Aside from P. indicus and its small molecule marker hypaphorine, caffeine was detected in Palaui honey beautifully reflecting the way of life of native Agtas who manage a small coffee plantation. The abundance of caffeine, however, is higher in stingless honey samples from Tanay, Rizal where Coffea trees have been extensively included in restoration activities over the past few decades. Our results imply the possibility of using honey as an ecological monitoring tool while generating baseline chemical information that reflects the state of Philippine forests. Furthermore, the identification of unique chemical components in forest honey can be further used in programs that assist indigenous communities in safeguarding the ownership and origin of forest honey sources.},
}
@article {pmid41640395,
year = {2026},
author = {Deane, DC and Hui, C and McGeoch, M},
title = {An Ecological Definition and Objective Threshold for Differentiating Small Fragments.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73054},
pmid = {41640395},
issn = {2045-7758},
abstract = {In an increasingly fragmented natural world, understanding how different ecological phenomena vary with patch size has many motivations. Examples include the assembly of biodiversity, ecosystem service provision and the suitability of fragments for habitat specialist species. A common approach to such questions divides fragments into small and large size classes for separate analysis. However, lack of an objective definition and means to differentiate 'small' from 'large' patches limits our ability to compare findings across studies, arguably impeding progress toward any unified views. Because larger and smaller fragments tend, on average, to respectively over-represent narrow- and wide-range species, an 'area for unbiased species representation' (AUSR) can be defined at some intermediate fragment size predicted to contain species at incidence frequencies approximating that of the overall landscape. A central tendency for AUSR has previously been estimated for patchy habitats (islands, habitat islands and fragments), providing a benchmark to compare this threshold of small fragment size between studies. However, if AUSR can be readily determined within individual study systems, it would also provide an objective threshold to separate small and large fragments under the AUSR definition. Here we assess this potential for 138 published datasets from various fragmented landscapes using an index comparing species incidence frequencies in each fragment with that of the overall landscape. Regressing this index on fragment area yielded an estimate for AUSR in over 90% of cases, suggesting broad applicability as an objective way to separate fragments into two size classes. Regression slopes provide further information on the relative representation of narrow- vs. wide-range species, with ~80% being numerically consistent with the overall negative trend. Requiring only the same data as the island species-area relationship, AUSR can provide useful insights on the relative importance of narrow- vs. wide-ranging species for studies of patch-size dependence in ecological phenomena.},
}
@article {pmid41642108,
year = {2026},
author = {Venkatraman, S and Pongchaikul, P and Balasubramanian, B and Anurathapan, U and Meller, J and Tohtong, R and Hongeng, S and Chutipongtanate, S},
title = {Transcriptomic Correlation Identifies Cell Model Representatives for MYCN-Amplified Pediatric Neuroblastoma, Downstream Impact of Model Choice on Functional Interpretation, and Potential Drug Repositioning Candidates.},
journal = {Omics : a journal of integrative biology},
volume = {30},
number = {3},
pages = {134-145},
doi = {10.1177/15578100261419486},
pmid = {41642108},
issn = {1557-8100},
mesh = {Humans ; *Neuroblastoma/genetics/drug therapy/pathology/metabolism ; *N-Myc Proto-Oncogene Protein/genetics ; Cell Line, Tumor ; *Transcriptome ; Gene Amplification ; *Drug Repositioning ; Gene Expression Regulation, Neoplastic/drug effects ; Gene Expression Profiling ; Child ; Antineoplastic Agents/pharmacology ; },
abstract = {Neuroblastoma (NB) is the most common extracranial solid malignancy of children, and MYCN amplification defines a high-risk subtype with poor outcomes. Although widely used in preclinical drug discovery, NB cell lines are often selected based on availability rather than the molecular characteristics of patient-derived tumors, leading to a critical translational gap between experimental outcomes and clinical relevance. To address this, we developed a rank-based transcriptomic correlation framework to assess the concordance between patient-derived tumors (n = 642; combined from the SEQC/MAQC-III and TARGET cohorts) and publicly available NB cell lines (n = 39). This system-level analysis enabled the identification of cell model representatives (CMRs) that closely recapitulate the gene expression landscapes of clinical tumors. COG-N-557, SMS-KAN, and NB-SD emerged as the top CMRs for MYCN-amplified tumors, whereas COG-N-549, FELIX, and SK-N-SH were identified for MYCN-nonamplified tumors. Pathway enrichment analyses indicated that MYCN-amplified CMRs retain key transcriptional programs involved in neuronal development and tumor proliferation, supporting their biological relevance. Leveraging these models, we integrated pharmacogenomic connectivity mapping and drug-gene network analyses to uncover kinase inhibitors and epigenetic modulators as promising therapeutic candidates capable of targeting MYCN-driven transcriptional programs, despite MYCN being an undruggable oncogene. In conclusion, this study addresses a fundamental systems biology and translational research gap by establishing a data-driven framework for selecting NB cell lines that accurately reflect patient-derived tumor biology with direct implications for prioritizing therapeutically relevant drug candidates. Future studies should prioritize the top CMRs as in vitro models to enhance translational relevance and accelerate precision drug discovery in high-risk pediatric NB.},
}
@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.},
}
@article {pmid41643370,
year = {2026},
author = {Jiajun, C and Xiaojuan, X and Shiyan, C and Xiaoli, Y and Yan, Z and Junfang, Z and Zhiliang, Z and Daqiang, Y and Yanling, Q},
title = {PFOA and co-exposure with PFOS induce AMPK-dependent hypoglycemia in mice: integrated evidence from physiology, multi-omics, and molecular docking.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110076},
doi = {10.1016/j.envint.2026.110076},
pmid = {41643370},
issn = {1873-6750},
mesh = {*Fluorocarbons/toxicity ; Animals ; Molecular Docking Simulation ; Mice ; *Alkanesulfonic Acids/toxicity ; Male ; *Caprylates/toxicity ; Mice, Inbred C57BL ; *Hypoglycemia/chemically induced ; *Environmental Pollutants/toxicity ; AMP-Activated Protein Kinases/metabolism ; Multiomics ; },
abstract = {Per- and polyfluoroalkyl substances, notably perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS), are persistent environmental contaminants with increasing evidence of metabolic toxicity. However, their effects on glucose homeostasis and the underlying mechanisms remain unclear. In this study, we investigated the metabolic consequences of PFOA, PFOS and co-exposure in male C57BL/6 mice for 28 days. Physiological indicators, including fasting blood glucose and hepatic glycogen, were evaluated, followed by transcriptomic, metabolomic, and molecular docking analyses. We found that PFOA and PFOS co-exposure significantly induced hypoglycemia and reduced hepatic glycogen content. Transcriptomic and metabolomic profiling revealed enriched pathways related to glucose metabolism, with the AMPK signaling pathway identified as a central mediator. Notably, PFOA and co-exposure upregulated glycolytic and fatty acid oxidation genes, while suppressing glycogen synthesis regulators. Molecular docking further indicated that both PFOA and PFOS could bind to adiponectin receptors (AdipoR1/2), potentially disrupting normal receptor-mediated AMPK activation. Together, these findings establish an AdipoR1/2-AMPK-mediated mechanism for PFAS-induced glucose metabolic disruption, particularly under PFOA or co-exposure. We provide the integrated physiological and mechanistic evidence linking PFAS exposure to AMPK-dependent hypoglycemia, highlighting the need for metabolic health risk assessments of PFAS mixtures in the environment.},
}
@article {pmid41644669,
year = {2026},
author = {White, SL and Brasher, MS and Pattee, J and Zhou, W and Chapman, S and Jee, YH and Bell, CC and Jamil, TL and Barrio, M and Arehart, CH and Evans, LM and Hirbo, J and Cox, NJ and Straub, P and Namba, S and Bertucci-Richter, E and Guare, L and Edris, A and Morris, S and Mulford, AJ and Zhang, H and Fennessy, B and Tobin, MD and Chen, J and Williams, AT and John, C and van Heel, DA and Mathur, R and Finer, S and Moksnes, MR and Brumpton, BM and Åsvold, BO and Peculis, R and Rovite, V and Konrade, I and Wang, Y and Crooks, K and Chavan, S and Fisher, MJ and Rafaels, N and Lin, M and Shortt, JA and Sanders, AR and Whiteman, DC and MacGregor, S and Medland, SE and Thorsteinsdóttir, U and Stefánsson, K and Karaderi, T and Egan, KM and Bocklage, T and McCrary, HC and Riedlinger, G and Salhia, B and Shriver, C and Phan, MD and Farlow, JL and Edge, S and Kaur, V and Churchman, ML and Rounbehler, RJ and Brock, PL and Ringel, MD and Pividori, M and Schweppe, R and Raeburn, CD and Walters, RG and Chen, Z and Li, L and Matsuda, K and Okada, Y and Zöllner, S and Verma, A and , and Preuss, MH and Kenny, E and Hendricks, AE and Fishbein, L and Kraft, P and Daly, MJ and Neale, BM and , and , and , and , and Martin, AR and Cole, JB and Haugen, BR and , and Gignoux, CR and Pozdeyev, N},
title = {Global multi-ancestry genome-wide analyses identify genes and biological pathways associated with thyroid cancer and benign thyroid diseases.},
journal = {Nature genetics},
volume = {58},
number = {2},
pages = {307-316},
pmid = {41644669},
issn = {1546-1718},
support = {R00HG011898//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; R00 HG011898/HG/NHGRI NIH HHS/United States ; I01 BX006252/BX/BLRD VA/United States ; CO-J-24-170//Colorado University | UC Denver | Colorado Clinical and Translational Sciences Institute (CCTSI)/ ; R21 CA282380/CA/NCI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; UL1 TR002535/TR/NCATS NIH HHS/United States ; R00 HG012222/HG/NHGRI NIH HHS/United States ; 1R21CA282380//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; R01 AG046938/AG/NIA NIH HHS/United States ; R25 DC021948/DC/NIDCD NIH HHS/United States ; P30 CA177558/CA/NCI NIH HHS/United States ; NNF20OC0062294//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
mesh = {Humans ; *Genome-Wide Association Study ; *Thyroid Neoplasms/genetics/pathology ; *Genetic Predisposition to Disease ; *Thyroid Diseases/genetics ; Multifactorial Inheritance/genetics ; Polymorphism, Single Nucleotide ; Graves Disease/genetics ; },
abstract = {Thyroid diseases are common and highly heritable. We performed a meta-analysis of genome-wide association studies from 19 biobanks for five thyroid diseases: thyroid cancer (ThC), benign nodular goiter, Graves' disease, lymphocytic thyroiditis and primary hypothyroidism. We analyzed genetic association data from ~2.9 million genomes and identified 313 known and 570 new independent loci linked to thyroid diseases. We discovered genetic correlations between ThC, benign nodular goiter and autoimmune thyroid diseases (rg = 0.16-0.97). Telomere maintenance genes contributed to benign and malignant thyroid nodular disease risk, whereas cell cycle, DNA repair and damage response genes were associated with ThC. We propose a paradigm that explains genetic predisposition to benign and malignant thyroid nodules. We found polygenic risk score associations with ThC risk of structural disease recurrence, tumor size, multifocality, lymph node metastases and extranodal extension. Polygenic risk scores identified individuals with aggressive ThC in a biobank, creating an opportunity for genetically informed population screening.},
}
@article {pmid41648011,
year = {2025},
author = {Rappazzo, AC and Lo Giudice, A and Giannarelli, S and Rizzo, C and Tomei, A and Ghezzi, L and Cairns, WRL and Azzaro, M and Papale, M},
title = {Diverging contaminant profiles and prokaryotic assemblages in Arctic and Antarctic lake sediments.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1722478},
pmid = {41648011},
issn = {1664-302X},
abstract = {INTRODUCTION: Persistent organic pollutants (POPs) and trace metals are increasingly recognized as critical drivers of ecological change in polar environments. However, their combined impact on sediment microbial communities remains largely unexplored.<br><br>METHODS: We analyzed sediments from 12 high-latitude lakes and ponds, five from the Arctic (Svalbard) and seven from the Antarctic (South Shetland Islands/Deception Island), to examine contaminant profiles (polychlorinated biphenyls [PCBs] and trace metals) and prokaryotic community structure using 16S rRNA gene amplicon sequencing. Finally, we assessed the associations between the identified communities and detected pollutants, and compared these associations across lakes and sites.<br><br>RESULTS: The results revealed distinct chemical signatures between poles: Arctic sediments were mainly contaminated by polycyclic aromatic hydrocarbons (&#x2211;PAHs, 18.5-685.7 ppb; phenanthrene was the most abundant), whereas Antarctic sediments showed relatively higher concentrations of chlorobenzenes (&#x2211;CBs, 1.9-3.6 ppb) and polychlorinated biphenyls (&#x2211;PCBs, 0.9-1.4 ppb), with 2-methylnaphthalene as the most abundant PAH. Manganese was the most abundant metal in both regions, reaching 760 ppm in the Arctic, while elevated arsenic and lead characterized specific Antarctic sites. Amplicon sequencing identified five dominant phyla (i.e., Actinobacteriota, Bacteroidota, Alpha- and Gammaproteobacteria, and Desulfobacterota) with significant compositional shifts between poles.<br><br>DISCUSSION: Notably, the distinct contaminant signatures between regions appeared to be associated with shifts in microbial community composition, suggesting that both the type and intensity of POP and metal exposure may influence bacterial diversity and ecological functions in polar lake sediments. These findings provide a robust baseline for Arctic-Antarctic comparisons, positioning polar lakes as sensitive sentinels of contaminant-driven ecological change. They also underscore the urgent need for functional studies and long-term monitoring to evaluate ecosystem resilience under accelerating climate change.},
}
@article {pmid41648310,
year = {2026},
author = {Szenei, J and Burke, A and Liong, A and Korenskaia, A and Lukowski, AL and Ziemert, N and Nikel, PI and Leão, PN and Moore, BS and Weber, T and Blin, K},
title = {Computational pipeline reveals nature's untapped reservoir of halogenating enzymes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41648310},
issn = {2692-8205},
support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; R35 GM159745/GM/NIGMS NIH HHS/United States ; },
abstract = {Microbial halogenated natural products (hNPs) hold ecological, agricultural, and biomedical relevance. The hNP-producing potential of the organism can be assessed by the precise prediction of biosynthetic enzymes, yet the detailed annotations of halogenases are often missing from genomic and metagenomic data. We created a manually curated database (https://halogenases.secondarymetabolites.org/) containing information on the halide-specificity, role, and position of verified catalytic residues and results of the mutagenesis studies of more than 120 experimentally validated or in silico inferred halogenases. The collection of experimental data supports a computational pipeline that allows the family-, substrate-, and halide-scope-level annotation of halogenating enzymes by relying on catalytic residues, conserved motifs, and profile Hidden Markov Models (pHMMs). Our analysis with sequence similarity networks (SSNs) highlighted several underexplored clusters in the UniRef50 database. Such finding was a halogenase from Rhodopirellula baltica (RhobaVHPO) previously labelled as a hypothetical chloroperoxidase, which clustered apart from the known chloroperoxidases and bromoperoxidases, but accepted chloride and preferred bromide. Our database and workflow provide extensive and scalable solutions for the systematic and precise annotation of halogenating enzymes in genomic and metagenomic data. The in-depth categorization of halogenases will improve the chemical structure prediction of microbial hNPs, supporting ecological assessments and natural product discovery.},
}
@article {pmid41649413,
year = {2026},
author = {Jo, S and Lee, HG and Nam, DH and Park, C},
title = {Use of metabarcoding detects the rapid onset of cultivation bias in the culture-based profiling of marine sediment bacterial communities.},
journal = {Letters in applied microbiology},
volume = {79},
number = {3},
pages = {},
doi = {10.1093/lambio/ovag020},
pmid = {41649413},
issn = {1472-765X},
support = {RS-2025-02217886//National Research Foundation of Korea/ ; RS-2025-02309093//National Research Foundation of Korea/ ; },
mesh = {*Geologic Sediments/microbiology ; *DNA Barcoding, Taxonomic/methods ; *Bacteria/genetics/classification/growth &amp; development/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; DNA, Bacterial/genetics/chemistry ; Biodiversity ; Phylogeny ; },
abstract = {When cultivation-based microbiology is used to isolate strains from environmental samples, the cultured populations may not represent ecologically relevant taxa in the source community. To address this, we employed pre-cultivation metabarcoding to establish a baseline community profile and detect cultivation bias. Using time-resolved cultivation of marine sediment bacteria, we demonstrated the need for initial community characterization. Sediment-derived microbiomes were cultured in Marine Broth 2216 and analyzed using 16S rRNA gene metabarcoding at 0, 6, 12, 18, and 24 h. A rapid 10-fold reduction in alpha diversity was observed within the 6 h (from 1029 amplicon sequence variants to 34-106), with the genus Vibrio reaching near-complete dominance (>95%) from 18 to 24 h, while environmentally dominant taxa such as Acinetobacter were quickly excluded. This dramatic shift illustrates that, without baseline characterization, cultivation-induced artifacts cannot be clearly distinguished from ecologically meaningful patterns. Fast-growing generalists can quickly outcompete ecologically significant taxa, distorting isolation outcomes and hindering the recovery of functionally important microorganisms. We show that metabarcoding at 0 h can identify cultivation biases, help interpret isolation results, and suggest targeted strategies for recovering ecologically relevant taxa. This integrated approach facilitates more accurate recovery and analysis of functionally significant microbial diversity.},
}
@article {pmid41649635,
year = {2026},
author = {Zhou, L and Qian, J and Liu, Y and Zhang, J and Zhang, K and Zhu, X},
title = {Simulation and optimization of multiple permeable reactive barriers (multi-PRBs) for acid mine drainage (AMD) based on machine learning.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {3},
pages = {143},
pmid = {41649635},
issn = {1573-2983},
support = {No. 2022YFC3702203//National Key R&amp;D Program of China/ ; },
mesh = {*Machine Learning ; *Mining ; *Water Pollutants, Chemical/chemistry ; Neural Networks, Computer ; Computer Simulation ; Models, Theoretical ; Drainage ; },
abstract = {Multiple permeable reactive barriers (multi-PRBs) are an effective in-situ technology for acid mine drainage (AMD) treatment. However, their practical implementation is hindered by unclear mechanisms and a lack of decision models. In this study, a coupled processes numerical model was developed to simulate the synergistic removal of TFe and SO42[-] through multi-PRBs with the optimized sequence of limestone, followed by biochar and then D201 resin. Machine learning integrated with the Non-dominated Sorting Genetic Algorithm (ML-NSGAII) was proposed for optimization, in which a Backpropagation Neural Network (BPNN) served as a highly accurate surrogate model (R[2] > 0.99) to predict system performance, reducing the computational load by 99.7% compared to conventional methods. Spearman correlation analysis and SHAP model interpretation revealed hydraulic load and filler size as the most influential parameters. Application of the TOPSIS-entropy weight method to the Pareto-optimal solution set yielded a final design that significantly enhanced system service life and treatment capacity while reducing costs. This research provides a practical and computationally efficient strategy for designing multi-PRBs for AMD treatment.},
}
@article {pmid41652929,
year = {2026},
author = {Pérez-Granados, C and Morant, J and Darras, KFA and Marín-Gómez, OH and Mendoza, I and Muñoz-Mohedano, MA and Santamaría-García, E and Bastianelli, G and Márquez-Rodríguez, A and Budka, M and Bota, G and De la Peña-Rubio, JM and de la Morena, ELG and Santa-Cruz, M and de la Nava, P and Fernández-Tizón, M and Sánchez-Mateos, H and Barrero, A and Traba, J and Osiejuk, TS and Hart, PJ and Navine, AK and Montoya Muñoz, AF and de Araujo, CB and Rosa, GLM and Denóbile Torres, IM and Camargo Catalano, AL and Simões, CR and Llusia, D and Morales, MB and Acebes, P and Medina, JA and Brown, N and Astaras, C and Karmiris, I and Navarrete, E and Cauchoix, M and Barbaro, L and Funosas, D and Arend, D and Müeller, S and González-García, F and González-Romero, A and Mammides, C and Pontikis, M and Jacuzzi, G and Olden, JD and Bombaci, SP and Marcacci, G and Jacot, A and Zurano, JP and Gangenova, E and Varela, D and Di Sallo, F and Zurita, GA and Atemasov, A and Tremblay, JA and Lamarre, V and Hutschenreiter, A and Monroy-Ojeda, A and Díaz-Vallejo, M and Chaparro-Herrera, S and Briers, RA and Sousa-Lima, R and Pinheiro, T and da Silva, WC and Calvente, A and Molin, AD and Antonelli, A and Gogoleva, S and Palko, I and Trọng, HV and Lage Duarte, MH and Dos Santos Saturnino, N and Silva, SR and Rainho, A and Lopes, P and Schuchmann, KL and Marques, MI and de Oliveira, AS and Littlewood, NA and Tuanmu, MN and Cheng, YR and Chao, H and Kepfer-Rojas, S and Aguilera, AL and Brotons, L and Feldman, MJ and Imbeau, L and Panwar, P and Weed, AS and Deshwal, A and da Paz, RV and Salustio-Gomes, C and Oliveira-Júnior, DD and Lima-Santos, CS and Pichorim, M and Pan, W and Goodale, E and Attisano, A and Theuerkauf, J and Sebastián-González, E},
title = {WABAD: A world annotated bird acoustic dataset for passive acoustic monitoring.},
journal = {Ecology},
volume = {107},
number = {2},
pages = {e70317},
pmid = {41652929},
issn = {1939-9170},
mesh = {Animals ; *Birds/physiology ; *Vocalization, Animal/physiology ; *Acoustics ; *Environmental Monitoring/methods ; *Databases, Factual ; },
abstract = {Under the current global biodiversity crisis, there is a need for automated and noninvasive monitoring techniques that can gather large amounts of data cost-effectively at various ecological scales, from local to large spatial scales. These data can then be analyzed to inform stakeholders and decision-makers. One such technique is passive acoustic monitoring, which is commonly coupled with automatic identification of animal species based on their sound. Automated sound analyses usually require the training of sound detection and identification algorithms. These algorithms are based on annotated acoustic datasets which mark the occurrence of sounds of species inside sound recordings. However, compiling large annotated acoustic datasets is time-consuming and requires experts, and therefore, they normally cover reduced spatial, temporal, and taxonomic scales. This data paper presents WABAD, the World Annotated Bird Acoustic Dataset for passive acoustic monitoring. WABAD is designed to provide the public, the research community, and conservation managers with a novel and globally representative annotated acoustic dataset. This database includes 5047 min of audio files annotated to species-level by local experts with the start and end time and the upper and lower frequencies of each identified bird vocalization in the recordings. The database has a wide taxonomic and spatial coverage, including information on 91,931 vocalizations from 1192 bird species recorded at 72 recording sites in 29 recording locations (mainly countries) and distributed across 13 biomes. WABAD can be used, for example, for developing and/or validating automatic species detection algorithms, answering ecological questions, such as assessing geographical variations on bird vocalizations, or comparing acoustic diversity indices with species-based diversity indices. The dataset is published under a Creative Commons Attribution 4.0 International license that permits redistribution and reuse on the condition that the original work is properly credited.},
}
@article {pmid41653553,
year = {2026},
author = {Ghosh, A and Bhakta, S and Kapse, N and Dhakephalkar, PK and Patra, C and Gorain, B},
title = {Micro/nanoplastic-mediated gut dysbiosis and its impact on cardiac and neuroimmune function in zebrafish model: A multi-omics approach.},
journal = {The Science of the total environment},
volume = {1017},
number = {},
pages = {181443},
doi = {10.1016/j.scitotenv.2026.181443},
pmid = {41653553},
issn = {1879-1026},
mesh = {Animals ; *Zebrafish ; *Dysbiosis/chemically induced ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; Heart/drug effects ; Multiomics ; },
abstract = {The pervasive distribution of micro- and nanoplastics (M/NPs) across ecosystems necessitates a mechanistic investigation into their toxicological consequences. Chronic exposure to M/NPs through combined intestinal uptake and branchial contact in aquatic animals disrupts epithelial barrier integrity, alters gastric secretions and luminal pH, and induces microbial dysbiosis, evidenced by the depletion of commensal taxa and expansion of pathogenic strains. These local perturbations trigger systemic sequelae, including neurotoxicity and cardiotoxicity. Consequences on cross-species analyses demonstrate translational concordance, as human studies similarly link M/NP bioaccumulation with inflammatory bowel disease, cognitive decline, and cardiovascular dysfunction. Integrative multi-omics approaches, encompassing transcriptomic, metabolomic, and microbiome analyses, have begun to elucidate the molecular cascades underpinning M/NP toxicity, providing high-resolution insights into host-microbe-environment interactions. Notwithstanding these advances, critical gaps remain in chronic exposure modelling, capturing particle heterogeneity, and ensuring ecological realism. In this context, zebrafish (Danio rerio) provide a uniquely tractable system for gnotobiotic rearing, microbial transplantation, and live imaging, thereby enabling causal inference and functional validation in real-time. Collectively, this review establishes zebrafish as a pivotal model for elucidating M/NP-induced gut dysbiosis, neurotoxicity, and cardiotoxicity. Multi-omics analyses and translational evidence reveal systemic inflammation, immune-metabolic disruptions, and mechanistic links to human health, providing a foundation for targeted research, regulatory frameworks, and interventions to mitigate environmental M/NP exposure.},
}
@article {pmid41653831,
year = {2026},
author = {Jano, T and Sayed, AN and Hossen, MM and Sardianos, C and Hamila, R and Bensaali, F and Varlamis, I and Dimitrakopoulos, G},
title = {Closing the loop: A systematic review of artificial intelligence in circular e-waste management.},
journal = {Waste management (New York, N.Y.)},
volume = {214},
number = {},
pages = {115392},
doi = {10.1016/j.wasman.2026.115392},
pmid = {41653831},
issn = {1879-2456},
mesh = {*Artificial Intelligence ; *Waste Management/methods ; *Electronic Waste/analysis ; },
abstract = {The proliferation of technological advancements, knitted with volatile consumption patterns and poor end-of-life management of discarded electronics, is currently outpacing sustainability transitions, putting increasing strain on finite material resources and heightening ecological vulnerability. This, in turn, has made electronic waste a stealth contributor to climate change with adverse impacts on the environment, economy, and society at large. This reality underscores the urgent need for a strategic shift from linear waste-disposal methods to circular pathways, where Artificial Intelligence (AI) can build more sustainable feedback loops. At the nexus of AI and circular e-waste management, this study systematically reviews 147 articles from 2019 to October 2025. The analysis reveals a steady increase in AI adoption, particularly in deep learning-based detection and classification applications. To structure the evidence from the literature, a six-tier taxonomy is proposed, encompassing AI methods, lifecycle stages, data, waste types, limitations, challenges, and future pathways and opportunities. Beyond technical interventions, systemic and operational barriers that demand strategic levers to address regulatory ambiguities, legislative gaps, managerial inefficiencies, and logistical fragmentation are elucidated. These challenges underpin data availability and generalizability, as well as the lack of standardization, interoperability gaps, and barriers to the ethical and regulatory adoption of AI. In practice, these constraints limit the development of uncertainty-aware electronic waste systems capable of functioning under realistic operational dynamics. To this end, the paper reframes AI-based systems from terminal sinks to regenerative loops, aligning technological progress with sustainable electronic waste management.},
}
@article {pmid41655849,
year = {2026},
author = {Losiewicz, OM and Wen, A and Cohen, ZD and Akre, S and Bui, AAT and Craske, MG},
title = {Negative emotional inflexibility underlies biological inflexibility: An ecological momentary assessment and passive digital sensing study.},
journal = {Journal of affective disorders},
volume = {402},
number = {},
pages = {121352},
doi = {10.1016/j.jad.2026.121352},
pmid = {41655849},
issn = {1573-2517},
mesh = {Humans ; *Ecological Momentary Assessment ; Male ; Female ; Adult ; *Emotions/physiology ; *Heart Rate/physiology ; Middle Aged ; Bayes Theorem ; Young Adult ; *Major Depressive Disorder/physiopathology/psychology ; },
abstract = {Emotional flexibility, thought to reflect the ability to adapt to internal and external environmental stimuli, is associated with psychological well-being. Emotional inertia and network density, defined as stability and interconnectedness, respectively, of emotions, are aspects of emotion dynamics that represent low emotional flexibility. Studies examining biological substrates of emotional persistence are largely limited to emotional inertia and non-depressed samples. Heart-rate variability (HRV) is a transdiagnostic biomarker for psychopathology thought to be associated with emotional flexibility. This study examined whether emotional inertia and network density were associated with HRV in adults with moderate-to-severe depression (N = 315). Participants completed three 8-day epochs of ecological momentary assessment (EMA) five times daily. Smartwatches measured HRV throughout the study. Emotional inertia and idiographic networks were calculated separately for EMA-rated negative and positive affect. Bayesian dynamic structural equation models with noninformative prior distributions examined the association between emotional inertia and HRV; hierarchical linear modeling examined associations between network density and HRV. Both daytime and bedrest HRV were inversely associated with contemporaneous network density of negative emotions. HRV was not associated with inertia, positive network density, or average EMA-reported affect, though it was associated with age, antidepressant medication, and physical exercise. This was the first study to examine HRV in relation to these emotion dynamics in a depressed sample. The results suggest that experiencing a variety of negative emotions within a short period of time may be associated with underlying biological inflexibility. Future studies should examine the directionality and mechanisms behind this effect and explore potential clinical interventions.},
}
@article {pmid41659429,
year = {2026},
author = {Vallecillo-Zuniga, ML and Akeefe, A and Brown, DG and Wahlig, TA and Marchetti, M and Heiner, T and Davis, KL and Nieznanski, C and Flynn, A and Leung, DT},
title = {Longitudinal Changes in Nasal and Oral Microbiome and Antimicrobial Resistance Gene Profiles in Response to Human Fecal Microbiota Transplantation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41659429},
issn = {2692-8205},
support = {UM1 TR004409/TR/NCATS NIH HHS/United States ; UL1 TR002538/TR/NCATS NIH HHS/United States ; S10 OD034321/OD/NIH HHS/United States ; T32 HG008962/HG/NHGRI NIH HHS/United States ; S10 OD021644/OD/NIH HHS/United States ; T32 HL105321/HL/NHLBI NIH HHS/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; },
abstract = {The gut-lung axis describes interactions between intestinal and respiratory mucosal systems through microbial, metabolic, and immune pathways, but the systemic impact of gut-targeted therapies on upper respiratory tract (URT) communities remains underexplored. We conducted a longitudinal study in adult patients undergoing fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infection (CDI) alongside healthy controls. Fecal, nasal, and oral samples were collected at baseline (Day 0) and on Days 14 and 56 following FMT. Shotgun metagenomic sequencing was performed to quantify microbial diversity, taxonomic composition, and the abundance of antimicrobial resistance genes (ARGs). FMT was associated with increased gut diversity and decreased levels of key intestinal taxa commonly considered pathobionts, including Klebsiella spp., Escherichia spp., Shigella spp., and Klebsiella pneumoniae. At the phylum level, fecal Bacteroidota increased, while Mucoromycota decreased following treatment. Post-FMT nasal microbiome changes included reduced richness and diversity, expansion of Moraxella, and decreases in taxa linked with respiratory colonization, including Staphylococcus aureus and Streptococcus pneumoniae. By Day 56, nasal communities partially recovered toward healthy profiles. Baseline nasal ARG abundance decreased following FMT, particularly among β-lactam, aminoglycoside, and fluoroquinolone resistance genes, and remained comparable to healthy controls by Day 56. In contrast, the oral microbiome and oral resistome remained largely stable, with only minor fluctuations, and no consistent increases in respiratory pathobiont-associated taxa. In summary, FMT was associated with broader effects beyond the gut, including changes in the URT microbial ecology and antimicrobial resistance profiles. Together, these findings are consistent evidence of gut-lung microbial interactions, linking intestinal dynamics with respiratory microbial composition and antimicrobial resistance patterns.},
}
@article {pmid41660072,
year = {2026},
author = {Katapally, TR and Elsahli, N and Ibrahim, ST and Bhawra, J},
title = {Human-centered AI to promote youth mental health: a serendipitous natural experiment enabled by a digital health platform.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20772},
pmid = {41660072},
issn = {2167-8359},
mesh = {Humans ; Adolescent ; *Mental Health ; Male ; Female ; *Artificial Intelligence ; *Health Promotion/methods ; Rural Population ; Mobile Applications ; Longitudinal Studies ; Digital Health ; },
abstract = {BACKGROUND: Health systems are struggling to deliver timely preventive care, particularly for marginalized populations, necessitating integration across health, education, and social services. For Indigenous youth in rural communities, fragmented services, isolation, and limited culturally safe options worsen mental health disparities. Interactive technologies, particularly human-centered artificial intelligence (AI)-enabled digital health platforms grounded in human-computer interaction (HCI), can enable remote interaction with citizens and decision-makers. This study investigated a serendipitous natural experiment to assess varying levels of platform nudging on Indigenous youth compliance in a longitudinal intervention.<br><br>METHOD: This study emerged from the final year of a 5-year initiative embedding a culturally appropriate digital health intervention into school curricula in rural Indigenous communities. While the broader aim was to assess long-term mental health outcomes, an unexpected system disruption assessment of digital nudging on compliance. The platform featured two interfaces: a citizen-facing mobile app for ecological assessments and nudges, and a scientist dashboard for monitoring engagement and triggering nudges. Youth received three nudges: (1) daily system-triggered reminders to complete assessments, (2) weekly non-personalized messages (e.g., land-based activity reminders), and (3) weekly personalized "Best Picture" messages showcasing youth-submitted images. The disruption created four phases: Phase 1 included all nudges; Phase 2 removed non-personalized and personalized nudges; Phase 3 reintroduced them; Phase 4 removed only personalized nudges. Data were analyzed using one-way analysis of variance (ANOVA) with Tukey post hoc tests in R 4.4.2.<br><br>RESULTS: Compliance, measured by completed mobile ecological prospective assessments (mEPAs), varied significantly across most phases. Comprehensive nudging (Phase 1) yielded the highest completion rates and fastest response times, which declined following the removal of personalized scientist-triggered nudges. Loss of personalized scientist-triggered nudges had the most substantial impact on compliance.<br><br>CONCLUSIONS: Consistent system-triggered reminders and personalized "Best Picture" nudges were most effective in sustaining compliance. Findings highlight the importance of integrating personalized, two-way communication features into digital health platforms to strengthen engagement in rural Indigenous communities. By enabling real-time interaction between youth and scientists, the platform supported integration across health, education, and research sectors. Its human-controlled backend and customizable citizen-facing interface reflect principles of human-centered AI, emphasizing trust and autonomy. This approach offers a scalable model for ethical, effective digital interventions that balance technological precision and participant agency.},
}
@article {pmid41661144,
year = {2026},
author = {Miller-Viacava, N and Apoux, F and Ferriere, R and Friedman, NR and Mullet, TC and Sueur, J and Willie, J and Lorenzi, C},
title = {Modulation statistics of natural soundscapesa).},
journal = {The Journal of the Acoustical Society of America},
volume = {159},
number = {2},
pages = {1263-1289},
doi = {10.1121/10.0039892},
pmid = {41661144},
issn = {1520-8524},
mesh = {*Acoustics ; Animals ; *Ecosystem ; *Sound ; Time Factors ; Sound Spectrography ; *Vocalization, Animal ; Signal Processing, Computer-Assisted ; Biodiversity ; },
abstract = {Modulation statistics of "natural soundscapes" were estimated by calculating the modulation power spectrum (MPS) of a database of acoustic samples recorded in nine pristine terrestrial habitats for four moments of the day and two contrasting periods, differing in precipitation level. In particular, a set of statistics estimating low-pass quality, starriness, separability, asymmetry, modulation depth, and 1/ftα temporal-modulation power-law relationships were calculated from the MPS of the samples and related to geographical, meteorological factors and diel variations. MPS were found to be generally low-pass in shape in the modulation domain with most of their modulation power restricted to low temporal (<10-20 Hz) and spectral modulations (<0.5-1 cycle/kHz). Modulation statistics were distinguished between habitats irrespective of moment of the day and precipitation period with a greater role of modulation depth and starriness. Separability and starriness were found to be related to the global biodiversity decrease from tropical to polar regions, suggesting that the lack of joint high spectral and fast temporal modulations and MPS complexity are important features that may characterise "biophony," the collective sound produced by animals in a given habitat. These findings may help guide research on monitoring auditory behaviours and underlying mechanisms expected to exploit regularities of natural scenes.},
}
@article {pmid41662068,
year = {2026},
author = {Sacco, MJ and Divita, G and Coale, K and Goldman, HH and Rosé, CP},
title = {An ecological model in support of an ontology of mental functioning.},
journal = {PLOS mental health},
volume = {3},
number = {1},
pages = {e0000407},
pmid = {41662068},
issn = {2837-8156},
abstract = {Health records contain rich sources of mental health data that can be used to evaluate disability and health care outcomes. However, a lack of behavioral health ontologies focused on daily life activity functioning has impeded development of clinical informatic tools to extract mental functioning information. We aim to present the theoretical foundation and conceptual model upon which the Ecological Mental Functioning Ontology (EMFO) was built to facilitate natural language processing (NLP) to extract mental functioning information in free-text clinical records. Subject matter experts operationally defined mental functioning, and a related theoretical perspective was established. Face validity of a proposed model was obtained using an iterative grounded theory approach. An annotation schema based on the model was constructed and tested using manual annotation and consensus on datasets of real and synthetic clinical notes. An annotation schema, based on the Ecological Model of Mental Functioning (EMMF), was shown to be robust when using NLP methods to identify and extract mental functioning information in real and synthetic behavioral health clinical notes. Mental functioning is a complex phenomenon that is fully conceptualized within an ecological milieu encompassing the dynamic transactive relationship between the person, the nature and demands of activities the person participates in, and the external contextual and environmental factors within which the activities take place. By operationalizing mental functioning, the EMMF provided a conceptual roadmap to develop the EMFO and NLP methods that identify and extract mental functioning activity information in clinical records.},
}
@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.},
}
@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.},
}
@article {pmid41664026,
year = {2026},
author = {Kim, H and Heo, SJ and Park, S and Lee, J and Do, G and Park, JY},
title = {Predicting suicidal and self-harm ideation using ecological momentary assessment: deep learning analysis in a general population sample.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {192},
pmid = {41664026},
issn = {1471-244X},
support = {RS-2023-KH135442//Ministry of Health and Welfare/ ; },
abstract = {BACKGROUND: Suicidal and self-harm ideation are major risk factors for suicide but are often difficult to detect, particularly in non-clinical populations. Ecological Momentary Assessment (EMA) offers a real-time, low-burden method for monitoring psychological states, yet its predictive value outside clinical settings remains unclear.<br><br>OBJECTIVE: To evaluate whether brief, indirect daily EMA data collected via a smartphone app can predict suicidal and self-harm ideation two weeks later in a general population sample.<br><br>METHODS: A total of 499 adults in Korea completed 28 days of EMA using the BIG4&#x2009;+&#x2009;app, reporting on seven daily items related to mood, sleep, appetite, concentration, fatigue, and loneliness. Suicidal and self-harm ideation were assessed using the CESD-R at baseline, 2 weeks, and 4 weeks. A recurrent neural network with Long Short-Term Memory (LSTM) architecture was trained on two-week EMA sequences, using 10-fold cross-validation.<br><br>RESULTS: The combined model using EMA and baseline data achieved an AUC of 0.873 for suicidal ideation and 0.821 for self-harm ideation. Predictive accuracy exceeded an AUC of 0.75 by day 6. Participants with ideation consistently showed lower scores on all EMA items. The study achieved a 94% compliance rate.<br><br>CONCLUSIONS: Brief, indirect EMA data can predict near-term suicidal and self-harm ideation in a general population. These findings support the feasibility of smartphone-based EMA as a scalable and non-intrusive tool for early detection of suicide risk.<br><br>CLINICAL TRIAL NUMBER: Not applicable.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12888-026-07815-6.},
}
@article {pmid41664417,
year = {2026},
author = {De Camargo, E and Schindler, S and Zülke, AE and Glaesmer, H and Hinz, A and Engel, C and Wirkner, K and Riedel-Heller, SG and Schomerus, G and Sander, C},
title = {Rest Assured: The Association of Structural, Functional Support, and Loneliness With Subjective Sleep Health.},
journal = {Journal of sleep research},
volume = {},
number = {},
pages = {e70303},
doi = {10.1111/jsr.70303},
pmid = {41664417},
issn = {1365-2869},
support = {713-241202//Freistaat Sachsen/ ; 14505/2470//Freistaat Sachsen/ ; },
abstract = {Sleep is increasingly understood as a socially embedded phenomenon. This study examined how structural and functional aspects of social support, as well as loneliness, relate to sleep health in a German sample of middle-aged adults (N = 5388). Drawing on the socio-ecological model of sleep health, we assessed the contributions of social support dimensions while accounting for age, sex, and socioeconomic status, as well as psychological covariates. The results of the binary logistic regression showed that functional support (ESSI), friend network size (LSNS6), and loneliness (CES-D item 14) significantly (p < 0.001) predicted sleep health (PSQI), while family network size did not. The portion of explained variance was small (4%-5%). Results remained robust after adjusting for age, sex, and socioeconomic status, but no longer when including psychological covariates (GAD-7, SWLS, CES-D), in which case only the friend network size remained significant (p = 0.019). Women were significantly more affected by poor sleep health than men, and with higher socioeconomic status, fewer people reported suffering from poor sleep (all: p < 0.001). Additional subgroup analysis revealed higher age as a risk factor for worse sleep health in women only, while the friend network was only relevant in men. Our findings highlight the importance of distinguishing between structural and functional dimensions of social support in sleep health research and interventions, and suggest a potential sex-by-age interaction. Future research should promote equity by including diverse populations and longitudinally examine how social support, especially friend networks, affects sleep across genders, ages, and contexts.},
}
@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 = {},
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.},
}
@article {pmid41666224,
year = {2026},
author = {Yang, B and Molton, I and Humbert, A and Baylor, C and Gregg, E and Ehde, D and Sullivan, J and Lanz, E and Schiller, M and Hurvitz, P and Lee, D},
title = {Environmental influences on community participation among people with multiple sclerosis: A mixed methods study.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0342678},
pmid = {41666224},
issn = {1932-6203},
mesh = {Humans ; *Multiple Sclerosis/psychology ; Female ; Male ; Middle Aged ; Adult ; *Community Participation ; Focus Groups ; Geographic Information Systems ; *Environment ; Aged ; },
abstract = {OBJECTIVE: To examine the influence of environmental factors (EFs) and personal factors (PFs) on community participation among people with multiple sclerosis (PwMS) and identify areas for improvement.<br><br>METHODS: A mixed methods explanatory sequential design was used. A secondary data analysis of patient-reported outcomes and Global Positioning System (GPS) data was completed using multiple linear regression analysis to examine associations between five EFs, five PFs, and six community participation outcomes in 100 PwMS. Four focus groups were completed with 12 PwMS who use mobility aids and 12 who do not to understand how EFs affected community participation experiences. Thematic analysis was used.<br><br>RESULTS: Regression results showed significant associations between PFs and five community participation outcomes (R2&#x2009;=&#x2009;13% - 48%, p&#x2009;<&#x2009;0.05), and EFs explained an additional 11% variation in satisfaction with participation and 11% in GPS-derived measures of activity space, after adjusting for PFs (&#x394;R&#xb2;&#x2009;=&#x2009;0.11, p&#x2009;<&#x2009;0.05). Among individual EFs, after accounting for PFs, perceived financial resources was associated with ability to participate (B&#x2009;=&#x2009;1.46, p&#x2009;=&#x2009;0.018), and satisfaction with participation (B&#x2009;=&#x2009;3.12, p&#x2009;<&#x2009;0.001). Social support (B&#x2009;=&#x2009;-1.05, p&#x2009;=&#x2009;0.022) and neighborhood safety (B&#x2009;=&#x2009;1.3, p&#x2009;=&#x2009;0.007) were associated with activity space. Qualitative findings revealed that mobility aid users experienced increased challenges in the built environment, and non-users reported more concerns about the attitudinal environment. They also described how environmental support enabled participation despite functional declines. Acceptance and adaptation were useful strategies, but participants called for improvements in the built environment, information access, MS specialty care, and public attitudes towards disability.<br><br>CONCLUSION: Community participation among PwMS is influenced by both PFs and EFs. Statistically, EFs uniquely affected participation satisfaction and activity space, while qualitative findings revealed major barriers and highlighted needs for improvement in physical, social, and attitudinal environments.},
}
@article {pmid41666339,
year = {2026},
author = {Liu, Y and Wu, X and Le, X and Cheng, H and Peng, Q and Wen, L and Hou, H and Hayat, K and Liu, W and Yin, S},
title = {Multiomics Insights into the Ecotoxicological Effects of Soil Microplastics on Crop Plants.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {7},
pages = {5832-5844},
doi = {10.1021/acs.jafc.5c11305},
pmid = {41666339},
issn = {1520-5118},
mesh = {*Soil Pollutants/toxicity/metabolism ; *Crops, Agricultural/metabolism/drug effects/genetics/chemistry/growth &amp; development ; *Microplastics/toxicity/metabolism ; Ecotoxicology ; Metabolomics ; Soil/chemistry ; Multiomics ; },
abstract = {Microplastics (MPs) have become pervasive contaminants. This is due to plastic mulching, wastewater irrigation, and sludge application. Concentrations of MPs in intensive farming regions have been recorded at 41,741 particles/kg. MPs are absorbed by crop roots and leaves and then travel to reproductive organs. In these organs, they cause oxidative stress, genotoxicity, and toxicity, which disrupts nutrient uptake, photosynthesis, and crop yield. This review summarizes 20 years (2003-2024) of studies on MP-distribution in soil-crop systems and their phytotoxicity mechanisms, highlighting the pioneering role of multiomics methods. Genomic analyses show that MPs cause DNA damage and change the expression levels of stress-response genes. Transcriptomics identifies disrupted pathways. These pathways are in carbohydrate metabolism, plant hormones, and antioxidant defense. Proteomics uncovers post-translational modifications. These affect nutrient transporters. Metabolomics further highlights disturbances in glycolysis, amino acid synthesis, and ROS-scavenging metabolites. Despite these advances, integrating multiomics data sets to elucidate systemic "gene-protein-metabolite" networks remains challenging. Key knowledge gaps include MP-protein binding mechanisms, the development of crop-specific biomarkers, and the interaction of MPs with costressors. Future research should prioritize integrated transcriptomic-metabolomic profiling to identify stress-response pathways, use X-ray crystallography to map MP-protein interactions, and develop MP-resilient crop varieties. Multiomics integration is essential for decoding the toxicity of the MPs and formulating mitigation strategies to safeguard the sustainability of agriculture.},
}
@article {pmid41667953,
year = {2026},
author = {Guccione, C and Sfiligoi, I and Gonzalez, A and Shaffer, JP and Kazachkova, M and Weng, Y and McDonald, D and Shah, SC and Minot, SS and Paulson, TG and Grady, WM and Alexandrov, LB and Knight, R and Curtius, K},
title = {Community assembly modeling of the microbiome within Barrett's esophagus and esophageal adenocarcinoma.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41667953},
issn = {1471-2164},
support = {AGA2022-13-05//AGA Research Foundation/ ; 2019-67013-29137//National Institute of Food and Agriculture/ ; RG103468//University of California, San Diego/ ; P30 CA023100/NH/NIH HHS/United States ; ICX002027A//U.S. Department of Veterans Affairs/ ; 5K12GM068524-17/NH/NIH HHS/United States ; T32 CA067754/CA/NCI NIH HHS/United States ; IK2 CX002027/CX/CSRD VA/United States ; R01 CA270235/NH/NIH HHS/United States ; R01 CA270235/CA/NCI NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; },
abstract = {UNLABELLED: Computational modeling of somatic evolution, a process shaped by ecology and impacting both host cells and microbial communities in the human body, can capture important dynamics driving carcinogenesis. Here we considered models for esophageal adenocarcinoma (EAC), a cancer that has dramatically increased in incidence over the past few decades in Western populations, with high case fatality rates due to late-stage diagnoses. Despite advancements in genomic analyses of the precursor Barrett’s esophagus (BE), prevention of late-stage EAC remains a significant clinical challenge. Previous microbiome studies in BE/EAC have focused on quantifying static microbial abundance differences rather than determining population dynamics. Using whole genome sequencing data from a total of 505 esophageal samples, we first applied a robust bioinformatics pipeline to extract non-host DNA reads, mapped these putative reads to microbial taxa, and retained those taxa with high genomic coverage. When applying mathematical models of demographic stochasticity to sequential stages of progression to EAC, we observed evidence of neutral dynamics in community assembly within normal esophageal tissue and BE, but not EAC. In a large case–control study of BE patients who progressed to EAC versus BE patients with non-cancer outcomes (NCO) during follow-up (mean = 10.5 years), we found that Helicobacter pylori deviated significantly from the neutral expectation in BE NCO only, suggesting that factors related to H. pylori or H. pylori infection itself may influence EAC risk. Additionally, stochastic simulations incorporating selection recapitulated non-neutral behaviors observed. Formally modeling dynamics during progression holds promise in clinical applications by offering a deeper understanding of microbial involvement in cancer development.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12545-w.},
}
@article {pmid41668731,
year = {2025},
author = {Gao, H and Li, J and Liu, L and Gu, Z and Yu, H and Xing, D and Zhao, T and Li, C},
title = {Multi-omics profiling reveals associations between gut microbiota and olfactory gene expression in mosquitoes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1745848},
pmid = {41668731},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Culex/microbiology/genetics/physiology ; Metagenomics ; *Smell/genetics ; Gene Expression Profiling ; Arthropod Antennae/metabolism ; Transcriptome ; Computational Biology ; Multiomics ; },
abstract = {INTRODUCTION: The interplay between gut microbiota and host physiological processes has been extensively studied in vertebrates, where it plays a crucial role in regulating appetite, emotion, immunity, and other physiological functions. However, whether a similar regulatory mechanism exists in insects remains unclear, especially regarding the long-distance regulation of olfactory function. This study focused on three Culex subspecies (Culex quinquefasciatus, Culex pipiens pallens, and Culex pipiens molestus) that are closely related but exhibit significant differences in olfaction-dependent ecological habits. By integrating antennal transcriptomic and gut metagenomic data, we systematically analyzed the expression characteristics of olfactory-related genes, the structure of gut microbial communities, and their intrinsic associations.<br><br>METHODS: We integrated antennal transcriptomic and gut metagenomic sequencing to analyze olfactory-related gene expression, gut microbial community structure, and their intrinsic associations in male and female individuals of the three Culex subspecies. Bioinformatics analyses included differential gene screening, functional enrichment, microbial taxonomic annotation, and Spearman correlation analysis.<br><br>RESULT: The results showed that a large number of sex-specific and species-specific differentially expressed genes (DEGs) were identified in the antennae of the three Culex subspecies. Among these, 345 DEGs were shared sex-specific genes across species, which were significantly enriched in pathways such as odor binding, signal transduction, and xenobiotic metabolism. At the phylum level, the&#xa0;gut microbial composition was dominated by Proteobacteria, Bacteroidetes, and Firmicutes, showing a conserved structure; at the genus level, 11 dominant&#xa0;genera (including Wolbachia, Elizabethkingia, and Asaia) exhibited distinct species-specific distribution patterns. Diversity analysis revealed that&#xa0;the gut&#xa0;microbial richness of male individuals was significantly higher than that of&#xa0;females, and the &#x3b2;-diversity showed an obvious "sex clustering" pattern.Correlation analysis further indicated that 152 DEGs were significantly correlated with 107 microbial genera. Among them, olfactory-related genes were closely associated with several core genera (e.g., Wolbachia, Asaia, Serratia). Gut microbes may remotely regulate the expression and function of&#xa0;olfactory genes in antennae through metabolites or signaling molecules, thereby influencing mosquito behaviors such as host localization, mating, and oviposition.<br><br>DISCUSSION: This study reveal the intrinsic association between gut microbes and olfactory function in Culex mosquitoes, providing a new perspective for understanding the "microbe-host" cross-organ regulatory mechanism and laying a theoretical foundation for the development of novel mosquito vector control strategies based on microbial or olfactory interference.},
}
@article {pmid41669161,
year = {2026},
author = {Akre-Bhide, S and Cohen, ZD and Welborn, A and Zbozinek, TD and Craske, MG and Bui, A},
title = {Detecting momentary reward and affect with real-time passive digital sensor data.},
journal = {JAMIA open},
volume = {9},
number = {1},
pages = {ooag005},
pmid = {41669161},
issn = {2574-2531},
abstract = {OBJECTIVES: This study explores the capability of passive digital sensor data from smartphones and smartwatches to predict self-reported ecological momentary assessments (EMA) of affect, motivation, interest, and pleasure in activities in an unseen test sample.<br><br>MATERIALS AND METHODS: Data were collected from 245 depressed participants with high-to-low anhedonia (195 train, 50 test) generating 23 812 EMA sessions. Machine learning models were used to assess the ability of behavioral and physiological features, aggregated over windows of 15 minutes to 3 hours, to predict momentary subjective states.<br><br>RESULTS: For 12 of 15 EMA questions asked, machine learning models exceeded random chance in the fully-held-out test sample, suggesting detectable signals between passive measures and subjective states. Dependent on the sensor type, the optimal aggregation periods ranged from 15 minutes to 3 hours, with generally at least two hours of data being required. Subgroup analyses revealed variations in model performance by demographics, depression severity, and anhedonia severity.<br><br>CONCLUSION: This study establishes the feasibility of using passive digital sensing to detect momentary subjective states, providing a baseline for scalable, non-invasive mental health monitoring.},
}
@article {pmid41671148,
year = {2026},
author = {Buczek, DJ and Kabir, W and Lindstedt, K and Mäklin, T and Thorpe, HA and Suzuki, Y and Corander, J and Samuelsen, &#xd8; and Sundsfjord, A},
title = {Sequence type and strain-level detection of Klebsiella pneumoniae in culture-enriched bacterial metagenomes: comparative performance of mSWEEP and StrainGE bioinformatic tools.},
journal = {Microbial genomics},
volume = {12},
number = {2},
pages = {},
pmid = {41671148},
issn = {2057-5858},
mesh = {*Klebsiella pneumoniae/genetics/classification/isolation &amp; purification ; *Computational Biology/methods ; *Metagenome ; Humans ; Whole Genome Sequencing ; Phylogeny ; Klebsiella Infections/microbiology ; Genome, Bacterial ; },
abstract = {Klebsiella pneumoniae is a major cause of human infections and is frequently associated with antimicrobial resistance (AMR). Carriage of K. pneumoniae in the gut is a major risk factor for infection and a reservoir for the spread of high-risk clonal lineages and associated AMR determinants. Accurate detection of K. pneumoniae at the subspecies level is therefore essential to better understand K. pneumoniae gut colonization ecology and clonal dissemination. We analysed two recently developed bioinformatic tools, mSWEEP and StrainGE, for sequence type (ST) detection of K. pneumoniae in culture-enriched sweep metagenomes compared to single-colony whole-genome sequencing (WGS). We show that both mSWEEP and StrainGE perform highly accurate ST detection, concordant with culture in 46/49 and 44/49 samples with WGS-detected single STs, respectively, as well as in 2/3 samples with two WGS-detected STs. Within-sample ST diversity was detected in 19 and 15 samples by mSWEEP and StrainGE, respectively, highlighting a major advantage of these tools over conventional single-colony WGS. StrainGE could also reconstruct accurate phylogenetic relationships between strains of the same ST for 2/3 different STs tested. Additionally, assembly of the genomes provides better resolution of ST detection by mSWEEP. Together, our results show that both mSWEEP and StrainGE are accurate tools for the detection and analysis of K. pneumoniae STs from mixed bacterial samples.},
}
@article {pmid41676438,
year = {2025},
author = {Liu, Y and Ise, Y and Takami, H and Urakawa, R and Tateno, R and Toyoda, A and Ohte, N and Shi, W and Jiang, L and Isobe, K},
title = {Soil pH modulates microbial nitrogen allocation in soil via compositional and metabolic shifts across forests in Japan.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70054},
pmid = {41676438},
issn = {2996-9514},
abstract = {Ammonium release (ammonification) and uptake (immobilization) by soil microbial communities are fundamental processes of forest nitrogen (N) cycling, representing major N fluxes that influence plant productivity and ecosystem N retention. However, because these processes involve diverse metabolic pathways distributed across many taxa, they are difficult to evaluate using gene- or taxon-specific approaches, and it remains unclear how microbial community structure governs the patterns of these processes. In this study, we examined how the abundance, taxonomic composition, richness, and metabolic capabilities of microbial communities regulate ammonium-related N cycling processes across a wide range of forests in Japan, using rRNA gene sequencing and quantification, shotgun metagenomics, and [[15]]N tracer assays. Across the full gradients of soil pH and N content, microbial abundance was primarily correlated with the absolute rates of N cycling processes, while taxonomic composition and richness were more strongly correlated with N allocation-that is, the balance among ammonium release, ammonium uptake, and subsequent nitrification. Soils with higher pH supported taxonomic compositions linked to enhanced ammonium release and nitrification, whereas lower-pH soils hosted compositions associated with greater ammonium uptake and retention. Notably, the regulatory influence of taxonomic composition on N allocation was pronounced within the higher-pH range but diminished within the lower-pH range. Despite this environmental dependency, N allocation by soil microbial communities was ultimately constrained by their overall metabolic capabilities. In higher-pH soils, microbial communities were enriched in metabolic functions related to nutrient acquisition and respiratory N transformations, supporting increased ammonium release and N mobility. By contrast, microbial communities in lower-pH soils were enriched in stress-adaptive functions, which promoted ammonium retention and limited N transformations-thereby diminishing the regulatory influence in N cycling. Together, our findings provide a mechanistic understanding of how microbial community structure and metabolic capabilities regulate ammonium-related N cycling processes across forests under varying environmental conditions.},
}
@article {pmid41677035,
year = {2026},
author = {Jiménez-Castro, L and López-Laguna, A and Férnandez-Ortuño, D and Pérez-García, A and Polonio, &#xc1;},
title = {LUCID: An Integrative Approach for Target Discovery and dsRNA Design in Plant Fungal Pathogens.},
journal = {Plant biotechnology journal},
volume = {24},
number = {6},
pages = {3597-3615},
pmid = {41677035},
issn = {1467-7652},
support = {PY20_00048//AYUDAS A LA I+D+i EN EL &#xc1;MBITO DEL PLAN ANDALUZ DE INVESTIGACI&#xd3;N, DESARROLLO E INNOVACI&#xd3;N (PAIDI 2020)/ ; PID2022-136240OB-C21//MICIU/AEI/10.13039/501100011033 and ERDF/EU/ ; },
mesh = {*RNA, Double-Stranded/genetics ; *Botrytis/genetics/pathogenicity ; *Plant Diseases/microbiology ; Fungicides, Industrial/pharmacology ; Fungal Proteins/genetics/metabolism ; *Fungi/genetics/pathogenicity ; Plants/microbiology ; Computational Biology/methods ; },
abstract = {Phytopathogenic fungi pose an escalating threat to global food security and ecosystem stability, as resistance and environmental concerns diminish the effectiveness of conventional fungicides. Double-stranded RNA (dsRNA)-based fungicides offer a species-specific, eco-friendly alternative. We introduce LUCID (Locating Uncovered, conserved, and Indispensable for pathogenicity Determinants), a computational pipeline that accelerates the development of RNAi-based biofungicides by integrating target identification with dsRNA design and off-target prediction. LUCID employs a dual-branch strategy to identify both Conserved Essential Proteins (CEPs) and Conserved Non-Annotated Proteins (CNAPs), leveraging transcriptomic data and comparative genomics across diverse fungal species. Validation in Botrytis cinerea demonstrated high efficacy, with 67% of proposed targets successfully silenced and an average silencing efficiency of 96%. Additionally, coupling LUCID with advanced protein language models (PLMs) revealed a novel pathogenicity determinant in B. cinerea: a putative mediator complex protein. LUCID offers a scalable, species-agnostic framework for designing sustainable fungicides, enabling rapid, targeted control of fungal diseases with minimal ecological impact.},
}
@article {pmid41677795,
year = {2026},
author = {Gaio, D and Tackmann, J and Perez-Molphe-Montoya, E and Näpflin, N and Patsch, D and Malfertheiner, L and Peluso, ME and von Mering, C},
title = {Enhanced semantic classification of microbiome sample origins using large language models (LLMs).},
journal = {GigaScience},
volume = {15},
number = {},
pages = {},
pmid = {41677795},
issn = {2047-217X},
support = {310030_192567/SNSF_/Swiss National Science Foundation/Switzerland ; 310030_192569/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Microbiota/genetics ; *Semantics ; Metadata ; Computational Biology/methods ; Humans ; Large Language Models ; },
abstract = {BACKGROUND: Over the past decade, central sequence repositories have expanded significantly in size. This vast accumulation of data holds value and enables further studies, provided that the data entries are well annotated. However, the submitter-provided metadata of sequencing records can be of heterogeneous quality, presenting significant challenges for re-use. Here, we test to what extent large language models (LLMs) can be used to cost-effectively automate the re-annotation of sequencing records against a simplified classification scheme of broad ecological environments with relevance to microbiome studies, without fine-tuning. This effort directly contributes to improving the FAIRness-findability, accessibility, interoperability, and reusability-of microbiome sequencing metadata, thereby enhancing their "AI readiness" for downstream computational analyses.<br><br>RESULTS: We focused on sequencing samples taken from the environment, for which metadata is important. We employed OpenAI Generative Pre-trained Transformer models, and assessed scalability, time- and cost-effectiveness, as well as performance against a diverse, hand-curated benchmark with 1,000 examples that span a wide range of complexity in metadata interpretation. Annotation performance markedly outperformed that of a baseline, manually curated, non-ML keyword-based approach. Changing models (or model parameters) has only minor effects on performance, but prompts need to be carefully designed to match the task. Furthermore, when we compared proprietary OpenAI models with open-weight alternatives (e.g., Qwen, meta-Llama, and Microsoft-Phi-4), we found comparable accuracy for both biome and sub-biome classification, indicating that open-weight architectures can match the performance of proprietary models for large-scale ecological metadata re-annotation. We validated the pipeline with 1,000 hand-curated samples, and we applied the optimized pipeline to 2 million sequencing records from the environment, providing coarse-grained yet standardized sample origin annotations covering the globe.<br><br>CONCLUSIONS: Our work demonstrates the effective use of LLMs to simplify and standardize annotation from complex biological metadata.},
}
@article {pmid41678209,
year = {2026},
author = {Colnaghi, M and Santos, FP and Van Lange, PAM and Balliet, D},
title = {The ecological origins of collectivism and individualism.},
journal = {Psychological review},
volume = {},
number = {},
pages = {},
doi = {10.1037/rev0000610},
pmid = {41678209},
issn = {1939-1471},
support = {//European Research Council; Horizon Europe/ ; },
abstract = {Interdependent subsistence styles, such as rice farming, are thought to underlie the evolution of collectivistic cultures, which emphasize collective welfare over individual gains. Rice farming can produce mutual dependence within communities but also create conflicting interests, as people cooperate to provide valuable public goods. However, current theories of the origins of collectivism fail to address the interplay between mutual dependence and conflict. As a consequence of these limitations, the evolutionary dynamics of collectivism and its association with cooperation are still unclear. We advance a theoretical model to study the evolution of cultural traits that enhance people's valuations of collective welfare, one of the key features of collectivistic cultures. Our model investigates the evolutionary dynamics of cooperation and cultural evolution in ecologies with distinct interdependence structures. We find evidence that higher degrees of mutual dependence facilitate the evolution and persistence of collectivism. However, the degree of conflicting interests also plays a crucial role in driving the diffusion and maintenance of collectivistic norms. In particular, the selective advantage of collectivism is strongest when people experience some degree of conflict of interests, an effect that is magnified by heightened mutual dependence. These results clarify how variation in interdependence could underlie the ecological origins of collectivism, lending support to and expanding the scope of current theories of the cultural evolution of cooperation. More broadly, the framework presented here elucidates how fitness interdependence can be influenced by different ecological factors, and, in turn, influence the evolution of social behaviors. (PsycInfo Database Record (c) 2026 APA, all rights reserved).},
}
@article {pmid41678582,
year = {2026},
author = {Cleanclay, WD and Kernyuy, FB and Kintung, IF and Yensii, NG and Chick, JA and Obi, AMM},
title = {Evaluating paratransgenesis using engineered symbiotic bacteria for Plasmodium inhibition in mosquito vectors: A systematic review.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {2},
pages = {e0013654},
pmid = {41678582},
issn = {1935-2735},
mesh = {Animals ; *Mosquito Vectors/parasitology/microbiology ; *Anopheles/parasitology/microbiology ; *Symbiosis ; *Bacteria/genetics/metabolism ; *Malaria/prevention &amp; control/transmission ; Mosquito Control/methods ; Plasmodium falciparum/drug effects ; *Plasmodium ; },
abstract = {Malaria is a significant health problem in the world and has been increased by the emerging resistance to insecticides and antimalarial drugs. New measures must therefore be implemented as an emergency to break the cycle of Plasmodium parasite transmission by the Anopheles mosquitoes. This systematic review assessed the effectiveness of paratransgenesis, an engineering approach that utilizes symbiotic microbes to deliver antiplasmodial molecules into the midgut of the mosquito as a transmission-blocking agent. PubMed, ScienceDirect, and Web of Science were searched in accordance with the PRISMA guidelines, yielding 1,289 records. Ten eligible studies were then included after screening. The chosen articles studied bacterial and fungal symbionts, such as Asaia, Serratia, Pantoea, Enterobacter, and Aspergillus oryzae, that have been engineered to produce effector proteins, such as Scorpine, EPIP, Defensin, and SM1-2 peptides. The delivery of oral sugar meals was always associated with colonization of the mosquito midguts, and results reported high levels of inhibition of oocysts or sporozoites in the mosquitoes. Scorpine was the strongest and most commonly used effector with a high level of up to 97.8% inhibition of P. falciparum oocysts in various microbial systems. The combination of two or multiple-effector approaches increased the efficacy in some cases, surpassing 89% parasite inhibition. The risk of bias measurement showed moderate variation in the methods, yet it was in favor of the sound findings. All evidence suggests that paratransgenesis is a potentially important malaria control tool, complementing existing approaches to malaria control. Nevertheless, ecological safety, microbial stability, and field validation are the key obstacles before the translation to large-scale use.},
}
@article {pmid41678735,
year = {2026},
author = {Jjingo, D and Walakira, A and Hashim, S and Cheickna, C and Galiwango, R and Kibet, C and Kivunike, FN and Mboowa, G and Kakembo, FE and Ayodele, B and Entfellner, JD and de Villiers, S and Wambui, K and Fatumo, S and Chikowore, T and Mukisa, J and Ssekagiri, A and Bbosa, N and Mulindwa, J and Kyobe, S and Nsubuga, M and Kebirungi, G and Katagirya, E and Mwesigwa, S and Lujumba, I and Kamulegeya, R and Kirimunda, S and Kanyerezi, S and Kiyaga, S and Sserwadda, I and Kiberu, D and Bagaya, BS and Okwir, J and Nabisubi, P and Nabakooza, G and Atwine, MT and Sserunjogi, R and Julius, R and Quiñones, M and McCarthy, M and Cruz, P and Noble, K and Whalen, CJ and Hurt, D and Giovanni, MY and Tartakovsky, M and Ssemwanga, D and Kitayimbwa, JM and Reynolds, SJ and Whalen, CC and Kambugu, A and Hanchard, NA and Jian, L and Amoako-Yirenkyi, P and Mardon, G and Jordan, IK and Salifu, SP and Wele, M and Adebiyi, E and Shaffer, JG and Doumbia, S and Kateete, DP and Skelton, M and Mulder, N and Kayondo, JK and Masiga, D and , },
title = {Pathways, outputs and impact of NIH-supported bioinformatics and genomics graduate trainees in Africa.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {41678735},
issn = {1477-4054},
support = {U2R TW010673/TW/FIC NIH HHS/United States ; UE5 TW012526/TW/FIC NIH HHS/United States ; },
mesh = {*Computational Biology/education ; *Genomics/education ; United States ; Africa ; Humans ; *National Institutes of Health (U.S.) ; *Education, Graduate ; Biomedical Research ; },
abstract = {Global biomedical and health research is increasingly relying on genomic and computational approaches, largely driven by the increasing volumes of nucleic acid sequencing. Concurrently, epidemiological studies and clinical records are generating enormous amounts of data amenable to disease modeling, machine learning, and artificial intelligence techniques. Bioinformatics and data science expertise is therefore essential for improved population health. Accordingly, in 2012, the US National Institutes of Health (NIH) in partnership with the Wellcome Trust, and with support from the African Society for Human Genetics, initiated the H3Africa (Human Heredity and Health in Africa) consortium. One of its key goals was to build capacity among African scientists to lead research on genetic and environmental contributors to health and disease across the continent. In 2017, the NIH provided funding to support the establishment of four graduate bioinformatics training programs across five African universities. Over seven years, these programs enrolled multiple trainees (n > 270), with >110 earning Master's degrees and >20 completing PhDs in Bioinformatics. It is thus timely to evaluate the outcomes and impact of these programs, particularly regarding graduation rates, career trajectories, and the institutions and research domains their alumni are serving. We also assess employment outcomes and the nature of the research they are enabling (n > 110 peer-reviewed articles). We additionally include the progress and outputs of the programs' instructors, which were partially enabled by program resources, networks, and trainees. Overall, this review paints valuable insights into the pioneering role of NIH extramural support in shaping Africa's biomedical research landscape.},
}
@article {pmid41679645,
year = {2026},
author = {Di Bidino, R and Dutta Majumdar, A and Pegg, M and Mahon, R and Papavero, SC and Mueller, D},
title = {Implications of Incorporating Environmental Sustainability Into Health Technology Assessment for Digital Health Technologies.},
journal = {Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research},
volume = {29},
number = {4},
pages = {595-599},
doi = {10.1016/j.jval.2026.01.019},
pmid = {41679645},
issn = {1524-4733},
mesh = {*Technology Assessment, Biomedical/methods ; Humans ; *Digital Technology ; *Telemedicine ; *Conservation of Natural Resources/methods ; Artificial Intelligence ; Digital Health ; },
abstract = {Health technology assessment (HTA) must increasingly incorporate environmental sustainability (ES) to ensure digital health technologies (DHTs) deliver true value for both population and planetary health. Existing HTA frameworks inadequately capture the upstream and downstream environmental implications of DHTs, overlooking critical factors such as energy consumption, data storage, water usage, and electronic waste. Using a few examples on telehealth platforms, electronic health records, and artificial intelligence-driven diagnostic tools, we illustrate how these technologies can reduce carbon emissions and other pollutants by limiting patient travel and optimizing resource use. We review current HTA frameworks, identify ongoing initiatives, and highlight gaps and challenges in integrating ES into value assessment. Traditional HTA models provide limited guidance for incorporating broad environmental factors, risking underestimation of DHTs' environmental impacts and potentially undermining health systems' net-zero commitments by 2050. To address these issues, in this commentary, we propose targeted investment in frameworks, streamlined environmental data collection, and stronger cross-sector collaboration. Systemic inclusion of ES can reduce inequalities, support ethical supply chains, and incentivize developers to design lower-impact technologies, positioning HTA as a driver of sustainable digital health innovation. By embedding environmental metrics, health systems can better balance clinical benefits, economic efficiency, and ecological responsibility, thereby advancing both human and planetary health.},
}
@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 {pmid41682587,
year = {2026},
author = {Sandeep, A and Jayarathna, S and Sandaruwan, S and Samarappuli, V and Meedeniya, D and Perera, C},
title = {Context-Aware Multi-Agent Architecture for Wildfire Insights.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {3},
pages = {},
pmid = {41682587},
issn = {1424-8220},
abstract = {Wildfires are environmental hazards with severe ecological, social, and economic impacts. Wildfires devastate ecosystems, communities, and economies worldwide, with rising frequency and intensity driven by climate change, human activity, and environmental shifts. Analyzing wildfire insights such as detection, predictive patterns, and risk assessment enables proactive response and long-term prevention. However, most of the existing approaches have been focused on isolated processing of data, making it challenging to orchestrate cross-modal reasoning and transparency. This study proposed a novel orchestrator-based multi-agent system (MAS), with the aim of transforming multimodal environmental data into actionable intelligence for decision making. We designed a framework to utilize Large Multimodal Models (LMMs) augmented by structured prompt engineering and specialized Retrieval-Augmented Generation (RAG) pipelines to enable transparent and context-aware reasoning, providing a cutting-edge Visual Question Answering (VQA) system. It ingests diverse inputs like satellite imagery, sensor readings, weather data, and ground footage and then answers user queries. Validated by several public datasets, the system achieved a precision of 0.797 and an F1-score of 0.736. Thus, powered by Agentic AI, the proposed, human-centric solution for wildfire management, empowers firefighters, governments, and researchers to mitigate threats effectively.},
}
@article {pmid41683185,
year = {2026},
author = {Song, D and Song, L and Zhong, X and Wu, Y and Zhang, Y and Yang, L},
title = {Integrated Molecular Informatics and Sensory-Omics Study of Core Trace Components and Microbial Communities in Sauce-Aroma High-Temperature Daqu from Chishui River Basin.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41683185},
issn = {2304-8158},
support = {MTXYTD202501//Science and Technology Innovation Team of Moutai Institute/ ; QianKeHeJiChu-ZD[2025]018//Guizhou Provincial Basic Research Program (Natural Science)/ ; ZunShiKeHe HZ Zi[2023]112//The Fund of Zunyi Technology and Big data Bureau, Moutai Institute Joint Science and Technology Research and Development Project/ ; mygccrc[2022]011, mygccrc[2022]013//Research Foundation for Scientific Scholars of Moutai Institute/ ; XYNJ20240104//Moutai Institute &amp; Guangdong Li'er'an Chemical Industry Group Co., Ltd/ ; },
abstract = {Flavor-relevant trace volatiles and microbial communities were examined in six sauce-aroma high-temperature Daqu samples. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) quantified 210 trace volatile compounds across 14 chemical classes. Orthogonal partial least squares discriminant analysis (OPLS-DA) with variable importance in projection (VIP) screening was integrated with sensory scoring, correlation analysis, and molecular docking to an olfactory receptor model. Volatile profiles showed clear stratification in total abundance. Pyrazines dominated the high-total group. Tetramethylpyrazine served as a major driver. Sensory evaluation indicated that aroma explained overall quality best. (E)-2-pentenal and dimethyl trisulfide showed significant positive associations with aroma and overall scores. In the olfactory receptor, the polar residue module that provides directional constraints for Daqu odor activation was formed by Ser75, Ser92, Ser152, Ser258, Thr74, Thr76, Thr98, Thr200, Gln99, and Glu94. The hydrogen-bond or charge network was further reinforced by Arg150, Arg262, Asn194, His180, His261, Asp182, and Gln181. The core discriminant set comprised acetic acid, hexanoic acid, (E)-2-pentenal, nonanal, decanal, dimethyl trisulfide, trans-3-methyl-2-n-propylthiophane, 2-hexanone oxime, ethyl linoleate, propylene glycol, 2-ethenyl-6-methylpyrazine, 4-methylquinazoline, 5-methyl-2-phenyl-2-hexenal, and 1,2,3,4-tetramethoxybenzene. Sequencing revealed higher bacterial diversity than fungal. Bacillus and Kroppenstedtia were dominant bacterial genera. Aspergillus, Paecilomyces, Monascus, and Penicillium were major fungal genera. Correlation patterns suggested that Bacillus and Monascus were positively linked to acetic acid and 1,2,3,4-tetramethoxybenzene. Together, these results connected chemical fingerprints, sensory performance, receptor-level plausibility, and microbial ecology. Concrete targets are provided for quality control of high-temperature Daqu.},
}
@article {pmid41683461,
year = {2026},
author = {Chen, H and Li, Y and Chen, Q and Chen, C and Hu, Y},
title = {Methodologies for Assessing Chemical Toxicity to Aquatic Microorganisms: A Comparative Review.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {3},
pages = {},
pmid = {41683461},
issn = {1420-3049},
mesh = {*Aquatic Organisms/drug effects ; Microalgae/drug effects ; Bacteria/drug effects ; *Toxicity Tests/methods ; *Water Pollutants, Chemical/toxicity ; Fungi/drug effects ; Viruses/drug effects ; },
abstract = {Aquatic ecological issues have garnered significant attention in recent years, driving the demand for convenient, effective, and systematic assessment methods in environmental risk evaluation. This review provides a comprehensive introduction to methodologies for assessing the toxicity of chemicals toward aquatic microorganisms, which include viruses, bacteria, fungi, protozoa, and algae. Among these, microalgae are commonly used as model organisms due to their relative simplicity. The article details conventional biological methods, general chemical techniques, modern instrumental analyses, and informatics approaches, with a particular focus on algae and bacteria as model organisms for toxicity assessment. The principles, advantages, and limitations of each method are discussed, along with examples of their application in various contexts. Biological methods offer direct visualization, convenience, and rapid results, while modern instrumental techniques enable mechanistic insights at molecular and biochemical levels. Informatics methods facilitate toxicity evaluation in complex systems. While aquatic microorganisms encompass viruses, fungi, protozoa, bacteria, and algae, this review primarily focuses on bacteria and algae as model organisms due to their ecological relevance, sensitivity, and widespread use in standardized assays.},
}
@article {pmid41683590,
year = {2026},
author = {Li, F and Jin, W and Cheng, H and Wu, F and Pan, Y and Zhu, D and Xu, S and Zhou, C and Zhang, B and Chakraborty, A and Roy, A and He, S},
title = {Transcriptomic Responses of Sclerodermus alternatusi Yang to Ultraviolet (UV) Stress of Different Wavelengths.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683590},
issn = {1422-0067},
support = {CSTB2025NSCQ-GPX0267//the Natural Science Foundation Project of Chongqing/ ; CSTB2024NSCQ-MSX0676//the Natural Science Foundation Project of Chongqing/ ; },
mesh = {Animals ; *Ultraviolet Rays/adverse effects ; *Transcriptome/radiation effects ; *Stress, Physiological/radiation effects/genetics ; Gene Expression Profiling ; *Wasps/genetics/radiation effects ; Gene Ontology ; },
abstract = {Ultraviolet (UV) radiation is a significant environmental stressor that exerts profound impacts on insect physiology, behaviour and survival. Although some insects can use UV light for spatial orientation and navigation, it can induce DNA damage, oxidative stress, and impair critical biological functions, ultimately reducing ecological fitness. Sclerodermus alternatusi Yang (Hymenoptera: Bethylidae) is a dominant ectoparasitoid of the early instar larvae of Monochamus alternatus and plays a key role in the biological control of this pest in forestry systems; however, it faces intense UV exposure in the field environment. Despite its ecological importance, the molecular mechanisms underlying its responses to UV-induced stress remain poorly understood. In this study, newly emerged adult wasps (within 24 h post-eclosion) were exposed to UVA (365 nm) and UVC (253.7 nm) radiation for 9 h under controlled laboratory conditions. Total RNA was extracted from treated and control individuals for transcriptomic analysis using RNA-Seq. A total of 505 differentially expressed genes (DEGs) were identified; gene ontology enrichment analysis revealed that UVA exposure significantly upregulated genes involved in cellular respiration and oxidative phosphorylation, suggesting an enhanced metabolic response. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that UV stress modulates energy metabolism through the activation of oxidative phosphorylation and thermogenesis-related pathways, highlighting the reallocation of energy resources in response to UV-induced stress. To validate the RNA-Seq data, four representative DEGs were selected for quantitative real-time PCR (RT-qPCR) analysis. The qPCR results were consistent with the transcriptomic trends, confirming the reliability of the sequencing data. Collectively, this study provides a comprehensive overview of the molecular response mechanisms of S. alternatusi to UV stress, offering novel insights into its environmental adaptability and laying a theoretical foundation for its application in biological pest control under field conditions.},
}
@article {pmid41683863,
year = {2026},
author = {Ren, S and Lv, G},
title = {A Transcriptome Study on Seed Germination of Nitraria roborowskii Kom.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683863},
issn = {1422-0067},
mesh = {*Germination/genetics ; Gene Expression Regulation, Plant ; *Transcriptome ; *Seeds/genetics/growth &amp; development ; Gene Expression Profiling ; Plant Dormancy/genetics ; Gene Ontology ; Computational Biology/methods ; Plant Proteins/genetics ; Molecular Sequence Annotation ; },
abstract = {Nitraria roborowskii Kom. seeds possess pronounced deep dormancy traits. Analyzing changes in gene expression before and after dormancy release is of great significance for elucidating the mechanisms underlying seed dormancy. In this study, transcriptome sequencing and bioinformatics analysis were conducted on N. roborowskii seeds both before and after dormancy release using high-throughput Illumina NovaSeq 6000 sequencing technology. The key findings are as follows: (1) A total of 215,303 transcripts and 84,450 unigenes were obtained through de novo assembly. (2) Comparative analysis revealed 16,130 significantly differentially expressed unigenes during germination, with 10,776 upregulated and 5354 downregulated. Gene Ontology (GO) enrichment analysis indicated that these differentially expressed genes (DEGs) were primarily associated with biological processes and molecular functions, mainly involved in metabolic processes and catalytic activities. (3) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were predominantly enriched in pathways such as plant hormone signal transduction and starch and sucrose metabolism. Specifically, among the downregulated genes, 126 were linked to plant hormone signal transduction, 110 to phenylpropanoid biosynthesis, 108 to starch and sucrose metabolism, 27 to flavonoid biosynthesis, 20 to plant hormone signal transduction, 6 to phenylpropanoid metabolism, 14 to starch and sucrose metabolism, and none to flavonoid biosynthesis.},
}
@article {pmid41686497,
year = {2026},
author = {Wu, Z and Liu, Y and Zhu, M and Zeng, J and Labat, D and Meng, F},
title = {SWAT-WASP coupled modeling of ammonia nitrogen in rare earth mining watersheds.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {93},
number = {3},
pages = {273-295},
pmid = {41686497},
issn = {0273-1223},
support = {41861002//National Natural Science Foundation of China/ ; 2022A15150112010//Natural Science Foundation of Guangdong Province/ ; //2023 Annual Guangdong Provincial Higher Education Teaching Reform Project/ ; },
mesh = {*Mining ; *Nitrogen/analysis ; *Metals, Rare Earth ; *Ammonia/analysis ; *Water Pollutants, Chemical ; *Environmental Monitoring/methods ; China ; Rivers/chemistry ; Models, Theoretical ; },
abstract = {High concentrations of ammonia nitrogen (NH4[+]-N) are a dominant water pollutant in ionic rare earth mining basins, threatening aquatic ecosystems and drinking-water safety. To quantify these dynamics, this study developed a coupled SWAT-WASP model for the upper Dongjiang River Basin (UDRB), integrating remote sensing and long-term monitoring data; the model was calibrated and validated with 2016-2018 monthly observations, and quantitative evaluation via Nash-Sutcliffe Efficiency (NSE) and Percent Bias (PBIAS) showed good performance (runoff: NSE = 0.77-0.80; NH4[+]-N: SWAT NSE = 0.56-0.61, SWAT-WASP NSE = 0.65-0.87), confirming its reliability. 2022 simulations revealed strong NH4[+]-N spatial heterogeneity, with concentrations >1.8 mg L[-1] near mining zones versus <0.5 mg L[-1] in upstream natural areas; geodetector analysis identified population density combined with industrial-agricultural activity as the top driver of spatial differentiation (q > 0.40), while interactions between precipitation, temperature, and land use further amplified variability. Overall, the SWAT-WASP framework provides a robust tool for evaluating NH4[+]-N dynamics and supports targeted pollution control and ecological restoration in rare earth mining watersheds.},
}
@article {pmid41687859,
year = {2026},
author = {Spagnesi, A and Gilardoni, S and Salzano, R and Feltracco, M and Ulgelmo, B and Maetzke, R and Ardini, F and Grotti, M and Coppolaro, VLM and Viglezio, T and Montaguti, S and Scoto, F and Spolaor, A and Gambaro, A and Barbante, C and Barbaro, E},
title = {Emerging contaminants during arctic rain-on-snow events: A case study from the 2023-24 Ny-Ålesund campaign.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {395},
number = {},
pages = {127790},
doi = {10.1016/j.envpol.2026.127790},
pmid = {41687859},
issn = {1873-6424},
mesh = {*Environmental Monitoring ; Arctic Regions ; *Air Pollutants/analysis ; *Rain/chemistry ; *Snow/chemistry ; Flame Retardants/analysis ; Aerosols/analysis ; Pesticides/analysis ; Norway ; Svalbard ; },
abstract = {The Svalbard Archipelago has undergone rapid warming in recent decades, increasing the frequency and intensity of Rain-on-Snow (ROS) events. While the physical and ecological consequences of ROS in the Arctic have been extensively documented, their role in modulating the atmospheric fate of emerging contaminants remains poorly understood. This study investigates the chemical signature of four ROS events during the 2023-24 field campaign in Ny-Ålesund (Kongsfjorden, Svalbard, Norway), focusing on the behaviour of emerging pollutants across pre-, during-, and post-event phases. By combining aerosol and wet deposition data with meteorological variables and air mass back-trajectories, we explore the potential of ROS to act as removal mechanisms for benzothiazole derivatives, tris(2-carboxyethyl) phosphine (TCEP) as flame retardant, pesticides, and haloacetic acids. The results highlight a substantial variability in contaminant patterns across events and suggest the influence of synoptic-scale air mass origin and local meteorological conditions. Diagnostic ratios and inorganic ion proxies provide insight into possible atmospheric transformation pathways and transport processes. This study provides the first detailed chemical characterisation of aerosol and depositions during Rain-On-Snow events, establishing a preliminary framework to better understand the complex interactions between ROS and contaminant cycling in a warming Arctic. This work contributes to ongoing efforts to clarify the mechanisms of atmospheric scavenging under changing climate conditions.},
}
@article {pmid41690269,
year = {2026},
author = {Paton, L and Kiesel, S and Elinkmann, M and Clases, D and Fernandez-Mendoza, F and Feldmann, J},
title = {The formation of bioavailable Hg in a pipeline: An initial investigation into Hg bioaccumulation resulting from oil and gas decommissioning.},
journal = {The Science of the total environment},
volume = {1019},
number = {},
pages = {181526},
doi = {10.1016/j.scitotenv.2026.181526},
pmid = {41690269},
issn = {1879-1026},
mesh = {*Mercury/metabolism/analysis ; *Water Pollutants, Chemical/metabolism/analysis ; *Environmental Monitoring ; Bioaccumulation ; },
abstract = {Mercury (Hg) released during offshore pipeline decommissioning may pose ecological risks, yet little is known about its chemical form and biological impact. We examined how Hg[0] can react on and subsequently be released from laboratory-generated steel pipeline material to interact with marine algae, focusing on chemical speciation, transformation, and cellular uptake. Laboratory exposures of the marine algae, Isochrysis galbana, to pipeline-derived Hg showed accumulation up to 109 mg kg[-1] dry weight, as determined by cold vapour atomic fluorescence spectrometry (CV-AFS). Single-cell inductively coupled plasma mass spectrometry (SC ICP-MS) confirmed substantial cell-associated Hg, with bimodal distributions suggesting distinct uptake or surface-association pathways. Although classical growth and photosynthetic parameters did not consistently reveal toxicity, Hg exposure altered cell populations and aggregation behaviour, indicating sublethal but ecologically relevant effects. Our findings demonstrate that through interactions with pipeline material Hg[0] can be transformed into species which have an increased likelihood of bioaccumulation.},
}
@article {pmid41693104,
year = {2026},
author = {Iannella, M and Cittadino, V and Bernabò, I and Romano, A and Biondi, M and Serva, D},
title = {Biodiversity-driven spatial conservation planning to delineate temporally stable regions.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {40},
number = {3},
pages = {e70244},
doi = {10.1111/cobi.70244},
pmid = {41693104},
issn = {1523-1739},
support = {//European Union/ ; NBFC-CN_00000033,CUPB63C22000650007//NextGenerationEU/ ; },
mesh = {*Conservation of Natural Resources/methods ; *Biodiversity ; Animals ; *Caudata/physiology ; Geographic Information Systems ; Models, Biological ; Models, Theoretical ; },
abstract = {The accelerating loss of biodiversity underscores the critical need for effective conservation strategies, particularly in the face of climate change and anthropogenic pressures. We devised a conservation planning framework that adopts a temporal stacking approach to species distribution models and landscape connectivity analyses. These models and analyses were derived from an integrated modeling and post-modeling GIS workflow and used to identify and propose conservation priority areas, also quantifying the proportion of these areas covered by existing protected areas (PAs). We applied the approach, as an example, to the genus Salamandrina, the oldest Salamandridae clade, because of its conservation and biogeographic importance. Our approach can be applied to any taxon. Specifically, we introduced and identified the steady core regions (i.e., areas predicted to remain ecologically suitable for the next 50 years) for Salamandrina. The geographic configuration of these areas, including their clustering and fragmentation degree, differed between distance-informed and distance-uninformed approaches along the Apennine chain. Those occurred in nationally designated PAs (few, large patches) and Natura 2000 sites (many and small patches), but steadiness values were generally low (often <5 out of 13), indicating scarce legal protection of temporally stable areas. We therefore propose 2 strategies to delineate areas currently unprotected that should be prioritized to reach the 30% of territories protected by 2030: increasing existing PA boundaries by estimating buffer distances and inferring stable areas outside current PAs, which we term half-century stable proposed protected areas (HCSPPAs). The buffering approach indicated a required 1-km expansion. The HCSPPAs clustered near existing PAs in northern and central Italy. In southern Italy, they were fewer and more dispersed, ranging from close to distant locations relative to current PAs. Our approach aligns with the European Union's 2030 Biodiversity Strategy and the global 30×30 conservation target because it provides a flexible and spatially informed framework to prioritize biodiversity conservation and strengthen long-term species' protection.},
}
@article {pmid41695296,
year = {2025},
author = {Crowley, LM and Barclay, MVL and Smith, MN and Brown, PMJ and Roy, HE and , and , and , and , and , and , and , },
title = {The genome sequence of the 24-spot ladybird, Subcoccinella vigintiquattuorpunctata (Linnaeus, 1758) (Coleoptera: Coccinellidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {698},
pmid = {41695296},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Subcoccinella vigintiquattuorpunctata (24-spot ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence has a total length of 532.03 megabases. Most of the assembly (97.41%) is scaffolded into 15 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 18.91 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 {pmid41698895,
year = {2026},
author = {Sound, JK and Bianchini, G and Ashok, TA and Rad-Menéndez, C and Green, DH and Sánchez-Baracaldo, P and Leney, AC},
title = {Mass spectrometry reveals the evolutionary conservation of phycobiliprotein complexes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41698895},
issn = {2041-1723},
support = {BB/T015640/1, BB/S019456/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/M01116X/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Phycobiliproteins/metabolism/chemistry/genetics ; Mass Spectrometry/methods ; *Cyanobacteria/metabolism/genetics ; *Evolution, Molecular ; Phylogeny ; Proteomics/methods ; Phycocyanin/metabolism/chemistry/genetics ; Phycobilisomes/metabolism ; Bacterial Proteins/metabolism/genetics/chemistry ; Photosynthesis ; Computational Biology ; },
abstract = {Cyanobacteria are a highly taxonomically and ecologically diverse group of oxygenic phototrophs that have colonized many different environments on our planet. Despite their differences, almost all cyanobacteria rely on highly efficient light-harvesting protein complexes, termed phycobilisomes, for effective photosynthesis. Phycobilisomes, along with the phycobiliproteins that make them up, have maintained their function throughout evolutionary history while also diversifying to optimize energy capture and transfer in different conditions. Here, we use a combination of evolutionary proteomics, phylogenomics, and structural bioinformatics to probe how phycobiliproteins have maintained their function while adapting to different habitats. Using high-resolution native mass spectrometry, we show that the two most abundant phycobiliprotein complexes, phycocyanin and allophycocyanin, are highly dynamic. Moreover, upon mixing phycobiliproteins from cyanobacterial strains representing diverse environments and evolutionary lineages, heterologous phycobiliprotein complexes rapidly form, comprising building blocks from different cyanobacterial strains. Bioinformatics and structural prediction methods allow us to identify critical residues involved in these interactions. We thus demonstrate that key structural features within the phycobiliprotein components have remained conserved over three billion years of cyanobacterial evolution, ensuring effective photosynthesis across a wide variety of natural environments.},
}
@article {pmid41698967,
year = {2026},
author = {Osada, Y and Miya, M and Araki, H and Doi, H and Kasai, A and Masuda, R and Minamoto, T and Seino, S and Takahara, T and Yamamoto, S and Yamanaka, H and Aizu-Hirano, M and Fukaya, K and Fukuchi, T and Gotoh, RO and Hori, M and Iida, M and Imaizumi, T and Kajita, T and Kanbe, T and Kenta, T and Kobayashi, Y and Matsuura, T and Mizumoto, H and Motomura, H and Murakami, H and Nohara, K and Oka, SI and Sado, T and Senou, H and Shibukawa, K and Sunobe, T and Takahashi, H and Takayama, K and Tanaka, K and Yamakawa, H and Yokoyama, S and Yoon, S and Kondoh, M},
title = {Large-scale environmental DNA survey reveals niche axes of a regional coastal fish community.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {3276},
pmid = {41698967},
issn = {2045-2322},
support = {19H05641//JSPS KAKENHI Grants/ ; 20H03311//JSPS KAKENHI Grants/ ; JPMJCR13A2//JSPS CREST program/ ; },
mesh = {Animals ; *Fishes/genetics ; Biodiversity ; *Ecosystem ; *DNA, Environmental/analysis/genetics ; Japan ; },
abstract = {The concept of the ecological niche, defined as the basic habitat requirements for a species, is central to understanding species geographic distributions and predicting their responses to environmental change. However, identifying the essential niche for large regional communities remains a challenge because niche axes can be "hidden" by the complexity of the underlying ecological processes. Here, applying advanced species distribution modelling to nationwide environmental DNA survey data, we identified hidden niche axes of the Japanese coastal fish community and investigated the response diversity to these axes. Our survey detected 1,220 coastal fish species. The hidden niche axes collectively explained most of the variation in fish biodiversity and revealed five biogeographic boundaries for the regional community. These niches of the Japanese fish community may primarily relate to several processes due to ocean currents, such as environmental filters, transport from source areas and dispersal barriers. We also found that the response diversity to niche axes was positively correlated with species richness, although local communities with particularly high response diversity were geographically biased. A better understanding of the niche axes of the regional ecological community should help to mitigate the loss of biodiversity and ecosystem services caused by ongoing environmental change.},
}
@article {pmid41699677,
year = {2026},
author = {Prakofjewa, J and Conte, L and Ludwig, D and Šarka, P and Centorrino, P and Kalle, R and Sõukand, R},
title = {"I know a lot about medicinal plants. I read, I watch, and I search": towards hybrid knowledge systems in the modern era.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {22},
number = {1},
pages = {14},
pmid = {41699677},
issn = {1746-4269},
support = {grant agreement N&#xb0; 714874//Horizon 2020 Framework Programme/ ; },
mesh = {*Plants, Medicinal ; Humans ; Female ; Male ; Adult ; Middle Aged ; Ethnobotany ; Lithuania ; *Knowledge ; Aged ; *Health Knowledge, Attitudes, Practice ; Medicine, Traditional ; },
abstract = {BACKGROUND: Hybrid knowledge systems are central to community negotiations of environmental, social, and epistemic pressures. In multilingual borderland areas, interactions between local ecological knowledge (LEK), formal, and popular knowledge systems remain underexplored, despite their importance for the persistence and transformation of medicinal plant use today.<br><br>METHODS: We conducted 67 semi-structured interviews and participant observation in 21 rural settlements of the Vilnius region (Lithuania), an area bordering Belarus, focusing on the two largest local groups, Lithuanians (LT) and Poles (PL). Detailed Use Reports (n&#x2009;=&#x2009;1446) on medicinal plant use were coded by the origin of knowledge, classified as local, formal, or popular, and the degree of hybridisation was quantified using the Shannon-Wiener diversity index and hybridisation metrics. Sociodemographic variables (age, gender, education, and multilingualism) were tested for associations with hybridisation using Spearman's &#x3c1; and Student's t-tests.<br><br>RESULTS: A total of 139 medicinal taxa were recorded, of which 68 (49%) were shared between the two groups. Overall, recorded medicinal plant knowledge remained primarily grounded in LEK, sustained through intergenerational transmission. Compared with PL, LT interviewees drew on a broader mix of knowledge-origin domains (H'&#x2009;=&#x2009;0.97 vs 0.52) and combined them more often (HD&#x2009;=&#x2009;0.195 vs 0.059). In total, 39 taxa showed hybrid use, predominantly in the LT group. Hybridisation was negatively associated with age but positively correlated with the number of listed plants and their reported uses, while multilingualism showed a near-significant positive trend.<br><br>CONCLUSIONS: The study suggests that medicinal plant knowledge has evolved here through hybridisation, a process whose consequences are context-dependent, offering opportunities for revitalisation but also a risk of displacement. Dialogic exchanges across families, communities, languages, and media expand people's plant repertoire and strengthen community adaptive capacity. Yet when these exchanges lead to excessive standardisation, they risk eroding the diversity of local traditions. Ethnobotanical research must therefore go beyond documenting popular and formal knowledge sources to interrogate how linguistic and sociopolitical contexts condition the emergence of hybrid knowledge systems, privileging certain forms while rendering others transformed or marginalised.},
}
@article {pmid41700573,
year = {2026},
author = {Fifield, K and Thomas, R and Dawe-Lane, E and Kusosa, R and O'Connor, E and Cummins, N and Pollak, TA and Wykes, T and Easton, A and Simblett, SK},
title = {COPE-EMBRACE: Coping with stress after encephalitis using real-time assessment.},
journal = {Neuropsychological rehabilitation},
volume = {},
number = {},
pages = {1-35},
doi = {10.1080/09602011.2026.2619548},
pmid = {41700573},
issn = {1464-0694},
abstract = {Encephalitis can cause acquired brain injury due to inflammation, leading to cognitive issues and fatigue, exacerbating daily stress. Knowledge of real-time stress coping mechanisms among people post-encephalitis and how this relates to depression is limited. Ecological momentary assessment (EMA) may address limitations in standardized cross-sectional self-report assessments. This study evaluates the feasibility and acceptability of collecting EMA data on mood and coping. Twenty adults post-encephalitis (12 women, age range 26:67) completed daily and self-initiated EMA for mood and coping over 4 months, and post-study interviews explored acceptability using framework analysis. Average daily compliance rate was 79.3% (range 37.3-97.5%), showing EMA's feasibility, though low self-initiated EMA usage indicated challenges. Linear mixed-effects model revealed significant relationships between coping style and depression levels within individuals and over time. Framework analysis categorized two themes: "Encephalitis experience and its relationship to stress response" and "Experience of EMA: barriers and facilitators'. Qualitative analysis indicated acceptability for the m-Path app and measuring daily mood. Results suggest long-term daily EMA is feasible for collecting mood and coping in adults with encephalitis. However, patient and public involvement should be utilized to establish suitability. Following adaptations, EMA may serve as a psychological intervention targeting stress coping in daily life.},
}
@article {pmid41701933,
year = {2026},
author = {MacLellan, A and Takano, K},
title = {Exploring the Cognitive and Behavioral Risks and Maintenance Factors of Hikikomori: Protocol for an Ecological Momentary Assessment Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e81384},
pmid = {41701933},
issn = {1929-0748},
mesh = {Humans ; Adult ; *Ecological Momentary Assessment ; Adolescent ; Young Adult ; Male ; Middle Aged ; Female ; Japan ; *Cognition ; *Social Isolation/psychology ; Internet Addiction Disorder/psychology ; Anxiety/psychology ; Affect ; Depression/psychology ; },
abstract = {BACKGROUND: Hikikomori is a state of social withdrawal first identified in Japan and is gaining interest globally. Classically, hikikomori is described as a state of isolation within one's home, though recent conceptualizations have proposed a continuum of severity. Hikikomori frequently shares symptoms with depression, social anxiety, autism, and schizophrenia, as well as internet and gaming disorders. Clinical case studies and cross-sectional studies suggest that dysfunctional emotion regulation, familial support, and internet behaviors are proposed to contribute to the onset and maintenance of a withdrawn state, though they have not been explored longitudinally.<br><br>OBJECTIVE: This study aims to investigate affective, behavioral, and cognitive correlates of hikikomori symptoms, and how daily mood, social enjoyment, familial support, and internet usage may maintain a socially withdrawn state.<br><br>METHODS: A minimum of 84 participants aged between 18 and 60 years will complete self-report measures of hikikomori symptoms, internet addiction, depression, anxiety, autism, and fear of offending others before participating in 14 days of ecological momentary assessment surveys. Surveys will be delivered 5 times per day from 8 AM to 10 PM, measuring mood, internet behavior, familial relationships, social interaction frequency, anticipatory and consummatory enjoyment, sleep quality, and physical activity. Participants will repeat the self-report measure of hikikomori symptoms postmonitoring period.<br><br>RESULTS: Recruitment began in November 21, 2025. Data collection and analysis are scheduled to be completed by summer 2026, with the results also scheduled to be available by the end of summer 2026. Correlation and multiple regression analyses will investigate whether internet addiction, social anxiety, expressive suppression, fear of offending others, daily mood, internet use, social enjoyment, and familial support predict hikikomori symptoms. Time-lagged network analyses will explore the temporal dynamics of these relationships, and how these differ in those with high and low levels of hikikomori symptoms. Finally, time-lagged logistic regressions will explore which factors predict future social behavior.<br><br>CONCLUSIONS: This study will be the first to investigate currently proposed mechanisms underlying hikikomori, while also exploring the time-varying relationships between affect and social behavior. The results will provide initial evidence for factors that predict hikikomori symptoms, explore candidate mechanisms underlying hikikomori, and identify potential maintenance factors as targets for intervention.},
}
@article {pmid41702108,
year = {2026},
author = {Ma, D and Yu, Y and Wang, Y and Wang, Q and Lin, Z},
title = {Multi-scale analysis of ecosystem service values and their driving factors based on MGWR: A case study of Yellow River Delta efficient ecological economic zone.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119886},
doi = {10.1016/j.ecoenv.2026.119886},
pmid = {41702108},
issn = {1090-2414},
mesh = {*Ecosystem ; *Rivers ; *Conservation of Natural Resources/methods ; China ; *Environmental Monitoring/methods ; Climate Change ; },
abstract = {The Yellow River basin has recently experienced intensified pressures from climate change and anthropogenic activities, causing severe ecological degradation and compromised ecosystem security. Enhanced ecological protection is critically important for maintaining regional equilibrium and sustainable development. The Yellow River Delta High-Efficiency Economic Development Zone was examined to investigate multi-grid-scale ecosystem service value (ESV) spatial patterns and drivers (2005-2020). ESV was first calculated using the equivalent factor method at 3 km, 7 km, and 10 km scales. Spatial distribution characteristics were subsequently revealed through autocorrelation analysis. Finally, spatial heterogeneity induced by natural and socio-economic drivers was analyzed using MGWR local regression coefficients. The results indicate that: (1) During 2005-2020, land-use ESV ranked: water bodies > farmland > grassland > forest > unutilized land > construction land, with eastern high-ESV zones expanding and southern low-ESV areas increasing; (2) Significant positive spatial autocorrelation (Moran's I > 0, Z > 2.58) was observed, weakening with scale. High-high clusters occurred in ecological-economic zones, contrasting low-low clusters in human activity areas, with stable overall patterns despite scale variations; (3) Significant spatial heterogeneity was driven by natural (DEM, slope; p < 0.05) and socio-economic factors, with GDP and population density gaining prominence by 2020; (4) Significant drivers increased dynamically from 9 (2005) to 12 (2020), confirming temporal evolution. This work establishes a scientific foundation for deltaic ecological restoration and informs precision conservation policies, with broader implications for global ecosystem sustainability.},
}
@article {pmid41702871,
year = {2026},
author = {Wen, M and Ma, X and Chen, J and Wu, J and Wu, F and Ma, R and Peng, R},
title = {Composition, Structure, and Diversity of Rhizosphere Soil Microbial Community in Saffron (Crocus sativus) Affected by Root Bulb Rot.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-07-25-1456-RE},
pmid = {41702871},
issn = {0191-2917},
abstract = {Fusarium oxysporum, first identified in Yunnan Province as the causal agent of saffron corm rot, causes a destructive soil-borne disease that has become a devastating threat to saffron cultivation in Shangri-La, causing over 50% mortality. This pathogen infects saffron corms, leading to vascular browning and rot, ultimately causing plant death and severe production losses. Given the crucial role of the rhizosphere microbiome in plant immunity and soil ecology, deciphering pathogen-microbiome interactions is essential for developing sustainable disease-control strategies. High-throughput sequencing of ITS/16S rRNA (Illumina MiSeq) was combined with arbuscular mycorrhizal fungi (AMF) analysis to compare the community structures of fungi, bacteria, and AMF in the rhizosphere of healthy and diseased saffron. The effects of soil physicochemical factors on microbiome assembly were systematically evaluated. The rhizosphere microbiome of diseased plants was significantly dysregulated: (1) pathogen-related taxa (e.g., Lauriomyces) proliferated, while saprotrophic functional taxa (e.g., Mortierella elongata) underwent community restructuring; (2) disease-suppressive taxa (e.g., fususidium) were enriched, while symbiotic mycorrhizal fungi (AMF) essential for nutrient acquisition sharply declined; (3) the soil parameter-microbiome relationship changed under different health conditions:available phosphorus (AP) and available potassium (AK) drove the aggregation of pathogenic soil fungi, while pH/organic matter (OM) dominated the aggregation of healthy soil fungi; (4) Knufia and Phomopsis were important taxa regulating soil ammonia oxidation and plant vitality. Fusarium infection disrupts the rhizosphere balance by inhibiting beneficial symbionts and promoting the colonization of pathogenic or saprotrophic microorganisms, ultimately compromising the innate resistance of saffron. Our findings reveal the rhizosphere ecological mechanism underlying corm rot progression and provide a microbiome informatics framework for the selection of biocontrol agents and rhizosphere engineering. Moreover, the worker safety benefits from the reductions in psychic emanations mandate industry adoption.},
}
@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 = {15},
number = {3},
pages = {e0134625},
pmid = {41705859},
issn = {2576-098X},
support = {2020/11534-0, 2022/15112-8, and 2017/03172-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 88887.514375/2020-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
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.},
}
@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 &amp; 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.},
}
@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},
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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.},
}
@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},
support = {P2C HD041041/HD/NICHD NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; R01 NR017605/NR/NINR NIH HHS/United States ; },
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.<br><br>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.<br><br>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.<br><br>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.<br><br>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 {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, G&#x160; 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 ; *Data Science ; Developing Countries ; *Global Health ; *Research ; },
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.},
}
@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 &amp; 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.<br><br>AIM: To estimate the association between ORA visits and self-reported stress using geographical ecological momentary assessment (gEMA) with refined multi-sourced ORA boundaries.<br><br>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.<br><br>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 (&#x2264; 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.<br><br>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.},
}
@article {pmid41714862,
year = {2026},
author = {McInerney, AM and Schmitz, N and Matthews, M and Deschênes, SS},
title = {The impact of sleep and movement behaviour on daily mood in people with type 2 diabetes: A smartphone-based digital phenotyping study.},
journal = {Diabetic medicine : a journal of the British Diabetic Association},
volume = {43},
number = {5},
pages = {e70269},
pmid = {41714862},
issn = {1464-5491},
support = {//Ad Astra Fellows PhD Studentship/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/psychology/physiopathology ; Male ; Female ; *Smartphone ; Middle Aged ; *Affect/physiology ; *Sleep/physiology ; Ecological Momentary Assessment ; Aged ; *Exercise/physiology/psychology ; Accelerometry ; Geographic Information Systems ; Adult ; Phenotype ; Movement/physiology ; Sleep Quality ; Actigraphy ; },
abstract = {OBJECTIVE: To examine how sleep and movement behaviours, measured on smartphones via ecological momentary assessment (EMA), GPS and accelerometer, impact subsequent daily mood in people with type 2 diabetes (T2D) compared to those without.<br><br>METHODS: Sixty-one participants with (n&#x2009;=&#x2009;32) and without (n&#x2009;=&#x2009;29) T2D underwent 2 months of smartphone-based data collection through phone sensors (GPS, accelerometer) and EMAs. Daily sleep, movement and mood (happiness, sadness, stress, anger) were assessed. Dynamic structural equation modelling examined the impact of sleep and movement on subsequent mood, adjusted for age, gender and employment status.<br><br>RESULTS: We found 18 significant within-person effects between smartphone-derived behaviour and subsequent mood, with 17 within-person effects indicating behaviour had a positive effect on mood. For people with and without T2D, higher physical activity, better sleep quality and visiting more locations predicted increased happiness, and higher physical activity predicted lower sadness. However, unique behaviour-mood effects were also found for each group, such as greater actigraphy-derived step count predicting greater anger in people with T2D (0.13 [0.05, 0.2]) but having no effect for those without.<br><br>CONCLUSIONS: Though effects were small, results indicate smartphone-derived behaviour influences daily mood for both people with and without T2D, but that the nuances of these relationships may differ. If daily mood correlates differ between people with and without T2D, digital phenotyping for early detection and intervention may need to be tailored to those with T2D.},
}
@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 {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.<br><br>OBJECTIVE: Our aim was to investigate prevalence, risk factors, and geographic variation of tree pollen sensitization in the United States.<br><br>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.<br><br>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.<br><br>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 {pmid41719082,
year = {2026},
author = {Gao, M and Liu, KJ},
title = {A REsampling and Visual EvALuation Method to Detect and Map Local Model Violations During Biomolecular Sequence Analysis.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {33},
number = {4},
pages = {482-498},
doi = {10.1177/15578666261424921},
pmid = {41719082},
issn = {1557-8666},
mesh = {Phylogeny ; Animals ; *Sequence Alignment/methods ; Algorithms ; *Computational Biology/methods ; Evolution, Molecular ; *Models, Genetic ; Computer Simulation ; },
abstract = {A fundamental assumption in phylogenetics and phylogenomics is that a single, global evolutionary model can adequately characterize the substitution processes operating across all sites in a molecular sequence alignment. However, this assumption is frequently violated in practice due to heterogeneity in evolutionary processes, leading to local model mis-specification and potential bias in downstream inference. While a variety of statistical and machine learning-based approaches have been developed to address this issue, these methods often rely on restrictive model assumptions or are designed for narrowly scoped applications, limiting their generalizability across diverse datasets and evolutionary contexts. Here, we present REVEAL ("REsampling and Visual EvALuation"), a general-purpose statistical framework for detecting and localizing model mis-specification in biomolecular sequence data. REVEAL operates without introducing additional assumptions beyond those inherent to standard global model-based analyses. It employs sequence-aware statistical resampling to construct a local support matrix along the sequence alignment, facilitating the identification of site-level model violations. Through extensive simulation experiments, we demonstrate that REVEAL achieves robust control of both type I and type II errors, with precision of 90% or greater and recall of 85% or greater across diverse evolutionary scenarios involving different sources of model heterogeneity, varying dataset sizes in terms of sequence length and number of taxa, and other experimental factors. We further apply REVEAL to genomic data from mouse and mosquito, uncovering localized model violations that are consistent with previously reported biological signals. These results establish REVEAL as a flexible and effective tool for evaluating model adequacy in phylogenetic and phylogenomic analyses.},
}
@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 &amp; bioelectronics},
volume = {302},
number = {},
pages = {118537},
doi = {10.1016/j.bios.2026.118537},
pmid = {41722362},
issn = {1873-4235},
mesh = {*Weevils/chemistry ; Animals ; *Pheromones/chemistry ; *Volatile Organic Compounds/chemistry ; Humans ; HEK293 Cells ; *Biosensing Techniques/instrumentation/methods ; *Fatty Alcohols/chemistry ; },
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 {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.},
}
@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 {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 &amp; technology},
volume = {60},
number = {9},
pages = {7011-7025},
doi = {10.1021/acs.est.6c00346},
pmid = {41728910},
issn = {1520-5851},
mesh = {*Kainic Acid/analogs &amp; derivatives ; Estuaries ; Diatoms ; Eutrophication ; Ecosystem ; Food Chain ; Animals ; Phytoplankton ; Environmental Monitoring ; },
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 {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 &amp; purification ; *Anti-Inflammatory Agents/pharmacology/isolation &amp; 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.<br><br>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.<br><br>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.<br><br>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-&#x3b1; signaling.<br><br>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.},
}
@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},
pmid = {41730638},
issn = {1347-4715},
mesh = {Japan/epidemiology ; Humans ; *Hospitalization/statistics &amp; 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.<br><br>METHODS: We used the data of the Longevity Improvement &amp; 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.<br><br>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 &#x2265;65 years regardless of mental disorders, and that the temperature-related attributable fractions were also higher in persons aged <65 years.<br><br>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.},
}
@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.},
}
@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 {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},
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.},
}
@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},
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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>DERR1-10.2196/88759.},
}
@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.},
}
@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},
mesh = {Humans ; Male ; Female ; *Ecological Momentary Assessment ; Middle Aged ; Adult ; Treatment Outcome ; Inpatients ; *Depression/therapy ; Surveys and Questionnaires ; *Major Depressive Disorder/therapy ; Psychiatric Status Rating Scales ; },
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 {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 {pmid41741663,
year = {2026},
author = {Pankararu, CJ and Teixidor-Toneu, I and Odonne, G and Asante, F and Bandeira, SO and Barrera-Bello, &#xc1;M 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 {pmid41742654,
year = {2026},
author = {Zhang, Z and Li, X and Li, J and Liu, Q and Li, W and Liu, J and Liu, D and Wang, L and Yan, Z and Fu, P and Yu, F},
title = {metaRLK 2.0: An updated database of plant receptor-like kinases developed with structure- and deep learning-based functional annotation and classification.},
journal = {Plant communications},
volume = {7},
number = {5},
pages = {101781},
pmid = {41742654},
issn = {2590-3462},
mesh = {*Deep Learning ; *Databases, Protein ; *Plants/enzymology/genetics ; *Plant Proteins/chemistry/metabolism/genetics ; *Protein Kinases/metabolism/chemistry/genetics ; Molecular Sequence Annotation ; },
abstract = {Receptor-like kinases (RLKs) are the largest class of signal transduction proteins in plants and play crucial roles in adaptation to diverse ecological environments. The previously published metaRLK database contains 311 581 RLKs from 508 plant species; however, 13% lack clear domain or family assignments, and structural features are not systematically integrated. Here, we present metaRLK 2.0, a structure-enhanced RLK resource that integrates large-scale structure-based annotation, fold classification, network analysis, and semantic functional inference. Structural reannotation identified 677 distinct domain types, increasing the number of recognized types by 62.7%. CATH-based classification revealed that RLK domains are enriched in rigid β-fold architectures. A structural similarity network identified 70 newly defined RLK families, 50 of which are predicted to be associated with plant cell wall-related processes. Overall, 8% of previously unclassified RLKs were assigned to known or newly defined families. MetaRLK 2.0 provides an expanded, structure-informed platform for the exploration of RLK diversity, evolution, and structure-function relationships and serves as a comprehensive resource for future research in plant receptor biology.},
}
@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.<br><br>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.<br><br>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&#x2009;=&#x2009;10) completed 30 sessions using a tablet device, while the TV intervention group (n&#x2009;=&#x2009;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.<br><br>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&#x2009;=&#x2009;0.044). No significant between-group differences were observed in HADS scores.<br><br>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 {pmid41747692,
year = {2026},
author = {Liu, Y and Fan, Q and Wang, B and Gao, Q and Chen, Y and Jing, X and Qu, H and Qi, D and Pang, M and Wang, W},
title = {Dual effects of 6PPD at environmentally relevant concentrations on freshwater algae: Multi-omics reveals a shift in survival strategies from lipid-mediated adaptation to carbon-energy reallocation.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141599},
doi = {10.1016/j.jhazmat.2026.141599},
pmid = {41747692},
issn = {1873-3336},
mesh = {*Carbon/metabolism ; *Water Pollutants, Chemical/toxicity ; Fresh Water ; *Microalgae/drug effects/metabolism ; Metabolomics ; Adaptation, Physiological/drug effects ; Lipid Metabolism/drug effects ; Proteomics ; Energy Metabolism/drug effects ; Multiomics ; },
abstract = {The widespread use of the tire antioxidant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) has resulted in its ubiquitous occurrence in aquatic environments, posing a significant ecological risk. However, the molecular effects and adaptive mechanisms of freshwater microalgae in response to environmentally relevant concentrations of 6PPD remain poorly understood. Employing a multi-omics approach, combining proteomics and metabolomics with physiological-biochemical analyses, this study investigated the holistic effects exerted by 6PPD on Tetradesmus obliquus during an 8-day static exposure simulating environmental attenuation. A significant hormetic effect was observed, with growth stimulation at environmentally relevant concentrations (≤10 μg/L, peaking at 0.1 μg/L with a 32.26 % increase) and inhibition at higher concentrations (≥100 μg/L). These different responses were associated with distinct molecular signatures. At 0.1 μg/L, lipid-mediated adaptive responses were activated via coordinated regulation of sphingolipid and glycerophospholipid metabolism, enhanced EPS production, adjusted amino acid and purine salvage pathways to support cellular structure and growth. At 100 μg/L, 6PPD induced a survival-oriented metabolic state, where impaired photosynthesis, mitochondrial function and membrane homeostasis were accompanied by a redirection of carbon-energy utilization toward starch and sucrose metabolism, pentose phosphate pathway, and Calvin cycle intermediate turnover, suggesting a shift toward cellular survival at the expense of structural maintenance and cell proliferation. Distinct from the passive signaling interference or transient stress responses observed in previous research, this study elucidates an active metabolic strategy integrating lipid-mediated adaptation and carbon-energy reallocation for algal survival, emphasizing the importance of considering sublethal molecular responses in ecological risk assessments of emerging contaminants.},
}
@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 {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 {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 {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.},
}
@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},
mesh = {Humans ; Hawaii ; *Wearable Electronic Devices/statistics &amp; numerical data ; *Ecological Momentary Assessment ; *Substance-Related Disorders/diagnosis/psychology ; Adult ; Female ; Male ; Computational Biology/methods ; Middle Aged ; Grounded Theory ; Data Collection ; Young Adult ; },
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 {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.},
}
@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.},
}
@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 {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 &amp; 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.},
}
@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},
mesh = {Animals ; *Water Pollutants, Chemical/toxicity ; Monte Carlo Method ; Quantitative Structure-Activity Relationship ; *Cosmetics/toxicity ; Algorithms ; Fishes ; Daphnia/drug effects ; Aquatic Organisms/drug effects ; Toxicity Tests/methods ; Chlorophyceae/drug effects ; },
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 {pmid41762813,
year = {2026},
author = {Hu, M and Li, R and Tian, Y and Huang, L and Chen, X and Liu, L and Li, G and Hao, L and Zheng, Y},
title = {Integrating multi-omics reveals the mechanisms of elevated [CO2] enhances salt tolerance of tobacco plants with a photosynthetic regulatory network.},
journal = {Plant physiology and biochemistry : PPB},
volume = {232},
number = {},
pages = {111160},
doi = {10.1016/j.plaphy.2026.111160},
pmid = {41762813},
issn = {1873-2690},
mesh = {*Nicotiana/metabolism/physiology/genetics ; *Photosynthesis/drug effects/physiology ; *Carbon Dioxide/metabolism/pharmacology ; *Salt Tolerance/physiology ; Metabolomics ; Plant Leaves/metabolism ; Multiomics ; },
abstract = {Abiotic stresses often occur concurrently with global changes, especially the combination of salt stress and elevated CO2 concentration ([CO2]) is a common phenomenon in salt-affected soils throughout the world. The synergistic regulatory mechanisms of tobacco (Nicotiana tabacum L.) plants in response to combined salt stress and elevated [CO2] are still poorly understood. This study aimed to reveal the potential mechanisms of elevated [CO2] modulating leaf photosynthesis of tobacco plants subjected to salt stress by integrating physiological, transcriptional, and metabolomics analyses. The results showed that elevated [CO2] significantly enhanced the photosynthetic and carbon assimilation capacity of tobacco plants by increasing the carboxylation efficiency of Rubisco, which counteracted damage to the photosynthetic system, mitigated water imbalance, and reduced ion toxicity caused by salt stress, thus alleviating the negative physiological effects on tobacco plants. This response was mechanistically linked to metabolic reprogramming: glyoxylate-derived succinate entered the tricarboxylic acid cycle to support adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH) production for antioxidant enzymes, while intermediates served as precursors for sucrose synthesis. At the same time, elevated [CO2] promoted photosynthetic carbon fixation, leading to a heightened triose phosphate flux toward starch and sucrose biosynthesis and accumulation. These carbohydrates functioned as osmoprotectants, conserving energy that would otherwise be expended in antioxidant synthesis. Thus, under future climate scenarios where elevated [CO2] coincides with intensified soil salinization, salt-induced suppression of photosynthetic carbon assimilation should be rigorously accounted for to avoid overestimation of the CO2 fertilization effect. This study provides novel insights into plant salt tolerance mechanisms, guiding precision breeding and exogenous modulation strategies for stress-resilient crops.},
}
@article {pmid41762815,
year = {2026},
author = {Liu, Y and Ge, J and Liu, Z and Yang, S and Li, X and Ismaeel, N},
title = {Multi-omics profiling unveils drought adaptation mechanisms in the peat moss Sphagnum palustre.},
journal = {Plant physiology and biochemistry : PPB},
volume = {232},
number = {},
pages = {111104},
doi = {10.1016/j.plaphy.2026.111104},
pmid = {41762815},
issn = {1873-2690},
mesh = {*Droughts ; *Sphagnopsida/metabolism/genetics/physiology ; Transcriptome ; *Adaptation, Physiological ; Gene Expression Regulation, Plant ; Plant Proteins/metabolism/genetics ; Gene Expression Profiling ; Photosynthesis ; Metabolomics ; Multiomics ; },
abstract = {Under the influence of global climate change, it is anticipated that the incidence and extent of drought conditions will increase in numerous regions across the globe. Sphagnum palustre, a dominant species in peatlands, is instrumental in maintaining hydrological regulation and enhancing carbon sequestration. However, the mechanisms underlying its drought response remain poorly characterized at the molecular and metabolic levels. This study analyzed the response of S. palustre to drought stress through integrated physiological, transcriptomic, and metabolomic approaches. Physiological results indicated that drought reduced the relative water content, chlorophyll and soluble protein content, while increased the content of soluble sugars and malondialdehyde, and antioxidant enzyme activity. Transcriptomic profiling identified 21,145 differentially expressed genes (DEGs) under drought stress. The DEGs associated with photosynthesis were significantly down-regulated, whereas those involved in other key pathways, such as hormone signal transduction, cutin and wax biosynthesis, and phenylalanine and linoleic acid metabolism, were significantly up-regulated. A total of 3668 differentially abundant metabolites were detected, with a significant accumulation of phenylpropanoids and flavonoids. Integrated multi-omics analyses highlight that S. palustre employs osmotic adjustment to enhance antioxidant defense, triggering adaptive responses through soluble sugar accumulation, hormone signaling, phenylpropanoid and flavonoid biosynthesis, and activation of ATP-binding cassette transporters. These findings provide insights into bryophytes drought adaptation, facilitating predictions of peatland ecosystem resilience and guiding conservation strategies under climate change.},
}
@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.},
}
@article {pmid41764240,
year = {2026},
author = {Stocco, A and Piras, P and Barbiero, G and Pranovi, F and Pinna, S},
title = {Ecosystem structure influences human health outcomes as the basis for green prescriptions.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41764240},
issn = {2045-2322},
mesh = {Humans ; *Ecosystem ; *Conservation of Natural Resources/methods ; Male ; Female ; Pilot Projects ; Middle Aged ; Adult ; },
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 {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 {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},
mesh = {*Soil Microbiology ; *Soil Pollutants/analysis ; *Coal Mining ; *Metals, Heavy/analysis ; *Environmental Monitoring ; Soil/chemistry ; *Microbiota ; Bacteria ; },
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 {pmid41766583,
year = {2026},
author = {Jastrzebski, JP and Gawronska, M and Babis, W and Quaranta, M and Czopek, D},
title = {PMScanR: An R Package for the Large-Scale Identification, Analysis, and Visualization of Protein Motifs.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {33},
number = {3},
pages = {379-384},
doi = {10.1177/15578666261423966},
pmid = {41766583},
issn = {1557-8666},
mesh = {Amino Acid Motifs ; *Software ; *Proteins/chemistry/genetics ; *Computational Biology/methods ; Databases, Protein ; *Sequence Analysis, Protein/methods ; Algorithms ; Amino Acid Substitution ; Humans ; },
abstract = {Proteins play a crucial role in biological processes, with their functions closely related to structure. Protein functions are often associated with specific motifs, which are short amino acid sequences exhibiting particular patterns. Most bioinformatics tools focus on identifying known motifs and they lack the ability to analyze the impact of single substitutions on entire domains or motifs. To address these limitations, we developed PMScanR (Protein Motif Scanner in R), an R package that automates the prediction and evaluation of the impact of single amino acid substitutions on protein motif occurrence in large datasets. In addition, existing tools do not support comparative analysis of multiple motifs across multiple sequences-a key feature that PMScanR was designed to provide. The package integrates various methods to facilitate motif identification, characterization, and visualization. It includes functions for running PS-Scan, a PROSITE database tool. Additionally, PMScanR supports format conversion to GFF, enhancing downstream analyses such as graphical representation and database integration. The library offers multiple visualization tools, including occurrence plots, sequence logos, and pie charts, enabling a deeper understanding of motif distribution and conservation. Through its integration with PROSITE, PMScanR provides access to up-to-date motif data, making it a valuable tool for biological and biomedical research, particularly in protein function annotation and therapeutic target identification. PMScanR is freely available under the GPL license and is distributed through Bioconductor (https://bioconductor.org/packages/PMScanR) and GitHub (https://github.com/prodakt/PMScanR).},
}
@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},
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 {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 {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 = {11},
number = {3},
pages = {815-831},
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)/ ; },
mesh = {*Trichoderma/genetics/classification/physiology ; Genome, Fungal ; Agriculture ; Phylogeny ; *Phenomics ; Spores, Fungal/genetics ; Phenotype ; Biological Evolution ; Ecology ; Plant Diseases/microbiology/prevention &amp; control ; },
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 {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},
mesh = {Humans ; Male ; Brazil/epidemiology ; Female ; *Particulate Matter/adverse effects/analysis ; Retrospective Studies ; *Air Pollution/adverse effects/analysis ; Middle Aged ; Adult ; Aged ; *Cardiovascular Diseases/mortality ; Risk Factors ; *Cerebrovascular Disorders/mortality ; Young Adult ; *Environmental Exposure/adverse effects ; Air Pollutants/analysis/adverse effects ; Residence Characteristics ; Myocardial Ischemia/mortality ; },
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).<br><br>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.<br><br>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 &#x2265; 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).<br><br>RESULTS: Approximately 91% of the 4.7 million residents (&#x2265; 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 &#xb1; 1.7; 95% CI = 3.5-4.2; male = 4.6 &#xb1; 2.1; 95% CI = 4.1-4.9), particularly in individuals aged &#x2265; 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).<br><br>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 {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},
pmid = {41779521},
issn = {1678-4464},
mesh = {Humans ; Brazil/epidemiology ; Adolescent ; Male ; Female ; Child ; *Self-Injurious Behavior/epidemiology/mortality/economics ; Hospitalization/statistics &amp; numerical data ; Young Adult ; Child, Preschool ; Sex Distribution ; Socioeconomic Factors ; Age Distribution ; Infant ; },
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 {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 Grozinger, 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},
pmid = {41779788},
issn = {1091-6490},
support = {101133983//More4nature/ ; },
mesh = {*Biodiversity ; *Conservation of Natural Resources/methods ; Ecosystem ; *Environmental Monitoring/methods ; Humans ; },
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 {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},
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.},
}
@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.},
}
@article {pmid41785249,
year = {2026},
author = {Pucci, N and Kaan, AM and Ujčič-Voortman, J and Verhoeff, AP and Zaura, E and Mende, DR},
title = {Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1013185},
pmid = {41785249},
issn = {1553-7358},
mesh = {Humans ; *Mouth/microbiology ; Infant ; *Microbiota/genetics ; Female ; Phylogeny ; Metagenome/genetics ; Metagenomics ; Male ; Streptococcus/genetics/classification ; Longitudinal Studies ; Computational Biology ; },
abstract = {Early-life oral microbiome development is a complex community assembly process that influences long-term health outcomes. Nevertheless, microbial functions and interactions driving these ecological processes remain poorly understood. In this study, we analyze oral microbiomes from a longitudinal cohort of 24 mother-infant dyads at 1 and 6 months postpartum using shotgun metagenomics. We identify two previously undescribed Streptococcus and Rothia species to be among the most prevalent, abundant and strongly co-occurring members of the oral microbiome of six-month-old infants. By leveraging metagenome-assembled genomes (MAGs) and genome-scale metabolic models (GEMS) we reveal their genomic and functional characteristics relative to other infant-associated species and predict their metabolic interactions within a network of co-occurring oral taxa. Our findings highlight unique functional features, including genes encoding adhesins and carbohydrate-active enzymes (CAZymes). Metabolic modeling identified potential exchange of key amino acids, particularly ornithine and lysine, between these species, suggesting metabolic cross-feeding interactions that may explain their co-abundance across infant oral microbiomes. Overall, this study provides key insights into the functional adaptations and microbial interactions shaping early colonization in the oral cavity, providing testable hypotheses for future experimental validation.},
}
@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 {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 = {23},
number = {3},
pages = {663-672},
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 Cient&#xed;fico e Tecnol&#xf3;gico (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)/ ; ECF 137/2020//Environment and Conservation Fund (ECF)/ ; UIDB/00329/2020//NOVA | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; 05K2022//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 05K2019//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
mesh = {*Ants/anatomy &amp; histology/genetics ; *Biodiversity ; Male ; Female ; Animals ; *Phenomics/methods ; *Phylogeny ; X-Ray Microtomography ; },
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 {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 = {232},
number = {4},
pages = {},
pmid = {41788053},
issn = {1943-2631},
support = {//U.S. Department of Agriculture (USDA)/ ; //National Institute of Food and Agriculture/ ; #2022-70412-38454//Agricultural Genome to Phenome Initiative/ ; #2021-70412-35233//Agricultural Genome to Phenome Initiative/ ; #2020-70412-32615//Agricultural Genome to Phenome Initiative/ ; #2019-67021-29920//USDA NIFA FACT/ ; #2024-51181-43233//USDA NIFA/ ; 2320675//NSF BII/ ; //the Trees In Peril Project funded by the Nature Conservancy/ ; },
mesh = {Phenotype ; *Plants/genetics ; *Genomics/methods ; *Software ; Climate Change ; *Biological Evolution ; Ecosystem ; *Genome, Plant ; },
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 {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 = {},
pmid = {41790499},
issn = {2057-5858},
mesh = {*Vitamin B 12/metabolism/biosynthesis/genetics ; *Mesorhizobium/genetics/metabolism ; *Synechococcus/genetics/metabolism/growth &amp; 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.},
}
@article {pmid41791164,
year = {2026},
author = {Ding, Y and Wang, W and Luo, T and Song, Y and Gao, Y and Zhang, Z and Zhao, H and Wang, H and Li, H},
title = {Multi-omics evaluation of grape microbial diversity and natural wine flavor metabolites under extra-simplified eco-viticulture.},
journal = {Food chemistry},
volume = {510},
number = {},
pages = {148671},
doi = {10.1016/j.foodchem.2026.148671},
pmid = {41791164},
issn = {1873-7072},
mesh = {*Wine/analysis/microbiology ; *Vitis/microbiology/metabolism/chemistry/growth &amp; development ; *Flavoring Agents/metabolism/chemistry/analysis ; Microbiota ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Volatile Organic Compounds/metabolism/chemistry/analysis ; Metabolomics ; Fruit/microbiology/chemistry/metabolism ; Fermentation ; Biodiversity ; Taste ; *Fungi/classification/isolation &amp; purification/metabolism/genetics ; Odorants/analysis ; Soil Microbiology ; Multiomics ; },
abstract = {Ecological viticulture with minimal intervention is increasingly emphasized for sustainable wine production, but its effects on grape microbial communities and wine flavor metabolism remain insufficiently understood. This study investigated vineyard soil/grape-associated microbiota and wine flavor metabolites under conventional management (CM) and extra-simplified eco-viticulture (ES) across 2023-2025 vintages. Results showed that ES positively influenced soil microbial diversity and grape epidermal bacterial diversity, while reducing epidermal fungal diversity relative to CM. Spontaneous fermentation (SF) enriched organic acids, amino acids, and their derivatives, whereas inoculated fermentation (IF) accumulated glycolysis/TCA cycle intermediates and nucleosides. Volatile metabolomics revealed that ES-S natural wine had higher levels of terpenoids, aldehydes, and heterocyclic compounds with distinct floral/fruity aromas (rOAV>1), while IF wines were dominated by alcohols, esters, and ketones with homogeneous ripe fruit/mushroom notes. Collectively, extra-simplified eco-viticulture enhanced microbial diversity and drove more complex flavor metabolites in natural wines, providing a sustainable strategy for high-quality wine production.},
}
@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 = {7},
number = {2},
pages = {100586},
pmid = {41793007},
issn = {2666-2477},
mesh = {Humans ; *Genome-Wide Association Study/methods ; *Genomics/methods ; Multifactorial Inheritance ; Polymorphism, Single Nucleotide ; Models, Genetic ; Phenotype ; },
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 genome-wide association studies (GWASs) 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 the 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 GWASs 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 existing in widely used biobanks such as the UK Biobank and the Health and Retirement Study.},
}
@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.},
}
@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.},
}
@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 {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 {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.<br><br>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.<br><br>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.<br><br>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 {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, MH},
title = {Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
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 f&#xfc;r 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.},
}
@article {pmid41801038,
year = {2026},
author = {Manninen, J and Korhonen, A and Johnson, KL and Tahvonen, O and Luukkonen, A and Saarenpää, M and Puhakka, R and Uimonen, L and Kummola, L and Skevaki, C and Renz, H and Rajaniemi, J and Laitinen, OH and Roslund, MI},
title = {Playgrounds as microbial interfaces: strategies to enhance soil microbiomes and support healthy childhoods.},
journal = {mSystems},
volume = {11},
number = {4},
pages = {e0166225},
pmid = {41801038},
issn = {2379-5077},
support = {346136//Strategic Research Council/ ; //Stiftung f&#xfc;r Pathobiochemie und Molekulare Diagnostik/ ; CALM-QE project MIRACUM consortium of the Medical Informatics Initiative//Bundesministerium f&#xfc;r Bildung und Forschung/ ; Hospital Partnership Programme//Deutscher Akademischer Austauschdienst/ ; //Deutsche Gesellschaft f&#xfc;r Internationale Zusammenarbeit/ ; //Deutsche Forschungsgemeinschaft/ ; 346137//Strategic Research Council/ ; 346138//Strategic Research Council/ ; //Universities of Giessen and Marburg Lung Center (UGMLC)/ ; //Deutsches Zentrum f&#xfc;r Lungenforschung/ ; //Uniklinikum Giessen und Marburg/ ; //Stiftung f&#xfc;r Pathobiochemie und Molekulare Diagnostik/ ; //Bundesministerium f&#xfc;r Gesundheit/ ; //State of Hesse/ ; },
mesh = {Humans ; *Soil Microbiology ; *Microbiota ; Child ; *Play and Playthings ; },
abstract = {Emerging evidence suggests that reduced exposure to biodiversity, including rich environmental microbiota, is associated with negative outcomes in the health and well-being of children. Biodiversity loss not only impacts individual health but also poses significant threats to planetary health. It destabilizes systems that regulate climate, purify air and water, maintain soil fertility, and support plant and microbial life essential for environmental health. Here, we review the scientific evidence on microbiome-supportive strategies in eco-centric, child-friendly playground environments. Investigating how environmental features influence soil microbiomes and exposure pathways could provide insights into how playgrounds function as living interfaces. These are places where environmental microbes shape children's microbial colonization patterns, immune and endocrine regulatory systems, while also contributing to ecosystem services such as biodiversity support and pollutant mitigation-particularly relevant given that many pollutants are known to disrupt immune and endocrine functions in children. These dynamics have far-reaching implications for child well-being, preventive health strategies, physical activity, environmental literacy, and broader sustainability. A multi-omic systems approach offers a critical pathway to uncover the ecological and health-related impacts of nature-associated microbial exposure and characterize host-microbiome interactions underlying immune and endocrine regulation, brain development, cognition, and stress-related disorders. Our review highlights a lack of such integrative studies, underscoring the need to advance this line of research to inform evidence-based, sustainable, and health-promoting urban design.},
}
@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},
pmid = {41802001},
issn = {1932-6203},
mesh = {Ethiopia ; *Geographic Information Systems ; *Crops, Agricultural/growth &amp; 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.},
}
@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 = {12},
number = {3},
pages = {520-531},
pmid = {41803388},
issn = {2055-0278},
mesh = {*Trees/physiology ; *Plant Leaves/growth &amp; development/metabolism ; *Rainforest ; *Climate Change ; Photosynthesis ; Remote Sensing Technology ; Models, Biological ; South America ; },
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 {pmid41805696,
year = {2026},
author = {Veith, T and Beck, RJ and Brown, JS and Andor, N},
title = {Inverse game theory characterizes frequency-dependent selection driven by karyotypic diversity in triple-negative breast cancer.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1013897},
pmid = {41805696},
issn = {1553-7358},
mesh = {*Triple Negative Breast Neoplasms/genetics ; Humans ; Female ; *Game Theory ; Cell Line, Tumor ; Animals ; DNA Copy Number Variations/genetics ; Mice ; Computational Biology ; Karyotyping ; Karyotype ; },
abstract = {Chromosomal instability, characterized by pervasive copy number alterations (CNAs), significantly contributes to cancer progression and therapeutic resistance. CNAs drive intratumoral genetic heterogeneity, creating distinct subpopulations whose interactions shape tumor evolution through frequency-dependent selection. Here, we introduce ECO-K (Ecological-Karyotypes), an inverse game theory framework that quantifies frequency-dependent interaction coefficients among karyotypically defined subpopulations under the assumption that their fitness is frequency-dependent. Applying this approach to serially-passaged, triple-negative breast cancer cell lines and patient-derived xenografts (PDXs), we estimated interaction matrices consistent with the observed time-series dynamics. In one PDX lineage, the inferred matrices consistently assigned large interaction coefficients to a subpopulation characterized by chromosome 1 loss and chromosome 14p gain, suggesting it may act as an ecological hub within the frequency-dependent model. Our framework provides testable predictions of intratumoral ecological dynamics, highlighting opportunities to strategically target key subpopulations to disrupt tumor evolution.},
}
@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},
pmid = {41805908},
issn = {1553-7358},
mesh = {*Host-Pathogen Interactions/genetics/physiology ; *Models, Biological ; *Biological Evolution ; *Disease Resistance/genetics ; Computational Biology ; Animals ; Humans ; },
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 {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.},
}
@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 = {26},
number = {1},
pages = {},
pmid = {41814333},
issn = {1472-6963},
mesh = {Humans ; Italy/epidemiology ; *COVID-19/epidemiology ; *Sentinel Surveillance ; *Hospitalization/statistics &amp; numerical data/trends ; *Hospitals/statistics &amp; numerical data ; SARS-CoV-2 ; },
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 {pmid41818283,
year = {2026},
author = {Brun-Usan, M and Latorre, R and Buscalioni, &#xc1;D and Alcorlo, P and Marugán-Lobón, J},
title = {Algorithmic reconstruction of trophic networks from open-access species lists reveals key organisms in real ecosystems.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1014061},
pmid = {41818283},
issn = {1553-7358},
mesh = {*Algorithms ; *Ecosystem ; *Food Chain ; Computational Biology/methods ; *Models, Biological ; Animals ; Biodiversity ; Databases, Factual ; Data Mining/methods ; Wetlands ; },
abstract = {Biotic interactions, crucial for understanding the ecology and evolution of species, are often conceptualized as ecological networks. However, the complexity of real ecosystems poses challenges for empirical inference, and theoretical interaction models, while informative, frequently fail to undergo empirical validation. This dual limitation creates a gap between theoretical and empirical approaches in portraying ecosystem dynamics and identifying (and protecting) key species, which are critical for conservation efforts and ecosystem management. In order to bridge this operational gap, we present a novel automated protocol capable of generating realistic trophic networks, including multilayer ones, using non-curated, freely-available species lists from real ecosystems as input data. As a proof-of-concept, we applied this method to the species lists contained in the RAMSAR database of wetland ecosystems. Our data mining algorithm enriches these species lists with functional traits, such as body size, habitat, and diet, by integrating information directly sourced from online biodiversity databases. Subsequently, a modified version of the Allometric Niche Model is used to sort species within the trophic network according to their functional traits and ecological roles. After demonstrating the algorithmic robustness of our method and the biological plausibility of the resulting ecological networks, we illustrate its potential to characterize, in a cost-efficient manner, the structure of real-world ecosystems and to identify the organisms that are crucial for maintaining that structure. In this case study, our findings indicate that the robustness of wetland ecosystems often depends on medium-sized, highly mobile organisms occupying intermediate trophic levels.},
}
@article {pmid41819291,
year = {2026},
author = {Kalimuthu, S and Muthusamy, A},
title = {MobiRes: An integrative pipeline for resistome risk prediction through mobilome profiling.},
journal = {Journal of microbiological methods},
volume = {244},
number = {},
pages = {107448},
doi = {10.1016/j.mimet.2026.107448},
pmid = {41819291},
issn = {1872-8359},
mesh = {Humans ; *Metagenomics/methods ; DNA Transposable Elements/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Animals ; *Bacteria/genetics/drug effects ; Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Bacterial/genetics ; Microbiota/genetics ; Machine Learning ; *Computational Biology/methods ; Metagenome ; Bacteriophages/genetics ; Risk Assessment ; Feces/microbiology ; },
abstract = {Antimicrobial resistance (AMR) poses a significant global health challenge, with the environment serving as a crucial reservoir and conduit for resistance determinants. Although antibiotic resistance genes (ARGs) have been extensively studied in environmental contexts, systematic approaches for assessing and prioritizing the risks associated with mobile genetic elements (MGEs), such as plasmids, phages, transposons, and integrative elements (IEs), remain unclear. To address this gap, we present MobiRes, an open-source computational framework designed to predict resistome risk by integrating information from the mobilome and microbiome. The pipeline was evaluated using a wide range of publicly available metagenomic datasets spanning diverse environments, including wastewater, poultry, soil, sediments, and human fecal samples. To validate the framework, statistical analyses and machine learning models were applied to evaluate the role of MGEs in driving ARG dissemination. The pipeline identified transposons as the dominant MGE class while capturing environment-specific variation in plasmid, phage, and IE -associated ARGs. Transposon-associated ARGs showed the most consistent environmental differentiation (ANOVA p = 0.0017; Kruskal-Wallis p = 0.018), whereas plasmid and phage-associated ARGs varied moderately (p = 0.015-0.040) and IE-associated ARGs remained comparatively stable across environments (p > 0.05). The Random Forest (RF) model achieved an AUC of 0.82, and subsequent feature importance and SHapley Additive exPlanations (SHAP) analyses revealed that transposon abundance is the primary factor driving ARG dissemination across diverse environments. By integrating host, mobility, and ecological factors, MobiRes provides a scalable and One Health-oriented framework for comprehensive AMR risk assessment. This pipeline is publicly available at https://github.com/santhiyakc17/MobiRes_Pipeline.},
}
@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 &amp; 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.<br><br>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.<br><br>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.<br><br>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.},
}
@article {pmid41825203,
year = {2026},
author = {Fu, Q and Dai, H and Wang, J and Zheng, S and Zhou, Y and Liu, H and Xu, F and Cheng, C and Jiang, H and Qian, Y and Zhang, S and Liu, L and Zheng, H and Li, Y and Zhang, L and Chen, Y and Cheng, X and Yang, T},
title = {Multi-omics analysis of dynamic profiles in response to various nutrient loads provides novel insights into obesity.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {59},
number = {},
pages = {106607},
doi = {10.1016/j.clnu.2026.106607},
pmid = {41825203},
issn = {1532-1983},
mesh = {Humans ; *Obesity/metabolism/microbiology/blood ; Male ; Female ; Adult ; Postprandial Period/physiology ; *Nutrients ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Metabolomics/methods ; *Diet ; Proteomics ; Feeding Behavior ; Overweight ; Body Mass Index ; Multiomics ; },
abstract = {BACKGROUND&amp; AIMS: Obesity is a global health issue driven by improper nutrient intake and metabolic dysregulation. The complexity of dietary components and the dynamic nature of postprandial metabolism limit our understanding of how different nutrient loads associated with obesity. This study aims to characterize the dynamic metabolic responses to nutrient intake using multi-omics approaches, assess the influence of dietary habits and gut microbiota, and evaluate the acute obesity-risk signature (AORS) associated with different macronutrients.<br><br>METHODS: We conducted a mixed meal tolerance test (MMTT) in 147 non-diabetic individuals (54 controls, 38 overweight, 55 obese). Blood samples were collected at multiple time points for untargeted metabolomics, lipidomics, proteomics, and hormone assays. Gut microbiota was profiled via metagenomic sequencing. A separate single macronutrient tolerance test (SMNTT) involving glucose, whey protein, butter, and olive oil was performed in 24 healthy volunteers to compare acute metabolic responses and derive an AORS based on postprandial multi-omics data.<br><br>RESULTS: Postprandial multi-omic analytes showed stronger associations with obesity indicators than fasting measures. Distinct temporal changes in metabolites, lipids, and proteins were observed across different BMI groups, with enrichment in pathways such as bile acid biosynthesis, triglyceride metabolism, and complement activation. Dietary habits and gut microbiota significantly influenced postprandial metabolic profiles, with specific metabolites and proteins mediating their effects on obesity. In SMNTT, glucose load exhibited the lowest AORS among isocaloric macronutrients (0.1082 &#xb1; 0.1917 %). Gut microbiota composition further modulated metabolic responses, with olive oil showing divergent AORS between Bacteroides- and Prevotella-dominated enterotypes (p = 0.043).<br><br>CONCLUSION: Postprandial multi-omics provides superior insights into obesity pathophysiology compared to fasting measurements. Our findings reveal that dietary habits and gut microbiota significantly influence postprandial metabolism and obesity risk, and demonstrate that different macronutrients confer distinct AORS values, which are further modified by an individual's gut microbiota composition. This underscores the potential for personalized nutritional strategies based on dynamic metabolic responses and microbial ecology.},
}
@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 = {89},
number = {1},
pages = {},
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/ ; },
abstract = {UNLABELLED: This study investigates the archaeal lipid distribution in freshwater springs with a particular focus on lipidomic profiles as ecological indicaters. Cultivation-independent approaches were employed to analyze organisms that had not yet been cultivated in the laboratory. Shotgun lipidomics of 21 springs in western and central part of Slovakia revealed more than 100 characteristic archaeal lipids, from which three biomarker groups were selected: (i) core lipids containing archaeol and glycerol dialkyl glycerol tetraethers (GDGT), including their mono and dihydroxy derivatives; (ii) mono- to tetra-glycosides of archaeol and GDGTs; and (iii) six phosphoarchaeols (archaeol-based phospholipids). Statistical analyses classified springs into three categories: cold (temperature < 20 °C), warm (> 30 °C), and radioactive (a subset of cold springs with ˃100 Bq/L radioactivity). Significant shifts in the ratios of archaeal lipids were correlated with the temperature and radioactivity, demonstrating the sensitivity of lipidomic profiling to environmental parameters. Moreover, tandem mass spectrometry identified a previously undescribed metabolite, archaeol-based dimethylphosphatidylethanolamine. The applied method provides rapid and highly sensitive tools for screening the presence of archaea, detecting as few as several thousand cells per liter, and offers new insights into the ecology of archaeal communities in groundwater environments.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02720-7.},
}
@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 = {42},
number = {3},
pages = {},
pmid = {41826799},
issn = {1367-4811},
support = {T32 DK137525/DK/NIDDK NIH HHS/United States ; R01LM013438//National Institutes of Health of the United States/ ; },
mesh = {*Neoplasms/genetics/pathology ; Humans ; Mutation ; *Genetic Fitness ; *Computational Biology/methods ; *Evolution, Molecular ; Tumor Microenvironment/genetics ; },
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.<br><br>RESULTS: We present estimating evolutionary events through single-timepoint sequencing (TEATIME), 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.<br><br>R implementation of TEATIME is available on GitHub (https://github.com/liliulab/TEATIME) and Zenodo (https://zenodo.org/records/17422174).},
}
@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.},
}
@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.},
}
@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},
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.},
}
@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 &amp; 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},
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},
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.},
}
@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.},
}
@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 = {},
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.},
}
@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 = {298},
number = {},
pages = {124273},
doi = {10.1016/j.envres.2026.124273},
pmid = {41839346},
issn = {1096-0953},
mesh = {*Pollen ; *Poaceae ; *Allergens/analysis ; *Environmental Monitoring/methods ; *Air Pollutants/analysis ; Forecasting ; Germany ; Models, Theoretical ; Climate ; Cities ; Spain ; },
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. Moreover, 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 Forest, 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 NNETAR and/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 may 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 = {14},
number = {1},
pages = {},
pmid = {41840729},
issn = {2049-2618},
support = {JPMJND2206//Japan Science and Technology Agency/ ; },
mesh = {*Metagenome ; *Metadata ; *Microbiota/genetics ; *Metagenomics/methods ; Molecular Sequence Annotation ; Databases, Genetic ; *Bacteria/classification/genetics ; Software ; Phylogeny ; Computational Biology/methods ; },
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.<br><br>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&#x2009;>95% completeness and&#x2009;<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&#x2009;~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty.<br><br>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},
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.},
}
@article {pmid41841726,
year = {2026},
author = {Laakso, H and Hashem Taha, M and Flegal, M and Surette, J and Mysara, M and Klokov, D},
title = {Impact of chronic low-dose external gamma- and internal tritium beta-irradiation on the gut microbiome in the context of intestinal tumorigenesis in Apc[Min/+] mice.},
journal = {mSystems},
volume = {11},
number = {4},
pages = {e0115625},
pmid = {41841726},
issn = {2379-5077},
support = {//Connexus Nuclear Inc/ ; //Atomic Energy of Canada Limited/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/radiation effects ; Mice ; *Gamma Rays/adverse effects ; *Beta Particles/adverse effects ; *Tritium/adverse effects ; *Carcinogenesis/radiation effects ; Male ; Dose-Response Relationship, Radiation ; Cytokines/blood ; Female ; *Intestinal Neoplasms/microbiology ; *Colorectal Neoplasms/microbiology ; Disease Models, Animal ; },
abstract = {UNLABELLED: The gut microbiome (GM) plays an essential role in health, and its dysbiosis can increase the risk of colon cancer. While the detrimental effects of high-dose ionizing radiation on GM have been documented, little is known about the effects of low doses, including from internal exposure to tritium, which is produced by nuclear power generation and emits beta radiation, making it a public concern. We examined the effects of chronic irradiation with internal tritium beta radiation or external [60]Co gamma radiation on GM and intestinal tumorigenesis in the Apc[Min/+] mouse model of colorectal cancer. Mice were exposed to tritiated drinking water (HTO) or gamma radiation at cumulative doses of 0, 10, 100, and 2,000 mGy, followed by intestine, blood plasma, and fecal sample collections at 12, 16, and 20 weeks of age. HTO- and gamma-exposed cohorts had distinct tumor size and multiplicity patterns, with non-monotonous dose-responses. Complex patterns of blood cytokine changes with age, dose, and type of irradiation were recorded. GM analyses using 16S rRNA amplicon sequencing revealed significant changes in alpha and beta diversity in irradiated mice compared to controls, indicating altered microbial dynamics. HTO and gamma radiation induced distinct microbiome changes that did not correlate with tumor and blood cytokine readouts. Our results suggest that chronic exposure to low-dose gamma- or internal HTO beta radiation can affect GM in a radiation type and dose-dependent non-linear manner. Our results provide novel insight into the effects of low-dose gamma- and tritium beta radiation on GM and a possible association with tumorigenesis.<br><br>IMPORTANCE: Low-dose ionizing radiation is one of the few environmental stressors that simultaneously reshapes host physiology and the structure-function landscape of resident microbiomes, yet mechanistic insight at ecologically relevant doses has been scarce. By integrating longitudinal 16S rRNA profiling, multiplex cytokine analyses, and quantitative tumor phenotyping in the Apc[Min/+] mouse model, our study demonstrates that continuous exposure to either external [60]Co &#x3b3;-photons or tritium beta particles perturbs gut microbial community structure in radiation-quality-specific ways and that these shifts track with, and sometimes precede, complex, non-monotonic changes in intestinal tumor burden. The work expands the traditional radiobiology focus from host-centric DNA damage to a systems-level view in which microbe-host-radiation interactions form a dynamic network influencing early colorectal carcinogenesis.},
}
@article {pmid41844600,
year = {2026},
author = {Xie, H and Hu, J and Zhao, X and Chen, J and Yue, X and Zhou, C and Navarro-Muñoz, JC and Jiang, J and Tang, X and Zhao, F and Hatmaker, EA and Rokas, A and Barber, AE and Drott, MT and Keller, NP and Zhang, Q and van der Hooft, JJJ and Medema, MH and Li, P},
title = {Large-scale multi-omics profiling reveals environmental and evolutionary drivers of fungal phylogeographic and metabolic diversity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41844600},
issn = {2041-1723},
mesh = {Phylogeography ; *Aspergillus flavus/genetics/metabolism/classification ; Phylogeny ; Metabolomics/methods ; Metabolome/genetics ; China ; Genome, Fungal ; Mycotoxins/metabolism/genetics/biosynthesis ; Evolution, Molecular ; Genome-Wide Association Study ; Multiomics ; },
abstract = {Chemical innovation is essential for fungi to adapt to ever-changing ecological environments. However, the environmental and evolutionary drivers of fungal metabolic differentiation remain ambiguous. Here, we show the phylogeographic diversity of 1052 Aspergillus flavus strains across four continents, as conducted through phylogenetic and biogeographical analysis, including 544 newly sequenced strains from China. These strains exhibit varying levels of population-specific mycotoxin production, as determined by population metabolomics analysis. We report a toxigenic subpopulation from China, identified through comparative population genomics analysis. Pan-metabolome analysis reveals strong phylogeographic metabolic patterns associated with specific ecological niches. Low-mycotoxin production clades harbor distinct uncharacterized biosynthetic gene clusters and produce different specialized metabolites instead. This discrepancy is only partially explained by variation in biosynthetic pathway genes, and changes in regulation and primary metabolism appear to mainly drive differentiation of specialized metabolite profiles across fungal populations, as indicated by pangenome profiling, metabolites-genome-wide association study, genotype-environment association study, pan-transcriptome analysis, and gene knockout experiments. Altogether, our results reveal how environmental shifts drive the fungal metabolic evolution, and provide insights for predicting the risk of harmful fungal outbreaks and for biogeographically-informed, precise control measures.},
}
@article {pmid41845564,
year = {2026},
author = {Zhang, Y and Wang, DD},
title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644682},
pmid = {41845564},
issn = {1949-0984},
support = {K99 DK119412/DK/NIDDK NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; U54 AG089325/AG/NIA NIH HHS/United States ; RF1 AG083764/AG/NIA NIH HHS/United States ; },
mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Animals ; *Diet ; Metabolomics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Proteomics ; Multiomics ; },
abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.},
}
@article {pmid41847797,
year = {2026},
author = {Basta, S and Montagnani, E and Bertamino, M and Balzarotti, N and Mordeglia, M and Crepaldi, M and Parmiggiani, A and Tacchino, C and Gori, M},
title = {Multisensory integration in action: Improving goal-directed movement in children with motor impairments.},
journal = {Perception},
volume = {},
number = {},
pages = {3010066261431229},
doi = {10.1177/03010066261431229},
pmid = {41847797},
issn = {1468-4233},
abstract = {Perinatal and pediatric brain damages in children, such as those caused by perinatal stroke, often results in motor and sensory impairments that compromise autonomy and quality of life. Such conditions may also disrupt multisensory integration, which is essential for goal-directed actions. While previous studies have examined multisensory processing using laboratory-based paradigms, they often lacked ecological validity. To address this issue, we developed MSICLIMB, a novel climbing wall equipped with smart holds that emit auditory (A), visual (V), and audiovisual (VA) cues, which enables the study of multisensory integration in a dynamic, action-oriented context. We compared children with motor impairments to typically developing peers, measuring their reaching times (RT) in response to randomly presented sensory cues. Children with motor impairments exhibited significantly slower RT across all conditions. However, both groups showed faster RT to multisensory stimuli, highlighting the facilitative effect of multisensory integration. RTs improved over trials, particularly in the clinical group, suggesting learning potential. Age was also a significant factor, with older children demonstrating faster responses and reduced group differences. MSICLIMB is an innovative tool that can be used to assess and potentially train multisensory integration through ecologically valid sensorimotor tasks. It has promising applications in both clinical and typical populations.},
}
@article {pmid41848748,
year = {2026},
author = {Rowland, T and FitzGerald, R and Challenger, E and Dickinson, L and Else, LJ and Walker, L and Hale, C and Shaw, V and Kelly, C and Lyon, R and Gibney, J and Dhamani, K and Irwin, M and Enever, Y and Tetlow, M and Wood, W and Reynolds, H and Chiong, J and Osanlou, O and Pertinez, H and Bullock, K and Greenhalf, W and Owen, A and Lalloo, DG and Jacobs, M and Hiscox, JA and Jaki, T and Mozgunov, P and Saunders, G and Griffiths, G and Khoo, SH and Fletcher, TE and , },
title = {Optimal Dose and Safety of Intravenous Favipiravir in Hospitalized Patients With COVID-19: A Dose-Escalating, Randomized Controlled Phase Ib Study.},
journal = {Clinical pharmacology and therapeutics},
volume = {119},
number = {6},
pages = {1650-1661},
pmid = {41848748},
issn = {1532-6535},
support = {75F40120C00085//US Food and Drug Administration/ ; NIHR300576//National Institute for Health and Care Research/ ; //National Institute for Health Research Southampton Biomedical Research Centre/ ; MR/V028391/1/MRC_/Medical Research Council/United Kingdom ; MR/W005611/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00040/03/MRC_/Medical Research Council/United Kingdom ; 221590/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Female ; Middle Aged ; Male ; *COVID-19 Drug Treatment ; Aged ; *Pyrazines/administration &amp; dosage/adverse effects/pharmacokinetics ; *Antiviral Agents/administration &amp; dosage/adverse effects/pharmacokinetics ; Aged, 80 and over ; *Amides/administration &amp; dosage/adverse effects/pharmacokinetics ; Dose-Response Relationship, Drug ; Administration, Intravenous ; SARS-CoV-2 ; Hospitalization ; COVID-19 ; Treatment Outcome ; },
abstract = {AGILE (NCT04746183) is a Phase Ib/IIa platform, evaluating candidates to treat COVID-19. Candidate Specific Trial 6 evaluated the safety and optimal dose of a novel intravenous formulation of favipiravir in a dose-escalating, open-label, randomized, controlled, Bayesian adaptive Phase Ib trial. Hospitalized adults with PCR-confirmed SARS-CoV-2 infection, within 14 days of symptomatic COVID-19 were randomized 2:1 in groups of 6 (n = 4 favipiravir, n = 2 standard of care) to ascending doses of intravenous favipiravir twice daily (b.i.d.) for 7 days or standard of care. Clinical data, safety evaluations, virology and pharmacokinetic samples were collected. The primary outcome was safety. Secondary outcomes included clinical, pharmacokinetic and virological endpoints. Twenty-four participants enrolled between September 10, 2022 and November 1, 2023 [10/24 female; median age 74 years (range 52-93)]. Favipiravir was well tolerated despite a high background rate of unrelated adverse events. No dose limiting toxicities were observed, with a model-predicted dose limiting toxicity risk of 16.8% and probability of unacceptable toxicity of 2.7% at the highest dose level. No serious adverse events were deemed related to favipiravir but an expected association with asymptomatic, transient hyperuricemia was observed. Favipiravir exposures increased disproportionally to dose with significant accumulation in plasma, but with marked variability between participants within each cohort. This novel formulation of favipiravir was safe at sustained high doses that reached pre-specified pharmacokinetic targets in a study group with frailty and complex health profiles. We consider doses up to 2,400 mg b.i.d. to be safe for further evaluation.},
}
@article {pmid41850510,
year = {2026},
author = {Naveesh, YB and Suresh, KP and Chethan, AJ and Patil, AV and Archana, CA and Nandan, AS and Patil, SS and Krishnamoorthy, P and Siju, SJ},
title = {Spatial Modeling of Anthrax Risk in India's Agro-Climatic Zones: A Future Perspective.},
journal = {Acta tropica},
volume = {278},
number = {},
pages = {108063},
doi = {10.1016/j.actatropica.2026.108063},
pmid = {41850510},
issn = {1873-6254},
mesh = {*Anthrax/epidemiology/veterinary ; India/epidemiology ; Animals ; *Climate Change ; Humans ; Livestock ; Zoonoses/epidemiology ; Agriculture ; Climate ; },
abstract = {Climate change is altering ecosystems, posing a risk of major impact for both human and animal health. Emerging zoonotic diseases, such as anthrax, are particularly vulnerable to changes in climate and biodiversity. anthrax, a classic zoonotic disease, disproportionately affects vulnerable pastoralist communities. This research assessed how changing climatic variables influence the geographical spread of anthrax outbreaks in the Indian condition, a region confronting rapid climate impacts. The study also compared the effect of climate variables with traditional factors like livestock population distribution and soil-moisture balance in determining anthrax risk. MaxEnt, a machine learning model which maximizes entropy of the probability distribution was used to predict anthrax suitability under Indian climatic conditions. The results identified climatic variables like rainfall, soil moisture, soil pH, temperature humidity index (THI), land surface temperature (LST) and livestock density are critical in modeling anthrax suitability. These outcomes emphasize the key role of warming climatic events driven by raising temperature and more frequent and intense extreme weather events heatwaves, droughts and floods in shaping anthrax ecology in India. Further indicate that strategies targeting conserving megafauna diversity in agriculture ecosystems and enhancing livestock health in small and medium-sized herds could mitigate the disease's risks. This study underscores the growing significance of climate in anthrax distribution and suggests that biodiversity conservation and better livestock management could play key roles in reducing future anthrax incidences.},
}
@article {pmid41852747,
year = {2026},
author = {Yi, X and Lu, Y and Li, J and Xu, D and Xiao, X and Xie, F},
title = {The source-based health risk assessment of toxic elements in soils from coal resource-depleted city.},
journal = {iScience},
volume = {29},
number = {3},
pages = {114963},
pmid = {41852747},
issn = {2589-0042},
abstract = {A variety of anthropogenic activities have caused soils pollution with potentially toxic elements (PTEs) during the transformation of coal resource-exhausted areas, which pose potential health risks to humans. Take a typical Chinese coal resource-exhausted city as the research object, 93 topsoil samples were collected and PTEs concentrations were quantified using ICP-MS. The results indicated that the over-standard rates of Pb and Zn were 53.8% and 33.4%, respectively, with their elevated concentrations primarily concentrated in the southwestern part of the study area, likely due to complex industrial activities. Industrial activities (24.0%), road dust (24.1%), and copper smelting-natural weathering mixed source (22.4%) contribute relatively more to soil pollution. Moreover, industrial activities and road dusts were identified as the main risk sources, indicating that local stakeholders should take measures to control road traffic and industrial emissions.},
}
@article {pmid41853458,
year = {2026},
author = {Sanguila, MB and Labaja, ACO and Bernstein, JM and Brown, RM},
title = {An updated herpetological inventory of the Agusan Marsh Wildlife Sanctuary, eastern Mindanao Island, Philippines.},
journal = {ZooKeys},
volume = {1272},
number = {},
pages = {203-251},
pmid = {41853458},
issn = {1313-2989},
abstract = {A formal synthesis of the occurrence of herpetofauna species in Agusan Marsh Wildlife Sanctuary remained scant since the documentation of historical records by E.H. Taylor in the early 20[th] century. Here, an updated checklist of the Agusan Marsh herpetofauna is provided. 49 species (16 amphibians and 33 reptiles) are recorded from the Agusan Marsh's peat and freshwater swamp forests, specifically, amphibians in the families Bufonidae, Ceratobatrachidae, Dicroglossidae, Microhylidae, Megophryidae, Ranidae, and Rhacophoridae; lizards in the families Agamidae, Gekkonidae, Dibamidae, Scincidae, and Varanidae; snakes in the families Colubridae, Cyclocoridae, Psammodynastidae, Pareidae, Pythonidae, Typhlopidae, and Viperidae; and a turtle in the family Geoemydidae. Our Shannon Diversity Indices calculations suggest that diversity might be declining, but more surveys are needed to sample the total species richness of the Agusan Marsh Wildlife Sanctuary. Our checklist highlights 14 new records (6 amphibians, 8 reptiles) and the presence of four invasive alien species in Agusan Marsh. Given the tremendous historical significance of the region, Agusan Marsh may represent one of the most significant focal study sites for assessing the impacts of historical land use and climate change in the Philippines. This work also demonstrates the importance of temporally sequential survey-resurveys for updating baseline biodiversity data to inform management decisions and conservation actions for this unique wetland ecosystem in Southeast Asia.},
}
@article {pmid41856776,
year = {2026},
author = {Clostres, E and Penno, C and El-Amrani, A and Daburon, V and Gazengel, K and Monard, C and Daval, S},
title = {Bioinformatic and experimental analyses revealed pathogen-derived pathoPEP candidates predicted to control plant miRNA expression and infection.},
journal = {RNA (New York, N.Y.)},
volume = {32},
number = {6},
pages = {915-929},
doi = {10.1261/rna.080819.125},
pmid = {41856776},
issn = {1469-9001},
mesh = {*MicroRNAs/genetics ; *Gene Expression Regulation, Plant ; *Plant Diseases/genetics/parasitology ; Computational Biology/methods ; *Brassica napus/genetics/parasitology/microbiology ; *Plasmodiophorida/pathogenicity/genetics/metabolism ; *Host-Pathogen Interactions/genetics ; *RNA, Plant/genetics ; },
abstract = {The partners of an ecological association tend to copy the biological system of their hosts. We hypothesized that microorganisms, particularly pathogens, have acquired the ability to express short peptides (pathoPEPs) homologous to host miPEPs, thus modulating the expression of the corresponding host microRNA (miRNA) and the function of miRNA-targeted genes. The pathosystem involving interactions between Brassica napus and its pathogen Plasmodiophora brassicae was studied. The data set contains RNA-seq and ribosomal profiling from two plant genotypes inoculated with one pathogen isolate. Using in silico analysis, we identified three putative pathoPEPs produced by P. brassicae and their targeted plant miRNA genes. A link between the level of infection of B. napus by P. brassicae and the expression of pathoPEPs and their targeted miRNA genes was found, with the expression of the latter two being inversely related. Finally, we identified differential expression and translation of genes predicted to be targets of pathoPEP-regulated miRNAs. These genes, involved in auxin pathway, immune defense, root architecture, or carbohydrate metabolism, are thought to enable P. brassicae, through its pathoPEPs, to hijack plant's metabolic pathways (e.g., hormonal pathways, sugar synthesis, root morphology), thereby facilitating its invasion. Using in silico approaches, the involvement of miPEPs from this host-pathogen system as a host post-transcriptional regulatory pathway is described herein for the first time.},
}
@article {pmid41856919,
year = {2026},
author = {Ferreira, MS and Rossi, RC and Batista, S and Sena, K and Bairos-Novak, KR and Shoma, SF and Leiner, NO and Astúa, D and Coulson, G and Fisher, DO and Harrison, ND and Willmer, JNG and Silva, GR and Cupolillo, G and Vieira, MV and Vieira, EM and Püttker, T and Figueiredo, MSL and Dickman, CR},
title = {The Marsupial Database: A comprehensive dataset on the ecology and life history of American and Australasian marsupials.},
journal = {Ecology},
volume = {107},
number = {3},
pages = {e70358},
doi = {10.1002/ecy.70358},
pmid = {41856919},
issn = {1939-9170},
support = {153700/2024-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico - CNPq/ ; 307457/2025-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico - CNPq/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; //Funda&#xe7;&#xe3;o de Amparo a Ci&#xea;ncia e Tecnologia do Estado de Pernambuco (FACEPE)/ ; //Funda&#xe7;&#xe3;o Carlos Chagas de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; //Foundation for Research Support of Minas Gerais State (FAPEMIG)/ ; //Australian Alumni Grants Round 2023-2024/ ; },
mesh = {Animals ; *Marsupialia/physiology/classification/genetics ; *Databases, Factual ; Australasia ; Americas ; *Ecosystem ; *Life History Traits ; },
abstract = {Marsupials are an important but typically neglected group of mammals that have been overlooked in many comparative analyses of vertebrate ecology and life history evolution. In order to address this knowledge bias, we have developed The Marsupial Database. The Marsupial Database contains traits for a phylogenetically diverse set of 414 extant and recently extinct (last 200 years) species from all seven modern marsupial orders (Dasyuromorphia, Didelphimorphia, Diprotodontia, Microbiotheria, Notoryctemorphia, Paucituberculata, Peramelemorphia) native to 34 countries in the Americas and Australasia. The database comprises 11,054 records of 35 traits describing anatomical, physiological, phenological, and reproductive characteristics, as well as information on species' ecology and current conservation status. Data were collected from 41 sources, comprising published databases and other relevant sources of information. By providing a centralized repository of marsupial ecological and life history traits, The Marsupial Database facilitates analyses of ecological and evolutionary patterns within the group, and also encourages inclusion of marsupials in comparative studies of mammals, vertebrates, and the entire animal kingdom. The Marsupial Database is free from copyright or proprietary restrictions. Please cite this data paper when using the data in publications or scientific presentations.},
}
@article {pmid41858257,
year = {2026},
author = {Geerts, MM and Curto, M and Alverson, AJ and Stone, J and Gante, HF},
title = {Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70128},
pmid = {41858257},
issn = {1755-0998},
support = {STG/21/044//KU Leuven Research Fund/ ; 11Q4724N//Fonds Wetenschappelijk Onderzoek/ ; UIDP/50027/2020//InBIO Program&#xe1;tico FUI 2020-2023/ ; DEB-2331644//Division of Environmental Biology/ ; },
mesh = {*Metagenomics/methods ; *Diatoms/genetics/classification ; Phylogeny ; *Computational Biology/methods ; *DNA, Environmental/genetics ; *Eukaryota/genetics/classification ; Metagenome ; *Biodiversity ; Czech Republic ; Fresh Water/microbiology ; },
abstract = {Genome assembly graphs contain valuable yet frequently overlooked information that can enhance assembly completeness by revealing contig connectivity. Here, we demonstrate how leveraging these information-rich structures enables the discovery of hidden microeukaryotic diversity in environmental DNA shotgun metagenomic datasets. While GetOrganelle has previously been used for organellar genome assembly from isolated tissues, we present its first application to water eDNA metagenomic data, using diatoms as an example. We tested the efficiency of this organellar genome assembly tool on three freshwater eDNA metagenomic datasets with varying diatom abundances, finding that GetOrganelle alone yields fragmented scaffolds due to mixed-species complexity. By implementing manual disentanglement of assembly graphs, we successfully recovered complete organellar genomes from these assemblies. From high-abundance bloom samples, we recovered complete plastomes of Stephanodiscus hantzschii with 99.9% pairwise identity across distant geographical locations (USA and Czech Republic). From a lower abundance non-bloom sample, we reconstructed a potentially novel Cyclotella plastome with only 94.0% identity to its closest available reference, Cyclotella atomus. Our assembly quality assessment confirmed effective manual disentanglement even at low diatom abundances. By integrating sequence similarity, gene order conservation and phylogenetic analysis, we achieved robust species-level resolution and resolved previous taxonomic uncertainties. Our findings demonstrate that mining eDNA metagenomic data with GetOrganelle reveals previously hidden microeukaryotic diversity and provides higher taxonomic resolution than traditional binning methods. This approach proves especially valuable for microeukaryotes, where reference organellar genomes remain underrepresented in existing databases.},
}
@article {pmid41860640,
year = {2026},
author = {Kandadai, S and Dadhwal, VK},
title = {Large-scale spatial assessment of soil organic carbon, pH and their interrelation in Indian agricultural soils using Soil Health Card big data.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {4},
pages = {},
pmid = {41860640},
issn = {1573-2959},
mesh = {India ; *Soil/chemistry ; *Carbon/analysis ; *Environmental Monitoring/methods ; Agriculture ; Hydrogen-Ion Concentration ; Big Data ; },
abstract = {Large-scale soil sampling efforts have been undertaken in India since 2015 under the Soil Health Card (SHC) scheme. This study integrates 39 million+ soil measurements from SHC into a geospatial framework to study two important soil properties - Soil Organic Carbon (SOC) content and pH. The study provides maps of mean and uncertainty at village level for SOC content and pH in surface (0-15 cm) agriculture soils in India, and further analyzes the varying relationship between them across major Agro-Ecological Regions (AERs) in the country. The resultant spatial SOC layer also gave an opportunity to assess two global SOC maps - 1. SoilGrids (250 m) and 2. Global Soil Data for Earth System Modelling (GSDE-30 arcsec). Mean SOC content in different AERs varied from 0.39% to 1.06% while mean pH varied from 5.4 to 8.0. An AER-wise analysis indicated a spatially varying relationship between SOC and pH with 11 AERs showing negative correlation and 4 showing positive and no correlation each. The mean SOC contents from GSDE were around half that of SHC for most AERs, while those estimated by SoilGrids were more than twice that of SHC in 16 of the 19 AERs. The implications of these results for Indian SOC stock estimates and climate change mitigation potential are discussed in this paper. Overall, SHC data can complement and augment large scale soil datasets. It can find applications in a diverse set of fields like soil monitoring, carbon budgeting, soil zonation studies, as well as in crop and carbon cycle modelling studies.},
}
@article {pmid41861932,
year = {2026},
author = {Piva, E and Pacchini, S and Kholdihaghighi, S and Stoilova, V and Drago, L and Baroni, F and Fogliano, C and Irato, P and Schumann, S and Santovito, G},
title = {Can Antarctic fish face marine heatwave-like events? Exploring cardiac physiology of Trematomus bernacchii using bio-loggers and stress biomarkers.},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {305},
number = {},
pages = {110511},
doi = {10.1016/j.cbpc.2026.110511},
pmid = {41861932},
issn = {1532-0456},
mesh = {Animals ; Antarctic Regions ; *Perciformes/physiology/metabolism ; Biomarkers/metabolism ; Glutathione Peroxidase/metabolism/genetics ; *Heart/physiology ; Fish Proteins/metabolism/genetics ; *Hot Temperature ; Heat-Shock Response ; Heart Rate ; Stress, Physiological ; Myocardium/metabolism ; Body Temperature ; },
abstract = {Rising seawater temperatures fundamentally reshape marine ecosystems, with the Southern Ocean exhibiting vulnerability to climatic perturbations. Antarctic teleosts have evolved under near-constant sub-zero conditions, developing unique physiological adaptations. In this study, responses of Trematomus bernacchii, an endemic Antarctic fish, to three successive marine heatwave-like events were addressed. Using implantable bio-loggers, core body temperature and heart rate were monitored over 15 days, revealing a statistically significant positive correlation between core body temperature and cardiac performance, with an approximately 25% increase per °C. Molecular analyses of cardiac tissue revealed a sequential antioxidant response. An early upregulation of gpx4 suggests immediate mitochondrial protection against lipid peroxidation, while the subsequent induction of gpx1, prdx3, and prdx5 indicates a broader cytosolic defence. Furthermore, the marked decoupling between elevated gpx1 transcript levels and diminished Selenium-dependent glutathione peroxidase activity highlights a hitherto unrecognised post-transcriptional regulatory mechanism under acute thermal stress. Our findings suggest that T. bernacchii activates a sequential, organ-specific stress response to short-term warming, which may allow it to overcome episodic heatwaves.},
}
@article {pmid41861947,
year = {2026},
author = {Guo, J and Liang, X and Lei, W and Zhang, Z and Shen, Y and Han, S and Wang, H and Qian, Y and Nie, B and Wang, L and He, S},
title = {Contrasting microbial sources of soil N2O emissions revealed by metagenomics in natural and agricultural soils along the Yellow River.},
journal = {Environmental research},
volume = {299},
number = {},
pages = {124311},
doi = {10.1016/j.envres.2026.124311},
pmid = {41861947},
issn = {1096-0953},
mesh = {*Soil Microbiology ; *Nitrous Oxide/analysis/metabolism ; Metagenomics ; Soil/chemistry ; Agriculture ; Denitrification ; Nitrification ; Archaea/metabolism/genetics ; Rivers ; China ; Bacteria/metabolism ; },
abstract = {Soil nitrous oxide (N2O) emission is a potent greenhouse gas source, yet the dominant production pathway (nitrification vs. denitrification) and its microbial mechanisms in regions like the Yellow River Basin remain unclear, particularly under different land uses. In this study, we integrated qPCR quantification, metagenomic sequencing and binning, as well as microbial network analysis to investigate the dominant microbial processes and regulatory mechanisms underlying potential soil N2O production. Results showed that denitrification dominated regional potential N2O production (N2ODen, 56.71 ± 102.94 nmol/(kg·h)), significantly exceeding nitrification (N2ONif, 4.34 ± 4.27 nmol/(kg·h)). On average, both N2ODen (115.34 ± 143.60 nmol/(kg·h)) and N2ONif (5.29 ± 4.42 nmol/(kg·h)) in natural soils were higher than in cultivated soils (28.56 ± 62.52 and 3.88 ± 4.22 nmol/(kg·h), respectively). Mechanistically, natural soils were enriched with ammonia-oxidizing archaea (AOA) and incomplete denitrifiers (e.g., Acidobacteriota), which, along with a higher norB/nosZ and more stable co-occurrence network, favored N2O accumulation. In cultivated soils, microbial community stability was reduced; however, they were enriched with strong N2O reducers (e.g., Pseudomonadota, Gemmatimonadota), resulting in lower potential N2O production. Altitude, total nitrogen, and pH collectively influenced the potential N2O emission patterns by regulating functional genes and microbial metabolism. This study provides a scientific basis for regional greenhouse gas mitigation from a microbial ecology perspective.},
}
@article {pmid41871796,
year = {2026},
author = {Beigel, K and Bringhurst, B and Greenwold, M and Kellner, K and Seal, JN},
title = {Non-reciprocal coevolution in a fungus-gardening ant.},
journal = {Molecular phylogenetics and evolution},
volume = {220},
number = {},
pages = {108608},
doi = {10.1016/j.ympev.2026.108608},
pmid = {41871796},
issn = {1095-9513},
mesh = {Animals ; *Ants/microbiology/genetics/classification ; *Symbiosis/genetics ; Phylogeny ; *Biological Coevolution ; *Biological Evolution ; Fungi/genetics ; },
abstract = {Symbioses are often characterized by nonrandom associations between hosts and symbionts. Hosts may obtain symbionts horizontally from the environment or vertically from a parent or sometimes use both methods. Macroevolutionary examinations of fungus-gardening ants and their fungi have shown either a 1:1 coevolution model or a 'diffuse' model between ant host and fungal symbionts. However, some of these conclusions may have been based on using relatively conservative molecular markers, which could obscure cryptic variation. The use of whole genome approaches potentially offer more power in elucidating coevolutionary history. In this study, we examined patterns of coevolution in a single species (Trachymyrmex septentrionalis) using genomic and experimental approaches. We tested whether ant-fungal specificity patterns reflected either 1:1 or diffuse models of coevolution. While we report significant co-phylogenetic signal among intraspecific ant host and fungal symbiont lineages, we found evidence of 1:1 coevolution in some lineages and diffuse in others. These conclusions were supported by the results of experiments where newly mated T. septentrionalis queens were forced to grow novel fungi that suggested that not all fungi are equivalent symbionts and would require specialized hosts. Thus, within a single ant species, there is a mixed support for both models.},
}
@article {pmid41872050,
year = {2026},
author = {de Guinea, M and Landesman, R and Madden, JR and Bugnyar, T and Bartan, Y and Nathan, R},
title = {Integrating Lab- and Field-Based Approaches to Decipher Individuals' Response to Anthropogenic Change.},
journal = {Ecology letters},
volume = {29},
number = {3},
pages = {e70366},
pmid = {41872050},
issn = {1461-0248},
support = {3-17405//Ministry of Science of Israel/ ; 2715/23//Israel Science Foundation/ ; //Hebrew University of Jerusalem/ ; },
mesh = {Animals ; Israel ; *Crows/physiology ; *Anthropogenic Effects ; *Behavior, Animal ; Risk-Taking ; Humans ; Human Activities ; Geographic Information Systems ; },
abstract = {The global expansion of human activities increasingly exposes wild animals to novel, potentially threatening conditions. Consistent behavioural responses to perceived risk may be detrimental to wildlife, either by limiting foraging opportunities or by overexposing them to lethal hazards. We examine the relationship between risk responses, movement patterns and survival in fan-tailed ravens (Corvus rhipidurus) inhabiting Israel's Dead Sea coastline. We found consistent individual differences assessed through controlled laboratory assays (novel food, objects, environment and foraging near humans) and even stronger consistencies in the wild via GPS-derived movement metrics. While risk-prone ravens remained near tourist sites and travelled less, risk-averse individuals foraged farther towards the edge of their home ranges, avoiding human activity. Further, risk-averse individuals were more likely to survive over extended periods than risk-prone individuals. As anthropogenic change accelerates, variation in consistent risk-taking behaviour could determine individuals' capacity to adapt and survive and consequently shape population composition and persistence.},
}
@article {pmid41873765,
year = {2026},
author = {Chothani, S and Ruiz-Orera, J and Tierney, JAS and Swirski, MI and Tjeldnes, H and Kok, LW and Clauwaert, J and Deutsch, EW and Alba, MM and Aspden, JL and Baranov, PV and Bazzini, AA and Bruford, EA and Brunet, MA and Cardon, T and Carvunis, AR and Casola, C and Choudhary, JS and Dean, K and Faridi, P and Fierro-Monti, I and Fournier, I and Frankish, A and Gerstein, M and Hubner, N and Jiang, Y and Kellis, M and Martinez, TF and Menschaert, G and Ni, P and Orchard, S and Roucou, X and Rozowsky, J and Salzet, M and Siragusa, M and Slavoff, S and Ternette, N and Vizcaino, JA and Wacholder, A and Wu, W and Xie, Z and Yang, YT and Moritz, RL and Valen, E and Mudge, J and van Heesch, S and Prensner, JR and Rackham, OJL},
title = {An expanded reference catalog of translated open reading frames for biomedical research.},
journal = {Nucleic acids research},
volume = {54},
number = {6},
pages = {},
pmid = {41873765},
issn = {1362-4962},
support = {//Morgan Adams Foundation/ ; OFYIRG23jan-0034/MOH-001340//National Medical Research Council/ ; //Chad Carr Pediatric Brain Tumor Center/ ; CRC/SFB-1470-B03//Deutsche Forschungsgemeinschaft/ ; R01 GM087221/NH/NIH HHS/United States ; R24 GM148372/NH/NIH HHS/United States ; //EMBL/ ; //DIPG/DMG Research Funding Alliance/ ; //European Union/ ; U24HG003345/HG/NHGRI NIH HHS/United States ; DBI-2324882//National Science Foundation/ ; //Book for Hope Foundation/ ; 2U24HG007234-13/HG/NHGRI NIH HHS/United States ; //Dutch Cancer Society/ ; 108749/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; //Chan Zuckerberg Foundation/ ; S10 OD026936/NH/NIH HHS/United States ; GR-24-008//Lindonlight Collective/ ; DBI-1933311//National Science Foundation/ ; GR-24-012//Lindonlight Collective/ ; //Yuvaan Tiwari Foundation/ ; U41 HG007234/HG/NHGRI NIH HHS/United States ; //Hyundai Hope on Wheels Foundation/ ; U24 HG003345/HG/NHGRI NIH HHS/United States ; K08-CA263552-01A1/CA/NCI NIH HHS/United States ; /NWO_/Dutch Research Council/Netherlands ; //CureSearch for Cancer Research/ ; /NH/NIH HHS/United States ; //Tough2gether Foundation/ ; 223745/Z/21/Z//Wellcome/ ; //University of Michigan Rogel Cancer Center/ ; V2024-013//V Foundation for Cancer Research/ ; AdG788970//European Union/ ; //European Molecular Biology Laboratory/ ; MRI-1920268//National Science Foundation/ ; },
mesh = {*Open Reading Frames/genetics ; Humans ; Molecular Sequence Annotation ; *Biomedical Research ; Databases, Genetic ; *Protein Biosynthesis ; Genome, Human ; },
abstract = {Non-canonical (i.e. unannotated) open reading frames (ncORFs) have until recently been omitted from reference genome annotations, despite evidence of their translation, limiting their incorporation into biomedical research. To address this, in 2022, we initiated the TransCODE consortium and built the first community-driven consensus catalog of human ncORFs, which was openly distributed to the research community via Ensembl-GENCODE. While this catalog represented a starting point for reference ncORF annotation, major technical and scientific issues remained. In particular, this initial catalog had no standardized framework to judge the evidence of translation for individual ncORFs. Here, we present an expanded and refined catalog of the human reference annotation of ncORFs. By incorporating more datasets and by lifting constraints on ORF length and start codon, we define a comprehensive set of 28 359 ncORFs that is nearly four times the size of the previous catalog. Furthermore, to aid users who wish to work with ncORFs with the strongest and most reproducible signals of translation, we utilized a data-driven framework (i.e. translation signature scores) to assess the accumulated evidence for any individual ncORF. Using this approach, we derive a subset of 10 127 ncORFs with translation evidence on par with canonical protein-coding genes, which we refer to as the primary set. This set can serve as a reliable reference for downstream analyses and validation, with a particular emphasis on high quality. Overall, this update reflects continuous community-driven efforts to make ncORFs accessible and actionable to the broader research public, and further iterations of the catalog will continue to expand and refine this resource.},
}
@article {pmid41875400,
year = {2026},
author = {Teich, MC and Escobari, B and Rehbein, M},
title = {Utilizing large language models to construct a dataset of Württemberg's 19th-century fauna from historical records.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344181},
pmid = {41875400},
issn = {1932-6203},
mesh = {*Biodiversity ; *Language ; *Databases, Factual ; History, 19th Century ; Animals ; Large Language Models ; },
abstract = {Constructing datasets on past biodiversity from historical sources is crucial for understanding long-term ecological changes. Typically, compiling such datasets relies on prior knowledge of the sources' composition and requires considerable manual effort. To overcome these challenges, we implement an automated approach based on prompted large language models (LLMs) to detect mentions of species in texts from 19th-century Württemberg and link these mentions to identifiers in the GBIF database. Based on our evaluation, we find that LLMs can reliably identify species in the texts with high recall (92.6%) and precision (95.3%), while providing estimates of the correct species identifier with considerable accuracy (83.0%). As our approach is easily scalable and adaptable to other contexts and languages, it offers a promising way to advance dataset generation from historical material using limited resources.},
}
@article {pmid41875615,
year = {2026},
author = {Kesavan, D and Meenatchi, R and Mohanakrishna, R and Tripathi, A and B S, Y and Narayanane, S and Gupta, S and Yadav, P and Pasupuleti, M and Mani, G and Balachandran, KRS and Rangamaran, VR and Verma, P and Kumar, AG and Vinithkumar, NV and Gopal, D and Pazhani, GP and Arockiaraj, J},
title = {Metagenomic mining of microbial communication genes from Indian deep-sea sediments using a quorum sensing- and quenching-related protein database.},
journal = {Marine genomics},
volume = {86},
number = {},
pages = {101245},
doi = {10.1016/j.margen.2026.101245},
pmid = {41875615},
issn = {1876-7478},
mesh = {*Quorum Sensing/genetics ; *Geologic Sediments/microbiology ; Metagenomics ; Indian Ocean ; *Metagenome ; *Bacterial Proteins/genetics ; Databases, Protein ; Bacteria/genetics ; *Microbiota ; },
abstract = {Cell-to-cell communication among microbes plays a key role in environmental adaptation and highly contributes to global biogeochemical cycling. However, microbial communication systems in deep-sea sediments, where diverse microbial communities employ quorum sensing (QS) and quorum quenching (QQ) mechanisms to regulate ecological interactions, remain largely understudied. Their distribution patterns and functional dynamics in deep-sea ecosystems are poorly understood. This study investigated QS and QQ communication systems alongside microbial community distribution in Arabian Sea sediments collected from depths of 334, 492, 550, and 992 m across the northern and southern Arabian Sea. Shotgun metagenomic sequencing was performed in conjunction with a curated QS- and QQ-related protein (QSP) database. Both individual assemblies and metagenome-assembled genomes (MAGs) were analyzed to comprehensively identify communication-associated proteins. In total, around 359 QSPs were detected across four sediment samples. Shallow sediments (334 and 492 m) exhibited greater abundance and diversity of QS and QQ elements, particularly acyl-homoserine lactone (AHL)-driven QS systems and acylase/lactonase-based QQ systems, indicating active microbial interactions. In contrast, deeper sediments (550 and 992 m) displayed reduced diversity of canonical QS elements with enrichment of autoinducer-2 (AI-2), diffusible signal factor (DSF), and cyclic-di-GMP signalling pathways, suggesting adaptive mechanisms conducive to oligotrophic and high-pressure conditions of deep-sea. Correlation analyses revealed potential intra- and inter-system associations among QS regulators and QQ enzymes, indicating complex regulatory networks. MAG-derived protein analyses detected conserved catalytic motifs, and molecular docking supported functional interactions with signal molecules. Overall, these findings provide a preliminary overview of QS and QQ related genes in deep sea sediments of the Arabian Sea and suggest potential variability in microbial communication systems within these environments.},
}
@article {pmid41876258,
year = {2026},
author = {Lee, MJ and DiRenzo, GV and Diao, C and Seltmann, KC},
title = {Leveraging local species data, a global database, and an occupancy model to explore bee-plant interactions.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {36},
number = {2},
pages = {e70221},
pmid = {41876258},
issn = {1939-5582},
support = {2102006//Division of Biological Infrastructure/ ; },
mesh = {Bees/physiology ; Animals ; *Pollination ; *Models, Biological ; Databases, Factual ; Flowers/anatomy &amp; histology ; *Magnoliopsida/physiology ; },
abstract = {Global declines in bee populations are threatening the ecosystem services they provide, including pollination. Many bee-plant interactions are understudied, producing an incomplete understanding of resulting ecosystem-level vulnerabilities. The last decade has generated a wealth of opportunistic data originating from natural history collection records, published ecological datasets, and citizen/community science initiatives in online databases such as Global Biotic Interactions (GloBI). Here, we explore hypotheses related to bee-plant interactions and detection processes using the GloBI database, curated checklists of bee and flowering plant species, and an occupancy model. We hypothesized that larger, social bees would visit a larger number of plant species, while smaller, solitary bees would visit fewer. We also predicted that flowers with open, bowl-like shapes would attract a greater diversity of bee visitors compared to closed shapes. Further, we hypothesized that both floral and bee traits, such as bright colors and conspicuous patterns, would increase detectability, and that different data collection methods would vary in their ability to capture bee-plant interactions. Lastly, we hypothesized that the interaction network generated by the output of the occupancy model, which accounted for imperfect bee-plant detection, would yield more interactions, thereby increasing measures of evenness and decreasing nestedness and specialization, as compared to the network generated from recorded interaction data. We found that smaller bees exhibited higher probabilities of plant interactions than larger bees, but we did not find evidence that bee sociality influenced the probability of interacting with plants. We found that blue flowers and closed (not-bowl-shaped) flowers had higher probabilities of bee-plant interaction than other flower colors or bowl-shaped flowers, respectively. We also found that larger bee size, blue flowers, bowl shapes, and community science sources were associated with higher detection probabilities of bee-plant interactions. Lastly, the interaction network generated by the occupancy model output showed higher levels of evenness, nestedness, and connectance than the network generated by the GloBI data. Our study is among the first to utilize occupancy modeling to directly model species' interactions, leverage aggregated, open-source databases and expert checklists, and highlight the influence of detection and collection biases on our understanding of ecological interactions.},
}
@article {pmid41877557,
year = {2026},
author = {Pastore, EP and De Rango, F},
title = {Foundation and Multimodal Models for Drug Discovery in Molecular Informatics: Principles, Evaluation, and Practical Guidance.},
journal = {Molecular informatics},
volume = {45},
number = {3},
pages = {e70027},
pmid = {41877557},
issn = {1868-1751},
mesh = {*Drug Discovery/methods ; *Models, Molecular ; Humans ; *Cheminformatics/methods ; },
abstract = {Foundation and multimodal models are rapidly becoming a core methodology in molecular informatics, particularly for drug discovery, by leveraging large-scale pretraining across sequences, graphs, 3D structures, and text. This mini-review provides practical guidance on when these models help, how to choose representations and data, and how to design pretraining and adaptation pipelines for real-world use. We clarify what qualifies as a foundation model in chemistry; compare chemical language models, graph-based architectures, and 3D equivariant networks; review multimodal strategies that connect molecules with proteins, pockets, and natural language; and summarize diffusion-based generative modeling. We also emphasize rigorous evaluation, discussing realistic splitting protocols, distribution shift, activity cliffs, uncertainty calibration, and conformal prediction in the context of widely used benchmarks.},
}
@article {pmid41879155,
year = {2026},
author = {Rauhöft, L and Tomazatos, A and Eisenbarth, A and Tóth, GE and Martins Afonso, SM and Doumba-Ndalembouly, AG and Duve, P and Lange, U and Meyer, P and Adegnika, AA and Ramharter, M and Schmidt-Chanasit, J and Cadar, D and Renz, A and Sauer, FG and Lühken, R},
title = {Evaluation of 4 adult trap types including the newly developed VectorCube for surveillance of multiple vector groups.},
journal = {Journal of medical entomology},
volume = {63},
number = {2},
pages = {},
pmid = {41879155},
issn = {1938-2928},
support = {01Kl2022//Federal Ministry of Education and Research of Germany/ ; },
mesh = {Animals ; *Insect Vectors ; *Insect Control/instrumentation/methods ; Germany ; Gabon ; },
abstract = {Comprehensive risk assessment for vector-borne disease requires effective monitoring of various vector groups. However, this depends on the traps' ability to capture multiple vector families. This study compares 3 commercially available traps, BG-Sentinel 2, BG-Trap Station as a combination of a BG-Pro and Gravid trap, and the Encephalitis Virus Surveillance trap, with the VectorCube, a newly developed prototype. Multiple openings enable multidirectional vector capture, and color cues can be easily attached and changed. All traps were tested under a uniform, carbon dioxide flow rate at 10 sampling sites (6 in Germany and 4 in Gabon) using a 4 × 4 Latin square design. Each site completed at least 1 full Latin square rotation, resulting in 48 trap comparison days. A total of 3,477 blood-seeking insects from 6 families were captured: 2,797 Culicidae, 324 Simuliidae, 268 Ceratopogonidae, 76 Muscidae, 8 Glossinidae, and 4 Psychodidae. Most Culicidae were collected with the BG-Sentinel 2 followed by the VectorCube. The VectorCube captured the majority of Simuliidae, Muscidae, and Glossinidae observed in this study, while Psychodidae were exclusively collected with BG-Sentinel 2 and BG-Trap Station in Gabon. Mean family richness per trapping session was highest in the VectorCube, followed by BG-Sentinel 2, BG-Trap Station, and Encephalitis Virus Surveillance trap. Overall, the VectorCube and BG-Sentinel 2 demonstrated the highest performance in vector abundance and diversity, driven primarily by high Culicidae catches, whereas captures of non-mosquito hematophagous Diptera occured at lower frequencies and were more site-dependent, including sporadic captures of larger-bodied vectors such as Muscidae and Glossinidae.},
}
@article {pmid41880602,
year = {2026},
author = {Issa, M and Yang, O and Doeve, J and Arcot, S and Chang, A and Amara, S and Bhakta, SH and Baber, I and Shali, K and Dweik, Q and Hung, TKW},
title = {Development and Evaluation of a Human-in-the-Loop Data Curation Training Program to Support a Digital Clinical Trial Platform: Descriptive Feasibility Study.},
journal = {JMIR formative research},
volume = {10},
number = {},
pages = {e81257},
pmid = {41880602},
issn = {2561-326X},
mesh = {Humans ; Feasibility Studies ; *Data Curation/methods ; *Clinical Trials as Topic ; Workflow ; *Medical Oncology/education ; },
abstract = {BACKGROUND: LookUpTrials is a clinician-facing digital platform designed to support point-of-care navigation of institution-specific oncology clinical trials, incorporating artificial intelligence-assisted summarization and search functionalities. While embedding curated trial knowledge tools in community oncology workflows is feasible, the human infrastructure required to sustain high-quality, up-to-date trial data over time remains underexplored.<br><br>OBJECTIVE: This study aimed to evaluate the feasibility of a structured training program embedding trainees within a supervised human-in-the-loop workflow for oncology clinical trial data curation in support of the LookUpTrials digital platform.<br><br>METHODS: We conducted a descriptive feasibility evaluation of a cohort-based training and workflow model. A total of 10 undergraduate trainees curated publicly available trial information from institutional portals and ClinicalTrials.gov across 5 academic medical centers. Trial throughput and participant experiences were summarized descriptively.<br><br>RESULTS: Over 10 months, trainees curated 2503 oncology clinical trial entries across 5 institutions, with processing rates increasing over time. Participants reported that structured onboarding and peer support facilitated engagement with data curation workflows.<br><br>CONCLUSIONS: Standardized human-in-the-loop workflows for clinical trial data stewardship can be implemented with individuals without prior clinical trials or informatics experience when supported by structured training and quality assurance. This study complements prior feasibility work on embedding trial knowledge tools in community oncology settings by focusing on the sustainability of the underlying content pipeline. Further evaluation is needed to assess scalability across institutions and durability over longer periods of platform maturation.},
}
@article {pmid41880737,
year = {2026},
author = {Han, T and He, Q and Zhai, G and Cai, X},
title = {Antimicrobial discovery from underexplored environments: unlocking specialized metabolism.},
journal = {Current opinion in microbiology},
volume = {91},
number = {},
pages = {102745},
doi = {10.1016/j.mib.2026.102745},
pmid = {41880737},
issn = {1879-0364},
mesh = {*Drug Discovery/methods ; *Bacteria/metabolism/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology/isolation &amp; purification ; Humans ; Archaea/metabolism/genetics ; Multiomics ; Synthetic Biology ; },
abstract = {The discovery of antibiotics transformed modern medicine and extended the average human lifespan by decades. However, the initial golden era of antibiotic discovery has significantly waned, a decline aggravated by the relentless evolution of drug resistance among human pathogens, ultimately driving the current global antimicrobial resistance (AMR) crisis. The repeated rediscovery of known compounds from conventional soil-derived microbes underscores the urgent need for new strategies and ecological frontiers.Here, we review emerging directions in antibiotic discovery that collectively address this innovation gap. Refined cultivation techniques such as co-culture and iChip have reactivated rare taxa and yielded novel scaffolds like teixobactin. Multi-omics and synthetic biology approaches now enable culture-independent access to cryptic biosynthetic gene clusters from the vast uncultivated microbial majority. Most recently, artificial intelligence (AI) has expanded the search frontier to neglected taxa such as archaea and even evolutionary timeframes through paleoproteome mining. Overall, these innovations signal a new era of intelligent, data-driven antibiotic discovery. The integration of ecology, omics, synthetic biology, and AI provides a sustainable framework to replenish the antibiotic pipeline and mitigate the growing threat of AMR.},
}
@article {pmid41883743,
year = {2025},
author = {Greenwell, SA and Curran, LS and Poe, CE and Klein, M and Yao, X and Ortyl, BK and Shih, PC and Nelson, EJ and Boustani, M and Dexter, P and Miled, ZB and Schootman, M and Dickinson, S and Unverzagt, FW and Jordan, EJ},
title = {Protocol for assessing urban-rural environmental stress disparities in ADRD through ecological momentary assessment (AURESIA).},
journal = {Alzheimer's &amp; dementia. Behavior &amp; socioeconomics of aging},
volume = {1},
number = {4},
pages = {},
pmid = {41883743},
issn = {2997-3805},
support = {R01 NS139192/NS/NINDS NIH HHS/United States ; },
abstract = {INTRODUCTION: Consistent exposure to environmental stressors increases the risk of Alzheimer's disease and related dementias (ADRD). Little is known about the timing, location, and nature of these stressors. We outline the protocol for an ongoing study using a novel ecological momentary assessment app to evaluate environmental stressors in urban and rural adults with mild cognitive impairment (MCI).<br><br>METHODS: We assess cognitive status at baseline and follow-up appointments for 2 years. During a 2-week stress-reporting period, participants self-report environmental stressors. We monitor physiological data via Smartwatch. The app collects geospatial data, which we analyze via spatiotemporal regression models.<br><br>RESULTS: The study will take 3 years to complete.<br><br>DISCUSSION: This study will advance knowledge of when, where, and what stressors occur among older adults and will underscore targets for intervention at individual and neighborhood levels to prevent progression from MCI to ADRD and reduce urban-rural disparities in older adults.},
}
@article {pmid41886482,
year = {2026},
author = {Bagic, M and Šajina, A and Bradshaw, WJ and Valenzano, DR},
title = {AEGIS: Individual-based modeling of life history evolution.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1014109},
pmid = {41886482},
issn = {1553-7358},
mesh = {*Biological Evolution ; *Life History Traits ; Animals ; Computational Biology/methods ; *Software ; Computer Simulation ; *Models, Biological ; },
abstract = {Nature presents a staggering diversity of life history strategies, ranging from rapid to slow onset of sexual maturity, short or long life, low or high number of offspring, and much more. Each species-specific life history trait reflects on the one hand specific adaptations to unique environments, e.g., nutrient availability, predation, parasite load, seasonality; and on the other hand, depends on past demographic constraints, such as population bottlenecks, migrations, etc. Studying life history diversity in nature and in the laboratory ultimately aims to identify the ecological, demographic, and intrinsic causes contributing to species-specific growth rate distributions, lifetime reproductive outcomes, as well as lifespans. However, for most species, we cannot rewind the evolutionary and demographic past to identify the causal chain of events leading to the present life history traits. We can infer past events only by sampling extant populations. In silico evolution has the advantage of providing complete time resolution for the events driving life history evolution and enables to directly test the impact of ecological and demographic variables on the evolution of life history traits. We developed AEGIS (Aging of Evolving Genomes In Silico), a software for individual-based modeling of life history trait evolution at the genotype and phenotype level. AEGIS models life history traits evolution in response to a set of factors, including resource availability, extrinsic mortality induced by predators or parasites, different levels of germline mutation rates, population size, sexual vs. asexual reproduction, and more. AEGIS serves as a powerful tool to model life history evolution and allows for parameter inference against ground truths. AEGIS can help generate estimates for the evolution of different life history traits, such as age-dependent mortality and reproduction, in response to different selective pressures and intrinsic genetic constraints.},
}
@article {pmid41888547,
year = {2026},
author = {Zhao, A and Huang, M and Cheng, Y and Li, Q and Cai, H and Bi, Y and Wang, A and Du, X and Ding, X},
title = {Multi-omics reveals the involvement of endophytes in the growth of Moso bamboo (Phyllostachys edulis) shoots.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41888547},
issn = {2399-3642},
mesh = {*Endophytes/physiology/genetics ; *Plant Shoots/microbiology/growth &amp; development/genetics ; Plant Growth Regulators/metabolism ; Plant Roots/microbiology/growth &amp; development/genetics ; *Poaceae/microbiology/growth &amp; development/genetics ; Transcriptome ; Gene Expression Profiling ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Gene Expression Regulation, Plant ; Multiomics ; },
abstract = {Moso bamboo (Phyllostachys edulis) exhibits extraordinary speed of growth. While its anatomical and hormonal features have been well studied, the contribution of microbial interactions to its rapid growth remains largely unknown. Here, we integrated 16S rRNA and ITS amplicon sequencing, phytohormone measurements, and root transcriptome analysis across four developmental stages and three plant compartments (shoot top, shoot bottom, and root). We show that microbial diversity and network complexity were strongly shaped by tissue type and developmental stage, with early-stage roots and shoot meristems exhibiting strong immune filtering and later stages showing a marked increase in diversity. Network analysis revealed highly complex microbial associations in nutrient-limited shoot tops during dormancy, suggesting influenced cooperation among endophytes. In roots, hormone levels were tightly correlated with microbial dynamics, and transcriptome analysis identified 153 hormone-related genes that are differentially expressed across developmental stages, including stage-specific activation of AUX/IAA and SAUR families. A plant-microbe-hormone interaction network highlighted associations between auxin-related genes and growth-promoting genera such as Paenibacillus. Together, these findings reveal that endophytes likely modulate hormone signaling to facilitate rapid shoot elongation, providing insights into the unique developmental program of Moso bamboo.},
}
@article {pmid41890765,
year = {2026},
author = {Bartholomeeusen, K and Affaticati, F and Willems, E and Dhondt, E and Bartholomeus, E and Maestri, A and Ly, S and Veasna, D and Ogunjimi, B and Meysman, P and Laukens, K and Cantaert, T and Ariën, KK},
title = {Identification of a TCR signature in peripheral blood derived CD4+ T cells, associated with chronic chikungunya disease, suggests a conducive, female-biased, background immune profile.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1739100},
pmid = {41890765},
issn = {1664-3224},
mesh = {Humans ; *CD4-Positive T-Lymphocytes/immunology/metabolism ; Female ; *Chikungunya Fever/immunology ; Adult ; Male ; *Receptors, Antigen, T-Cell/genetics/immunology ; Middle Aged ; Chronic Disease ; *Chikungunya virus/immunology ; Young Adult ; Sex Factors ; Adolescent ; },
abstract = {INTRODUCTION: Chronic chikungunya disease (CCD) is characterized by persistent inflammatory joint pains following acute chikungunya virus (CHIKV) infection in about half of the patients . CD4[+] T cells have been implicated in CCD pathogenesis, yet disease-associated T cell receptor (TCR) signatures remain undefined.<br><br>METHODS: Peripheral blood CD4[+] T cells were collected from 65 Cambodian participants six months after RTqPCR-confirmed CHIKV infection during the 2020 outbreak, including chronic (n=16), non-chronic (n=16), and control (n=33) individuals. TCR &#x3b1;, &#x3b2;, &#x3b3;, and &#x3b4; CDR3 regions were sequenced and clustered using ClusTCR. Differential enrichment was assessed by Fisher's exact test. L1-regularized logistic regression incorporating age, gender, and TCR clone counts was used to identify non-redundant TCR signatures.<br><br>RESULTS: Eight TCR clusters were differentially enriched between chronic and non-chronic patients. Chronic disease was associated with increased TRAV9-2 and TRAV41.2 and decreased TRAV41.3 and TRBV18 clone counts. Female controls exhibited higher baseline TRAV9-2 frequencies, suggesting a pre-existing, female-biased immune background associated with CCD susceptibility.<br><br>DISCUSSION: A distinct CD4[+] TCR signature detectable six months post-infection characterizes patients who develop CCD. The association of TRAV9-2 with chronic disease and its enrichment in females suggests an underlying immune predisposition rather than persistent virus-driven expansion. These findings support a role for CD4[+] T cells in CCD pathophysiology and identify candidate TCR-based biomarkers for disease risk stratification.},
}
@article {pmid41890980,
year = {2026},
author = {Shi, Y and Sanderson, H and Chuan, J and Khan, IUH and Sunohara, M and Craiovan, E and Lapen, DR and Diarra, M and Chen, W},
title = {Dual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101384},
pmid = {41890980},
issn = {2352-7714},
abstract = {Freshwater systems embedded in agricultural landscapes serve as dynamic reservoirs and conduits for fecal-associated microbes, zoonotic pathogens, and antimicrobial resistance (ARG) and virulence factor (VF) genes. Yet factors that govern their densities and diversity remain a research challenge. From 2016 to 2021, we conducted a longitudinal water surveillance in an agriculturally dominated river basin in eastern Ontario, Canada; characterizing fecal-associated bacterial communities using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Agricultural drainage ditches consistently harbored higher fecal-associated bacterial diversity with pronounced seasonal shifts; i.e., higher levels during larger flow periods in spring and fall. Elevated discharge was associated with enrichment of genera containing zoonotic or opportunistic pathogens, such as those in Pseudomonas, Sphingomonas, and Massilia. Conditionally rare taxa (CRTs), although typically low in abundance, accounted for ∼12.6% of all pathogen-associated genera and disproportionately contributed to community turnover, highlighting their role as transient reservoirs of microbial risk. Shotgun metagenomics detected 27 ARGs, primarily at mixed-use sites, and 14 VFs, mainly in agricultural ditches. Clinically relevant β-lactamase genes (e.g., oxa, imp, sme) co-occurred with metal-resistance operons, a pattern suggestive of possible co-selection, although selective agents were not directly measured. Although the prevalence of ARG and VF was low (<5% of samples), their ecological context indicates potential transmission pathways. Limited overlap in ARGs between short-read and metagenome-assembled genome (MAG)-based profiling reflects their complementary strength: gene-level sensitivity versus host-resolved analysis. Together, these findings demonstrate the utility of integrated amplicon and shotgun metagenomic surveillance for proactive One Health risk assessment in agricultural watersheds.},
}
@article {pmid41890999,
year = {2026},
author = {Suez, E and Fox, SJ},
title = {Basic Baseline model design choices can substantially influence performance in collaborative forecast hubs.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {41890999},
abstract = {Over the past decade, outbreak forecasting has become an increasingly used tool to assist public health decision-making during epidemics. Collaborative forecast hubs, where multiple teams submit predictions in real-time, are the gold standard for such efforts. For each hub, a Baseline model is used as a performance benchmark for other models. Although the Baseline is understood as a naïve forecast, its design is subjective, and the impact of model design decisions remains understudied. We evaluated how three Baseline specification decisions influence forecast performance on trend models that forecast based on historically observed dynamics: (1) the amount of historical data used for training, (2) whether the data are transformed, and (3) whether forecasts follow a flatline variant (constant predictions) or a drift variant (allowing a slope). Retrospective forecasts were generated for multiple years across four surveillance targets: COVID-19, influenza and RSV hospital admissions, and weighted influenza-like illness percentage. For wILI, we additionally compared trend baselines with a seasonal baseline model leveraging long-term historical patterns. Model specification significantly altered performance. The optimal performing model across targets was a flatline model that used the most recent 6-12 transformed observations. The optimal model outperforms the current standard Baseline used in many forecast hubs by an average of 9.6% (range: 3.7-12.9%) across forecast targets, and it outperformed the seasonal baseline model by 32.3% across nine influenza seasons. Our results demonstrate that subjective Baseline design decisions can materially influence forecast accuracy and, consequently, the perceived rankings of models within collaborative forecast hubs. Based on the varying approaches and their performance differences, these findings highlight the need for increased transparency in Baseline model specifications and support the routine inclusion of multiple benchmark models within collaborative forecast hubs.},
}
@article {pmid41893962,
year = {2026},
author = {Li, W and Shan, B and Chen, L and Wang, W and Hao, W},
title = {Spatiotemporal impact of new urbanization on ecological environment quality-a case study of Shandong Province.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {4},
pages = {},
pmid = {41893962},
issn = {1573-2959},
support = {12YJA790019//Humanities and Social Science Fund of the Ministry of Education of the People's Republic of China/ ; 51608309//National Natural Science Foundation of China/ ; },
mesh = {*Urbanization/trends ; China ; *Environmental Monitoring ; *Conservation of Natural Resources ; Cities ; Spatio-Temporal Analysis ; *Ecosystem ; Sustainable Development ; },
abstract = {Studying the ecological impacts of urbanization is crucial for advancing regional sustainable development. This study, based on panel data of ecological environment and new urbanization in Shandong Province (2000-2022), employed Global Principal Component Analysis to calculate improved Remote Sensing Ecological Index (GRSEI) and ecological environment index, and applied spatial panel regression models to analyze the spatiotemporal impacts of new urbanization on the ecological environment quality (EEQ). The results showed that: (1) From 2000 to 2022, the GRSEI of cities in Shandong Province exhibited a U-shaped evolution trend, first declining and then rising. The trend of environmental pressure in central Shandong was largely consistent with that of the GRSEI. Environmental protection across the province steadily improved, resulting in a gradual enhancement of EEQ, with coastal cities outperforming inland ones. (2) There was a significant positive correlation between EEQ and various indicators of new urbanization. Among them, indicators such as per capita retail sales of consumer goods and per capita education expenditure showed the strongest correlation with EEQ, reaching the 0.001 significance level. (3) The spatial panel regression results indicated that variables including the proportion of urban population, green coverage rate of built-up areas, and social urbanization score had significant positive effects on EEQ. Per capita GDP and economic urbanization exhibited negative impacts before 2018 but shifted to positive effects after 2019. This indicates that Shandong Province's urbanization shifted from a "pollution-intensive growth" model to a "green development" model, promoting the continuous improvement of EEQ.},
}
@article {pmid41894444,
year = {2026},
author = {Aguadé-Gorgorió, G and Kéfi, S},
title = {Emergent coexistence and the limits of reductionism in ecological communities.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1014116},
pmid = {41894444},
issn = {1553-7358},
mesh = {*Models, Biological ; *Ecosystem ; Computational Biology ; Biodiversity ; Ecology ; Computer Simulation ; },
abstract = {Understanding the extent to which the species composition of a community can be explained by pairwise interactions is a long-standing question in ecology. Recent observations have revealed that stable microbial communities contain a high number of species that cannot coexist in pairs, providing new empirical elements to explore this question from a fresh perspective. Here, using species-rich models of ecological communities with pairwise interactions alone, we show that emergent coexistence arises naturally in an extent that is consistent with empirical observations. Interestingly, this phenomenon does not require additional mechanisms like intransitive or higher-order interactions; rather, coexistence can arise from the dense networks of indirect effects. As diversity increases, we show that indirect effects can become so intricate that pairwise interactions decouple from community composition, revealing a fundamental limit to reductionist explanations of coexistence. Our findings provide the theoretical foundations to understand how simple pairwise interactions can lead to emergent coexistence patterns in ecological communities.},
}
@article {pmid41895565,
year = {2026},
author = {Chen, J and Zhang, W and Li, J and Zhang, Y and Jin, W and Zhan, X and Yu, X and Zeng, H},
title = {Sulfur-based electron donor driven autotrophic denitrification for nitrate removal: Mechanisms, performance, and nitrous oxide emission.},
journal = {Environmental research},
volume = {299},
number = {},
pages = {124329},
doi = {10.1016/j.envres.2026.124329},
pmid = {41895565},
issn = {1096-0953},
mesh = {*Denitrification ; *Nitrous Oxide/analysis ; Autotrophic Processes ; *Nitrates ; *Sulfur/chemistry ; *Waste Disposal, Fluid/methods ; Electrons ; Wastewater ; },
abstract = {Sulfur-driven autotrophic denitrification (SAD), an organic-free biological nitrogen removal process driven by sulfur-based electron donors (SEDs), offered advantages including low energy consumption, low sludge yield, and reduced greenhouse gas emissions. The sulfur-based compounds, with their abundant global reserves and cost-effectiveness, serve as utilizable electron donors for advanced nitrogen removal in wastewater treatment and polluted water remediation. Research on a variety of SEDs and SAD processes had expanded significantly, yet documentation of their large-scale implementation remained scarce in industrial practice. This paper presented a comprehensive review of the research and application of SADs over the past two decades. It summarized and compared the physicochemical properties and nitrogen removal performance of various SEDs, and evaluated their economic and environmental impacts. Moreover, the key factors affecting SAD efficiency were identified, along with feasible solutions to support its large-scale applications. Nitrous oxide (N2O) emissions were considered a critical indicator for evaluating the sustainability of future wastewater treatment technologies. Therefore, this study also examined the N2O emission characteristics from SAD processes, highlighting their potential for low-carbon applications, and further proposed strategies to mitigate N2O emissions. Finally, the review outlined future research directions and prospects of SAD, providing insights to filter material development and guide process design in engineering applications. This study systematically evaluated the merits and constraints of SAD, delineating critical application bottlenecks while identifying potential unresolved scientific challenges demanding further investigation.},
}
@article {pmid41896196,
year = {2026},
author = {He, W and Bolnick, DI and Scarpino, SV and Eliassi-Rad, T},
title = {Hypergraph representations of single-cell RNA sequencing data for improved cell clustering.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {4},
pages = {},
pmid = {41896196},
issn = {1367-4811},
support = {#2133740//National Science Foundation/ ; },
mesh = {*Single-Cell Analysis/methods ; Algorithms ; Cluster Analysis ; *Sequence Analysis, RNA/methods ; Humans ; Computational Biology/methods ; Gene Expression Profiling ; Gene Regulatory Networks ; },
abstract = {MOTIVATION: Single-cell RNA sequencing (scRNA-seq) data analysis is often performed using network projections that produce co-expression networks. These network-based algorithms are attractive because regulatory interactions are fundamentally network-based and there are many tools available for downstream analysis. However, most network-based approaches have two major limitations. First, they are typically unipartite and therefore fail to capture higher-order information. Second, scRNA-seq data are often sparse, so most algorithms for constructing unipartite network projections are inefficient and may overestimate co-expression relationships, or may under-utilize the sparsity when clustering (e.g. with cosine distance). To address these limitations, we propose representing scRNA-seq expression data as hypergraphs, which are generalized graphs where a hyperedge can connect more than two nodes. In this context, hypergraph nodes represent cells, and hyperedges represent genes. Each hyperedge connects all cells in which its corresponding gene is actively expressed, indicating the expression of that gene across different cells. The resulting hypergraph can capture higher-order information and appropriately handle varying levels of data sparsity. This representation enables clustering algorithms to leverage higher-order relationships for improved cell-type differentiation.<br><br>RESULTS: To distinguish cell types using hypergraph representations of scRNA-seq data, we introduce two novel clustering algorithms: (i) Dual-Importance Preference Hypergraph Walk (DIPHW) and (ii) Co-expression and Memory-Integrated Dual-Importance Preference Hypergraph Walk (CoMem-DIPHW). DIPHW is a new hypergraph-based random walk algorithm that computes cell embeddings by considering the relative importance of genes to cells and cells to genes, incorporating a preference exponent to facilitate clustering. CoMem-DIPHW integrates two unipartite projections, the gene co-expression and cell co-expression networks, along with the cell-gene expression hypergraph derived from single-cell abundance count data into the random walk model. The advantage of CoMem-DIPHW is that it accounts for both local information from single-cell gene expression and global information from pairwise similarity in the two co-expression networks. We benchmark the performance of our algorithms against established and state-of-the-art deep learning approaches using both real-world and simulated scRNA-seq data. Real-world datasets include cells from the human pancreas, mouse pancreas, human brain, and mouse brain tissues. We also use a ground-truth labeled cell-type annotation dataset based on human lung adenocarcinoma cell lines. Quantitative evaluation shows that CoMem-DIPHW consistently outperforms established algorithms and state-of-the-art deep learning algorithms for cell-type clustering. Our proposed algorithms show the greatest improvement on scRNA-seq data with weak modularity. Moreover, CoMem-DIPHW successfully annotates clusters with biologically relevant cell types. Our results highlight the utility of hypergraph representations in the analysis of scRNA-seq data.<br><br>Our methods are implemented in Python and available on GitHub (https://github.com/wanhe13/CoMem-DIPHW) and archived at Zenodo (https://doi.org/10.5281/zenodo.18927437).},
}
@article {pmid41896497,
year = {2026},
author = {Sowmya, and N, AA and J, R and R, A and Chalannavar, RK},
title = {Urban dispersion-driven land use change detection using GIS-based buffer gradient and Shannon's entropy analysis in Dakshina Kannada District, India.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {4},
pages = {},
pmid = {41896497},
issn = {1573-2959},
mesh = {India ; *Geographic Information Systems ; *Environmental Monitoring/methods ; *Urbanization ; Entropy ; Cities/statistics &amp; numerical data ; Agriculture ; *Conservation of Natural Resources ; Forests ; },
abstract = {Rapid and often unregulated urban expansion in ecologically sensitive coastal districts poses challenges to environmental integrity and urban resilience. This study quantifies land use/land cover (LULC) change and urban dispersion in Dakshina Kannada district, India, from 2000 to 2024 using multi-temporal Landsat 7 ETM+ and Landsat 8 OLI imagery, Geographic Information Systems (GIS), and Shannon's entropy. Six LULC categories-agricultural land, forest, built-up land, water bodies, barren land, and sand-were classified using a supervised maximum likelihood approach, achieving overall accuracies > 89% and Kappa coefficients > 0.82 by Error-matrix approach. Results indicate a substantial increase in built-up land (792.9%) over the study period, primarily at the expense of agricultural land, alongside notable forest-agriculture transitions. Shannon's entropy values (0.74-0.77) suggest a moderately dispersed urban form. The 2000-2014 period exhibits higher spatial dispersion and polycentric expansion, while a marginal decline in entropy during 2014-2024 indicates a relative shift toward spatial consolidation. Gradient and buffer-based directional analyses reveal pronounced growth along southeast, south, and northeast corridors aligned with major transport routes, with limited expansion toward the western coastal margin due to ecological and regulatory constraints. Unlike conventional entropy-based studies, this analysis integrates buffer-gradient and directional entropy assessment at the district scale, improving detection of peri-urban and corridor-oriented growth. The findings highlight a transition from dispersed to relatively consolidated urban expansion and underscore the importance of integrated spatial planning to balance development pressures with ecological conservation in rapidly urbanizing coastal regions.},
}
@article {pmid41898837,
year = {2026},
author = {Li, S and Chiodi, C and Maucieri, C and Della Lucia, MC and Zardinoni, G and Ravi, S and Squartini, A and Concheri, G and Geng, G and Wang, Y and Stevanato, P},
title = {Profiling Soil-Plant-Microbial Communities: DNA and Multi-Omics Techniques.},
journal = {Genes},
volume = {17},
number = {3},
pages = {},
pmid = {41898837},
issn = {2073-4425},
mesh = {*Soil Microbiology ; Rhizosphere ; Metagenomics/methods ; *Microbiota/genetics ; *Plants/microbiology/genetics ; Genomics/methods ; Metabolomics/methods ; Plant Roots/microbiology/genetics ; Crops, Agricultural/microbiology/genetics ; Multiomics ; },
abstract = {Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches-marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays-and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge-cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.},
}
@article {pmid41901676,
year = {2026},
author = {Vukasinovic, D and Maksimovic, M and Tanaskovic, S and Marinkovic, J and Cirkovic, A and Jakovljevic, B and Ilic Zivojinovic, J and Radak, D and Vlajinac, H},
title = {Predictors of Late Adverse Outcomes After Carotid Endarterectomy.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {3},
pages = {},
pmid = {41901676},
issn = {1648-9144},
mesh = {Humans ; *Endarterectomy, Carotid/adverse effects/statistics &amp; numerical data ; Female ; Male ; Aged ; Retrospective Studies ; Risk Factors ; Middle Aged ; Myocardial Infarction/etiology/epidemiology ; Stroke/etiology/epidemiology ; *Postoperative Complications/etiology/epidemiology/mortality ; Aged, 80 and over ; Cohort Studies ; Carotid Stenosis/surgery ; Proportional Hazards Models ; Age Factors ; },
abstract = {Background and Objectives: Although carotid endarterectomy (CEA) is the gold standard in the treatment of carotid disease, a higher frequency of adverse outcomes can reduce its benefit. The aim of the present study is to identify factors related to myocardial infarction, stroke, death and restenosis as the late adverse outcomes of CEA. Materials and Methods: The retrospective cohort study included 1597 CEAs that were performed in 1533 consecutive patients at the Vascular Surgery Clinic in Belgrade from 2012 to 2017. Late adverse outcomes within 4 years after CEA were available for the majority of them. Data for myocardial infarction and stroke were available for 1223 CEAs, data for death for 1305 CEAs, and data for restenosis for 1162 CEAs. The association between possible risk factors and late adverse outcomes of CEA was analyzed using univariate and multivariate Cox and logistic regression analyses. Results: During follow-up, myocardial infarction occurred after 55, stroke after 68, death after 103 and restenosis after 121 CEAs. Two factors were the most frequent predictors of late adverse outcomes, i.e., the patient's age and diabetes mellitus (DM). Age predicted all late adverse outcomes except restenosis, and DM predicted all of them. A predictor of myocardial infarction, besides age (HR 1.08, 95% CI 1.05-1.11) and DM (HR 1.60, 95% CI 1.11-2.29), was peripheral arterial disease (HR 1.81, 95% CI 1.17-2.78) in personal history. Predictors were only age (HR 1.04, 95% CI 1.01-1.08) and DM (HR 1.68, 95% CI 1.03-2.72) for stroke, as well as for death (HR 1.17, 95% CI 1.12-1.21 and HR 1.94, 95% CI 1.17-3.21, respectively). For restenosis, in addition to DM (HR 1.78, 95% CI 2.62), predictors were hyperlipidemia (HR 3.52, 95% CI 1.27-9.76) and urgent surgery (HR 3.51, 95% CI 1.06-11.65). Conclusions: CEA should be performed with special caution in the elderly and diabetic patients. Modification of other risk factors and precise medical therapy are necessary to reduce possible adverse outcomes.},
}
@article {pmid41902137,
year = {2026},
author = {Yang, Y and Nakagawa, R and Shinoda, R and Santo, H and Oyama, K and Ohkawa, T and Okura, F},
title = {Talking with Actionbits-A Part-Enhanced VLM for Action and Interaction Recognition in Animals.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {6},
pages = {},
pmid = {41902137},
issn = {1424-8220},
support = {JPMJFR206F//Japan Science and Technology Agency/ ; JP23H05491//Japan Society for the Promotion of Science/ ; JP25K03140//Japan Society for the Promotion of Science/ ; JP21H04914//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Behavior, Animal/physiology ; },
abstract = {Understanding animal actions and interactions is essential for behavior analysis and ecological monitoring. Although large-scale in-the-wild datasets have advanced animal action recognition, existing methods still struggle with fine-grained motion, spatial relations, and multi-individual interactions. To address these challenges, we introduce AIRA, a unified framework for Action and Interaction Recognition in Animals. Built upon a vision-language model (VLM), AIRA learns in an action-centered representation space defined by body parts and their corresponding motions, thereby improving robustness to background noise and enabling cross-species generalization via a unified mammal-centric part ontology. To model actions, we treat body parts and motion as primary cues and introduce Actionbit tokens-compact representations for parts and motions generated by a large language model (LLM) that encode which parts move and how. We further propose Part-Enhanced Prompt Fine-tuning (PEPF) to make the VLM explicitly sensitive to part and pose cues. Within PEPF, the Action-actionbit Alignment (AbA) module enriches action representations with fine-grained part-motion semantics, and Part-Vision Prompting (PVP) extracts keyframes through action-aware prompting. Experiments across multiple benchmarks show consistent improvements in both action and interaction recognition, highlighting the importance of action-centered adaptation and relational reasoning for understanding animal behavior in the wild.},
}
@article {pmid41903906,
year = {2026},
author = {Vitale, G and Ruiz-Sagalés, M and Chosson, V and Halldórsson, SD and Borrell, A and Aguilar, A and Sigurðsson, GM and Corami, F and Barbante, C and Garcia-Garin, O},
title = {Occurrence of microplastics across tissues in North Atlantic fin whales (Balaenoptera physalus).},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {397},
number = {},
pages = {128026},
doi = {10.1016/j.envpol.2026.128026},
pmid = {41903906},
issn = {1873-6424},
mesh = {Animals ; *Microplastics/metabolism/analysis ; *Water Pollutants, Chemical/metabolism/analysis ; *Environmental Monitoring ; *Fin Whale/metabolism ; Iceland ; },
abstract = {As long-lived filter-feeders, baleen whales integrate and reflect changes in ocean contamination, including exposure to microplastics (MPs). This study reports the occurrence of MPs in multiple tissues of North Atlantic fin whales (Balaenoptera physalus) collected off southwestern Iceland in 2023. Five tissues (blubber, muscle, liver, lung, and kidney) from eight individuals were analyzed using the Micro-FTIR and Micro-Raman spectroscopy under strict contamination control. MPs occurred in 32.5% of the samples (13/40; n = 16 particles), predominantly as blue fragments (75%) with an average length of 67.2 ± 33.8 μm. Polyester, polyethylene, and polypropylene were the most common polymers. Although overall tissue differences were minimal, blubber contained the highest MP abundance and longer average particles than other tissues. These findings provide evidence of MP tissue-specific accumulation within a mysticete species and highlight the need to clarify the mechanisms and implications of MP accumulation in marine megafauna.},
}
@article {pmid41904765,
year = {2026},
author = {Barman, S and Sarkar, BC},
title = {Assessment of ecological environment quality under urbanization: an RS and GIS-based analysis of Jalpaiguri Planning Area in West Bengal, India.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {4},
pages = {},
pmid = {41904765},
issn = {1573-2959},
mesh = {*Urbanization ; *Geographic Information Systems ; India ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; *Ecosystem ; *Conservation of Natural Resources ; },
abstract = {The ecological environment plays a crucial role in maintaining the balance and sustainability of ecosystems, particularly in the context of rapid urbanization. This study investigates the impact of urban growth on ecological environment quality in the Jalpaiguri Planning Area, a rapidly urbanizing area that has been overlooked in previous research. Using remote sensing and geographic information system, this study employed the Remote Sensing Ecological Index (RSEI) to quantitatively assess ecological environment quality by integrating key biophysical properties such as greenness, wetness, dryness, and surface temperature using multi-temporal Landsat data from 1991 to 2021. The results revealed a significant deterioration in eco-environment quality with a decline in mean RSEI values from 0.70 to 0.45. Areas with moderate to excellent ecological quality declined over time, while poor and fair quality zones increased, especially in the urban core and surrounding areas. Moran's I increased from 0.332 to 0.389, suggesting an increasing spatial dependence and clustering of ecological conditions, indicative of growing environmental polarization. Local indicators of spatial association highlighted a decreasing trend in High-High clusters and an expansion of Low-Low clusters, indicating degradation in greenness and wetness due to intensified built-up development. The outcomes of regression analysis revealed a strong and consistent negative correlation between growing built-up areas and RSEI, with correlation coefficients ranging from -0.76 to -0.86 over the study period. The results support targeted planning interventions, including protection of green and blue spaces, control of unplanned built-up expansion, and integration of RSEI-based ecological monitoring into urban planning for informed decision-making.},
}
@article {pmid41905022,
year = {2026},
author = {Benschop, KSM and Zwagemaker, F and Andersson-Li, L and Andrés, C and Antón, A and Berengua, C and Berginc, N and Bessaud, M and Bisseux, M and Bujaki, E and Canning, B and Christiansen, CB and Couderé, K and Broberg, EK and Cassidy, H and Castilletti, C and Celma, C and Cinek, O and Deézsi-Magyar, N and Eis-Hübinger, AM and Flipse, J and Jiřincová, H and Gatej, R and Georgieva, I and Giardina, F and González-Sánchez, A and Hack, B and Helfferich, J and Hutchings, S and Hietanen, E and Hönemann, M and Virant, MJ and Kalogera, E and Johannesen, CK and Kenicer, J and Kleines, M and Lagarejos, E and Landaas, ET and Kandulu, CC and Xavier López Labrador, F and Lunar, MM and Maier, M and Majumdar, M and Martin, J and McClure, CP and Muñoz-Almagro, C and Ošep, A and Øverbø, J and Palminha, P and Papa, A and Pariani, E and Pellegrinelli, L and Pietsch, C and Piralla, A and Poljak, M and Pomari, E and Prats-Méndez, I and Rector, A and Reuter, G and Riess, M and Ruta, S and Schibler, M and Nilsen, HS and Simmonds, P and Sourvinos, G and Szomor, K and Susi, P and Tabain, I and Vallely, P and von Eije, KJ and Weil, M and Wieczorek, M and Wollants, E and Wolthers, KC and Zuckerman, NS and Fischer, TK and Harvala, H},
title = {Next generation sequencing approaches for the detection and characterization of enteroviruses in clinical, public health, and research settings: Expert view of the European non-polio enterovirus network (ENPEN).},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {184},
number = {},
pages = {105940},
doi = {10.1016/j.jcv.2026.105940},
pmid = {41905022},
issn = {1873-5967},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Enterovirus Infections/diagnosis/virology/epidemiology ; *Enterovirus/genetics/isolation &amp; purification/classification ; Europe ; Public Health ; Computational Biology/methods ; Genome, Viral ; },
abstract = {Enteroviruses (EVs) are a common cause of a wide spectrum of infectious diseases, ranging from mild respiratory illnesses to severe neurological conditions, particularly affecting children. Current molecular methods, such as 5'UTR-based PCR for detection and (partial) VP1 gene sequencing for typing, are widely utilized. However, Next-Generation Sequencing (NGS), and bioinformatics offer a comprehensive alternative, enabling full-genome analyses for improved virus characterization, genomic epidemiological surveillance, and outbreak investigation. Despite its advantages, implementation of NGS poses challenges, particularly in standardizing and optimizing laboratory workflows (wet-lab) and bioinformatics analyses (dry-lab), methods that are not often readily accessible in many laboratories. Here, we discuss the potential of NGS as a tool for EV detection/characterization in clinical virology, public health, and research settings. We provide practical options for actions for implementing NGS to advance the understanding and management of enterovirus infections. These recommendations are based on expert discussions during the recent European non-polio enterovirus network (ENPEN) workshop held in Corfu, Greece, on 23-24 May 2024, aiming to guide harmonization of NGS practices across clinical, public health, and research settings.},
}
@article {pmid41907146,
year = {2026},
author = {Wang, H and Fan, K and Li, Y and Wang, Z and Wang, S and Zheng, G},
title = {Ambient Cold and Mortality in Pan-Arterial Diseases: A Nationwide Ecological Analysis of CDC WONDER Data.},
journal = {Vascular health and risk management},
volume = {22},
number = {},
pages = {589152},
pmid = {41907146},
issn = {1178-2048},
mesh = {Humans ; United States/epidemiology ; *Peripheral Arterial Disease/mortality/diagnosis ; Middle Aged ; Risk Factors ; *Cold Temperature/adverse effects ; Seasons ; Male ; Databases, Factual ; Aged ; Time Factors ; Female ; Adult ; Risk Assessment ; *Aortic Aneurysm/mortality/diagnosis ; *Aortic Dissection/mortality/diagnosis ; *Atherosclerosis/mortality/diagnosis ; Centers for Disease Control and Prevention, U.S. ; },
abstract = {INTRODUCTION: Pan-arterial diseases, including atherosclerosis (AS), aortic aneurysm and dissection (AAD), and peripheral arterial disease (PAD), impose a substantial global health burden. Although ambient temperature has been implicated in individual arterial conditions, its association with mortality across the pan-arterial spectrum remains incompletely understood.<br><br>OBJECTIVE: To evaluate the association between ambient temperature and mortality from pan-arterial diseases across the United States.<br><br>METHODS: We analysed mortality data for adults aged &#x2265;25 years with AS, AAD, or PAD in the United States CDC WONDER database from 1999 to 2023. Age-adjusted mortality rates (AAMR) and average annual percent change (AAPC) were estimated. Monthly air-temperature metrics (1999-2023) were linked at the United States Census region level. Seasonal variation was assessed using analysis of variance. Associations between temperature and mortality were examined using Spearman correlation, Poisson regression with lag structures, and distributed lag non-linear models (DLNM), with results expressed as relative risks (RR) per 10&#xb0;F increase in temperature.<br><br>RESULTS: Between 1999 and 2023, AAMRs declined for AS, AAD, and PAD, yet mortality burden remained substantial. Mortality from all three conditions was consistently higher in winter than in summer across Census regions. Monthly mean temperature was inversely correlated with crude mortality for pan-arterial diseases (P < 0.05). In the Northeast, cumulative RR per +10&#xb0;F across lags 0-3 months was 0.919 for AS, 0.945 for AAD, and 0.953 for PAD, with similar patterns observed in other regions. DLNM analyses demonstrated a predominantly cold-related excess risk, with acute effects and regional heterogeneity at higher temperatures.<br><br>CONCLUSION: Lower ambient temperatures are associated with increased mortality from pan-arterial diseases in the United States. These findings highlight shared vulnerability to cold exposure across arterial diseases and support winter-focused preventive and healthcare preparedness strategies.},
}
@article {pmid41913298,
year = {2026},
author = {Adeogun, AO and Izekor, RT and Babalola, AS and Oyeniyi, TA and Adetunji, O and Adesoye, OA and Wahedi, J and Busari, LO and George, A and Ajayi, S and Chabi, J and Awolola, ST},
title = {Spatial distribution of the 2La chromosomal inversion in Anopheles gambiae populations across Nigeria: ecological associations and implications for malaria control.},
journal = {Tropical medicine and health},
volume = {54},
number = {1},
pages = {},
pmid = {41913298},
issn = {1348-8945},
abstract = {BACKGROUND: Chromosomal inversions are key drivers of local adaptation and ecological diversification in Anopheles gambiae, the principal malaria vector in sub-Saharan Africa. Among these, the 2La inversion is associated with tolerance to aridity, behavioural variation, and insecticide resistance. However, large-scale data on inversion frequency and ecological association remain scarce in Nigeria. This study investigated the spatial distribution of 2La inversion frequencies in An. gambiae and their relationship with ecological zones across the country.<br><br>METHODS: A total of 1200 Anopheles mosquitoes were collected across 12 states representing Nigeria's major ecozones. 2La inversion karyotypes were determined by PCR, and allele frequencies were analysed in relation to ecological zones, latitude, and ecological gradients. Spatial mapping and statistical analyses were performed using R version 4.4.<br><br>RESULTS: Morphological identification and species-specific PCR revealed 999 An. gambiae s.l., comprising An. gambiae s.s. (39.7%), An. coluzzii (51.5%), and An. arabiensis (8.7%). A total of 399 An. gambiae s.s. was karyotyped. From the An. gambiae s.s. population karyotyped, a distinct south-north cline in inversion frequency was observed. The 2La/2La homokaryotype predominated in arid northern ecozones (Sahelian and Sudan savannas), whereas 2La&#x2009;+&#x2009;/2La&#x2009;+&#x2009;was dominant in humid southern forests and mangrove regions. The heterokaryotype 2La/2La&#x2009;+&#x2009;occurred at moderate frequencies in transitional zones (Osun-Taraba corridor). Linear regression analyses confirmed significant correlations between inversion frequency and latitude (R[2]&#x2009;=&#x2009;0.68-0.73, P&#x2009;<&#x2009;0.001). Generally, the allele frequencies from 2La karyotyping did not deviate significantly from Hardy-Weinberg equilibrium expectations (P&#x2009;>&#x2009;0.05) except in Bayelsa and Kebbi States.<br><br>CONCLUSION: This study provides the first nationwide evidence linking 2La inversion polymorphism to ecological adaptation of An. gambiae in Nigeria. The inversion likely enhances vector survival across diverse habitats, contributing to spatial variation in malaria transmission. These findings have direct operational relevance for Nigeria's National Malaria Elimination Programme (NMEP), indicating that vector-control effectiveness may vary by ecological context. Integrating ecotype- and region-specific evidence into NMEP planning could improve intervention targeting. Continuous genomic surveillance will be essential to sustain malaria control gains.},
}
@article {pmid41915641,
year = {2026},
author = {Pierides, I and Kramml, HM and Waldherr, S and Weckwerth, W},
title = {Kernel-DMD for multiome data integration and control.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1014029},
pmid = {41915641},
issn = {1553-7358},
mesh = {Photosynthesis/physiology ; *Computational Biology/methods ; Computer Simulation ; Algorithms ; Models, Biological ; },
abstract = {Research in multiome data integration comes with the challenge of high-dimensionality and a small sample size in time series data. Traditional statistical tools often fail to capture true functional modules in large molecular networks, resulting in spurious associations. Dynamical systems theory overcomes this hurdle by assuming the biological system follows a trajectory that can be modelled in such a way that the interactions in the network have a causal nature and pertain to mechanistic processes. Here we use kernel-DMD, a data-driven dynamical systems tool for time series data, for multiome network integration in the exotic plant species Clusia. We uncover differing modes of photosynthesis that correspond to the C3-like or strong CAM dynamics of two species, Clusia major and Clusia rosea and implement a control strategy that enables the in silico phenocopying between the two species. We demonstrate the applicability of the Koopman operator to multiome data integration, uncover drivers of plasticity in molecular networks and also identify key biomarkers that could potentially establish more resilient forms of photosynthesis, such as CAM, for the introduction of new crop bioengineering possibilities in C3 plants.},
}
@article {pmid41918090,
year = {2026},
author = {Wei, L and Lin, J and Xie, Z and Chu, Y and Chai, S and Han, Y},
title = {Beyond green: how city greenspace shapes health outcomes in China.},
journal = {BMC public health},
volume = {26},
number = {1},
pages = {},
pmid = {41918090},
issn = {1471-2458},
support = {KYYW202338//Basic Scientific Research Foundation of Wenzhou Medical University/ ; SKODJ2309//Talent Research Startup Project of Wenzhou Medical University/ ; },
abstract = {BACKGROUND: Urban greenspace is increasingly acknowledged as a vital component of sustainable urban development. While being exposed to greenspace is associated with a lower risk of chronic diseases, the specific health effects of different types and functions of greenspace remain unclear. As a distinct category with clear boundaries, high accessibility, and multiple functions, urban parks may play a particularly important role in promoting health, yet research focusing specifically on urban parks remains limited, and the underlying mechanisms are still unclear.<br><br>METHODS: The data were obtained from the China Health and Retirement Longitudinal Study (CHARLS), the China Longitudinal Aging Social Study (CLASS), and the China Urban Construction Statistical Yearbook for 2016, 2018, and 2020. Spatial autocorrelation analysis was applied to identify clustering patterns and hot/cold spots of chronic disease prevalence and greenspace resources (including park area and green coverage). A Multiscale Geographically and Temporally Weighted Regression (MGTWR) model was applied to quantify the influence of green coverage and park area on chronic disease prevalence, supported by geographic information system (GIS) mapping to visualize spatial distributions.<br><br>RESULTS: Chronic disease prevalence followed an inverted U-shaped trend from 2016 to 2020, peaking in 2018. High-high clustering and hot spot shifted cyclically from the southwest to the northeast and back. Areas with high park greenspace remained consistently concentrated in the Bohai Rim and Pearl River Delta metropolitan regions, while those with high green coverage transitioned from the Yangtze River Delta and Pearl River Delta to the Middle Yangtze River urban agglomeration and finally to the southwestern ecological zone. The MGTWR model indicated a marginal effect: in eastern regions with ample green infrastructure, expanding greenspace yields limited returns, whereas in the less-green western regions, further development produces more significant health improvements.<br><br>CONCLUSIONS: It is recommended to adopt tailored chronic disease prevention strategies, focusing on high-risk areas. Urban planning should prioritize equitable access to greenspace rather than merely expanding their area. Long-term environmental health monitoring is also advised to better capture the lagged effects of ecological improvements. This research provides evidence for transforming green infrastructure into health assets, supporting equitable urban planning to reduce the burden of chronic diseases.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12889-026-27006-y.},
}
@article {pmid41919563,
year = {2026},
author = {Afridi, R and Ibrahim, M and Yaqoob, M and Ahmad, W},
title = {Synergistic Effect of Glyphosate and Polyethylene Microplastics on Culturable Gut Microbiota Alterations in Zebrafish.},
journal = {Environmental toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1002/tox.70091},
pmid = {41919563},
issn = {1522-7278},
abstract = {The coexistence of emerging pollutants, that is, microplastics (MPs) and pesticides poses significant threat to aquatic organisms. This study investigated the combined effects of polyethylene microplastics (PE-MPs) and glyphosate on the gut microbiome of zebrafish. Following a 21-day exposure, 16S rRNA sequencing revealed that co-exposure caused the most significant disruption, surpassing the individual effects of each stressor. Co-exposure resulted in the lowest alpha diversity and a distinct microbial community structure, characterized by the depletion of A. veronii and a marked enrichment of opportunistic pathogens like A. hydrophila. Clear separation of all exposed groups from controls, with the co-exposure group forming the most distinct cluster was observed in non-metric multi-dimensional scale analysis. Specifically, a higher number of ASVs were differentially abundant in the co-exposure group compared to the individual exposures. In the MPs group, Aeromonas species were markedly replaced by Enterobacter species. Glyphosate significantly enriched A. hydrophila species in the gut. Treatment-specific clustering, with Enterobacter species associated with MPs, and A. hydrophila with glyphosate and co-exposure groups were observed in Heatmap analysis. The findings indicate that microplastics not only act as direct stressors but also as glyphosate carriers, leading to amplified, non-additive shifts in the gut microbiome and posing a heightened ecological risk.},
}
@article {pmid41919872,
year = {2026},
author = {Santos, FS and Carvalho, MS and Costa, JSDD},
title = {Trend of avoidable mortality due to circulatory system diseases and ischemic heart diseases in Rio Grande do Sul (2000-2023): an ecological analysis.},
journal = {Revista da Associacao Medica Brasileira (1992)},
volume = {72},
number = {1},
pages = {e20250627},
pmid = {41919872},
issn = {1806-9282},
mesh = {Humans ; Brazil/epidemiology ; Middle Aged ; Female ; Male ; Aged ; Adult ; *Myocardial Ischemia/mortality ; *Cardiovascular Diseases/mortality ; Sex Distribution ; Age Distribution ; Mortality/trends ; },
abstract = {OBJECTIVE: The aim of this study was to analyze trends in avoidable mortality due to circulatory system diseases and ischemic heart diseases among individuals aged 30-69 years across the health macro-regions of Rio Grande do Sul, Brazil, from 2000 to 2023.<br><br>METHODS: An ecological time-series study was conducted using data from the Mortality Information System and Department of Informatics of the Unified Health System, with calculation of age- and sex-adjusted mortality coefficients.<br><br>RESULTS: A reduction in mortality from circulatory system diseases and ischemic heart diseases was observed among women in almost all macroregions, except for the Central-West. Among men, decreasing trends in mortality from circulatory system diseases were identified, except in the Vales macro-region and in the state overall. Mortality was higher among men and increased with age, with the highest coefficients observed in the South, Central-West, and Metropolitan macro-regions.<br><br>CONCLUSION: A downward trend in mortality was observed despite population aging, which may be attributed to health policies that strengthened the Unified Health System, including the expansion of the Family Health Strategy, the Hypertension and Diabetes Mellitus Care Reorganization Plan, and the Popular Pharmacy Program, as well as measures for chronic disease control and health promotion.},
}
@article {pmid41920852,
year = {2026},
author = {Kim, H and Kim, S and Kimbrel, JA and Morris, MM and Mayali, X and Buie, CR},
title = {Multidimensional scaling informed by F-statistic: Visualizing grouped microbiome data with inference.},
journal = {PLoS computational biology},
volume = {22},
number = {4},
pages = {e1014102},
pmid = {41920852},
issn = {1553-7358},
mesh = {*Microbiota ; *Computational Biology/methods ; Algorithms ; Humans ; Multivariate Analysis ; },
abstract = {Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. In this study, we introduce a new MDS-based ordination method, "F-informed MDS," which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community's response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.},
}
@article {pmid41921320,
year = {2026},
author = {Huang, DQ and Zhou, S and Jia, Y and Yan, Y and Lu, H},
title = {Deciphering pharmaceutical resistance in sulfur-driven autotrophic denitrification: an integrated multi-omics artificial intelligence-driven structural biology approach.},
journal = {Water research},
volume = {298},
number = {},
pages = {125834},
doi = {10.1016/j.watres.2026.125834},
pmid = {41921320},
issn = {1879-2448},
mesh = {*Denitrification ; *Sulfur/metabolism ; Autotrophic Processes ; *Artificial Intelligence ; Ibuprofen ; Multiomics ; },
abstract = {Sulfur-driven autotrophic denitrification (SdAD) is a promising low-carbon technology for nitrogen removal; however, its stability and adaptive mechanisms under pharmaceutical stress remain poorly understood. In this study, ibuprofen (IBU) was used as a representative pharmaceutical to investigate the response of an SdAD system. Throughout the 210-day operational period, the system demonstrated exceptional functional robustness, maintaining high sulfide (97.46 ± 3.18%) and inorganic nitrogen (99.17 ± 4.34%) removal efficiencies across IBU concentrations ranging from environmentally relevant levels to elevated shock loads (100-2000 μg/L). Underpinning this macroscopic stability, community-level analyses revealed that instead of succumbing to inhibition, the SdAD microbiome actively reorganized its composition and topological structure to accommodate the selective pressure. This adaptation was characterized by enhanced microbial diversity and stress-induced network modularity (particularly at 100-500 μg/L), alongside strengthened cooperative interactions between sulfur-oxidizing bacteria and denitrifiers. To unravel the specific molecular drivers of this resilience, we integrated AlphaFold-based structural modeling with machine learning-coupled molecular docking. This enabled us to resolve the three-dimensional structure of sulfide: quinone oxidoreductase (SQR) and perform the first structure-function analysis of SQR within an SdAD context under pharmaceutical stress, revealing that arginine residues serve as key interaction hotspots for IBU binding. Consistent with this binding mechanism, multi-omics data further corroborated a systemic adjustment involving the coordinated regulation of sulfur oxidation genes and the transcriptional upregulation of arginine biosynthesis pathways. Overall, these findings shed light on how the SdAD community mitigates pharmaceutical toxicity through a multi-tiered strategy involving ecological network reorganization and metabolic compensation. Methodologically, this work highlights the value of integrating artificial intelligence-driven structural biology with multi-omics analyses to decode the mechanisms of contaminant resistance in biological wastewater treatment systems.},
}
@article {pmid41924063,
year = {2026},
author = {Sánchez, D and Martinho, DV and Figueiredo, A and Barrera-Díaz, J and Sousa, H and Ordoñez-Saavedra, N and Ramos, S and Gouveia, &#xc9;R and Campos, P and Sarmento, H},
title = {Perceptions of Colombian Olympic coaches on talent identification and development in sport: a qualitative study.},
journal = {Frontiers in psychology},
volume = {17},
number = {},
pages = {1712976},
pmid = {41924063},
issn = {1664-1078},
abstract = {INTRODUCTION: Studies examining talent identification and development have primarily focused on athletic samples. However, there is limited literature addressing the determinants of talent from coaching perspectives. The aim of this study was to characterize the perspectives of coaches regarding talent identification and development among Colombian elite coaches.<br><br>METHODS: The research adopted a qualitative, interpretative approach, utilizing semi-structured interviews. The guide was validated through expert review and interviews conducted with 10 coaches who have Olympic experience. Thematic analysis was conducted for data analysis using NVivo software (version 14) and a deductive-inductive content analysis approach based on the ecological dynamics theoretical framework.<br><br>RESULTS: The results were organized into three main categories of constraints: (1) related to the athlete; (2) related to the task; and (3) related to environment. Participants highlighted the importance of physical, technical, tactical, and, above all, psychological skills in talent identification. Coaches also emphasized that talent should not be viewed as static but as a dynamic construct influenced by biological maturation and environmental factors. Deliberate practice and play were considered complementary in sport development, with early diversification of sporting experiences being highly valued by Olympic coaches. Family involvement, institutional support, and socioeconomic stability emerged as critical elements to ensure the continuity and sustainability of the process.<br><br>CONCLUSION: The geographic and ethnic diversity of Colombia was recognized as a factor that can facilitate talent identification and development although structural challenges such as infrastructure shortages and the lack of coordinated national policies continue to limit the development of elite athletes. The talent development model in Colombia should consider the interrelationships between different constraints to effectively identify and develop athletes for elite-level competition.},
}
@article {pmid41926843,
year = {2026},
author = {Yang, D and Zhou, N and Du, F and Zhou, Z and Wang, W and Shu, Y and Ji, Q and Zhu, Z},
title = {Biomass prediction and invasion assessment of Spartina alterniflora driven by remote sensing big data.},
journal = {Marine pollution bulletin},
volume = {228},
number = {},
pages = {119602},
doi = {10.1016/j.marpolbul.2026.119602},
pmid = {41926843},
issn = {1879-3363},
mesh = {*Introduced Species ; *Remote Sensing Technology ; *Biomass ; Wetlands ; *Poaceae ; *Environmental Monitoring/methods ; China ; Big Data ; Ecosystem ; },
abstract = {Coastal wetlands, as one of the three major ecosystems on Earth, play a critical role in maintaining biodiversity and ecological balance. In recent years, the invasive species Spartina alterniflora has rapidly spread along China's coastal areas, posing a considerable threat to coastal wetland ecosystems. Based on marine remote sensing big data, this study integrated multi-source remote sensing imagery and multi-site observational characteristics to develop a standardized dataset for estimating S. alterniflora biomass, and created corresponding automated identification and remote sensing inversion methods for biomass estimation. Systematic monitoring in the Hangzhou Bay area revealed that between 2019 and 2022, S. alterniflora biomass density continued to increase, with a maximum annual expansion area reaching 1135.7 ha, a northward shift in distribution centroid, and edge-expansion patterns dominating the spread. However, from 2023 to 2024, with enhanced artificial control measures, its distribution area sharply decreased from a peak of 3387.1 ha to 608.1 ha, accompanied by a significant reduction in biomass. This research demonstrates the effectiveness of combining remote sensing technology with machine learning algorithms for biomass monitoring, provides a scientific basis for developing effective management strategies against invasive species, and holds important practical significance for the conservation and restoration of coastal wetland ecosystems.},
}
@article {pmid41930519,
year = {2026},
author = {Han, L and Gu, H and Chen, M and He, Z and Jia, Y and Feng, Y and Li, J and Zhu, Y and Zou, Y},
title = {Text mining and machine learning based health risk prediction for soil polycyclic aromatic hydrocarbons at typical coal-fired industrial sites in china.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141934},
doi = {10.1016/j.jhazmat.2026.141934},
pmid = {41930519},
issn = {1873-3336},
mesh = {*Polycyclic Aromatic Hydrocarbons/analysis/toxicity ; China ; Risk Assessment ; *Machine Learning ; *Soil Pollutants/analysis/toxicity ; Data Mining ; Humans ; Coal ; Environmental Monitoring ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants posing significant threats to the environment and human health, particularly at active coal-fired industrial sites (coking, steel smelting, and thermal electric power generation) in China. However, for active industrial enterprises, effectively predicting PAHs exposure risks at the national scale remains challenging due to spatial uncertainty of contamination distribution and difficulties in the acquisition of large-scale monitoring data. This study introduces a multidisciplinary framework integrating text mining, probabilistic risk assessment, and machine learning to predict and assess health risks of PAHs in soils at these active industrial sites. Text mining extracted comprehensive PAHs-related data from literature, forming a national database with over 1600 entries. Probabilistic risk assessment with Monte Carlo simulation (1000 iterations per sample) revealed that 32% of historically reported sites in the text-mined database exceeded the acceptable target risk (ATR = 1 ×10[-6]), with benzo[a]pyrene (BaP) and dibenzo[a,h]anthracene (DahA) emerging as primary risk drivers, while non-carcinogenic risks were mostly below safety thresholds (hazard quotient < 1). Four machine learning algorithms including Support Vector Machine (SVM), Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Light Gradient Boosting Machine (LightGBM) were evaluated for risk classification, with LightGBM achieving optimal performance (accuracy: 98.88%, ROC-AUC: 1.0000). Feature importance analysis identified enterprise insured population, regional atmospheric CO concentration, and particulate emission limits as key predictors. National-scale prediction for 1263 sites identified 15.30% exceeding the ATR, predominantly concentrated in eastern and central China. Industry-specific analysis showed coking plants (39.40%) and steel smelting facilities (38.00%) exhibited higher proportions of sites exceeding the ATR than thermal power plants (22.60%), reflecting process-specific PAHs generation patterns. This framework provides an efficient, scalable approach for PAHs risk assessment and management at coal-fired sites in China, offering a replicable model for similar environmental challenges globally.},
}
@article {pmid41931472,
year = {2026},
author = {Kim, Y and Faivre, B and Boulinier, T and Sineau, C and Galon, C and Moutailler, S and Bournez, L and Métras, R},
title = {A Bayesian modelling framework for estimating tick-borne pathogen transmission dynamics at the host-tick interface.},
journal = {PLoS computational biology},
volume = {22},
number = {4},
pages = {e1014146},
pmid = {41931472},
issn = {1553-7358},
mesh = {Bayes Theorem ; Animals ; *Tick-Borne Diseases/transmission/microbiology ; *Ticks/microbiology ; *Models, Biological ; Birds/parasitology ; Computational Biology ; Host-Pathogen Interactions ; },
abstract = {Understanding the transmission dynamics of tick-borne pathogens at the host-tick interface is challenged by the presence of multiple pathways for tick infection, including (i) host-to-tick transmission, (ii) tick-to-tick (cofeeding) transmission, and (iii) pre-existing infection through vertical transmission or prior feeding. Assessing parameters governing these pathways is critical for identifying the main transmission drivers and, consequently, key prevention and control points. Here, we developed a Bayesian modelling framework that estimates key parameters describing the probability of each transmission pathway and assesses associated factors, including bird species, tick life stage and engorgement level, by jointly modelling transmission at the host-tick interface using data collected in field studies that sample hosts and their ticks. First, by fitting the model to simulated host-tick infection data, we demonstrated the framework's ability to recover the parameter values underlying these data. Model performance improved significantly when more information was available on variability in cofeeding probability among individual ticks, highlighting the value of testing all collected ticks and recording their spatial distribution on the host in relation to each other. Second, we fitted the model to field data collected at the bird-tick interface in Northeast France in 2023, focusing on Borrelia garinii, B. valaisiana, and Anaplasma phagocytophilum as case pathogens. For all three pathogens studied, models including cofeeding transmission explained the data significantly better than models that did not. Engorgement level was significantly and positively associated with the probability of bird-to-tick transmission for A. phagocytophilum. Finally, the estimated parameters, such as the probability of A. phagocytophilum infection in birds and the probability of Borrelia or Anaplasma infection in ticks before feeding, were comparable to values from an external dataset, not used for model fitting. Our framework provides a valuable foundation for future research to understand tick-borne pathogen transmission dynamics based on epidemiological and ecological field data collected at the host-tick interface.},
}
@article {pmid41931547,
year = {2026},
author = {Weyna, A and Mullon, C and Lehmann, L},
title = {Directional and disruptive selection in populations structured by class and continuous ontogeny under incomplete plasticity.},
journal = {PLoS computational biology},
volume = {22},
number = {4},
pages = {e1013591},
pmid = {41931547},
issn = {1553-7358},
mesh = {Female ; Male ; *Selection, Genetic ; Biological Evolution ; Animals ; *Models, Genetic ; Computational Biology ; Body Size/genetics ; Sexual Selection ; },
abstract = {Many organisms undergo ontogeny, whereby individuals change in state (e.g., in size, morphology, or condition) as they age. Understanding the evolution of traits influencing ontogeny is challenging because their fitness effects unfold across an individual's lifetime and may differ between classes such as sexes. Here, we analyse selection on non-plastic traits (e.g., fixed resource allocation strategies) that determine the development of dynamical states throughout life (e.g., body size), with consequences for fecundity and survival in age- and class-structured populations. Using invasion analysis, we derive expressions for directional and disruptive selection that decompose into age- and class-specific components. This allows us to identify convergence stable trait values, assess whether they are uninvadable or potentially experience evolutionary branching, and pinpoint the age and class pathways through which correlational and disruptive selection act. Applying our results to a model of growth under size-mediated sexual selection, we show how selection on growth rates distributes across ages and sexes, and how its relative strength depends on genetic correlations, individual ploidy and life-history. We also show how sex-specific developmental trade-offs and constraints can generate disruptive selection on male growth and favour the evolution of alternative male life histories. More broadly, our results highlight how adaptation is mediated by the interaction of development and demography, and provide tools to investigate how conflicts across ages and classes may influence senescence, sexual dimorphism, and the diversification of ontogenetic strategies.},
}
@article {pmid41932416,
year = {2026},
author = {Mattern, N and Brandt, N and Bräuer, AU and Steinhoff, LM and Wree, A and Scherberich, J and Windfelder, AG and Kampschulte, M and Krombach, GA and Heiss, C and Windhorst, A and Lips, KS},
title = {Altered bone structure in Niemann-Pick Type C1 mice, especially in females.},
journal = {Bone},
volume = {208},
number = {},
pages = {117879},
doi = {10.1016/j.bone.2026.117879},
pmid = {41932416},
issn = {1873-2763},
mesh = {Animals ; Female ; *Niemann-Pick Disease, Type C/pathology/drug therapy/diagnostic imaging/genetics ; Niemann-Pick C1 Protein ; Male ; Mice ; *Bone and Bones/pathology/diagnostic imaging/drug effects ; X-Ray Microtomography ; Mice, Knockout ; 1-Deoxynojirimycin/analogs &amp; derivatives/pharmacology/therapeutic use ; Intracellular Signaling Peptides and Proteins ; 2-Hydroxypropyl-beta-cyclodextrin ; Pregnanolone/pharmacology/therapeutic use ; Femur/pathology/diagnostic imaging/drug effects ; *Sex Characteristics ; },
abstract = {Niemann-Pick type C disease (NPC) is a rare lysosomal storage disorder belonging to the group of sphingolipidoses and is caused by a genetic defect affecting cholesterol trafficking. Since other sphingolipidoses with lipid accumulations show disrupt bone, this study investigated bone structure in an Npc1 mouse model and assessed whether pharmacological treatments (miglustat, 2-hydroxypropyl-β-cyclodextrin [HPßCD], and combination therapy including allopregnanolone) affected it. Femora from Npc1[-]/[-] mice of postnatal day (P) 65 were analysed using histology, histomorphometry and micro-CT. Additionally, femur and vertebral bodies of mice from P30, P40 and P65 were examined by real-time RT-PCR. Histomorphometric findings revealed a significantly reduced relative bone area in female Npc1[-]/[-] mice compared to wild-type mice. Micro-CT analysis confirmed this by demonstrating deteriorated trabecular bone structures in female Npc1[-]/[-] mice. Following treatment, particularly with combination therapy, an improvement in the bone microarchitecture was observed. Differences relative to wild-type mice were often no longer detectable. Furthermore, there was some evidence that combi therapy also increased the relative numbers of osteoblasts and osteoclasts. Since real-time RT-PCR indicated low expression of osteoclast and osteocyte targets cathepsin K and connexin-43, respectively, a stimulation of bone cells might decelerate postnatal disease progression. While at P30, sphingosine-kinase-1 (SphK1) expression was increased in female Npc1[-]/[-] mice, it decreased in femur at P40 and in vertebral bodies at P65. This decline was not measured in male Npc1[-]/[-] mice revealing a sex-dependent decline of bone structures in female Npc1[-]/[-] mice. Overall, disease-modifying treatment regimens targeting lipid storage improved bone microarchitecture in a sex-dependent manner.},
}
@article {pmid41932645,
year = {2026},
author = {Sakakibara, H and Ohkubo, N and Yamasaki, K and Tahara, M and Nakamura, K and Akata, K and Ikegami, H and Jotatsu, T and Okawara, M and Fujino, Y and Matsuda, S and Fushimi, K and Mukae, H and Yatera, K},
title = {Clinical and epidemiological characteristics of hospitalized patients with Diphyllobothriasis in Japan: A nationwide administrative database study.},
journal = {Parasitology international},
volume = {114},
number = {},
pages = {103276},
doi = {10.1016/j.parint.2026.103276},
pmid = {41932645},
issn = {1873-0329},
mesh = {Humans ; Japan/epidemiology ; Male ; Female ; *Diphyllobothriasis/epidemiology/drug therapy/parasitology ; Adult ; Retrospective Studies ; Middle Aged ; *Hospitalization/statistics &amp; numerical data ; Incidence ; Seasons ; Young Adult ; Adolescent ; Child, Preschool ; Child ; Animals ; Aged ; Praziquantel/therapeutic use ; Infant ; Databases, Factual ; Diphyllobothrium ; },
abstract = {Diphyllobothriasis, a fish-borne infection caused by broad tapeworms and transmitted through the consumption of raw or undercooked fish, continues to pose a public health concern in Japan. However, nationwide epidemiological data on hospitalized patients are limited. We conducted a retrospective analysis using the Japanese Diagnosis Procedure Combination (DPC) inpatient administrative database from April 2014 to March 2021. Hospitalized patients with diphyllobothriasis were identified using the ICD-10 code B700. Demographic characteristics, clinical presentations, treatment patterns, temporal trends, and geographic distribution were evaluated. Population-standardized incidence rates were calculated per 100,000 population by prefecture. A total of 340 unique hospitalized patients were included. The mean age was 36.6 years, and 65.0% were male. The highest incidence rates were observed in Toyama, Kyoto, Kagawa, Ishikawa, and Nara prefectures. Seasonality was evident, with peaks in late spring and summer. Overt anemia and severe complications were uncommon. Praziquantel was administered in 73.2% of cases, and endoscopic procedures for worm removal were rare. This nationwide DPC-based study demonstrates marked geographic heterogeneity and clear seasonal patterns in hospitalized diphyllobothriasis in Japan, with a predominance among working-age adults. Population-standardized incidence rates provide an alternative perspective on regional patterns among hospitalized cases than absolute case counts. These findings enhance understanding of the inpatient burden and real-world management of diphyllobothriasis in contemporary Japan. (212 words).},
}
@article {pmid41933172,
year = {2026},
author = {Legaz, A and Moguilner, S and Barttfeld, P and Cuadros Castro, J and Galván Rial, DS and Migeot, J and Farina, FR and Gonzalez-Gomez, R and Salazar-Londoño, S and de Souza Azzi, T and Alcauter, S and Amoruso, L and Anghinah, R and Bakr, M and Behrens, MI and Bruno, MA and Cardona, JF and Chen, C and Colliot, O and Custodio, N and d'Acremont, Q and Debette, S and Dzianok, P and Güntekin, B and Huguet, J and Jarne, C and Joliot, M and Karageorgiou, E and Khedr, EM and Koopowitz, SM and Kublik, E and Lee, J and Aksman, L and Lopez, S and Margaretic, P and Matallana, D and Matis, S and Miltiadous, A and Novotni, G and Orio, P and Parra, MA and Reppermund, S and de Paula França Resende, E and Salum, GA and Slachevsky, A and Ortiz, ALS and Takada, LT and Toh, AQ and Tzallas, A and Wen, W and Whelan, R and Yener, G and Zegarra Valdivia, JA and Alexoudi, A and Arshad, F and Atta, H and Avila-Funes, JA and Santos, JB and Bruña, R and Castelblanco-Toro, SM and Chino Vilca, BN and Coronel-Oliveros, C and Crivello, F and Cruzat, J and Dellavale, D and Dhooge, C and Di Caterina, G and Escudero, J and Esquivias Farias, JM and Eze, LU and Evans, TE and Farombi, T and Fernández, A and Fittipaldi, S and Portillo, F and Martinic, GF and García, AM and Garcia-Cordero, I and Gaurav, R and Godoy, ME and Gonzalez Campo, C and González Hernández, A and Hanoğlu, L and Hazelton, JL and Herzog, R and Ikiz, B and Njamnshi, AK and Landin-Romero, R and López, ME and Maito, MA and Medel, V and Sepúlveda, JPM and Ochoa Gómez, JF and Ogbuagu, C and de Oliveira, MO and Ozansoy, M and Palma-Espinosa, J and Hilal, S and Zhou, JH and Escudero, SDP and Pitman, JK and Prado, P and Ramírez González, D and Reyes, P and Santamaría García, H and Schröder, J and Sitt, JD and Soliman, RK and Soto-Añari, M and Thanissery, N and Ito, LT and Tsuchida, A and Tzourio, C and Yırıkoğulları, H and Yokoyama, JS and Aguillon, D and Miller, B and Alladi, S and Jiang, Y and Navarro, A and Babiloni, C and Huepe Artigas, D and Piguet, O and Sosa, PAV and Mostert, CM and Tahmasian, M and Li, P and Hu, K and Genon, S and Stein, DJ and Maestú, F and Pievani, M and Salama, M and Brodaty, H and Sachdev, PS and Lawlor, B and Eyre, HA and Miranda, JJ and Baez, S and Tagliazucchi, E and Duran-Aniotz, C and Hernandez, H and Ibanez, A},
title = {The exposome of brain aging across 34 countries.},
journal = {Nature medicine},
volume = {32},
number = {5},
pages = {1838-1851},
pmid = {41933172},
issn = {1546-170X},
support = {R01 AG057234/AG/NIA NIH HHS/United States ; S10OD032285, R01AG080473, RF1AG087965 and RF1AG088003//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AG051125, U01AG064948//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
mesh = {Humans ; *Brain/pathology/physiology ; *Aging/pathology/physiology ; Male ; Female ; Aged ; *Exposome ; Middle Aged ; Cognitive Dysfunction/pathology ; Alzheimer Disease/pathology/epidemiology/physiopathology ; Aged, 80 and over ; Cross-Sectional Studies ; },
abstract = {The physical and social exposome affects human aging, and brain clocks may track its effects. However, most studies neglect multidomain exposures (physical, social and political) across diverse settings globally and their associations with brain aging. In this study, we characterized the associations between 73 country-level physical and social exposomal factors and multimodal brain age in 18,701 participants from 34 countries (healthy individuals and those with Alzheimer's disease, frontotemporal lobar degeneration or mild cognitive impairment). Exposome effects were assessed using generalized additive models and meta-analytic frameworks. Aggregated exposome models explained up to 15.5-fold more variance than individual exposures (delta Akaike information criterion (ΔAIC): 2,034-3,127). Physical exposome was primarily associated with accelerated structural brain aging (limbic, subcortical and cerebellar regions), whereas social exposome was more strongly associated with functional brain aging (frontotemporal and limbic networks). Exposome burden accounted for 3.3-9.1-fold higher risk of accelerated aging, exceeding effects of clinical diagnoses. Findings were out-of-sample validated in cross-sectional and longitudinal designs, remained consistent across clinical subgroups and persisted after adjustment for demographics, age correction bias, cognition, scanner type and data quality. The exposome accelerates brain aging in health and disease, underscoring the need to address physical, social and political inequities.},
}
@article {pmid41934536,
year = {2026},
author = {O'Leary, BC and Fonseca, C and Casal, G and Cornet, CC and Córdova, FE and Furlan, E and Hawkins, JP and de Juan, S and Krause, T and Pérez, G and Simide, R and Trégarot, E and Roberts, CM},
title = {Eight recommendations for advancing blue Nature-based Solutions.},
journal = {Ambio},
volume = {},
number = {},
pages = {},
pmid = {41934536},
issn = {1654-7209},
support = {869710//Horizon 2020/ ; },
abstract = {Crises narratives surrounding the societal challenges of biodiversity loss, climate change, and human health and well-being dominate current debates in global environmental politics. These challenges are deeply interconnected and require transformative and integrated change. Marine and coastal Nature-based Solutions (blue NbS) are an opportunity to minimise harmful human impacts on these ecosystems while providing co-benefits to people and nature. However, uptake of the approach is currently slow despite the urgency of addressing global challenges. For blue NbS to become a key tool for environmental management, integrated social-ecological advice on action for practitioners is required, alongside guidance for new research. Here, we present eight recommendations to help advance further research, development, and implementation of effective blue NbS. Recommendations are broadly grouped into three themes: (1) objectives, (2) function, and (3) mechanisms. Through these, we aim to encourage dialogue into strategic blue NbS implementation and research that supports solution-focussed narratives.},
}
@article {pmid41939925,
year = {2026},
author = {Tong, H and Tian, Z and Zhang, N and Liu, X and Zhu, H and Jing, L and Wang, L},
title = {Construction and Validation of a Prediction Model for Sustained Smoking Cessation in Patients with Chronic Obstructive Pulmonary Disease.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {21},
number = {},
pages = {554995},
pmid = {41939925},
issn = {1178-2005},
mesh = {Humans ; *Smoking Cessation/psychology ; *Pulmonary Disease, Chronic Obstructive/diagnosis/physiopathology/psychology/therapy/epidemiology ; Male ; Female ; Middle Aged ; Aged ; Risk Factors ; *Smoking/adverse effects/psychology/epidemiology ; Risk Assessment ; *Decision Support Techniques ; Reproducibility of Results ; Time Factors ; Predictive Value of Tests ; Recurrence ; *Nomograms ; China/epidemiology ; Treatment Outcome ; Surveys and Questionnaires ; Age Factors ; },
abstract = {OBJECTIVE: To identify factors associated with smoking relapse or non-attempt within one year in COPD patients and to develop a predictive model for early identification of high-risk individuals to guide targeted interventions.<br><br>METHODS: Based on the health ecology model, a questionnaire integrating factors affecting smoking cessation was developed. We enrolled 221 COPD patients from a tertiary hospital in Tianjin and categorized them into smoking cessation success or failure groups. Mann-Whitney U-tests, &#x3c7;[2] -tests, and logistic regression were used to identify predictors. A nomogram prediction model was developed using significant factors. Model performance was evaluated via calibration plot, Hosmer-Lemeshow test, concordance index (C-index), decision curve analysis (DCA), and clinical impact curve (CIC).<br><br>RESULTS: Among 221 patients, 92 successfully quit smoking and 129 failed. Multivariate analysis identified age (OR = 0.922, P < 0.001), GOLD grade (OR = 0.257, P < 0.001), and death anxiety score (OR = 0.930, P = 0.001) as protective factors against cessation failure, while depression score (OR = 1.107, P < 0.001) and quit-smoking partner complaints score (OR = 1.075, P < 0.001) were risk factors. The prediction model demonstrated good discrimination (C-index = 0.876) and calibration (Hosmer-Lemeshow test P = 0.350). DCA and CIC confirmed the model's clinical utility.<br><br>CONCLUSION: Younger age, mild/moderate GOLD grade, higher depression score, lower death anxiety, and higher partner complaints increase the risk of smoking cessation failure in COPD patients. The developed model facilitates early identification of high-risk patients for targeted intervention to improve quit rates.},
}
@article {pmid41940893,
year = {2026},
author = {Liao, Y and Wang, B and Li, Y and Ni, W and Li, X and Hu, S},
title = {Establishment of the chromid database and analysis of evolutionary research.},
journal = {Molecular genetics and genomics : MGG},
volume = {301},
number = {1},
pages = {},
pmid = {41940893},
issn = {1617-4623},
mesh = {*Evolution, Molecular ; Phylogeny ; *Genome, Bacterial/genetics ; *Databases, Genetic ; *Bacteria/genetics/classification ; Polymorphism, Single Nucleotide ; Metagenomics/methods ; Computational Biology/methods ; },
abstract = {In bacterial multireplicon genomes, in addition to the main chromosome, there is a widespread class of secondary replicons with a distinct evolutionary status known as chromids. These elements possess plasmid-like replication and partitioning systems, while their nucleotide composition and gene functions are highly similar to those of the main chromosome. Therefore, chromids are considered to play important roles in the evolution of bacterial genome architecture and in environmental adaptation. With advances in long-read sequencing technologies and breakthroughs in bioinformatics methods, metagenomic data resources have been greatly expanded. Using our previously developed automated tool, "Chromid-Finder", we systematically identified and collected chromid sequences from large-scale metagenomic assemblies. These data were then uniformly curated, classified, and centrally managed to construct a public database platform dedicated to chromids-Chromid Database. On this basis, we conducted comprehensive analyses of the evolutionary and genetic characteristics of chromids. Phylogenetic analyses revealed the overall evolutionary landscape of chromids. Variation analyses showed that SNP distributions on chromids exhibit clear and well-organized patterns, depicting a dynamic population that is continuously adapting to the environment through fine-scale sequence tuning and non-coding regulatory mechanisms. Structural variation analyses further identified several hotspot regions significantly enriched in key genes related to metabolic functions, nutrient acquisition, and antibiotic resistance. The distribution patterns of recombination events suggest that their occurrence is likely driven primarily by non-phylogenetic factors such as environmental conditions and ecological niches. In addition, systematic quantification of heritable mobile genetic elements indicated that the number of integrative and conjugative elements (ICEs) largely determines the overall mobile element burden within chromids.},
}
@article {pmid41941010,
year = {2026},
author = {Tan, M and Li, X and Nian, R and Song, X and Dong, J and Qu, J and Hao, M},
title = {Spatial distribution, contamination characteristics and health hazard potential of soil potentially toxic elements under different reclamation modes in coal mining subsidence areas.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {5},
pages = {},
pmid = {41941010},
issn = {1573-2959},
support = {2025JCXKSK11//the Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Soil Pollutants/analysis ; *Coal Mining ; *Environmental Monitoring ; China ; Soil/chemistry ; Metals, Heavy/analysis ; Risk Assessment ; Humans ; Environmental Pollution/statistics &amp; numerical data ; },
abstract = {Potentially toxic elements (PTEs) pollution of reclamation soils is becoming an important issue in coal mining subsidence areas due to its impacts on environment and human health. To investigate the spatial and temporal distribution, pollution characteristics, bioaccumulation, ecological and health risk of the soils under different reclamation modes in coal mining subsidence areas, 126 soil samples and 42 crop samples were collected and analyzed from coal gangue filling areas (CG), lake sediment filling areas (LS) and land leveling areas (LL). While the results showed that PTEs concentrations were lower than the soil environment quality risk control standard-indicating a low risk of soil pollution for this agricultural land-the levels of heavy metals in the three reclamation areas all exceeded, to varying degrees, the background values for Jiangsu Province. This exceedance of the background levels still poses an ecological risk. The distributions in the soil profile of PTEs had no obvious regularity and the PTEs concentrations also fluctuated irregularly with the extension of the reclamation time. The Cd and Hg were in "moderate pollution" while other analyzed metals were in "no pollution to medium pollution" based on the mean values of Igeo. Soil PTEs pollution status followed the sequence of CG (PLI = 1.85) > LS (PLI = 1.55) > LL (PLI = 0.97). Meanwhile, the results of the RI revealed that the CG, LS, and LL area were ecologically in "considerable risk" (RI: 535.97 to 314.57), "moderate risk" (RI: 218.90 to 51.71), and "low risk" (RI: 126.33 to 59.11). In addition, crops had a strong enrichment capacity for Cd, and Hg in the CG, LS, and LL areas. Health risk assessment showed that the non-carcinogenic health risks were not expected for adults while the children were prone to non-carcinogenic health risks. The new exploration can provide some insight into the contamination characteristics, ecological and human health risk of soil PTEs under different reclamation modes, which is useful for soil pollution prevention and reclamation planning.},
}
@article {pmid41942569,
year = {2026},
author = {Connolly, JA and Del Carratore, F and Schmidt, K and Bisesi, AT and Martinson, JNV and Chua, J and Kuhs, M and Boneza, MM and Heinsch, SC and Kinkel, LL and Smanski, MJ and Harcombe, WR and Breitling, R and Takano, E},
title = {Multi-omics analysis of interspecies interactions in a soil Streptomyces community provides functional insights into siderophore ecology.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41942569},
issn = {2045-2322},
support = {NE/T010959/1//UK Research and Innovation/ ; 1935458//National Science Foundation/ ; },
mesh = {*Streptomyces/metabolism/genetics ; *Siderophores/metabolism ; *Soil Microbiology ; Metabolomics/methods ; Iron/metabolism ; *Microbiota ; Deferoxamine/metabolism ; Transcriptome ; Multigene Family ; Multiomics ; },
abstract = {Streptomyces are key contributors to soil microbiome function, known for their biosynthetic diversity. While advances in -omics technologies have improved our understanding of microbiome composition and metabolic potential, the mechanisms underpinning interspecies interactions remain poorly resolved. Here, we investigate the molecular basis of interactions among four sympatric Streptomyces soil microbiome isolates, focusing on phenotypic, metabolomic and transcriptomic responses. Co-culture experiments revealed that one isolate, strain A, exhibited pronounced phenotypic changes when grown alongside each of the other three strains. Untargeted metabolomics and RNA-seq analyses showed that strain A undergoes distinct metabolic and transcriptional shifts depending on its partner, with the strongest response elicited by strain C. Despite all four strains possessing a conserved desferrioxamine biosynthetic gene cluster, only strain C constitutively produced desferrioxamine B (DFO-B), a hydroxamate siderophore, indicating a role for iron bioavailability in the interaction. Supplementation with DFO-B or iron mimicked the growth stimulation of strain A observed in co-culture with strain C, and CRISPR base editing of desD in strain C abolished both DFO production and the phenotypic induction of strain A. However, transcriptomic profiles of strain A varied significantly depending on the partner strain, with distinct sets of biosynthetic gene clusters and metabolic pathways activated in response to strains B and C, suggesting additional cues beyond DFO-B. In contrast, strain D did not elicit growth stimulation in its partners, and itself showed downregulation of amino acid and carbon metabolism when co-cultured with strain C. These findings indicate that Streptomyces interactions are not only mediated by siderophore piracy but also involve complex, strain-specific molecular responses. Our findings demonstrate that Streptomyces interactions are highly strain-specific and only partly mediated by siderophore piracy, with DFO-B acting as a potent interspecies cue. The divergent molecular responses to different partners suggest nuanced mechanisms of microbial sensing and competition. These insights advance our understanding of microbial crosstalk and highlight the ecological and evolutionary complexity of siderophore-mediated interactions. By integrating transcriptomics, metabolomics, and biochemical assays, we present a robust framework for dissecting microbial interactions, with implications for microbiome engineering and synthetic community design.},
}
@article {pmid41942613,
year = {2026},
author = {Du, Q and Guo, G and Li, H and Sun, J and Hu, Z},
title = {Overlying strata movement characteristics and water conducting fracture zone height prediction for deep coal mining in arid Western China.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41942613},
issn = {2045-2322},
support = {2025QN1104//Fundamental Research Funds for the Central Universities/ ; 2025M771776//China Postdoctoral Science Foundation/ ; 51974292//National Natural Science Foundation of China/ ; },
abstract = {The deep mining of coal seams in the central Ordos Basin, a critical arid region of western China, is governed by the unique mechanical behavior of ultra-thick, weakly cemented sandstones of the Cretaceous Zhidan Group, which challenge classical overburden control theories. To elucidate the deformation mechanisms of this special overburden and assess its implications for groundwater protection, this study integrates physical similarity simulation, laboratory rock-mechanical testing, microstructural analysis, and distinct-element numerical modeling (UDEC). A 1:500 similarity model simulated the stratigraphic sequence and mining progression. Results reveal that during single-panel extraction, the main roof initiates deformation at a 150 m face advance, with subsidence reaching 5.55 m at a 300 m mining width. Under multi-panel continuous mining, the high-position weakly cemented sandstones exhibit large-scale coordinated bending and plastic flow, forming a distinctive “subsidence–rotation” deformation pattern that propagates upward. Triaxial tests confirm the rock’s low strength and high confining-pressure sensitivity, with peak strength ranging from 27.8 to 71.1 MPa, cohesion of 6.7 MPa, and an internal friction angle of 38.7°. Failure modes transition from tensile splitting at low confinement to shear and plastic flow at higher pressures. Microstructural analyses (SEM/EDS) identify well-rounded quartz grains, extensive intergranular pores, and weak calcite–feldspar cements, explaining the observed high deformability and low bearing capacity. UDEC simulations of multi-panel mining captured progressive horizontal separation, stress redistribution, and composite tensile–shear failure. The water-conducting fracture zone (WCFZ) is shown to develop upward to the base of the Jurassic Anding Formation, with a maximum height of 186 m when the width-to-depth ratio exceeds 1.5. These findings characterize the deformation features of weakly cemented overburden and establish a mechanical basis for predicting the WCFZ, providing critical insights for overburden management and groundwater resource protection in deep coal mining under arid conditions.},
}
@article {pmid41943093,
year = {2026},
author = {Adeogun, AO and Adetunji, O and Babalola, AS and Izekor, RT and Oyeniyi, TA and Adesoye, O and Wahedi, J and Busari, LO and Aniekeme, G and Ajayi, S and Chabi, J and Awolola, ST},
title = {Spatial eco-climatic gradients drive adaptive 2La chromosomal inversion polymorphism in Anopheles coluzzii, a major malaria vector in Nigeria.},
journal = {International journal of health geographics},
volume = {25},
number = {1},
pages = {},
pmid = {41943093},
issn = {1476-072X},
mesh = {Animals ; *Anopheles/genetics ; *Chromosome Inversion/genetics ; Nigeria/epidemiology ; *Malaria/epidemiology/genetics/transmission ; *Mosquito Vectors/genetics ; *Polymorphism, Genetic/genetics ; *Climate ; Ecosystem ; },
abstract = {BACKGROUND: Chromosomal inversions are important genetic mechanisms that facilitate local adaptation, ecological flexibility, and behavioural variation in mosquito populations. In Anopheles coluzzii, a dominant malaria vector in West Africa, the 2La inversion has been associated with desiccation tolerance, thermal resistance, and insecticide resistance. Despite Nigeria's ecological diversity and substantial malaria burden, the spatial distribution and clinal dynamics of 2La inversion polymorphism in An. coluzzii remain poorly characterized. This study investigated the distribution of 2La inversion karyotypes across major Nigerian ecozones and examined their association with climatic gradients.<br><br>METHODS: Larvae of Anopheles mosquitoes were sampled across 12 states representing Nigeria's southern, central, and northern ecological zones. Species identification was conducted morphologically and confirmed with PCR diagnostics. The 2La inversion was determined using established molecular assays, and allele frequencies were analyzed with respect to ecozone and climatic gradients. Spatial distribution maps and statistical analyses, including correlation and clinal trend assessment, were done in R version 4.4.<br><br>RESULTS: A clear geographic structuring of 2La inversion polymorphism was observed in An. coluzzii populations. The 2La/2La homokaryotype was strongly predominant in the northern Sahelian and Sudan savanna ecozones, reflecting adaptation to hot and arid conditions. In contrast, the standard 2La+/2La+ arrangement was predominant in humid southern forest and mangrove regions. The heterokaryotype (2La/2La+) occurred at intermediate frequencies within the central transitional belt, where ecological gradients overlap. Karyotype frequencies exhibited a pronounced latitudinal cline, with heterozygosity peaking in central Nigeria. The spatial patterns indicate that climatic pressures, particularly aridity and humidity, might be a major determinant of inversion distribution in An. coluzzii from Nigeria.<br><br>CONCLUSION: This study provides the first detailed nationwide characterization of 2La inversion polymorphism in An. coluzzii across Nigeria's ecological zones. The strong alignment between inversion frequency and eco-climatic gradients highlights the role of chromosomal rearrangements in promoting vector survival and ecological fitness. These adaptive patterns have significant implications for malaria control, as inversion-mediated adaptability may influence resting behaviour, insecticide response, and vector persistence under climate change. Integrating chromosomal inversion surveillance into entomological monitoring frameworks will be essential for designing ecologically tailored vector control strategies in Nigeria.},
}
@article {pmid41946726,
year = {2026},
author = {Funosas, D and Massol, E and Bas, Y and Schmidt, S and Bennett, D and Arend, D and Gebhard, A and Barbaro, L and König, S and Font, RC and Sannier, D and Deroussen, F and Sueur, J and Trilar, T and Forstmeier, W and Roger, L and Matheu, E and Guzik, P and Barataud, J and Pelozuelo, L and Puissant, S and Mueller, S and Schuller, B and Montoya, JM and Triantafyllopoulos, A and Cauchoix, M},
title = {A finely annotated dataset for the automated acoustic identification of European Orthoptera and Cicadidae.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07150-1},
pmid = {41946726},
issn = {2052-4463},
support = {ANR-23-CPJ1-0174-01//Association Nationale de la Recherche et de la Technologie (National Association for Research and Technology)/ ; ANR-21-CE03-0002//Association Nationale de la Recherche et de la Technologie (National Association for Research and Technology)/ ; ANR-21-ESRE-0014//Association Nationale de la Recherche et de la Technologie (National Association for Research and Technology)/ ; ANR-23-CPJ1-0174-01//Association Nationale de la Recherche et de la Technologie (National Association for Research and Technology)/ ; P1-0255//The Slovenian Research and Innovation Agency (ARIS)/ ; },
abstract = {Mounting evidence points to widespread declines in insect abundance and diversity across European terrestrial ecosystems, highlighting an urgent need for effective large-scale monitoring methods. Passive acoustic monitoring enables the monitoring of sound-producing insects at an unprecedented temporal and spatial scale by remotely capturing sounds such as orthopteran stridulations and cicada timbalizations. However, current automated recognition tools for European insect sounds remain limited, and developing algorithms capable of reliably identifying diverse species requires large, ecologically heterogeneous acoustic datasets. Here we present a dataset of 11,224 recordings covering 193 orthopteran and 24 cicada species from North, Central, and temperate Western Europe. It combines coarsely labeled recordings, for which we can only infer the presence, at some point, of their target species (weak labeling), with finely annotated recordings that specify the time and frequency range of each insect sound (strong labeling). This dataset complements existing online resources and supports the advancement of automated acoustic classification for orthopterans and cicadas, aiding biodiversity monitoring efforts across Europe.},
}
@article {pmid41950154,
year = {2026},
author = {Araujo, TKA and Maranhão, TA and Frota, MMCD and Sousa, GJB and Rocha, MIF and Pereira, MLD and Ferreira, LFO and Lira Neto, JCG},
title = {Trend and prediction of congenital syphilis in Brazil in the 21st century: A time series study.},
journal = {Revista gaucha de enfermagem},
volume = {47},
number = {},
pages = {e20250112},
doi = {10.1590/1983-1447.2026.20250112.en},
pmid = {41950154},
issn = {1983-1447},
mesh = {Humans ; Brazil/epidemiology ; *Syphilis, Congenital/epidemiology ; Incidence ; Forecasting ; Infant, Newborn ; Female ; Time Factors ; Pregnancy ; },
abstract = {OBJECTIVE: To investigate the temporal trend of congenital syphilis in Brazil in the 21st century and to estimate its behavior from 2023 to 2030.<br><br>METHOD: Ecological time series study using secondary data extracted from the Informatics Department of the Unified Health System (DATASUS) from 2001 to 2022. The temporal evolution of congenital syphilis was analyzed using crude incidence calculation and the standardized mean incidence rate. Statistical techniques such as Joinpoint and Autoregressive Integrated Moving Average were used for time-series analysis and case projections.<br><br>RESULTS: Over the 22-year period, 302,759 cases of congenital syphilis were reported in Brazil, 51.1% of which occurred between 2017 and 2022. The incidence rate rose from 1.3 in 2001 to 10.3 cases per 1,000 live births in 2022. The temporal analysis showed that four of the five regions showed an increasing trend during the study period. By 2030, projections indicate growth in rates in Brazil (8.3%) and in the following regions: South (11.2%), Southeast (10.5%), North (9.2%), Central-West (8.0%), and Northeast (6.8%).<br><br>CONCLUSION: An increase in incidence rates was observed in Brazil and its regions. The temporal analysis showed an upward trend, and projections through 2030 show an increase in cases.},
}
@article {pmid41952219,
year = {2026},
author = {Gedeon, CI and Váczi, O and Knauer, F and Árvai, M and Suchentrunk, F},
title = {What drives population fluctuations of European ground squirrels in Hungary?.},
journal = {Frontiers in zoology},
volume = {23},
number = {1},
pages = {},
pmid = {41952219},
issn = {1742-9994},
support = {LIFE24-NAT-HU-CitellusLIFE-101202727//European Commission/ ; },
abstract = {BACKGROUND: Understanding and predicting the dynamics of rodent populations, particularly for endangered or pest species, requires knowledge of potential background factors. We collected long-term data on the abundance of European ground squirrels, Spermophilus citellus, in 64 colonies as part of the Hungarian Biodiversity Monitoring System to investigate the abiotic factors that could explain the spatial and temporal dynamics of populations in Hungary. We used information theory-based modelling and multi-model inference to investigate the effects of environmental and climate variables on relative population densities, using monitoring records of burrow counts as proxies for density collected annually between 2000 and 2018. We examined data carefully for any clues of inconsistencies, errors, or missing data, which resulted in 57% of the complete dataset.<br><br>RESULTS: Our generalised additive models (GAM) with splines identified geographical location, year, and principal components reflecting winter temperature, precipitation, and summer temperature to affect population densities. Contour plots derived from the best GAM model uncovered increasing density in the Kiskuns&#xe1;g and Kisalf&#xf6;ld meso-regions with favourable water management characteristics and decreasing densities in the northern and southern regions, which in fact, cover floodplain of River Tisza and other flash-flood regions. Ambient temperature and precipitation of the wettest and warmest months during hibernation and summer contributed most to counts fluctuations, though these factors were dwarfed by spatial effects. Increased temperatures and aridification in the Kiskuns&#xe1;g, because of the warming Pannonian ecoregion, seemed to positively affect counts.<br><br>CONCLUSIONS: Analysis of our reduced dataset indicated unidentified local factors or a spatial effect on demographic variability of ground squirrel populations. Those fluctuations underscore the necessity of research and management on local populations to identify the reasons of declines and adapt management accordingly to stop or change decreasing population trajectories.},
}
@article {pmid41955025,
year = {2026},
author = {Li, J and Chen, S and Wu, Z and Wang, H and Xia, R and Meng, J and Zhang, Y},
title = {Response to "Addressing biases and limitations in feature attribution for circRNA modification profiling".},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
pmid = {41955025},
issn = {1477-4054},
mesh = {*RNA, Circular/genetics/metabolism ; Humans ; *Computational Biology/methods ; },
abstract = {This response addresses the comments raised by Souichi Oka and colleagues in their Letter to the Editor titled "Addressing biases and limitations in feature attribution for circRNA modification profiling." We clarify that two independent XGBoost models were used for distinct purposes in our analysis: one for predicting RNA modification events from nanopore-derived signal features and another for feature attribution using genome-derived sequence features extracted through the m6AlogisticModel framework. We further note that Shapley Additive Explanations (SHAP) was employed as an exploratory interpretability tool rather than as definitive evidence of causal biological mechanisms. We appreciate the constructive methodological suggestions provided and acknowledge that integrating complementary analytical strategies may further enhance the robustness of computational studies of circRNA modifications.},
}
@article {pmid41955211,
year = {2026},
author = {Palma, FAG and Ruiz Cuenca, P and Khalil, H and Brito, PL and Reis das Virgens, MN and Arouca, MG and Mota Santos, A and Santos de Oliveira, D and Alzete Lòpez, YA and Santiago, DCC and Begon, M and Giorgi, E and Costa, F and Lustosa, R},
title = {Collaborative mapping: Perceived environmental risk of leptospirosis in Urban communities in Salvador, Brazil.},
journal = {PLOS global public health},
volume = {6},
number = {4},
pages = {e0006113},
pmid = {41955211},
issn = {2767-3375},
abstract = {Environmental risks disproportionately affect socially vulnerable populations, yet most studies on urban leptospirosis have not captured residents' perceptions of these risks. We conducted a cross-sectional study between August 2018 and March 2019 across four communities in Salvador, Brazil (Marechal Rondon, Alto do Cabrito, Nova Constituinte, and Rio Sena) using a collaborative mapping approach to explore residents' perceptions of environmental health risks. The majority of participants identified sewage as the primary health risk (26-39% across communities), followed by garbage (22-28%), while leptospirosis itself was perceived as a high-risk problem by very few participants (0-4%). We found no spatial concordance between areas perceived as high risk for leptospirosis and households testing positive for the disease, nor between areas perceived as high rat risk and the locations of positive rat traps and track plates. However, a higher density of rubbish piles was observed in areas residents identified as high rubbish risk, suggesting that perceptions do reflect some on-the-ground realities. Collaborative mapping proved an effective method for capturing individual perceptions of environmental health risks and promoting community participation in generating locally relevant information. The disconnect between perceived and actual transmission risk may reflect that residents are more attuned to the broader social and environmental determinants of leptospirosis, such as sanitation and waste, than to the disease itself, a distinction that warrants further investigation to better integrate community knowledge into disease prevention and control strategies.},
}
@article {pmid41956682,
year = {2026},
author = {Cao, R and Yan, X and Ma, Y and Li, A and Du, H and Zhou, Q and Xu, Y},
title = {Coupling ensemble learning with multi-omics: a novel data-driven strategy for Daqu quality assessment and validation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 2},
pages = {119028},
doi = {10.1016/j.foodres.2026.119028},
pmid = {41956682},
issn = {1873-7145},
mesh = {Fermentation ; *Fermented Foods/microbiology/analysis ; *Machine Learning ; *Food Microbiology ; Quality Control ; Taste ; Food Quality ; Odorants/analysis ; Ensemble Learning ; Multiomics ; },
abstract = {Daqu, a fermentation starter for traditional fermented foods, is produced by complex microbial communities; it is generally evaluated using conventional methods based on subjective sensory perception and limited physicochemical indicators. These approaches have several limitations, including poor consistency and low repeatability, making it challenging to meet industrial demands for a transition from "experience-driven" to "science-driven" quality control. In this study, medium-high temperature Daqu for strong-aroma-type Baijiu was selected as the research object, and we aimed to establish a quality evaluation model for it by the integration of multidimensional fermentation data. Additionally, multi-omics analysis was combined to validate key functional microorganisms, thereby revealing their mechanisms of action. The results indicate that the fermentation functions of Daqu are predominantly driven by eukaryotic microorganisms characterized by "low abundance and high expression." Rhizomucor and Saccharomycopsis were identified as core contributors to hydrolases. An ensemble learning model (temperature-based Gradient Boosting + physicochemical XGBoost + flavor-based Linear Regression) was established to achieve rapid quality grading of Daqu. Daqu quality was substantially improved by targeted inoculation with core functional fungi, thereby verifying the effectiveness of the model. Accordingly, in this study, a systematic research paradigm of "multi-omics analysis → machine learning modeling → microbial targeted validation" was established, allowing the transformation of experience-dependent "ecological art" into interpretable, quantifiable, and predictable "synthetic ecological engineering." The study findings are expected to provide a generalizable methodology for addressing quality evaluation issues in traditional fermented foods.},
}
@article {pmid41957200,
year = {2026},
author = {Spiliotis, K and Russo, L and Siettos, C and Giannino, F},
title = {Numerical bifurcation analysis of turing and symmetry broken patterns of a PDE model for vegetation dynamics.},
journal = {Journal of mathematical biology},
volume = {92},
number = {5},
pages = {},
pmid = {41957200},
issn = {1432-1416},
mesh = {*Models, Biological ; Mathematical Concepts ; Biomass ; *Ecosystem ; *Plant Development ; Water/metabolism ; Computer Simulation ; },
abstract = {We study the mechanisms of pattern formation for vegetation dynamics in water-limited regions. Our analysis is based on a set of two partial differential equations (PDEs) of reaction-diffusion type for the biomass and water, and one ordinary differential equation (ODE) describing the dependence of the toxicity on the biomass. We perform a linear stability analysis in the one-dimensional finite space, we derive analytically the conditions for the appearance of Turing instability that gives rise to spatio-temporal patterns emanating from the homogeneous solution, and provide its dependence with respect to the size of the domain. Furthermore, we perform a numerical bifurcation analysis in order to study the pattern formation of the inhomogeneous solution, with respect to the precipitation rate, thus analyzing the stability and symmetry properties of the emanating patterns. Based on the numerical bifurcation analysis, we have found new patterns, which form due to the onset of secondary bifurcations from the primary Turing instability, thus giving rise to a multistability of asymmetric solutions.},
}
@article {pmid41959695,
year = {2026},
author = {Celeste, J and Sevilleja, JE and Bongolan, VP and Rivera, RL and Caoili, SE and de Castro, R},
title = {COVID-19 mortality in the Philippines: province-level ecological analysis, 2020-2023.},
journal = {Western Pacific surveillance and response journal : WPSAR},
volume = {17},
number = {1},
pages = {1-12},
pmid = {41959695},
issn = {2094-7313},
mesh = {Humans ; Philippines/epidemiology ; *COVID-19/mortality ; Aged ; SARS-CoV-2 ; Middle Aged ; Incidence ; Male ; Adult ; Female ; },
abstract = {OBJECTIVE: To investigate COVID-19 mortality in Philippine provinces from 2020 to 2023.<br><br>METHODS: Crude mortality rate (CMR), age-standardized mortality rate (ASMR) and age-specific mortality rate were computed for 84 areas (82 provinces and 2 cities) using COVID-19 surveillance data from the Philippine Department of Health, which captured data about confirmed deaths occurring between 20 January 2020 and 9 May 2023. Provinces were ranked by their ASMR. A correlation analysis was conducted to identify possible predictors of COVID-19 mortality. Among the factors investigated were the incidence of poverty, population density, proportion of the population considered elderly (aged &#x2265;&#xa0;65 years), hospital bed density and COVID-19 testing rates.<br><br>RESULTS: Eight of the 10 provinces that had the highest COVID-19 ASMRs were located in the Luzon island group. The province with the highest ASMR was Benguet in Northern Luzon (207.83 deaths/100&#xa0;000 population), and the lowest rate was in Tawi-Tawi in Southwestern Mindanao (2.22 deaths/100&#xa0;000 population). The incidence of poverty was negatively correlated with COVID-19 mortality, while hospital bed density and COVID-19 testing rates were positively correlated with CMRs and ASMRs.<br><br>DISCUSSION: This analysis provides a starting point for investigating COVID-19 mortality in Philippine provinces. The ranking of provinces by their ASMR is useful for directing future epidemiological investigations and, coupled with the results of the correlation analysis, provides insight into the factors that may have impacted COVID-19 mortality in the Philippines. Our analysis suggests that COVID-19 mortality patterns can partly be explained by the streetlight effect and factors linked to the availability of and access to health care.},
}
@article {pmid41959754,
year = {2026},
author = {Nande, A and Levy, MZ and Hill, AL},
title = {Understanding patterns of variant emergence and spread in an ongoing epidemic.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {41959754},
abstract = {The COVID-19 pandemic saw successive emergence and global spread of novel viral variants, exhibiting enhanced transmissibility or evasion of immunity. While the genotypic and phenotypic basis of SARS-CoV-2 variants have been extensively characterized, the evolutionary factors governing their patterns of emergence are less well understood. In this study we systematically investigated how the invasion dynamics of viral variants depend on variant phenotype (increased transmissibility or immune evasion), source (local evolution vs importation), the timing of introduction, the distribution of population susceptibility, and the contact network structure. Using a stochastic multi-strain epidemic model, we find that strains with only a transmission advantage are more likely to emerge earlier in the epidemic, and rapidly and predictably dominate the viral population. In contrast, immune-escape variants tend to linger at low prevalence for extended time periods after emergence, avoiding detection, until a critical amount of immunity has built up in the population and they begin to rapidly outcompete existing strains. We find that two common features of realistic human contact networks-heterogeneity in contacts (overdispersion) and clustering-lead to more punctuated evolutionary dynamics. This work provides insight into past dynamics of SARS-CoV-2 variants and can help define planning scenarios for future epidemic modeling efforts.},
}
@article {pmid41964702,
year = {2026},
author = {Bouzada, N and Ababou, A and Senouci, F and Chenaoui, A and Bouthiba, A},
title = {Influence of water quality on the composition and distribution of riparian vegetation in the Cheliff River, Algeria.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {5},
pages = {},
pmid = {41964702},
issn = {1573-2959},
mesh = {Algeria ; *Rivers/chemistry ; *Environmental Monitoring ; *Water Quality ; *Plants/classification ; *Water Pollutants, Chemical/analysis ; Ecosystem ; },
abstract = {This ecological study was conducted along the Cheliff River in northwestern Algeria to evaluate how water quality shapes riparian plant communities. Floristic surveys and water quality analyses were performed at ten stations across the upstream and downstream sections. The hierarchical classification distinguished four main vegetation units: the Centaurium-Sonchus (CS) unit, associated with downstream sites affected by urban wastewater; the Plantago-Medicago-Lolium (PML) unit, linked to upstream agricultural runoff; the Solanum-Melissa-Bryonia (SMB) unit, reflecting industrial influence with high sulfates and nitrates; and the Aster-Atriplex-Nicotiana (AAN) unit, indicating alkaline conditions. Redundancy analysis (RDA) confirmed that these assemblages were strongly correlated with environmental gradients, explaining 60.6% of the species-environment variation. Key drivers included pH, conductivity, nitrates, orthophosphates, and iron, which successfully differentiated pollution gradients from urban, agricultural, and industrial sources. The dominance of nitrophilous and ruderal species in highly disturbed areas signals advanced ecological degradation, while several taxa demonstrated strong tolerance to pollutants, highlighting their bioindicator potential. These findings validate the use of macrophyte communities for monitoring water quality and provide a scientific basis for managing Mediterranean river ecosystems.},
}
@article {pmid41964929,
year = {2026},
author = {Arboleda-Baena, C and Corrêa, FB and Saraiva, JP and Castillo-Rivadeneira, S and Kasmanas, JC and Chatzinotas, A and Jurburg, SD},
title = {HVRLocator: a computationally efficient tool for identifying hypervariable regions in large 16S rRNA datasets.},
journal = {GigaScience},
volume = {15},
number = {},
pages = {},
pmid = {41964929},
issn = {2047-217X},
support = {//HMC/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Software ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; *DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Metabarcoding of the 16S rRNA gene is widely used to assess microbial diversity due to its cost-effectiveness and efficiency. However, publicly available 16S rRNA metabarcoding datasets often lack standardized metadata, particularly information on the sequenced hypervariable regions or primers used, which are critical to their accurate reuse. To address this, we present HVRLocator, a computational tool that (1) identifies the start and end positions of 16S rRNA amplicons, (2) determines their corresponding hypervariable regions, and (3) detects the presence of primer sequences. This tool was validated on four datasets comprising 41,513 samples generated with different primers and sequencing platforms.<br><br>RESULTS: HVRLocator can process archived 16S rRNA sequences from NCBI SRA at an average rate of 6.5 samples per minute. Validation showed it reliably detects amplicon start and end positions across datasets sequenced with different primers and platforms, achieving 100% accuracy within single-platform studies and correctly revealing length heterogeneity across platforms. It also flagged misannotated metadata and problematic sequences, underscoring its value as a sequence data curation tool. Finally, HVRLocator can select comparable sequences to build large 16S rRNA amplicon databases spanning the same hypervariable region, facilitating cross-study comparisons.<br><br>CONCLUSION: HVRLocator overcomes unreliable metadata by accurately identifying 16S rRNA amplicon start and end positions, determining hypervariable regions, and detecting primer sequences, enabling accurate curation and large-scale processing of 16S rRNA data for reliable and reproducible microbial studies, syntheses, and meta-analyses.},
}
@article {pmid41966053,
year = {2026},
author = {Hu, H and Qu, Z and Liu, Y and Zhu, L and Mei, Z and Chen, XL},
title = {AI-driven fungicide design: From target identification to field application.},
journal = {Plant communications},
volume = {7},
number = {5},
pages = {101850},
pmid = {41966053},
issn = {2590-3462},
mesh = {*Fungicides, Industrial/pharmacology/chemistry ; *Artificial Intelligence ; *Plant Diseases/microbiology/prevention &amp; control ; *Fungi/drug effects ; Drug Resistance, Fungal ; Crops, Agricultural/microbiology ; },
abstract = {Plant pathogenic fungi pose a severe threat to global agriculture, causing substantial yield losses in staple crops and jeopardizing food safety through mycotoxin contamination. Conventional fungicide development is hindered by high costs, lengthy timelines, and the rapid evolution of fungal resistance, which outpaces conventional discovery workflows. Although artificial intelligence (AI) offers transformative potential to address these bottlenecks, its application in plant pathology remains fragmented and lacks integration of agriculture-specific constraints such as field stability, ecological safety, and resistance management. This review introduces the AI-driven fungicide design (AIFD) platform, a comprehensive framework comprising four interdependent components: a plant pathogen-specific data ecosystem, a modular microservice technical architecture, a linear multiphase development workflow, and a specialized resistance prediction workflow. We synthesize key technological advances across the fungicide development pipeline, from target identification and virtual screening to molecular optimization and field validation, with an emphasis on AI methodologies adapted to agrochemical requirements rather than pharmaceutical standards. Despite substantial advances, critical challenges persist, including scarce high-quality training data for understudied pathogens, limited model adaptability across diverse agroecosystems, poor interpretability that hinders stakeholder trust, and accessibility barriers for resource-constrained researchers. Future directions emphasize the integration of real-time field data, explainable AI to facilitate regulatory acceptance, and inclusive design strategies aimed at bridging the laboratory-to-field gap. By aligning computational innovation with agricultural priorities, AIFD platforms can accelerate the discovery of resistance-breaking, environmentally benign fungicides, thus offering a viable pathway toward sustainable crop protection and enhanced global food security.},
}
@article {pmid41968734,
year = {2026},
author = {Sandin, MM and Walde, M and Henry, N and Forn, I and Simon, N and Berney, C and Massana, R and Richter, DJ},
title = {OligoN-Design: A Simple and Versatile Tool to Design Specific Probes and Primers From Large Heterogeneous Datasets.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70140},
pmid = {41968734},
issn = {1755-0998},
support = {2021BP00068//Generalitat de Catalunya/ ; 101103530//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 464344344//Deutsche Forschungsgemeinschaft/ ; 101082304//European Union under the Horizon Europe Programme/ ; PID2023-152955NA-I00/ERC_/European Research Council/International ; PID2022-137508NB-I00/ERC_/European Research Council/International ; 2021 SGR 00751//Departament de Recerca i Universitats de la Generalitat de Catalunya/ ; },
mesh = {*DNA Primers/genetics ; *Computational Biology/methods ; *Software ; High-Throughput Nucleotide Sequencing/methods ; *Oligonucleotide Probes/genetics ; },
abstract = {High-throughput environmental DNA sequencing has ushered ecological and evolutionary studies into the big data era. With thousands to millions of DNA sequences, designing taxon-specific oligonucleotides is a current bottleneck of molecular studies that rely on primers for Polymerase Chain Reactions (PCRs) or probes for Fluorescence in situ Hybridization (FISH). No software currently exists to design specific oligonucleotides starting from a custom set of sequences. Existing tools rely on specific databases, alignments or phylogenetic trees, or cannot accommodate increasingly large molecular environmental datasets. Here we present oligoN-design, a versatile tool to design oligonucleotides specific to a set of target sequences while minimizing predicted binding to non-target sequences. OligoN-design is simple, reproducible and adaptable to high-throughput sequencing data analyses. It requires only two fasta files as input, one containing target taxa and the other containing non-target taxa. Using standard bioinformatic formats, it integrates easily with other tools such as BLAST, VSEARCH or MAFFT. OligoN-design allows a range of strategies that we present in detail, from an unsupervised end-to-end usage all the way to a detailed and thorough expert usage. Starting with large, comprehensive ribosomal databases that are widely used by the community (i.e., PR2, SILVA) and the unsupervised function, we were able to replicate known taxa-specific oligonucleotides in under 30 min and up to 6 GB of RAM on a personal laptop. OligoN-design, available at github.com/MiguelMSandin/oligoN-design under GNU General Public Licence version 3.0, is easily installed via bioconda bioconda.github.io/recipes/oligon-design/README.html.},
}
@article {pmid41969650,
year = {2026},
author = {Zhu, H and Ma, P and Yuan, Y and Chen, Y and Shi, H and Huang, C and Zhou, Y and Jing, R and Cao, M and Zhang, D and Luo, Y},
title = {Integrated mechanistic and bioinformatics analysis of a traditional Chinese medicine compound MangHuang solution against Candida albicans.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1737769},
pmid = {41969650},
issn = {2235-2988},
mesh = {*Candida albicans/drug effects/genetics ; Biofilms/drug effects/growth &amp; development ; *Antifungal Agents/pharmacology ; Computational Biology/methods ; Staphylococcus aureus/drug effects ; *Drugs, Chinese Herbal/pharmacology/chemistry ; Microbial Sensitivity Tests ; Medicine, Chinese Traditional ; Escherichia coli/drug effects ; Anti-Bacterial Agents/pharmacology ; Tannins/pharmacology ; },
abstract = {INTRODUCTION: The growing prevalence of drug-resistant pathogens urgently calls for new treatment strategies. Traditional Chinese medicine (TCM) formulas, with their multi-targeted mechanisms of action, offer promising alternative options for antimicrobial therapy. This study aims to evaluate the antimicrobial activity of the TCM formula MangHuang solution (MH) after content detection of tannin, composed of Rhei Radix et Rhizoma, Natrii Sulfas, and Galla Chinensis, and to elucidate its antifungal mechanism against Candida albicans through integrated multi-omics analysis.<br><br>METHODS: MH and its individual or combined components were prepared and evaluated for their inhibitory effects on Staphylococcus aureus, Escherichia coli, and Candida albicans, and their antimicrobial activity was assessed. Transmission electron microscopy (TEM), biofilm formation experiments, and multi-omics analysis were used to investigate the antifungal mechanism of MH against C. albicans.<br><br>RESULTS: MH demonstrated potent and rapid antibacterial activity. Biofilm formation was significantly inhibited, manifested by reduced cell surface hydrophobicity, weakened initial adhesion capacity, and impaired biofilm maturation processes. Transcriptome and metabolome analyses revealed significant alterations in key metabolic pathways, particularly ABC transporters, amino acid biosynthesis, and protein-related pathways.<br><br>DISCUSSION: MH exhibits potent antifungal activity against C. albicans through a multi-target mechanism, primarily affecting biofilm formation and intracellular metabolic processes. The integration of multi-omics approaches provides strong evidence for the potential clinical application of MH as an effective antifungal agent.},
}
@article {pmid41972477,
year = {2026},
author = {Mammides, C and Gu, H and Nimalrathna, TS and Avicena, NR and Papadopoulos, H and Campos-Arceiz, A},
title = {Emerging applications of large language models in ecology and conservation science.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {},
number = {},
pages = {e70287},
doi = {10.1111/cobi.70287},
pmid = {41972477},
issn = {1523-1739},
support = {CAS-SEABRI: #Y4ZK111B05//Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences/ ; 202503AM140014//The Wisdom Yunnan Project/ ; E3ZKFF9B//4th Five-Year Plan of the Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences/ ; //High-End Foreign Experts Program of the Yunnan Revitalization Talents Support Plan/ ; H20250434//National Foreign Expert Project/ ; 202505AO120035//Yunnan Provincial Foreign Expert Project/ ; },
abstract = {Large language models (LLMs) mark a major development in artificial intelligence, with potentially transformative implications for ecology and conservation science. Built on advanced deep-learning architectures, these models can support a wide range of tasks. We reviewed emerging applications of LLMs, drawing on the wider scientific literature and practical use cases. We found that LLMs can streamline ecological workflows and accelerate evidence-based conservation by supporting the extraction of ecological information from unstructured sources, enabling natural-language interaction with structured databases and facilitating large-scale literature syntheses. They can also be used to leverage publicly available data for ecological insights, for example, through automated monitoring of news reports. They can enhance biodiversity monitoring through integration with edge devices, such as camera traps, and can assist with analytical tasks, such as code generation, and improve scientific communication and support outreach, for example, through custom models trained on domain-specific information. Other potential applications include policy analysis and decision support, such as simulating interactions among stakeholders with multiagent systems. However, the rapid adoption of LLMs also raises technical and ethical challenges, including inaccurate or biased outputs caused by hallucinations and imbalances in training data. Such limitations can also contribute to poor out-of-distribution performance and the underrepresentation of minority viewpoints. Additional concerns include limited transparency and reproducibility due to their black-box nature, high technical complexity, and computational demands, which may exacerbate access inequalities, the risk of deskilling, and environmental impacts. To mitigate these challenges, we recommend a set of best practices, including careful model selection, effective prompt engineering, retrieval-augmented generation to improve factual accuracy and representation, human-in-the-loop validation, and broader efforts to promote inclusive development, capacity building, and appropriate governance. When applied thoughtfully, LLMs can serve as a valuable addition to the ecologists' toolkit, enhancing scientific capacity and supporting efforts toward achieving global biodiversity goals.},
}
@article {pmid41973532,
year = {2026},
author = {Devasahayam, BRF and Poeschl, Y and Uthe, H and Rennert, R and Hartmann, L and Deising, HB},
title = {Confrontations between Aspergillus nidulans and microbial biocontrol agents cause differential regulation of secondary metabolism and synthesis of chemicals toxic to human kidney and colon cells.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {5},
pages = {e0218025},
pmid = {41973532},
issn = {1098-5336},
support = {//German Centre for Integrative Biodiversity Research (iDiv)/ ; },
mesh = {*Aspergillus nidulans/metabolism/genetics/physiology ; Humans ; *Secondary Metabolism ; *Biological Control Agents/metabolism/pharmacology ; HEK293 Cells ; HCT116 Cells ; *Microbial Interactions ; },
abstract = {Microbial interactions in agricultural ecosystems are chemically dynamic, with significant implications for ecological balance and crop protection. As synthetic fungicides face increasing regulatory and resistance challenges, applying microbial biological control agents (MBCAs) presents a potential alternative crop-protection strategy. However, the chemical and toxicological consequences of such applications remain poorly understood. Using the model ascomycete Aspergillus nidulans, the response to confrontations with twelve microbial partners, including bacterial and fungal MBCAs, plant pathogens, and phylloplane isolates was studied. Dual-culture assays revealed distinct interaction patterns, and transcriptome profiling showed confrontation-specific activation of secondary metabolite biosynthetic gene clusters (SMBGCs), with up to 50 SMBGCs differentially expressed in A. nidulans. Complementary untargeted LC-MS/MS identified hundreds of unique secondary metabolites (SMs), including compounds structurally resembling synthetic fungicides, including azoles and piperidines. Notably, cytotoxicity assays using human HEK-293 and HCT-116 cell lines revealed that SM mixtures from confrontations of A. nidulans with Bacillus subtilis or Trichothecium roseum exhibited significant toxicity, with IC50 values as low as 52 µg/mL. These findings demonstrate that microbial confrontations can trigger the production of diverse and specific sets of SMs, including compounds representing potential human health risks. This study underscores the need for confrontation-informed toxicological assessments in MBCA regulation and highlights the importance of developing safer biocontrol strategies in agriculture.IMPORTANCEThis study shows fundamental changes at the transcriptome and metabolome level in the ubiquitous fungus Aspergillus nidulans confronting various microorganisms, including microbial biological control agents. Strong modulations of transcript abundances of genes belonging to secondary metabolism gene clusters correlated with the formation of a vast array of novel secondary metabolites. Compounds formed in some confrontations were toxic to human cells, questioning the consumer safety of applying microbial biological control agents.},
}
@article {pmid41973730,
year = {2026},
author = {Dahlin, KJ and Ebey, K and Vinson, JE and Drake, JM},
title = {Nonlinear effects of noise on outbreaks of mosquito-borne diseases.},
journal = {PLoS computational biology},
volume = {22},
number = {4},
pages = {e1013466},
pmid = {41973730},
issn = {1553-7358},
mesh = {*Disease Outbreaks/statistics &amp; numerical data ; Animals ; Humans ; *Vector Borne Diseases/epidemiology/transmission ; Mosquito Vectors ; *Culicidae ; Stochastic Processes ; Basic Reproduction Number ; Nonlinear Dynamics ; *Noise ; Models, Biological ; Computational Biology ; Climate Change ; Mosquito-Borne Diseases ; },
abstract = {Mosquito-borne diseases are a significant and growing public health burden globally. Predictions about the spread and impact of mosquito-borne disease outbreaks can help inform direct control and prevention measures. However, climate change is expected to increase weather variability, potentially shaping the future of mosquito-borne disease outbreaks globally. In this study, we sought to determine the effects of demographic and environmental noise (stochasticity) on the duration and size of outbreaks predicted by models of mosquito-borne disease. We developed a demographically and environmentally stochastic Ross-Macdonald model to assess how noise affects the probability of an outbreak, the peak number of cases, and the duration of outbreaks at increasing levels of the basic reproduction number (R0) and environmental noise strength. Increasing environmental noise reduces the risk of endemic disease from 100% down to almost 0%, but the largest outbreaks occur at intermediate environmental noise levels. In this case, if an outbreak dies out, it ends quickly. In the presence of noise, R0 alone is insufficient to definitively predict whether an outbreak occurs. Surprisingly, our modelling results suggest that the dramatic effect on mosquito populations from increases in the frequency of extreme environmental conditions could reduce the risk of endemic disease and epidemics in some settings.},
}
@article {pmid41974379,
year = {2026},
author = {Weseman, CE and Siegle, E and Boxrud, B and Shankman, SA and Reddy, M and Griffith, JW and Ashaie, SA},
title = {Validating an aphasia-accessible ecological momentary assessment for daily depressive affect: A preliminary investigation.},
journal = {Journal of affective disorders},
volume = {407},
number = {},
pages = {121783},
doi = {10.1016/j.jad.2026.121783},
pmid = {41974379},
issn = {1573-2517},
support = {K23 DC020757/DC/NIDCD NIH HHS/United States ; },
mesh = {Humans ; *Ecological Momentary Assessment ; Male ; *Aphasia/psychology/complications ; Female ; Middle Aged ; Aged ; *Depression/diagnosis/psychology ; Feasibility Studies ; Adult ; Mobile Applications ; Reproducibility of Results ; Affect ; Stroke/psychology/complications ; Quality of Life/psychology ; Surveys and Questionnaires ; },
abstract = {BACKGROUND: Up to 60% of individuals with aphasia have post-stroke depression, resulting in worse quality of life. However, extant measures of depression in aphasia are insufficient, and people with aphasia are often excluded from studies of depression due to a lack of valid assessment tools. Ecological momentary assessment (EMA) involves brief, repeated surveys that capture fluctuations in the real world, and may be adapted for individuals with communication impairments. We created a novel, aphasia-accessible EMA of affective depressive symptoms and evaluated its feasibility and usability in a sample of people with aphasia.<br><br>METHODS: 27 people with aphasia (Western Aphasia Battery-Aphasia Quotient (WAB-AQ) range: 32.9-97.4) completed a six-item EMA survey assessing positive and negative affect through the app m-Path four times per day for 14&#xa0;days (up to 56 assessments). We analyzed feasibility, validity, and user experience of the app and surveys.<br><br>RESULTS: Participants completed 89.6% of the EMA surveys, indicating strong compliance and feasibility. EMA items correlated strongly with the Center for Epidemiologic Scale-Revised and Patient-Reported Outcomes Measure Information System (PROMIS) Depression measures, reflecting high convergent validity. Participants gave positive feedback about their experience using the app and answering the survey questions.<br><br>CONCLUSIONS: These results suggest that EMA is a useful tool for identifying affective symptoms of depression in people with aphasia and could be a way to address the gap in mental health care for people with aphasia. Future research should include more diverse samples as well as add passive, ecologically valid measures of depression.},
}
@article {pmid41974724,
year = {2026},
author = {Lydon, EC and Deosthale, P and Glascock, A and Phan, HV and Osborne, CM and Leroue, MK and Allen, J and Mick, E and Wagner, BD and DeRisi, JL and Ambroggio, L and Mourani, PM and Langelier, CR},
title = {Host-microbiome archetypes differentiate infection from pathogen carriage in the human lower airway.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71863-5},
pmid = {41974724},
issn = {2041-1723},
support = {R01HL155418//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL124103//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI182308//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
abstract = {Distinguishing lower respiratory tract infection (LRTI) from incidental pathogen carriage (IPC) is clinically challenging. The immunologic and microbial factors defining the states of LRTI and IPC are poorly understood. Here, we perform host-microbe metatranscriptomic profiling of tracheal aspirates from 326 mechanically ventilated children with clinically adjudicated LRTI (n = 207), IPC (n = 70), or non-infectious respiratory failure (n = 49). In the airway microbiome, LRTI shows reduced alpha diversity and taxonomic richness, while IPC displays greater bacterial abundance, enrichment in respiratory anaerobes, and increased metabolic activity. At the host level, patients with LRTI exhibit a distinct lower airway transcriptional signature of innate and adaptive immune activation compared to those with IPC, who have similar transcriptional profiles to uninfected controls. Mediation analyses suggest the airway microbiome influences the host response to pathogens. An integrated host-microbe metatranscriptomic classifier accurately discriminates LRTI from IPC and controls (AUC = 0.89, 95% confidence interval (CI) 0.85-0.92). The single gene FABP4, encoding a macrophage-associated lipid chaperone and recently described pneumonia biomarker, performs similarly when combined with alpha diversity; FABP4 protein alone achieves an AUC = 0.88 (95% CI 0.82-0.93). Together, our findings reveal distinct ecological and immunologic archetypes defining LRTI and IPC, and support data-driven, biology-informed LRTI diagnostics incorporating host and microbial features.},
}
@article {pmid41975475,
year = {2026},
author = {Floridia, T and Mendoza, JN and Fantinato, E and Zocchi, DM and Barbasetti di Prun, L and Sõukand, R and Mattalia, G},
title = {Local farmers, custodians of wild food plant knowledge and uses in the touristified Venice Lagoon.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {22},
number = {1},
pages = {},
pmid = {41975475},
issn = {1746-4269},
mesh = {Humans ; *Farmers ; *Plants, Edible ; *Knowledge ; Italy ; Male ; Female ; Middle Aged ; Ethnobotany ; Adult ; Tourism ; Conservation of Natural Resources ; },
abstract = {BACKGROUND: The islands of Sant'Erasmo and Vignole, nestled in the Venice Lagoon, are biocultural refugia, where local ecological knowledge (LEK) of local communities, vital for wetland conservation, is being eroded by factors such as rural depopulation, globalization and touristification. This study investigates Local Gastronomic Knowledge (LGK) of Wild Food Plants (WFPs) among farmers and fishers to determine how occupation specialization influences knowledge distribution. It also investigates the ability of farmers to transform LGK into an economic resource by creating (or entering) niche economies, even though being immersed in a touristified and globalized context.<br><br>METHODS: From 2022 to 2025, semi-structured interviews were conducted with 18 farmers (Sant'Erasmo and Vignole) and 31 fishers of the Venice lagoon.<br><br>RESULTS: We documented 39 wild plant taxa, focusing on folk taxonomy, culinary preparations, and sale of WFPs. A significant occupational knowledge gap was identified: 94% of farmers utilized wild plants (with 70% of them also involved in their sale), naming 39 taxa, whereas fishers reported minimal knowledge representing only 10% of the sample (three out of 31 interviewed) and naming 2 out of the 39 documented taxa, confirming that LGK is tied to everyday contact with specific resources. Farmers demonstrated a very specialized knowledge, including 35% of uses previously unrecorded at the regional or national level.<br><br>CONCLUSIONS: The findings of this study reveal that LGK among farmers, thus people who live in close connection with the soil and vegetation of the Venice lagoon, is still vivid and it is increasingly economically valued. The study also shows a sharp distinction in the LGK on WFPs between farmers and fishers, revealing a strong knowledge specialization tied to their primary occupation, essential in a context of rural depopulation and touristification, for identifying knowledge hotspots and supporting the resilience of local economies. Furthermore, the economic valorization of WFPs (through their incorporation into local short food supply chains) may further encourage their continued use and LGK transmission. We believe this may empower farmers and facilitate the expansion of WFP markets, shedding light on a positive narrative that sees farmers as active custodians of LGK, rather than as passively subjected to globalization, especially in tourist areas as the Venice lagoon is.},
}
@article {pmid41978890,
year = {2026},
author = {Pereira Belúcio, L and Reyes Flores, CA and Leão de Oliveira, L and Frederico Mortati, A and Batista Rodrigues, D and Vieira Feitoza, G and André, T and Schöngart, J and Fernandez Piedade, MT and Cavalcanti da Cunha, A},
title = {Soil physicochemical gradient from headwaters to flooded riparian zones in the Falsino River, Eastern Amazonia.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20882},
pmid = {41978890},
issn = {2167-8359},
mesh = {*Rivers/chemistry ; *Soil/chemistry ; *Floods ; Brazil ; Geographic Information Systems ; Environmental Monitoring/methods ; Hydrology ; },
abstract = {This study investigates the edaphic-hydrological gradients of riparian zones in the Falsino River basin, Eastern Amazon. We defined 21 sampling units based on water body order (2nd to 4th) to capture edaphic and hydrological variation. Maximum river level values (MRL) were represented using limnimetric rulers as proxy of flood pulse intensity, and physicochemical analysis was performed on 378 soil samples. The topographic measurements by Global Positioning System (GPS) and Shuttle Radar Topography Mission (SRTM) quantified basin levels and the results were compared. Results reveal a clear spatial pattern, with MRL increasing with tributary order and decreasing elevation. Flood pulse intensity strongly influenced soil texture and acidity, while variables such as organic matter and phosphorus were weakly associated. The inverse relationship between elevation and MRL highlights the topographic control on hydrological dynamics, although elevation alone did not explain most soil variations. Both GPS and SRTM showed strong agreement, validating their use in low-relief Amazonian landscapes. Sample plot delimitation along the basin's longitudinal profile facilitated the evaluation of abiotic attribute relationships. This research provides novel insights into how hydro-topographic interactions shape riparian soil properties, offering a practical framework for hydropedological assessments in remote tropical basins.},
}
@article {pmid41983802,
year = {2026},
author = {Rudgers, JA and Gherardi, LA and Yogi, P and Bacigalupa, M and Miller, TEX and Blais, JJ and Bolin, L and Collins, SL and Hou, E and Luo, Y and Morales, JO and Pockman, WT and Richardson, AD and Villatoro-Castañeda, M and Wesely, NK and Whitney, KD and Zhou, Y},
title = {Precipitation variability interacts with mean precipitation to restructure a semiarid grassland community.},
journal = {Ecology},
volume = {107},
number = {4},
pages = {e70365},
doi = {10.1002/ecy.70365},
pmid = {41983802},
issn = {1939-9170},
support = {1655499//Division of Environmental Biology/ ; 2425290//Division of Environmental Biology/ ; },
mesh = {*Grassland ; *Rain ; *Plants/classification ; Biodiversity ; Climate Change ; Time Factors ; },
abstract = {Climate forecasts project change not only in the mean of climate variables but also in their variance. If these dual changes interact, then future ecological dynamics will be difficult to predict using current experimental approaches, which typically change the mean or impose a single extreme event, such as drought. We designed a new field experiment to factorially reduce mean precipitation and increase its interannual variability. Across 4 years, drier, more variable precipitation additively reduced aboveground primary productivity by 48%-69% and interactively reduced the dominant plant species, but had no effect on the plant species predicted to dominate in the future, which could lead to state transition. Drier, more variable precipitation also interactively reduced biodiversity more than either climate factor alone, with 37%-42% fewer plant species than under ambient conditions, a pattern that matched declining richness during the past 20 years of ongoing climate change. Drier, more variable precipitation restructured the composition and spatiotemporal variation of the plant community. Altered precipitation mean or variance affected 14% of plant species, with eight species sensitive to the mean × variance interaction. Results suggest that future forecasts of plant community structure may be inadequate if they fail to incorporate climate mean × variance interactions.},
}
@article {pmid41985106,
year = {2026},
author = {Sun, Q and Lin, Y and Ping, Q and Zhao, Y and Wang, X and Wang, L and Li, Y},
title = {Breaking the Pharmaceutical-ARG Nexus in Wastewater: Mechanistic Insights into Risk Mitigation by a Novel Riboflavin/Ultraviolet/Peracetic Acid Disinfection Process Unveiled by Multiomics.},
journal = {Environmental science &amp; technology},
volume = {60},
number = {16},
pages = {12501-12513},
doi = {10.1021/acs.est.5c16102},
pmid = {41985106},
issn = {1520-5851},
mesh = {*Wastewater ; *Disinfection ; Riboflavin ; Peracetic Acid ; Ultraviolet Rays ; Water Pollutants, Chemical ; Drug Resistance, Microbial/genetics ; Water Purification ; Pharmaceutical Preparations ; Multiomics ; },
abstract = {Wastewater treatment plants (WWTPs) serve as critical reservoirs and dissemination hotspots for pharmaceuticals and antibiotic resistance genes (ARGs), posing significant threats to environmental and public health. In this study, a novel riboflavin/ultraviolet/peracetic acid (RF/UV/PAA) disinfection process was developed to enhance the removal of these emerging contaminants. The process achieved superior performance in degrading 29 pharmaceuticals and eliminating 106 ARGs and 13 mobile genetic elements (MGEs), attributed to the action of both radical and non-radical species. The underlying risk mitigation potential was further elucidated through multiomics analyses. The results revealed that the RF/UV/PAA process suppresses ARG dissemination through a triple-mechanism pathway, directly inactivating host bacteria; blocking vertical gene transfer; enhancing pharmaceutical removal, which alleviates the selection pressure for resistance; and disrupting horizontal gene transfer (HGT) through MGE destruction and alterations in membrane permeability, extracellular polymeric substance secretion, adenosine triphosphate synthesis, and cellular motility. Notably, our results also suggest that non-antibiotic pharmaceuticals promote the MGE-mediated HGT of ARGs, challenging the conventional antibiotic-centric paradigm. This study not only establishes RF/UV/PAA disinfection as an effective technology for the synergistic removal of pharmaceuticals and ARGs in wastewater but also provides critical mechanistic insights to mitigate ARG dissemination via WWTP effluents.},
}
@article {pmid41985608,
year = {2026},
author = {Guo, Q and Ding, C and Ding, Z and Luan, J and Meng, Q and Cai, M and Dong, C and Pan, Y and Yu, J and Liang, F},
title = {A data mining-based screening and prioritization of PFAS in wastewater treatment plants across China.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {398},
number = {},
pages = {128129},
doi = {10.1016/j.envpol.2026.128129},
pmid = {41985608},
issn = {1873-6424},
mesh = {China ; *Wastewater/chemistry ; *Water Pollutants, Chemical/analysis ; *Fluorocarbons/analysis ; *Environmental Monitoring/methods ; *Waste Disposal, Fluid ; Data Mining ; Risk Assessment ; Humans ; },
abstract = {Numerous per- and polyfluoroalkyl substances (PFAS) existed in effluent of wastewater treatment plants (WWTP) generate potential risk to ecosystem and human health. It is imperative to evaluate the characteristic and potential risk of PFAS from WWTP comprehensively. The risk prioritization based on data mining method was established to compile the reference PFAS and corresponding concentrations in municipal WWTP (M-WWTP) and industrial WWTP (I-WWTP) across China over 17 years. The annual publication frequency of PFAS increased significantly, indicating the major concern over time. Totally, 370 PFAS compounds were identified from 960 publications, of which 107 PFAS with concentrations were detected from M-WWTP, and 55 PFAS with concentrations were identified in I-WWTP. Most PFAS categories from M-WWTP and I-WWTP were concentrated on PFCA and PFSA. It's worth noting that there existed negative removal for PFAS contaminants from WWTP, suggesting the precursors in influent could be transformed into PFAS by biodegradation in following treatment processes. The ecological and human health risk of PFAS, including PFOS, PFOA and FOSA, etc., with risk quotient (RQ) > 0.3 and exposure activity ratio (EAR) > 0.001, in effluent from WWTPs could be generated to the receiving water environment. PFAS, including PFOS, PFOA, 6:2 FESA, FOSA, PFHpA, PFTrDA, MeFBSAA, have high prioritization index based on environmental health (EHPI) scores in effluent of M-WWTP, while 6:2 Cl-PFESA, PFDA, 8:2 Cl-PFESA, FOSA, PFOS, 6:2 diPAP have high EHPI scores in effluent of I-WWTP, indicating that these PFAS should be focused on and further prioritized for removal and control. Finally, the PFAS from M-WWTP and I-WWTP in China over the past 17 years were comprehensively compiled by text mining, which provides the reference for screening and identifying PFAS in WWTP. The prioritization of PFAS also offered the foundation for following goal analysis, supervision and administration.},
}
@article {pmid41987215,
year = {2026},
author = {Yan, M and Firkins, J and Guo, J and Relling, A and Yu, Z},
title = {Genome-resolved multi-omics provide new insights into microbial nitrogen utilization by the rumen microbiota.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41987215},
issn = {2049-2618},
mesh = {*Rumen/microbiology ; Animals ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Sheep/microbiology ; Ammonia/metabolism ; *Gastrointestinal Microbiome ; Genomics/methods ; Genome, Bacterial ; *Microbiota ; Multiomics ; },
abstract = {BACKGROUND: Optimizing nitrogen (N) utilization in ruminant production systems holds both economic and environmental significance. However, traditional paradigms of N metabolism, derived primarily from well-studied model rumen bacteria, do not fully reflect the diverse and complex N metabolism in the rumen ecosystem.<br><br>RESULTS: To address this gap, we utilized comparative genomics and genome-resolved multi-omics analyses using a curated set of microbial genomes to investigate N assimilation and regulation in rumen microbes. We discovered that well-established mechanisms of ammonia assimilation and regulation, such as the glutamine synthetase (GS)/glutamate synthase (GOGAT) pathways and their regulatory proteins, are absent in many of the predominant rumen microbes, which likely utilize alternative pathways for ammonia assimilation. These findings challenge the applicability of E. coli-based N regulation models to rumen bacteria in response to ammonia availability. We further linked polysaccharide utilization and ammonia assimilation across hundreds of rumen microbial species. Furthermore, we identified specific microbial species involved in ureolysis and denitrification, as well as phages carrying auxiliary metabolic genes involved in N assimilation. Using an animal trial involving 11 pairs of lamb twins in a crossover design, we demonstrated that dietary crude protein (CP) at 10% and 13% had minimal impact on rumen microbiome composition and expression of N assimilation genes. Instead, changes in concentrate levels altered N assimilation, notably increasing expression of amino acid biosynthesis pathways.<br><br>CONCLUSION: These findings indicate a nuanced, species-specific microbial response to dietary interventions, highlighting the limitations of traditional N metabolism models applied to rumen microbes and the need for more granular studies of rumen microbial ecosystems.},
}
@article {pmid41987236,
year = {2026},
author = {Chen, X and Xie, B and Cui, Y and Li, H and Wang, X and Zhou, J and Lu, Z},
title = {Impact of environmental and socioeconomic factors on the prevalence of and DALYs due to cutaneous leishmaniasis globally from 1990 to 2021 based on remote sensing and GIS technologies.},
journal = {Parasites &amp; vectors},
volume = {19},
number = {1},
pages = {},
pmid = {41987236},
issn = {1756-3305},
mesh = {Humans ; *Leishmaniasis, Cutaneous/epidemiology ; Geographic Information Systems ; Prevalence ; *Remote Sensing Technology ; Socioeconomic Factors ; *Disability-Adjusted Life Years ; Global Health ; Spatio-Temporal Analysis ; Environment ; Global Burden of Disease ; },
abstract = {BACKGROUND: Leishmaniasis, a parasitic disease caused by Leishmania spp., is a major public health threat. The synergistic effects of environmental and socioeconomic factors on the global distribution of leishmaniasis are unknown.<br><br>METHODS: Applying epidemiological data on cutaneous leishmaniasis (CL) from the Global Burden of Disease 2021 database, we used spatial autocorrelation and standard deviation ellipses to explore the spatiotemporal clustering and migration patterns of CL. Four remote sensing-retrieved environmental factors and five socioeconomic factors were selected for analysis. Spearman's correlation coefficient was used to screen for factors correlated with the prevalence of and disability-adjusted life years (DALYs) due to CL. Ordinary least squares (OLS), geographically weighted regression (GWR) and geographically and temporally weighted regression (GTWR) were used to assess the impact of the influencing factors on the prevalence of and DALYs due to CL.<br><br>RESULTS: From 1990 to 2008, the global prevalence of and DALYs due to CL exhibited significant positive spatial autocorrelation (Z&#x2009;>&#x2009;1.96, P&#x2009;<&#x2009;0.05). Prevalence and DALYs both had one cold spot, located in northern Africa, and two hot spots, located in Central America and Central Asia. Temperature, infant mortality rate (IMR) and humidity were significantly positively correlated with the prevalence of and DALYs due to CL, whereas gross domestic product (GDP) and surface solar radiation (SSR) were significantly negatively correlated with the latter. The GTWR model demonstrated the best regression performance, with adjusted R[2] values for prevalence reaching 0.841, 0.984, 0.839 and 0.972, and those for DALYs reaching 0.816, 0.966, 0.837 and 0.972 in Asia, Europe, the Americas and Africa, respectively. Regression coefficients further quantified the individual contributions of each factor to the prevalence of and DALYs due to CL, which could provide a scientific basis for governments to implement targeted control of CL.<br><br>CONCLUSIONS: To our knowledge, this study is the first to analyze the global spatiotemporal distribution patterns of the prevalence of and DALYs due to CL and quantitatively study the spatiotemporal effects of environmental and socioeconomic factors on CL on a global scale. Environmental (temperature, SSR and humidity) and socioeconomic (GDP and IMR) factors were significantly correlated with the prevalence of and DALYs due to CL. The GTWR model outperformed the GWR and OLS models, further confirming the spatiotemporal effects of influencing factors on CL.},
}
@article {pmid41989469,
year = {2026},
author = {Shchyogolev, S and Muratova, A and Turkovskaya, O and Matora, L},
title = {The Rieske dioxygenase system in Achromobacter: in silico studies of the protein structure and substrate interactions.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {41989469},
issn = {1432-072X},
mesh = {*Achromobacter/enzymology/genetics/chemistry ; *Bacterial Proteins/chemistry/metabolism/genetics ; Substrate Specificity ; *Dioxygenases/chemistry/metabolism/genetics ; Protein Conformation ; Computational Biology ; Computer Simulation ; Models, Molecular ; Amino Acid Sequence ; },
abstract = {Using a set of protein sequences of the class IIB Rieske dioxygenase system of the Achromobacter insolitus LCu2 strain, known for its ability to degrade pollutants, large-scale bioinformatic assessments of the potential of Achromobacter as an effective tool for bioremediation were performed. More than 100 homologues and isoforms of proteins in this system have been identified in various species of the genus Achromobacter. The reproducibility and stability of their 3D structures with ions and coenzymes, predicted using the AlphaFold 3 program, were established despite significant changes in protein sequences with a percentage identity of ≈ 20-99% within the genus. Using AlphaFold 3 and DeepPeptide programs and considering the experimental 3D structures of Rieske dioxygenase proteins of various bacterial classes from the PDB database, presumable propeptides were identified for the first time in achromobacteria at the N- and C-termini of the protein precursors. Their possible functions include participation in the folding, maturation, stabilization of proteins, and regulation of their activity. The genomic context of the proteins in the type strains of Achromobacter species revealed a conservative clustering pattern. Along with the stability of the protein 3D structures, this may contribute to the conservation of the functional activity of the enzymes as the strains adapt to their respective ecological niches. The interactions of the substrates with the enzyme and isoenzyme in the catalytic domain of the dioxygenase were characterized Using AutoDock Vina, which showed that their substrate specificity remained virtually unchanged. Overall, a wide range of Achromobacter strains suitable for biodegradation (bioremediation) was identified.},
}
@article {pmid41989870,
year = {2026},
author = {Zhu, YC and Deng, Y and Zeng, JQ},
title = {Effects of concurrent Helicobacter pylori infection and small intestinal bacterial overgrowth on the gut microbiota and metabolic profiles: A multi-omics study.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {73},
number = {2},
pages = {201-210},
doi = {10.1556/030.2026.02894},
pmid = {41989870},
issn = {1588-2640},
mesh = {Humans ; *Helicobacter Infections/microbiology/metabolism/complications ; Female ; *Helicobacter pylori/physiology ; *Intestine, Small/microbiology ; *Gastrointestinal Microbiome ; Male ; Multiomics ; Feces/microbiology ; *Metabolome ; Middle Aged ; Adult ; *Bacteria/classification/growth &amp; development/genetics/isolation &amp; purification/metabolism ; Aged ; },
abstract = {This study investigated the synergistic effects of Helicobacter pylori (Hp) infection and small intestinal bacterial overgrowth (SIBO) on the gut microbiota structure and metabolic profiles and elucidate the underlying pathophysiological mechanisms. Forty-two patients with gastrointestinal symptoms were recruited and assigned to group A (Hp+ SIBO+), B (Hp+ SIBO-), C (Hp- SIBO+), or D (Hp- SIBO-) based on their Hp infection and SIBO status. Fecal samples were collected for metagenomic sequencing and untargeted metabolomic analysis. The associations between microbiota and metabolites were evaluated using alpha/beta diversity analysis, differential species screening, metabolite identification, and Procrustes/Spearman correlation analysis. Neither Hp infection nor SIBO significantly altered the alpha or beta diversity of the gut microbiota (both P > 0.05). However, specific shifts in microbial abundance were observed. Specifically, the abundance of short-chain fatty acid-producing bacteria such as Megamonas was significantly decreased in the SIBO+ groups. Metabolomic analysis revealed significant enrichment of inflammatory metabolites (e.g., prostaglandin derivatives) in group A, disordered bile acid conjugates (e.g., chenodeoxycholylisoleucine) and nucleotide metabolism in SIBO+ groups, and abnormal lipid/carbohydrate metabolism pathways in Hp+ groups. Multi-omics integration analysis indicated a strong coupling between the microbial structure and metabolic profiles (Procrustes analysis, P < 0.05). In group A, the abundance of Faecalibacterium and Hominenteromicrobium was negatively correlated with bile acid levels, suggesting impaired bile acid transformation. Hp infection and SIBO might synergistically exacerbate gut ecological and metabolic disorders by reshaping specific microbiota and metabolic networks (enhanced inflammatory response, disrupted bile acid circulation). Their co-occurrence produces additive effects, which could explain the aggravated clinical symptoms. This study provides a theoretical basis for interventions targeting microbiota-metabolite interactions, such as probiotics and bile acid modulators.},
}
@article {pmid41990227,
year = {2026},
author = {Parween, S and Nagarajan, AP and Alghamdi, AK and Eida, AA and Lafi, FF and Albanna, L and Salem, N and Abu-Irmaileh, B and Pirzada, ZA and Siddique, S and Garrido-Oter, R and Schulze-Lefert, P and Saad, MM and Hirt, H},
title = {Desert Plant Endophyte Genome Database: a curated repository of endophytic bacterial genomes across arid ecosystems.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {41990227},
issn = {1758-0463},
support = {BAS/1/1062-01-01//KAUST/ ; },
mesh = {*Endophytes/genetics ; *Desert Climate ; *Genome, Bacterial ; *Databases, Genetic ; *Plants/microbiology ; *Ecosystem ; *Bacteria/genetics ; },
abstract = {Microbial communities associated with desert plants play a pivotal role in enhancing host survival under extreme environmental stressors, including drought, salinity, and nutrient limitation. The Desert Plant Endophyte Microbial Collection is one of the largest curated repositories of 2500 cultivable endophytic bacteria isolated from 23 native desert plant species across Saudi Arabia, Jordan, and Pakistan. Representing a broad spectrum of arid microhabitats from inland deserts and mountain wadis to coastal mangroves and date palm oases, the collection supports integrative studies on microbial ecology and plant-microbe interactions in water-limited ecosystems. A central component of this initiative is the Desert Plant Endophyte Genome Database, which currently hosts whole-genome sequences of 534 endophytic bacterial isolates annotated with extensive ecological metadata, assembly statistics, functional traits, and host associations. The database interface provides tools for genome exploration, metadata filtering, and functional gene mining, enabling users to identify taxa and traits of agronomic interest, particularly for applications in sustainable agriculture and sustainable desert revegetation. By combining genomic, ecological, and functional data, the Desert Plant Endophyte Genome Database serves as a foundational platform for the development of targeted microbial inoculants and fosters data-driven research into desert microbiomes and plant resilience mechanisms.},
}
@article {pmid41990455,
year = {2026},
author = {James, SH and Galvan, T and Raugh, IM and Allen, DN and Condray, R and Strauss, GP},
title = {Ethnoracially incongruent environments predict state increases in negative symptoms of schizophrenia:Evidence from geocoding and digital phenotyping.},
journal = {Journal of psychiatric research},
volume = {198},
number = {},
pages = {294-300},
doi = {10.1016/j.jpsychires.2026.04.007},
pmid = {41990455},
issn = {1879-1379},
mesh = {Humans ; Male ; *Schizophrenia/physiopathology/ethnology/diagnosis ; Female ; Adult ; *Ecological Momentary Assessment ; Middle Aged ; Geographic Information Systems ; *Social Environment ; *Schizophrenic Psychology ; },
abstract = {BACKGROUND: Cultural contexts, such as whether one's immediate environment is ethnoracially congruent, are known to influence emotional expression, emotional experience, motivation, and social behavior in healthy individuals. However, it is unclear whether such cultural factors play a role in state exacerbations in negative symptoms that occur in schizophrenia (SZ).<br><br>AIMS: The current study combined GPS data, environmental geocoding, and ecological momentary assessment (EMA) to test the hypothesis that ethnoracial incongruence encountered in daily-life situations predicts state increases in negative symptoms in SZ.<br><br>METHOD: Participants included outpatients with SZ (n&#xa0;=&#xa0;37) and healthy controls (CN: n&#xa0;=&#xa0;41) with marginalized ethnoracial identities who completed EMA and passive digital phenotyping recordings. Geolocation was used to pair participant GPS location at the time of completing EMA symptom surveys with geocoded measures of that location's ethnoracial density based on government census records. Ethnoracial congruence was determined in relation to the match between a participant's identified ethnoracial identity and the ethnoracial density of their location at the time of EMA survey.<br><br>RESULTS: Results indicated that ethnoracially incongruent contexts were associated with state increases in negative symptoms in individuals with SZ, but not CN.<br><br>CONCLUSIONS: These findings suggest that interactions between one's own ethnoracial identity and the ethnoracial context of the current environment contributes to negative symptom exacerbations in SZ. Identity factors are not typically considered in the assessment and treatment of negative symptoms in SZ, but it would be beneficial to do so.},
}
@article {pmid41991539,
year = {2026},
author = {Lionello, P and Di Fant, V and Pasquier, U and Tosi, L and Cozannet, GL and Nicholls, RJ and Cramer, W and Cremades, R and Giupponi, C and Hinkel, J and Sfriso, A and Teatini, P and Vafeidis, AT and Umgiesser, G and Haasnoot, M},
title = {Long-term adaptation pathways for Venice and its lagoon under sea-level rise.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41991539},
issn = {2045-2322},
support = {Pathways2Resilience project (101093942)//European Union's Horizon 2020/ ; Adapt@Ve Programme//Fondazione Eni Enrico Mattei/ ; },
abstract = {The substantial risks posed to Venice and its lagoon by ongoing and projected sea-level rise (SLR) require unprecedented long-term adaptation strategies. We map the evolution of development pathways and the progressive shrinking of the solution space as SLR advances, identifying adaptation tipping points and analysing the relative pros and cons of alternative measures. The analysis highlights trade-offs among environmental quality, heritage preservation, social well-being and relevant Sustainable Development Goals, and costs increasing with SLR. With present insufficient greenhouse gas mitigation policies, the current open lagoon strategy, with mobile barriers and multiple accommodation measures, is likely to encounter hard limits within the current century. Follow-up strategies include ring-dikes isolating the city from the rest of the lagoon, or a closed lagoon with permanent coastal dams, each preserving different combinations of values while entailing major ecological and socio-cultural transitions. Under extreme SLR, relocation of monuments to suitable inland areas and abandonment would be the only remaining strategy, which might become unavoidable in the 22nd century under current climate policies and an Antarctic ice-sheet collapse. Rapid mitigation could still avoid the most disruptive long-term outcomes.},
}
@article {pmid41992918,
year = {2026},
author = {Luijten, M and Herzler, M and Affourtit, F and Allen, D and Ashraf, MW and Ball, N and Berggren, E and Berndt, S and Billat, PA and Cöllen, E and Colbourne, J and Marco, M and Currie, R and Diemar, MG and Dirven, H and Dreser, N and Escher, SE and Gardner, I and Gozalbes, R and Hahn, S and Heiland, A and Hempt, C and Hendriks, G and Henschel, O and Husøy, T and Islam, B and Jensen, KA and Kamp, H and Karakitsios, S and Kass, GEN and Kumar, V and Landsiedel, R and Loret, T and Lundquist, P and Mahony, C and Marx-Stoelting, P and Moné, MJ and Ottenbros, I and Ouédraogo, G and Pastor, M and Sachana, M and Schmeisser, S and Scholz, S and Schütte, K and Sullivan, K and Tangianu, S and Tristram, A and Turner, J and Vinken, M and Vlaanderen, J and van de Water, B and White, A and Leist, M},
title = {Stakeholder input towards further refinement and consolidation of the alternative safety profiling algorithm (ASPA) for next generation risk assessment (NGRA).},
journal = {ALTEX},
volume = {},
number = {},
pages = {},
doi = {10.14573/altex.2603121},
pmid = {41992918},
issn = {1868-8551},
abstract = {Next-generation risk assessment (NGRA) aims to enable transparent, reproducible chemical safety assessments based on human-relevant, animal-free new approach methodologies (NAMs). The Alternative Safety Profiling Algorithm (ASPA) was developed within the ASPIS cluster to provide an algorithmic workflow that structures problem formulation, evidence integration, and decision-making across three main pillars-hazard, ADME (toxicokinetics), and exposure. To refine ASPA, a stakeholder workshop was organized. Four breakout groups systematically reviewed corresponding workflow sections, identifying strengths, conceptual gaps, and opportunities for harmonization. Across groups, participants endorsed ASPA's modular, technology-neutral nature and its focus on standardizing processes rather than prescribing specific test batteries. The hazard pillar discussions emphasized a sensitive, hypothesis-generating Tier 1, complemented by a specific, mechanistic Tier 2, capable of deriving points of departure (PoDs). ADME experts supported a physiology-based kinetic (PBK) modelling strategy, advancing from generic towards more complex models, using mechanistic information and experimental data. The exposure group proposed refinements for transparent, tiered exposure modelling, with emphasis on realistic worst-case scenarios and explicit uncertainty communication. Cross-pillar discussions highlighted the importance of feedback loops between all pillars, and the documentation of decision points to achieve consistency and defensibility. The workshop outcomes informed three parallel developments: (i) algorithmic refinement and re-design toward the next ASPA version, (ii) the creation of detailed guidance for each building block, and (iii) the establishment of practical case studies to demonstrate workflow implementation. This report already contains a first case study (developmental neurotoxicity assessment of desnitro-imidacloprid). These advances increase the operability, transparency, and regulatory readiness of ASPA.},
}
@article {pmid41993749,
year = {2026},
author = {Malik, V and AlJarullah, A and Alsubait, T and Ikram, A and Goyal, SB and Khan, M},
title = {Explainable artificial-intelligence-based hyperspectral image analysis for leaf disease detection in intercropping system.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1789542},
pmid = {41993749},
issn = {1664-462X},
abstract = {INTRODUCTION: Intercropping regimes enhance the efficiency of land use and ecological sustainability but present serious problems to automated disease analysis since the overlapping canopy and the similarity of symptoms in crop species are visually indistinguishable.<br><br>METHODS: This work presents an explainable artificial intelligence (XAI)-based hyperspectral analysis on leaf disease in intercropping systems. The framework combines the spectral-spatial feature generators that utilize transformers including vision transformer (ViT), Swin transformer, pyramid vision transformer (PVT), and detection transformer (DETR) to identify nuanced biochemical and structural changes in crop combinations for maize-soybean and pea-cucumber. In order to reduce spectral redundancy and high dimensionality, an enhanced greedy political optimization (EGPO) algorithm is used as a wrapper-based feature selection strategy. A capsule spatial shift neural network (CSSNet) is used to predict the classification of diseases. Explainable AI methods, such as Local Interpretable Model-agnostic Explanations (LIME) and SHapley Additive exPlanations (SHAP) feature attribution analysis and gradient-weighted class activation mapping (Grad-CAM) visualization of disease-relevant regions, provide model transparency. The DETR + EGPO + CSSNet framework is tested on the conventional feature selection methods.<br><br>RESULTS AND DISCUSSION: The results or findings on publicly available hyperspectral datasets on intercropping show an average recall of 99.998% with high region consistency (Dice score: 99.997%) of activation maps and expert-marked disease regions. These findings affirm that the proposed framework is highly accurate, stable, and interpretable to identify subtle and overlapping disease in leaves in a complex system of intercropping.},
}
@article {pmid41994308,
year = {2026},
author = {van Gerrevink, MJ and Veraverbeke, S and Cooperdock, S and Potter, S and Zhong, Q and Moubarak, M and Virkkala, AM and Goetz, SJ and Mack, MC and Randerson, JT and Schutgens, N and Turetsky, MR and van der Werf, GR and Rogers, BM},
title = {Climate impacts from North American boreal forest fires.},
journal = {Nature geoscience},
volume = {19},
number = {4},
pages = {455-461},
pmid = {41994308},
issn = {1752-0894},
abstract = {The boreal forest biome is warming rapidly, impacting disturbance regimes and global climate. Boreal forest fires have intensified, initiating both climate warming (positive) and climate cooling (negative) impacts across spatial and temporal scales. Here we estimate climate impacts from boreal fires in Alaska and western Canada between 2001 and 2019 using integrated net radiative forcing metrics combining greenhouse gas and aerosol emissions from combustion, vegetation recovery, greenhouse gas emissions from fire-induced permafrost thaw and changes in surface albedo over a 70-year period. We find that fires across Alaska contributed, on average, to net climate warming (0.35 ± 4.66 W m[-2] of burned area; one standard deviation), while fires across Canada contributed to net cooling (-2.88 ± 4.17 W m[-2] of burned area; one standard deviation). Climate-warming fires occur preferentially in dry, high-elevation, steep permafrost landscapes with high pre-fire black spruce coverage and combust more carbon per unit area. Climate-cooling fires are driven by longer spring snow exposure and occur more frequently in continental regions near the treeline. This fine-scale characterization of component and net radiative forcing advances our understanding of the biogeophysical impacts of fires on high-latitude climate and highlights the need to prioritize fire management in carbon-rich permafrost regions to curb long-term warming.},
}
@article {pmid41994310,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Water Carpet, Lampropteryx suffumata (Denis &amp; Schiffermiiller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {304},
pmid = {41994310},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Lampropteryx suffumata (the Water Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 581.6 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 16.48 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,663 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 {pmid41995560,
year = {2026},
author = {Demirtaş, Y and Şahinöz, T},
title = {Trends and determinants of tuberculosis incidence in Turkey: A secondary data analysis.},
journal = {Medicine},
volume = {105},
number = {16},
pages = {e48278},
pmid = {41995560},
issn = {1536-5964},
mesh = {Humans ; Turkey/epidemiology ; Incidence ; *Tuberculosis/epidemiology ; Longitudinal Studies ; Female ; Male ; Adult ; Socioeconomic Factors ; Linear Models ; Social Determinants of Health ; Risk Factors ; Secondary Data Analysis ; },
abstract = {Tuberculosis remains a major public health concern, with incidence rates influenced by social determinants of health. Although tuberculosis incidence in Turkey has declined markedly in recent decades, the factors associated with this decline have not been comprehensively evaluated at the country-level. This study aimed to examine trends in tuberculosis incidence in Turkey from 1982 to 2021 and to identify determinants of tuberculosis incidence rates between 2000 and 2021, considering variables categorized under composite development, economic indicators, population, and health services. A longitudinal ecological study was conducted using secondary data to examine trends and determinants of tuberculosis incidence in Turkey. Univariate and multivariable linear regression were employed to evaluate the associations between tuberculosis incidence rates and 10 selected variables. Tuberculosis incidence in Turkey declined substantially over the 40-year period analyzed, with an overall decrease of 86.6% and sharper reductions observed in certain intervals. In multivariable linear regression, only the Human Development Index remained independently associated with tuberculosis incidence (β = -1.041, P < .001), indicating that higher Human Development Index values were associated with lower tuberculosis incidence rates in Turkey. These findings indicate that tuberculosis incidence in Turkey has declined alongside changes in human development, as reflected by the composite Human Development Index.},
}
@article {pmid41997124,
year = {2026},
author = {Shi, M and Patti, GJ and Gunter, MJ and Govindan, R and Lansdorp-Vogelaar, I and Wang, T and Townsend, JP and Colditz, GA and Belkaid, Y and Cao, Y},
title = {Accelerating discovery of cancer causes for prevention in the era of rising early-onset cancers.},
journal = {Cell},
volume = {189},
number = {8},
pages = {2232-2253},
doi = {10.1016/j.cell.2026.03.019},
pmid = {41997124},
issn = {1097-4172},
support = {U24 NS132103/NS/NINDS NIH HHS/United States ; R01 HG007175/HG/NHGRI NIH HHS/United States ; OT2 CA297576/CA/NCI NIH HHS/United States ; UM1 DA058219/DA/NIDA NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; R37 CA246175/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Neoplasms/prevention &amp; control/epidemiology/etiology/genetics ; Age of Onset ; Risk Assessment ; },
abstract = {Cancer in younger adults is rising globally, with notable birth-cohort effects. This epidemiological shift underscores the urgent need to accelerate the identification of novel causes and underlying biological networks, with the aim of translating these insights into prevention and interception strategies. In this perspective, we revisit the major milestones in the discovery of cancer causes and outline challenges that hinder progress. To address these challenges, we advocate closer integration of epidemiologic and mechanistic studies and propose three interconnected frameworks that extend current epidemiologic approaches: a tissue ecosystem-anchored framework for cancer cause discovery, a biological state-based framework for precision cancer risk assessment, and a dynamic framework to characterize cancer preventability. This roadmap aims to stimulate conceptual, resource, and methodological advances to accelerate cancer etiology research and prevention in the era of rising early-onset cancers.},
}
@article {pmid41998806,
year = {2026},
author = {Tang, R and Wang, J and Zhang, Z and Li, Y and Lan, Y and Fan, Z},
title = {Temporal Shifts in Gut Microbiota and Host Immunity During Chronic Diarrhea in an Infant Rhesus Macaque: A Longitudinal Case Study Based on Multi-Omics.},
journal = {Journal of medical primatology},
volume = {55},
number = {3},
pages = {e70074},
doi = {10.1111/jmp.70074},
pmid = {41998806},
issn = {1600-0684},
support = {2023NSFSC1935//Sichuan Province Science and Technology Support Program/ ; 32370450//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Macaca mulatta/immunology ; *Gastrointestinal Microbiome ; *Diarrhea/veterinary/microbiology/immunology ; *Monkey Diseases/immunology/microbiology ; Longitudinal Studies ; Transcriptome ; Male ; Anti-Bacterial Agents/therapeutic use ; Female ; Chronic Disease ; Multiomics ; },
abstract = {Diarrhea remains a major health challenge in captive rhesus macaques (RMs; Macaca mulatta), particularly among infants, yet the dynamic interplay between gut microbiota and host immune responses during disease progression remains poorly understood. Here, we conducted a longitudinal multi-omics study on a captive infant RM, analyzing 25 fecal metagenomes and 18 blood transcriptomes across diarrheal, antibiotic treatment, and recovery phases. Our results demonstrated that disease state was the primary driver of gut microbiota variation. The diarrheal phase was characterized by a significant reduction in microbial α-diversity and marked expansion of multidrug-resistant Enterobacteriaceae, including Escherichia, Shigella, and Salmonella, accompanied by severe depletion of probiotic genera such as Lactobacillus and Bifidobacterium. Correspondingly, antibiotic resistance genes targeting fluoroquinolones and cephalosporins accumulated substantially during diarrhea, explaining the limited efficacy of empirical antibiotic therapy. Blood transcriptome analysis revealed heightened innate immune activation, evidenced by upregulation of interferon-related genes, alongside suppression of adaptive immune pathways including interleukin-5 signaling. Integrated correlation analysis uncovered synchronized host-microbiome interactions, with inflammatory gene expression positively associated with opportunistic pathogens and negatively correlated with beneficial commensals. Clinical recovery coincided with re-establishment of probiotic populations, reduction in resistance gene burden, and normalization of immune function. These findings demonstrate that infant macaque diarrhea profoundly disrupts both gut microbial ecology and systemic immunity, supporting management strategies that prioritize targeted antimicrobial intervention and microbiome restoration over prolonged empirical antibiotic use in captive primates.},
}
@article {pmid41999115,
year = {2026},
author = {Zhang, Y and Zhang, H and Akashi, H and Albouy, CP and Andres, KJ and Barquín, J and Brantschen, J and Connon, RE and Craine, JM and Gleeson, D and Goldenberg-Vilar, A and González-Ferreras, AM and Hatzenbuhler, C and Hupało, K and Hyde, J and Iwasaki, W and Johnson, MD and Katz, AD and Kuzovlev, VV and Larson, CE and Lecaudey, LA and Leese, F and Leray, M and Li, F and Macher, TH and Mauvisseau, Q and Morán-Luis, M and Nester, G and Quintero, H and Ravelomanana, T and Chacko, MR and Saccò, M and Sales, N and Schenekar, T and Schletterer, M and Schmidt, S and Schulte, NO and Schütz, R and Sperry, JH and Stevens, ER and Stinson, SA and Weiss, S and Xia, F and Zhang, H and Zhang, S and Zhong, W and Zong, S and Pellissier, L and Zhang, X and Altermatt, F},
title = {Integrated Reanalysis of Global Riverine Fish eDNA Datasets Shows Robustness and Congruence of Biodiversity Conclusions.},
journal = {Molecular ecology},
volume = {35},
number = {8},
pages = {e70340},
pmid = {41999115},
issn = {1365-294X},
support = {2022YFC32021001//National Key Research and Development Program of China/ ; 2021YFC3201003//National Key Research and Development Program of China/ ; 42507382//National Natural Science Foundation of China/ ; 310030_197410//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 31003A_173074//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Biodiversity ; Animals ; *Fishes/genetics/classification ; *DNA, Environmental/genetics ; DNA Barcoding, Taxonomic ; Rivers ; Computational Biology ; Ecosystem ; },
abstract = {The analysis of environmental DNA (eDNA) has revolutionized biodiversity assessments in aquatic ecosystems, enabling non-invasive monitoring of fish communities across diverse regions. However, the global comparability of these eDNA datasets remains ambiguous due to heterogeneous sampling protocols and bioinformatic workflows across studies, making it difficult to assess how robust and comparable the biodiversity patterns inferred from these datasets actually are. Here, we conducted a meta-analysis of 58 riverine fish eDNA metabarcoding studies, covering 1818 sampling sites worldwide, to evaluate the robustness of eDNA-derived biodiversity patterns. We found that species richness estimates and metrics of community structure derived under a common bioinformatic workflow were overall consistent with those of original analyses, despite the relatively high variability in bioinformatic analyses in the respective original studies. Contrastingly, congruence of species identity varied more extensively across datasets, mostly reflecting different completeness and regional relevance of reference databases. Restricting taxonomic assignment to basin-specific species pools improved species identification accuracy, while datasets lacking publicly accessible or well-curated reference data were more prone to mismatches. Year of sampling had a positive effect on taxonomic congruence, such that more recent studies showed increased robustness, also reflecting improved reference database coverage and enhanced species-level identification over time and overall method congruence in more recent years. Overall, the suitability and potential of eDNA for global biodiversity monitoring is corroborating overall robust biodiversity estimates, irrespective of the bioinformatic approaches. Our study underlines the effectiveness and need for further harmonization of bioinformatic workflows and strengthened region-specific reference databases for improved taxonomic resolution and comparability across studies.},
}
@article {pmid42000490,
year = {2026},
author = {Kahraman, &#xdc;O and Üçağaç, A and İnal, V and Mucahit Aydin, },
title = {Dynamic environmental management and liability attribution using an AlphaZero-Bayes framework: Intelligent decision support for multi-agent risk systems.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129672},
doi = {10.1016/j.jenvman.2026.129672},
pmid = {42000490},
issn = {1095-8630},
mesh = {Bayes Theorem ; *Decision Support Techniques ; },
abstract = {Attributing liability in environmental systems involving multiple strategic actors poses significant challenges for policy-makers and regulators, particularly under conditions of uncertainty, feedback dynamics, and distributed responsibility. Traditional deterministic models of causation are often inadequate for such complex contexts. In this study, we propose a novel hybrid framework that integrates AlphaZero-based reinforcement learning with Bayesian probabilistic inference to construct an intelligent decision support system for multi-agent environmental liability attribution. Our primary motivation is to solve the very difficult legal causality puzzles in environmental fields by making a Gestalt leap, offering more legitimate, intelligent and consistent solutions than those currently found in the literature. While this work does not exhaust the full landscape of such puzzles, its principal contribution is to stimulate further inquiry and open new horizons for computational legal reasoning. The framework introduces a Dynamic Causation Index (DCI) that quantifies each agent's simulated contribution to ecological harm and updates their posterior responsibility using Bayesian inference. AlphaZero models the actors' long-term strategic behavior within environmental and regulatory environments, while the Bayesian layer incorporates historical priors and likelihoods derived from simulation outcomes. This enables both counterfactual analysis and probabilistic responsibility estimation, overcoming key limitations in current environmental decision-making practices. We apply this framework to a hypothetical river pollution case study involving three industrial facilities, demonstrating how the model supports transparent, proportionate, and adaptive allocation of liability. The results show that Factory B bears the highest causal share (55.1%), followed by Factory A (37.5%) and Factory C (7.4%), based on their strategic leverage and posterior responsibility estimates. The results illustrate how strategic leverage and probabilistic confidence can be combined to enhance environmental governance and intervention planning. The proposed methodology offers a scalable and explainable approach to regulatory design and system-level environmental accountability, with potential applications across sustainability science, environmental law, and intelligent governance.},
}
@article {pmid42002129,
year = {2026},
author = {Chen, S and Tian, L and Ming, R and Yang, Y and Wang, Y and Lu, P},
title = {Combined effects of thifluzamide and lead at environmental concentrations on Xenopus laevis tadpoles: Phenotypic and multi-omics insights.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {399},
number = {},
pages = {128124},
doi = {10.1016/j.envpol.2026.128124},
pmid = {42002129},
issn = {1873-6424},
mesh = {Animals ; *Xenopus laevis/physiology ; Larva/drug effects ; *Lead/toxicity ; *Water Pollutants, Chemical/toxicity ; Molecular Docking Simulation ; *Fungicides, Industrial/toxicity ; Phenotype ; Multiomics ; },
abstract = {Thifluzamide (TF) is a widely used fungicide for controlling sheath blight in rice and is frequently detected in aquatic environments. Lead (Pb) may show toxicity to aquatic organisms due to its persistence and bioaccumulation. However, currently studies on the impacts of these two pollutants on aquatic organisms remain limited. To explore their toxic effects and potential risks to amphibians, the present study investigates the single and combined toxicities of TF and Pb at environmentally relevant concentrations on Xenopus laevis tadpoles, based on a multi-omics approach and molecular docking simulations. The results demonstrated that TF and Pb impaired tadpole growth and development, induced oxidative stress and triggered inflammatory responses, and disrupted normal locomotor behavior. Transcriptomic and metabolomic analyses indicated that the signaling pathways (FoxO, MAPK and Cytokine-cytokine receptor interaction) associated with the toxic effects of TF and Pb, as well as metabolic pathways (Histidine metabolism, Purine metabolism, and Alanine, aspartate, and glutamate metabolism) were significantly affected. Molecular docking simulations indicate a higher binding affinity between inflammation-related proteins and their corresponding receptors. Moreover, these adverse effects on tadpoles were more pronounced under combined exposure. In conclusion, we clarified the toxic effects and potential toxic mechanisms of amphibian larvae exposure to Pb and TF. These results provide a scientific foundation for assessing the ecological risks of complex pollutant mixtures in aquatic ecosystems.},
}
@article {pmid42002290,
year = {2026},
author = {Jadin, RC and Orlofske, SA},
title = {AN ACTIVE LEARNING PROJECT FOR TEACHING BIOINFORMATICS, PHYLOGENETICS, AND PARASITOLOGY.},
journal = {The Journal of parasitology},
volume = {112},
number = {2},
pages = {203-208},
doi = {10.1645/25-19},
pmid = {42002290},
issn = {1937-2345},
mesh = {*Phylogeny ; *Parasitology/education ; *Computational Biology/education ; *Problem-Based Learning ; Humans ; Animals ; Curriculum ; },
abstract = {This article describes an active learning project designed for implementation in general biology, ecology, evolution, and parasitology courses. It involves individual or group-based tasks in which students role-play as various types of biologists to solve real-world parasitology problems through molecular data analysis. Specifically, students are provided with a scenario and a molecular data set to analyze, which involves performing bioinformatic tasks to construct a phylogenetic tree. Students use MEGA software to explore, create, and illustrate a phylogenetic analysis of parasites with GenBank sequences. The resulting phylogenetic tree helps identify an "unknown" taxon and provides the evidence required to address the scenario and answer the posed question. By fostering a deeper understanding of evolutionary processes and bioinformatics tools, this project not only enhances students' knowledge of parasitology but also prepares them to tackle complex, interdisciplinary challenges in global health, biodiversity conservation, and beyond, shaping the next generation of scientists capable of addressing the urgent issues facing our world.},
}
@article {pmid42003557,
year = {2026},
author = {Zu, B and Zhang, Y and Yu, Z and Li, B and Cheng, S and Du, M and Li, R and Liu, C and Zhou, B},
title = {miR-184/hamp-Mediated Cardiotoxicity and Hepatotoxicity in Offspring Zebrafish Following Paternal Exposure to Environmentally Relevant Concentrations of Tris(1,3-dichloro-2-propyl) Phosphate.},
journal = {Environmental science &amp; technology},
volume = {60},
number = {17},
pages = {12814-12824},
doi = {10.1021/acs.est.6c00486},
pmid = {42003557},
issn = {1520-5851},
mesh = {Animals ; Zebrafish ; *MicroRNAs/metabolism ; Male ; *Paternal Exposure ; Cardiotoxicity ; Female ; Liver/drug effects ; *Hepcidins/metabolism ; Organophosphorus Compounds ; },
abstract = {Recently, increasing attention has been focused on the intergenerational toxicity of environmental contaminants. Tris(1,3-dichloro-2-propyl)phosphate (TDCIPP) is a widely detected contaminant in aquatic environments, but its paternally mediated intergenerational toxicity in vertebrates has remained insufficiently elucidated. In this study, zebrafish at 50 days postfertilization (dpf) were exposed to environmentally relevant concentrations (55, 550, and 5500 ng/L) of TDCIPP for 150 days. Following exposure, the males were paired with unexposed females, and cardiotoxicity and hepatotoxicity were assessed in the offspring larvae. It was found that TDCIPP accumulated in F0 testes but not in the offspring embryos. Furthermore, paternal exposure to TDCIPP led to an increased heart rate, abnormal cardiac morphology, and significantly elevated ventricular wall thickness in the offspring zebrafish. Additionally, lipid metabolism disorders, abnormal liver morphology, and functional impairment were also observed in the offspring. Moreover, paternal exposure to TDCIPP down-regulated the expression of the hepcidin antimicrobial peptide gene (hamp) in the offspring larvae, leading to iron overload, which might contribute to the observed cardiotoxicity and lipid metabolism disorders in the offspring, as well as the subsequent development of hepatotoxicity. Furthermore, the up-regulation of miR-184 in F0 testes and offspring larvae accounted for the suppression of hamp expression following paternal exposure to TDCIPP. Our findings reveal that paternal exposure to TDCIPP induces up-regulation of miR-184 in F0 testes, and this overexpressed microRNA can be transmitted to the offspring, subsequently inhibiting hamp expression, leading to iron overload and consequently contributing to cardiotoxicity and hepatotoxicity in the offspring.},
}
@article {pmid42004444,
year = {2026},
author = {Ossendorf, G and Tekelemariam, MG and Taipale, N and Groos, AR and Negash, A and Cnuts, D and Akçar, N and Vockenhuber, C and Tariku, ZK and Kahsay, TH and Rots, V and Vogelsang, R},
title = {Human occupation of the Afroalpine Bale Mountains at the onset of the African Humid Period.},
journal = {Landscape ecology},
volume = {41},
number = {4},
pages = {75},
pmid = {42004444},
issn = {0921-2973},
abstract = {CONTEXT: The reasons for the intermittent human use of harsh Afroalpine environments in prehistory remain unclear. High-resolution glacial and archaeological chronologies from Ethiopia's Bale Mountains now offer insights into landscape change and human adaptations at high altitudes.<br><br>OBJECTIVES: This study investigates the behavioral signatures of human occupation in Africa's largest alpine environment around 15,000&#xa0;years ago, focusing on local site use and integration into regional networks amid deglaciation and the abrupt onset of African Humid Period wet conditions.<br><br>METHODS: This research integrates surface exposure dating of moraine boulders and radiocarbon dating of archaeological rock shelter deposits with detailed analyses of lithic materials from three stratified sites in the Bale Mountains. We use multivariate statistical analyses of electron microprobe data to determine the geochemical provenance of obsidian artifacts. Lithic technological analysis is based on systematic recording of artifact attributes to reconstruct key stages of production. Functional analyses include use-wear and residue studies conducted using stereomicroscopy, reflected light microscopy, and scanning electron microscopy (SEM-EDX).<br><br>RESULTS: This study provides a detailed reconstruction of the final deglaciation phase in the Bale Mountains and identifies distinct patterns of lithic acquisition, production, and use across three contemporaneous sites. Dimtu, located on the formerly glaciated plateau and representing the highest known stratified archaeological site in Africa, is distinguished by a focus on the production of rare but specific pointed flakes. Simbero exhibits standardized backed tool production and evidence of hafting, while the Webi Gestro assemblage includes bladelets and notched tools; wear on unretouched bladelets indicates their use in transverse and longitudinal motions for processing activities and possibly as projectile elements. Geochemical results reveal obsidian exchange between high altitudes and lowlands, suggesting extensive social networks reinforced by technological and behavioral parallels.<br><br>CONCLUSIONS: Human strategies at high altitudes closely mirror contemporaneous lowland behavior, revealing synchronous patterns across ecological zones. Similar patterns during other periods point to broader systemic dynamics. Conventional refugium-based explanations fail to fully capture these patterns, highlighting the need to examine diachronic shifts in the scale, connectivity, and intensity of prehistoric networks across ecozones.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10980-026-02337-8.},
}
@article {pmid42007577,
year = {2026},
author = {Cai, ZF and Liu, B and Yin, TT and Ma, C and Han, ZT and Gu, LH and Zhang, C and Wu, F and Liu, LS and Shi, X and Wang, XQ and Wu, RN and Xie, LZ and Bai, Y and Zhang, YC and Zhang, SR and Gu, LJ and Wang, MS and Xie, GL and Cheng, WK and Lu, JG and Luo, Y and Li, SB and Ashari, H and Zein, MSA and Han, JL and Singchat, W and Srikulnath, K and Zhang, YP and Peng, MS},
title = {Harnessing Deep Learning in Searching Wild Relatives of Domestic Animals.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70133},
pmid = {42007577},
issn = {1755-0998},
support = {2022YFC2602500//National Key Research and Development Program of China/ ; 2024YFD1200700//National Key Research and Development Program of China/ ; 202503AP140028//Yunnan International Joint Laboratory for Conservation and Gene Mining of Genetic Resources/ ; 2021FY100200//Science and Technology Basic Resources Investigation Program of China: "Wild Germplasm Collection and Preservation in the Greater Gaoligong Mountains"/ ; 32001091//National Natural Science Foundation of China/ ; //Ministry of Higher Education, Science, Research and Innovation, Thailand/ ; RUP_Climate68_No.9//Thailand Science Research and Innovation/ ; //Chinese Academy of Sciences/ ; //Kunming Institute of Zoology, Chinese Academy of Sciences,/ ; },
mesh = {Animals ; *Deep Learning ; *Animals, Domestic/genetics/classification ; *Chickens/genetics/classification ; Polymorphism, Single Nucleotide ; *Animals, Wild/genetics/classification ; Sus scrofa/genetics ; Genomics/methods ; Genetic Variation ; Swine/genetics ; *Computational Biology/methods ; },
abstract = {Wild relatives of domestic animals are crucial reservoirs of genetic diversity, yet pervasive hybridization with domestic animals poses significant conservation challenges. Here, we developed a deep learning-based pipeline, consisting of a multi-layer perceptron for SNP panel selection and a Deep &amp; Cross Network for model training, to discern wild relatives from their closely related domestic animals using genomic SNP data. Leveraging the 1960 genomes from 164 red jungle fowl (RJF; Gallus gallus) and 1796 domestic chicken samples, we applied this pipeline to yield the RJF identification model based on a 285-SNP panel. We employed this model to characterize domestic chickens, RJF, and hybrids in the independent genomic datasets from contemporary samples and historical specimens, respectively. The accuracy was 97.8% for historical samples with missing genotypes. The benchmarking multiple hybrid detection tools indicated that the RJF identification model was effective and practical. The further application to the genomic data from wild boar (Sus scrofa), domestic pigs, and their hybrids validated the pipeline. Our method has potential in not only monitoring genetic diversity in wild relatives of domestic animals but also supporting animal genetic resource conservation and management.},
}
@article {pmid42008016,
year = {2026},
author = {Yoneda, K},
title = {Comprehensive identification and subcellular localization prediction of carbonic anhydrases in the marine haptophyte Tisochrysis lutea based on a refined genome annotation.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42008016},
issn = {1432-072X},
support = {23K14001//Japan Society for the Promotion of Science/ ; },
mesh = {*Carbonic Anhydrases/genetics/metabolism/chemistry ; *Haptophyta/genetics/enzymology ; Molecular Sequence Annotation ; Proteome/genetics ; Genome ; Computational Biology ; Photosynthesis ; },
abstract = {The marine haptophyte Tisochrysis lutea is a commercially important microalga known for its production of high-value lipids and carotenoids. While the CO2-concentrating mechanism (CCM) is essential for efficient photosynthesis in marine environments, its molecular basis in haptophytes remains poorly understood despite their ecological and industrial importance. In the present study, I first assessed proteome completeness of the latest gene models of T. lutea and subsequently re-annotated the reference genome to refine these models. I then identified the complete repertoire of carbonic anhydrases (CAs). The re-annotated models significantly improved the proteome-level BUSCO completeness from 76.7% to 89.9% and resolved previously fragmented sequences, resulting in 17,205 protein-coding genes with markedly reduced fragmentation. Within this refined proteome, I identified 16 CA genes across six distinct classes: one α-, five β-, three γ-, two δ-, one θ-, and four ι-type CAs. Subcellular localization was predicted using an integrated bioinformatic pipeline (SignalP, TargetP, ASAFind2, HECTAR, and DeepLoc-2), which suggested a complex compartmentalization of inorganic carbon interconversion. Notably, TlδCA1 and TlιCA3 exhibited high expression levels and were predicted to localize to the plasma membrane and plastid, respectively, indicating their pivotal roles in the CCM of T. lutea. Furthermore, structural analysis revealed unique features in haptophyte CAs, such as specific transmembrane domain configuration in δ-CA and conserved domain repeats in ι-CAs. These findings provide a molecular framework for understanding the CCM machinery in T. lutea, offering a robust genomic platform for future metabolic engineering aimed at enhancing carbon fixation efficiency in marine haptophytes.},
}
@article {pmid42009284,
year = {2026},
author = {Macrina, L and Terraneo, TI and McFadden, CS and Sabino, A and Oury, N and Barreca, F and Vicario, S and Samimi-Namin, K and Knop, D and Rodrigue, M and Pieribone, V and Baird, AH and Berumen, ML and Reimer, JD and Paulay, G and Benzoni, F},
title = {Beyond Tubipora musica: Phylogenomics unveils the overlooked diversity and endemism of the hermatypic octocoral genus Tubipora.},
journal = {Molecular phylogenetics and evolution},
volume = {221},
number = {},
pages = {108622},
doi = {10.1016/j.ympev.2026.108622},
pmid = {42009284},
issn = {1095-9513},
mesh = {*Phylogeny ; *Anthozoa/genetics/classification/anatomy &amp; histology ; Animals ; Indian Ocean ; *Biodiversity ; Pacific Ocean ; Phylogeography ; Sequence Analysis, DNA ; Coral Reefs ; Australia ; },
abstract = {Although scleractinians are typically considered the main reef-building corals, a few octocoral taxa also contribute to coral reef framework formation. The genus Tubipora deposits hard calcareous skeletons organised in tubes connected by horizontal stolonic platforms constituted of fused sclerites. The genus is broadly distributed across the tropical Indo-Pacific, but its diversity and evolutionary history remain poorly understood. Most recent treatments have recognized only the type species Tubipora musica, albeit historically ten species have been named. Here, using an integrative approach combining morphological and phylogenomic (based on Ultra-Conserved Elements and exon loci) analyses of 136 Tubipora colonies collected across six marine provinces in the Indo-Pacific, we delimited 15 morphologically distinct and genetically strongly supported lineages. All lineages retrieved in our results exhibited restricted geographic distributions, limited to single areas, highlighting potential regional endemism. Endemic diversification is suggested by sister species restricted to the Red Sea, Madagascar, and Eastern Australia, as well as regional diversification in Arabia, the Western Indian Ocean, and the Western Pacific. Our results reveal deep diversification within the Western Pacific and are consistent with colonization of the Western Indian Ocean by a single clade that subsequently diversified there. Accordingly, these findings underscore the need for broader sampling across the Indo-Pacific to assess Tubipora diversity and diversification and highlight the power of genomics in clarifying species boundaries and evolutionary relationships, providing a foundation towards the taxonomic revision of Tubipora. Accurate species definition is essential for biodiversity assessment and conservation planning, particularly for reef-building taxa that may include geographically restricted lineages vulnerable to environmental change, ultimately enhancing our ability to monitor and mitigate such impacts on these organisms.},
}
@article {pmid42011984,
year = {2026},
author = {Chelaru, IA and Ciausu, RA and Savuca, A and Ureche, C and Nicoara, MN and Ciobica, AS and Andronic, GA and Ambrosie, RM and Ureche, D},
title = {Effects of environmentally relevant ibuprofen and valproic acid exposure on zebrafish behavior.},
journal = {Biomolecules &amp; biomedicine},
volume = {},
number = {},
pages = {},
doi = {10.17305/bb.2026.14030},
pmid = {42011984},
issn = {2831-090X},
abstract = {Active pharmaceutical ingredients (APIs) are increasingly entering aquatic environments due to human and veterinary use, wastewater discharges, and inadequate waste containment, raising significant concerns for both ecosystems and human health. Ibuprofen and valproic acid are among the pharmaceuticals detected in surface waters, primarily due to incomplete metabolism and the limited removal efficiency of conventional wastewater treatment systems. Ibuprofen, readily available over the counter, is frequently found in high concentrations, while valproic acid, which is available only by prescription, is detected less often, likely reflecting its more restricted use. This study employed the established behavioral ecotoxicology model, Danio rerio, to investigate the effects of environmentally relevant concentrations of ibuprofen (20 µg L-1) and valproic acid (3 µg L-1) on zebrafish (8 months old) after 96 hours of exposure. Both compounds influenced locomotor and anxiety-related endpoints, with changes in social preference primarily associated with valproic acid exposure. Single compound exposures resulted in reduced total distance traveled and average velocity, while combined exposure did not differ from the control group, indicating no additive locomotor impairment. Inactivity duration decreased in both individual treatments, most significantly with valproic acid, whereas the mixture produced no significant effect. Only ibuprofen reduced counterclockwise rotations, suggesting a mild anxiolytic-like response. Given the ecological importance of social cohesion and locomotor performance in predator avoidance, foraging, and reproduction, such behavioral disruptions may compromise population stability. These findings highlight the necessity of integrating behavioral endpoints and considerations of mixture toxicity into ecological risk assessments of pharmaceutical contaminants in aquatic systems.},
}
@article {pmid42012361,
year = {2026},
author = {Jiang, Y and Wang, X and Wei, M and Zhu, W and Liu, L and Zheng, H and Tang, S},
title = {Indirect reciprocity with environmental feedback.},
journal = {Chaos (Woodbury, N.Y.)},
volume = {36},
number = {4},
pages = {},
doi = {10.1063/5.0334029},
pmid = {42012361},
issn = {1089-7682},
abstract = {Indirect reciprocity maintains cooperation in stranger societies by mapping individual behaviors onto reputation signals via social norms. Existing theoretical frameworks assume static environments with constant resources and fixed payoff structures. However, in real-world systems, individuals' strategic behaviors not only shape their reputation but also induce collective-level resource changes in ecological, economic, or other external environments, which, in turn, reshape the incentives governing future individual actions. To overcome this limitation, we establish a co-evolutionary framework that couples moral assessment, strategy updating, and environmental dynamics, allowing the payoff structure to dynamically adjust in response to the ecological consequences of collective actions. We find that this environmental feedback mechanism helps lower the threshold for the emergence of cooperation, enabling the system to spontaneously transition from a low-cooperation state to a stable high-cooperation regime, thereby reducing the dependence on specific initial conditions. Furthermore, while lenient norms demonstrate adaptability in static environments, norms with strict discrimination are shown to be crucial for curbing opportunism and maintaining evolutionary resilience in dynamic settings. Our results reveal the evolutionary dynamics of coupled systems involving reputation institutions and environmental constraints, offering a new theoretical perspective for understanding collective cooperation and social governance in complex environments.},
}
@article {pmid42014086,
year = {2026},
author = {Martins, BH and Franco, AMA and Soriano-Redondo, A and Acácio, M and Catry, I},
title = {From inexperience to proficiency: age-related improvements shape the use of novel anthropogenic food subsidies in a long-lived bird.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2069},
pages = {},
doi = {10.1098/rspb.2025.1884},
pmid = {42014086},
issn = {1471-2954},
support = {//InBIO/ ; //Natural Environment Research Council/ ; //Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Animals ; *Birds/physiology ; *Feeding Behavior ; Waste Disposal Facilities ; Age Factors ; Anthropogenic Effects ; Geographic Information Systems ; },
abstract = {Worldwide, humans have altered ecosystems not only by reducing and changing the distribution of resources but also by providing new foraging opportunities to wildlife. However, little is known about the early-life development and maintenance of new foraging behaviours, which are crucial for species to adapt to human-induced environmental changes. Using a longitudinal global positioning system (GPS)-tracking dataset from 71 adult and 147 juvenile white storks (Ciconia ciconia) tracked for up to 6 years, this study investigates shifts in the exploitation of landfill resources during ontogeny and explores whether selective survival, within-individual improvements or both shape the emergence of this behaviour. Landfill use was found to increase with age. From their second year of life onwards, white storks visit landfills more often than in their first year, forage more in areas with abundant organic waste and reduce their foraging energy expenditure. Overall, this study reveals that the age-related increase in the use of anthropogenic food sources is driven primarily by within-individual improvements operating most strongly in early life, rather than by selective survival of individuals that most frequently and proficiently use landfill sites. As more species rely on anthropogenic food subsidies, this work highlights how opportunistic species cope with and adapt to human-driven environmental change, influencing individual lifetime decisions and potentially impacting population dynamics.},
}
@article {pmid42014453,
year = {2026},
author = {Treichel, NS and Pauvert, C and Séneca, J and Pjevac, P and Berry, D and Penders, J and Hitch, TCA and Clavel, T},
title = {Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.},
journal = {Nature microbiology},
volume = {11},
number = {5},
pages = {1233-1244},
pmid = {42014453},
issn = {2058-5276},
support = {460129525//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 445552570//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 10.55776/DOC69//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 10.55776/COE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; },
mesh = {*Metagenomics/methods ; *Benchmarking ; *Bacteria/genetics/classification ; *Metagenome ; *High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Genome, Bacterial ; Phylogeny ; Shotgun Sequencing ; },
abstract = {Shotgun metagenomics can provide both taxonomic and functional insights, but benchmarking is necessary to determine the sequencing depth appropriate for specific analyses. Here we used complex mixtures of DNA from cultured bacteria and analysed taxonomic composition, strain-level resolution and functional profiles at up to 11 sequencing depths (0.1-50.0 Gb). Reference-based analysis provided accurate strain-level taxonomy at 0.5-1.0 Gb. By contrast, de novo metagenome-assembled genome (MAG) reconstruction required deep sequencing (>10 Gb), and even MAGs deemed high quality by standard metrics were chimeric, with 54.5-81.8% accurately representing original strains, depending on the bioinformatic approach. Functionally, 2 Gb provided reliable insights at the pathway level for each of the mock communities tested, but sufficient proteome coverage was achieved only at or above 10 Gb. Library preparation and host DNA contamination were identified as confounders in shallow metagenomic analysis. This analysis highlights the potential and limitations of shallow metagenomics and provides guidance to accurately capture strain-level diversity using MAGs.},
}
@article {pmid42017006,
year = {2026},
author = {Bai, Y and Song, P and Wen, S and Zhu, H and Wang, Y and Wang, H and Feng, X and Ma, B and Ergu, D and Liu, F},
title = {A Hybrid Machine Learning Framework to Improve Morphological Trait Recovery in Avian Datasets.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73173},
pmid = {42017006},
issn = {2045-7758},
abstract = {Missing data in morphological trait datasets pose a persistent challenge to ecological and evolutionary research, frequently compromising model inference and predictive accuracy. We propose THORBFNN, a three-stage hybrid imputation framework that integrates regularized K-means clustering, Radial Basis Function Neural Networks (RBFNNs), and hierarchical Bayesian optimization to accurately recover missing avian morphological traits. The framework partitions species into clusters using regularized K-means, enhancing the preservation of local morphological structure through inter-cluster separation. Within each cluster, RBFNNs model nonlinear dependencies among traits using input features selected by Pearson correlation with the target trait. Key hyperparameters such as the number of clusters and RBF width are optimized via hierarchical Bayesian optimization to balance generalization and model complexity. When applied to a global avian trait dataset comprising over 10,000 individuals and 11 morphological traits, THORBFNN outperforms K-nearest neighbors and Random Forest imputation across four focal traits, achieving higher R [2] and lower errors (THORBFNN: R [2] = 0.9003, RMSE = 0.1652, MAE = 0.1096; KNN: R [2] = 0.8864, RMSE = 0.1668, MAE = 0.1248; Random Forest: R [2] = 0.8573, RMSE = 0.2134, MAE = 0.1584). Ablation experiments comparing models trained on complete cases versus mean-imputed data confirm that THORBFNN captures genuine trait covariation rather than statistical artifacts. THORBFNN requires no phylogenetic information and scales efficiently to datasets with thousands of individuals, offering a practical pathway for integrating machine learning into biodiversity trait analysis.},
}
@article {pmid42018599,
year = {2026},
author = {Li, Y and Nielsen, BF and Levin, SA and Te Velthuis, AJW and Grenfell, BT},
title = {Spatio-temporal modelling of in vitro influenza A virus infection: The impact of defective interfering particles on the type I interferon response.},
journal = {PLoS computational biology},
volume = {22},
number = {4},
pages = {e1014198},
pmid = {42018599},
issn = {1553-7358},
support = {DP2 AI175474/AI/NIAID NIH HHS/United States ; },
mesh = {*Interferon Type I/immunology/metabolism ; *Influenza A virus/immunology/physiology/genetics/pathogenicity ; Humans ; *Defective Viruses/immunology ; Virus Replication/immunology ; *Influenza, Human/immunology/virology ; *Models, Biological ; Spatio-Temporal Analysis ; Computational Biology ; Animals ; Immunity, Innate ; Stochastic Processes ; },
abstract = {Defective interfering particles (DIPs) are incomplete viral genomes that modulate infection by competing with wild-type viruses and activating the innate immune response. Activation of the immune response leads to the production of cytokines and chemokines, including type I interferon (IFN), which restricts viral growth and may cause cell death. How DIPs interact with type I interferon (IFN) in spatially structured environments remains unclear. Focusing here on influenza A viruses, we developed a spatially explicit, stochastic model of in vitro viral infection that integrates virus and DIP replication, IFN signalling, and alternative dispersal modes. We find that: (1) our model captures the ring-like and patchy plaque morphologies observed experimentally; (2) IFN production peaks at an intermediate DIP ratio, reflecting a trade-off between early immune activation and sufficient co-infection; and (3) even a small fraction of long-range spread by virus and DIPs enables escape from the immune-based containment despite long-range IFN diffusion; this causes stronger antiviral responses but earlier peaks in virus egress at similar levels of cell loss. The model is available as an interactive platform: https://shiny-spatial-infection-app-production.up.railway.app/.},
}
@article {pmid42019450,
year = {2026},
author = {Guo, Z and Wang, Z and Liu, Y and Wang, M and Ma, H and Wang, Z and Zhang, S and Chang, Y and Ge, H and Li, C and Yang, H and Miao, H and Zhang, X and Cui, P},
title = {Early-life and lifelong exposure to environmentally relevant enrofloxacin reorganizes a proteobacteria-centered gut-lipid-resistome steady state in marine medaka.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142146},
doi = {10.1016/j.jhazmat.2026.142146},
pmid = {42019450},
issn = {1873-3336},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Enrofloxacin/toxicity ; *Water Pollutants, Chemical/toxicity ; Lipid Metabolism/drug effects ; *Oryzias/microbiology ; *Anti-Bacterial Agents/toxicity ; *Proteobacteria/drug effects/genetics ; Intestines/drug effects/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Environmental fluoroquinolone residues such as enrofloxacin (ENR) are increasingly detected in coastal waters, yet the persistence of low-dose effects on gut ecosystem organization remains unclear. We compared an early-life window exposure (5 μg/L ENR, 20-35 days post-hatch; depurated to 150 dph) with a lifelong exposure (5 μg/L ENR from fertilization to 150 dph) in marine medaka (Oryzias melastigma), using an environmentally realistic upper-bound concentration reflecting aquaculture-impacted conditions. We integrated intestinal histology and ultrastructure, inflammatory and lipid-metabolic transcriptional programs, intestinal fatty-acid profiles, 16S rRNA and 2bRAD-M characterization of the gut microbiota and antibiotic-resistance genes. Both regimens increased intestinal hypertrophy or densification and rewired communities into more positively connected, Proteobacteria-centered networks. Lifelong exposure produced a pronounced shift in intestinal lipid programming, marked by enhanced lipogenesis and reduced fatty-acid catabolism, together with selective changes in fatty-acid composition and desaturation balance. Early-life window exposure left persistent, albeit weaker, adult signatures in intestinal morphology, microbial network topology, and lipid-related transcription after prolonged withdrawal. Across cohorts, Proteobacteria indicator taxa covaried with inflammatory and lipid gene modules and with coordinated resistance-gene modules, consistent with a Proteobacteria-rich gut-lipid-resistome steady state. These findings indicate that ENR at an environmentally realistic upper-bound concentration reflecting aquaculture-impacted and hotspot contamination scenarios can durably reorganize host-microbe-resistome linkages, supporting re-evaluation of "no-effect" thresholds for antibiotic pollution from a One Health perspective.},
}
@article {pmid42020482,
year = {2026},
author = {Sun, X and Guan, J and Meng, L and Wang, C and Chen, N and Wei, T and Xing, S},
title = {Predicting future habitat suitability of Smilax glabra under climate change scenarios.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42020482},
issn = {2045-2322},
mesh = {*Smilax/growth &amp; development/physiology ; *Climate Change ; *Ecosystem ; China ; Geographic Information Systems ; },
abstract = {The rhizome of Smilax glabra Roxb., known as Smilacis glabrae Rhizoma, is extensively used in Traditional Chinese Medicine for relieving dampness and other health issues. The growth patterns and geographical distribution of S. glabra are significantly influenced by ecological conditions. This study used the maximum entropy (MaxEnt) modeling approach in combination with the geographic information system (GIS) software (ArcMap) to evaluate and predict the influence of climate change on the geographical distribution of S. glabra. The potential suitable habitats under two greenhouse gas emission scenarios (SSP126 and SSP370) were forecast for two future timeframes (2041-2060 and 2061-2080) by analyzing species occurrence records and environmental factors. Jackknife method was employed to assess the significance of environmental variables, and those contributing ≥ 1.0% to the model were considered as major driving factors. S. glabra is widely distributed in the southern provincial regions of the Yangtze River Basin in China. Currently, the suitable habitat covers 1,755,900 km[2]. In the predicted future climate scenarios, the suitable habitat area is projected to extend to a maximum of 1,915,400 km[2]. The distribution of S. glabra is significantly influenced by rainfall, daily temperature variation, and soil clay composition. Moreover, under both the projected climate scenarios, the core of suitable habitats for S. glabra were predicted to migrate southward. Overall, our findings offer a scientific basis for developing conservation approaches and optimize their spatial distribution management of the genetic sources of S. glabra.},
}
@article {pmid42021765,
year = {2026},
author = {Boyes, D and Crowley, LM and McCulloch, J and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Acorn Weevil, Curculio glandium (T.Marsham, 1802) (Coleoptera: Curculionidae).},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {178},
pmid = {42021765},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Curculio glandium (Acorn Weevil; Arthropoda; Insecta; Coleoptera; Curculionidae). The genome sequence has a total length of 1 121.34 megabases. Most of the assembly (97.77%) is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 21.61 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 {pmid42022432,
year = {2026},
author = {Hanf-Dressler, T and Nouioua, R and Thomisch, K and Cazau, D and de Selys Longchamps, S and Darras, KFA},
title = {Software Tools for Passive Acoustic Monitoring in Aquatic and Terrestrial Bio- and Ecoacoustics: A Living Systematic Review.},
journal = {F1000Research},
volume = {15},
number = {},
pages = {48},
pmid = {42022432},
issn = {2046-1402},
mesh = {*Software ; *Acoustics ; *Environmental Monitoring/methods ; Ecosystem ; Biodiversity ; },
abstract = {Biodiversity monitoring is crucial for understanding species trends and their responses to anthropogenic change. Passive acoustic monitoring (PAM) offers a scalable, non-invasive approach to capture ecological information across large spatial and temporal scales. However, it generates vast amounts of audio recordings, whose management and analysis present technical challenges. To support diverse user needs in ecoacoustic research, a growing number of software tools have emerged, but the landscape remains fragmented and difficult to navigate. We provide a systematic overview of software tools used for soundscape assessment across terrestrial, freshwater, and marine environments. We screened peer-reviewed literature and complemented it with database cross-checking to identify and categorize tools according to four PAM data workflow components: data management, signal pre-processing, visualisation and navigation, and acoustic analysis. We found 221 available tools of which 174 were explicitly designed for PAM. Most tools were freely accessible (83%) with only a smaller fraction being commercial (12%) or limited access (5%). Terrestrial research accounted for most software mentions (476 studies), followed by aquatic (319) and cross-realm (64) studies. Nearly half (45%) were package-based frameworks within R, Python, or MATLAB. Acoustic analysis was the most represented workflow component, while only 40 tools covered all four of them. This diversity illustrates the field's rapid technical growth but also its redundancy and methodological fragmentation: to date, many tools target only a subset of workflow components and replicate similar functionalities. Despite this, the prevalence of PAM-dedicated software indicates increasing specialization and technical maturity within ecoacoustics. Our structured inventory underscores the need for greater collaboration and continuity in software development, promoting the improvement and accessibility of existing tools rather than further proliferation. This living systematic review, provides a practical, biannually updated reference for tool selection and fosters transparency, comparability, and cooperation across bioacoustic and ecoacoustic research communities.},
}
@article {pmid42022830,
year = {2026},
author = {Agbajelola, V and Raghavan, RK},
title = {A systematic review and meta-analysis of population-based anthrax prevalence in Africa with a one health narrative synthesis of outbreak surveillance.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1792476},
pmid = {42022830},
issn = {2296-2565},
mesh = {*Anthrax/epidemiology ; Humans ; Africa/epidemiology ; Prevalence ; *Disease Outbreaks/statistics &amp; numerical data/veterinary ; Animals ; *One Health ; *Population Surveillance ; Cross-Sectional Studies ; },
abstract = {BACKGROUND: Anthrax remains a persistent public health, veterinary, and ecological challenge in Africa, sustained by fragmented surveillance systems characterized by underreporting, limited diagnostic capacity, and weak cross-sectoral coordination. The absence of integrated surveillance across human, livestock, wildlife, and environmental interfaces constrains accurate burden estimation and timely outbreak response.<br><br>METHODS: We conducted a systematic review and meta-analysis following PRISMA guidelines to synthesize available evidence on anthrax epidemiology in Africa. Studies published between January 2000 and February 2025 were identified from PubMed and Web of Science. Observational studies reporting primary epidemiological data in humans, livestock, wildlife, or environmental samples were eligible. Quantitative synthesis was restricted to cross-sectional studies reporting extractable prevalence data. Pooled estimates were generated using a logit-transformed random-effects model (REML), with heterogeneity assessed using I [2] and &#x3c4;[2] statistics. Studies not meeting meta-analytic criteria were synthesized narratively within a One Health framework.<br><br>RESULTS: Ten cross-sectional studies comprising 19,955 samples and 2,079 confirmed anthrax cases were included in the meta-analysis. The crude aggregated prevalence was 9.88% (95% CI: 9.46%-10.30%). The pooled prevalence from the logit-transformed random-effects model was 20% (95% CI: 8%-44%). Substantial heterogeneity was observed (I [2] = 98.2%), indicating marked epidemiological variability across ecological settings, host populations, and surveillance systems. Narrative synthesis further highlighted wildlife outbreaks and environmental persistence of Bacillus anthracis, though such studies remain comparatively scarce.<br><br>CONCLUSION: The available evidence on anthrax in Africa is limited, geographically uneven, and highly heterogeneous. The pooled estimate should therefore be interpreted as a summary measure of reported prevalence rather than a precise continental burden estimate. These findings underscore persistent transmission within fragmented surveillance systems and support strengthened One Health-based approaches integrating human, animal, wildlife, and environmental health sectors to improve surveillance, early detection, and coordinated response across Africa.},
}
@article {pmid42025279,
year = {2026},
author = {Shen, A and Shen, W and Zhu, Y and Zeng, J},
title = {Multi-omics investigation of the molecular response of typical bloom-forming species Prorocentrum shikokuense to stoichiometric phosphorus limitation under a high nitrogen-to-phosphorus ratio.},
journal = {Marine environmental research},
volume = {218},
number = {},
pages = {108071},
doi = {10.1016/j.marenvres.2026.108071},
pmid = {42025279},
issn = {1879-0291},
mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism/analysis ; *Dinoflagellida/physiology/genetics ; *Eutrophication ; China ; Phytoplankton ; Transcriptome ; Multiomics ; },
abstract = {Nitrogen and phosphorus are essential nutrients for marine phytoplankton, with their ratio critically influencing ecosystem dynamics. The high nitrogen-to-phosphorus (N/P) ratio in the East China Sea (ECS) results in stoichiometric phosphorus limitation, which is a primary constraint on phytoplankton growth. Nevertheless, the dinoflagellate Prorocentrum shikokuense can form persistent, large-scale blooms even when dissolved inorganic phosphorus concentrations are low. The molecular mechanisms behind its adaptation to stoichiometric P limitation under high N/P ratios remain unclear. This study applied multi-omics analyses to investigate the response of P. shikokuense to stoichiometric P limitation under a high N/P ratio. We identified 431 differentially expressed genes (DEGs: 139 up, 292 down), 617 differentially expressed proteins (DEPs: 135 up, 482 down), and 217 differentially accumulated metabolites (DAMs: 51 up, 166 down). Integrated analysis revealed 61 metabolic pathways common to at least two omics layers. Key enriched pathways included photosynthesis, oxidative phosphorylation, nucleotide metabolism, and nitrogen metabolism. Pathways related to genetic information processing were downregulated, and energy metabolism was constrained. This subsequently suppressed nitrogen transport, assimilation, allocation, and secondary metabolism. In summary, these results elucidates the transcriptional, proteomic, and metabolic adjustments enabling P. shikokuense to thrive under stoichiometric P limitation based on a high N/P ratio. These findings provide a scientific basis for understanding its bloom dynamics in the ECS waters subject to stoichiometric P limitation under high N/P ratios.},
}
@article {pmid42026820,
year = {2026},
author = {Melendez, D and Şapcı, AOB and Bafna, V and Mirarab, S},
title = {SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70145},
pmid = {42026820},
issn = {1755-0998},
support = {//Minderoo Foundation/ ; },
mesh = {*Genetic Variation ; Animals ; *Genetics, Population/methods ; *Conserved Sequence ; *DNA/genetics ; Invertebrates/genetics/classification ; *Computational Biology/methods ; Vertebrates/genetics/classification ; },
abstract = {Ultraconserved elements (UCEs) provide ideal candidates for targeted sequencing and cost-effective acquisition of genome-wide data. While UCEs have been widely used in phylogenetic studies to reconstruct evolutionary relationships, their use in population-level research has been limited. This limited application stems from uncertainty over whether UCEs can capture the levels of genetic variation needed to answer population genomic questions central to ecology and biodiversity research. The concern is that, by definition, UCEs are highly conserved and may therefore lack sufficient within-species variation. The more variable flanking regions (400-750 bp from the UCE core) contain informative polymorphisms, though diversity decreases near the core. Thus, any naive estimator of genetic diversity that ignores this conservation will have an underestimation bias. In this paper, we introduce SPrUCE: Sigmoid Pi requiring UCEs, a reference-free method that estimates nucleotide diversity π $$ \pi $$ from aligned UCE data. SPrUCE corrects underestimation bias by modelling the change in diversity away from the UCE core using a Gompertz function. The model accounts for the bias introduced by the conserved core and allows for more accurate per-site diversity estimates. We tested SPrUCE on UCE alignments from a range of taxa, including invertebrates and vertebrates (finches, honeybees, sheep and smelt). SPrUCE produces diversity values consistent with whole-genome derived estimates that require an assembled reference. It is fast, scalable, and effective even with missing data. Its modelling approach enables accurate population-level assessments of genetic diversity, offering a new and reliable option for conservation and population genetics.},
}
@article {pmid42027768,
year = {2026},
author = {Ylinampa, TA and Kõljalg, U},
title = {The Orbitoscope, a six-axis macro-imaging robot for photogrammetric 3D-digitization of insects and other small specimens.},
journal = {ZooKeys},
volume = {1277},
number = {},
pages = {137-155},
pmid = {42027768},
issn = {1313-2989},
abstract = {Natural history collections contain vast numbers of small, fragile specimens whose morphology is difficult to capture using conventional 2D-imaging. Photogrammetric 3D-reconstruction from multi-view photographs can preserve surface colour and enable scaled measurement, but at macro magnification it typically requires dense viewpoint coverage with high overlap and extended depth-of-field (EDOF) imagery. Existing robotic systems often achieve viewpoint variation by rotating and tilting the specimen, which can be limiting for elongated, heavy, or fragile mounts and for objects whose geometry may change when reoriented. We present the Orbitoscope, an open-source six-axis macro-imaging robot that keeps the specimen stationary while moving the camera in translation (X-Y-Z) and orientation (A-B) around it, with a dedicated stacking axis (C) to acquire focus stacks automatically. We demonstrate the workflow by digitizing six insect specimens and generating scaled, textured 3D models suitable for preservation, measurement, and online dissemination. Basic measurement validation on one specimen showed a mean absolute percent error of 0.52% (max. 0.88%) relative to calibrated microscope reference measurements. Hardware, software, and documentation are openly released, with detailed build and operation instructions archived separately as a technical package.},
}
@article {pmid42030493,
year = {2026},
author = {Wei, S and Van, S and Shia, C and Gancz, M and Camenga, D and Aneni, K and Marks, A and Hieftje, K},
title = {Psychophysiological Responses in Virtual Reality for Assessing Current Nicotine Use and Future Addiction Risk Among Young Adults: Protocol for a Mixed Methods Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e89382},
pmid = {42030493},
issn = {1929-0748},
support = {K23 DA059638/DA/NIDA NIH HHS/United States ; },
mesh = {Humans ; Young Adult ; Adolescent ; Pilot Projects ; *Virtual Reality ; Male ; Craving/physiology ; Female ; Heart Rate/physiology ; *Tobacco Use Disorder/psychology/diagnosis/physiopathology ; Galvanic Skin Response ; Cues ; *Vaping/psychology ; *Behavior, Addictive/psychology ; *Psychophysiology/methods ; },
abstract = {BACKGROUND: Nicotine addiction among youth is a continuing public health concern, and vaping serves as a major pathway to nicotine use. Conventional assessments of craving and addiction risk rely on self-reports, which are prone to bias and lack sensitivity to real-time processes. Virtual reality (VR) enables controlled cue exposure while capturing real-time multimodal data, including subjective experiences, behavioral patterns, and physiological responses, which offer a more implicit and dynamic approach to identifying addiction risk.<br><br>OBJECTIVE: This pilot study examines whether subjective craving and psychophysiological responses (eg, eye gaze, heart rate, and electrodermal activity) to vaping-related cues in VR can distinguish young adults who vape from those who do not. Our secondary objective is to explore associations between these multimodal biomarkers and self-reported measures of craving, dependence, motivation to quit, and susceptibility to initiate vaping.<br><br>METHODS: Bespoke VR scenes were developed with input from a youth advisory board to ensure ecological validity. Forty young adults aged 18 to 21 years (20 vapers and 20 nonvapers) will complete a single laboratory session. Participants will experience 3 VR scenes (neutral baseline, vaping cues without social pressure, and vaping cues with social pressure in counterbalanced order). Eye gaze, heart rate, and electrodermal activity will be recorded continuously. Participants will complete standardized assessments of craving, sense of presence, and social presence in VR after each cue scene, followed by a short interview at the end. Quantitative data will be analyzed using mixed-model ANOVAs, correlation metrics, and exploratory regularized regression analyses to examine relationships between physiological responses, behavioral measures, and vaping status.<br><br>RESULTS: The project received institutional review board approval in August 2025 and was registered publicly in the Open Science Framework in November 2025. Development of the VR stimuli was completed in December 2025. Participant recruitment and data collection began in February 2026, and 7 participants have been enrolled as of March 2026.<br><br>CONCLUSIONS: This protocol outlines a pilot study integrating immersive VR and multimodal biometrics to examine vaping cue reactivity in young adults. The findings will guide the development and evaluation of VR-based psychophysiological tools for identifying early markers of nicotine use risk. This work will also lay the foundation for adapting the approach to younger adolescents to support scalable early detection and prevention of nicotine addiction and initiation.},
}
@article {pmid42032815,
year = {2026},
author = {Min, J and Ning, Y and Pope, NS and Baumdicker, F and Kern, AD},
title = {Neural posterior estimation for population genetics.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyag107},
pmid = {42032815},
issn = {1943-2631},
support = {R01 HG010774/HG/NHGRI NIH HHS/United States ; R01 HG012473/HG/NHGRI NIH HHS/United States ; R35 GM148253/GM/NIGMS NIH HHS/United States ; },
abstract = {Simulation-based inference methods are increasingly being used in population genetics due to their flexibility and ability to be applied in settings where likelihood-based methods are intractable. Perhaps the best known such method is Approximate Bayesian Computation (ABC); however, its popularity is offset by its shortcomings which include computational expense and an unfortunate inability to efficiently fit models to high-dimensional summaries of the data. An alternative approach that solves these issues is supervised machine learning (ML); however, ML methods generally do not yield Bayesian uncertainty estimates of the quantities they predict. Here, we apply a recently introduced method, neural posterior estimation (NPE), that combines the best facets of ABC and supervised ML by training a neural network to estimate the posterior distribution of a population genetics model. We first compare neural posterior estimation with other inference methods for a variety of population genetic tasks, and show that neural posterior estimators yield posterior distributions with high accuracy and efficiency. We compare learned posterior distributions given raw genotypes and various summary statistics as input data. Additionally, we apply neural posterior estimation for demographic inference for simple and more complex models to highlight its application, including an analysis of demographic history in Drosophila melanogaster. Finally, we provide a user friendly workflow that enables others to perform neural posterior estimation on their own genetic data.},
}
@article {pmid42037082,
year = {2026},
author = {Spöri, Y and Flot, JF},
title = {Champuru 2: Improved Scoring of Alignments and a User-Friendly Graphical Interface.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70110},
pmid = {42037082},
issn = {1755-0998},
mesh = {*Software ; *Computational Biology/methods ; *Sequence Alignment/methods ; User-Computer Interface ; Computer Graphics ; *Sequence Analysis, DNA/methods ; Internet ; Algorithms ; },
abstract = {Champuru is a web-based software tool that helps determine the two sequences present in mixed Sanger chromatograms obtained by simultaneously sequencing two DNA templates of unequal lengths. A previous version (Champuru 1.0) was published as a simple Perl CGI (Common Gateway Interface) application, but the server hosting it was decommissioned, which prompted us to update Champuru and develop it further. The new Champuru 2, implemented in Haxe and hosted at GitHub Pages, offers an improved graphical user interface as well as more sophisticated algorithms to compute alignment scores, making it more efficient at detecting the most likely alignment positions between forward and reverse traces. It also compares the distribution of alignment scores to the theoretical expectation for the comparison of two random sequences and uses this comparison to calculate p-values for the offset pairs it detects. Moreover, Champuru 2 now makes it possible to analyse other offset pairs than the one detected as most likely by the selected algorithm. Champuru 2 is freely accessible at https://eeg-ebe.github.io/Champuru/, including both a graphical user interface (running a JavaScript version transpiled from the Haxe source code) and a compiled command-line version (obtained by transpiling the Haxe source code into C++).},
}
@article {pmid42038460,
year = {2026},
author = {Li, J and Wang, QY},
title = {Multi-omics insights into mosquito insecticide resistance for integrated vector management.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21083},
pmid = {42038460},
issn = {2167-8359},
mesh = {*Insecticide Resistance/genetics ; Animals ; *Mosquito Vectors/genetics/drug effects ; *Mosquito Control/methods ; *Insecticides/pharmacology ; Genomics ; Multiomics ; },
abstract = {Escalating insecticide resistance in mosquito vectors threatens the durability of vector-borne disease control and increasingly constrains the effectiveness of core interventions. This resistance is a multilayered adaptive phenotype arising from the combined action of target-site substitutions that reduce insecticide sensitivity, transcriptional and enzymatic upregulation of detoxification systems that enhance xenobiotic metabolism, cuticular and behavioral changes that limit exposure and penetration, and transporter-mediated efflux, with additional modulation by microbiota and local environmental conditions that shape phenotypic expression in the field. Current integrated vector management (IVM) strategies aim to mitigate resistance through operationally guided deployment of dual-active-ingredient or synergist-treated nets, indoor residual spraying with rotations or mixtures, integration of larval source management and habitat modification, and incorporation of nonchemical tools such as Wolbachia releases and genetic control, supported by routine resistance surveillance. However, much of the existing evidence remains fragmented, with an overreliance on a narrow set of insecticide classes and a limited number of genetic markers, variable phenotyping and performance metrics across settings, and insufficient prospective linkage between molecular signals and intervention impact under real transmission ecologies. Multi-omics frameworks provide a route to move beyond single-locus screening toward network-level reconstruction of resistance biology, enabling discovery of predictive biomarkers, pathway signatures, and metabolic readouts that can be translated into actionable diagnostics and locally optimized decision rules. Looking forward, omics-enabled precision surveillance integrated with field-deployable assays, standardized benchmarks, and model-informed adaptive management could support closed-loop resistance mitigation in which operational choices are continuously refined to preserve long-term intervention efficacy within IVM programs.},
}
@article {pmid42040854,
year = {2026},
author = {Kietzka, GJ and Pryke, JS and Gaigher, R and Samways, MJ and Hui, C},
title = {Evaluating Conservation Corridor Success for Rare and Common Dragonflies Using Zeta Diversity.},
journal = {Ecology and evolution},
volume = {16},
number = {4},
pages = {e73251},
pmid = {42040854},
issn = {2045-7758},
abstract = {Conservation corridors connect natural areas, aiming to mitigate the effects of land transformation. However, their influence on biodiversity, particularly species turnover, remains poorly understood. This study evaluates the impact of conservation corridors on riverine ecosystems and their associated dragonfly assemblages. We assessed species richness and applied the zeta diversity framework to evaluate species turnover across multiple sites, thereby providing insights into how these corridors influence dragonfly community composition relative to natural areas. The research was conducted in the KwaZulu-Natal Midlands of South Africa, covering 104 freshwater sites within natural grasslands and timber plantation corridors. At each site, a 100 m transect adjacent to a river was sampled twice, focusing on recording adult male dragonflies and six environmental variables. Drivers of species richness were analysed using generalised additive models and generalised linear models. Multi-site generalised dissimilarity models were run to examine changes in zeta diversity along environmental gradients and to partition the contributions of different factors to compositional turnover. A total of 37 species were recorded, with one species exclusive to natural areas and four unique to corridors. Dragonfly assemblages were influenced more by stochastic processes than by environmental gradients. Although factors such as site distance, differences in water temperature, dissolved oxygen, shade and rock cover affected turnover, they explained little variation in both rare and common species. Species richness was higher in corridors and consistently declined with increasing shade cover. Neither the presence of corridors nor invasive alien vegetation influenced species turnover, indicating that corridors function similarly to natural habitats. This study demonstrates the crucial role of conservation corridors in preserving dragonfly diversity in altered landscapes. Our findings support continued investment in corridor implementation and management for biodiversity conservation and demonstrate the utility of the zeta diversity framework for understanding species turnover dynamics.},
}
@article {pmid42041468,
year = {2026},
author = {Gerolimos, N and Kiskira, K and Sfyroera, E and Tsoumas, J and Alevizos, V and Plakantonaki, S and Foka, M and Priniotakis, G},
title = {Integrating Biomimetic Reasoning Into Early-Stage Design Thinking for Sustainable Textile Development.},
journal = {Biomimetics (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
pmid = {42041468},
issn = {2313-7673},
abstract = {This study explores the potential of biomimetic reasoning to inform early-stage design thinking, with a focus on enhancing the consideration of material utilization and textile waste. While sustainability efforts within the field of textiles are often focused on recycling and end-of-life management strategies, it is important to recognize that a substantial proportion of final waste-related outcomes are determined during the conceptual design stage and the initial prototyping iterations. This study investigates the potential of organizational principles derived from natural systems to inform the definition of problems, the generation of ideas, and early conceptual prototyping. This is achieved by the introduction of ecological constraints and material life-cycle awareness in conjunction with user-centered requirements. To address the conceptual gap between biological forms and manufacturing, biomimicry is approached as a mode of systemic reasoning, utilizing topological skeletonization as a tool for logic extraction rather than formal imitation, with emphasis placed on continuity, modularity, and adaptive organization. This computational proof-of-concept employs a Particle Swarm Optimization (PSO) framework, utilizing biological venation as a topological guide to demonstrate how distinct organizational logics influence pattern configuration while incorporating manufacturing-inspired constraints (such as path continuity and density) as optimization penalties. The findings are exploratory in nature and are confined to the computational domain; while the study utilizes proxy indicators to simulate potential textile behaviors, it acknowledges the lack of direct experimental validation of physical fabrication as a current limitation. By framing waste as an outcome of upstream design choices, this paper contributes a methodological perspective. This perspective places biomimetic design thinking as a reflective tool within sustainable and regenerative design practice. It also supports earlier engagement with ecological considerations in textile development.},
}
@article {pmid42047788,
year = {2026},
author = {Gambetta Vianna, J and Ceccardi, E and Benedetti, B and Oh, JK and Di Carro, M and Pizzini, S and Magi, E},
title = {Assessing emerging contaminants in Antarctic benthic marine fauna: a dual mass spectrometry investigation combining targeted and suspect screening approaches.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {42047788},
issn = {1618-2650},
support = {PNRA18_00216-B2//Ministero dell'Universit&#xe0; e della Ricerca, National Program of Research in Antarctica, Italy/ ; },
abstract = {Antarctica hosts a highly endemic and diverse benthic marine fauna. Despite this biodiversity, the Antarctic marine food web remains structurally simple, rendering the ecosystem particularly vulnerable to environmental stressors. Benthic organisms, due to their sedentary nature, long lifespans, and close interaction with the sediment-water interface, are widely regarded as effective sentinels of ecological change. In this study, we extended a previously validated QuEChERS-based extraction protocol, originally developed for Adamussium colbecki organisms, to assess its applicability across additional Antarctic benthic taxa, including Sphaerotylus antarcticus, Odontaster validus, Trematomus bernacchii, and Laternula elliptica. The extraction method was used in combination with LC-MS/MS analysis for the determination of emerging contaminants in both targeted and suspect screening modes. Method performance was evaluated for 23 targeted emerging contaminants (ECs), yielding recovery rates of 58-116% and matrix effects between 62 and 108% for most compounds, confirming the method's suitability for taxonomically diverse matrices. Samples collected during Antarctic expeditions from 2018 to 2022 revealed the presence of multiple ECs, including perfluorooctanoic acid (PFOA), caffeine, pharmaceuticals and personal care products (PPCPs), and UV filters. Complementarily, a preliminary suspect screening via high-resolution mass spectrometry was attempted, revealing the potential presence of a broader spectrum of drugs, PPCPs, and lifestyle-related compounds in all studied species. This work represents one of the first applications of a QuEChERS-based analytical framework for ECs detection in Antarctic marine fauna, offering a reliable approach for long-term contaminant monitoring in one of the planet's most fragile ecosystems.},
}
@article {pmid42050104,
year = {2026},
author = {Rubin, L and Nowack, R and Lang, F and Stiasny, P and Puhlmann, H},
title = {Deadwood effects on dissolved organic carbon in forest soils depend on bedrock type, tree species, and microclimate.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42050104},
issn = {2045-2322},
abstract = {Deadwood plays an important role in the forest carbon cycle by supplying dissolved organic carbon to the underlying soils. Yet, the extent to which this effect varies across different site conditions remains insufficiently understood. We monitored dissolved organic carbon at multiple soil depths beneath European beech and Norway spruce logs at sites with contrasting bedrock types over 2.5 years, comparing them with adjacent control plots. Concentrations were consistently elevated beneath deadwood, but the magnitude of the increase varied with bedrock type, tree species, and depth, and was influenced by soil temperature and moisture. Differences between deadwood and control were minor beneath the forest floor but pronounced in the upper mineral soil (15 cm), with the strongest increase (+ 90%) observed at the silicate site. When separating by tree species, this increase was driven by beech deadwood, while spruce showed little effect. At the silicate site, concentrations declined markedly between 15 and 30 cm, suggesting enhanced retention or processing in deeper layers. The effect of soil moisture on DOC was similar between deadwood and control plots, but temperature effects differed. These results indicate that the contribution of deadwood to soil carbon inputs is context-dependent, varying with tree species and soil properties.},
}
@article {pmid42053508,
year = {2026},
author = {Tandon, D and De Farias, TM and Allard, PM and Defossez, E},
title = {METRIN-KG: A knowledge graph integrating plant metabolites, traits, and biotic interactions.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag051},
pmid = {42053508},
issn = {2047-217X},
abstract = {BACKGROUND: In recent years, biodiversity data management has emerged as a critical pillar in global conservation efforts. Today, the ability to efficiently collect, structure, and analyze biodiversity data is central to breakthroughs in conservation, drug development, disease monitoring, ecological forecasting, and agri-tech innovation. However, due to the vastness and heterogeneity of biodiversity data, it is often confined to databases for specific research areas in isolated formats and disconnected from other relevant resources. Crucial components of such data in kingdom Plantae comprise of metabolomes-the vast array of compounds produced by plants; traits-measurable characteristics of plants that influence their growth, survival, and reproduction, and that affect ecosystem processes; and biotic interactions-relationships of plants with other living organisms, affecting the ecosystem functions.<br><br>RESULTS: In this work, we present METRIN-KG (MEtabolomes, TRaits, and INteractions-Knowledge Graph) a powerful data resource simplifying the integration of diverse and heterogeneous data resources such as plant metabolomes, traits, and biotic interactions.<br><br>CONCLUSIONS: The proposed knowledge graph provides an interface to interactively search for data relating plant metabolomes, traits, and interactions. This, in turn, will facilitate development of research questions in life-sciences. In this context, we provide representative case studies on how to frame queries that can be used to search for relevant data in the knowledge graph.},
}
@article {pmid42054418,
year = {2026},
author = {Arnold, CRK and Kong, AC and Winter, AK and Moss, WJ and Patenaude, BN and Ferrari, MJ},
title = {Individual and population level uncertainty interact to determine the performance of outbreak surveillance systems.},
journal = {PLoS computational biology},
volume = {22},
number = {4},
pages = {e1013309},
pmid = {42054418},
issn = {1553-7358},
mesh = {Humans ; *Disease Outbreaks/statistics &amp; numerical data ; Measles/epidemiology/diagnosis ; Uncertainty ; Computer Simulation ; Computational Biology ; *Population Surveillance/methods ; Stochastic Processes ; Incidence ; },
abstract = {BACKGROUND: Outbreak detection frequently relies on imperfect individual-level case diagnosis. Both outbreaks and cases are discrete events that can be misclassified and uncertainty at the case level may impact the performance of outbreak alert and detection systems. Here, we describe how the performance of outbreak detection depends on individual-level diagnostic test characteristics and population-level epidemiology, and describe settings where imperfect individual-level tests can achieve consistent performance comparable to "perfect" diagnostic tests.<br><br>METHODOLOGY: We generated a stochastic SEIR model to simulate daily incidence of measles (i.e., true) and non-measles (i.e., noise) febrile rash illness. We modeled non-measles sources as either independent static (Poisson) noise, or dynamical noise consistent with an independent SEIR process (e.g., rubella). Defining outbreak alerts as the exceedance of a threshold by the 7-day rolling average of observed test positives, we optimized the threshold that maximized outbreak detection accuracy across sets of noise structures and magnitudes, diagnostic test accuracy (consistent with either a perfect test, or proposed rapid diagnostic tests), and testing rates.<br><br>CONCLUSIONS: The optimal threshold for each diagnostic test typically increased monotonically with testing rate. With static noise, outbreak detection with RDT-like and perfect tests achieved accuracies of 90%, with comparable delays to outbreak detection. With dynamical noise, the accuracy of perfect test scenarios was superior to those achieved with RDTs (&#x2248; 90% vs.&#x2009;&#x2264;&#x2009;80%). Outbreak detection accuracy declined as dynamical noise increased and leads to permanent alert status with RDT-like tests at very high noise. The performance of an outbreak detection system is highly sensitive to the structure and the magnitude of the background noise. Depending on the epidemiological context, outbreak detection using RDTs can perform as well as perfect tests.},
}
@article {pmid42055456,
year = {2026},
author = {Bohling, SM and Musharoff, S and Gunn, LH},
title = {Advances and opportunities for computational interrogation of plant proteins.},
journal = {The Plant journal : for cell and molecular biology},
volume = {126},
number = {3},
pages = {e70899},
pmid = {42055456},
issn = {1365-313X},
support = {DE-SC0024175//U.S. Department of Energy/ ; },
mesh = {*Plant Proteins/metabolism/genetics/chemistry ; *Computational Biology/methods ; *Plants/metabolism/genetics ; },
abstract = {Plants exhibit remarkable biochemical and physiological diversity, and are capable of adapting to a wide range of environmental conditions and stresses. This complexity makes them essential systems for understanding how life responds to a changing climate. Plant proteins are the molecular engines that carry out the reactions, signalling and regulation underlying these adaptive processes. However, studying plant proteins remains constrained by limited experimental throughput and the challenges of genetic manipulation, which vary widely across species. While synthetic biology and heterologous expression systems have expanded opportunities to investigate plant proteins, in planta studies are still limited by the availability and efficiency of genetic transformation methods. Computational approaches offer a powerful complement to experimental research by generating high-throughput, testable hypotheses that can accelerate discovery of plant protein function. In recent years, the power, versatility and ease of use of computational tools for protein research have expanded dramatically. These methods now enable detailed predictions of protein structure, dynamics and interactions, as well as insights into their evolutionary history and mechanistic function. In this review, we highlight the expanding computational toolkit for plant protein analysis, emphasising both established and emerging approaches. We summarise recent successes where computational methods have provided key biological insights into plant protein function and highlight the potential of such methods for scientific discovery in plant research. By integrating computation with experimentation, plant biology can overcome current limitations to studying plant proteins and move more rapidly toward a mechanistic understanding of plant processes, enabling advances in agriculture, ecology and climate resilience.},
}
@article {pmid42056177,
year = {2026},
author = {Agrawal, N and Mahrishi, M and Gupta, MK and Bohra, MK},
title = {Large scale multi-class pest image classification using structurally adapted DenseNet architecture.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49685-8},
pmid = {42056177},
issn = {2045-2322},
abstract = {The United Nations' Sustainable Development Goals, SDG 12: Responsible Consumption and Production, and SDG 13: Climate Action highlight the importance of environmental conservation and reducing pesticide use. Early and accurate pest identification is essential for implementing targeted pest control measures, which helps reduce unnecessary and incorrect pesticide use. While effective pest recognition and classification are crucial for ecological research and biodiversity conservation, traditional methods remain labor-intensive, time-consuming, and dependent on experts. Several deep learning techniques have been introduced in recent years, leading to more efficient and accurate identification and classification of crop pests. This research presents a structurally adapted DenseNet model for multi-class pest image classification based on dense connections. The model is fine-tuned through hyperparameters involving dense blocks and transition layers to perform consistently across three different datasets, including the IP102 dataset, which contains over 75,000 images of 102 pest species. The study also addresses dataset imbalance to prevent biased outcomes by deep learning models. The proposed structurally adapted model for fine-grained classification achieves 82.69% accuracy and 81.45% F1 score on the IP102 dataset, complementing existing advanced methods.},
}
@article {pmid42056695,
year = {2026},
author = {Kim, KM and Hwang, K},
title = {Phylogenomic Tree Reconstruction from Bacterial Genomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2981},
number = {},
pages = {221-233},
pmid = {42056695},
issn = {1940-6029},
mesh = {*Phylogeny ; *Genome, Bacterial ; *Genomics/methods ; *Bacteria/genetics/classification ; *Computational Biology/methods ; Software ; Databases, Genetic ; Gene Transfer, Horizontal ; },
abstract = {The recent, rapid expansion of available prokaryotic genomes has fueled significant advancements in phylogenomics within microbial ecology and evolution. However, comprehensive protocols for reconstructing phylogenomic trees from bacterial genomes remain scarce. To address this gap, we present a series of essential bioinformatics steps. This protocol begins with setting up a Docker environment to ensure consistent implementation across different operating systems. We demonstrate phylogenomic tree reconstruction using the Genome Taxonomy Database and its toolkits with five test genomes, which were retrieved from the NCBI database, quality-checked with CheckM, aligned using GTDB-Tk, and analyzed for tree reconstruction with RAxML. Genome-level phylogenetic analyses are often complicated by gene duplication, horizontal gene transfer, and computational demands that increase with the number of taxa. We discuss practical strategies for addressing these issues and highlight the value of orthologous gene concatenation in generating accurate phylogenomic trees.},
}
@article {pmid42056701,
year = {2026},
author = {Hernández-Morales, R and Luna, CCG and Lazcano, A and Becerra, A},
title = {Protein Architecture Comparisons and the Reconstruction of the Last Universal Common Ancestor (LUCA).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2981},
number = {},
pages = {309-322},
pmid = {42056701},
issn = {1940-6029},
mesh = {Phylogeny ; *Evolution, Molecular ; Archaea/genetics ; *Computational Biology/methods ; Bacteria/genetics ; *Proteins/chemistry/genetics ; },
abstract = {The Last Universal Common Ancestor (LUCA) represents an early stage of evolution that can be studied using phylogenetic and bioinformatic methods. Research efforts focus on reconstructing LUCA's genome, proteome, metabolism, habitat, ecological context, and timeline. A novel method developed by our group identifies structural homologs by comparing protein architectures, defined as the sequential arrangement of homologous domains within a protein. In our approach, proteins are considered homologous if they share identical domain types in the same N-to-C-terminal order. Homologous proteins with the same architecture found in the primary branches of both Bacteria and Archaea are potential candidates for those present in LUCA.},
}
@article {pmid42057267,
year = {2026},
author = {Dolk, H and Damase-Michel, C and Morris, J and Neville, A and Garne, E and Jordan, S and Rissmann, A and Coi, A and Folan, D and Broekstra, D and Broughan, JM and Bruneau, L and Cavero-Carbonell, C and den Hond, E and Gatt, M and Gissler, M and Khoshnood, B and Bielenska, AL and Nordeng, H and Odak, L and O'Mahony, M and Perthus, I and Richardson, JL and Rouget, F and Sichitiu, J and Tucker, D and Zymak-Zakutnya, N and Loane, M},
title = {The EUROmediCAT Network and Databases: A Resource for Pharmacovigilance in Pregnancy.},
journal = {Pharmacoepidemiology and drug safety},
volume = {35},
number = {5},
pages = {e70360},
pmid = {42057267},
issn = {1099-1557},
support = {//Seventh Framework Programme/ ; //Innovative Medicines Initiative/ ; //Ulster University/ ; },
mesh = {*Pharmacovigilance ; Pregnancy ; Humans ; Female ; *Databases, Factual/statistics &amp; numerical data ; *Abnormalities, Drug-Induced/epidemiology/etiology ; Europe/epidemiology ; Registries ; Adverse Drug Reaction Reporting Systems/statistics &amp; numerical data ; Pregnancy Trimester, First ; *Drug-Related Side Effects and Adverse Reactions/epidemiology ; Pharmacoepidemiology/methods ; },
abstract = {BACKGROUND: The evidence gap relating to the risk of congenital anomalies (CA) associated with first trimester medication exposure in pregnancy is well recognized.<br><br>AIMS: We describe the EUROmediCAT network and databases, and the methodological approach to pregnancy pharmacovigilance.<br><br>MATERIAL AND METHODS: Multidisciplinary expertise includes CA diagnosis and epidemiology, pharmacoepidemiology, pharmacology and teratology. The EUROmediCAT central database comprises standardized data from 19 EUROCAT CA registries in 14 countries, including more than 40&#x2009;000 CA cases 1995-2021 with first trimester medication exposure data recorded, and a population coverage of 14.6&#x2009;million births, growing by more than 650&#x2009;000 births per year. The distributed database enables federated data analysis across eight countries which can link data from CA registries to electronic healthcare data, with population coverage of up to 900&#x2009;000 births per year for linkage to maternal prescriptions, of which 300&#x2009;000 births per year for linkage also to data on all births.<br><br>RESULTS: The databases have enabled a variety of study designs: case-malformed control studies, cohort studies, disease cohort studies, signal detection studies, prevalence and ecological studies, and medication utilization studies.<br><br>DISCUSSION: A key strength is that studies of CA risk can address accurately the specificity of risk by type of CA.<br><br>CONCLUSION: EUROmediCAT presents a unique data and expert resource for tackling the enormous evidence gap regarding the safety of medication during pregnancy.},
}
@article {pmid42057917,
year = {2026},
author = {Szentiványi, T and Bruszniczky, B and Biró, Z and Katona, K and Klein, &#xc1; and Bende, A and Bánáti, L and Vass, G and Lehotzky, P and Kovács, D and Földvári, G and Csivincsik, &#xc1; and Nagy, G and Nagy, RR and Miklós, M and Szabadi, KL and Szabó, &#xc9;S and Garamszegi, LZ},
title = {Unwelcome guests: Nematodes of zoonotic and animal health importance in native and invasive carnivores of Hungary.},
journal = {Current research in parasitology &amp; vector-borne diseases},
volume = {9},
number = {},
pages = {100380},
pmid = {42057917},
issn = {2667-114X},
abstract = {Wild carnivores are important reservoirs of parasitic nematodes, several of which have veterinary and zoonotic significance. In Europe, the role of invasive carnivores in parasite circulation remains poorly understood. Here, we screened 371 individuals of six wild carnivore species from Hungary (red foxes, badgers, golden jackals, raccoons, raccoon dogs, and beech martens), using molecular markers (cox1 and S12), and detected five nematode parasites: Dirofilaria immitis, Crenosoma vulpis, Angiostrongylus vasorum, Thelazia callipaeda, and Spirocerca lupi. The highest prevalence was observed in badgers (32.0%) and red foxes (15.7%), while invasive raccoons also showed a relatively high infection rate (13.2%). Dirofilaria immitis was one of the most common nematode species detected: it was found in four host species, including the first confirmed cases in Hungarian badgers and invasive raccoons, extending the known host range of this parasite in central Europe. Importantly, T. callipaeda was recorded in red foxes and an invasive raccoon dog, representing the first invasive host records of this zoonotic eyeworm in Hungary. Crenosoma vulpis was identified in raccoons, suggesting invasive species may act as incidental carriers of endemic parasites. Both C. vulpis and D. immitis showed low host specificity. These findings indicate that invasive carnivores, particularly raccoons, may harbour unexpectedly high prevalence and play a greater role in local parasite networks than previously assumed. Our results highlight the epidemiological significance of both native and invasive carnivores in sustaining nematodes of zoonotic and veterinary importance in central Europe, stressing the need for continued surveillance in wild carnivores.},
}
@article {pmid42058737,
year = {2026},
author = {Liu, Q and Zhou, L and Yang, W and Liu, M and Liu, J},
title = {Associations between environmental exposure, lifestyle, and the risk of respiratory infections among 67890 adults: A population-based cohort analysis using UK Biobank data.},
journal = {Global health research and policy},
volume = {11},
number = {1},
pages = {43-50},
pmid = {42058737},
issn = {2397-0642},
mesh = {Humans ; Male ; Female ; *Life Style ; United Kingdom/epidemiology ; Middle Aged ; *Respiratory Tract Infections/epidemiology ; *Environmental Exposure/adverse effects/statistics &amp; numerical data ; Adult ; Cohort Studies ; Biological Specimen Banks ; Aged ; Risk Factors ; Proportional Hazards Models ; UK Biobank ; },
abstract = {BACKGROUND: Respiratory infections pose a major global health burden. While green spaces are generally thought to benefit respiratory health, research often overlooks the roles of private gardens and the interaction between environmental exposures and lifestyle behaviors. This study uses UK Biobank data to examine the integrated associations of environmental exposures, lifestyle habits, and respiratory infections.<br><br>METHODS: We conducted a large-scale cohort analysis based on UK Biobank data. Environmental exposures were assessed using geospatial data linked to residential addresses, including green space and domestic garden percentage (within 300&#x202f;m and 1000&#x202f;m buffers), natural environment accessibility, and coastal proximity. Cox proportional hazards regression models were used to estimate hazard ratios (HRs), adjusting for demographic characteristics (sex, age, BMI), socioeconomic status, and lifestyle behaviors (insomnia, smoking status, alcohol consumption, and physical activity).<br><br>RESULTS: A total of 46,288 healthy individuals and 21,602 patients with respiratory infection were included. Results revealed a scale-dependent "dual effect" of green space: higher greenspace percentage within a 300&#x202f;m buffer was protective (HR=0.93, 95% CI: 0.88-0.99), whereas within a 1000&#x202f;m buffer, it was associated with an increased risk (HR=1.10, 95% CI: 1.02-1.19). Domestic gardens and natural environments at 1000&#x202f;m were generally protective. Greater distance to the coast was associated with a lower risk of most respiratory infections but a potentially higher risk of tuberculosis. Male gender, older age, higher BMI, smoking, and insomnia were risk factors, while physical activity and alcohol consumption were associated with lower risks.<br><br>CONCLUSIONS: This study provides novel insights into the complex interplay between environmental exposures and lifestyle factors. The divergence between the protective effects of immediate greenness (300&#x202f;m) and the risks associated with broader vegetation coverage (1000&#x202f;m) suggests a trade-off between accessibility benefits and potential exposure to aeroallergens. Public health strategies should prioritize "low-allergen" urban planning and promote healthy lifestyles-particularly physical activity and smoking cessation-to mitigate respiratory infection risks.},
}
@article {pmid42059556,
year = {2026},
author = {Dunham, SJB and Willkeen, GA and Darby, B and Corley, JM and Hahn, A and Klapper, I and Bean, HD and Caverly, LJ and Thornton, CS and Martin, C and Quinn, RA and Widder, S and Bailey, BA and Wagner, BD and Garg, N and Planet, PJ and Hunter, RC and LiPuma, JJ and Rohwer, F and Whiteson, KL},
title = {The Guild Model of CF Airway Microbial Ecology.},
journal = {mBio},
volume = {},
number = {},
pages = {e0366825},
doi = {10.1128/mbio.03668-25},
pmid = {42059556},
issn = {2150-7511},
support = {R01 AI177613/AI/NIAID NIH HHS/United States ; },
abstract = {Ecological guilds are groups of organisms that utilize the same class of resources and occupy similar niches, regardless of their taxonomic identities. Here we propose the Guild Model for Cystic Fibrosis Airway Microbial Ecology, which considers the ecological function and wider role of each microbe in the ecosystem. This model consists of four functional guilds: (i) "Brewers" metabolize host-derived substrates (e.g., mucins) and produce fermentation products; (ii) "Drunkards" exploit the metabolic niche built by Brewers, consuming fermentation products and secreting exopolysaccharides to build biofilms; (iii) "Putrifiers" produce toxic compounds causing inflammation and tissue necrosis; and (iv) "Nihilists" are specialist pathogens characterized by intracellular or lytic life cycles and cytotoxin production. By focusing on microbial function and the broader community context, this model offers a refined framework for interpreting cystic fibrosis airway ecology. Although developed for CF, the Guild Model is adaptable to other diseases influenced by microbial ecology.},
}
@article {pmid42059572,
year = {2026},
author = {Zhang, J and Wang, X and Wang, D and Zheng, Z and Wang, H and Ma, L},
title = {Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.},
journal = {mSystems},
volume = {11},
number = {5},
pages = {e0080025},
pmid = {42059572},
issn = {2379-5077},
support = {42577239, 42277193//National Natural Science Foundation of China/ ; MEER-2024-10//Open Fund of Key Laboratory of Mine Ecological Effects and Systematic Restoration, Ministry of Natural Resources/ ; },
mesh = {*Deep Learning ; *Microbiota/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Ecosystem ; },
abstract = {Molecular profiling enabled by meta-omics technologies has significantly expanded our knowledge of microbial catalog across diverse environments. Increasing attention has now been focused on identifying ecologically significant taxa, particularly keystone that stabilize communities, rare taxa that underpin functional redundancy, and indicators that reflect environmental gradients. However, current pipeline methods remain limited in deciphering complex ecological relationships and modeling the evolution of community dynamics. As a transformative computational tool, deep learning (DL) offers novel strategies to address these challenges through autonomous feature extraction, nonlinear interaction modeling, and integration of multi-modal data sets. Nevertheless, there are still obstacles to the widespread adoption of DL for collaborative identification of specific microbial taxa, primarily including the intrinsic heterogeneity and imbalance of data sets, the difficulty of model generalization across diverse ecosystems, and the limited ecological interpretability of model outputs. This review summarizes existing research advances and proposes to build a unified DL framework for multi-modal data, exploring its implementation pathways, challenges, and potential coping strategies. The envisioned framework establishes a multi-task learning architecture for unified identification of keystone, rare, and indicator taxa, incorporating domain knowledge through ecological constraint layers and explainable AI modules, while providing flexible implementation pathways for heterogeneous data integration and model customization across microbial ecosystems. This framework has the potential to form a closed-loop verification in combination with synthetic microbial community experiments, reshape the paradigm of microbial community research, and promote the transition from empirical classification to mechanistic ecological cognition.},
}
@article {pmid42060700,
year = {2026},
author = {Niimi, R and Furusawa, C and Himeoka, Y},
title = {Population dynamics of generalist and specialist strategies under feast-famine cycles.},
journal = {PLoS computational biology},
volume = {22},
number = {4},
pages = {e1014265},
pmid = {42060700},
issn = {1553-7358},
mesh = {*Models, Biological ; Population Dynamics ; Computational Biology ; Nutrients/metabolism ; },
abstract = {Microbial populations exhibit a broad spectrum of nutrient utilization strategies, ranging from those utilizing diverse nutrients, called "generalists," to those highly adapted to specific nutrients, called "specialists." Identifying the conditions for the diversification of nutrient utilization strategies is one of the central questions in ecology. Previous theoretical studies have shown that trade-offs among different resource utilization functions in which cells cannot utilize broad types of substrates at nearly optimal efficiency are crucial for the emergence of diverse strategies. Additionally, in natural settings, nutrient availability often fluctuates over time, imposing another trade-off on the cells; cells that grow rapidly under nutrient-rich conditions tend to have a higher death rate under nutrient-poor conditions, leading to a growth-death trade-off. This additional trade-off can contribute to the emergence of diverse strategies. Here, we introduce a mathematical model that simultaneously incorporates the resource-use trade-off and the growth-death trade-off. Nutrient supply was modeled as discrete stochastic events, mimicking temporal changes in nutrient availability. We show that the phenotype with a higher ratio of growth rate to death rate dominates the population; that is, the strength of the growth-death trade-off plays a crucial role in the emergence of distinct strategies. We also found that a sparse and uncertain nutrient supply favors specialists, increasing their temporally averaged abundance. Our findings highlight the crucial role of temporal environmental variation and the resulting growth-death trade-off in driving diversification of microbial nutrient utilization strategies.},
}
@article {pmid42061074,
year = {2026},
author = {Yang, C and Liu, F and Zhang, C and Dong, J},
title = {Dual-functional carboxymethyl-β-cyclodextrin for enhanced peroxydisulfate/Fe[2+] removal of tetrachloroethylene in simulated groundwater.},
journal = {Journal of environmental management},
volume = {406},
number = {},
pages = {129733},
doi = {10.1016/j.jenvman.2026.129733},
pmid = {42061074},
issn = {1095-8630},
mesh = {*Groundwater/chemistry ; *Tetrachloroethylene/chemistry ; *beta-Cyclodextrins/chemistry ; Sulfates/chemistry ; Iron/chemistry ; Hydroxyl Radical/chemistry ; Water Purification/methods ; *Water Pollutants, Chemical/chemistry ; *Environmental Restoration and Remediation/methods ; },
abstract = {The removal of contaminants by peroxydisulfate (PDS)/Fe[2+] system is a promising groundwater decontamination technology, while the non-recyclability of Fe[2+] and the restricted mass transfer of contaminants in water limit the decontamination efficiency. Here, we developed carboxymethyl-β-cyclodextrin (CM-β-CD) to chelate Fe[2+] coupled with enhancing the solubization of contaminants in groundwater for efficient decontamination. Results showed that a 4.60-fold enhancement in the perchloroethylene (PCE) degradation rate following the addition of 1 g/L CM-β-CD to the PDS/Fe[2+] system. The ternary complex formed by CM-β-CD, Fe[2+] and PCE was confirmed via ultraviolet absorption spectra and nuclear magnetic resonance hydrogen spectrum. Electron paramagnetic resonance, complemented by chemical probe and radical quenching experiments, identified singlet oxygen ([1]O2), high-valent iron (Fe(IV)), and hydroxyl radicals ([•]OH) as the dominant reactive species in the PDS/Fe[2+]/CM-β-CD system, with relative contributions to PCE degradation quantified at 30.4%, 26.2%, and 18.1%, respectively. The presence of humic acid and common inorganic ions showed negligible effects on PCE degradation efficiency. The primary PCE degradation intermediate is dichloromethane, mediated by [1]O2, Fe(IV), and •OH, with mineralization occurring via dechlorination pathways. This study developed an environmentally sustainable remediation strategy utilizing CM-β-CD as a dual-functional agent for simultaneous Fe[2+] chelation and contaminant solubilization, enabling efficient groundwater decontamination.},
}
@article {pmid42068945,
year = {2026},
author = {Zhou, S and Wang, L and Cao, Y and Zhang, Z and Zhu, X and Luo, Y},
title = {Multi-omics elucidates how humic acid-biochar composite empowers sulfate-reducing bacteria for efficient biomineralization of cadmium and lead.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142208},
doi = {10.1016/j.jhazmat.2026.142208},
pmid = {42068945},
issn = {1873-3336},
mesh = {*Lead/metabolism/chemistry ; *Humic Substances ; *Cadmium/metabolism/chemistry ; Sulfates/metabolism/chemistry ; *Charcoal/chemistry ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; Biomineralization ; *Bacteria/metabolism/genetics ; Adsorption ; Oxidation-Reduction ; Multiomics ; },
abstract = {The HA&amp;BC-SRB composite, formed by immobilizing sulfate-reducing bacteria (SRB) onto a hybrid of humic acid (HA) and biochar (BC), achieved effective remediation of cadmium (Cd) and lead (Pb) through synergistic physicochemical and biological processes. The carrier provided a favorable microenvironment for bacterial activity (3.82 × 10[8] CFU g[-1]), with maximum adsorption capacities of 210.92 mg g[-1] for Pb and 137.04 mg g[-1] for Cd. Removal occurred primarily via monolayer chemisorption, involving sulfate reduction, extracellular polymeric substance complexation, and enzymatic electron transfer leading to stable sulfide precipitation. Immobilization induced substantial transcriptional reprogramming of metal detoxification and metabolic genes, accompanied by a metabolomic shift characterized by enhanced tricarboxylic acid cycle activity, oxidative phosphorylation, and glutathione metabolism. These changes collectively bolstered energy supply and antioxidant capacity. A strong correlation between differentially expressed genes and altered metabolites revealed a well-coordinated molecular network supporting biomineralization while preserving cellular integrity. This gene-metabolite coupling directly fuels the energy-intensive processes of sulfide precipitation and metal efflux, thereby enhancing biomineralization efficiency. Multi-omics integration confirmed that the carbon carrier primes SRB into a metabolically pre-adapted state, enabling a rapid and robust stress response. In soil trials, the system effectively transformed bioavailable heavy metals into stable residual fractions, reducing Cd and Pb accumulation in pakchoi plants by up to 85.12% and 66.88% respectively. These findings demonstrate that inducing a pre-adapted state in SRB through a functionalized carbon carrier offers a promising strategy to enhance bioremediation efficacy in metal-contaminated soils.},
}
@article {pmid42069314,
year = {2026},
author = {Yin, Q and Sun, J and Wu, QY and Wang, WL and Guan, Y},
title = {Hybrid membrane bioreactor-filler system enables efficient nitrogen removal from semiconductor wastewater through engineered microbial niche differentiation: Process optimization, biofilm-enhanced kinetics, and multi-omics insights.},
journal = {Bioresource technology},
volume = {454},
number = {},
pages = {134765},
doi = {10.1016/j.biortech.2026.134765},
pmid = {42069314},
issn = {1873-2976},
mesh = {*Biofilms ; *Bioreactors/microbiology ; *Nitrogen/isolation &amp; purification/metabolism ; *Wastewater/chemistry ; *Membranes, Artificial ; Kinetics ; *Semiconductors ; *Water Purification/methods ; Sewage/microbiology ; Denitrification ; Biomass ; Multiomics ; },
abstract = {Nitrogen removal from semiconductor wastewater is challenged by low carbon-to-nitrogen (C/N) ratios and the need for specialized microbial guilds to degrade organoamines including tetramethylammonium hydroxide (TMAH), N-methyl-2-pyrrolidone (NMP), and monoethanolamine (MEA). We hypothesized that creating distinct ecological niches within a single treatment system would shift microbial community assembly from stochastic to deterministic processes, selectively enriching specialized functional guilds and improving nitrogen removal without external carbon addition. To test this, we developed a hybrid system integrating a multi-stage anoxic-oxic (AOAO) process with a long sludge retention time (SRT) membrane bioreactor (MBR) and polyurethane fillers, creating three distinct ecological niches (suspended sludge, filler biofilm, and MBR biomass). Following process optimization with back-loaded hydraulic retention time (HRT) allocation and 150% internal recycle, the system achieved stable total nitrogen (TN) removal of 73% (effluent TN 7-9 mg L[-1]) without external carbon addition. Normalized stochasticity ratio (NST) analysis confirmed that the anoxic microenvironment within fillers shifted community assembly toward deterministic processes (NST = 37% vs. 76% in suspended sludge). This shift enriched Methanomethylovorans (5.1-fold) for anaerobic TMAH demethylation and Hyphomicrobium for methylotrophic denitrification. Untargeted metabolomics identified tryptophan and succinate depletion in filler biofilm, with strong metabolite-gene correlations (tryptophan-norB, r = 0.90; succinate-dmmA, r = 0.83) linking organoamine catabolism to respiratory denitrification. Co-occurrence network analysis confirmed tightly coupled anaerobic demethylation and denitrification modules in filler biofilm (216 edges, density 0.53). This work demonstrates that engineered niche differentiation can overcome carbon limitation in organoamine-rich industrial wastewater, providing a transferable design paradigm for carbon-efficient biological nitrogen removal.},
}
@article {pmid42070741,
year = {2026},
author = {Medernach, JP and Aleithe, P and Sanchez, X and Memmert, D and Henz, J},
title = {The priming Effect and its impact on sport performance and difficulty judgment: Evidence from Olympic Bouldering.},
journal = {Psychology of sport and exercise},
volume = {85},
number = {},
pages = {103147},
doi = {10.1016/j.psychsport.2026.103147},
pmid = {42070741},
issn = {1878-5476},
mesh = {Humans ; Female ; *Athletic Performance/psychology ; *Judgment ; Young Adult ; Adult ; *Mountaineering/psychology ; Cognition ; Adolescent ; },
abstract = {INTRODUCTION: Priming refers to the psychological phenomenon whereby a prior stimulus modulates cognitive processes and behavioural responses. To date, perceptual-cognitive mechanisms through which priming influences sporting performance remain underexplored. Olympic Bouldering provides a compelling and ecologically valid context for investigating psychological priming, as it involves perceptual-cognitive processes sensitive to priming while offering robust performance indicators and a controllable experimental environment. This study aimed to advance theoretical and empirical understanding of psychological priming by examining the impact of manipulated difficulty labels, assigned to boulders (short climbing routes) and serving as primes, on climbers' performance outcomes and their perceived difficulty judgments (targets).<br><br>METHODS: Twenty-eight female climbers previewed and attempted four boulders that were equivalent in movement demands and difficulty, but presented with manipulated difficulty labels: B1 (labelled easier than actual difficulty), B2 (true difficulty), B3 (labelled harder than actual difficulty), and B4 (no difficulty label). Measures included climbing performance and perceived boulder difficulty.<br><br>RESULTS: Among the boulders included in the priming manipulation (B1-B3), climbing performance (successful completion, number of attempts) was lowest in B3, labelled as most difficult (negative priming), and highest in B1, labelled as easiest (positive priming). Although all four boulders were of identical difficulty, participants perceived B3 as most difficult and B1 as easiest.<br><br>CONCLUSION: Findings indicate that priming through manipulated difficulty labels can influence athletes' climbing performance and perceived boulder difficulty. The study provides empirical evidence that exposure to prime stimuli can activate pre-existing internal representations, modulating both procedural and expectancy processes, and ultimately shaping sporting performance.},
}
@article {pmid42071145,
year = {2026},
author = {Pina-Martins, F and Poiares-Oliveira, G and Oliveira, J and Pesquita, C},
title = {FAIR Omics Data Management: Overview, Challenges, and Best Practices.},
journal = {Advances in experimental medicine and biology},
volume = {1504},
number = {},
pages = {187-204},
pmid = {42071145},
issn = {0065-2598},
mesh = {Humans ; *Data Management/standards/methods ; *Genomics/standards ; *Computational Biology/standards/methods ; Computer Security ; Metadata/standards ; },
abstract = {This chapter provides a comprehensive overview of FAIR principles applied to omics data management, addressing key challenges in handling large-scale, heterogeneous datasets while promoting reproducibility, collaboration, and open science practices. It covers essential strategies including Data Management Plans (DMPs), file organization, metadata standards, ontologies, repository selection, interoperability protocols, and security measures for privacy and ethics compliance. Best practices are outlined for achieving Findable, Accessible, Interoperable, and Reusable data, with recommendations for continuous improvement to support cross-omics integration and long-term data stewardship.},
}
@article {pmid42074365,
year = {2026},
author = {Seixas, AA and Chung, DP},
title = {Reintegrating the Human in Health: A Triadic Blueprint for Whole-Person Care in the Age of AI.},
journal = {International journal of environmental research and public health},
volume = {23},
number = {4},
pages = {},
pmid = {42074365},
issn = {1660-4601},
mesh = {Humans ; *Artificial Intelligence ; *Precision Medicine ; *Delivery of Health Care ; },
abstract = {Modern healthcare remains structurally and conceptually fragmented, with profound clinical and policy implications. At its root lies an ontological fracture: the prevailing biomedical model reduces patients to discrete biological systems (organs, biomarkers, and symptoms) detached from the psychological, social, and ecological contexts in which health and illness are experienced. This is compounded by epistemological fragmentation, where medical knowledge is compartmentalized into increasingly narrow specialties, limiting holistic understanding. These philosophical divisions manifest in downstream operational, informational, financial, and policy dysfunctions duplicative testing, misaligned incentives, disconnected care pathways, and population health failures. To address these multilevel fractures, we propose a unified architecture grounded in three interlocking components. First, the Precision and Personalized Population Health (P3H) framework offers a principle-based realignment toward care that is integrated, personalized, proactive, and population wide. P3H addresses the conceptual shortcomings of fragmented care by focusing on the full human trajectory across time, systems, and determinants. Second, General Purpose Technologies including artificial intelligence, biosensors, mobile diagnostics, and multimodal data systems enable the operationalization of whole-person care at scale, especially in low-resource settings. Third, the AI-WHOLE policy framework (Alignment, Integration, Workflow, Holism, Outcomes, Learning, and Equity) provides governance principles to guide ethical, equitable, and context-specific implementation. We argue that this triadic blueprint is particularly critical for Global South nations, where the lack of legacy infrastructure offers an opportunity for leapfrogging toward integrated, intelligent systems of care. Early models illustrate how policy-aligned, technology-enabled care rooted in whole-person principles can yield improvements in continuity, cost-efficiency, and chronic disease outcomes. This manuscript offers a systems-level strategy to overcome fragmentation and reimagine healthcare delivery, not only by refining clinical tools, but by redefining what it means to care for the human being in full.},
}
@article {pmid42074397,
year = {2026},
author = {Abasilim, OR and Nwosu, KOS and Akintimehin, OO and Ezeigwe, OJ and Dimgba, OO and Lama, M and Njoku, AH and Okoye, NC and Obekpa, EO},
title = {Food Insecurity and Adolescent Obesity in the United States: A Social Ecological Analysis of Multi-Level Risk Factors and Structural Inequities.},
journal = {International journal of environmental research and public health},
volume = {23},
number = {4},
pages = {},
pmid = {42074397},
issn = {1660-4601},
mesh = {Humans ; Adolescent ; *Food Insecurity ; United States/epidemiology ; Female ; Male ; *Pediatric Obesity/epidemiology/etiology ; Child ; Risk Factors ; Cross-Sectional Studies ; Poverty ; },
abstract = {While the association between food insecurity and adolescent obesity is well-established, the mechanisms through which these co-occurring public health crises are linked remain inadequately understood. Using the Social Ecological Model as a theoretical framework, this study examines how individual (physical activity), interpersonal (household food security), community (poverty level, residence), and societal (race/ethnicity) factors interact to influence adolescent weight outcomes. Cross-sectional data from 37,425 adolescents aged 12-17 years in the 2022-2023 National Survey of Children's Health using weighted multinomial logistic regression with interaction terms were used. Adolescents experiencing nutrition insecurity (adequate quantity but poor-quality food) had 41% higher odds of obesity (adjusted odds ratio (aOR) = 1.41; 95% CI: 1.20-1.65), while those with food insecurity (insufficient quantity) had 48% higher odds (aOR = 1.48; 95% CI: 1.08-2.02) compared to food-secure peers. Significant effect modification emerged across ecological levels: poverty below the 200% federal poverty level (FPL) significantly amplified the food insecurity-obesity relationship (interaction p < 0.001), Hispanic and Black adolescents demonstrated 49% and 78% higher obesity odds, respectively, independent of household food and nutrition security status, and physical activity showed protective effects that varied by food security context (interaction p = 0.003). These findings underscore the necessity of multi-level interventions addressing structural inequities alongside individual behaviors to combat adolescent obesity in food-insecure populations effectively.},
}
@article {pmid42075709,
year = {2026},
author = {Purgatová, S and Mangová, B and Selyemová, D and Krumpálová, Z and Chvostáč, M and Didyk, YM and Rajská, P and Kazimírová, M and Rusňáková Tarageľová, V},
title = {Sympatric Occurrence of Five Exophilic Tick Species in the Levice Region (Southwestern Slovakia) and Their Infection with Tick-Borne Pathogens.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {42075709},
issn = {2076-0817},
support = {APVV 22-0372//Slovak Research and Development Agency/ ; },
mesh = {Animals ; Slovakia/epidemiology ; *Tick-Borne Diseases/epidemiology/microbiology/parasitology/veterinary ; Sheep/parasitology ; Babesia/isolation &amp; purification/genetics ; Sympatry ; Rickettsia/isolation &amp; purification/genetics ; Theileria/isolation &amp; purification/genetics ; *Ticks/microbiology/parasitology ; *Tick Infestations/veterinary/epidemiology/parasitology ; },
abstract = {Among the 24 tick species documented in Slovakia, Ixodes ricinus is the most widespread and abundant. In some sites, 2-5 epidemiologically important tick species co-occur. Such sites represent hotspots for studying the co-circulation of tick-borne pathogens. Sympatric occurrence of five exophilic species (I. ricinus, Dermacentor reticulatus, D. marginatus, Haemaphysalis concinna, and H. inermis) was confirmed in the environs of the Žemberovce village (Levice region, south-western Slovakia). Here, the seasonal activity and abundance of questing ticks and the tick infestation of game and sheep were investigated. Questing ticks, spleens of game, and ticks removed from game and sheep were examined for the presence of tick-borne pathogens (Babesia spp., Theileria spp., Anaplasma phagocytophilum, Rickettsia spp., Borrelia burgdorferi s.l., and Borrelia miyamotoi) by molecular methods. Among the questing ticks, I. ricinus prevailed. Presence of Babesia crassa, B. microti, Rickettsia helvetica, R. raoultii, A. phagocytophilum, Borrelia afzelii, B. garinii, B. valaisiana, B. burgdorferi sensu stricto and B. miyamotoi was detected. Dermacentor marginatus, I. ricinus and H. concinna were collected from sheep. They were infected with A. phagocytophilum, A. ovis, R. slovaca, and R. raoultii. Anaplasma phagocytophilum was detected in all examined red deer and roe deer and in 55.6% of wild boar. All cervids were positive for Theileria spp. Infestation of game with all five tick species, with a predominance of I. ricinus, was confirmed. In these ticks, A. phagocytophilum, R. helvetica, R. raoultii, Babesia sp. hc-hlj212, B. crassa, B. microti, Babesia spp. and B. miyamotoi were detected. This study confirmed the presence of B. crassa in Slovakia for the first time. The investigated area, with the co-occurrence of five exophilic tick species and a wide spectrum of tick-borne pathogens, represents an epidemiologically important hotspot with the risk of infections of humans and domestic animals.},
}
@article {pmid42076550,
year = {2026},
author = {Khazaei, M and Raeisi, K and Fiedler, P and Croce, P and Zappasodi, F and Comani, S},
title = {Suppressing Non-Stationary Motion Artefacts in Mobile EEG Using Generalized Eigenvalue Decomposition.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {8},
pages = {},
pmid = {42076550},
issn = {1424-8220},
support = {101007521//European Union's Horizon 2020 research and innovation programme under the Marie Sk&#x142;odowska-Curie grant/ ; 01QE2316C, 13GW0721C//German Federal Ministry of Research, Technology and Space/ ; 57712119//German Academic Exchange Service/ ; },
mesh = {Humans ; *Electroencephalography/methods ; Artifacts ; Signal Processing, Computer-Assisted ; *Brain/physiology ; Motion ; Algorithms ; Movement/physiology ; Male ; },
abstract = {Mobile EEG enables investigating brain activity during real-world behaviour, but remains susceptible to motion artefacts, limiting signal interpretability and the use of advanced analytical techniques. Methods developed for removing motion-related artefacts induced by periodic activity like cycling, walking or juggling showed degraded performance with increasing movement variability and speed. To fill this gap, we developed a method based on generalized eigenvalue decomposition (GED) to identify and suppress highly variable, non-periodic-especially transient-artefacts due to very rapid, free full body movements of different types, as they occur during sports practice. By leveraging the contrast between covariance matrices of artefactual and resting-state EEG segments, this approach isolates motion-related components for removal during multichannel EEG signal reconstruction. The method was validated on two ecological datasets featuring stereotyped head and body movements and dynamic table tennis. Comparison with state-of-the-art technique showed superior performance of our method in terms of signal-to-error ratio (SER), artefact-to-residue ratio (ARR), brain spectral power preservation and computation time. Sensitivity analysis was applied to demonstrate the method's robustness to parameter changes. These findings highlight the potential of the proposed method as a robust, generalizable approach for motion artefact suppression in mobile EEG, particularly when applied in extreme recording conditions like during active sports activity.},
}
@article {pmid42077975,
year = {2026},
author = {Zhang, ZS and Ding, Y and Cao, KJ and Guo, ZZ and Zhou, SX and Lu, ZP and Dong, JL},
title = {Urban building carbon emissions based on BIM-LCA-GIS.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1713246},
pmid = {42077975},
issn = {2296-2565},
mesh = {China ; Humans ; *Geographic Information Systems ; *Carbon/analysis ; *Construction Materials ; *Environmental Monitoring/methods ; Carbon Footprint/statistics &amp; numerical data ; Cities ; Urbanization ; },
abstract = {With the continuous advancement of China's urbanization process and building technologies, traditional cast-in-situ construction methods have become increasingly incompatible with the concepts of green and healthy development due to significant energy consumption and carbon emissions generated throughout their entire lifecycle, including material production, construction processes, and related upstream and downstream industrial activities, while the advantages of the prefabricated building model have become increasingly prominent in this context; to address the need for in-depth carbon emission analysis of prefabricated buildings, this paper develops an integrated carbon emission analysis model integrating Building Information Modeling (BIM), Life Cycle Assessment (LCA), and Geographic Information Systems (GIS), applies this model to conduct in-depth analysis of carbon emissions at each stage of the prefabricated building's lifecycle to acquire accurate and specific carbon emission data, and adopts three analytical methods, input-output analysis, and ecological footprint analysis-to perform spatial analysis on the collected data, specifically combining BIM models with the LCA framework to quantify and assess the impacts of different building materials and structural components on energy efficiency and the surrounding environment and using the three computational methods for spatial carbon emission analysis; this integrated model effectively achieves accurate quantification and in-depth analysis of carbon emissions at each lifecycle stage of prefabricated buildings, obtaining specific and reliable carbon emission data and clarifying the spatial distribution characteristics and influencing factors of carbon emissions through spatial analysis; the research findings thus provide valuable insights and practical references for future initiatives to promote low carbon and energy efficient building practices and advance the development of low-carbon buildings, while the established integrated analysis model overcomes the limitations of single-method analysis and improves the accuracy and comprehensiveness of carbon emission analysis for prefabricated.},
}
@article {pmid42081716,
year = {2026},
author = {Eliasson, ET and Sutori, S and Mura, F and Ortiz, V and Catrambone, V and Hadlaczky, G and Todorov, I and Alfeo, AL and Cardi, V and Cimino, MGCA and Mioni, G and Raya, MA and Valenza, G and Carli, V and Gentili, C},
title = {Curiosity in a Novel Virtual Reality Scenario and Its Association With Symptoms of Depression: Observational Pilot Investigation.},
journal = {JMIR formative research},
volume = {10},
number = {},
pages = {e80120},
pmid = {42081716},
issn = {2561-326X},
mesh = {Humans ; *Virtual Reality ; Pilot Projects ; Female ; Male ; *Exploratory Behavior/physiology ; Adult ; *Depression/psychology ; Young Adult ; Self Report ; Middle Aged ; },
abstract = {BACKGROUND: Curiosity plays a fundamental role in human learning, development, and motivation, and emerging evidence suggests that reduced curiosity is linked to poorer mental health outcomes, including depressive symptoms (DS). However, to date, the majority of curiosity research relies on self-report assessments and thus risks biased reporting. Virtual reality (VR), a novel tool increasingly used within mental health research and treatment, might represent a potent tool for offering ecologically valid insights into curiosity-driven behaviors while circumventing issues related to self-report assessments, including demand characteristics and recall bias.<br><br>OBJECTIVE: The study aimed to enhance the assessment of curiosity by using a novel VR environment and to examine its relevance to DS. Specifically, we tested 2 hypotheses using a novel VR environment: first, that curiosity, as assessed through spontaneous exploratory interactions and behaviors in VR, positively correlates with self-reported curiosity, and second, that VR-based curiosity is inversely associated with DS.<br><br>METHODS: This exploratory study used an observational design that included 100 volunteers. All participants completed self-reported assessments of DS and curiosity before engaging in a novel VR scenario. Although progression in the virtual environment required solving cognitive tasks, these were embedded as structural elements rather than framed as the primary objective. Instead, participants' free explorations and interactions with objects formed the basis for the 4 curiosity metrics used in this study. After VR exposure, participants completed a questionnaire assessing cybersickness symptoms.<br><br>RESULTS: Hypothesis 1 was not supported, as only one curiosity metric, namely object interactions, was positively associated with one aspect of curiosity relating to motivation to seek new knowledge and experiences. Further, diminishing significance after correction for multiple testing warranted caution. Results relating to hypothesis 2 indicated partial support, in that object interaction was significantly associated with DS while controlling for age, sex, and cybersickness levels. Sensitivity analyses showed no associations between object interactions and self-reported anxiety and stress symptoms.<br><br>CONCLUSIONS: VR may be a potent tool for assessing exploratory behaviors in a controlled, yet ecologically valid, environment that avoids issues related to self-report. However, whether such motivations translate to established curiosity constructs warrants further research. This study also provided preliminary insights into how assessing exploratory interactions in VR may be a promising avenue that could enhance the understanding of the etiology and assessment of DS-particularly its early stages.},
}
@article {pmid42081988,
year = {2026},
author = {Gao, N and Cheng, Q and Guo, R},
title = {Spatiotemporal variations and prediction analysis of decadal series carbon storage in coastal city based on GEE.},
journal = {Environmental research},
volume = {302},
number = {},
pages = {124595},
doi = {10.1016/j.envres.2026.124595},
pmid = {42081988},
issn = {1096-0953},
mesh = {China ; Cities ; *Environmental Monitoring/methods ; *Carbon/analysis ; *Carbon Sequestration ; Urbanization ; Models, Theoretical ; Spatio-Temporal Analysis ; Geographic Information Systems ; },
abstract = {Quantifying carbon storage dynamics in rapidly urbanizing coastal cities is critical for regional climate mitigation. This study integrated Google Earth Engine (GEE), Random Forest classification, InVEST, and PLUS models to reconstruct land-use trajectories (2014-2024) and simulate carbon storage scenarios (2034) for Panjin City, a saline-alkali wetland-urban complex in Northeast China. Total carbon storage declined 11.91% (3.01 × 10[7]t to 2.65 × 10[7]t), driven primarily by conversion of high-carbon Cropland (94.24 t/ha) and Forestland (224.84 t/ha) to low-carbon Residentialland (13.97 t/ha). Landscape fragmentation intensified (ED +4.0%, SHDI -2.8%), while Structural Equation Modeling revealed that urbanization (Nighttime Light) exacerbates carbon loss indirectly through vegetation degradation (NDVI coefficient = 0.518). Multi-scenario simulations for 2034 show the "Ecological Protection" scenario yields maximum carbon storage (2.65 × 10[7]t), while "Urban Priority" yields minimum (2.44 × 10[7]t)-a 7.93% divergence. These findings suggest that coastal management should prioritize the preservation of native soil carbon pools over artificial vegetation compensation, utilizing ecological red lines as a practical pathway for sustainable development.},
}
@article {pmid42083045,
year = {2026},
author = {Bertram, H and Jawad, M and Michanski, S and Tiemann, I and Schmitt, AO and Gültas, M},
title = {Whole-genome resequencing data of the Ixworth chicken breed.},
journal = {BMC research notes},
volume = {19},
number = {1},
pages = {},
pmid = {42083045},
issn = {1756-0500},
mesh = {Animals ; *Chickens/genetics ; *Breeding ; Male ; *Whole Genome Sequencing ; *Genome ; Polymorphism, Single Nucleotide ; Germany ; Genetic Variation ; },
abstract = {OBJECTIVES: The Ixworth chicken is a British dual-purpose breed and mostly maintained by small-scale farmers. Due to legislation regarding the ban on male chick culling in European countries, such as in Germany, renewed interest has arisen in rearing dual-purpose chickens that provide both meat and eggs from the same genetic line. This dataset was generated within the scope of projects aiming to evaluate the viability of dual-purpose breeds for sustainable and welfare-oriented poultry production. One of the objectives was to characterize the genetic potential of the Ixworth chicken as a model for breeding programs that combine conservation and practical use in ecological farming systems.<br><br>DATA DESCRIPTION: Liver samples from 49 male Ixworth chickens were collected after scheduled slaughter at the Campus Frankenforst of the Faculty of Agricultural, Nutritional and Engineering Sciences of the University of Bonn, Germany. Genomic DNA was extracted and subjected to whole-genome resequencing using the Illumina NovaSeq 6000 platform. The dataset provides high-resolution genomic information on a rare breed with a pure dual-purpose background. This resource represents the first public sequencing dataset of the Ixworth chicken and thus offers a valuable foundation for future studies on genetic diversity, conservation genomics, and breeding strategies for sustainable poultry production.},
}
@article {pmid42083334,
year = {2026},
author = {Ye, JF and Zheng, S and Liu, PL},
title = {Multifunctional Online Medical Record Use and Patient Empowerment: Examining the Mediating Role of Patient-Centered Communication Across the Life Span in the Greater China Region.},
journal = {Health communication},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/10410236.2026.2668013},
pmid = {42083334},
issn = {1532-7027},
abstract = {The Greater China region represents the fastest-growing market for online medical records (OMR) implementation. However, the implications of these technologies for patient-centered care remain unclear. This study examined the relationships among different types of OMR usage (online patient-provider interactions, health information management, self-health management, and decision-making), patient-centered communication (PCC), and patient empowerment using a national sample (N = 6,271) of patients from Mainland China, Taiwan, Hong Kong, and Macao. Results revealed that OMR usage for online patient-provider interactions, self-health management, and decision-making was associated with patient empowerment among younger (18-34) and middle-aged (35-59) cohorts, with PCC mediating these relationships. eHealth literacy (eHL) moderated the relationship between self-health management and PCC in younger and middle-aged cohorts, while also moderating the association between decision-making and PCC across all age cohorts. Framed within the ecological model of health communication and life span perspectives, these findings suggest that future OMR studies would benefit from more nuanced and dialectical approaches. Practical implications are also discussed.},
}
@article {pmid42089043,
year = {2026},
author = {Johnston, JM and Perkins, E and Glynn, PD and von Stackelberg, K and Hope, BK and Harwell, MC},
title = {Interoperability to Improve Science-Based Decision Making: Adapting a Risk Analysis Framework to Improve Translational Environmental Health Science.},
journal = {Electronics},
volume = {15},
number = {3},
pages = {574},
pmid = {42089043},
issn = {2079-9292},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
abstract = {The protection of human and ecological health has become more challenging because of the myriad of human and climate stressors, and the sustainability of our social, economic, and environmental systems would be enhanced by further defensible risk assessment. There are scientific, technological, and cultural challenges to interoperability, bridging the necessary disciplines and integrating data from the genome to globe. Interoperability makes possible the use and reuse of data and modeling approaches and is a contemporary and rapidly progressing area advancing toxicology and exposure science. We present a coherent vision of human and ecological risk assessment, including the types of information and modeling science to create knowledge and apply it for improved decision-making. We focus on science-based decision-making, emphasizing decisions where science is the primary or sole driver, as in human toxicology and ecological risk assessment. This contrasts with decision-making where science has a minor role, if at all, in weighing decision options. We also examine the barriers that exist in the creation and application of systems thinking. We identify: the (1) needs and challenges for the application of a systems approach to informing decisions; (2) case studies that illustrate informatics needs for 21st-century science-based decision-making; and (3) recommendations on how to progress towards a systems approach to informing decisions.},
}
@article {pmid42089848,
year = {2026},
author = {DiFiore, G and Martin, H and Mitchell, JA and Barnett, I and Wiebe, D and Basner, M and Fiks, AG and Glanz, K and Mayne, SL},
title = {Association of Stress and Neighborhood Social Context With Actigraphy-Measured and Self-Reported Adolescent Sleep Outcomes.},
journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jadohealth.2026.02.022},
pmid = {42089848},
issn = {1879-1972},
abstract = {PURPOSE: Chronic stress and unfavorable neighborhood environments may increase adolescents' risk for poor sleep. Few studies have examined whether neighborhood social environments moderate associations of adolescents' perceptions of stress with actigraphy-measured and self-reported sleep outcomes.<br><br>METHODS: In a cross-sectional study of adolescents aged 15-18 (n = 163) years, perceived stress (10-item Perceived Stress Scale) and perceived neighborhood collective efficacy and safety were assessed via survey. Over 14 days, actigraphy measured nightly sleep duration and timing, while ecological momentary assessment (EMA) measured daily stress, self-reported sleep problems, and sleep environment disruptions. Multivariable mixed effects regression estimated associations of stress and neighborhood social factors with nightly sleep patterns and self-reported sleep outcomes, while multivariable linear regression estimated associations with sleep variability (intraindividual standard deviation of each sleep measure).<br><br>RESULTS: Higher 10-item Perceived Stress Scale scores and daily EMA-reported stress were associated with more variable sleep duration, onset, and offset timing, and higher and more variable sleep problem scores. Daily EMA-reported stress was also associated with earlier sleep timing. Higher neighborhood collective efficacy was associated with less variable sleep duration and timing, and lower and less variable sleep problem scores. Neighborhood collective efficacy and safety moderated associations between stress and several sleep outcomes (e.g., stronger associations between stress and sleep variability were present among adolescents with low neighborhood safety or collective efficacy).<br><br>DISCUSSION: Lower perceived stress and higher neighborhood collective efficacy were associated with less variable sleep patterns and lower sleep problem scores. Results suggest positive neighborhood social environments may moderate the relationship of stress with adolescent sleep variability.},
}
@article {pmid42090291,
year = {2026},
author = {Kong, L and Song, Q and Liang, S and Huang, H and Wei, H and Zhu, S and Wang, Y and Lin, H and Chen, Y and Su, R and Huang, L and Chen, H and Peng, Y and Zhao, Z and Li, Y and Wang, D and Zhao, J and Chen, B and Zhu, H and Dai, Q and Guo, Y and Luo, H and Hou, M and Zhao, B and Ma, T and Luo, K},
title = {Multi-omics analysis uncovers the molecular basis of "golden-thread" formation in Phoebe zhennan stems.},
journal = {Cell reports},
volume = {45},
number = {5},
pages = {117359},
doi = {10.1016/j.celrep.2026.117359},
pmid = {42090291},
issn = {2211-1247},
mesh = {Multiomics ; Flavonoids/biosynthesis/metabolism ; *Plant Stems/metabolism/genetics ; Gene Expression Regulation, Plant ; },
abstract = {Phoebe zhennan is an endangered and endemic tree species in China, renowned for its distinctive "golden-thread nanmu" wood with exceptional economic, ecological, and cultural value. However, the molecular basis underlying this unique wood trait remains poorly understood. Here, we report a telomere-to-telomere genome assembly of P. zhennan, spanning 919.42 Mb with a contig N50 of 84.44 Mb. Integrated metabolomic analyses identify morin, a flavonol compound, as a major contributor to the "golden-thread" phenotype. Functional characterization through enzymatic assays and transient overexpression reveals that PzF3'HL plays a central role in morin biosynthesis. Transcriptomic and single-nucleus RNA sequencing (RNA-seq) analyses further demonstrate age-dependent and xylem-specific activation of flavonoid pathway genes, driving flavonoid accumulation. Additionally, we reconstruct potential regulatory networks involved in flavonoid biosynthesis in P. zhennan stems. These findings provide critical insights into the genetic and biochemical mechanisms of "golden-thread nanmu" formation, offering valuable resources for the conservation and molecular breeding of P. zhennan.},
}
@article {pmid42091644,
year = {2026},
author = {Iqbal, M and Yaro, D and Apeanti, WO and Akuamoah, SW and Aljohani, A and Gouadria, S and Ceesay, B},
title = {Optical soliton solutions of the nonlinear coupled Konno-Oono system by using the new analytical approach and modulation instability analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51821-3},
pmid = {42091644},
issn = {2045-2322},
abstract = {This study primarily aims to apply the Riccati equation rational expansion method (REREM) to the nonlinear coupled Konno-Oono system (NCKOS) in order to construct novel and flexible optical soliton solutions. In addition, the modulation instability of the NCKOS is examined. The NCKOS represents current-field strings that interact with an external magnetic field. By employing REREM, we obtain various new types of solutions, including hyperbolic, bright, dark, periodic, kink and anti-kink, peakon, bell-shaped, and many other solitary wave structures. Several physical illustrations of some of the derived solutions are provided to enhance clarity. The findings demonstrate that the proposed technique is more powerful, efficient, and effective for investigating the solutions of other complex nonlinear models. Furthermore, the newly obtained solutions have potential applications in hydrodynamics, solid-state physics, cosmology, ecology, and quantum electronics.},
}
@article {pmid42091994,
year = {2026},
author = {Oba, Y and Doi, H},
title = {Macroecological assessment of invasive species impact on Japanese lake fish communities using eDNA metabarcoding.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46585-9},
pmid = {42091994},
issn = {2045-2322},
support = {22K18429//JSPS KAKENHI/ ; },
abstract = {Biological invasion has negative effects on ecological interaction such as competition and predation. The ecological impacts on native communities may also affect two processes that are important in determining community structures, namely, the environmental and spatial processes. Here, we used lake fish species compositions estimated using environmental DNA metabarcoding to investigate the effects of invasive species composition on the native community and on the processes that determine it. The results of PERMANOVA indicated that the native fish assemblage patterns significantly changed along invasive species compositions. Furthermore, it was observed that the diversity of invasive species acted as a potent ecological filter, driving native fish communities towards biological homogenisation. Distance-based Redundancy Analysis revealed that invasive species alter the relationship between ecological communities and their environment. The study suggests invasive species may obscure distinct environmental signals, potentially by having broader environmental tolerances than native species. A comparison of the relative importance of environmental factors and spatial structure in determining species composition between communities, fish species composition in lakes is more strongly influenced by environmental factors than spatial structure, although the predictive power of these factors varies with the presence of invasive species and is most evident in native-only communities. Our results suggest that the need to understand the impacts of invasive species on native species not only through direct effects, but also the complex effects involving the diversity level of invasive species.},
}
@article {pmid42092045,
year = {2026},
author = {Rehder, J and Timm, I and Berretz, G and Reinhard, I and Neubauer, AB and Güntürkün, O and Takano, K and Bierbauer, W and Cabrita, M and Bourke, M and Smyth, J and Kim, J and Michalak, J and Curtiss, J and Pannicke, B and Gallagher, JB and Abrantes, AM and Nakamura, T and Yamamoto, Y and Cook, P and Wieland, LM and von Haaren-Mack, B and McCormick, B and Hachenberger, J and Vetrovsky, T and Henwood, B and Poppe, L and Sudeck, G and Hollands, L and Goldschmidt, AB and Martire, L and Kanning, M and Maher, JP and Li, YM and Reininghaus, U and Berli, C and Seiferth, C and Hevel, DJ and Leger, K and Staiano, AE and Zeeck, A and Calza, S and Liao, Y and Ruissen, GR and , and Schwerdtfeger, AR and Haucke, M and Pham, LT and Liu, S and Thomas, MC and Meyer-Lindenberg, A and Dunton, GF and Elavsky, S and Ebner-Priemer, UW and Giurgiu, M and Packheiser, J and Reichert, M},
title = {An individual participant data meta-analysis of how physical activity relates to affective well-being in daily life.},
journal = {Nature human behaviour},
volume = {},
number = {},
pages = {},
pmid = {42092045},
issn = {2397-3374},
support = {01EW2404A//Bundesministerium fr Bildung und Forschung (Federal Ministry of Education and Research)/ ; 01EW2404A//Bundesministerium fr Bildung und Forschung (Federal Ministry of Education and Research)/ ; 01GL1719A/B//Bundesministerium fr Bildung und Forschung (Federal Ministry of Education and Research)/ ; TRR265, project C05//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; U.S. R01 AG026010//U.S. Department of Health; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 3092;51000-056-04A//U.S. Department of Agriculture (United States Department of Agriculture)/ ; CZ.02.1.01/0.0/0.0/16_019/0000798//Ministerstvo ;kolstv, Ml;de;e a T;lov;chovy (Ministry of Education, Youth and Sports)/ ; },
abstract = {Physical inactivity constitutes a pressing societal problem. To realize physical activity's (PA) potential as a key health resource, mechanisms of PA engagement need to be understood. Laboratory and interventional studies documented that exercise relates to affective well-being (AWB) and suggested that AWB may shape PA behaviour. Digitalization enabled the investigation of how PA relates to AWB in everyday life, but findings from individual studies are ambiguous. Here we compiled 67 datasets (55.2% of eligible records) including 321,345 smartphone-based AWB ratings and nearly 1,000,000 h of accelerometer-measured PA (N = 8,223 participants) until December 2023 to clarify the nature and extent of PA-AWB associations. One- and two-stage individual participant data meta-analyses reveal that momentary AWB is associated with both prior (within, r = 0.05, 99.2% confidence intervals (CI) 0.03 to 0.06; between, r = 0.08, 99.2% CI 0.04 to 0.12) and subsequent (within, r = 0.04, 99.2% CI 0.03 to 0.05; between, r = 0.08, 99.2% CI 0.04 to 0.13) short-term PA in everyday life. Within persons, PA displays a positive association with energetic arousal, positive affective states and valence, yet a negative relation to calmness. The practical effect sizes are comparable to other daily life activities, with energetic arousal evincing the strongest relation to PA. Considerable heterogeneity in associations across individuals can be partially explained by sociodemographic moderators. Between participants, PA relates to positive affective states. The results document the critical relevance of PA-AWB relations in everyday life. They can contribute to the revision and development of health behaviour models and establish a starting point to approach behavioural, physiological and neuronal mechanisms underlying PA-AWB associations.},
}
@article {pmid42092788,
year = {2026},
author = {Ng'ang'a, SI and Ward, JA and Rossiter, SJ and Faulkes, CG and Bougiouri, K and McHugo, GP and Cotterill, FPD and Nyachieo, A and Thalmann, O and Medugorac, I and Krebs, S and Sonstegard, TS and Hanotte, O and Bradley, DG and Vaughan-Smith, G and MacHugh, DE and Frantz, LAF},
title = {Accurate imputation of African cattle genomes using a diverse reference panel.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42092788},
issn = {1471-2164},
mesh = {Animals ; Cattle/genetics ; Polymorphism, Single Nucleotide ; *Genome ; Whole Genome Sequencing ; Genotype ; *Genomics/methods ; Africa ; },
abstract = {BACKGROUND: In cattle, most commercial single-nucleotide polymorphism (SNP) genotyping arrays have been shown to be suboptimal for capturing genomic variation in non-European populations, particularly in African cattle. Low-coverage whole-genome sequencing (LCWGS) followed by imputation provides a cost-effective method for genotyping that is more adaptable and can outperform genotyping arrays.<br><br>RESULTS: Here, we generate a high-quality reference imputation panel representative of the complex ancestries of cattle populations in Africa to enable the deployment of LCWGS. To do so, we generated 116 high-coverage (between 20&#x2012;24&#xd7;) new African cattle genomes, representing most cattle breeds across the continent. We combined this data with publicly available genomes from other regions to build a reference panel that comprised over 3,300 cattle genomes from 133 cattle populations, thus capturing the genetic diversity of domestic cattle across the world. After applying a high filtering step to remove poor genome sequences with very low sequence coverage, we retained 1,882 with an average coverage of 7&#xd7;. We show that the imputation pipeline implemented, based on this reference panel, provides highly accurate genotypes of common (>&#x2009;99% accuracy) and rare (>&#x2009;98% accuracy) variants in genome coverage as low as 0.5&#xd7;.<br><br>CONCLUSION: This panel provides an important new resource for genetic improvement and conservation of African cattle populations.},
}
@article {pmid42093056,
year = {2026},
author = {Itoh, H and Shimoji, H and Nakane, D and Jang, S and Kikuchi, Y},
title = {Soil pH as an external filter shaping stink bug-Burkholderia gut symbiosis.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42093056},
issn = {2049-2618},
support = {19K15724//Japan Society for the Promotion of Science/ ; 22H05065//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Symbiosis ; *Burkholderia/physiology/isolation &amp; purification/genetics/classification ; *Soil/chemistry ; Hydrogen-Ion Concentration ; *Soil Microbiology ; *Gastrointestinal Microbiome ; *Heteroptera/microbiology ; },
abstract = {BACKGROUND: Many animals and plants establish intimate symbiotic relationships with specific microorganisms acquired from the environment. Given the immense diversity of environmental microbiomes, selecting appropriate partners from such a vast microbial pool poses a critical challenge for host organisms. To meet this challenge, hosts have evolved sophisticated internal partner-choice mechanisms that ensure stable associations with beneficial microbes. However, because these symbionts primarily inhabit external environments, environmental conditions themselves are also expected to influence the establishment of symbiosis. Despite this expectation, the mechanistic role of external environmental filters in shaping the intended symbiosis remains largely unexplored. Focusing on stink bugs, which acquire their symbiotic bacteria from soil each generation, we investigated how soil properties influence the establishment of gut symbiosis in terrestrial insects.<br><br>RESULTS: Microbiome analyses confirmed that Burkholderia sensu lato overwhelmingly dominates a specific gut organ in six stink bug species from the superfamilies Coreoidea and Lygaeoidea, including serious agricultural pests (relative abundance ranging from 74.5 to 100%). Rearing experiments with isolated Burkholderia revealed that insects were strictly dependent on this symbiont; failure to acquire it from soil severely reduced host growth and reproduction, indicating that the availability of symbionts from soil can represent an ecological constraint. Field surveys identified patches of exceptionally high stink bug density in weedy fields with soil pH&#x2009;<&#x2009;7.0, whereas such aggregations were absent in fields with pH&#x2009;&#x2265;&#x2009;7.0. Laboratory experiments with collected field soils showed that the abundance of Burkholderia in soils was negatively correlated with soil pH, and stink bugs readily acquired their symbionts from soils with pH&#x2009;<&#x2009;7.0 but rarely from soils with pH&#x2009;&#x2265;&#x2009;7.0. Experimental manipulations of soil pH followed by rearing experiments confirmed that increasing soil pH to 7-8 markedly suppressed symbiont acquisition by the host, likely by impairing symbiont growth and motility.<br><br>CONCLUSIONS: We demonstrate that, beyond host-intrinsic mechanisms, a soil chemical property can act as an externally filter that constrains symbiont acquisition prior to colonization inside the host in a stink bug-Burkholderia symbiosis. This finding highlights how local environmental conditions can shape the assembly of environmentally acquired insect-microbe symbioses. Video Abstract.},
}
@article {pmid42094442,
year = {2026},
author = {De Paolis Kaluza, MC and Ramola, R and Joshi, P and Piovesan, D and Reade, W and Orchard, S and Martin, MJ and Ignatchenko, A and , and Rost, B and Orengo, CA and Robinson-Rechavi, M and Durand, D and Brenner, SE and Greene, CS and Mooney, SD and Friedberg, I and Radivojac, P},
title = {Advances in Protein Function Prediction from the Fifth CAFA Challenge.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42094442},
issn = {2692-8205},
abstract = {The Critical Assessment of Functional Annotation (CAFA) is a long-standing community effort to independently assess computational methods for protein function prediction, to highlight well-performing methodologies, to identify bottlenecks in the field, and to provide a forum for the dissemination of results and exchange of ideas. In its fifth round (CAFA5) of triennial challenges, a partnership with Kaggle Inc. facilitated participation from a large community of data scientists and computational biologists through a competitive prospective challenge on the crowdsourcing platform. In this work, we present an in-depth analysis of the submitted predictions and report improvements in accuracy over all methods from the previous CAFA challenges. We further introduce a new evaluation setting for proteins with pre-existing (incomplete) annotations and identify the need for methods that better leverage existing annotations to predict those that will be discovered later. Finally, we characterize the prospective evaluation framework by examining performance on a strict set of unpublished annotations and across intermediate database releases. Our results indicate that recent developments in the field, such as the availability of protein language models and accurately predicted 3D structures, as well as the growth of experimental annotations through biocuration, have all contributed to performance improvements.},
}
@article {pmid42095939,
year = {2026},
author = {Al Nashib, MN and Raji, SV},
title = {Assessment of industrial effluent impact and hydrological dynamics of the Meghadri Gedda surplus channel using SWAT and GIS.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {5},
pages = {},
pmid = {42095939},
issn = {1573-2959},
mesh = {*Environmental Monitoring/methods ; India ; *Water Pollutants, Chemical/analysis ; *Industrial Waste/analysis/statistics &amp; numerical data ; Geographic Information Systems ; Hydrology ; },
abstract = {The Meghadri Gedda surplus channel, Visakhapatnam, India, is an important waterway originating from Meghadri Gedda reservoir and flowing into the Bay of Bengal, which is heavily impacted by the surrounding industries. This present study adopts a novel integrated technique that combines SWAT-based hydrological modeling with detailed physicochemical characterization of industrial effluents to evaluate both watershed processes and pollution impacts in an industrially influenced catchment. Furthermore, a comparative assessment of industrial-treated effluent quality against CPCB standards was included in this study, an aspect that has received limited attention in previous studies in this region. SWAT model was used in this study to analyze the spatial distribution and hydrological process around the MG catchment area. The physicochemical properties of industrial effluents and channel water were analyzed to assess the extent of industrial pollution and its impact on the MG surplus channel. Industrial effluents from Coromandel Fertilizers Limited and rain C-II carbon showed remarkable physicochemical characteristics such as low pH of 1.02 at ETP inlets, high TDS value up to 5020mg/L, and elevated chloride concentrations up to 148,890 mg/L. The values of BOD and COD also crossed the CPCB limits with 4875 mg/L BOD and 1232 mg/L COD, indicating a notable organic load. Alkalinity concentrations in both batches vary from 80 to 720 mg/L, and desalination-reject magnesium concentrations exceed the standard limits of CPCB. The catchment area received annual precipitation of 1363.6 mm with a runoff of 966.49 mm, which indicates a remarkable portion of rainfall contributing to channel water flow. Only 21.32 mm of groundwater recharge was calculated, while evapotranspiration was high at 229.8 mm. Annually, 16.84 mg/ha nutrient losses by crop were substantially high due to nitrate leaching and phosphorus runoff.},
}
@article {pmid42096535,
year = {2026},
author = {Walker, K and Shenkin, A and Malhi, Y},
title = {Diameter-driven variation in wood CO2 efflux across the stems and crowns of three temperate broadleaf tree species.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpag060},
pmid = {42096535},
issn = {1758-4469},
abstract = {A major constraint on modelling woody-tissue CO2 efflux is the scarcity of datasets that adequately represent its variability and underlying drivers. We intensively sampled CO2 efflux along the vertical profile of nine temperate broadleaf trees across three species and found substantial longitudinal variation. We partitioned the flux into growth and maintenance-associated components; accordingly we use 'efflux' for measurements and 'respiration' only for the derived components. Expressing efflux by wood volume, surface area, and sapwood volume each offered insight to the underpinning of the flux. However, efflux was most strongly associated with surface area, particularly in medium and large branches, and across both growth and maintenance respiration. In small branches, where sapwood dominates, this surface-area scaling weakens, suggesting maintenance respiration shifts from surface-area to volume-based scaling, while growth respiration remains associated with surface-area. Sapwood depth, tree ring width, and the relative contributions of growth and maintenance respiration explained much of the variation in efflux, though additional biological and physical factors, such as CO2 diffusion from sap and variation in sapwood parenchyma, likely also contribute. These findings represent an important step towards reducing uncertainty in the spatial scaling of woody-tissue CO2 efflux by linking within tree variation in respiration to underlying anatomical and growth-related controls.},
}
@article {pmid42098484,
year = {2026},
author = {Hanan, MS and Abbas, S},
title = {Climate-induced shifts and lengthening of growing seasons across Pakistan's major vegetation types.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {5},
pages = {},
pmid = {42098484},
issn = {1573-2959},
mesh = {Pakistan ; Seasons ; *Climate Change ; *Environmental Monitoring ; *Plant Development ; Ecosystem ; Temperature ; },
abstract = {Pakistan's diverse ecology, ranging from arid to semi-arid zones and mountainous regions, makes vegetation phenology highly sensitive to climate variability. However, a long-term assessment of phenological shifts across its major ecological zones remains limited at national-scale. This study provides the first consistent nationwide analysis of changes in vegetation phenology metrics from 2001 to 2023, including the start of season (SOS), length of season (LOS), and end of season (EOS). The assessment focused on natural and semi-natural vegetation classes, excluding croplands, to understand climate-driven phenological responses. The MODIS phenology product was used to extract phenological indicators, while vegetation land cover types were derived from the MODIS land cover type product. The impact of climate variability on phenology was assessed using temperature and solar radiation data from the ECMWF ERA5 (European Centre for Medium-Range Weather Forecasts Reanalysis 5) and precipitation data from CHIRPS (Climate Hazards Group InfraRed Precipitation with Station data). Temporal trends in phenological events and climatic variables were analyzed at seasonal and annual scales, with correlations assessed between each climatic driver and phenological parameters. Results indicated variation in SOS (May to August) and EOS (November to March), reflecting phenological differences across different vegetation types across the biomes. A significant trend of delayed SOS (0.10 days/year) and EOS (0.40 days/year) was observed. SOS onset for grassland and savannas were negatively correlated with temperature (-0.424 and -0.422), and consistently indicated negative association with solar radiation across all vegetation types, suggesting an earlier SOS with warmer temperature and bright sunny conditions. Among the divergent vegetation classes (mixed forests, open and close shrublands, and savannas and woody savannas), within-season precipitation showed positive correlations with EOS and LOS (r = 0.455-0.727), indicating moisture-constrained growing season length. Soil moisture exhibited stronger associations with EOS and LOS, particularly in mixed forests (EOS r = - 0.557, LOS: r = -0.71) with higher significance than with SOS, suggesting a greater role in regulating senescence and growing season duration than green-up onset. These asymmetric phenological responses to different climate controls suggest the complex influence of climatic conditions at different stages of vegetation growth, varying across vegetation types and landscapes. The reliance on the MODIS phenology product may introduce uncertainties, suggesting further validation and independent phenology observation across the landscape.},
}
@article {pmid42098613,
year = {2026},
author = {Alfiky, A and Dora, SA},
title = {TrichoBase: a standardized genomic resource for comparative genomics of Trichoderma species.},
journal = {BMC genomic data},
volume = {27},
number = {1},
pages = {},
pmid = {42098613},
issn = {2730-6844},
mesh = {*Trichoderma/genetics/classification ; *Genomics/standards ; *Genome, Fungal ; Molecular Sequence Annotation ; DNA Transposable Elements ; *Databases, Genetic ; },
abstract = {The ecological versatility of the fungal genus Trichoderma spans roles from mycoparasite to saprotroph, presenting a compelling model to investigate how genomic variation underpins niche adaptation. However, comparative genomic studies of Trichoderma are hampered by inconsistent annotation methods across independently sequenced genomes, complicating direct cross-species analysis. To address this, we developed and applied a unified, evidence-based annotation pipeline integrating RNA-seq and homology data to six key species spanning the genus's ecological range (T. asperellum, T. harzianum, T. virens, T. reesei, T. longibrachiatum, and T. citrinoviride). This work presents 'TrichoBase', a consistently annotated genomic resource comprising standardized gene models, functional annotations, and comparative profiles. Using this comparable dataset, we confirm and quantitatively refine the correlation between transposable element (TE) accumulation and genome size expansion. We further demonstrate that TE-rich genomes of mycoparasitic strains are enriched in carbohydrate-active enzymes (CAZymes) and biosynthetic gene clusters (BGCs), while saprotrophic opportunistic lineages show streamlined profiles. Notably, the resource reveals patchy phylogenetic distributions of specific BGC families, such as sorbicillinoid and brefeldin A-like clusters. We provide the complete resource including annotation files, analysis scripts, and a reproducible pipeline to serve as a foundational dataset for future functional genomics and ecological studies in Trichoderma.},
}
@article {pmid42101816,
year = {2026},
author = {Hailekiros, F and Mitiku, M and Mekonnon, M and Bishaw, T and Abebe, A and Kelly-Hope, LA},
title = {Lessons from the field: adapting lymphatic filariasis morbidity mapping and patient care amidst conflict in Ethiopia.},
journal = {International health},
volume = {18},
number = {3},
pages = {324-327},
pmid = {42101816},
issn = {1876-3405},
mesh = {*Elephantiasis, Filarial/epidemiology/prevention &amp; control ; Ethiopia/epidemiology ; Humans ; Morbidity ; *Armed Conflicts ; Patient Care ; },
abstract = {Conflict in Ethiopia has prevailed in recent years and is impeding the implementation of lymphatic filariasis elimination activities for morbidity management and disability prevention. This led to the need for alternative approaches to ensure safe and effective implementation. Here, we outline the challenges that were faced (e.g., insecurity, restricted travel to external field teams, limited in-person training, direct patient care). First, we describe what potential solutions were discussed and decided. Second, we summarise the planned adapted strategy and how it was implemented through central-level planning, supervision, courier-based data transfer, and centralised data management. Third, we highlight what worked well, what did not, and key lessons learned. Finally, we outline areas for future consideration, including for example, the importance of global and national standard guidelines, and a better understanding of type and intensity of the conflict to help with realistic and safe planning.},
}
@article {pmid42102146,
year = {2026},
author = {Kovács, B and Barabás, G and Meszéna, G and Szathmáry, E and Szilágyi, A},
title = {The ecology and evolution of sub-exponential replicators.},
journal = {PLoS computational biology},
volume = {22},
number = {5},
pages = {e1014247},
pmid = {42102146},
issn = {1553-7358},
mesh = {*Biological Evolution ; Computational Biology ; Ecology ; Origin of Life ; Computer Simulation ; *Evolution, Molecular ; },
abstract = {Systems of oligonucleotide chemical replicator molecules provide some of the finest, empirically realizable models of prebiotic evolution. Yet, a full understanding of their eco-evolutionary implications is hampered by conflicting assumptions, modeling strategies, and therefore predictions in the literature. Here we construct a model of these systems that accounts for the reversible association of templates and copies, ultimately leading to self-inhibition and sub-exponential growth. We show that, contrary to predictions from simplified model descriptions, there are well-defined limits on the attainable diversity of different replicator species. We also demonstrate that increasing the overall concentration of the system increases diversity, but counterintuitively, an analogous increase in the available resource concentration has the opposite effect. Most notably, if an exponentially-growing replicator is also present in the system, it absorbs any increase in the total replicator concentration, while the concentrations of the sub-exponential replicators remain unchanged. In the context of prebiotic evolution, this means that in high-concentration local environments, an exponential replicator can reach disproportionately high concentrations even if its copying rate is lower than that of the sub-exponential replicators. In a variable environment, this can lead to the eventual stochastic extinction of its competitors, with the exponentially growing species taking over the community.},
}
@article {pmid42102276,
year = {2026},
author = {Ramjan, S and Blum, M and Tseng, RY and Davey, K and Shereen, AD and Nomura, Y},
title = {Feasibility of Integrating Wearable Devices and Ecological Momentary Assessment for Real-Time Environmental Exposure Estimation: Proof-of-Concept Study.},
journal = {JMIR formative research},
volume = {10},
number = {},
pages = {e86615},
pmid = {42102276},
issn = {2561-326X},
mesh = {Humans ; *Ecological Momentary Assessment ; Female ; *Wearable Electronic Devices/statistics &amp; numerical data ; Feasibility Studies ; Male ; Adolescent ; *Environmental Exposure/analysis ; Young Adult ; Pilot Projects ; Proof of Concept Study ; Geographic Information Systems ; Air Pollution/analysis ; Heart Rate ; Exercise ; },
abstract = {BACKGROUND: Environmental exposures such as heat and air pollution are critical determinants of health, yet traditional assessment methods rely on stationary monitors or residential address proxies that fail to capture the exposures that individuals experience throughout the day.<br><br>OBJECTIVE: This pilot study aimed to assess the feasibility of integrating ecological momentary assessment (EMA), wearable devices, and continuous GPS tracking to capture real-time environmental exposures and to explore associations with concurrent health outcomes.<br><br>METHODS: In total, 7 young adults (aged approximately 16 to 24 years; 5/7, 71% female) wore Fitbit Charge 6 watches from July 2025 to August 2025 (mean 28.1, SD 1.1 days), recording sleep quality and duration, resting heart rate, breathing rate, heart rate variability, and physical activity. GPS location measured at up to 5-minute intervals (mean 19.7, SD 25.8 measurements per day) was linked to ambient temperature, humidity, and air pollution data (particulate matter <2.5 um or <10 um in diameter, nitrogen dioxide, sulfur dioxide, ozone, and carbon monoxide) derived from monitoring stations, satellites, and climate models using data-integration algorithms accessed via an application programming interface. EMA surveys administered 3 times per day captured participants' emotional states and location (inside or outside). Feasibility targets were &#x2265;3 GPS measurements per day, &#x2265;1 survey completed per day, and complete sleep data on &#x2265;50% of days. We examined exploratory bivariate correlations between environmental exposures, physiological measures, and self-reported mood, adjusting for multiple comparisons using false discovery rate correction.<br><br>RESULTS: Of the 7 participants, 5 (71%) met predefined feasibility targets. Mean compliance included 565 (SD 457) GPS coordinates per participant, 1.4 (SD 0.2) EMA surveys per day, and complete Fitbit sleep data on 64% (SD 27%) of days. Surveys identified barriers to compliance, including perceived complexity of the system and forgetting to put the Fitbit watch back on after removing it. Exploratory correlations (6/7, 86% of participants with complete Fitbit data) revealed associations between nitrogen dioxide and heat exposure and reduced heart rate variability (a marker of parasympathetic tone), and between air pollutants (sulfur dioxide) and increased negative emotions. Heat exposure showed a paradoxical pattern of lower self-reported sadness but reduced heart rate variability with higher levels of heat exposure. Given the small sample size, these correlations should be considered preliminary and hypothesis generating rather than definitive findings.<br><br>CONCLUSIONS: This study demonstrates that the multimodal integration of wearable devices, GPS tracking, and EMA is feasible for capturing real-time environmental exposures and concurrent health outcomes in young adults. This approach addresses critical exposure misclassification issues in environmental health research that relies on residential addresses as proxies. Preliminary patterns suggest complex relationships between environmental exposures and both physiological and emotional outcomes, warranting further investigation in larger, more diverse samples. This approach could inform future personalized environmental health interventions.},
}
@article {pmid42103987,
year = {2026},
author = {Kargarandehkordi, A and Jaiswal, A and Banerjee, A and Qian, Y and Slade, CR and Sun, Y and Islam, T and Tadesse, HB and Kostrinsky-Thomas, A and Park, C and Sarkar, U and Khoong, EC and Nguyen, N and Xu, XO and Phillips, KT and Benzo, RM and Aguilera, A and Zhang, H and Doshi-Velez, F and Washington, P},
title = {Personalized modeling of stress and blood pressure reactivity using mobile health data.},
journal = {Npj mental health research},
volume = {},
number = {},
pages = {},
doi = {10.1038/s44184-026-00210-9},
pmid = {42103987},
issn = {2731-4251},
support = {2516767//National Science Foundation (NSF)/ ; U54GM138062//National Institute of General Medical Sciences (NIGMS)/ ; MedRes-2023-00002689//Hawai'i Community Foundation/ ; },
abstract = {Psychological stress is a key driver of short-term blood pressure (BP) elevations and cardiovascular risk, yet its moment-to-moment impact in daily life remains difficult to predict. In this longitudinal observational study, we collected multimodal data from 20 adults with self-reported hypertension, including continuous wearable-derived heart rate and activity, ecological momentary assessment (EMA) stress ratings, and ambulatory BP measurements in free-living conditions. The dataset comprised 3694 EMA responses and 3812 BP measurements collected over approximately four weeks per participant (mean 24.1 ± 8.5 days). We evaluated whether participant-specific ("personalized") models outperform a single pooled population model. Two prediction tasks were examined: (i) prediction of near-term BP elevations from wearable signals and stress EMA responses and (ii) prediction of self-reported stress from wearable signals and BP. Across both tasks, personalized models consistently improved predictive performance. For BP prediction, personalized models achieved a mean AUROC of 0.803, exceeding the population model by 0.235, while for stress prediction they achieved a mean AUROC of 0.849, exceeding the population model by 0.208. These findings suggest that personalized wearable-based models can capture individual patterns of stress and BP dynamics, with direct implications for precision mental health assessment and just-in-time adaptive intervention design in future work.},
}
@article {pmid42106069,
year = {2026},
author = {Nakamura, K and Ohkubo, N and Yamasaki, K and Tahara, M and Akata, K and Ikegami, H and Nishida, C and Okawara, M and Fujino, Y and Matsuda, S and Fushimi, K and Mukae, H and Yatera, K},
title = {Epidemiology and clinical characteristics of hospitalized patients with echinococcosis in Japan: A nationwide administrative database study.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {32},
number = {6},
pages = {102991},
doi = {10.1016/j.jiac.2026.102991},
pmid = {42106069},
issn = {1437-7780},
mesh = {Humans ; Male ; Japan/epidemiology ; Female ; Aged ; Retrospective Studies ; Middle Aged ; *Echinococcosis/epidemiology/therapy/diagnosis ; *Hospitalization/statistics &amp; numerical data ; Databases, Factual ; Aged, 80 and over ; Adult ; Length of Stay/statistics &amp; numerical data ; Albendazole/therapeutic use ; Young Adult ; Child ; Adolescent ; },
abstract = {BACKGROUND: Echinococcosis is a rare but potentially life-threatening parasitic disease caused by Echinococcus species. In Japan, epidemiological data are mainly derived from notification-based surveillance, and large-scale nationwide analyses focusing on hospitalized patients remain limited. This study aimed to clarify the nationwide epidemiology and clinical characteristics of hospitalized patients with echinococcosis in Japan using an administrative database.<br><br>METHODS: We conducted a retrospective nationwide study using the Japanese Diagnosis Procedure Combination database. Hospitalized patients diagnosed with echinococcosis between April 1, 2014, and March 31, 2021, were identified. Data on age, sex, geographic distribution, affected organs, comorbidities, treatments, Japan Coma Scale score, and length of hospital stay were extracted and analyzed.<br><br>RESULTS: A total of 170 hospitalized patients coded for echinococcosis were included after exclusion of duplicate cases. The median age was 65.5 years, and 51% were male. Hepatic involvement was observed in 90% of patients, followed by pulmonary (4%), cutaneous (2%), cerebral (2%), and osseous (2%) involvement. Surgical treatment was frequently performed, including hepatectomy in 48% and cholecystectomy in 24% of patients, while albendazole therapy was administered in 21%. Most patients were from the Hokkaido region (85%), followed by the Kanto region (8%). The average annual number of hospitalized patients was approximately 24.<br><br>CONCLUSION: Echinococcosis remains a clinically relevant parasitic disease in Japan, particularly in Hokkaido, and often requires hospitalization and surgical intervention. Nationwide administrative data provide valuable insights into the real-world clinical burden of echinococcosis.},
}
@article {pmid42106747,
year = {2026},
author = {Ullah, I and Alrhmoun, M and Gillani, SW and Prakofjewa, J and Zhang, L and Mattalia, G and Amin, HIM and Yebouk, C and Moola, F and Corvo, P and Sõukand, R and Kalle, R and Sulaiman, N and Pieroni, A},
title = {When minority language persistence is not enough: the decline of foraging knowledge in German- and Ladin-speaking Alpine communities of Northern Italy.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13002-026-00906-4},
pmid = {42106747},
issn = {1746-4269},
abstract = {Local ecological knowledge is an essential element of the Alpine biocultural diversity and is often linked to minority languages. However, its continuity does not necessarily correspond to the persistence of these languages. This study investigates how knowledge of wild plants (and mushrooms) is transmitted and transformed among three minority-language communities in the Italian Alps: Cimbrian, Mòcheno, and Ladin speakers. Ethnobotanical data were collected through structured interviews between 2022 and 2025 and compared with historical records from the 1980s documenting the use of wild plants for food, medicinal purposes, and herbal teas. The results reveal a marked decline in traditional plant-related practices despite the continued use and institutional support of minority languages. Plants once central to household herbal repertoires, such as Achillea millefolium L., Artemisia absinthium L., and Sambucus nigra L. which are now marginal or abandoned. However, a limited set of herbal teas remains culturally significant. Conversely, mushroom foraging and the gathering of wild fruits remain comparatively resilient, supported mainly by communal land-use institutions (usi civici) that foster ecological engagement and intergenerational learning. Overall, the study highlights a paradox of biocultural resilience: linguistic vitality alone does not safeguard embodied ecological knowledge. Sustaining Alpine cultural and environmental heritage, therefore, requires integrated approaches that address language, environment, governance, and socio-economic change together.},
}
@article {pmid42107872,
year = {2026},
author = {Velavan, TP and Schmidt-Chanasit, J},
title = {When rare zoonoses travel: Andes virus, hantavirus cardiopulmonary syndrome, and the preparedness gap.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {169},
number = {},
pages = {108778},
doi = {10.1016/j.ijid.2026.108778},
pmid = {42107872},
issn = {1878-3511},
abstract = {The perspective discusses how the suspected Andes virus (ANDV) associated hantavirus cluster on the expedition cruise ship MV Hondius illustrates a critical preparedness gap in managing rare zoonotic infections in mobile, closed, and medically constrained settings. Focusing on the reported multi-country cluster involving severe hantavirus cardiopulmonary syndrome, deaths, and international passenger dispersal, it highlights the associated diagnostic, clinical, and epidemiological challenges. The perspective also explains why ANDV is distinct among hantaviruses, including its documented potential for limited person-to-person transmission during close and prolonged contact, with insights into the virology and pathogenesis of ANDV. Additionally, it highlights ecological exposure hazards in Patagonia, rodent reservoirs, clinical progression, the necessity for laboratory confirmation, candidate severity biomarkers such as IL-6 and intestinal fatty acid-binding protein, and the lack of specific antiviral therapy. Furthermore, it discusses risk factors, including European ethnicity and host genetic susceptibility linked to αVβ3 integrin variation. Overall, this perspective argues that expedition travel, maritime medicine, One Health surveillance and outbreak preparedness must be better integrated in order to detect, investigate and manage rare but high-consequence zoonotic infections before they escalate into international public health events.},
}
@article {pmid42108288,
year = {2026},
author = {Yan, C and Zhang, F and Long, C and Yin, Y and Wang, L},
title = {A Brief Review of Microbial Omics: Methods and Perspectives.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {1-20},
pmid = {42108288},
issn = {1940-6029},
mesh = {*Genomics/methods ; *Metabolomics/methods ; *Proteomics/methods ; *Microbiota/genetics ; *Computational Biology/methods ; Single-Cell Analysis/methods ; Artificial Intelligence ; Transcriptome ; Metagenomics/methods ; },
abstract = {Microbial omics has progressed from isolated genomic analyses into a comprehensive, integrated multi-omics framework, profoundly advancing our understanding of microbial complexity and functionality. This mini-review systematically outlines the core technologies within microbial omics-including genomics, transcriptomics, proteomics, and metabolomics-by introducing their fundamental principles, common experimental workflows, and state-of-the-art bioinformatic strategies. We particularly highlight the emergence of single-cell microbial omics as a transformative methodology that resolves molecular and functional heterogeneity within communities, enabling the identification of rare taxa, strain-level microdiversity, and specialized functional roles that are obscured in bulk analyses. Furthermore, we discuss how artificial intelligence (AI)-driven tools are revolutionizing the interpretation of high-dimensional omics data, uncovering latent biological patterns, improving predictive modeling of microbial behavior, and facilitating the translation of microbiome insights into clinical and environmental applications. The review concludes by comparing the strengths, limitations, and optimal use cases of each omics layer and single-cell approach while also addressing ongoing technical challenges and future directions in the field.},
}
@article {pmid42108290,
year = {2026},
author = {Li, B and Xu, J and Zhao, T and Yang, X and Yin, Q and Zou, Y},
title = {Metagenomic Data Preprocessing and Quality Control.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {43-61},
pmid = {42108290},
issn = {1940-6029},
mesh = {*Metagenomics/methods/standards ; Quality Control ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Software ; Workflow ; *Metagenome ; *Computational Biology/methods ; },
abstract = {Accurate metagenomic analysis relies on clean and well-processed sequencing reads. This chapter presents a concise four-step workflow for preprocessing: raw data assessment, adapter and quality filtering, host DNA removal, and final clean-read evaluation. By standardizing these essential procedures, researchers can minimize contamination, reduce technical bias, and ensure reliable inputs for assembly and downstream metagenomic analyses.},
}
@article {pmid42108291,
year = {2026},
author = {Li, B and Yang, X and Zhao, T and Xu, J and Meng, Q and Yin, Q and Zou, Y},
title = {Metagenomic Assembly and Gene Prediction.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {63-89},
pmid = {42108291},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Metagenome ; *Computational Biology/methods ; Molecular Sequence Annotation ; Contig Mapping/methods ; Software ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Metagenomic assembly and gene prediction connect quality-controlled reads to downstream microbiome analyses. This chapter outlines core assembly strategies, including per-sample versus co-assembly and short-read versus hybrid approaches, and highlights key parameters and metrics for evaluating assembly quality. Gene prediction from contigs and the construction of nonredundant gene catalogs are introduced as fundamental steps for representing community coding potential. The resulting contigs and gene sets provide essential input for metagenome-assembled genome (MAG) reconstruction, as well as taxonomic and functional annotation in subsequent chapters.},
}
@article {pmid42109270,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Buff Arches, Habrosyne pyritoides (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {480},
pmid = {42109270},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Habrosyne pyritoides (the Buff Arches; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 400.6 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.59 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,018 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 {pmid42110286,
year = {2026},
author = {Lin, C and Xu, E and He, J and Tang, Y and Xiong, Y and Pu, Y},
title = {Digital health readiness among rural hypertensive patients: a latent profile analysis.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1786213},
pmid = {42110286},
issn = {2296-2565},
mesh = {Humans ; *Hypertension/therapy ; Female ; Male ; Cross-Sectional Studies ; Middle Aged ; *Rural Population/statistics &amp; numerical data ; China ; Aged ; *Telemedicine/statistics &amp; numerical data ; Surveys and Questionnaires ; Adult ; Digital Health ; },
abstract = {BACKGROUND: Driven by the rapid advancements in big data and artificial intelligence technologies, digital health tools have become deeply integrated into healthcare systems, offering novel pathways for blood pressure control and management. However, rural patients with hypertension face greater obstacles in accessing and utilizing digital technologies due to disparities in healthcare resources, education levels, and digital infrastructure. This study aims to identify latent classes of digital health readiness among rural hypertensive patients and explore their predictors based on the Health Ecological Model using latent profile analysis.<br><br>METHODS: This cross-sectional study followed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines and collected data from 980 rural hypertensive patients across three townships in Hunan Province, China. Relevant factors were identified based on the Health Ecological Model. Research instruments included a General Information Questionnaire (23 items), the Social Support Rating Scale (10 items), the Cardiovascular Disease Risk Perception Assessment Tool (1 item), and the Digital Health Readiness Questionnaire (18 items). Latent profile analysis was employed to identify distinct subgroups of digital health readiness, and multivariate logistic regression analysis was used to determine predictive factors for each class.<br><br>RESULTS: Latent profile analysis revealed three distinct subtypes of digital health readiness among rural hypertensive patients: Low Digital Health Readiness group (n&#x202f;=&#x202f;247, 25.2%), Moderate Digital Health Readiness group (n&#x202f;=&#x202f;533, 54.4%), and High Digital Health Readiness group (n&#x202f;=&#x202f;200, 20.4%). Multivariate logistic regression analysis demonstrated that age, duration of hypertension, number of chronic comorbidities, activities of daily living, regular exercise, awareness of "digital health," cardiovascular disease risk perception, number of children, social support rating, educational level, employment status, physician recommendation to use information-based blood pressure management devices, and home wireless network coverage were significant factors influencing digital health readiness.<br><br>CONCLUSION: These findings underscore the characteristics associated with lower digital health readiness. Rural healthcare institutions should develop tailored interventions targeting the specific vulnerabilities of different hypertensive patient populations and strengthen social support systems to enhance digital health readiness among rural patients with hypertension.},
}
@article {pmid42113306,
year = {2026},
author = {Mazza, V and Latini, L and Burini, G and De Donno, R and Scalvini, M and Benedetti, D and Liuzzo, M and Grignani, G and Nascetti, G and Malavasi, S and Tricarico, E and Canestrelli, D and Carere, C},
title = {Heads and tails of individual differences: the role of environmental complexity in cognitive development of juvenile lobsters.},
journal = {Animal cognition},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10071-026-02062-4},
pmid = {42113306},
issn = {1435-9456},
support = {PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN project PL-ASTICI (20223EETLW)//Ministero dell'Universit&#xe0; e della Ricerca/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//European Union - Next Generation EU/ ; CN_00000033, CUP J83C22000860007//National Biodiversity Future Center - 'NextGenerationEU'/ ; CN_00000033, CUP J83C22000860007//National Biodiversity Future Center - 'NextGenerationEU'/ ; },
abstract = {Experiencing environmental complexity during early life is fundamental for vertebrate neural development, with profound and often irreversible effects on later behavioural and cognitive outcomes. However, studies on the early stages of invertebrate development are scanty. European lobsters (Homarus gammarus) are routinely reared in captivity for subsequent release in the context of restocking and stock-enhancement. The impoverished captive conditions they experience may exert long-term effects on their development, ultimately impairing their success after release. Here we tested the effects of environmental complexity during early life on learning (N = 38) and personality (N = 132) of juvenile lobsters. Lobsters experienced a full enrichment (with both substrate and shelter), a partial enrichment (either substrate or shelter), or bare standard conditions as a control. We assessed lobsters' exploration and activity patterns via repeated open field tests, quantified their learning in a double T-maze, and investigated the possible presence of a speed-accuracy/flexibility trade-off in decision-making. We found that juvenile lobsters raised in enriched environments were more active compared to lobsters raised in control conditions. They were also faster in taking decisions and in correcting erroneous ones compared to controls, while decision speed did not predict the accuracy of its outcome. Finally, while all lobsters reached the learning criterion, the effects of environmental treatment on learning speed were only detectable in individuals that developed a wild-type morphological phenotype (i.e. asymmetrical claws), who showed a higher information-seeking tendency and required more trials. Overall, these results indicate a key role of early-life experience of environmental complexity in the development of behavioural and cognitive traits that can drive success in the wild.},
}
@article {pmid42118451,
year = {2026},
author = {Langraf, V and Čerteková, S and Kučka, M and Petrovičová, K and Ražná, K},
title = {The impact of Triticum aestivum L. cultivation management on genomic polymorphism of Harpalus rufipes and Silpha obscura assessed by RAPD markers.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {42118451},
issn = {2676-8607},
abstract = {Beetle genetics is becoming increasingly important in research on agricultural ecosystems, not only from a basic biological perspective but also for practical applications in pest management, biodiversity, and agroecosystem sustainability. Our study analyzed the genetic variability of beetle populations (Harpalus rufipes and Silpha obscura) under two types of agricultural management systems-organic and conventional-using RAPD markers. Out of six tested markers (OPB 5, OPB 8, OPB 11, OPB 12, OPB 14, and OPB 18), three markers (OPB 11, OPB 14, and OPB 18) demonstrated clear genetic differentiation between beetle samples collected from organically and conventionally cultivated wheat. The results of DNA fingerprinting and t-SNE analysis confirmed the formation of two genetic clusters corresponding to the management type. Jaccard similarity coefficient values indicated moderate to strong genetic similarity within individual management systems, while similarity between systems was weaker. These findings suggest that agronomic practices influence the genetic structure of beetle populations, likely due to ecological and anthropogenic factors such as pesticide use and landscape modification. The study emphasizes the importance of molecular markers in assessing population-level responses to agroecosystem management and their contribution to sustainable agriculture.},
}
@article {pmid42118833,
year = {2026},
author = {Fares, M and McFarlane, M and Parry, RH and Arif, R and Clarke, AT and Kamel, W and Davies, K and Datta-Savage, R and Schwarz-Linek, U and Bell-Sakyi, L and Petit, MJ and Schnettler, E and Castello, A and Kohl, A and Brennan, B},
title = {SFTSV NSs protein is a tick antiviral RNAi response suppressor.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {20},
pages = {e2524728123},
pmid = {42118833},
issn = {1091-6490},
support = {210462/Z/18/Z//Wellcome Trust (WT)/ ; MC_UU_00034/4//UKRI | Medical Research Council (MRC)/ ; MC_UU_00034/8//UKRI | Medical Research Council (MRC)/ ; MRF2022950//Medical Research Future Fund/ ; BB/P024270/1//UKRI | Biotechnology and Biological Sciences Research Council (AFRC)/ ; 223743/Z/21/Z//Wellcome Trust (WT)/ ; 890970//EC | Horizon 2020 Framework Programme (H2020)/ ; TTU 01.708//Deutsches Zentrum f&#xfc;r Infektionsforschung (DZIF)/ ; 101001634//EC | European Research Council (ERC)/ ; MR/R021562/1//UKRI | Medical Research Council (MRC)/ ; MC_UU_00034/2//UKRI | Medical Research Council (MRC)/ ; MC_UU_12014/8//UKRI | Medical Research Council (MRC)/ ; MC_UU_00034/4//UKRI | Medical Research Council (MRC)/ ; MR/W018608/1//UKRI | Medical Research Council (MRC)/ ; },
mesh = {Animals ; *RNA Interference ; *Viral Nonstructural Proteins/metabolism/genetics ; Virus Replication ; *Phlebovirus/genetics/physiology/immunology ; Humans ; *Ticks/virology/immunology ; RNA, Small Interfering/genetics/metabolism ; Severe Fever with Thrombocytopenia Syndrome/virology ; Cell Line ; },
abstract = {Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging tick-borne phenuivirus causing high mortality in humans. While the nonstructural protein NSs is dispensable for replication in interferon-deficient mammalian cells, we demonstrate that NSs is essential for viral replication in tick cells. SFTSV infection triggers canonical Dicer-2-mediated antiviral RNA interference (RNAi) in tick cells, producing virus-derived small interfering RNAs (siRNAs) that target viral transcripts for degradation. We show that NSs functions as a viral suppressor of RNAi by selectively engaging and depleting single-stranded RNAs derived from 22-nucleotide siRNAs, likely limiting their incorporation into RNA-induced silencing complexes (RISC). Complementation with a heterologous RNAi suppressor (p19 protein) partially rescues replication of NSs-deficient virus, validating the RNAi-suppressive function of NSs. These findings reveal that successful tick-borne viral replication requires host-specific immune evasion strategies and establish NSs-mediated RNAi suppression as essential for SFTSV persistence in arthropod vectors.},
}
@article {pmid42120019,
year = {2026},
author = {De Pascalis, F and Ventura, F and Grémillet, D and Benvenuti, A and Pisu, D and Pala, D and Rubolini, D and Cecere, JG},
title = {Storm petrels trade movement speed for information gain.},
journal = {Biology letters},
volume = {22},
number = {5},
pages = {},
doi = {10.1098/rsbl.2026.0108},
pmid = {42120019},
issn = {1744-957X},
support = {//Italian Ministry for the Ecological Transition (MiTE)/ ; //Biodiversa+/ ; //European Biodiversity Partnership/ ; //European Commission/ ; //National Aeronautics and Space Administration (NASA)/ ; },
mesh = {Animals ; *Birds/physiology ; *Flight, Animal ; Wind ; Geographic Information Systems ; },
abstract = {Animals travelling through air or water can benefit from surrounding flows. This is evident in procellariforms, oceanic birds capable of undertaking some of the longest journeys in the animal kingdom despite the need to periodically return to the nest. While airflow negotiation is well understood for larger species relying on dynamic soaring, less is known for the smallest species, which use flapping flight. Using GPS-tracking, we investigated wind use of the 28 g Mediterranean storm petrel (Hydrobates pelagicus melitensis). Birds actively searched for crosswind support at meso- (tens of kilometres) and macroscales (hundreds of kilometres). However, this reliance on crosswinds was associated with lower groundspeeds and a full compensation mechanism for drift during homing, implying an increased energy expenditure. Yet, crosswind support may facilitate navigation via a cognitive odour map and improve prey detection through olfaction, increasing the likelihood of intersecting odour plumes. These results indicate that storm petrels could face a trade-off between movement efficiency and information gain. Overall, our study offers new perspectives on the adaptations required to sustain aerial life in the marine realm and highlights the adaptability of seabirds in exploiting the windscape through strategic flow negotiation.},
}
@article {pmid42120905,
year = {2026},
author = {Srivastava, A and Bhola, A and Frnda, J and Rozhon, J and Prakash, P and Singh, S and Chauhan, V},
title = {Deep convolutional models for robust multi-crop disease recognition in real-world conditions.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52369-y},
pmid = {42120905},
issn = {2045-2322},
support = {09I05-03-V02-00013//Recovery and Resilience Plan for Slovakia/ ; },
abstract = {Crop diseases significantly reduce agricultural output and are a serious problem, especially in the parts of the world where diagnostic experts are not readily available. Deep learning has recently shown us that it is possible for a computer to identify plant diseases directly from images of the leaves. Nevertheless, to make such solutions available on the web or mobile devices one has to really think about how heavy the calculations will be, how easy the user interface should be, and also the limit on the data used. Here is a paper on a web-based applied deep learning system for disease detection in multiple crops. The system detects disease in eight crops Apple, Banana, Grape, Mango, Cauliflower, Tomato, Potato, and Corn with each crop having several disease classes and healthy samples. Three transfer-learning-based CNN architectures MobileNetV3, EfficientNetB4, and ResNet50 were compared for classification performance on the public datasets collected from PlantVillage, Kaggle, and Mendeley. Considering class-wise accuracy, prediction time, and deployment scenarios, MobileNetV3 was picked as the main model to be integrated into the system. To compensate for the differences in image quality often found in pictures taken by users, an optional super-resolution preprocessing step with Real-ESRGAN is added and quantitatively assessed. Disease prediction with spectral activation maps (Grad-CAM) enhances the model's interpretability by highlighting image areas where the disease is detected. The resulting model is embedded in a multilingual Progressive Web Application (PWA). The platform enables users to submit their crop images and receive predicted disease names and treatment options, which are generated by a Large Language Model (LLM) using structured disease metadata. The research acknowledges dataset bias and limitations in extrapolating from curated datasets to the general real-world setting although it reports very good performance of the method on the test sets. In summary, the system proposed here is intended as a practical digital agriculture decision-support tool that demonstrates deployment feasibility and raises a few issues for future validation at the field level and improvement.},
}
@article {pmid42121019,
year = {2026},
author = {Fernández, H and Ojosnegros, S and Álvarez, JM and Vázquez, F and Goya, N and Quintanilla, LG and Flexas, J and Peña, A and Grossniklaus, U},
title = {Comprehensive in silico characterization of proteins associated with light responses, transport, and stress-related processes in the gametophyte of the fern Dryopteris affinis ssp. affinis.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42121019},
issn = {1471-2164},
mesh = {*Plant Proteins/metabolism/genetics ; *Dryopteris/genetics/metabolism/radiation effects/physiology ; *Germ Cells, Plant/metabolism/radiation effects ; *Stress, Physiological/genetics ; *Light ; Computer Simulation ; Computational Biology/methods ; Gene Expression Regulation, Plant ; Biological Transport ; },
abstract = {BACKGROUND: Fern gametophytes represent a key phase in the fern life cycle and play an essential role in establishment and persistence. Despite their ecological and developmental relevance, the molecular basis of gametophyte function remains poorly characterised, particularly in apogamous ferns. The growing availability of transcriptomic resources offers new opportunities to investigate the functional organisation of this life stage.<br><br>RESULTS: We conducted an in silico analysis of a previously published RNA-seq dataset obtained from gametophytes of the apogamous fern Dryopteris affinis ssp. affinis, focusing on a curated subset of protein candidates defined by stringent filtering criteria (E-value&#x2009;<&#x2009;1&#x2009;&#xd7;&#x2009;10&#x207b;&#xb9;&#x2070;&#x2070; and minimum sequence length&#x2009;>&#x2009;450&#xa0;bp). Following filtering, 1,160 proteins were retained and classified into three main functional categories-light-related processes, transport functions, and stress responses-representing key processes underlying gametophyte physiology and environmental adaptation. Light-associated proteins were primarily linked to photosynthesis, photorespiration, xanthophyll metabolism and photomorphogenesis, including components involved in photosystem assembly, chloroplast function and photoreceptor-mediated signalling. Transport-related proteins comprised a diverse set of membrane- and cytoplasm-associated transporters mediating the movement of sugars, amino acids, ions and other metabolites. In addition, numerous proteins associated with biotic and abiotic stress responses and plant immunity were detected. Protein-protein interaction analysis identified a small number of highly connected nodes, with MODIFIED TRANSPORT TO THE VACUOLE 1 (MTV17) emerging as the most connected protein, mainly supported by database- and text-mining-based evidence, suggesting a potential central role in intracellular transport-related processes.<br><br>CONCLUSIONS: This study presents a curated, high-confidence protein dataset that extends current knowledge of fern gametophyte molecular organisation. The functional categories and interaction patterns identified highlight core processes underlying gametophyte physiology and stress adaptation, and provide a resource for future functional, comparative and experimental studies in ferns and other early-diverging land plants.},
}
@article {pmid42123469,
year = {2026},
author = {Zhu, Y and Tang, K and Lin, M and Fanji, S and Zhang, S},
title = {A Comprehensive Larval microRNA Atlas of Hyphantria cunea Identifies Candidate miRNAs and Potential Molecular Targets for Green Pest Management.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123469},
issn = {1422-0067},
mesh = {Animals ; *MicroRNAs/genetics ; Larva/genetics/growth &amp; development ; Gene Expression Profiling ; Transcriptome ; *Moths/genetics/growth &amp; development ; RNA Interference ; Computational Biology/methods ; Gene Expression Regulation, Developmental ; High-Throughput Nucleotide Sequencing ; },
abstract = {Hyphantria cunea (Drury) causes extensive ecological damage primarily during its larval stages, characterized by voracious feeding and rapid dispersal. Given that conventional dsRNA-mediated RNA interference (RNAi) is generally recalcitrant in Lepidoptera, endogenous microRNAs (miRNAs) may represent an additional class of regulatory molecules worthy of systematic investigation. In this study, we utilized high-throughput sequencing to construct nine comprehensive miRNA libraries across three critical developmental milestones (three biological replicates per instar): the 1st, 4th, and 7th instars (L1, L4, and L7). A total of 1667 miRNA entries were catalogued, including 1080 known and 587 bioinformatically predicted, as yet unvalidated novel miRNA candidates. Comparative transcriptomic analysis revealed 52 differentially expressed miRNAs with significant stage-dependent profiles, with the most pronounced divergence observed between the L1 and L7 groups. Bioinformatic prediction identified 16,784 non-redundant target genes. GO and KEGG enrichment analyses indicated that the predicted target genes of these differentially expressed miRNAs were enriched in developmental and metabolic categories, including cellular development, protein digestion, and nutrient absorption, suggesting that these miRNAs may be associated with tissue remodeling and larval developmental transitions. Collectively, our findings expand the currently available miRNA resource for H. cunea and define stage-associated miRNA expression patterns during larval development. Rather than establishing direct functional roles, this work provides a framework and candidate molecules for future design of RNAi-based biopesticides.},
}
@article {pmid42127140,
year = {2026},
author = {Ubilla Pavez, P and Paz, A and Maynard, DS},
title = {Functional group classification using consensus clustering.},
journal = {PLoS computational biology},
volume = {22},
number = {5},
pages = {e1014278},
pmid = {42127140},
issn = {1553-7358},
mesh = {Cluster Analysis ; *Biodiversity ; *Computational Biology/methods ; Ecosystem ; Algorithms ; Models, Biological ; },
abstract = {Functional diversity is a fundamental aspect of community structure and composition, reflecting diversity and redundancy in ecological niches, functional roles, and environmental responses among species within a community. Despite its growing importance for quantifying ecosystem-level biodiversity, existing functional diversity metrics remain difficult to calculate and interpret, hindering their adoption and application beyond the scientific realm. One potential solution to this problem is to categorize species into functional groups based on their traits, which provides a simple, intuitive categorization of functional diversity that allows for the application of traditional species-based metrics. The functional-group approach, however, has several challenges that have limited its adoption, namely, the difficulty in identifying robust functional clusters, which can vary substantially due to trait variability, measurement error, and trait correlation. Here, to address these challenges, we present a multi-step consensus clustering method that integrates trait uncertainty and correlation into the classification of species into functional groups. Our approach proceeds in four main steps: (1) (re)sample trait data from an underlying distribution or with measurement error, (2) fit a Gaussian Mixture Model (to account for correlation) to each resample, (3) build a consensus matrix quantifying how often species pairs are grouped together across the noisy trait sample, and (4) apply traditional hierarchical clustering to this matrix and select the final groups. As a case study of this approach, we apply this method to a global dataset of 47,828 tree species using 18 traits, identifying 42 functional groups with distinct trait patterns and varying degrees of stability. We show how the resulting groups reflect underlying ecological trade-offs and phylogenetic structure, and we demonstrate how traditional diversity metrics (richness and Simpson's Index) can be applied to these functional groups to provide intuitive measures of functional group richness and functional redundancy. Collectively, this framework presents a scalable, interpretable approach for quantifying functional groups that embraces trait correlation and trait uncertainty, allowing for repeatable and intuitive quantification of functional biodiversity that can aid its adoption in biodiversity assessments by conservation and restoration organisations.},
}
@article {pmid42128821,
year = {2026},
author = {Fukui, R and Watanabe, F and Tokutsu, K and Muramatsu, K and Fushimi, K and Matsuda, S and Okawara, M},
title = {Perioperative Outcomes Associated with Remimazolam Use in On-Pump Coronary Artery Bypass Grafting in Japan: A Nationwide Retrospective Cohort Study from 2020 to 2022.},
journal = {The Tohoku journal of experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1620/tjem.2026.J051},
pmid = {42128821},
issn = {1349-3329},
}
@article {pmid42129698,
year = {2026},
author = {Škorić, D and Davidović, D and Paunović, K and Ćirković, A and Jovanović, V and Vasiljević, N},
title = {Assessment of Serbian adults' diet through cluster analysis approach - findings from the national health interview survey.},
journal = {BMC public health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12889-026-27737-y},
pmid = {42129698},
issn = {1471-2458},
abstract = {BACKGROUND: The study aimed to assess the diet of Serbian adults using a cluster analysis approach and to determine the association of socio-demographic and other characteristics with the membership to the identified dietary clusters.<br><br>METHODS: This study represents a secondary analysis of data from the 2019 Serbian Health Interview Survey and it included 12755 adults. We used two-step cluster analysis in order to identify the existing dietary types or patterns in the Serbian population. Univariate and multivariable binary logistic regression analyses were used to test the association of the participants' socio-demographic characteristics, health status, body mass index, perceived impact of health risk factors and health-related behavior (physical activity, smoking, alcohol consumption) with the identified diet clusters.<br><br>RESULTS: Two diet clusters were identified, "more favourable" and "less favourable" one, the latter being slightly more prevalent. The main differences between the clusters were in the frequency of vegetables', fruit and milk and dairy products' consumption. More favourable diet type was associated with female sex, older age, higher income and education level, having a chronic illness/ illnesses, practicing healthy behaviors regarding physical activity and smoking and having a positive attitude towards health impact of diet and social activities.<br><br>CONCLUSIONS: The study findings could help in creating national dietary guidelines as well as health promotion activities tailored for specific population groups that account for their diet's characteristics.},
}
@article {pmid42135458,
year = {2026},
author = {Lin, N and Qian, Y and Wei, L and Dai, B and Peng, H and Ma, Y and Zhuang, S and Zhang, D},
title = {An autonomous intelligent mosquito sentinel for field-deployed surveillance.},
journal = {Communications engineering},
volume = {},
number = {},
pages = {},
doi = {10.1038/s44172-026-00685-6},
pmid = {42135458},
issn = {2731-3395},
support = {62475157//National Natural Science Foundation of China (National Science Foundation of China)/ ; 62475157//National Natural Science Foundation of China (National Science Foundation of China)/ ; 62475157//National Natural Science Foundation of China (National Science Foundation of China)/ ; 62475157//National Natural Science Foundation of China (National Science Foundation of China)/ ; RZ-RGZN-01-25-0957//Shanghai Municipal Commission of Economy and Informatization (Shanghai Municipal Working Committee of Economy and Informatization)/ ; RZ-RGZN-01-25-0957//Shanghai Municipal Commission of Economy and Informatization (Shanghai Municipal Working Committee of Economy and Informatization)/ ; RZ-RGZN-01-25-0957//Shanghai Municipal Commission of Economy and Informatization (Shanghai Municipal Working Committee of Economy and Informatization)/ ; RZ-RGZN-01-25-0957//Shanghai Municipal Commission of Economy and Informatization (Shanghai Municipal Working Committee of Economy and Informatization)/ ; },
abstract = {Mosquito-borne diseases pose a major public health challenge and require effective, scalable surveillance to guide targeted interventions. Existing monitoring techniques, ranging from manual morphological identification to acoustic, optical, and spectroscopic sensing, remain constrained by environmental sensitivity, labor demands, and limited ground-truth validation. Here, we present a fully autonomous, field-deployable platform, called automated intelligent mosquito sentinel (AIMS), integrating distributed mosquito monitoring outposts (MMOs) and a centralized analysis center (AC) for scalable, non-invasive mosquito surveillance. AIMS employs an adaptive event-triggering mechanism, optimized through feature engineering of colour and texture pairs, to enable energy-efficient detection with zero missed events and a false-positive rate below 1%. At the analytical level, a hierarchical gated residual network performs multitask classification of taxonomy and sex with accuracies of 99.51% at species and 98.02% for sex, demonstrating interpretable, biologically meaningful attention patterns. The self-powered architecture, robust wireless data transmission, and large-scale field dataset underpin reliable operation across diverse ecological settings. Together, these results show that AIMS can support scalable and sustainable mosquito surveillance and may also be useful for broader entomological monitoring and public health applications.},
}
@article {pmid42140124,
year = {2026},
author = {Lu, Y and Wu, Y and Zhang, H and Gao, D and Xie, H and Fu, S and Wang, H and Li, X},
title = {Multi-omics and in silico assessment of ecological risks posed by agrochemical coatings: Disruption of rhizosphere stress signaling and induction of bulb rot in Fritillaria cirrhosa.},
journal = {Ecotoxicology and environmental safety},
volume = {318},
number = {},
pages = {120276},
doi = {10.1016/j.ecoenv.2026.120276},
pmid = {42140124},
issn = {1090-2414},
mesh = {*Rhizosphere ; *Fritillaria/microbiology/drug effects/physiology ; *Plant Diseases/microbiology ; Molecular Docking Simulation ; *Agrochemicals/toxicity/adverse effects ; *Fungicides, Industrial/toxicity ; Fusarium ; Computer Simulation ; Soil Microbiology ; Signal Transduction/drug effects ; Metabolomics ; Multiomics ; },
abstract = {Agrochemical seed coatings are widely used to control soil-borne pathogens. However, their unintended ecological effects on rhizosphere interactions and plant health remain unclear. Here, we combined a field transplantation trial, multi-omics analyses, and molecular docking to investigate the effects of fungicide-based seed coatings on the rhizosphere microecology of Fritillaria cirrhosa.The field trial showed that coating treatment unexpectedly increased bulb rot incidence by 2.8-fold compared with untreated controls (P < 0.001). Multi-omics analyses further indicated that coating application disrupted rhizosphere microecology, as evidenced by a 25.1% decline in bacterial diversity, reduced network complexity, and enrichment of pathogenic Fusarium species. Metabolomic analysis revealed the accumulation of exogenous xenobiotics along with downregulation of pyrimidine metabolism pathway, suggesting altered plant-microbe chemical communication. Stress-related metabolites, including salicylic acid (SA), L-carnitine, and ethylmalonate, accumulated, whereas key signaling molecules, such as adenosine, monoacylglycerol (18:3), Lysophosphatidylethanolamine 15:1 were depleted (0.03-fold) in the treatment group. Moreover, the decrease in jasmonic acid coupled with an increase in SA suggests immune hijacking associated with necrotrophic pathogens such as Fusarium, a pathological cascade further supported by the accumulation of mycotoxins such as T-2 triol. Cross-domain network and molecular docking analyses further clarified interactions between hub metabolites and the microbial community. Notably, adenosine exhibited strong binding affinities (< -6.0 kcal/mol) to both plant defense-related proteins (JOX2 and CotA laccase) and fungal pathogenicity targets, indicating a key role for endogenous plant defense signals in maintaining rhizosphere ecological balance. Collectively, these findings provide robust correlative evidence linking agrochemical seed coatings to rhizosphere microecological dysbiosis, characterized by reduced metabolite-mediated recruitment of beneficial microbiota and disrupted interkingdom signaling. This pathogen-favoring environment highlights the often-overlooked ecological impacts of seed coatings and underscores the urgent need for microbiome-compatible disease management strategies in perennial bulbous crop production.},
}
@article {pmid42142637,
year = {2026},
author = {Adeboye, SO and Nwinyi, OC and Ayanda, OI},
title = {Insecticide resistance and malaria transmission: divergent effects on Anopheles vector competence.},
journal = {Microbial pathogenesis},
volume = {217},
number = {},
pages = {108557},
doi = {10.1016/j.micpath.2026.108557},
pmid = {42142637},
issn = {1096-1208},
abstract = {The global reduction of malaria burden through the use of insecticides in the form of insecticide-treated nets (ITNs) or indoor residual spraying has been challenged with insecticide resistance among species of Anopheles mosquitoes. The challenge is due to resistance mechanisms such as target site mutation, metabolic resistance, cuticular thickening, and behavioral resistance. Despite few studies reporting significant influence of insecticide exposure on vector competence-a mosquito's ability to infect, harbour, and transmit Plasmodium - the relationship between insecticide exposure in mosquitoes and vector competence remains poorly understood and underexplored. While some studies have reported on the impairment of parasite development in mosquitoes, some others concluded that vector competence in mosquitoes is enhanced by insecticide exposure. This review therefore reports on recent knowledge about the effects of insecticide resistance on vector competence for malaria transmission in Anopheles populations. We argue that the integration of omics-based approaches that embrace ecological reality is crucial for addressing current contradictions observed and accurately predicting epidemiological implications of insecticide resistance in malaria transmission.},
}
@article {pmid42144599,
year = {2026},
author = {Kouba, M and Stehlíková Sovadinová, S and Tulis, F and Ševčík, M and Bartošová, J and Korpimäki, E and Bartoš, L},
title = {Sibling cooperation in boreal owls during the post-fledging dependence period.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-026-02626-3},
pmid = {42144599},
issn = {1741-7007},
abstract = {BACKGROUND: Many vertebrates develop in the company of their siblings, a social context that profoundly influences their life histories and phenotypes. While avian begging behaviour in parent-offspring conflict and sibling competition/cooperation have been largely studied in nestlings, the fledglings' begging remains under-researched, despite the continued dependency of young birds throughout the post-fledging dependence period (PFDP). Siblings typically maintain close proximity during the PFDP, a pattern that might be explained by the following four mutually non-exclusive hypotheses: competition over the prey delivered by parents (competition, H1), mutual affection established during the nestling period (cooperation-friendship, H2), various antipredation behaviours (cooperation-antipredation, H3) or begging negotiation about whose need is greater (cooperation-negotiation, H4).<br><br>RESULTS: We radio-tracked 123 boreal owl (Aegolius funereus) fledglings from 34 nests over 6&#xa0;years in Czechia and Finland and recorded daily inter-sibling distances throughout the PFDP. Distances were longer in Czechia than in Finland during both night (82&#x2009;&#xb1;&#x2009;81 vs 56&#x2009;&#xb1;&#x2009;65&#xa0;m; mean&#x2009;&#xb1;&#x2009;SD) and day (75&#x2009;&#xb1;&#x2009;109 vs 64&#x2009;&#xb1;&#x2009;86&#xa0;m). In both areas, distances increased with an augmenting time gap in tracking, siblings' age and the number of present siblings at night but decreased during the day. These consistent patterns across different environments indicate that the life history of the target species prevails over the environmental effects. Consistent with the predictions of the cooperation-antipredation hypothesis (H3), the mean inter-sibling distances were shorter in Finland compared to Czechia during both day and night, and inter-sibling distances were shorter within larger sibling flocks during the day. The cooperation-negotiation hypothesis (H4) is supported by the finding that vocally begging siblings were closer to each other than their non-begging counterparts.<br><br>CONCLUSIONS: Our results demonstrate, for the first time, that sibling cooperation can occur during the PFDP, when offspring are vulnerable to predators, both during diurnal roosting and at night while begging for food. We conclude that the inter-sibling distances in boreal owls during the PFDP are maintained because siblings cooperate through collective antipredation behaviour during diurnal roosting and through collective negotiation over access to the indivisible prey items delivered by their parent during nocturnal activity.},
}
@article {pmid42149110,
year = {2026},
author = {Kutambe, BM and Patel, PD and Chizani, K and Silungwe, N and Kukacha, C and Carey, ME and Meiring, JE and Laurens, MB and Gordon, MA and Ashton, PM},
title = {Genomic analysis of Salmonella Typhi from a typhoid conjugate vaccine trial.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
pmid = {42149110},
issn = {2057-5858},
mesh = {*Salmonella typhi/genetics/isolation &amp; purification/drug effects/classification/immunology ; Humans ; *Typhoid-Paratyphoid Vaccines/immunology/administration &amp; dosage ; *Typhoid Fever/prevention &amp; control/microbiology ; Child, Preschool ; Infant ; Whole Genome Sequencing ; Child ; Vaccines, Conjugate/immunology ; Malawi ; Genome, Bacterial ; Double-Blind Method ; Male ; Female ; Genomics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Background. Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, continues to pose a major public health challenge in many low- and middle-income countries. The World Health Organization recommended typhoid conjugate vaccine (TCV) use in countries with a high burden of disease and/or high rates of antimicrobial resistance (AMR). Recent introductions of TCVs into national immunization programmes are expected to substantially reduce this burden. However, the impact of vaccine introduction on pathogen populations has not been widely investigated.Methods. To fill this research gap, we analysed the genomes of isolates from a trial in Malawi. A Phase 3, double-blind, randomized, controlled trial enrolled 28,130 healthy children aged 9 months through 12 years of age to receive either TCV (Typbar-TCV, Bharat Biotech) or meningococcal A conjugate vaccine (MenA). We conducted Illumina whole-genome sequencing and compared isolates from the TCV intervention arm to the MenA control arm with regard to (i) S. Typhi lineage distribution, (ii) AMR profile, (iii) mutations in genes associated with Vi capsule biosynthesis and expression and (iv) phylogenetic population structure.Results. We obtained high-quality genome sequences for 136 S. Typhi isolates (24 from the TCV arm, 112 from the MenA arm). Of these, 135 (99%) belonged to lineage L4.3.1.1.EA1. Isolates from the two arms were intermixed across multiple sub-clades. Nearly all isolates (135 out of 136) carried genes encoding resistance to ampicillin, cotrimoxazole and chloramphenicol. Non-synonymous mutations in the quinolone resistance determining region were identified in five isolates (three GyrA S83F; two GyrA S464F), and no statistically significant difference in prevalence of these mutations was observed between study arms (Fisher's exact test, P=0.25). Mutations in Vi capsule-associated genes were detected in 11 out of 112 (9%) MenA isolates and 1 out of 24 (4%) TCV isolates (Fisher's exact test, P=0.67). Fifteen MenA cases were hospitalized, two of whom had Vi-associated mutations. In one of these cases, the Vi mutation has previously been associated with increased virulence in a murine model; however, there was no significant association between tested Vi mutations and hospitalization (P>0.91).Conclusions. We identified no clinically meaningful genomic differences between S. Typhi isolates from participants vaccinated with TCV or MenA, and no Vi-negative S. Typhi were detected. These findings suggest no detectable short-term evolutionary impact of TCV on circulating S. Typhi populations in this Phase 3 trial. However, given the limited follow-up period and S. Typhi's relatively slow substitution rate, continued genomic surveillance in this population after national TCV introduction in 2023 is essential to detect evolutionary responses to vaccine pressure.},
}
@article {pmid42149935,
year = {2026},
author = {Kyomuhangi, I and Mustafa, A and Hawkes, FM},
title = {A systematic review comparing the performance of alternative blackfly (Simulium) trapping methods against the standard human landing catch (HLC) for onchocerciasis surveillance.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {5},
pages = {e0014359},
pmid = {42149935},
issn = {1935-2735},
mesh = {*Simuliidae/physiology/parasitology ; Animals ; *Onchocerciasis/prevention &amp; control/epidemiology/transmission ; Humans ; *Insect Control/methods/instrumentation ; *Insect Vectors/parasitology ; },
abstract = {Despite decades of control efforts, onchocerciasis remains a major public health concern in Africa, the Americas, and Yemen. Human Landing Catch (HLC) is the primary method for collecting blackflies and is central to surveillance. However, HLC raises ethical concerns due to collectors' exposure to painful and potentially infectious bites and faces operational challenges in areas of very low or high transmission. Consequently, several alternative blackfly trapping methods have been investigated, but no comprehensive synthesis comparing their effectiveness against standard HLC across studies has been conducted. Therefore, we performed a systematic review comparing the performance of alternative blackfly traps with standard HLC. A systematic review (PROSPERO registration number: CRD420261294895) of literature published in Scopus, PubMed, and Web of Science up to December 2025 was supplemented by an expert-provided reference list. From 166 records, 62 were screened, and 13 studies (comprising 79 comparisons with standard HLC) met inclusion criteria. Alternative traps included light traps, Bellec traps, tent traps baited with humans or cows, Esperanza Window Traps, Host Decoy Traps, electric nets, and modified HLC. Most comparisons (75.9%) found alternative traps to be less effective than standard HLC, with statistical analyses often supporting these differences, although nearly half lacked formal significance testing. Variation in study design-including trap placement, rotation, and trapping duration-and inconsistent reporting of key variables such as season, habitat, and species limited direct comparisons. Some studies indicated that increasing trap density or deployment duration of Esperanza Window Traps could improve effectiveness. While HLC remains the most effective method, its ethical and operational limitations highlight the need for reliable alternatives. Most existing traps underperform relative to HLC, but modifications based on deeper understanding of blackfly behaviour and ecology could improve performance. Future research should focus on standardizing trap evaluation methods, exploring species-specific behaviours, and assessing scalability to develop ethical, scalable tools for onchocerciasis surveillance.},
}
@article {pmid42149938,
year = {2026},
author = {Lindsley, IC and Juman, MM and Seifert, SN and Gibb, R and Albery, GF and Jephcott, F and Restif, O},
title = {Host-virus association databases as tools for understanding viral spillover at varying scales.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {5},
pages = {e0013343},
pmid = {42149938},
issn = {1935-2735},
mesh = {Humans ; Animals ; *Hemorrhagic Fever, Ebola/virology/epidemiology/transmission ; Ebolavirus/physiology ; *Lassa Fever/virology/epidemiology/transmission ; *Databases, Factual ; *Zoonoses/virology/epidemiology ; Africa South of the Sahara/epidemiology ; Lassa virus/physiology ; Viruses ; *Host-Pathogen Interactions ; },
abstract = {Large host-virus association databases are increasingly used to explore broad questions in disease ecology, particularly around host range, pathogen diversity, and the potential for spillover. While these databases have been instrumental in large-scale synthesis of host-pathogen biogeography and zoonotic risk, their potential role in addressing fine-scale questions about pathogen prevalence, maintenance, and transmission dynamics remains underexplored. In this study, we build on previous efforts to assess how different types of data, including both entries in databases and the original studies they draw from, can support targeted research on zoonotic spillover. We selected two zoonotic diseases, Ebola virus disease and Lassa fever, which are characterised by recurrent spillover events and outbreaks in sub-Saharan Africa. We searched the VIRION database for entries corresponding to the respective viral taxa, the genus Orthoebolavirus and the species Mammarenavirus lassaense, and used these entries as case studies. We evaluated the extent to which databases capture crucial contextual metadata, such as spatial and temporal resolution, negative results, and measures of viral load. Guided by a conceptual framework of factors that lead to spillover, we demonstrate that while host-virus databases are valuable for addressing high-level patterns, fine-scale investigations of spillover require specific studies with detailed epidemiological data. Our study adds to a growing body of literature offering practical recommendations for database users and managers and highlights how these tools can be used as starting points in spillover research.},
}
@article {pmid42151772,
year = {2026},
author = {Witzke, S and Zabbarov, J and Kleissl, M and Iversen, P and Renard, BY and Baum, K},
title = {Selecting synthetic data for successful simulation-based transfer learning in dynamical biological systems.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {42151772},
issn = {1471-2105},
mesh = {*Machine Learning ; Computer Simulation ; *Computational Biology/methods ; *Systems Biology/methods ; },
abstract = {BACKGROUND: Accurate prediction of the temporal dynamics of biological systems is crucial for informing timely and effective interventions, e.g., in ecological or epidemiological contexts, or for treatment adjustments in therapy. While machine learning has proven its capabilities in generalizing the underlying non-linear dynamics of such systems, unlocking its predictive power is often restrained by the limited availability of large, curated datasets. To supplement real-world data, informing machine learning by transfer learning with synthetic data derived from simulations using ordinary differential equations has emerged as a promising solution. However, the success of this approach highly depends on the designed characteristics of the synthetic data.<br><br>RESULTS: We suggest scrutinizing these characteristics, such as size, diversity, and noise, of ordinary differential equation-based synthetic time series datasets. Here, we demonstrate how to systematically evaluate the influence of such design choices on transfer learning performance. We conduct a proof-of-concept study on three simple, but widely used systems and four real-world datasets. We find a strong interdependency between synthetic dataset size and diversity effects. Good transfer learning settings heavily rely on real-world data characteristics as well as the data's coherence with the dynamics of the model underlying the synthetic data. We achieve a performance improvement of up to 95% in mean absolute error for simulation-based transfer learning compared to non-informed deep learning.<br><br>CONCLUSIONS: Our work emphasizes the relevance of carefully selecting properties of synthetic data for leveraging the valuable domain knowledge contained in ordinary differential equation models for machine-learning based predictions. The code is available at https://github.com/DILiS-lab/opt-synthdata-4tl .},
}
@article {pmid42153706,
year = {2026},
author = {Borren, NZ and Paulides, E and Klaassen, MAY and Alm, E and Xavier, RJ and Janneke van der Woude, C and Ananthakrishnan, AN},
title = {Microbiome-Directed Therapy for Fatigue in Quiescent Inflammatory Bowel Disease: A Randomized Placebo-Controlled Trial of Multi-Strain Probiotic Supplementation.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000004056},
pmid = {42153706},
issn = {1572-0241},
abstract = {INTRODUCTION: Fatigue is a challenging symptom for patients with inflammatory bowel diseases (IBD). Emerging evidence links alterations in the gut microbiome with fatigue in IBD, highlighting the potential of microbiome-targeted treatments. Our aim was to evaluate the clinical efficacy and biological effects of a multi-strain probiotic supplementation on fatigue in patients with quiescent IBD.<br><br>METHODS: This multi-center, placebo-controlled, randomized controlled trial included patients with quiescent IBD, defined as being in clinical remission and a colonoscopy within 1 year which demonstrated no active disease, and with significant fatigue (FACIT-F score < 43). Patients were randomized to receive either probiotics (Ecologic&#xae; BARRIER, containing 9 different bacterial strains) or placebo for 12 weeks. Gut microbiome and serum metabolome were analyzed at baseline and at the end of the study.<br><br>RESULTS: Our study enrolled 100 patients (52 Crohn's disease (CD), 44 ulcerative colitis (UC), 4 IBD-unspecified) with quiescent IBD and with a mean age of 41 years; 61% were women. After 12 weeks, 29.4% of the probiotic group and 40.0% of the placebo group met criteria for no fatigue (p=0.34). However, all participants reported an improvement in fatigue (p<0.001) with the most striking change noted at 4 weeks in both groups. Probiotic treatment led to beneficial shifts in gut microbiome and serum metabolome composition, particularly an increase in Bifidobacterium animalis after 12 weeks.<br><br>DISCUSSION: While 12 weeks of probiotic administration was not associated with relief of fatigue in patients with quiescent IBD, we observed beneficial alterations in the gut microbiome and serum metabolome. ClincialTrials.gov number, NCT03266484.},
}
@article {pmid42155086,
year = {2026},
author = {Akarapimand, P and Lin, JC and Scott, IU and Baxter, SL},
title = {Broadband Access and Ophthalmologist Density in the United States: Cross-Sectional Questionnaire Study.},
journal = {JMIR public health and surveillance},
volume = {12},
number = {},
pages = {e88473},
pmid = {42155086},
issn = {2369-2960},
mesh = {Humans ; United States ; Cross-Sectional Studies ; Surveys and Questionnaires ; *Ophthalmologists/supply &amp; distribution/statistics &amp; numerical data ; Female ; Male ; *Health Services Accessibility/statistics &amp; numerical data ; Adult ; Middle Aged ; Rural Population/statistics &amp; numerical data ; *Internet Access/statistics &amp; numerical data ; },
abstract = {BACKGROUND: Rural US communities experience disproportionately high rates of visual disability yet have limited access to ophthalmologists. Teleophthalmology may help address these gaps, but its effectiveness depends on broadband connectivity. The relationship between broadband access and ophthalmologist density has not been well characterized.<br><br>OBJECTIVE: The aim of this study is to quantify the association between household broadband access-defined as subscription rates or connection prevalence-and county-level ophthalmologist density and to identify sociodemographic predictors of access.<br><br>METHODS: We conducted an ecological study of all 3141 US counties using 2019 data from the American Community Survey, Area Health Resources File, and National Center for Health Statistics (NCHS). Broadband access was the primary exposure; ophthalmologist count with county population as an offset was the outcome. The primary analysis used negative binomial regression, adjusting for urbanicity, income, education, age, sex, race/ethnicity, unemployment, and insurance status. Sensitivity analyses included population-weighted linear regression and state fixed effects models. County-level heatmaps illustrated geographic patterns.<br><br>RESULTS: Median household broadband access was 56.6%, ranging from 72.2% in the most urban counties (NCHS category 1) to 49.1% in the most rural (NCHS category 6). In unadjusted negative binomial regression, each 10-percentage-point increase in broadband access was associated with a 68% higher ophthalmologist rate (incidence rate ratio=1.68, 95% CI 1.61-1.76; P<.001). After adjustment, each 10-percentage-point increase was associated with a 46% higher rate (incidence rate ratio=1.46, 95% CI 1.37-1.56; P<.001). Sensitivity analyses were consistent with primary analysis. Regions with both low broadband access and zero ophthalmologist density were concentrated in the South, Mountain West region, and Alaska.<br><br>CONCLUSIONS: Broadband access is strongly associated with ophthalmologist availability across US counties, independent of sociodemographic factors. Areas lacking ophthalmologists also tend to lack broadband adoption, creating compounded barriers to both in-person and teleophthalmic care. Efforts to expand broadband may support more equitable access to vision services in underserved regions.},
}
@article {pmid42156649,
year = {2026},
author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Gopal, D},
title = {Exploring the Ocean's Microbial World: Techniques and Protocols for Microbiome Research.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {33-46},
pmid = {42156649},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Oceans and Seas ; *Seawater/microbiology ; Computational Biology/methods ; },
abstract = {Marine microbiomes play a crucial role in oceanic ecosystems, influencing biogeochemical cycles, climate regulation, and marine biodiversity. Accurate characterization of these microbial communities requires standardized protocols for sample collection, processing, sequencing and data analysis. This chapter provides a comprehensive guide to essential methodologies for marine microbiome research including field sampling strategies, DNA and RNA extraction techniques, high-throughput sequencing approaches (such as 16S rRNA amplicon sequencing and metagenomics) and bioinformatics pipelines for data interpretation. Additionally, we discuss quality control measures, best practices for reproducibility, and challenges associated with marine microbiome profiling. By adopting standardized methodologies, researchers can generate reliable, comparable datasets that enhance our understanding of marine microbial ecology and its broader environmental implications.},
}
@article {pmid42156650,
year = {2026},
author = {Miliotis, G and Tumeo, A},
title = {Shotgun Metagenomic Analysis of Microbial Community Dynamics in Wastewater Treatment Through Constructed Wetlands.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {47-73},
pmid = {42156650},
issn = {1940-6029},
mesh = {*Wetlands ; *Metagenomics/methods ; *Wastewater/microbiology ; *Water Purification/methods ; *Microbiota/genetics ; Metagenome ; Computational Biology/methods ; Water Microbiology ; },
abstract = {Constructed wetlands (CWs) offer a sustainable, nature-based solution to wastewater treatment, supporting diverse and dynamic microbial communities that drive nutrient cycling, pollutant degradation, and pathogen removal. This chapter presents an end-to-end methodology for performing shotgun metagenomic analyses on microbial populations from CW influent and effluent. We detail approaches for site selection, sample collection, filtration, DNA extraction, and the incorporation of positive and negative controls to ensure reproducibility and data quality. Two modular bioinformatic workflows encompassing quality control, assembly, taxonomic/functional annotation, and metagenome-assembled genome recovery are described alongside options for detecting antimicrobial resistance genes, pathogens, toxins, and plasmids. In addition, an example workflow for the calculation of alpha and beta diversity is provided. Guidelines for data standardization, replication, and compliance with community-driven reporting standards (MIMS, MIMAG) are also included. Incorporating this protocol will facilitate standardized, reproducible insights into CW microbial dynamics, thereby informing ecological understanding and guiding practical interventions that enhance wastewater treatment efficacy and improve public health outcomes.},
}
@article {pmid42156652,
year = {2026},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Computational Microbial and Viral Ecology Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {83-141},
pmid = {42156652},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics/classification ; Virome ; Bacteriophages/genetics ; Bacteria/genetics ; Archaea/genetics ; },
abstract = {The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed that interactions between diverse groups of community members such as archaea, bacteria, and viruses (bacteriophages) are common and have significant impacts on entire microbiomes. Thus, to have a well-developed understanding of microbes as they naturally exist in the environment, biological entities of all kinds must be studied together. While numerous protocols for metagenome analysis exist, comprehensive published protocols for the simultaneous analysis of viruses and prokaryotes together are scarce. Further, as bioinformatic methods for microbiology rapidly advance, existing metagenomic tools and pipelines require frequent re-evaluation. This ensures the adherence to best practices for microbiome and metagenomic data analysis. Here, we offer an expansive approach for the joint analysis of bulk sequence data from a mixed microbial community (metagenomes) and viral-sized fraction communities (viromes). This chapter serves as a beginner's-level guide for researchers with limited bioinformatics expertise who wish to engage in multiscale metagenome and virome analyses. We cover steps from initial study design to sequence read processing, metagenome assembly, quality control, virus identification, microbial and viral genome binning, taxonomic characterization, species-level clustering, and host-virus predictions. We also provide the bioinformatic scripts used in our workflow for reuse in one's own computational methods. Lastly, we discuss additional approaches a researcher can take after processing data with this workflow.},
}
@article {pmid42156659,
year = {2026},
author = {Zhang, S and McCullough, HC and Song, HS},
title = {Predicting Interspecies Metabolic Dependencies in Microbial Communities by Integrating Flux Coupling Analysis with SteadyCom.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {261-276},
pmid = {42156659},
issn = {1940-6029},
mesh = {*Metabolic Networks and Pathways ; Software ; Algorithms ; *Microbiota ; *Computational Biology/methods ; *Metabolic Flux Analysis/methods ; Models, Biological ; },
abstract = {Microbial communities play a pivotal role in a wide range of ecological processes and engineered systems. The level of complexity in analyzing microbial communities necessitates the use of predictive mathematical models such as genome-scale metabolic networks. To identify metabolic interdependence among member species within microbial communities, we present a recently developed computational tool combining two existing approaches: SteadyCom and Flux Coupling Analysis (FCA). Both approaches leverage genome-scale metabolic networks as their primary inputs, albeit for distinct objectives. SteadyCom is a community modeling tool used to estimate flux distributions and metabolite exchanges within and across species, respectively, by constraining individual specific growth rates to be equal. In contrast, FCA has been used to identify the causal relationships among reactions with a primary focus on the analysis of individual metabolic networks, i.e., what reactions must be active for a target reaction to be active. The combination of these two approaches allows us to find how metabolic reactions in individual species are coordinated as an interacting community. Without any additional computations, the implementation of this algorithm also provides information on what reactions are blocked in the network. We provide all the information needed to implement these coupled computational tools in a Python Jupyter notebook.},
}
@article {pmid42156661,
year = {2026},
author = {Nawaz, A and Schaefer, JL and Centler, F},
title = {Dynamic Simulation of Growth and Cross-Feeding in Microbiomes with μbialSim.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {317-330},
pmid = {42156661},
issn = {1940-6029},
mesh = {*Microbiota ; Computer Simulation ; Software ; *Models, Biological ; Microbial Interactions ; Bioreactors/microbiology ; Computational Biology/methods ; },
abstract = {Microbial cells in natural environments are typically embedded in microbial communities consisting of few to many different species. Close proximity and high diversity of neighboring cells facilitate manifold interactions on several layers, from substrate competition, exchange of genetic material, to metabolic cross-feeding. The complexity of these ecological interaction networks makes microbiomes notoriously difficult to study. While microbiome dynamics can routinely be elucidated by meta-omics technologies, pinpointing mechanisms driving these observed dynamics remains a challenge. Mechanistic mathematical modeling with its ability to focus on individual interactions and exploring their isolated impact on overall dynamics has emerged as a suitable tool in this context. Here, we use μbialSim, an open-source simulator that extends the Flux Balance Analysis approach to microbial communities, considering substrate competition and metabolic cross-feeding but neglecting any other microbial interactions. Assuming a well-mixed bioreactor environment, simulated trajectories enable the analysis of growth behavior of individual microbiome members, dynamics of intracellular enzymatic fluxes across all species, as well as the analysis of cross-feeding behavior and how it changes over time. The MATLAB implementation of μbialSim is available from https://github.com/fcentler/microbialSim .},
}
@article {pmid42157207,
year = {2026},
author = {Dhir-Hewitt, E and Newlands, F and Shafran, R and Stephenson, T and Richards-Belle, A and Dalrymple, E and Chalder, T and Ford, T and Fox-Smith, L and Heyman, I and N Ladhani, S and G Semple, M and Segal, TY and Swann, O and Whittaker, E and , and Pinto Pereira, SM},
title = {Exploring post-Covid-19 condition in children and young people 3.5 years after infection: a mixed-methods analysis from the CLoCk study.},
journal = {BMC public health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12889-026-27520-z},
pmid = {42157207},
issn = {1471-2458},
support = {ES/T00200X/1//ESRC-BBSRC Soc-B Centre for Doctoral Training/ ; MR/Y009398/1//UK Medical Research Council Senior Non-clinical fellowship/ ; },
abstract = {BACKGROUND: Comprehensive data on the persistence of Post-COVID-19 Condition (PCC; also known as Long COVID) and its impact on children and young people (CYP), incorporating their own perspective, is crucial to enhance our understanding of the condition, improve service provision and inform clinical management.<br><br>METHODS: We examine long-term symptoms, health, and well-being among CYP persistently meeting PCC criteria up to 3.5-years after SARS-CoV-2 infection (when they were aged between 11-to-17-years), using a mixed-methods approach. 68 CYP from the CLoCk study who persistently met PCC criteria at 3- (April-June 2021), 6- (July-September 2021), 12- (January-March 2022), and 24-months (January-March 2023) post-infection were invited to complete an additional follow-up (October-November 2024). The survey assessed current symptoms and health status using validated measures, and symptom experiences through open-text responses. Quantitative data were analysed descriptively; qualitative data were analysed using thematic framework analysis. Findings were integrated using a convergent parallel design.<br><br>RESULTS: 50 CYP completed the survey; of these 42 (84%) responders continued to meet the PCC definition 3.5-years post-infection. All 42 (100%) reported tiredness and 34 (81%) reported 5&#x2009;+&#x2009;symptoms 3.5-years post-infection. Qualitative analysis reinforced tiredness as a central symptom, alongside co-occurring symptoms that impact daily life. While quantitative and qualitative findings largely converged, context as to why CYP reported high levels of impact were only available from qualitative data.<br><br>CONCLUSIONS: CYP with PCC persisting for 3.5-years post-infection experience multiple symptoms of wide-ranging severity and disruption to daily life, education and social participation.},
}
@article {pmid42158411,
year = {2026},
author = {Akinyosoye, AD and Rotimi, SO and Olasehinde, OE and Oduselu, GO and Oranusi, SU and Akinnola, OO},
title = {Hemozoin-induced immunomodulation and prostate carcinogenesis: mechanisms and implications.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1786079},
pmid = {42158411},
issn = {2234-943X},
abstract = {Hemozoin (Hz) is a crystalline by-product, which is produced when the Plasmodium species destroy haemoglobin, and it is commonly recognised that it leads to how our bodies respond to malaria. Although we understand pretty well its immunological actions in infectious diseases, recent research indicates that chronic exposure to Hz may actually cause cancer by sustaining inflammation and altering the immune system. In this review, we examines how the relationship between the hemozoin induced immune changes contribute to prostate cancer development arises. The presence of Hz within the macrophages and dendritic cells can modulate inflammatory signalling pathways, including NF-kB, MAPK, and STAT3, particularly in the context of co-stimulation with parasite or host-derived ligands, thereby sustaining low-grade inflammation over time. These processes can result in amplified cell growth, inhibition of cell death, and genomic instability, which are typical of cancer. In addition, while several in vitro studies have reported that the purified hemozoin elicits weak or no cytokines, it has accumulated Hz amplify responses to infections or Toll-like receptor ligands, consistent with a primarily agonistic role. Hz is seen to direct macrophages to a tumour-promoting M2, suppress cytotoxic T-cells, and increase the performance of regulatory T cells, all of which are detrimental to the immune response against tumours. The connections between Toll-like receptor (TLR) signalling, oxidative stress, and PI3K/Akt/mTOR are also investigated in relation to the possibility of encouraging tumour development in prostate conditions. Epidemiologically, malaria endemic regions also report an increase in prostate cancer incidence, though this ecological overlap is subject to major cofounding, it raises the hypothesis that repeated exposure to malaria and subsequently Hz might contribute to prostate cancer, which necessitates further studies. In addition, improved malaria control, demographic ageing, coinfections, and other factors are likely to obscure any direct association. A better comprehension of these relationships may present the possibility of novel diagnostic measures and specific interventions.},
}
@article {pmid42158548,
year = {2026},
author = {Stratemann, C and Khorsandi, S and Swamy, S and Lin, L and King, B},
title = {Cross-sectional characterisation of housing and social service engagement prior to death among adults experiencing homelessness in Harris County, Texas, USA.},
journal = {BMJ public health},
volume = {4},
number = {2},
pages = {e003952},
pmid = {42158548},
issn = {2753-4294},
abstract = {INTRODUCTION: People experiencing homelessness are at disproportionate risk of premature mortality. In Harris County, Texas, USA, mortality has continued to rise despite reductions in unsheltered homelessness. The extent and timing of housing and social service engagement preceding these deaths remain poorly understood yet may help inform whether and how service engagement could play a role in prevention.<br><br>METHODS: This cross-sectional study included 417 adults who died while experiencing homelessness in Harris County between January 2021 and December 2022. Medical examiner records were probabilistically linked to the regional Homeless Management Information System (HMIS) to assess service engagement from January 2020 until death. Bivariate analyses compared decedents with and without HMIS records and among those in HMIS, individuals with and without recent service interactions (&#x2264;12 months before death).<br><br>RESULTS: The median age at death was 55 years. Just over half of decedents (53.48%) had an HMIS record but only 29.50% had a recent service interaction. The most frequently documented services were basic needs provision and case management while street outreach engaged the largest number of individuals. Significant racial and ethnic differences were observed, with Hispanic and non-Hispanic Asian decedents less likely to have used services compared with non-Hispanic Black and non-Hispanic White decedents.<br><br>CONCLUSION: Nearly half of those who died while experiencing homelessness had no documented service record, and fewer than one-third had any recent engagement, highlighting limited connection with services prior to death. Strengthening continuity and frequency of contact, expanding culturally responsive outreach and enhancing pathways to housing-focused services may support improved engagement and risk identification, though their implications for mortality require further investigation.},
}
@article {pmid42160376,
year = {2026},
author = {Long, C and Angulo, MT and Ogbunugafor, CB and Solé, R and Saavedra, S},
title = {Energetic constraints shape the diversity of feasible ecological networks.},
journal = {PLoS computational biology},
volume = {22},
number = {5},
pages = {e1014330},
pmid = {42160376},
issn = {1553-7358},
mesh = {*Models, Biological ; *Biodiversity ; *Ecosystem ; *Energy Metabolism/physiology ; Computational Biology ; Biomass ; Animals ; Ecology ; Computer Simulation ; },
abstract = {The relationship between energy supply and biodiversity is a longstanding question in ecology. Although a monotonic increase in diversity with energy availability is often assumed, unimodal species-energy relationships have been widely documented across ecosystems, and their origin from first principles remains unclear. Here, we develop a geometric framework that recasts ecological feasibility in explicitly energetic terms. By treating total energy supply as a system-level constraint on an energy-based network model, we define nested feasibility domains in the space of energy capture rates and quantify feasibility probabilities as their volume ratios. We show that the probability of initializing a feasible network increases monotonically and saturates with energy supply, whereas the probability of sustaining steady-state biomass follows a unimodal relationship-revealing a bounded energetic window within which network maturation is most likely. Extending this analysis to all candidate subcommunities via feasibility partitions, we find that different community sizes are most feasible at different energy levels, and that average diversity itself peaks at intermediate supply. Together, these results suggest that energetic constraints determine the diversity of ecological networks not through energy scarcity alone, but through the geometric interplay between external energy supply and internal energy exchange.},
}
@article {pmid42162297,
year = {2026},
author = {Khurana, MP and Tsui, JL and Gutierrez, B and Chopra, A and Scheidwasser, N and Zhu, HBH and Chang, SY and Duchêne, DA and Mills, C and Inward, RPD and Reddy, B and Brittain, J and Dasgupta, A and Sheldon, J and Githinji, G and Brownstein, JS and Monod, M and Ferretti, L and Bershan, S and Tietze, S and Ferres, L and Argimón, S and Dallman, TJ and Koua, E and Ratmann, O and Cauchemez, S and Meyers, LA and Su, L and Vespignani, A and Pronyk, P and O'Toole, &#xc1; and Rambaut, A and Loman, NJ and Holmes, EC and Flaxman, S and Mulder, N and Morgan, OW and Tegally, H and Gomez-Rodriguez, M and Shadbolt, N and Happi, C and Chand, M and Tessema, SK and Mbala-Kingebeni, P and Suchard, MA and Pybus, OG and Scarpino, SV and Bhatt, S and Kraemer, MUG},
title = {Global approaches to infectious disease surveillance and modeling.},
journal = {Nature medicine},
volume = {32},
number = {5},
pages = {1646-1660},
pmid = {42162297},
issn = {1546-170X},
mesh = {Humans ; *Communicable Diseases/epidemiology ; Global Health ; Disease Outbreaks ; *Population Surveillance/methods ; Information Dissemination ; },
abstract = {Human mobility, climate change and demographic trends increase the risk of pathogen spillover and expansion. Data that can inform our responses to outbreaks have increased in availability and volume, but access to highly confidential outbreak data and commercially sensitive contextual information remains difficult. Despite ongoing efforts to adopt global health data infrastructures and sharing protocols, there remain regulatory, logistical, human and computational barriers to data sharing. Federated approaches-in which data remain stored locally but analyses are performed across datasets from different sources-offer a potential way to address these challenges. While federated approaches have been used in some clinical and biomedical contexts, their adoption in infectious disease surveillance and modeling has been limited. Here, we discuss global approaches to infectious disease modeling and analysis, with a focus on federated methods. We outline how these can be used to address key epidemiological questions during outbreaks by enabling the secure use of multimodal data and integration with existing surveillance and modeling efforts. We summarize current methods for combining distributed and locally stored data and identify limitations, opportunities and organizational structures needed to achieve equitable global public health impacts.},
}
@article {pmid42162964,
year = {2026},
author = {Peng, C and Jiang, L and Huang, Z and Wei, X and Zhu, X and Liu, Z and Chen, Q and Shen, X and Gao, P and Jiang, C},
title = {MetaNet: a scalable and integrated tool for reproducible omics network analysis.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {6},
pages = {},
pmid = {42162964},
issn = {1367-4811},
support = {82341109//NSFC/ ; 82173645//NSFC/ ; //Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Software ; Multiomics/methods ; Algorithms ; *Computational Biology/methods ; Microbiota ; },
abstract = {MOTIVATION: Network analysis has become a central strategy for dissecting complex biological and environmental systems, particularly as modern omics technologies generate increasingly large and heterogeneous datasets. However, current tools often lack the scalability, flexibility, and native multi-omics support required for high-dimensional data analysis. We developed MetaNet, a high-performance R package that unifies network construction, visualization, and analysis across diverse omics layers.<br><br>RESULTS: MetaNet enables fast and scalable correlation-based network construction for datasets with more than 10&#x2009;000 features, providing over 40 layout algorithms, rich annotation utilities, and visualization options compatible with both static and interactive platforms. It further offers comprehensive topological and stability metrics for in-depth network characterization. Benchmarking shows that MetaNet delivers up to a 100-fold improvement in computation time and a 50-fold reduction in memory usage compared to existing R packages. We demonstrate its utility through two representative applications: (1) longitudinal microbial co-occurrence networks revealing airborne microbiome dynamics, and (2) an integrative exposome-transcriptome network of over 40&#x2009;000 features, uncovering distinct regulatory impacts of biological and chemical exposures. By offering a robust, reproducible, and biologically informed framework, MetaNet advances multi-omics network analysis across biological, ecological, and environmental domains.<br><br>AVAILABILITY: MetaNet package is freely available at https://github.com/Asa12138/MetaNet.},
}
@article {pmid42163451,
year = {2026},
author = {Afzal, Y and Nawaz, N and Khan, AA and Yousaf, MJ and Khan, MZ and Arif, E and Salahuddin, M and Mohamed, MA and Ullah, S},
title = {Sustainable Control of Carbon Emissions and Energy Consumption Through a Green Data Center Approach.},
journal = {TheScientificWorldJournal},
volume = {2026},
number = {1},
pages = {e1158756},
pmid = {42163451},
issn = {1537-744X},
abstract = {Data center management, the foundation of contemporary cloud computing, has made energy saving a top priority. Among other difficulties, the placement of virtual machines (VMs) has a major impact on data center resource and energy usage. Assigning VMs to physical machines (PMs) is a challenging NP-hard problem, especially in large-scale infrastructures where it is computationally infeasible to find an ideal solution. To solve the VM placement problem, the proposed study formulates it as a restricted optimization problem with the goal of preserving performance while lowering energy consumption. The explosive growth of data centers has resulted in higher energy consumption and higher carbon dioxide (CO2) emissions, which are a primary cause of climate change. Globally, governments, energy-focused organizations, and business executives have taken notice of this expanding environmental impact. This study provides a comprehensive analysis of data center energy consumption patterns, environmental effects, and trends in energy consumption. It also suggests doable energy-saving measures, such as installing energy-efficient infrastructure and upgrading air conditioning systems. The paper also presents an improved genetic algorithm-based method that is tailored for energy-conscious VM deployment, successfully striking a balance between computing economy and convergence accuracy. The suggested solution highly increased data centers' energy efficiency by incorporating this strategy within a profile-based virtual resource management model. Additionally, policy suggestions for sustainable data center management are delineated, advancing the more general objective of ecologically conscious cloud computing. Experimental results demonstrate that the proposed method achieves up to 50% reduction in execution time, 48% fewer generations for convergence, and approximately 7% reduction in energy consumption compared to traditional first fit decreasing (FFD) methods. Additionally, the integration of task classification improves energy efficiency by up to 15% and reduces the number of active PMs. These findings highlight the effectiveness of the proposed framework in enabling scalable, energy-efficient, and environmentally sustainable cloud data center management.},
}
@article {pmid42166193,
year = {2026},
author = {Sarzo, B and King, R and McCrea, R},
title = {Correcting random effect distributions to account for survivorship bias in individual heterogeneity Cormack-Jolly-Seber models.},
journal = {Biometrics},
volume = {82},
number = {2},
pages = {},
doi = {10.1093/biomtc/ujag086},
pmid = {42166193},
issn = {1541-0420},
support = {CD23/00090//WWF/ ; //European Union/ ; },
mesh = {*Models, Statistical ; Survival Analysis ; *Biometry/methods ; Computer Simulation ; Selection Bias ; Bias ; Animals ; Data Interpretation, Statistical ; },
abstract = {Survivorship (or selection) bias arises within statistical analyses where the observed data are subject to some underlying selection process prior to entry into the sampled data. For example, within capture-recapture studies, a primary selection mechanism is the survival until initial capture time. The common Cormack-Jolly-Seber model conditions on the first time an individual is observed, leading to potential survivorship bias. However, while the issue of survivorship bias has been well studied in many fields, there has been little exploration within the capture-recapture framework. In particular, we focus on individual (continuous) random effect Cormack-Jolly-Seber models, where it is assumed that individuals have different survival probabilities, specified to be from some common underlying distribution. We discuss the implications of the survivorship bias within the data collection process, and describe a novel modeling approach that accounts for the survivorship bias within an ecologically sensible manner. Using simulated data, we demonstrate the significant impact of ignoring the survivorship bias present in the data. We fit the corrected model to a guillemot data set and demonstrate that even with relatively mild selection bias, the individual heterogeneity variability is substantially underestimated when ignoring this survivorship bias.},
}
@article {pmid42170025,
year = {2026},
author = {Higashi, K and Ishikawa, H and Kurokawa, K and Mori, H},
title = {PZLAST-MAG: full length protein sequence similarity search server of large-scale MAG proteins.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag129},
pmid = {42170025},
issn = {2635-0041},
abstract = {MOTIVATION: Metagenome-assembled genomes (MAGs) provide access to novel protein sequences from uncultured microbes, offering invaluable resources for studying protein diversity, structure prediction, and evolutionary analysis. However, despite the explosive growth of MAG-derived protein data, tools enabling fast and accurate similarity searches against large-scale MAG protein datasets remain limited.<br><br>RESULTS: We present PZLAST-MAG, a web server for ultra-fast sequence similarity searches against 0.4 billion MAG-derived protein sequences (0.1 trillion amino acids) from over 210&#xa0;000 MAGs indexed in Microbiome Datahub. Implemented on PEZY-SC3 MIMD many-core processors, PZLAST-MAG achieves high accuracy and speed, with performance comparable to widely used tools such as DIAMOND and MMseqs2 based on our benchmark analyses. In addition to tabular alignments, PZLAST-MAG provides interactive visualizations of phylogenetic and environmental distributions and co-occurrence patterns of homologous proteins across MAGs. This combination enables rapid homolog mining of functionally important genes across diverse microbial lineages while simultaneously revealing their taxonomic and ecological contexts. Two use case analyses indicate its utility for homolog mining of metabolic enzyme genes and plasmid-derived genes.<br><br>PZLAST-MAG is provided as a web-based service and is freely available at https://pzlast.nig.ac.jp/pzlast/mag without requiring registration.},
}
@article {pmid42172047,
year = {2026},
author = {Delgado, LF and Ortís Sunyer, J and Laczny, CC and Hickl, O and May, P and Wilmes, P},
title = {PathoFact 2.0: an integrative pipeline for the prediction of antimicrobial resistance genes, virulence factors, toxins and toxin-associated proteins, and biosynthetic gene clusters in metagenomes.},
journal = {GigaScience},
volume = {15},
number = {},
pages = {},
pmid = {42172047},
issn = {2047-217X},
support = {C23/BM/18091896//Luxembourg National Research Fund/ ; ERC-CoG 863664/ERC_/European Research Council/International ; },
mesh = {*Virulence Factors/genetics ; *Multigene Family ; *Metagenome ; *Software ; Machine Learning ; *Drug Resistance, Bacterial/genetics ; *Computational Biology/methods ; Bacterial Toxins/genetics ; },
abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) and virulence factors (VFs) are central contributors to the global health crisis surrounding drug-resistant infections.<br><br>FINDINGS: We introduce PathoFact 2.0, an enhanced pipeline for improved ARG, VF, toxin, and biosynthetic gene clusters (BGCs) prediction. Key improvements include an updated machine learning (ML) model for VF identification, expanded hidden Markov model profiles for VFs and toxin-associated proteins, a new ML model for toxin and toxin-associated proteins identification, and the integration of antiSMASH 7.0 for predicting BGCs.<br><br>CONCLUSIONS: Our upgrades make PathoFact 2.0 a more powerful and user-friendly platform for predicting microbiome-based pathogenicity and resistance, providing a crucial tool for better understanding and addressing the challenges posed by antimicrobial resistance and infectious diseases.PathoFact 2.0 is available at https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2. It is compatible with Linux operating systems.},
}
@article {pmid42172597,
year = {2026},
author = {Bizzotto, EC and Raimondi, B and Rigamonti, I and Ceccon, S and Moggia, M and Marcomini, A and Trezzi, A},
title = {Evaluating biodiversity and ecosystem services offered by spontaneous revegetation in a restored quarry area in Tuscany.},
journal = {Integrated environmental assessment and management},
volume = {},
number = {},
pages = {},
doi = {10.1093/inteam/vjag086},
pmid = {42172597},
issn = {1551-3793},
abstract = {This study illustrates results of an ecological survey performed on a former quarry area, morphologically reshaped from late '90 s, through the use of red gypsum obtained as a by-product from the production cycle of a facility in Italy. After emplacement of the red gypsum in the former quarry, the area underwent spontaneous revegetation. To evaluate the ongoing restoration process and to document existing ecological values, a geopedological survey, a preliminary vegetation survey and preparation of a wildlife checklist were conducted in autumn 2023; additionally, desktop studies were carried out to identify the expected vegetation series and habitats for the area. A preliminary assessment was also carried out to identify the main Ecosystem Services currently provided by the subject area. The investigations showed that, although of its recent origin and the modest rate of pedological evolution, the area currently presents elements of high ecological value: the observed vegetation is consistent with the successional series expected for the area and the observed ecological features (in terms of vegetational structures, outcropping soils and more arid microclimatic conditions) introduce elements of habitat diversity with respect to the surrounding area (a dense wood), favoring therefore the presence of animal species adapted to habitats that are limiting for many. Specifically, the southern portion of the area displays a complex assemblage of different native plant species, while the northern part of the area is characterized by the presence of a dense bramble bush, species is of ecological value for wildlife since offering food/ refuge/ habitat/ pollination. Overall results thus indicate that the approach adopted in the restoration of the former quarry allowed a functional restoration of the area; on the basis of this work, key suggestions were provided to optimize the management of the restored area, meanwhile monitoring its temporal evolution.},
}
@article {pmid42173756,
year = {2026},
author = {Abraham, AJ and Duvall, ES and Moracho, E and Ruiz-López, MJ and Gilbert, L and Ellis-Soto, D and Prys-Jones, T and Marjakangas, EL},
title = {Double-edged dispersal: animal-mediated transport in the Anthropocene.},
journal = {Trends in ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2026.04.014},
pmid = {42173756},
issn = {1872-8383},
abstract = {Animals play important roles in dispersing seeds, nutrients, and microbes across Earth's surface. These transport functions connect ecosystems and shape fundamental dynamics, including community composition, productivity, and carbon storage. Yet humans have substantially altered resource availability, wildlife assemblages, and movement patterns, leading to some undesirable outcomes, including the spread of nonnative species, pollutants, and zoonotic pathogens. Although animals disperse multiple natural and anthropogenic objects simultaneously, people tend to champion or criticize animal dispersal functions individually. Such valuations paint an incomplete picture and may misguide management. Going forward, researchers must holistically consider all relevant dispersal forms, their interactions, and ecological outcomes together. Balancing trade-offs will help wildlife managers effectively harness animal-mediated dispersal for mitigating the climate, biodiversity, and emerging disease crises.},
}
@article {pmid42175284,
year = {2026},
author = {Tachnai, N and Hanan, G and Tamburis, O and Benis, A},
title = {Identification of Ecological and Human Health Indicators Based on Geographic and Spatial Mapping.},
journal = {Studies in health technology and informatics},
volume = {336},
number = {},
pages = {2066-2070},
doi = {10.3233/SHTI260615},
pmid = {42175284},
issn = {1879-8365},
mesh = {Humans ; *Geographic Mapping ; Europe ; *Health Status Indicators ; Spatial Analysis ; *Artificial Intelligence ; Geographic Information Systems ; },
abstract = {Addressing public health and environmental challenges in rapidly urbanizing areas requires identifying and analyzing relevant indicators. This study introduces an AI-powered framework for extracting and analyzing health and ecological indicators from biomedical literature. Using PubMed as a data source and Large Language Models, we processed 16,474 publications from 5 European regions related to the EU-funded OneAquaHealth project. We automated the identification of 41,377 unique georeferenced relationships between health and environmental indicators. Through dimensionality reduction and clustering, we elicited eight healthcare-focused clusters (e.g., chronic disease and mental health) and eight environmental-focused clusters (e.g., exposure to contaminants). Spatial patterns highlighted disparities in data density, with greater coverage in Western Europe and less in Africa and the Middle East. Our methodology demonstrates how extracting valuable, geographically based insights from unstructured biomedical text supports interdisciplinary research and helps decision-makers address health and environmental challenges.},
}
@article {pmid42176242,
year = {2026},
author = {Beccacece, L and Crocco, P and Torbidoni-Baldassari, B and Pallotti, S and Huang, J and Belloy, ME and Puca, AA and Bae, HT and Sebastiani, P and Passarino, G and Rose, G and Dato, S and Napolioni, V},
title = {Genetic associations with longevity in a Calabrian cohort: an exploratory genome-wide study.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {42176242},
issn = {2509-2723},
support = {D.D.104 2.02.2022; cod. 20227KNBEJ//European Union/ ; PNRR M4.C2.1.1//European Union/ ; },
abstract = {Human longevity is a complex trait shaped by genetic background and population-specific factors. Calabria, a region in Southern Italy with a high prevalence of centenarians and relative genetic isolation, is a valuable model for investigating the genetic architecture of extreme survival. Here, we performed a genome-wide association study of longevity in 705 Calabrian individuals, comparing long-lived subjects to younger controls using a mixed-model approach that accounts for relatedness and population structure. We identified 22 suggestive risk loci, among which one reached genome-wide significance. Although most loci did not replicate in external datasets, an intronic variant regulating proteasome-related gene expression was confirmed by meta-analysis. Based on the nominal significance of gene- and pathway-based analyses, it is possible to hypothesize that the biological processes potentially affecting longevity in this cohort might include proteostasis, maintenance of genome integrity, apoptosis, and insulin- and inflammation-related pathways. Notably, established longevity loci such as APOE and FOXO3 were not associated, underscoring population-specific genetic effects. Overall, our preliminary findings suggest that longevity in the Calabrian population arises from a combination of unique genetic influences and conserved aging-related mechanisms, providing new insights into the molecular basis of human lifespan extension.},
}
@article {pmid42176628,
year = {2026},
author = {Guo, R and Wang, HY and Zhong, CW and Ma, RR and Huang, J and Chen, J and Guan, XJ and Zheng, L and Shen, RF and Liu, MQ and Zhu, XF},
title = {Os79, a UDP-Glycosyltransferase, negatively regulates cadmium tolerance and accumulation in rice.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142376},
doi = {10.1016/j.jhazmat.2026.142376},
pmid = {42176628},
issn = {1873-3336},
abstract = {Cadmium (Cd) contamination in agricultural soils poses a significant threat to global food safety. Reducing grain Cd accumulation in rice, a primary dietary source of this toxic metal, is therefore an urgent priority. This study identified and characterized a novel UDP-glycosyltransferase gene, Os79 (LOC_Os04g12970), which functions as a key negative regulator of Cd tolerance and accumulation in rice. Using loss-of-function mutants (os79) generated by clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) and gain-of-function lines (Os79-OX), we demonstrate that a bidirectional genetic response governs Cd homeostasis: the loss of Os79 function enhances plant growth under Cd stress and significantly reduces Cd accumulation, whereas its overexpression exacerbates Cd sensitivity and accumulation. Subcellular localization analysis revealed that Os79 is localized to both the nucleus and cytoplasm. Its expression is rapidly induced at both transcriptional and protein levels upon Cd exposure. Mechanistically, the os79 mutants achieve reduced Cd toxicity through a tripartite coordinated response: (1) Transcriptional reprogramming of Cd transporters, where key uptake genes including Oryza sativa Iron-Regulated Transporter 1 (OsIRT1) and Oryza sativa Natural Resistance-Associated Macrophage Protein 5 (OsNRAMP5) are downregulated, whereas the vacuolar sequestration genes such as Oryza sativa Heavy Metal ATPase 3 (OsHMA3) are upregulated; (2) Enhanced cell-wall binding capacity, characterized by increased content of pectin and hemicellulose in root and shoot cell walls and their elevated Cd-binding ability; (3) Strengthened antioxidant defense, marked by elevated activities of peroxidase (POD) and catalase (CAT), which reduce hydrogen peroxide (H2O2) and malondialdehyde (MDA) levels and alleviate oxidative damage. Collectively, our findings reveal that Os79 negatively regulates an integrated detoxification network. Targeting Os79 presents a promising genetic strategy for developing low-Cd-accumulating rice varieties, contributing to safer food production in Cd-contaminated regions.},
}
@article {pmid42179991,
year = {2026},
author = {di Palma, A and Bellezza, M and Santisi, S and Giordano, R and Frosini, A and Pergola, E and Primi, C and Donati, MA},
title = {SAFESLOT: an experimental virtual reality protocol to examine flow, craving, and cognitive biases in gambling.},
journal = {Frontiers in psychiatry},
volume = {17},
number = {},
pages = {1787985},
pmid = {42179991},
issn = {1664-0640},
abstract = {Gambling-related harm comes out from dynamic interactions between craving, cognitive distortions, and physiological responses to gambling outcomes. These processes happen rapidly during play and are strongly influenced by the structural features of slot machine, yet they are seldom captured in real time using ecologically valid methods. Traditional research has relied mainly on self-report measures and simplified gambling simulations, limiting the ability to assess moment-to-moment changes in motivation, cognition, and arousal. The present study aims to address these limitations by developing SAFESLOT: a virtual slot machine designed ad hoc to examine behavioral and psychophysiological mechanisms underlying gambling disorder risk and to test whether interrupting gambling activity can attenuate craving and cognitive distortions. The study will recruit approximately 200 university students who will participate in a controlled virtual reality slot-machine task. The virtual environment replicates a realistic Video Lottery Terminal. The task will be composed by five gameplay sessions, each emphasizing a distinct feature of slot machines. Participants will be randomly assigned to one of three conditions: uninterrupted gambling, gambling interrupted by brief reflective pauses with questions concerning craving and perceived winning probability, and gambling interrupted without self-reflective prompts. During the task, continuous multimodal data will be collected, including psychophysiological signals, behavioral indicators such as reaction times, betting patterns, and eye-tracking measures. Psychological self-report assessments will be administered before and after the virtual gambling experience. Data analysis will combine classical statistical methods with machine learning techniques in order to identify patterns associated with changes in craving and gambling-related cognitive distortions. Our study aims to clarify how specific gambling outcomes influence craving, cognition, and arousal. The comparison between uninterrupted and interrupted gambling conditions will offer insights into the potential preventive value of brief reflective pauses in reducing automatic gambling responses. The findings may contribute to the development of evidence-based prevention and responsible gambling interventions.},
}
@article {pmid42183147,
year = {2026},
author = {Sofyantoro, F and Kusuma, WA and Wahyudi, ST and Lumbanraja, FR and Rahmawan, H and Rustamaji, HC and Kurniawan, DW and Rastuti, U and Putri, WA and Wibowo, WA and Priyono, DS and Yudha, DS and Raharjo, S and Nuringtyas, TR},
title = {Transcriptomic Insights Into the Evolution of Snake Venom: Mechanisms, Diversity, and Adaptation.},
journal = {Scientifica},
volume = {2026},
number = {},
pages = {8813839},
pmid = {42183147},
issn = {2090-908X},
abstract = {Snake venoms are evolutionarily refined biochemical arsenals composed of diverse toxins with complex functional roles in predation, defense, and competition. Over the past 2 decades, transcriptomic approaches have transformed venom research by enabling high-resolution insights into gene expression dynamics, molecular diversity, and the evolutionary mechanisms driving venom variation across lineages. In this review, we present a comprehensive synthesis of snake venom transcriptomics literature and propose a conceptual framework structured around three major axes: (1) gene family expansion through duplication and neofunctionalization; (2) regulatory complexity encompassing transcriptional, posttranscriptional, and epigenetic modulation; and (3) ecological selection pressures shaping venom profiles in response to diet, habitat, and interspecific interactions. We integrate findings from diverse taxa and technologies, including bulk RNA sequencing, long-read transcriptomics, and spatial or single-cell approaches, to highlight progress and gaps in current knowledge. A bibliometric analysis of 358 studies from 2002 to 2024 reveals significant growth in the field, with key contributions from institutions in the United States, Brazil, and Australia. Despite this progress, transcriptomic research remains geographically and taxonomically biased, with challenges in toxin annotation, data standardization, and integrative multiomics still unresolved. We conclude by emphasizing the growing role of integration with other omics approaches, advancements in single-cell transcriptomics, and the emerging potential of computational modeling in reconstructing venom evolution.},
}
@article {pmid42184080,
year = {2026},
author = {Qian, J and Zhou, L and Zhang, J and Zhang, K and Zhu, X},
title = {The removal effects and mechanism of sulfate from acid mine drainage using fly ash and sunflower heads composite biochar.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {8},
pages = {},
pmid = {42184080},
issn = {1573-2983},
support = {No. 2022YFC3702203//National Key R&amp;D Program of China/ ; },
mesh = {*Charcoal/chemistry ; *Coal Ash/chemistry ; *Sulfates/chemistry ; Mining ; *Water Pollutants, Chemical/chemistry ; Helianthus/chemistry ; Calcium Sulfate/chemistry ; Adsorption ; Kinetics ; Calcium Chloride/chemistry ; },
abstract = {To address the persistent challenge of sulfate (SO4[2-]) removal from acid mine drainage (AMD), a novel calcium-functionalized composite biochar (CaCl2-BC) was synthesized via the co-pyrolysis of sunflower heads, coal fly ash, and CaCl2. The composite prepared under optimal conditions (600 °C, 1:1 mass ratio) exhibited an exceptional SO4[2-] removal capacity of 188.73 mg/g. The removal kinetics followed the pseudo-second-order model, while the equilibrium data fitted the Langmuir isotherm well. Crucially, microscopic characterizations and Density Functional Theory (DFT) calculations explicitly decoded a synergistic "adsorption-precipitation" mechanism. The fly-ash-derived Si-O groups acted as high-affinity anchors (- 174.3 kJ/mol) to initially capture and enrich SO4[2-], effectively overcoming electrostatic repulsion. Subsequently, the surface-loaded CaCl2·2H2O phase served as a reactive engine, driving the in-situ crystallization of stable gypsum (CaSO4·2H2O). Comparative system matrix evaluations demonstrated that this synergy far exceeded the simple sum of individual components. Furthermore, CaCl2-BC sustained a formidable capacity of 147.56 mg/g in complex real AMD, while leaching tests confirmed its environmental safety. This study establishes a rigorous theoretical framework for mineral-carbon synergy and provides a highly practical material for industrial AMD remediation.},
}
@article {pmid42186944,
year = {2026},
author = {Patin, NV and Pitz, K and Kimbrough, K and Archer, F},
title = {Beyond Biodiversity: Incorporating Uncertainty Into Metabarcoding Data for Improved Inference of Ecological Relationships.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70160},
doi = {10.1111/1755-0998.70160},
pmid = {42186944},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Bayes Theorem ; },
abstract = {Metabarcoding sequence data from environmental DNA (eDNA) is rapidly expanding as a powerful method for biodiversity surveys. In order to interpret these data, tools are needed that account for the uncertainty associated with eDNA sampling, sequencing and analysis. The data resulting from eDNA marker gene analysis differ from many traditional methods of biodiversity surveys because they are highly complex, sparse and compositional. Methodological biases produce uncertainty at every step of the sampling and sequencing process. Thus, it is critical that users have a way of interpreting eDNA results that accounts for their compositional nature and models the uncertainty resulting from factors like patchy sampling, PCR amplification biases and variable sequencing depth. Here, we introduce MAMBO: Metabarcoding Analysis using Modeled Bayesian Occurrences. MAMBO simulates in silico replication and models the uncertainty surrounding the sequencing and analysis process. Further, it uses these modelled sequence count data to correlate two sets of marker genes with a Bayesian regression, facilitating the linkage of different groups targeted by these assays. Compared with correlational network analyses, MAMBO overcomes many of the limitations to robust statistical analyses of eDNA marker gene data and provides an opportunity for new insight into ecological patterns over space and time.},
}
@article {pmid42188046,
year = {2026},
author = {Tang, G and Guo, L and Liu, Z and Quan, Y},
title = {Hypothesis of the Causal Mechanisms Between Gut Microbiota and Neurodegenerative Diseases: An Elucidation from Evolutionary Perspective and Metabolic Consideration.},
journal = {Metabolites},
volume = {16},
number = {5},
pages = {},
pmid = {42188046},
issn = {2218-1989},
support = {Grant 32570777 and Grant 32300545//National Natural Science Foundation of China/ ; Grant 2662025XXPY004//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Growing evidence links gut microbiota dysbiosis to neurodegenerative diseases (NDs) such as Alzheimer's disease and Parkinson's disease, yet the field remains dominated by correlational observations rather than experimentally validated causal mechanisms. In this hypothesis-generating Perspective, we propose that causal inference in microbiota-associated neurodegeneration may be strengthened by combining two complementary lenses: evolutionary biomedicine and microbial metabolism. Because evolutionary information carries intrinsic temporal and causal structure, it can provide biological prior knowledge for inferring causal mechanisms of diseases. Human Accelerated Regions (HARs), genomic loci conserved across mammals but rapidly divergent in the human lineage, offer an anchor for identifying human-specific host-microbe co-evolutionary units relevant to NDs. We further hypothesize that microbial metabolites represent one class of mechanistically testable intermediates linking host genetic background, gut microbial ecology, and neurodegenerative phenotypes. This integrated evolutionary-metabolic perspective offers a tractable path from correlation toward mechanism in gut microbiota-ND research.},
}
@article {pmid42198074,
year = {2026},
author = {Yang, L and Chen, W and Mo, Z and Gao, X and Mo, M and Xia, C and Zhang, L},
title = {Spectral-YOLOv13: A Dual-Domain Vision-Mamba Sensing Framework for Fine-Grained Coral Health Assessment and Continuous Ecological Forecasting.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {10},
pages = {},
pmid = {42198074},
issn = {1424-8220},
support = {2024ZRBSHZ099//Ministry of Natural Resources/ ; 2024JCYJ074//Yantai Science and Technology Innovation Development Plan Basic Research Project/ ; },
mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; *Environmental Monitoring/methods ; Ecosystem ; Forecasting ; },
abstract = {Coral reefs are among the most important and vulnerable marine ecosystems worldwide. AI-powered underwater visual monitoring has become essential for effective reef conservation, yet current methods still face severe limitations: spectral ambiguity caused by underwater turbidity, fine-grained confusion in early coral health assessment, and discrete forecasting models that cannot represent continuous ecological degradation dynamics. To address these issues, we propose Spectral-YOLOv13, a dual-domain vision-Mamba sensing framework for high-precision coral health evaluation and continuous ecological forecasting. The framework incorporates three novel components: a Wavelet-Integrated Omni-Neck (WIO-Neck) to perform multi-scale spectral filtering and suppress turbidity-induced noise; a Contrastive Prototype Head (CP-Head) to enhance discriminability between visually similar health states; and a Bio-Mamba Predictor based on state-space models to capture long-term continuous health trajectories. Extensive experiments on the CR-Mix++ dataset demonstrate that Spectral-YOLOv13 achieves 53.8% mAP with strong robustness in turbid underwater environments. It reduces four-week forecasting error by 26.8% and maintains real-time inference speed at 112 FPS. This work provides a reliable and high-performance vision framework for practical underwater coral reef monitoring and proactive conservation management.},
}
@article {pmid42198519,
year = {2026},
author = {Ćućuz, V and Jovanović, G and Bezdan, T and Herceg Romanić, S and Mustać, B and Stojić, A and Perišić, M},
title = {Evaluating and Refining PCB Mixture Indicators in Marine Fish Through Explainable Artificial Intelligence.},
journal = {Toxics},
volume = {14},
number = {5},
pages = {},
pmid = {42198519},
issn = {2305-6304},
abstract = {Polychlorinated biphenyls (PCBs) remain a major concern in marine ecosystems, where bioaccumulation in fish occurs as complex congener mixtures whose dynamics challenge conventional indicator approaches. This study develops and evaluates a data-driven framework for refining mixture-based indicators of PCB contamination by integrating ensemble machine learning with explainable artificial intelligence. Focusing on PCB-138 as a target indicator of cumulative PCB burden, we analyse concentrations of 24 organochlorines together with biological covariates in four Mediterranean edible pelagic fish species (sardine, anchovy, horse mackerel, and chub mackerel). Comparative evaluation of indicator performance shows that alternative congener combinations, including i4 PCBs (-138, -153, -170, -180), i6 PCBs (-138, -153, -170, -180, -118, -123), and mixtures incorporating DDD and DDE, more effectively represent total PCB burden than traditional indicator groups. Clustering identifies two distinct bioaccumulation settings, characterized by high-concentration coherent congener effects and low-concentration heterogeneous responses, demonstrating that indicator performance depends on concentration range and mixture context. The study illustrates how interpretable machine learning approaches can serve as formal tools for indicator evaluation and optimisation, strengthening long-term monitoring and management of legacy contaminants in marine ecosystems, particularly under conditions of persistent exposure and renewed inputs from sediment remobilization and riverine transport.},
}
@article {pmid42200521,
year = {2026},
author = {Wright, RJ and Fisher, BR and Comeau, AM and Langille, MGI},
title = {From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001739},
pmid = {42200521},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Bacteria/classification/genetics ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Microbiota/genetics ; },
abstract = {Obtaining high precision while maintaining high recall is an ongoing problem for metagenomic taxonomic classification in microbial ecology research. Parameter adjustments can achieve this in simulated samples, but in real samples - especially from environments like marine and soil - the proportion of classified reads drops sharply with precision increases. We, therefore, suggest verification of metagenomic taxonomic classifications obtained from a tool like Kraken by mapping their assigned reads to reference genomes to assess genomic coverage. In simulations, filtering the identified species to only those with ≥0.5% reference genome coverage removed 99.7% of false-positive taxa. Applying this method to samples from real datasets requires a more nuanced approach that considers sequencing depth, whether the samples are high- or low-microbial biomass, and database completeness with respect to the sampled environment. Nevertheless, we show that clinically relevant Kraken-identified taxa, such as Helicobacter pylori identified in human stool samples, lack any reads mapping to their reference genome and are likely false positives driven by contaminating phage sequences within reference genomes. Similarly, in human blood and lung tumour datasets, only 18 and 11 species, respectively, have ≥1% reference genome coverage and likely represent sample collection or sequencing contaminants. Marine and soil samples pose additional challenges due to lower representation in reference databases, leading to low nucleotide identity between sequenced reads and reference genomes and similarity only at higher taxonomic ranks. We recommend genome coverage checking to researchers in all fields of microbial ecology and provide an open-source pipeline on GitHub (GeCoCheck): https://github.com/R-Wright-1/GeCoCheck.},
}
@article {pmid42201504,
year = {2026},
author = {Crompton, CJ and Wolfe, K and Tullo, A and Hoffman, P and Wolters, MK and MacPherson, SE},
title = {The impact of perceived human and computer interaction on collaborative learning: insights from the Map Task.},
journal = {Cognitive processing},
volume = {},
number = {},
pages = {},
pmid = {42201504},
issn = {1612-4790},
support = {PG-2020-035//Leverhulme Trust/ ; Engineering and Physical Sciences Research Council//Engineering and Physical Sciences Research Council/ ; },
abstract = {Learning new skills and information becomes more challenging as people get older, but learning collaboratively can provide benefits to learning in older age. Prior work has predominantly focused on improved learning in terms of accuracy and efficiency when interacting with another human compared to learning alone, while the potential benefits of a human learning with a computer are understudied. It has been reported that older adults learn more efficiently and accurately when they believe they are interacting with a human compared to a computer to perform the Barrier Task. In the current study, we examined the effect of agency on performance on the Map Task, a test that measures spatial cognition, where participants must orally collaborate to reproduce a route printed on one participant's map onto another's, and which is considered a more ecologically valid measure of real-life communication compared to other materials used to study collaborative learning. We used a Wizard-of-Oz paradigm, in which participants interacted with a computer system, but were told that they were interacting with either a human assistant or computer. Twenty-four older adult participants (aged 66-79 years) completed an adapted version of the Map Task with a (perceived) human partner or computer to plan and execute a route, doing so through conversation. Overall, participants engaged similarly with their human and computer partner, but recall was more accurate when the information had been provided by the human, compared to the computer. Participants' negative perceptions about the computer-provided information may have driven this effect. These findings may influence how voice-based learning systems are introduced to older end-users, and strategies for negotiating agency between the human user and the voice-based system, to influence collaborative learning in older age. Future work should attempt to replicate these findings in a larger sample.},
}
@article {pmid42203969,
year = {2026},
author = {Verma, P and Singh, S and Katiyar, R and Adhikari, D},
title = {Prioritizing restoration hotspots in riparian corridors using integrated spatial decision-support framework for targeted urban greening initiatives.},
journal = {Environmental management},
volume = {76},
number = {6},
pages = {},
pmid = {42203969},
issn = {1432-1009},
mesh = {*Conservation of Natural Resources/methods ; *Decision Support Techniques ; Rivers ; Urbanization ; India ; },
abstract = {Urban riparian corridors are increasingly degraded due to rapid urbanization. Yet spatial tools for prioritizing restoration remain limited, especially in data-poor regions. This study presents an Integrated Spatial Decision-Support Framework (ISDSF) that integrates high-resolution Sentinel-2, terrain and soil datasets within a principal component analysis (PCA)-weighted multi-criteria framework across a 500 m corridor of the river Gomati in Lucknow, India to generate a Composite Restoration Index (CRI) at 10 m resolution. The CRI revealed that 36.4% of the study area fell under high or very-high restoration priority classes, characterized by low NDVI/LAI, elevated LST, depleted SOC and increased bare/impervious surfaces. Ground surveys showed that higher CRI values were associated with reduced native species richness and increased invasive dominance, while Random Forest-based internal consistency assessment showed strong agreement between the CRI and its component indicators (R[2] = 0.97; RMSE = 0.01). By combining objective weighting, internal model checking and floristic ground-truthing, the framework provides a locally calibratable decision-support tool for targeting riparian restoration under urban pressure.},
}
@article {pmid42204167,
year = {2026},
author = {Saeedi, H},
title = {Gaps and drivers of global marine animal biodiversity from the surface to abyss.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42204167},
issn = {2041-1723},
mesh = {Animals ; *Biodiversity ; *Aquatic Organisms/classification/physiology ; Oceans and Seas ; Conservation of Natural Resources ; Humans ; Marine Biology ; Ecosystem ; },
abstract = {With advances in global biodiversity data sharing, particularly following the Census of Marine Life, understanding of marine biodiversity has improved but remains incomplete. The Ocean Biodiversity Information System and Global Biodiversity Information Facility host over 150 million marine occurrence records, enabling reassessment of global biodiversity and data gaps. Here, we compile a quality-controlled dataset of ca. 48 million records covering 184,141 marine animal species, representing ~87% of accepted World Register of Marine Species and 91% of Ocean Biodiversity Information System taxa. Generalised Linear and Additive Models assess how geoecological drivers and human impact influence species richness while accounting for sampling effort and spatial autocorrelation across depth and taxa. Approximately 50% of the global ocean remains insufficiently sampled, with more than 160 million km[2] below 200 m lacking data. Sampling is biased toward developed regions, especially the North Atlantic, with major gaps in equatorial and Global South regions. Central tropical areas (- 5° to 5°) contribute only <2.5% of global records, helping explain non-significant bimodal latitudinal patterns. Shallow-water richness is mainly associated with temperature, while deep-sea patterns relate to human impact (sampling intensity) and nitrate-driven remineralisation. These results highlight major global data gaps and the need for depth-explicit, bias-aware biodiversity assessment and monitoring to support conservation and the UN Ocean Decade.},
}
@article {pmid42204173,
year = {2026},
author = {Torres-Cambas, Y and Ambrus, A and Bán, M and Bánó, B and Basooma, A and Bremerich, V and Borgwardt, F and Čarf, M and Cernisencu, I and Cvijanović, G and Czeglédi, I and Domisch, S and Erős, T and Fehér, Z and Füstös, V and Geist, J and Hein, T and Jaćimović, M and Jähnig, SC and Kiss, B and Kubala, M and Lebar, K and Margaritova, BK and Marušić, M and Meulenbroek, P and Mihov, SD and Mozsár, A and Müller, Z and Nagel, C and Nichersu, I and Nikolić, D and Orlić, S and Pander, J and Pengal, P and Piria, M and Polyák, L and Preiszner, B and Rusjan, S and Sallai, M and Sallai, Z and Sály, P and Samu, A and Sasano, B and Schmidt-Kloiber, A and Sevcsik, A and Smederevac-Lalić, M and Specziár, A and Stoffers, T and Szalóky, Z and Szita, R and Takács, G and Takács, P and Teichert, M and Todorov, M and Tóth, B and Trichkova, T and Valić, D and Vitál, Z and Tschikof, M},
title = {The Danube Fish Database: documenting species distributions across a major European river basin.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42204173},
issn = {2052-4463},
mesh = {Animals ; *Fishes ; *Rivers ; Europe ; Conservation of Natural Resources ; Biodiversity ; *Databases, Factual ; Climate Change ; Introduced Species ; },
abstract = {The Danube River Basin (DRB) harbors the highest documented fish species richness of any European river, yet native populations face increasing threats from physical infrastructures that impede longitudinal and lateral connectivity, unsustainable fisheries, the introduction of non-native species, and climate change. Spanning across 19 countries, the DRB presents conservation challenges that demand coordinated, transboundary data sharing. The present database compiles and standardizes fish occurrence datasets that have been previously unavailable, fragmented and often restricted by federal agencies, research institutes, and conservation organizations, integrating also data from sources such as the Global Biodiversity Information Facility, the Joint Danube Surveys, the European Fish Index, and national monitoring programmes. It contains 133,131 occurrence records across 114 fish species, representing 30 families and 17 orders, with a temporal range from 1856 to 2024, organized into 39 columns. By supporting fish community conservation, invasive alien species monitoring, and climate impact assessments, this database provides a vital resource for developing evidence-based management strategies in the DRB.},
}
@article {pmid42205355,
year = {2026},
author = {Branco, D and Fernandes, MC and Bermúdez I Badia, S and Faria, AL},
title = {Emotional Daily Life Library (E-DLL): Validation of a database of 3D objects for emotion elicitation.},
journal = {International journal of clinical and health psychology : IJCHP},
volume = {26},
number = {2},
pages = {100690},
pmid = {42205355},
issn = {2174-0852},
abstract = {Research on emotional perception often relies on 2D stimuli or highly affective images, limiting ecological validity. We introduce the Emotional Daily Life Library (E-DLL), a database of 132 rotating 3D everyday objects with comprehensive perceptual, cognitive, and emotional normative ratings. In 52 adults, participants provided dimensional (valence-arousal-dominance) and categorical emotion ratings, alongside assessments of recognition, naming, familiarity, contact, usage, and visual complexity. Personality traits (NEO-FFI) and depressive symptoms (BDI-II) were measured to examine individual differences. Cumulative Link Mixed Models (CLMMs) revealed that valence ratings were negatively influenced by the interaction of Neuroticism and subclinical depressive symptoms. For arousal, higher Neuroticism and Conscientiousness demonstrated marginal positive associations, while dominance ratings were unaffected. Generalized Linear Mixed Models (GLMMs) for categorical labels indicated that while emotional attributions were primarily driven by stimulus properties, traits such as Neuroticism and Extraversion significantly predicted the perception of negative emotions (e.g., Sadness). Spearman correlations identified interrelationships among cognitive and perceptual dimensions, and redundant variables (Contact and Usage) were combined into a composite Object Interaction score. By integrating neutral, immersive 3D stimuli with rich multidimensional annotations, E-DLL provides a controlled and ecologically valid tool for experimental and clinical research. Its applicability includes cognitive training, VR-based interventions, and personalized neurorehabilitation platforms such as NeuroAIreh@b, supporting investigations of affective biases and optimizing daily life-oriented therapeutic interventions.},
}
@article {pmid42210915,
year = {2024},
author = {Boyes, D and Crowley, LM and , and , and , and , and , and , and , },
title = {The genome sequence of the Frosted Green moth, Polyploca ridens (Fabricius, 1787).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {545},
pmid = {42210915},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Polyploca ridens (the Frosted Green; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence has a total length of 493.60 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,321 protein-coding genes.},
}
@article {pmid42212592,
year = {2026},
author = {Wu, SN and Jiang, Y and Guan, W and Xu, C and Zeng, DX and Yan, B and Lv, J and Huang, C and Hu, J and Han, Y and Liu, Z},
title = {Global, regional, and national trends in blindness and vision loss, 1990-2021: a secondary ecological trend analysis based on modelled population estimates.},
journal = {Journal of global health},
volume = {16},
number = {},
pages = {04176},
pmid = {42212592},
issn = {2047-2986},
mesh = {Humans ; *Blindness/epidemiology ; Disability-Adjusted Life Years ; Female ; Prevalence ; *Global Health/statistics &amp; numerical data ; Male ; Middle Aged ; Adult ; Aged ; Adolescent ; Global Burden of Disease/trends ; Young Adult ; Child ; Child, Preschool ; Infant ; Aged, 80 and over ; Secondary Data Analysis ; Risk Factors ; },
abstract = {BACKGROUND: We aimed to provide global, regional, and national estimates of the burden of blindness and vision loss from 1990 to 2021, stratified by cause, age, and sociodemographic index (SDI).<br><br>METHODS: This population-based study used data from the 2021 Global Burden of Diseases, Injuries, and Risk Factors Study 2021 (GBD) study, covering 1990 to 2021. It evaluates the burden of blindness and vision loss based on prevalence, age-standardised prevalence rate (ASPR), disability-adjusted life years (DALYs), age-standardised DALY rate (ASR of DALY), and average annual percent changes (AAPCs).<br><br>RESULTS: Globally, the ASPR of blindness and vision loss increased from 12&#x2009;453.52 (95% uncertainty interval (UI)&#x2009;=&#x2009;10&#x2009;287.58, 15&#x2009;226.09) in 1990 to 15&#x2009;784.33 (95% UI&#x2009;=&#x2009;12&#x2009;761.44, 19&#x2009;502.32) in 2021, with an AAPC of 0.85 (95% confidence interval (CI)&#x2009;=&#x2009;0.7, 1.11, P&#x2009;<&#x2009;0.001). In contrast, the ASR of DALYs remained stable, changing from 342.01 (95% UI&#x2009;=&#x2009;237.87, 482.17) in 1990 to 342.78 (95% UI&#x2009;=&#x2009;224.21, 503.61) in 2021, with an AAPC of 0.05 (95% CI&#x2009;=&#x2009;-0.04, 0.2, P&#x2009;=&#x2009;0.298). Notably, near vision loss and cataract showed consistent increases, with AAPCs of 1.14 (95% CI&#x2009;=&#x2009;0.94, 1.51, P&#x2009;<&#x2009;0.001) and 0.25 (95% CI&#x2009;=&#x2009;0.16, 0.33, P&#x2009;<&#x2009;0.001), respectively. Blindness and vision loss prevalence was significantly higher in low and low-middle SDI regions compared to other SDI regions.<br><br>CONCLUSIONS: Global blindness and vision loss increased from 1990 to 2021, while DALYs stayed stable. Prevention should be tailored by region, country, gender, cause, and age.},
}
@article {pmid42213148,
year = {2026},
author = {Sun, Y and Tang, X and Shang, J and Wang, H and Qiu, D and Zhang, Y and Liu, JX},
title = {Prediction of multicategory miRNA-disease associations based on bidirectional hypergraph attention network and gated convolutional strategy.},
journal = {Journal of computer-aided molecular design},
volume = {40},
number = {1},
pages = {},
pmid = {42213148},
issn = {1573-4951},
mesh = {*MicroRNAs/genetics ; Humans ; *Computational Biology/methods ; Algorithms ; },
abstract = {Recent studies have shown that miRNAs undergo dynamic expression changes under pathological conditions and play diverse regulatory roles in disease progression. Accurately identifying their specific regulatory association types is essential for understanding disease mechanisms. However, most existing computational models mainly focus on association existence prediction or rely on node-centric representation learning, while insufficiently modeling fine-grained regulatory types and the semantic information carried by association edges. To address these limitations, we propose BGMMDA, a computational model for predicting multicategory miRNA-disease associations based on a bidirectional hypergraph attention network and a gated convolutional strategy. Specifically, multi-source similarity information and known miRNA-disease associations are first integrated to construct a weighted heterogeneous association graph. Then, candidate miRNA-disease associations are modeled as semantic hyperedges, and a bidirectional hypergraph attention network is designed to establish a closed-loop information propagation mechanism, enabling collaborative optimization between node representations and edge-level semantic representations. In addition, a gated convolutional strategy is introduced to selectively enhance informative pairwise features while suppressing noisy or redundant signals from the original association space. Finally, a unified multi-task loss function is used to improve type aware discrimination and representation stability. Experiments were conducted on the HMDD v3.2 dataset under two five-fold cross-validation settings. In the primary CVtype experiment, BGMMDA achieved Top-1 precision, Top-1 recall, and Top-1 F1 of 0.8711, 0.8700, and 0.8694, respectively. In the CVtriplet experiment, BGMMDA obtained an AUC of 0.9508 and an AUPR of 0.9503. Comparative experiments with five state-of-the-art methods demonstrate that BGMMDA achieves superior and more balanced performance in both regulatory type classification and potential association identification, confirming its effectiveness and practical applicability.},
}
@article {pmid42215097,
year = {2026},
author = {Wang, Z and Ding, Y and Cheng, S and Xun, Z and Li, Z and Zhu, M and Zhao, X and Hu, W and Meng, X and Zhang, S and Qiu, L},
title = {Integrating multi-omics to link core and region-specific microbiota to flavor metabolism in medium-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {238},
number = {},
pages = {119428},
doi = {10.1016/j.foodres.2026.119428},
pmid = {42215097},
issn = {1873-7145},
mesh = {Multiomics ; *Microbiota/physiology ; Fermentation ; *Alcoholic Beverages/microbiology/analysis ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis/metabolism ; China ; Metabolomics/methods ; *Food Microbiology ; *Taste ; *Flavoring Agents/metabolism ; Metagenomics ; Bacteria/metabolism/classification ; Temperature ; Fungi/metabolism/classification/genetics ; },
abstract = {Medium-temperature Daqu (MTD) is a critical fermentation starter for strong-aroma Baijiu, where its complex microbiota governs flavor development. We combined metagenomics with GC-MS metabolomics to analyze 15 MTD samples from six major producing regions in China, moving from descriptive profiling to mechanistic insight. Although microbial communities exhibited substantial regional variation, a conserved core microbiota emerged, consisting of eight fungal genera, including Aspergillus and Rhizopus, and five bacterial genera such as Bacillus. Beta diversity analysis indicated that producer-specific practices were more influential than geography in structuring these communities. Functional metagenomic profiling showed enriched pathways for carbohydrate, amino acid, and ester metabolism. Volatile metabolite analysis identified 94 compounds, primarily esters, with 12 common to all samples. We constructed multi-omics correlation networks to predict functional linkages, which notably connected genera like Talaromyces and Aspergillus to key flavor esters. Based on these predictions, we isolated Wickerhamomyces anomalus and Bacillus velezensis from Daqu. In vitro validation demonstrated their functional roles: W. anomalus produced ethyl acetate, while co-culturing B. velezensis with Saccharomyces cerevisiae significantly enhanced the yield of ethyl decanoate and ethyl laurate. This work delineates both the core and region-specific metabolic features of MTD and translates multi-omics correlations into confirmed microbial activities. It thereby establishes a targeted framework for identifying flavor-active microorganisms, offering a scientific foundation for quality control and directed bioaugmentation in Daqu production.},
}
@article {pmid42217290,
year = {2026},
author = {Kawahara, T and Yamaoka, Y and Fushimi, K and Fujiwara, T},
title = {Incidence of hospitalized abusive head trauma among infants in Japan, 2014-2022.},
journal = {Child abuse &amp; neglect},
volume = {178},
number = {},
pages = {108139},
doi = {10.1016/j.chiabu.2026.108139},
pmid = {42217290},
issn = {1873-7757},
abstract = {BACKGROUND: Abusive head trauma (AHT) is a leading cause of fatal maltreatment in infancy.<br><br>OBJECTIVE: To estimate the annual incidence of hospitalized AHT among infants in Japan from 2014 to 2022 and assess the impact of the COVID-19 pandemic and increasing male childcare-leave uptake.<br><br>PARTICIPANTS AND SETTING: Infants <1&#xa0;year old admitted to hospitals participating in the nationwide Diagnosis Procedure Combination (DPC) database in Japan.<br><br>METHODS: We conducted a retrospective study identifying AHT admissions using ICD-10 codes, and calculated annual incidence using census data. We compared pre-COVID-19 (2014-2019) and COVID-19 (2020-2022) periods and examined the ecological association between AHT incidence and national male childcare-leave uptake.<br><br>RESULTS: We identified 755 presumptive and 5019 possible AHT admissions across 10.4 million infant-years. Presumptive AHT incidence was 7.9/100,000 in 2014 and 10.5/100,000 in 2022, demonstrating year-to-year variation but no significant overall trend (P for trend&#xa0;=&#xa0;0.91). The incidence rate ratio for the COVID-19 period versus pre-COVID-19 was 0.95 (95% CI 0.81-1.12). No significant association was found between male childcare-leave uptake and AHT incidence (&#x3c1;&#xa0;=&#xa0;0.15, P&#xa0;=&#xa0;0.70).<br><br>CONCLUSIONS: Hospitalized AHT incidence in Japan did not change significantly over 9&#xa0;years. At the population level, neither the COVID-19 pandemic nor the increased uptake of male childcare leave was associated with a measurable change in the AHT burden.},
}
@article {pmid42217878,
year = {2026},
author = {Yao, Z and Chen, J and Gao, Z and Sheng, Y and Xiao, L and Liu, H and Liang, Y and Yan, W and Li, Z},
title = {Synergistic effects of nanoplastics and BDE-47 on glutathione dysregulation in rice: Insights from integrated multi-omics and computational modeling.},
journal = {Journal of environmental sciences (China)},
volume = {165},
number = {},
pages = {285-296},
doi = {10.1016/j.jes.2025.09.005},
pmid = {42217878},
issn = {1001-0742},
mesh = {*Halogenated Diphenyl Ethers/toxicity ; *Oryza/drug effects/physiology ; *Glutathione/metabolism ; Multiomics ; Computer Simulation ; },
abstract = {Understanding the combined toxicity mechanisms of polybrominated diphenyl ethers (PBDEs) and nanoplastics is essential for ecological risk management. This study integrated physiological, transcriptomic, metabolomic, and computational analyses to investigate the synergistic phytotoxicity of polyethylene (PE) nanoplastics and 2,2',4,4'-Tetrabromodiphenyl ether (BDE-47) in rice (Oryza sativa L.). Co-exposure synergistically intensified toxicity compared to isolated treatments, causing 14.8 %-42.8 % reductions (P < 0.001) in enzymatic antioxidants such as peroxidase (POD), catalase (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX) activities and non-enzymatic antioxidants oxidized glutathione (GSSG) and ascorbate (AsA) levels, alongside inhibited root and shoot growth. Transcriptomic data revealed suppressed expression of photosystem II genes (psbO, psbW), correlating with impaired photosynthesis, energy deficits, and growth restriction. Concurrently, glutathione biosynthesis genes (OsGLN2, OsGS1, OsGPX1/4) were downregulated, disrupting glutamine-to-glutathione (GSH) conversion. Metabolomic analysis confirmed 3.5-fold glutamate depletion and inhibited carbohydrate metabolism, indicating pollutant-induced oxidative stress. Molecular docking simulations identified OsGPX1 as BDE-47's binding target through hydrogen-bond interactions, which competitively blocked GSH binding to glutathione peroxidase (GPX). This demonstrated that nanoplastics act as chemical potentiators, amplifying PBDEs toxicity via enzyme inhibition and metabolic interference. Specifically, PE enhanced BDE-47's capacity to disrupt redox homeostasis and energy metabolism through direct protein interactions and pathway dysregulation. These findings would provide mechanistic insights into pollutant synergism, emphasizing the need to evaluate nanoplastic co-contaminants in environmental risk frameworks.},
}
@article {pmid42218298,
year = {2026},
author = {Schwemmer, P and Donnez, M and Mercker, M and Garthe, S and Boschert, M and Düttmann, H and Elts, J and Fartmann, T and Fiedler, W and Jiguet, F and Kämpfer, S and Korniluk, M and Kruckenberg, H and Krupiński, D and Marja, R and Piha, M and Rousseau, P and Rupprecht, V and Bocher, P},
title = {High annual-cycle repeatability suggests low flexibility to environmental changes in a near-threatened migratory shorebird.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42218298},
issn = {2399-3642},
mesh = {Animals ; *Animal Migration/physiology ; Seasons ; *Birds/physiology ; Environment ; Geographic Information Systems ; },
abstract = {Migratory species often repeat spatio-temporal patterns within their annual cycle. Although this may help to promote knowledge about local features and site quality, stereotyped behaviours may also create an ecological trap by preventing the flexibility required to adjust to environmental changes. Using a long-term international dataset, this study assesses 24 spatial and temporal parameters describing the repeatability of the entire migratory cycle in 94 individuals of the migratory near-threatened Eurasian curlew (Numenius arquata) that were tracked for up to 7 consecutive years using high-resolution GPS tags. Twenty-two parameters show significant repeatability, with the highest repeatability for use of the same breeding and wintering sites, indicating consistent faithfulness. All migration and stopover parameters during spring migration are also significantly repeatable, with lower repeatability for autumn migration, likely related to variable breeding success. The location of migration routes varies between consecutive years, but intra-individual similarity is significantly greater than inter-individual similarity. While the potential of adaptations to long-term environmental changes needs further studies (preferably including several cohorts of individuals) there are indications of a potentially maladaptive behaviour to short-term changes that should be carefully observed by site managers to conserve this near-threatened species.},
}
@article {pmid42220300,
year = {2026},
author = {Game, CA and Piechaud, N and Howell, KL},
title = {Deep blueprint: A literature review and guide to automated image classification for ecologists.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70271},
pmid = {42220300},
issn = {1365-2656},
support = {101034309//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; UKRI041//Natural Environment Research Council/ ; //Institute of Marine Research, Norway/ ; },
abstract = {Deep learning (DL) is a powerful tool to extract ecological information from large image datasets efficiently and consistently. However, applying these methods remains challenging, due in part to the complexity of DL workflows and the dynamic nature of available tools. To address this, we created a practical guide and review, focused on one of the fundamental tasks in automated image analysis: image classification. Our approach integrates commonly used software and highlights key steps-from image acquisition to annotated, model-ready datasets, to training, evaluation and deployment. It is modular and supported by a flexible code base (in Python, with R alternatives where possible) and Graphical User Interfaces (GUIs), enabling adaptation to different models and ecological objectives. The goal is to empower ecologists to confidently incorporate computer vision into their research. We illustrate this approach, using an open-source ROV dataset from the Norwegian Sea, featuring deep-sea biotopes defined by multivariate clusters of depth, substrate type, and associated species. To balance accessibility for users alongside performance, we focused on CNN models from the Ultralytics ML Platform (YOLO V.8 and V.11), comparing the full suite of architectures that range in complexity and efficiency. Cross-validation revealed high overall performances and that larger, more complex models are not always superior, with YOLO V.8m best (accuracy and macro-averaged performance metrics = ~0.97-0.98). Notably, high performances were achieved despite labels being based on both visual and external environmental predictors, suggesting visual features alone were sufficient for classification in this dataset. We highlight that the decision to deploy a model must be made in light of the study's objectives, with domain-based reasoning and experience guiding every stage of implementation. This work offers a practical blueprint for implementing DL in ecological research, promoting broader adoption and supporting reproducibility and more efficient, standardised, and sustainable monitoring; in this case of deep-sea biotopes, which is essential for marine spatial planning.},
}
@article {pmid42229176,
year = {2026},
author = {Asteraye, GB and Jobling, R and Jemberu, WT and Pinchbeck, G and Knight-Jones, TJD and Chaters, GL and Rushton, J},
title = {Estimating the economic value of working donkeys in Ethiopia.},
journal = {Preventive veterinary medicine},
volume = {254},
number = {},
pages = {106926},
doi = {10.1016/j.prevetmed.2026.106926},
pmid = {42229176},
issn = {1873-1716},
abstract = {There is limited empirical evidence on the quantitative economic contribution of donkeys to livelihoods, leading to their undervaluation and exclusion from policy. Here an enterprise budget analysis is embedded within a stochastic dynamic population model for three production systems in Ethiopia to evaluate system inputs, outputs and the economic contribution of donkeys. The model was parameterised using data from household surveys, focus group discussions and key informant interviews, supplemented by literature. The economic value of donkeys' (unpaid) homestead and agricultural services was estimated in terms of both monetary savings and conserved human labour hours. The benefits of donkey ownership significantly exceed the costs, with an average net return of USD 567 (95% PI: 479-660) per household per year. Donkeys provide essential unpaid labour, particularly in domestic agricultural and pastoral systems. Households saved an average of USD 498 (95% PI: 437-564) a year by utilising their own donkeys. Additionally, they reduce household labour demands by up to 16.5 hours per week, easing the workload on women and enabling children to attend school. In agriculture, donkeys support all production stages, providing an average of 53 days of work per year. This study demonstrates the importance of donkeys across Ethiopia's production systems and the need for investment in donkey health and welfare to sustain these benefits. Donkeys provide essential economic services, helping marginalised households with limited resources to significantly enhance their well-being and financial circumstances.},
}
@article {pmid42230871,
year = {2026},
author = {Pan, W and Gong, Y and Deng, W and Guo, G and Wan, Y and Khan, NM},
title = {Influence mechanisms of rock mass discontinuity density on mining-induced land subsidence.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-55895-x},
pmid = {42230871},
issn = {2045-2322},
support = {52404188//National Natural Science Foundation of China/ ; 2024D01C244//Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; TCYC2025//Tianchi Talent Recruitment Program of Xinjiang Uygur Autonomous/ ; 2023YFC3804200//National Key Research and Development Program of China/ ; },
abstract = {Surface subsidence induced by underground coal mining, together with the associated damage to surface infrastructure and a range of ecological impacts such as hydrological disturbance and vegetation degradation, collectively hampers the sustainable development of coal resource-based cities worldwide. What remains unclear, however, is how discontinuity density influences mining-induced surface subsidence (mining subsidence), which may render conventional analogy-based analysis methods inadequate for interpreting the anomalously low surface subsidence observed in the Ordos coalfield in China. In this study, we demonstrate that the stiffness of the overburden, represented by the uniaxial compressive strength of intact rock ([Formula: see text]), is not a sufficient indicator for subsidence estimation, and the discontinuity density may play a more influential role. To substantiate this claim, a series of UDEC models with varied discontinuity density and rock stiffness were built and calibrated, and the modeling results were compared with practical cases to assess their validity. The results indicate: (1) increasing discontinuity density leads to a systematic shift in the dominant overburden failure mode from intact rock deformation to block sliding, thereby reducing the reliability of [Formula: see text] as an indicator for subsidence estimation; (2) the applicability of [Formula: see text]-based analogy methods is conditional, being reliable primarily when discontinuity densities are comparable; and (3) higher discontinuity density reduces the width-to-depth ratio required for critical mining, which helps to explain the delayed and attenuated subsidence observed in deep coal mining areas of Ordos, China. The study provides useful insights for subsidence prediction and mining design, and contributes to a better understanding of subsidence mechanisms relevant to the sustainable development of coal resource-based cities.},
}
@article {pmid42232005,
year = {2026},
author = {Moreira, HG and Barreto, TC},
title = {Out-of-Hospital Excess Mortality From Cardiovascular Diseases During the COVID-19 Pandemic in Brazil.},
journal = {Cureus},
volume = {18},
number = {5},
pages = {e108136},
doi = {10.7759/cureus.108136},
pmid = {42232005},
issn = {2168-8184},
abstract = {BACKGROUND: The COVID-19 pandemic disrupted health systems worldwide; yet, the magnitude of collateral mortality occurring outside hospitals, particularly from cardiovascular disease (CVD), remains poorly characterized in low- and middle-income countries (LMICs). Brazil, which experienced one of the highest cumulative death tolls globally, offers a critical setting for quantifying this indirect burden.<br><br>METHODS: We conducted an ecological time-series analysis of all deaths recorded outside health care facilities (domicile or public thoroughfare) in Brazil from 2015 through 2021 using national mortality data from the Mortality Information System (SIM)/Department of Informatics of the Brazilian Unified Health System (DATASUS). Crude mortality rates and age-sex adjusted mortality rates were calculated and standardized to the 2022 Census population structure. Pre-pandemic (2015-2019) and pandemic (2020-2021) periods were compared descriptively.<br><br>RESULTS: Out-of-hospital deaths increased from a pre-pandemic mean of 313660 per year (151.6 per 100000 inhabitants) to 381720 per year (180.2 per 100000 inhabitants) during 2020-2021, representing an 18.8% increase. Age-sex adjusted cardiovascular out-of-hospital mortality rates, which had declined steadily from 53.43 per 100000 in 2015 to 47.16 per 100 000 in 2019, rose sharply to 53.48 per 100000 in 2020 and 54.53 per 100000 in 2021. The Southeast exhibited the steepest rate increase (+23%), whereas the Northeast maintained the highest overall proportion of out-of-hospital cardiovascular deaths. CVD remained the leading cause of death (115228; 29.8%), followed by external causes (65009; 16.8%) and ill-defined causes (62433; 16.1%). Ill-defined deaths increased by 44% between 2019 and 2021, suggesting substantial diagnostic gaps.<br><br>CONCLUSIONS: The pandemic period was associated with a substantial rise in out-of-hospital mortality in Brazil, reversing the prior declining trend in age-sex adjusted cardiovascular mortality. These findings underscore the need for resilient primary care networks and decentralized emergency response systems during public health emergencies.},
}
@article {pmid39198489,
year = {2024},
author = {Chanda, MM and Campbell, L and Walke, H and Salzer, JS and Hemadri, D and Patil, SS and Purse, BV and Shivachandra, SB},
title = {A thirty-year time series analyses identifies coherence between oscillations in Anthrax outbreaks and El Niño in Karnataka, India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19928},
pmid = {39198489},
issn = {2045-2322},
mesh = {*Anthrax/epidemiology ; India/epidemiology ; *Disease Outbreaks ; Animals ; *El Nino-Southern Oscillation ; Bayes Theorem ; Bacillus anthracis/isolation &amp; purification/pathogenicity ; Humans ; Livestock/microbiology ; },
abstract = {Anthrax is an economically important zoonotic disease affecting both livestock and humans. The disease is caused by a spore forming bacterium, Bacillus anthracis, and is considered endemic to the state of Karnataka, India. It is critical to quantify the role of climatic factors in determining the temporal pattern of anthrax outbreaks, so that reliable forecasting models can be developed. These models will aid in establishing public health surveillance and guide strategic vaccination programs, which will reduce the economic loss to farmers, and prevent the spill-over of anthrax from livestock to humans. In this study, correlation and coherence between time series of anthrax outbreaks in livestock (1987-2016) and meteorological variables and Sea Surface Temperature anomalies (SST) were identified using a combination of cross-correlation analyses, spectral analyses (wavelets and empirical mode decomposition) and further quantified using a Bayesian time series regression model accounting for temporal autocorrelation. Monthly numbers of anthrax outbreaks were positively associated with a lagged effect of rainfall and wet day frequency. Long-term periodicity in anthrax outbreaks (approximately 6-8 years) was coherent with the periodicity in SST anomalies and outbreak numbers increased with decrease in SST anomalies. These findings will be useful in planning long-term anthrax prevention and control strategies in Karnataka state of India.},
}
@article {pmid39198944,
year = {2024},
author = {Wang, HT and Li, HY and Lu, QW and He, SL},
title = {[Determination of eight neonicotinoid pesticides in wastewater by solid phase extraction combined with liquid chromatography-tandem mass spectrometry].},
journal = {Se pu = Chinese journal of chromatography},
volume = {42},
number = {9},
pages = {856-865},
pmid = {39198944},
issn = {1872-2059},
mesh = {*Tandem Mass Spectrometry/methods ; *Solid Phase Extraction/methods ; *Wastewater/chemistry/analysis ; *Neonicotinoids/analysis ; *Water Pollutants, Chemical/analysis ; Chromatography, Liquid/methods ; *Nitro Compounds/analysis ; Thiamethoxam/analysis ; Guanidines/analysis ; Thiazoles/analysis ; Pesticides/analysis ; Thiazines/analysis ; Oxazines/analysis ; },
abstract = {Neonicotinoid pesticides are a relatively new class of pesticides that have garnered significant attention owing to their potential ecological risks to nontarget organisms. A method combining solid phase extraction with liquid chromatography-tandem mass spectrometry (SPE-LC-MS/MS) was developed for the rapid and accurate detection of eight neonicotinoid pesticides (dinotefuran, E-nitenpyram, thiamethoxam, clothianidin, imidacloprid, imidaclothiz, acetamiprid, and thiacloprid) in wastewater. The chromatographic mobile phase and MS parameters were selected, and a single-factor method was used to determine the optimal column type, extraction volume, sample loading speed, and pH for SPE. The optimal parameters were as follows: column type, HLB column (500 mg/6 mL); sample extraction volume, 500 mL; sample loading speed, 10 mL/min; and sample pH, 6-8. The matrix effects of the wastewater samples were reduced by optimizing the chromatographic gradient-elution program, examining the dilution factor of the samples, and using the isotope internal standard calibration method. Prior to analysis, the wastewater samples were diluted 5-fold with ultrapure water for pretreatment. Subsequently, 2 mmol/L ammonium acetate aqueous solution containing 0.1% (v/v) formic acid and methanol was used as mobile phases for gradient elution on a ZORBAX Eclipse Plus C18 column (100 mm×2.1 mm, 1.8 μm). The samples were quantified using positive-ion multiple reaction monitoring (MRM) mode for 10 min. Imidacloprid-d4 was used as the isotope internal standard. The SPE process was further optimized by applying response surface methodology to select the type and mass of rinsing and elution solvents. The optimal pretreatment of the SPE column included rinsing with 10% methanol aqueous solution and elution with methanol-acetonitrile (1∶1, v/v) mixture (7 mL). The eight neonicotinoid pesticides showed satisfactory linearity within the relevant range, with linear correlation coefficients (r) all greater than 0.9990. The method detection limits (MDLs) ranged from 0.2 to 1.2 ng/L, and the method quantification limits (MQLs) ranged from 0.8 to 4.8 ng/L. The average recoveries of the eight neonicotinoid pesticides were in the range of 82.6%-94.2% at three spiked levels, with relative standard deviations (RSDs) ranging from 3.9% to 9.4%. Finally, the optimized method was successfully applied to analyze wastewater samples collected from four sewage treatment plants. The results indicated that the eight neonicotinoid pesticides could be generally detected at concentrations ranging from not detected (ND) to 256 ng/L. The developed method has a low MDL and high accuracy, rendering it a suitable choice for the trace detection of the eight neonicotinoid pesticides in wastewater when compared with other similar methods. The proposed method can be utilized to monitor the environmental impact and assess the potential risks of neonicotinoid pesticides in wastewater, thus promoting the protection of nontarget organisms and the sustainable use of these pesticides in agriculture.},
}
@article {pmid39202178,
year = {2024},
author = {de Llanza Varona, M and Martínez, M},
title = {Synergy Makes Direct Perception Inefficient.},
journal = {Entropy (Basel, Switzerland)},
volume = {26},
number = {8},
pages = {},
pmid = {39202178},
issn = {1099-4300},
support = {PID2021-127046NA-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CEX2021-001169-M MCIN/AEI/10.13039/501100011033)//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 2021-SGR-00276//Government of Catalonia/ ; },
abstract = {A typical claim in anti-representationalist approaches to cognition such as ecological psychology or radical embodied cognitive science is that ecological information is sufficient for guiding behavior. According to this view, affordances are immediately perceptually available to the agent (in the so-called "ambient energy array"), so sensory data does not require much further inner processing. As a consequence, mental representations are explanatorily idle: perception is immediate and direct. Here we offer one way to formalize this direct-perception claim and identify some important limits to it. We argue that the claim should be read as saying that successful behavior just implies picking out affordance-related information from the ambient energy array. By relying on the Partial Information Decomposition framework, and more concretely on its development of the notion of synergy, we show that in multimodal perception, where various energy arrays carry affordance-related information, the "just pick out affordance-related information" approach is very inefficient, as it is bound to miss all synergistic components. Efficient multimodal information combination requires transmitting sensory-specific (and not affordance-specific) information to wherever it is that the various information streams are combined. The upshot is that some amount of computation is necessary for efficient affordance reconstruction.},
}
@article {pmid39202353,
year = {2024},
author = {Maltseva, PY and Plotnitskaya, NA and Krivoruchko, AV and Beletskiy, AV and Rakitin, AL and Mardanov, AV and Ivshina, IB},
title = {Bioinformatics Analysis of the Genome of Rhodococcus rhodochrous IEGM 1362, an (-)-Isopulegol Biotransformer.},
journal = {Genes},
volume = {15},
number = {8},
pages = {},
pmid = {39202353},
issn = {2073-4425},
support = {24-14-20015//the Russian Science Foundation/ ; },
mesh = {*Rhodococcus/genetics/metabolism ; *Genome, Bacterial ; *Computational Biology/methods ; *Biotransformation/genetics ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Monoterpenes/metabolism ; },
abstract = {A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (-)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (-)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation.},
}
@article {pmid39205176,
year = {2024},
author = {Vanslembrouck, A and Jansen, S and De Witte, J and Janssens, C and Vereecken, S and Helms, M and Lange, U and Lühken, R and Schmidt-Chanasit, J and Heitmann, A and Müller, R},
title = {Larval Competition between Aedes and Culex Mosquitoes Carries over to Higher Arboviral Infection during Their Adult Stage.},
journal = {Viruses},
volume = {16},
number = {8},
pages = {},
pmid = {39205176},
issn = {1999-4915},
support = {G0G2319N//BiodivERsA/ ; CA17108//European Cooperation in Science and Technology/ ; 653316//European Union's Horizon 2020 research and innovation program/ ; Dubois-Brigu&#xe9; scholarship//Doctor Albert Dubois Foundation for tropical pathology/ ; },
mesh = {Animals ; *Culex/virology/growth &amp; development ; *Aedes/virology/growth &amp; development/physiology ; *Larva/virology ; *Mosquito Vectors/virology/growth &amp; development ; Arbovirus Infections/transmission/virology ; Arboviruses/physiology ; West Nile virus/physiology ; Female ; Chikungunya virus/physiology ; Encephalitis Virus, Japanese/physiology ; },
abstract = {The common house mosquito (Culex pipiens) is a native vector for West Nile virus (WNV). Invasive species like the tiger mosquito (Aedes albopictus) and Asian bush mosquito (Aedes japonicus) are rapidly spreading through Europe, posing a major threat as vectors for dengue, chikungunya (CHIKV), and Japanese encephalitis virus (JEV). These mosquitoes share a similar ecological niche as larvae, but the carry-over effects of aquatic larval interactions to the terrestrial adult stage remain largely unknown and their medical relevance requires further investigation. This study examines the context dependency of larval interactions among Aedes albopictus, Aedes japonicus, and Culex pipiens. The survival, development time, growth, and energetic storage were measured in different European populations within density-response (intraspecific) experiments and replacement (interspecific) experiments at 20 °C and 26 °C. Overall, Ae. japonicus was the weakest competitor, while competition between Ae. albopictus and Cx. pipiens varied with temperature. Adults emerging from this larval competition were infected as follows: Culex pipiens with WNV, Ae. albopictus with CHIKV, and Ae. japonicus with JEV. While no JEV infection was observed, mosquitoes experiencing interspecific interactions during their larval stages exhibited higher infection rates and viral RNA titers for CHIKV and WNV. This increased susceptibility to viral infection after larval competition suggests a higher risk of arbovirus transmission in co-occurring populations.},
}
@article {pmid39208193,
year = {2024},
author = {Naser, AY},
title = {Insights into hospitalization pattern for drug, medicament, and biological substance poisoning, adverse effect, and underdosing in Australia: An ecological study between 1998 and 2019.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0309362},
pmid = {39208193},
issn = {1932-6203},
mesh = {Humans ; *Hospitalization/statistics &amp; numerical data/trends ; Australia/epidemiology ; Female ; Male ; Adult ; Middle Aged ; Adolescent ; Aged ; Child ; Young Adult ; Poisoning/epidemiology ; Child, Preschool ; Infant ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Aged, 80 and over ; Databases, Factual ; },
abstract = {BACKGROUND: Drug, medicament, and biological substance poisoning, adverse effects, and underdosing are significant public health concerns. Gaining insight into the patterns and trends in hospitalizations caused by these occurrences is essential for the development of preventative initiatives, optimization of treatment regimens, and improvement of patient safety. The aim of this study is to examine the trend of hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019.<br><br>METHODS: This is an ecological descriptive study that examined hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019. A nationwide hospital admissions database was used for this study.<br><br>RESULTS: Between 1998 and 2019, a total of 683,869 hospital admission episodes were recorded in Australia. The overall annual number of hospital admissions for various reasons increased by 20.5% from 29,854 in 1998 to 35,960 in 2019, representing a decrease in hospital admission rate of 10.6% [from 158.69 (95% CI 156.90-160.49) in 1998 to 141.91 (95% CI 140.44-143.37) in 2019 per 100,000 persons, trend test, p<0.05]. Overnight-stay admissions accounted for 69.2% of the total number of hospital admissions, and 30.8% were same-day admissions. Rates of same-day hospital admission decreased by 13.3% [from 50.55 (95%CI 49.54-51.57) in 1998 to 43.81 (95%CI 43.00-44.63) in 2019 per 100,000 persons]. Rates of overnight-stay hospital admission decreased by 11.1% [from 108.14 (95%CI 106.66-109.63) in 1998 to 96.17 (95%CI 94.96-97.38) in 2019 per 100,000 persons]. Admissions related to antiepileptic, sedative-hypnotic and antiparkinsonism drugs was the most prevalent hospital admissions type accounting for 26.8%. Females were responsible for 418,751 hospital admission episodes, representing 61.5% of the total number of hospital admission.<br><br>CONCLUSION: This study found that while the overall annual number of admissions increased, the rate of admission decreased over the same period. The most common reasons for admissions were antiepileptic, sedative-hypnotic, and anti-parkinsonism drugs. The study also noted increases in admissions related to anaesthetics, therapeutic gases, hormones, and their synthetic substitutes. These findings suggest a concerning rise in the suboptimal use of these medications. In order to combat the increasing incidence of this type of admissions, it is imperative to strengthen public awareness initiatives on medicine safety and abuse.},
}
@article {pmid39208288,
year = {2024},
author = {Ishigohoka, J and Bascón-Cardozo, K and Bours, A and Fuß, J and Rhie, A and Mountcastle, J and Haase, B and Chow, W and Collins, J and Howe, K and Uliano-Silva, M and Fedrigo, O and Jarvis, ED and Pérez-Tris, J and Illera, JC and Liedvogel, M},
title = {Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure.},
journal = {Evolution; international journal of organic evolution},
volume = {78},
number = {12},
pages = {1916-1935},
doi = {10.1093/evolut/qpae117},
pmid = {39208288},
issn = {1558-5646},
support = {MFFALIMN0001//The Max Planck Society/ ; 395940726//Magnetoreception and Navigation in Vertebrates/ ; 407495230//DFG Research Infrastructure/ ; 423957469//Next Generation Sequencing Competence Network/ ; 1ZIAHG200398//Intramural Research Program of the NHGRI/ ; //Spanish Ministry of Science/ ; //Innovation and Universities/ ; PGC2018-097575-B-I00//The European Regional Development Fund/ ; },
mesh = {Animals ; *Haplotypes ; *Recombination, Genetic ; *Genetic Variation ; *Songbirds/genetics ; Selection, Genetic ; Genome ; },
abstract = {Genomic regions sometimes show patterns of genetic variation distinct from the genome-wide population structure. Such deviations have often been interpreted to represent effects of selection. However, systematic investigation of whether and how non-selective factors, such as recombination rates, can affect distinct patterns has been limited. Here, we associate distinct patterns of genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using a new reference genome assembly, whole-genome resequencing data and recombination maps. We find that distinct patterns of genetic variation reflect haplotype structure at genomic regions with different prevalence of reduced recombination rate across populations. At low-recombining regions shared in most populations, distinct patterns reflect conspicuous haplotypes segregating in multiple populations. At low-recombining regions found only in a few populations, distinct patterns represent variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns evolve neutrally by reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolutionary reduction of local recombination rate. The recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.},
}
@article {pmid39209112,
year = {2024},
author = {Ji, N and Kumar, A and Joe, W and Kuriyan, R and Sethi, V and Finkelstein, JL and Mehta, S},
title = {Prevalence and Correlates of Double and Triple Burden of Malnutrition Among Children and Adolescents in India: The Comprehensive National Nutrition Survey.},
journal = {The Journal of nutrition},
volume = {154},
number = {10},
pages = {2932-2947},
doi = {10.1016/j.tjnut.2024.08.021},
pmid = {39209112},
issn = {1541-6100},
mesh = {Humans ; India/epidemiology ; Adolescent ; Child ; Female ; Male ; Prevalence ; *Nutrition Surveys ; Child, Preschool ; *Malnutrition/epidemiology ; Nutritional Status ; Young Adult ; Overnutrition/epidemiology ; Socioeconomic Factors ; Child Nutrition Disorders/epidemiology ; },
abstract = {BACKGROUND: Limited information on the co-prevalence of undernutrition, micronutrient deficiencies, overnutrition, and abnormal levels of noncommunicable disease biomarkers at the same time in children and adolescents in India hinders efforts to comprehensively address their health.<br><br>OBJECTIVES: This study aimed to examine the prevalence and correlates of double burden of malnutrition (DBM) and triple burden of malnutrition (TBM) among children and adolescents (5-19 y) to inform policies and programs.<br><br>METHODS: A total of 17,599 children (5-9 y) and 16,184 adolescents (10-19 y) with available biomarker data from the Comprehensive National Nutrition Survey were included. Malnutrition was defined based on either undernutrition based on anthropometry, overnutrition/abnormal metabolic markers, and anemia/micronutrient deficiency. DBM was defined as the coexistence of any 2 forms of malnutrition. DBM+ was defined as the coexistence of undernutrition and/or micronutrient deficiency along with overnutrition. TBM was defined as having the coexistence of all 3 forms of malnutrition. The prevalence of DBM, DBM+, and TBM was estimated accounting for probabilistic selection. We used mixed-effect binomial regression to determine correlates of DBM/TBM in children and adolescents separately.<br><br>RESULTS: The prevalence of DBM, DBM+, and TBM was 50.8%, 37.2%, and 14.4%, respectively, in children and 53.4%, 36.1%, and 12.7%, respectively, in adolescents. The prevalence of DBM+ was significantly higher in girls compared to in boys in the 5-9 y age group. In children, being in a disadvantaged caste group, having a lower wealth index, having inadequate diet diversity, having no maternal schooling, and having a recent history of acute illness were associated with DBM. In adolescents, being in a disadvantaged caste group, maternal occupation, and lower paternal age were correlated with DBM. A similar set of variables was associated with TBM in both age groups.<br><br>CONCLUSIONS: The prevalence of DBM and TBM is substantial in children and adolescents in India and varies across states. Socioeconomic factors and acute illness were the main correlates for DBM and TBM.},
}
@article {pmid39209853,
year = {2024},
author = {Mi, J and Jing, X and Ma, C and Yang, Y and Li, Y and Zhang, Y and Long, R and Zheng, H},
title = {Massive expansion of the pig gut virome based on global metagenomic mining.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {76},
pmid = {39209853},
issn = {2055-5008},
mesh = {Animals ; Swine ; *Virome/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Viruses/genetics/classification/isolation &amp; purification ; *Genome, Viral ; Data Mining ; Metagenome ; Phylogeny ; },
abstract = {The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.},
}
@article {pmid39209912,
year = {2024},
author = {Yuan, R and Qu, Q and Lu, Z and Geng, X and Tian, S and Jin, Y and Gong, J and Ye, X and Tang, P and Chen, X},
title = {A chromosome-level genome assembly of the gall maker pest inquiline, Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae).},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {944},
pmid = {39209912},
issn = {2052-4463},
support = {32070467//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31920103005//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Chromosomes, Insect ; Genome Size ; *Genome, Insect ; *Hymenoptera/genetics ; Wasps/parasitology ; Datasets as Topic ; },
abstract = {Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae) is an inquiline of gall maker Aiolomorphus rhopaloides Walker (Hymenoptera: Eurytomidae). They are of significant economic significance and predominantly inhabit bamboo forest. So far, only four scaffold-level genomes have been published for the family Torymidae. In this study, we present a high-quality genome assembly of D. aiolomorphi at the chromosome level, achieved through the integration of Nanopore (ONT) long-read, Illumina pair-end DNA short-read, and High-through Chromosome Conformation Capture (Hi-C) sequencing methods. The final assembly was 1,084.56 Mb in genome size, with 1,083.41 Mb (99.89%) assigned to five pseudochromosomes. The scaffold N50 length reached 224.87 Mb, and the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) score was 97.3%. The genome contained 762.12 Mb of repetitive elements, accounting for 70.27% of the total genome size. A total of 18,011 protein-coding genes were predicted, with 17,829 genes being functionally annotated. The high-quality genome assembly of D. aiolomorphi presented in this study will serve as a valuable genomic resource for future research on parasitoid wasps. The results of this study may also contribute to the development of biological control strategies for pest management in bamboo forests, enhancing ecological balance and economic sustainability.},
}
@article {pmid39211527,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Small Square-spot, Diarsia rubi (Vieweg, 1790).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {210},
pmid = {39211527},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Diarsia rubi (the Small Square-spot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 624.9 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 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,173 protein coding genes.},
}
@article {pmid39213378,
year = {2024},
author = {Wang, M and Li, Z and Wang, H and Zhao, J and Zhang, Y and Lin, K and Zheng, S and Feng, Y and Zhang, Y and Teng, W and Tong, Y and Zhang, W and Xue, Y and Mao, H and Li, H and Zhang, B and Rasheed, A and Bhavani, S and Liu, C and Ling, HQ and Hu, YQ and Zhang, Y},
title = {A Quantitative Computational Framework for Allopolyploid Single-Cell Data Integration and Core Gene Ranking in Development.},
journal = {Molecular biology and evolution},
volume = {41},
number = {9},
pages = {},
pmid = {39213378},
issn = {1537-1719},
support = {//National Natural Science Foundation of China/ ; //National Key R&amp;D Program of China/ ; //Yangfan Project of Shanghai Science and Technology Commission/ ; //State Key Laboratory of Genetic Engineering/ ; //State Key Laboratory of Crop Gene Exploration and Utilization in Southwest/ ; //State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/ ; //Shanghai Key Laboratory of Agricultural Genetics and Breeding/ ; },
mesh = {*Single-Cell Analysis/methods ; *Polyploidy ; Animals ; Computational Biology/methods ; },
abstract = {Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome-divergent regulation in the context of cellular differentiation. However, analyzing single-cell data suffers from high error rates due to high dimensionality, noise, and sparsity, and the errors stack up in polyploid analysis due to the increased dimensionality of comparisons between subgenomes of each cell, hindering deeper mechanistic understandings. In this study, we develop a quantitative computational framework, called "pseudo-genome divergence quantification" (pgDQ), for quantifying and tracking subgenome divergence directly at the cellular level. Further comparing with cellular differentiation trajectories derived from single-cell RNA sequencing data allows for an examination of the relationship between subgenome divergence and the progression of development. pgDQ produces robust results and is insensitive to data dropout and noise, avoiding high error rates due to multiple comparisons of genes, cells, and subgenomes. A statistical diagnostic approach is proposed to identify genes that are central to subgenome divergence during development, which facilitates the integration of different data modalities, enabling the identification of factors and pathways that mediate subgenome-divergent activity during development. Case studies have demonstrated that applying pgDQ to single-cell and bulk tissue transcriptomic data promotes a systematic and deeper understanding of how dynamic subgenome divergence contributes to developmental trajectories in polyploid evolution.},
}
@article {pmid39213392,
year = {2024},
author = {Du, Q and Zhang, Z and Yang, W and Zhou, X and Zhou, N and Wu, C and Bao, J},
title = {CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {39213392},
issn = {1758-0463},
support = {31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; 31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; },
mesh = {Humans ; *Databases, Genetic ; *Data Curation/methods ; Genome-Wide Association Study/methods ; Genetic Predisposition to Disease ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; CRISPR-Cas Systems ; Disease/genetics ; },
abstract = {The field of understanding the association between genes and diseases is rapidly expanding, making it challenging for researchers to keep up with the influx of new publications and genetic datasets. Fortunately, there are now several regularly updated databases available that focus on cataloging gene-disease relationships. The development of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system has revolutionized the field of gene editing, providing a highly efficient, accurate, and reliable method for exploring gene-disease associations. However, currently, there is no resource specifically dedicated to collecting and integrating the latest experimentally supported gene-disease association data derived from genome-wide CRISPR screening. To address this gap, we have developed the CRISPR-Based Gene-Disease Associations (CBGDA) database, which includes over 200 manually curated gene-disease association data derived from genome-wide CRISPR screening studies. Through CBGDA, users can explore gene-disease association data derived from genome-wide CRISPR screening, gaining insights into the expression patterns of genes in different diseases, associated chemical data, and variant information. This provides a novel perspective on understanding the associations between genes and diseases. What is more, CBGDA integrates data from several other databases and resources, enhancing its comprehensiveness and utility. In summary, CBGDA offers a fresh perspective and comprehensive insights into the research on gene-disease associations. It fills the gap by providing a dedicated resource for accessing up-to-date, experimentally supported gene-disease association data derived from genome-wide CRISPR screening. Database URL: http://cbgda.zhounan.org/main.},
}
@article {pmid39218423,
year = {2025},
author = {Morris, JS},
title = {Tracking vaccine effectiveness in an evolving pandemic, countering misleading hot takes and epidemiologic fallacies.},
journal = {American journal of epidemiology},
volume = {194},
number = {4},
pages = {898-907},
pmid = {39218423},
issn = {1476-6256},
support = {UL1 TR001878/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Bias ; *COVID-19/prevention &amp; control/epidemiology ; *COVID-19 Vaccines/immunology ; *Pandemics/prevention &amp; control ; SARS-CoV-2/immunology ; Social Media ; *Vaccine Efficacy ; },
abstract = {With the emergence of Omicron during the pandemic and the establishment of antibody waning over time, vaccine effectiveness, especially against infection, declined sharply from the original levels seen after the initial rollout. However, studies have demonstrated that they still provided substantial protection vs severe/fatal disease even with Omicron and after waning. Social media has been rife with reports claiming vaccines provided no benefit and some even claiming they made things worse, often driven by simple presentations of raw observational data using erroneous arguments involving epidemiologic fallacies including the base rate fallacy, Simpson's paradox, and the ecological fallacy and ignoring the extensive bias especially from confounding that is an inherent feature of these data. Similar fallacious arguments have been made by some in promoting vaccination policies, as well. Generally, vaccine effectiveness cannot be accurately estimated from raw population summaries but instead require rigorous, careful studies using epidemiologic designs and statistical analysis tools attempting to adjust for key confounders and sources of bias. This article summarizes what aggregated evidence across studies reveals about effectiveness of the mRNA vaccines as the pandemic has evolved, chronologically summarized with emerging variants and highlighting some of the fallacies and flawed arguments feeding social media-based claims that have obscured society's collective understanding.},
}
@article {pmid39219129,
year = {2024},
author = {Xie, Z and Hu, D and Jiang, F and Fu, X and Li, R and Zheng, D and Zhao, L and Xu, J and Yuan, X and Bao, Y and Zhou, H and Wang, B and Wang, Q},
title = {Assessment of urban flood resilience based on the socio-ecological composite index model: a case study in Wuhua District, Kunming City, China.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {89},
number = {2},
pages = {252-270},
doi = {10.2166/wst.2023.413},
pmid = {39219129},
issn = {0273-1223},
mesh = {China ; *Floods ; *Cities ; Models, Theoretical ; Geographic Information Systems ; Socioeconomic Factors ; },
abstract = {Global climate change and rapid urbanization have increased the frequency of flooding, making urban flood resilience a critical objective. This article introduces a methodology for assessing urban flood resilience, utilizing a social-ecological synthesis index that integrates geographical and temporal data with Geographic Information System (GIS). The study focuses on ten administrative subdistricts in Wuhua District, Kunming City, China, and selects 18 social-ecological indicators. These indicators, chosen from social and ecological perspectives, are weighted using the entropy weight method to determine their significance in the assessment system. By combining scores for each subdistrict, the study quantifies flood resilience and creates a spatial distribution map using ArcGIS. Key findings reveal that out of the ten administrative subdistricts, five in Wuhua District, particularly in the core urban area of Kunming, demonstrate strong overall flood resilience. Influenced by social-ecological indicators, there is significant spatial differentiation in flood resilience within Wuhua District, with a decreasing trend radiating from the city center to areas farther from the urban core. The research indicates that regions with well-established transportation infrastructure, a wide distribution of government institutions, improved water management facilities, and a substantial population with higher education levels contribute significantly to enhancing urban flood resilience.},
}
@article {pmid39219859,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Ruby Tiger, Phragmatobia fuliginosa (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {124},
pmid = {39219859},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Phragmatobia fuliginosa (the Ruby Tiger; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 629.4 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,338 protein coding genes.},
}
@article {pmid39221442,
year = {2024},
author = {Morales, HE and Norris, K and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Groombridge, JJ and Gilbert, MTP and , and , and , and , },
title = {The genome sequence of the Mauritius kestrel, Falco punctatus (Temminck, 1821).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {312},
pmid = {39221442},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Falco punctatus (the Mauritius kestrel; Chordata; Aves; Falconiformes; Falconidae). The genome sequence is 1,279.3 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.34 kilobases in length.},
}
@article {pmid39221663,
year = {2024},
author = {Crawford, AD and Slavin, R and Tabar, M and Radhakrishnan, K and Wang, M and Estrada, A and McGrath, JM},
title = {Methodological approaches in developing and implementing digital health interventions amongst underserved women.},
journal = {Public health nursing (Boston, Mass.)},
volume = {41},
number = {6},
pages = {1612-1621},
doi = {10.1111/phn.13410},
pmid = {39221663},
issn = {1525-1446},
mesh = {Humans ; Female ; *Telemedicine ; Texas ; Vulnerable Populations ; Women's Health ; Medically Underserved Area ; Artificial Intelligence ; Adult ; Mobile Applications ; Digital Health ; },
abstract = {BACKGROUND: Minority populations are utilizing mobile health applications more frequently to access health information. One group that may benefit from using mHealth technology is underserved women, specifically those on community supervision.<br><br>OBJECTIVE: Discuss methodological approaches for navigating digital health strategies to address underserved women's health disparities.<br><br>Using an intersectional lens, we identified strategies for conducting research using digital health technology and artificial intelligence amongst the underserved, particularly those with community supervision.<br><br>We explore (1) methodological approaches that combine traditional research methods with precision medicine, digital phenotyping, and ecological momentary assessment; (2) implications for artificial intelligence; and (3) ethical considerations with data collection, storage, and engagement.<br><br>DISCUSSION: Researchers must address gendered differences related to health, social, and economic disparities concurrently with an unwavering focus on the protection of human subjects when addressing the unique needs of underserved women while utilizing digital health methodologies.<br><br>PUBLIC CONTRIBUTION: Women on community supervision in South Central Texas helped inform the design of JUN, the mHealth app we reported in the case exemplar. JUN is named after the Junonia shell, a native shell to South Texas, which means strength, power, and self-sufficiency, like the participants in our preliminary studies.},
}
@article {pmid39222055,
year = {2024},
author = {Xu, C and Wang, JC and Sun, L and Zhuang, LH and Guo, ZJ and Ding, QS and Ma, DN and Song, LY and Li, J and Tang, HC and Zhu, XY and Zheng, HL},
title = {Genome-Wide Identification of Pentatricopeptide Repeat (PPR) Gene Family and Multi-Omics Analysis Provide New Insights Into the Albinism Mechanism of Kandelia obovata Propagule Leaves.},
journal = {Plant, cell &amp; environment},
volume = {47},
number = {12},
pages = {5498-5510},
doi = {10.1111/pce.15132},
pmid = {39222055},
issn = {1365-3040},
support = {//This study was supported by the Natural Science Foundation of China (NSFC) (32171740, 31870581) and&#xa0;the National Key Research and Development Program of China (2017YFC0506102)./ ; },
mesh = {*Plant Leaves/genetics/metabolism ; *Genome-Wide Association Study ; *Plant Proteins/genetics/metabolism ; Multigene Family ; RNA Editing/genetics ; Rhizophoraceae/genetics/physiology ; Phylogeny ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Genes, Plant ; Genome, Plant ; Multiomics ; },
abstract = {Pentatricopeptide repeat (PPR) gene family constitutes one of the largest gene families in plants, which mainly participate in RNA editing and RNA splicing of organellar RNAs, thereby affecting the organellar development. Recently, some evidence elucidated the important roles of PPR proteins in the albino process of plant leaves. However, the functions of PPR genes in the woody mangrove species have not been investigated. In this study, using a typical true mangrove Kandelia obovata, we systematically identified 298 PPR genes and characterized their general features and physicochemical properties, including evolutionary relationships, the subcellular localization, PPR motif type, the number of introns and PPR motifs, and isoelectric point, and so forth. Furthermore, we combined genome-wide association studies (GWAS) and transcriptome analysis to identify the genetic architecture and potential PPR genes associated with propagule leaves colour variations of K. obovata. As a result, we prioritized 16 PPR genes related to the albino phenotype using different strategies, including differentially expressed genes analysis and genetic diversity analysis. Further analysis discovered two genes of interest, namely Maker00002998 (PLS-type) and Maker00003187 (P-type), which were differentially expressed genes and causal genes detected by GWAS analysis. Moreover, we successfully predicted downstream target chloroplast genes (rps14, rpoC1 and rpoC2) bound by Maker00002998 PPR proteins. The experimental verification of RNA editing sites of rps14, rpoC1, and rpoC2 in our previous study and the verification of interaction between Maker00002998 and rps14 transcript using in vitro RNA pull-down assays revealed that Maker00002998 PPR protein might be involved in the post-transcriptional process of chloroplast genes. Our result provides new insights into the roles of PPR genes in the albinism mechanism of K. obovata propagule leaves.},
}
@article {pmid39222062,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: coverage-based analysis for identification of microbiome.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
pmid = {39222062},
issn = {1477-4054},
support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; },
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}
@article {pmid39222768,
year = {2024},
author = {Yushin, N and Jakhu, R and Chaligava, O and Grozdov, D and Zinicovscaia, I},
title = {Evaluation of the potentially toxic elements and radionuclides in the soil sample of Novaya Zemlya in the Arctic Circle.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {361},
number = {},
pages = {124871},
doi = {10.1016/j.envpol.2024.124871},
pmid = {39222768},
issn = {1873-6424},
mesh = {Arctic Regions ; *Soil/chemistry ; Russia ; Environmental Monitoring/methods ; Soil Pollutants/analysis ; Thorium/analysis ; Cesium Radioisotopes/analysis ; Soil Pollutants, Radioactive/analysis ; Radiation Monitoring/methods ; Animals ; Birds ; Radioisotopes/analysis ; Radium ; },
abstract = {The study presented here elucidate the concentrations of radionuclides and potentially toxic elements in the soil samples around the Novaya Zemlya in the Russian Arctic zone, determined using HPGe gamma spectrometry, inductively coupled plasma optical emission spectrometry and direct mercury analyzer. The average detected concentrations for [226]Ra, [232]Th, [40]K, [235]U and [137]Cs were 36.40, 46.06, 768, 2.06 and 4.71 Bq/kg, respectively. At many sampling sites, the concentrations of potentially toxic elements (Zn, Cu, Pb, Cd, Ni, and Cr) were higher than the natural levels. Positive Matrix Factorization analysis revealed the contribution of oil dumps (32%), natural sources (16%), bird colonies (32%) and atmospheric deposition (20%) for elevated elements content. In the case of radionuclides, the natural occurring contamination (38%) was primary source followed by dumped material (32%) and bird colonies (30%). The radiological risk from radionuclides was relatively high, yet still under permissible levels. For potentially toxic elements, Fe was predominant non-carcinogenic pollutant and Ni emerged as major carcinogenic contaminant. Keeping in view the high content of some elements, future studies are required to keep the human and ecological risk low, and to establish scientific grounds for the contribution of settled bird species. The findings of the study advance the present knowledge about the contamination of the study area and lays the path for further effort.},
}
@article {pmid39224703,
year = {2024},
author = {Shi, Y and Zhang, W and Li, L and Wu, W and Li, M and Xiao, K and Wang, K and Sheng, Z and Xie, F and Wang, X and Shi, X and Tong, Y and Xie, L},
title = {Evaluation of phage-based decontamination in respiratory intensive care unit environments using ddPCR and 16S rRNA targeted sequencing techniques.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1442062},
pmid = {39224703},
issn = {2235-2988},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Klebsiella pneumoniae/virology/genetics ; *Intensive Care Units ; *Decontamination/methods ; *Bacteriophages/genetics ; Humans ; Polymerase Chain Reaction/methods ; Cross Infection/prevention &amp; control/microbiology ; Disinfectants/pharmacology ; Klebsiella Infections/prevention &amp; control/microbiology ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Klebsiella pneumoniae is a major cause of hospital-acquired infections (HAIs), primarily spread through environmental contamination in hospitals. The effectiveness of current chemical disinfectants is waning due to emerging resistance, which poses environmental hazards and fosters new resistance in pathogens. Developing environmentally friendly and effective disinfectants against multidrug-resistant organisms is increasingly important.<br><br>METHODS: This study developed a bacteriophage cocktail targeting two common carbapenem-resistant Klebsiella pneumoniae (CRKP) strains, ST11 KL47 and ST11 KL64. The cocktail was used as an adjunctive disinfectant in a hospital's respiratory intensive care unit (RICU) via ultrasonic nebulization. Digital PCR was used to quantify CRKP levels post-intervention. The microbial community composition was analyzed via 16S rRNA sequencing to assess the intervention's impact on overall diversity.<br><br>RESULTS: The phage cocktail significantly reduced CRKP levels within the first 24 hours post-treatment. While a slight increase in pathogen levels was observed after 24 hours, they remained significantly lower than those treated with conventional disinfectants. 16S rRNA sequencing showed a decrease in the target pathogens' relative abundance, while overall species diversity remained stable, confirming that phages selectively target CRKP without disrupting ecological balance.<br><br>DISCUSSION: The findings highlight the efficacy and safety of phage-based biocleaners as a sustainable alternative to conventional disinfectants. Phages selectively reduce multidrug-resistant pathogens while preserving microbial diversity, making them a promising tool for infection control.},
}
@article {pmid39224768,
year = {2024},
author = {Jentoft, S and Tørresen, OK and Tooming-Klunderud, A and Skage, M and Kollias, S and Jakobsen, KS and , and , and , and , and , },
title = {The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {189},
pmid = {39224768},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Gadus morhua (the Atlantic cod; Chordata; Actinopteri; Gadiformes; Gadidae). The genome sequence is 669.9 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 23,515 protein coding genes.},
}
@article {pmid39224879,
year = {2023},
author = {Boyes, D and Mulley, JF and , and , and , and , and , and , },
title = {The genome sequence of the Small Emerald, Hemistola chrysoprasaria (Esper, 1795).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {441},
pmid = {39224879},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Hemistola chrysoprasaria (the Small Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 438.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,512 protein coding genes.},
}
@article {pmid39225619,
year = {2024},
author = {Liu, Z and Sun, Y and Li, Y and Ma, A and Willaims, NF and Jahanbahkshi, S and Hoyd, R and Wang, X and Zhang, S and Zhu, J and Xu, D and Spakowicz, D and Ma, Q and Liu, B},
title = {An Explainable Graph Neural Framework to Identify Cancer-Associated Intratumoral Microbial Communities.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {11},
number = {41},
pages = {e2403393},
pmid = {39225619},
issn = {2198-3844},
support = {2020YFA0712400//National Key Research and Development Program of China/ ; 62272270//National Nature Science Foundation of China/ ; 11931008//National Nature Science Foundation of China/ ; ZR2023JQ002//Shandong Provincial Natural Science Foundation for Distinguished Young Scholars/ ; },
mesh = {Mice ; *Microbiota ; Animals ; *Neoplasms/microbiology ; *Neural Networks, Computer ; Humans ; Reproducibility of Results ; Disease Models, Animal ; },
abstract = {Microbes are extensively present among various cancer tissues and play critical roles in carcinogenesis and treatment responses. However, the underlying relationships between intratumoral microbes and tumors remain poorly understood. Here, a MIcrobial Cancer-association Analysis using a Heterogeneous graph transformer (MICAH) to identify intratumoral cancer-associated microbial communities is presented. MICAH integrates metabolic and phylogenetic relationships among microbes into a heterogeneous graph representation. It uses a graph transformer to holistically capture relationships between intratumoral microbes and cancer tissues, which improves the explainability of the associations between identified microbial communities and cancers. MICAH is applied to intratumoral bacterial data across 5 cancer types and 5 fungi datasets, and its generalizability and reproducibility are demonstrated. After experimentally testing a representative observation using a mouse model of tumor-microbe-immune interactions, a result consistent with MICAH's identified relationship is observed. Source tracking analysis reveals that the primary known contributor to a cancer-associated microbial community is the organs affected by the type of cancer. Overall, this graph neural network framework refines the number of microbes that can be used for follow-up experimental validation from thousands to tens, thereby helping to accelerate the understanding of the relationship between tumors and intratumoral microbiomes.},
}
@article {pmid39226337,
year = {2024},
author = {Rahman, AU and Tikhonov, G and Oksanen, J and Rossi, T and Ovaskainen, O},
title = {Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1011914},
pmid = {39226337},
issn = {1553-7358},
mesh = {*Algorithms ; *Computational Biology/methods ; *Software ; Models, Biological ; Machine Learning ; Computer Graphics ; Models, Statistical ; Humans ; },
abstract = {Joint species distribution modelling (JSDM) is a widely used statistical method that analyzes combined patterns of all species in a community, linking empirical data to ecological theory and enhancing community-wide prediction tasks. However, fitting JSDMs to large datasets is often computationally demanding and time-consuming. Recent studies have introduced new statistical and machine learning techniques to provide more scalable fitting algorithms, but extending these to complex JSDM structures that account for spatial dependencies or multi-level sampling designs remains challenging. In this study, we aim to enhance JSDM scalability by leveraging high-performance computing (HPC) resources for an existing fitting method. Our work focuses on the Hmsc R-package, a widely used JSDM framework that supports the integration of various dataset types into a single comprehensive model. We developed a GPU-compatible implementation of its model-fitting algorithm using Python and the TensorFlow library. Despite these changes, our enhanced framework retains the original user interface of the Hmsc R-package. We evaluated the performance of the proposed implementation across various model configurations and dataset sizes. Our results show a significant increase in model fitting speed for most models compared to the baseline Hmsc R-package. For the largest datasets, we achieved speed-ups of over 1000 times, demonstrating the substantial potential of GPU porting for previously CPU-bound JSDM software. This advancement opens promising opportunities for better utilizing the rapidly accumulating new biodiversity data resources for inference and prediction.},
}
@article {pmid39229001,
year = {2024},
author = {Obbard, DJ and , and , and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Drosophila limbata von Roser 1840.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {365},
pmid = {39229001},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Drosophila limbata (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 233.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.09 kilobases in length.},
}
@article {pmid39230451,
year = {2024},
author = {Hendrix, JG and Robitaille, AL and Kusch, JM and Webber, QMR and Vander Wal, E},
title = {Faithful pals and familiar locales: differentiating social and spatial site fidelity during reproduction.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1912},
pages = {20220525},
pmid = {39230451},
issn = {1471-2970},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; Female ; *Reproduction ; *Reindeer/physiology ; Newfoundland and Labrador ; Social Behavior ; Geographic Information Systems ; },
abstract = {Site fidelity-the tendency to reuse familiar spaces-is expected to improve fitness. Familiarity with the local environment is particularly crucial when resource demands or predation risk are high. Consequently, site fidelity often peaks during reproduction when energetic costs are high and offspring are vulnerable. For many species, the environment they experience is not solely a function of geography but also of the social environment. Social fidelity, the selection for familiar social environments, could constitute an independent or parallel strategy to spatial fidelity when considering behaviour at the spatial-social interface. Using global positioning system locations from caribou across Newfoundland, we tested whether females selected calving sites based on proximity to familiar conspecifics, in addition to geographical (spatial) fidelity. These strategies were synergistic, not alternative, and correlated across the population but more variable within individuals. We also tested whether either form of fidelity affected reproductive success. We failed to detect an effect of spatial or social fidelity on reproductive success in this population. Nevertheless, given the association between social and spatial fidelity and the demonstrated fitness consequences of site fidelity in other systems, familiar conspecifics and the potential benefits these social partners provide may be an underappreciated component driving site fidelity.This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.},
}
@article {pmid39233066,
year = {2024},
author = {Wen, J and Chuai, X and Xiang, A and Liu, Y and Wang, T and Luo, Y and Miao, L and Zhang, L and Li, J and Zhao, R},
title = {Re-identifying farmland carbon neutrality gap under a new carbon counting and the framework of regional interactions in China.},
journal = {The Science of the total environment},
volume = {952},
number = {},
pages = {175996},
doi = {10.1016/j.scitotenv.2024.175996},
pmid = {39233066},
issn = {1879-1026},
abstract = {The farmland ecosystem, with its numerous material cycles and energy flows, is an important part of the carbon cycle in terrestrial ecosystems. Focusing on the carbon neutrality of farmland is meaningful for mitigating global warming and serving national low-carbon strategies. This study enriches the carbon accounting items of farmland and establishes a new research framework to check the carbon neutrality of farmland from the aspect of regional interactions and, subsequently, the inequality among China's provinces. The results revealed that there is still a great gap in the capability of China[']s farmland to reach carbon neutrality, with a gap value of up to 10,503 × 10[4] t C. All of the provinces presented net carbon emissions, and the per unit area carbon neutrality gaps showed spatial regularity decreasing from the coastal regions to the inland areas. Anthropogenic carbon emissions on farmland played a dominant role compared with soil organic carbon. Five provinces had reduced interior-regional carbon emissions through grain trade, and the amounts were especially high for developed regions, such as Guangdong, Zhejiang, Beijing, Shanghai and Jiangsu. Sixteen provinces gained external carbon emissions through trade; these were the less developed regions located mainly in the north, such as Inner Mongolia, Hebei, Jilin, Heilongjiang and Xinjiang. Under regional inequality, 15 provinces added to the net amount of the carbon emissions generated in external regions, with China's megacities adding the highest percentage, especially Beijing, with 389.95 % compared with its original emissions. Inequality showed that most provinces had a moderate status. Sichuan and Hunan experienced weak advantages, and six provinces had disadvantages. Therefore, constructing compensation and trade-based rights and responsibilities traceability mechanisms is important.},
}
@article {pmid39233286,
year = {2024},
author = {Long, XB and Yao, CR and Li, SY and Zhang, JG and Lu, ZJ and Ma, DD and Jiang, YX and Ying, GG and Shi, WJ},
title = {Multiomics analysis reveal the impact of 17α-Ethinylestradiol on mortality in juvenile zebrafish.},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {286},
number = {},
pages = {110027},
doi = {10.1016/j.cbpc.2024.110027},
pmid = {39233286},
issn = {1532-0456},
mesh = {Animals ; *Zebrafish ; *Ethinyl Estradiol/toxicity ; *Water Pollutants, Chemical/toxicity ; Endocrine Disruptors/toxicity ; Transcriptome/drug effects ; Multiomics ; },
abstract = {17α-Ethinylestradiol (EE2) is known for its endocrine-disrupting effects on embryonic and adult fish. However, its impact on juvenile zebrafish has not been well established. In this study, juvenile zebrafish were exposed to EE2 at concentrations of 5 ng/L (low dose, L), 10 ng/L (medium dose, M), and 50 ng/L (high dose, H) from 21 days post-fertilization (dpf) to 49 dpf. We assessed their growth, development, behavior, transcriptome, and metabolome. The findings showed that the survival rate in the EE2-H group was 66.8 %, with all surviving fish displaying stunted growth and swollen, transparent abdomens by 49 dpf. Moreover, severe organ deformities were observed in the gills, kidneys, intestines, and heart of fish in both the EE2-H and EE2-M groups. Co-expression analysis of mRNA and lncRNA revealed that EE2 downregulated the transcription of key genes involved in the cell cycle, DNA replication, and Fanconi anemia signaling pathways. Additionally, metabolomic analysis indicated that EE2 influenced metabolism and development-related signaling pathways. These pathways were also significantly identified based on the genes regulated by lncRNA. Consequently, EE2 induced organ deformities and mortality in juvenile zebrafish by disrupting signaling pathways associated with development and metabolism. The results of this study offer new mechanistic insights into the adverse effects of EE2 on juvenile zebrafish based on multiomics analysis. The juvenile zebrafish are highly sensitive to EE2 exposure, which is not limited to adult and embryonic stages. It is a potential model for studying developmental toxicity.},
}
@article {pmid39233418,
year = {2024},
author = {Li, X and Zhang, LY and Wu, C},
title = {Vegetation changes and influencing factors in different watersheds of Henan Province based on GEE and geographic detectors.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {7},
pages = {1887-1896},
doi = {10.13287/j.1001-9332.202407.021},
pmid = {39233418},
issn = {1001-9332},
mesh = {China ; *Rivers ; *Ecosystem ; *Environmental Monitoring/methods ; Conservation of Natural Resources ; Plant Development ; Geographic Information Systems ; Plants ; },
abstract = {Clarifying vegetation changes and the driving factors can provide references for ecological restoration and sustainable social development. We analyzed vegetation distribution and trend changes in Henan Province and its basin zoning (Haihe River basin zoning, Yellow River basin zoning, Huaihe River basin zoning, Yangtze River basin zoning), with fractional vegetation cover data from 2000 to 2020 based on the Google Earth Engine platform, and by combining Theil-Sen Median trend analysis, Mann-Kendall test, and Hurst index. We also utilized factor detection and factor interaction to explore the individual and mutual influences of natural and anthropogenic factors on vegetation at different scales. The results showed that the fractional vegetation cover (FVC) in Henan Province exhibited a distribution pattern of higher coverage in the south and lower in the north during the study period, predominantly characterized by moderate to high vegetation coverage. The Yangtze River basin zoning had the highest coverage. FVC in Henan Province and its zoning exhibited a consistent pattern of fluctuating upward trends, with all areas showing significant improvement. Particularly, the Yangtze River basin zoning had the largest area of improvement. According to the Hurst index, apart from the possibility of continued improvement in the Huaihe River basin zoning, other zoning would be likely to shift from improvement to degradation in the future. Vegetation changes in Henan Province and its zoning were the result of combined effects of anthropogenic and natural factors, with the influence of these factors changing over time and the dominant factors varying by region. Anthropogenic factors such as land use/cover type and nighttime lighting had a stronger impact on vegetation than natural factors like elevation, slope, and annual mean low temperature. The interaction between factors, particularly between anthropogenic and natural factors, exhibited a nonlinear enhancing pattern.},
}
@article {pmid39233899,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Scarlet Tiger moth, Callimorpha dominula (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {31},
pmid = {39233899},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Callimorpha dominula (the Scarlet Tiger moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 658.1 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 15.45 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,234 protein coding genes.},
}
@article {pmid39233902,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Green Silver-lines, Pseudoips prasinana (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {117},
pmid = {39233902},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Pseudoips prasinana (the Green Silver-lines; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 1,125.7 megabases in span. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,065 protein coding genes.},
}
@article {pmid39235751,
year = {2025},
author = {Lemée, P and Bridier, A},
title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2852},
number = {},
pages = {289-309},
pmid = {39235751},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; },
abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.},
}
@article {pmid39239169,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Elephant Hawk-moth, Deilephila elpenor (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {104},
pmid = {39239169},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Deilephila elpenor (the Elephant Hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 414.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,748 protein coding genes.},
}
@article {pmid39240386,
year = {2025},
author = {Han, S and Hogue, W},
title = {Assessing Human Influence and Vegetative Dune Dynamics on Barrier Islands via Satellite Raster Classification.},
journal = {Environmental management},
volume = {75},
number = {3},
pages = {524-537},
pmid = {39240386},
issn = {1432-1009},
mesh = {Alabama ; Humans ; *Conservation of Natural Resources ; *Ecosystem ; Mississippi ; Climate Change ; Islands ; Satellite Imagery ; *Environmental Monitoring/methods ; Geographic Information Systems ; },
abstract = {Barrier islands support ecological diversity and offshore ecosystems and provide critical protection to coastal communities. Climate change has intensified the frequency and severity of hurricanes affecting these islands, leading to ongoing erosion. The primary goal of this study was to explore the relationship between human intervention such as development and construction and the vegetative dune systems on Gulf Coast barrier islands in Alabama and Mississippi, USA. This research employed two decades of satellite images of three neighboring barrier islands and employed GIS raster classification to track changes in the vegetative dune system in terms of: (1) dune coverage (surface area of the vegetation), (2) vegetative maturity (vegetation type), and (3) stability (fluctuations in the vegetative coverage over time). Time series and trend analyses were used to compare the results for three neighboring islands. The findings show that Dauphin Island, which features both commercial facilities and vacation homes, exhibited a decrease in total area over time, and had the lowest percentage of vegetative dune coverage and highest level of vegetative fluctuation. In contrast, Petit Bois and Horn Islands, which remain untouched by human activity, displayed significantly higher levels of vegetative maturity and coverage and comparatively less fluctuation. This research provides a foundation for those advocating for dune restoration strategies, development limitations, and conservation regulations as nature-based infrastructure solutions to combat erosion on barrier islands and serves as a point of entry for future inquiries in the field of environmental management.},
}
@article {pmid39240878,
year = {2024},
author = {Shipley, ON and Dabrowski, AJ and Bowen, GJ and Hayden, B and Pauli, JN and Jordan, C and Anderson, L and Bailey, A and Bataille, CP and Cicero, C and Close, HG and Cook, C and Cook, JA and Desai, AR and Evaristo, J and Filley, TR and France, CAM and Jackson, AL and Kim, SL and Kopf, S and Loisel, J and Manlick, PJ and McFarlin, JM and McMeans, BC and O'Connell, TC and Pilaar Birch, SE and Putman, AL and Semmens, BX and Stantis, C and Stricker, CA and Szejner, P and Trammell, TLE and Uhen, MD and Weintraub-Leff, S and Wooller, MJ and Williams, JW and Yarnes, CT and Vander Zanden, HB and Newsome, SD},
title = {Design, development, and implementation of IsoBank: A centralized repository for isotopic data.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0295662},
pmid = {39240878},
issn = {1932-6203},
mesh = {*Databases, Factual ; *Metadata ; Isotopes ; Internet ; },
abstract = {Stable isotope data have made pivotal contributions to nearly every discipline of the physical and natural sciences. As the generation and application of stable isotope data continues to grow exponentially, so does the need for a unifying data repository to improve accessibility and promote collaborative engagement. This paper provides an overview of the design, development, and implementation of IsoBank (www.isobank.org), a community-driven initiative to create an open-access repository for stable isotope data implemented online in 2021. A central goal of IsoBank is to provide a web-accessible database supporting interdisciplinary stable isotope research and educational opportunities. To achieve this goal, we convened a multi-disciplinary group of over 40 analytical experts, stable isotope researchers, database managers, and web developers to collaboratively design the database. This paper outlines the main features of IsoBank and provides a focused description of the core metadata structure. We present plans for future database and tool development and engagement across the scientific community. These efforts will help facilitate interdisciplinary collaboration among the many users of stable isotopic data while also offering useful data resources and standardization of metadata reporting across eco-geoinformatics landscapes.},
}
@article {pmid39242656,
year = {2023},
author = {Hui, C and Pyšek, P and Richardson, DM},
title = {Disentangling the relationships among abundance, invasiveness and invasibility in trait space.},
journal = {npj biodiversity},
volume = {2},
number = {1},
pages = {13},
pmid = {39242656},
issn = {2731-4243},
support = {89967//National Research Foundation/ ; NE/V007548/1//Natural Environment Research Council/ ; DP200101680//Australian Research Council/ ; 101059592//HORIZON EUROPE European Research Council/ ; EXPRO 19-28807X//Czech Science Foundation/ ; RVO 67985939//Czech Academy of Sciences/ ; RVO 67985939//Czech Academy of Sciences/ ; CZ.02.2.69/0.0/0.0/18_053/0017850//Ministry of Education, Youth, and Sports of the Czech Republic/ ; },
abstract = {Identifying conditions and traits that allow an introduced species to grow and spread, from being initially rare to becoming abundant (defined as invasiveness), is the crux of invasion ecology. Invasiveness and abundance are related but not the same, and we need to differentiate these concepts. Predicting both species abundance and invasiveness and their relationship in an invaded community is highly contextual, being contingent on the community trait profile and its invasibility. We operationalised a three-pronged invasion framework that considers traits, environmental context, and propagule pressure. Specifically, we measure the invasiveness of an alien species by combining three components (performance reflecting environmental suitability, product of species richness and the covariance between interaction strength and species abundance, and community-level interaction pressure); the expected population growth rate of alien species simply reflects the total effect of propagule pressure and the product of their population size and invasiveness. The invasibility of a community reflects the size of opportunity niches (the integral of positive invasiveness in the trait space) under the given abiotic conditions of the environment. Both species abundance and the surface of invasiveness over the trait space can be dynamic and variable. Whether an introduced species with functional traits similar to those of an abundant species in the community exhibits high or low invasiveness depends largely on the kernel functions of performance and interaction strength with respect to traits and environmental conditions. Knowledge of the covariance between interaction strength and species abundance and these kernel functions, thus, holds the key to accurate prediction of invasion dynamics.},
}
@article {pmid39242702,
year = {2023},
author = {Santangeli, A and Haukka, A and Morris, W and Arkkila, S and Delhey, K and Kempenaers, B and Valcu, M and Dale, J and Lehikoinen, A and Mammola, S},
title = {What drives our aesthetic attraction to birds?.},
journal = {npj biodiversity},
volume = {2},
number = {1},
pages = {20},
pmid = {39242702},
issn = {2731-4243},
abstract = {In the Anthropocene, the era when the imprint of humans on nature is pervasive across the planet, it is of utmost importance to understand human relationships with other species. The aesthetics of nature, and of species, is one of the values that plays a role in shaping human-nature relationships. Birds are ubiquitous across the world. The beauty of birds exerts a powerful tug on human emotions, and bird-rich areas attract scores of eco-tourists. People naturally find some birds more beautiful or interesting than others, but we currently lack a global understanding of the specifics of what makes a species aesthetically attractive. Here, we used a global citizen-science database on bird attractiveness covering nearly all extant bird species, to show that there are specific visual features that drive our aesthetic appeal for some bird species over others. First, our aesthetic attraction is highest for smaller birds with specific, vivid colors (e.g., blue and red, and departing from brown-grey) and extreme ornaments (a long crest or tail). Second, our aesthetic attraction is highest for species with broad ranges, possibly because such species may be more familiar to us. The features that make us attracted to a particular bird strongly align with broad human visual aesthetic preferences in modern society. Unveiling the visual features underpinning our aesthetic attraction to birds is a critical step towards optimizing conservation (e.g., via conservation marketing) and education campaigns, and leverage the cultural ecosystem service potential of birds.},
}
@article {pmid39242865,
year = {2023},
author = {Karakulak, A and Tepe, B and Dimitrova, R and Abdelrahman, M and Akaliyski, P and Alaseel, R and Alkamali, YA and Amin, A and Lizarzaburu Aguinaga, DA and Andres, A and Aruta, JJBR and Assiotis, M and Avanesyan, H and Ayub, N and Bacikova-Sleskova, M and Baikanova, R and Bakkar, B and Bartoluci, S and Benitez, D and Bodnar, I and Bolatov, A and Borchet, J and Bosnar, K and Broche-Pérez, Y and Buzea, C and Cassibba, R and Carbonell, MM and Chen, BB and Dimitrovska, GR and Công Doanh, D and Dominguez Espinosa, ADC and Edine, WG and Ferenczi, N and Fernández-Morales, R and Gaete, J and Gan, Y and Giolo, S and Giordani, RCF and Friehs, MT and Gindi, S and Gjoneska, B and Godoy, JC and Del Pilar Grazioso, M and Hancheva, C and Hapunda, G and Hihara, S and Husain, MS and Islam, MS and Janovská, A and Javakhishvili, N and Jovanović, V and Kabir, RS and Abdul Kadir, NB and Karl, J and Katović, D and Kauyzbay, Z and Kawashima, TD and Kazmierczak, M and Khanna, R and Khosla, M and Klicperová-Baker, M and Kozina, A and Krauss, SE and Landabur, R and Lefringhausen, K and Lewandowska-Walter, A and Liang, YH and Makashvili, A and Malik, S and Manrique-Millones, D and Mastrotheodoros, S and McGrath, B and Mechili, EA and Mejía, M and Mhizha, S and Michalek-Kwiecien, J and Miconi, D and Mohsen, F and Moreta-Herrera, R and Muhl, C and Muradyan, M and Musso, P and Naterer, A and Nemat, A and Neto, F and Neto, J and Palacio, LMA and Okati-Aliabad, H and Orellana, CI and Orellana, LM and Mishra, SK and Park, J and Pavlova, I and Peralta, E and Petrytsa, P and Pišot, S and Prot, F and Rasia, J and Rivera, R and Riyanti, BPD and Samekin, A and Seisembekov, T and Serapinas, D and Silletti, F and Sharma, P and Shukla, S and Skrzypińska, K and Šolcová, IP and Solomontos-Kountouri, O and Stanciu, A and Stefenel, D and Steinmetz, LCL and Stogianni, M and Stuart, J and Sudarnoto, LF and Sugimura, K and Sultana, S and Suryani, AO and Tair, E and Tavitian-Elmadjan, L and Thome, LD and Uka, F and Valickienė, RP and Walter, B and Wendt, GW and Yang, PJ and Yıldırım, E and Yu, Y and Yunes, MAM and Zanoni da Silva, M and Rudnev, M},
title = {Trust in government moderates the association between fear of COVID-19 as well as empathic concern and preventive behaviour.},
journal = {Communications psychology},
volume = {1},
number = {1},
pages = {43},
pmid = {39242865},
issn = {2731-9121},
support = {INV-003092/GATES/Gates Foundation/United States ; },
abstract = {With the COVID-19 pandemic, behavioural scientists aimed to illuminate reasons why people comply with (or not) large-scale cooperative activities. Here we investigated the motives that underlie support for COVID-19 preventive behaviours in a sample of 12,758 individuals from 34 countries. We hypothesized that the associations of empathic prosocial concern and fear of disease with support towards preventive COVID-19 behaviours would be moderated by trust in the government. Results suggest that the association between fear of disease and support for COVID-19 preventive behaviours was strongest when trust in the government was weak (both at individual- and country-level). Conversely, the association with empathic prosocial concern was strongest when trust in the government was high, but this moderation was only found at individual-level scores of governmental trust. We discuss how motivations may be shaped by socio-cultural context, and outline how findings may contribute to a better understanding of collective action during global crises.},
}
@article {pmid39244927,
year = {2024},
author = {Ibrahim, AS and Kuuire, V and Kepe, T},
title = {On mapping urban community resilience: Land use vulnerability, coping and adaptive strategies in Ghana.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122426},
doi = {10.1016/j.jenvman.2024.122426},
pmid = {39244927},
issn = {1095-8630},
mesh = {Ghana ; *Floods ; Humans ; *Cities ; Climate Change ; Urban Population ; Geographic Information Systems ; },
abstract = {Cities across the globe are prioritizing resilience in the wake of increasing climate change-related disasters. About 44% of these disasters are floods and their manifestation in cities is more pronounced, threatening urban social, ecological, and economic systems. This study draws on community resilience and participatory GIS, to examine land use vulnerability to flooding and local coping and adaptive strategies to achieve resilience. Using Ghana as a case study, the results show that participatory mapping offers community resilience benefits by providing context to community resilience challenges and potentials, enabling a deeper understanding of socio-environmental coupling that contributes to flood vulnerability and builds on community adaptive strategies through harnessing local community knowledge. We identified that topography, poor drainage and road network, rainfall variability, residents' land use practices, and land use planning conundrum drive disparities in land use vulnerability to flooding. Participants underscored the necessity of critical urban infrastructure in facilitating community adaptability to floods. The findings indicate that socio-spatial inequities threaten urban community resilience, especially in increasingly cosmopolitan urban contexts, by putting the marginalized urban population in a more vulnerable position. We recommend the prioritization of recognitional equity in community resilience planning efforts to allow for the targeting of resilient interventions that reflect and respect social differentiation in the urban environment so that outcomes will not exacerbate or generate new urban socio-spatial inequalities.},
}
@article {pmid39250076,
year = {2024},
author = {Zancolli, G and von Reumont, BM and Anderluh, G and Caliskan, F and Chiusano, ML and Fröhlich, J and Hapeshi, E and Hempel, BF and Ikonomopoulou, MP and Jungo, F and Marchot, P and de Farias, TM and Modica, MV and Moran, Y and Nalbantsoy, A and Procházka, J and Tarallo, A and Tonello, F and Vitorino, R and Zammit, ML and Antunes, A},
title = {Web of venom: exploration of big data resources in animal toxin research.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {39250076},
issn = {2047-217X},
support = {//European Cooperation in Science and Technology/ ; //Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Animals ; *Venoms ; *Internet ; *Computational Biology/methods ; *Big Data ; Databases, Factual ; },
abstract = {Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.},
}
@article {pmid39253482,
year = {2024},
author = {Mortzfeld, BM and Bhattarai, SK and Bucci, V},
title = {Expanding the toolbox: Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.12.05.570296},
pmid = {39253482},
issn = {2692-8205},
abstract = {Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally-produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered twelve previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella . Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e. Acinetobacter baumannii or Pseudomonas aeruginosa , providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.},
}
@article {pmid39255143,
year = {2024},
author = {Jiang, W and Windl, M and Tag, B and Sarsenbayeva, Z and Mayer, S},
title = {An Immersive and Interactive VR Dataset to Elicit Emotions.},
journal = {IEEE transactions on visualization and computer graphics},
volume = {30},
number = {11},
pages = {7343-7353},
doi = {10.1109/TVCG.2024.3456202},
pmid = {39255143},
issn = {1941-0506},
mesh = {Humans ; *Emotions/physiology ; *Virtual Reality ; Female ; Male ; *Computer Graphics ; Adult ; Young Adult ; User-Computer Interface ; Databases, Factual ; Video Recording ; },
abstract = {Images and videos are widely used to elicit emotions; however, their visual appeal differs from real-world experiences. With virtual reality becoming more realistic, immersive, and interactive, we envision virtual environments to elicit emotions effectively, rapidly, and with high ecological validity. This work presents the first interactive virtual reality dataset to elicit emotions. We created five interactive virtual environments based on corresponding validated 360° videos and validated their effectiveness with 160 participants. Our results show that our virtual environments successfully elicit targeted emotions. Compared with the existing methods using images or videos, our dataset allows virtual reality researchers and practitioners to integrate their designs effectively with emotion elicitation settings in an immersive and interactive way.},
}
@article {pmid39255272,
year = {2024},
author = {Sylla, A and Chevillon, C and Djidjiou-Demasse, R and Seydi, O and Campos, CAV and Dogbe, M and Fast, KM and Pechal, JL and Rakestraw, A and Scott, ME and Sandel, MW and Jordan, H and Benbow, ME and Guégan, JF},
title = {Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012435},
pmid = {39255272},
issn = {1553-7358},
mesh = {Humans ; *Ecosystem ; Mycobacterium ulcerans/pathogenicity ; Buruli Ulcer/transmission/microbiology ; Models, Biological ; Computational Biology ; Animals ; },
abstract = {Pathogens such as bacteria, fungi and viruses are important components of soil and aquatic communities, where they can benefit from decaying and living organic matter, and may opportunistically infect human and animal hosts. One-third of human infectious diseases is constituted by sapronotic disease agents that are natural inhabitants of soil or aquatic ecosystems. They are capable of existing and reproducing in the environment outside of the host for extended periods of time. However, as ecological research on sapronosis is infrequent and epidemiological models are even rarer, very little information is currently available. Their importance is overlooked in medical and veterinary research, as well as the relationships between free environmental forms and those that are pathogenic. Here, using dynamical models in realistic aquatic metacommunity systems, we analyze sapronosis transmission, using the human pathogen Mycobacterium ulcerans that is responsible for Buruli ulcer. We show that the persistence of bacilli in aquatic ecosystems is driven by a seasonal upstream supply, and that the attachment and development of cells to aquatic living forms is essential for such pathogen persistence and population dynamics. Our work constitutes the first set of metacommunity models of sapronotic disease transmission, and is highly flexible for adaptation to other types of sapronosis. The importance of sapronotic agents on animal and human disease burden needs better understanding and new models of sapronosis disease ecology to guide the management and prevention of this important group of pathogens.},
}
@article {pmid39255632,
year = {2024},
author = {Amenu, K and Daborn, C and Huntington, B and Knight-Jones, T and Rushton, J and Grace, D},
title = {Prioritization, resource allocation and utilization of decision support tools in animal health: Results of qualitative interviews with experts.},
journal = {Preventive veterinary medicine},
volume = {233},
number = {},
pages = {106333},
doi = {10.1016/j.prevetmed.2024.106333},
pmid = {39255632},
issn = {1873-1716},
mesh = {Animals ; *Resource Allocation ; Decision Support Techniques ; Health Priorities ; Decision Making ; Animal Husbandry/methods ; Surveys and Questionnaires ; },
abstract = {A follow up to an online questionnaire survey (in a kind of a sequential study design), qualitative assessment was made on the views of selected animal health experts on disease prioritization methods, resource allocation and use of decision-support tools. This was done through in-depth interviews with experts working for national or international organizations and sectors. A semi-structured question guide was formulated based on the information generated in the online questionnaire and a systematic content analysis of animal and human health manuals for disease prioritization and resource allocation. In-depth, one-on-one, online interviews on the process of disease prioritization, animal health decision-making, types of prioritization tools and aspects of improvements in the tools were conducted during March and April 2022 with 20 expert informants. Prioritization approaches reported by experts were either single criterion-based or multiple criteria-based. Experts appreciated the single-criterion-based approach (quantitative) for its objectivity in contrast to multicriteria prioritization approaches which were criticized for their subjectivity. Interviews with the experts revealed a perceived lack of quality and reliable data to inform disease prioritization, especially in smallholder livestock production systems. It was found that outputs of disease prioritization exercises do not generally directly influence resource allocation in animal health and highlighted the paucity of funding for animal health compared to other agricultural sectors. The experts considered that the available decision-support tools in animal health need improvement in terms of data visualization for interpretation, management decision making and advocacy. Further recommendations include minimizing subjective biases by increasing the availability and quality of data and improving the translation of disease prioritization outputs into actions and the resources to deliver those actions. DATA AVAILABILITY STATEMENT: The data can be obtained from the corresponding author upon request.},
}
@article {pmid39257281,
year = {2024},
author = {Calabrese, JM and Schüler, L and Fu, X and Gawel, E and Zozmann, H and Bumberger, J and Quaas, M and Wolf, G and Attinger, S},
title = {A novel, scenario-based approach to comparing non-pharmaceutical intervention strategies across nations.},
journal = {Journal of the Royal Society, Interface},
volume = {21},
number = {218},
pages = {20240301},
pmid = {39257281},
issn = {1742-5662},
support = {//Helmholtz-Gemeinschaft/ ; //Bundesministerium f&#xfc;r Bildung und Forschung/ ; //S&#xe4;chsisches Staatsministerium f&#xfc;r Wissenschaft und Kunst/ ; },
mesh = {*COVID-19/epidemiology/prevention &amp; control ; Humans ; New Zealand/epidemiology ; Switzerland/epidemiology ; Germany/epidemiology ; *SARS-CoV-2 ; Pandemics/prevention &amp; control ; },
abstract = {Comparing COVID-19 response strategies across nations is a key step in preparing for future pandemics. Conventional comparisons, which rank individual non-pharmaceutical intervention (NPI) effects, are limited by: (i) a focus on epidemiological outcomes; (ii) NPIs typically being applied as packages of interventions; and (iii) different political, economic and social conditions among nations. Here, we develop a coupled epidemiological-behavioural-macroeconomic model that can transfer NPI effects from a reference nation to a focal nation. This approach quantifies epidemiological, behavioural and economic outcomes while accounting for both packaged NPIs and differing conditions among nations. As a first proof of concept, we take Germany as our focal nation during Spring 2020, and New Zealand and Switzerland as reference nations with contrasting NPI strategies. Our results suggest that, while New Zealand's more aggressive strategy would have yielded modest epidemiological gains in Germany, it would have resulted in substantially higher economic costs while dramatically reducing social contacts. In contrast, Switzerland's more lenient strategy would have prolonged the first wave in Germany, but would also have increased relative costs. More generally, these findings indicate that our approach can provide novel, multifaceted insights on the efficacy of pandemic response strategies, and therefore merits further exploration and development.},
}
@article {pmid39257623,
year = {2024},
author = {Boyes, D and Januszczak, I and Lees, DC and , and , and , and , and , and , and , },
title = {The genome sequence of the White-pinion Spotted, Lomographa bimaculata (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {96},
pmid = {39257623},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Lomographa bimaculata (the White-pinion Spotted; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 554.7 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 16.66 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,749 protein coding genes.},
}
@article {pmid39257624,
year = {2024},
author = {Lohse, K and Vila, R and Hayward, A and , and , and , and , and , },
title = {The genome sequence of the Lulworth Skipper, Thymelicus acteon (Rottemburg, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {266},
pmid = {39257624},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Thymelicus acteon (the Lulworth Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 537.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,813 protein-coding genes.},
}
@article {pmid39257810,
year = {2024},
author = {Hartley, GA and Okhovat, M and Hoyt, SJ and Fuller, E and Pauloski, N and Alexandre, N and Alexandrov, I and Drennan, R and Dubocanin, D and Gilbert, DM and Mao, Y and McCann, C and Neph, S and Ryabov, F and Sasaki, T and Storer, JM and Svendsen, D and Troy, W and Wells, J and Core, L and Stergachis, A and Carbone, L and O'Neill, RJ},
title = {Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39257810},
issn = {2692-8205},
support = {P51 OD011092/OD/NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R01 HG010333/HG/NHGRI NIH HHS/United States ; },
abstract = {Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assembled centromeres in the Eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence this epigenetic feature is conserved in the absence of satellite arrays; nevertheless, we report a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, large structural variations define HLE centromeres and distinguish them from other gibbons. Combined with differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, we propose that a "perfect storm" of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.},
}
@article {pmid39262445,
year = {2023},
author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, &#xc5;J and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA},
title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {926},
pmid = {39262445},
issn = {2046-1402},
support = {T32 GM139782/GM/NIGMS NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; },
abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.<br><br>METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.<br><br>RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.<br><br>CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.},
}
@article {pmid39262678,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Brindled Flat-body, Agonopterix arenella (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {214},
pmid = {39262678},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Agonopterix arenella (the Brindled Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 545.8 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.},
}
@article {pmid39263387,
year = {2024},
author = {Deeleman-Reinhold, CL and Addink, W and Miller, JA},
title = {The genera Chrysillaand Phintelloidesrevisited with the description of a new species (Araneae, Salticidae) using digital specimen DOIs and nanopublications.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e129438},
pmid = {39263387},
issn = {1314-2828},
abstract = {BACKGROUND: Two Southeast Asian spider collections: that of Frances and John Murphy, now in the Manchester University Museum and the Deeleman collection, now at the Naturalis Biodiversity Center in Leiden constituted the basis of this analysis of Chrysilla Thorell, 1887 and related genera. The latter collection also includes many thousands of spiders obtained by canopy fogging for an ecological project in Borneo by A. Floren.<br><br>NEW INFORMATION: Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C.jesudasi Caleb &amp; Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam &amp; Benjamin, 2019, based on analysis of molecular data is validated by morphology. An interesting new species known only from the forest canopy in Borneo, Phintelloidesscandens sp. nov, is described based on both male and female specimens. Distinguishing chrysilline genera is mostly based on traditional somatic characters, e.g., habitus, carapace and abdomen patterns, mouthparts, and genital organs. The utility of two character systems for distinguishing chrysilline genera is highlighted: 1) the presence of a flexible, articulating embolic tegular branch (etb) in combination with the conformation of the characteristic construction of the epigyne in Chrysilla and Phintelloides; 2) presence of red colour on carapace and abdomen of live males and females, in combination with abundant blue/violet/white iridescent scales such as inChrysilla and Siler. The red colour usually gets lost in alcohol, hampering species identification of alcohol material. The genera Chrysilla andPhintelloidesare redefined. Specimens of the heretofore unknown female of Chrysilla deelemani Pr&#xf3;szy&#x144;ski &amp; Deeleman-Reinhold, 2010 are described. The male and female ofChrysillalauta and male of C.volupe are redescribed. The genus Chrysilla is diagnosed and discriminated from PhintellaB&#xf6;senberg &amp; Strand, 1906, SilerSimon, 1889, Phintelloides Kanesharatnam &amp; Benjamin, 2019 andProszynskiaKanesharatnam &amp; Benjamin, 2019. The structure of the female genital organ of Phintelloidesflavumi Kanesharatnam &amp; Benjamin, 2019 is scrutinized and the generic placement of Phintelloides is discussed. Males and females of one of the most variable species, Phintelloidesversicolor (C. L. Koch, 1846) are redescribed.Phintelloidesmunita(B&#xf6;senberg &amp; Strand, 1906) is removed from synonymy with P.versicolor. Phintellaleucaspis Simon 1903 (male, Sumatra) is synonymized withP.versicolor.Biodiversity data are increasingly reliant on digital infrastructure. By linking physical specimens to digital representations of their associated data, we can lower barriers to information flow. Here we demonstrate a workflow whereby persistent identifiers (PIDs) in the form of DOIs issued by DataCite are assigned to specimens. Recognized taxa are identified by their catalog of life identifier, or by registration in ZooBank where no catalog of life identifier is available. We demonstrate the use of nanopublications, creating a series of machine readable, scientifically meaningful assertions regarding the provenance and identification of cited specimens. All human agents associated with the specimen data are linked to a persistent identifier issued by either ORCiD or Wikidata.},
}
@article {pmid39264239,
year = {2024},
author = {Silva, M and Capps, S and London, JK},
title = {Community-Engaged Research and the Use of Open Access ToxVal/ToxRef In Vivo Databases and New Approach Methodologies (NAM) to Address Human Health Risks From Environmental Contaminants.},
journal = {Birth defects research},
volume = {116},
number = {9},
pages = {e2395},
pmid = {39264239},
issn = {2472-1727},
support = {P30 ES023513/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; *Environmental Pollutants ; *Databases, Factual ; Risk Assessment/methods ; Environmental Exposure/adverse effects ; United States ; United States Environmental Protection Agency ; Pesticides/adverse effects/toxicity ; },
abstract = {BACKGROUND: The paper analyzes opportunities for integrating Open access resources (Abstract Sifter, US EPA and NTP Toxicity Value and Toxicity Reference [ToxVal/ToxRefDB]) and New Approach Methodologies (NAM) integration into Community Engaged Research (CEnR).<br><br>METHODS: CompTox Chemicals Dashboard and Integrated Chemical Environment with in vivo ToxVal/ToxRef and NAMs (in vitro) databases are presented in three case studies to show how these resources could be used in Pilot Projects involving Community Engaged Research (CEnR) from the University of California, Davis, Environmental Health Sciences Center.<br><br>RESULTS: Case #1 developed a novel assay methodology for testing pesticide toxicity. Case #2 involved detection of water contaminants from wildfire ash and Case #3 involved contaminants on Tribal Lands. Abstract Sifter/ToxVal/ToxRefDB regulatory data and NAMs could be used to screen/prioritize risks from exposure to metals, PAHs and PFAS from wildfire ash leached into water and to investigate activities of environmental toxins (e.g., pesticides) on Tribal lands. Open access NAMs and computational tools can apply to detection of sensitive biological activities in potential or known adverse outcome pathways to predict points of departure (POD) for comparison with regulatory values for hazard identification. Open access Systematic Empirical Evaluation of Models or biomonitoring exposures are available for human subpopulations and can be used to determine bioactivity (POD) to exposure ratio to facilitate mitigation.<br><br>CONCLUSIONS: These resources help prioritize chemical toxicity and facilitate regulatory decisions and health protective policies that can aid stakeholders in deciding on needed research. Insights into exposure risks can aid environmental justice and health equity advocates.},
}
@article {pmid39264914,
year = {2024},
author = {Zhang, K and Cao, Y and Guo, X and Kong, F and Sun, H and Jing, T and Zhan, Y and Qi, F},
title = {Comparative transcriptome analysis of differentially expressed genes and pathways in male and female flowers of Fraxinus mandshurica.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0308013},
pmid = {39264914},
issn = {1932-6203},
mesh = {*Flowers/genetics/metabolism/growth &amp; development ; *Gene Expression Regulation, Plant ; *Gene Expression Profiling ; *Fraxinus/genetics ; *Transcriptome ; Signal Transduction/genetics ; Plant Proteins/genetics/metabolism ; Gene Ontology ; Genes, Plant ; },
abstract = {Fraxinus mandshurica Rupr. (F. mandshurica) is a dioecious tree species with important ecological and application values. To delve deeper into the regulatory pathways and genes responsible for male and female flowers in F. mandshurica, we conducted transcriptome sequencing on male and female flowers at four distinct stages. The analysis revealed that the female database generated 38,319,967 reads while the male database generated 43,320,907 reads, resulting in 2930 differentially expressed genes with 1441 were up-regulated and 1489 down-regulated in males compared to females. Following an analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), four distinct pathways (hormone signal transduction, energy metabolism, flavonoid biosynthesis, and photoperiod) linked to female and male flowers were identified. Subsequently, qRT-PCR verification revealed that FmAUX/IAA, FmEIN3, and FmA-ARR genes in hormone signal transduction pathway are related to female flower development. Meanwhile, FmABF genes in hormone signal transduction pathway, FmGS and FmGDH genes in energy metabolism pathway, FmFLS genes in flavonoid biosynthesis pathway, and FmCaM, FmCRY, and FmPKA genes in photoperiod pathway are related to male flower development. This study was the first to analyze the transcriptome of male and female flowers of F. mandshurica, providing a reference for the developmental pathways and gene expression levels of male and female plants.},
}
@article {pmid39264951,
year = {2024},
author = {Pfennig, T and Kullmann, E and Zavřel, T and Nakielski, A and Ebenhöh, O and Červený, J and Bernát, G and Matuszyńska, AB},
title = {Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012445},
pmid = {39264951},
issn = {1553-7358},
mesh = {*Photosynthesis/physiology ; *Synechocystis/metabolism/physiology ; *Light ; *Models, Biological ; Computational Biology ; Carbon Dioxide/metabolism ; Carbon Cycle/physiology ; Phycobilisomes/metabolism ; Computer Simulation ; },
abstract = {Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2. By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions for ensemble of parameter sets and found no physiological benefit of a model assuming phycobilisome detachment. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. We suggest gene targets for overexpression under different illuminations to increase the yield. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.},
}
@article {pmid39266599,
year = {2024},
author = {He, H and Boehringer, T and Schäfer, B and Heppell, K and Beck, C},
title = {Analyzing spatio-temporal dynamics of dissolved oxygen for the River Thames using superstatistical methods and machine learning.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21288},
pmid = {39266599},
issn = {2045-2322},
support = {VH-NG-1727//Helmholtz Association and the Networking Fund/ ; },
abstract = {By employing superstatistical methods and machine learning, we analyze time series data of water quality indicators for the River Thames (UK). The indicators analyzed include dissolved oxygen, temperature, electrical conductivity, pH, ammonium, turbidity, and rainfall, with a specific focus on the dynamics of dissolved oxygen. After detrending, the probability density functions of dissolved oxygen fluctuations exhibit heavy tails that are effectively modeled using q-Gaussian distributions. Our findings indicate that the multiplicative Empirical Mode Decomposition method stands out as the most effective detrending technique, yielding the highest log-likelihood in nearly all fittings. We also observe that the optimally fitted width parameter of the q-Gaussian shows a negative correlation with the distance to the sea, highlighting the influence of geographical factors on water quality dynamics. In the context of same-time prediction of dissolved oxygen, regression analysis incorporating various water quality indicators and temporal features identify the Light Gradient Boosting Machine as the best model. SHapley Additive exPlanations reveal that temperature, pH, and time of year play crucial roles in the predictions. Furthermore, we use the Transformer, a state-of-the-art machine learning model, to forecast dissolved oxygen concentrations. For long-term forecasting, the Informer model consistently delivers superior performance, achieving the lowest Mean Absolute Error (0.15) and Symmetric Mean Absolute Percentage Error (21.96%) with the 192 historical time steps that we used. This performance is attributed to the Informer's ProbSparse self-attention mechanism, which allows it to capture long-range dependencies in time-series data more effectively than other machine learning models. It effectively recognizes the half-life cycle of dissolved oxygen, with particular attention to critical periods such as morning to early afternoon, late evening to early morning, and key intervals between the 16th and 26th quarter-hours of the previous half-day. Our findings provide valuable insights for policymakers involved in ecological health assessments, aiding in accurate predictions of river water quality and the maintenance of healthy aquatic ecosystems.},
}
@article {pmid39267994,
year = {2024},
author = {Boyes, D and Broad, GR and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Oak Nycteoline moth, Nycteola revayana (Scopoli, 1772).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {258},
pmid = {39267994},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Nycteola revayana (the Oak Nycteoline moth; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 621.0 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,235 protein-coding genes.},
}
@article {pmid39268176,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the White Satin, Leucoma salicis (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {323},
pmid = {39268176},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Leucoma salicis (the White Satin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 733.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,222 protein coding genes.},
}
@article {pmid39269992,
year = {2024},
author = {O'Meara, BC and Beaulieu, JM},
title = {Noise leads to the perceived increase in evolutionary rates over short time scales.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012458},
pmid = {39269992},
issn = {1553-7358},
mesh = {*Computational Biology/methods ; Models, Genetic ; Biological Evolution ; Evolution, Molecular ; Animals ; Models, Statistical ; Humans ; },
abstract = {Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time. We show that plotting a noisy numerator divided by time versus time leads to the observed hyperbolic pattern; in fact, randomizing the amount of change over time generates patterns functionally identical to observed patterns. Ignoring errors can not only obscure true patterns but create novel patterns that have long misled scientists.},
}
@article {pmid39269993,
year = {2024},
author = {Golumbeanu, M and Briët, O and Champagne, C and Lemant, J and Winkel, M and Zogo, B and Gerhards, M and Sinka, M and Chitnis, N and Penny, M and Pothin, E and Smith, T},
title = {AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1011609},
pmid = {39269993},
issn = {1553-7358},
mesh = {Animals ; Humans ; *Malaria/transmission/prevention &amp; control ; *Anopheles/physiology ; *Mosquito Vectors/physiology ; *Mosquito Control/methods ; *Software ; Computational Biology ; Models, Biological ; },
abstract = {In recent decades, field and semi-field studies of malaria transmission have gathered geographic-specific information about mosquito ecology, behaviour and their sensitivity to interventions. Mathematical models of malaria transmission can incorporate such data to infer the likely impact of vector control interventions and hence guide malaria control strategies in various geographies. To facilitate this process and make model predictions of intervention impact available for different geographical regions, we developed AnophelesModel. AnophelesModel is an online, open-access R package that quantifies the impact of vector control interventions depending on mosquito species and location-specific characteristics. In addition, it includes a previously published, comprehensive, curated database of field entomological data from over 50 Anopheles species, field data on mosquito and human behaviour, and estimates of vector control effectiveness. Using the input data, the package parameterizes a discrete-time, state transition model of the mosquito oviposition cycle and infers species-specific impacts of various interventions on vectorial capacity. In addition, it offers formatted outputs ready to use in downstream analyses and by other models of malaria transmission for accurate representation of the vector-specific components. Using AnophelesModel, we show how the key implications for intervention impact change for various vectors and locations. The package facilitates quantitative comparisons of likely intervention impacts in different geographical settings varying in vector compositions, and can thus guide towards more robust and efficient malaria control recommendations. The AnophelesModel R package is available under a GPL-3.0 license at https://github.com/SwissTPH/AnophelesModel.},
}
@article {pmid39271747,
year = {2024},
author = {Shin, S and Baker, AJ and Enk, J and McKenna, DD and Foquet, B and Vandergast, AG and Weissman, DB and Song, H},
title = {Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21377},
pmid = {39271747},
issn = {2045-2322},
support = {DEB-1937815//National Science Foundation/ ; IOS-1253493//National Science Foundation/ ; DEB-1064082//National Science Foundation/ ; Hatch Grant TEX0-2-6584//U.S. Department of Agriculture/ ; },
mesh = {Animals ; *Phylogeny ; *Orthoptera/genetics/classification ; Transcriptome/genetics ; Computational Biology/methods ; DNA Probes/genetics ; Evolution, Molecular ; },
abstract = {Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.},
}
@article {pmid39271937,
year = {2024},
author = {Hansen, AJ and Burns, P and Ervin, J and Goetz, SJ and Hansen, M and Venter, O and Watson, JEM and Jantz, PA and Virnig, ALS and Barnett, K and Pillay, R and Atkinson, S and Supples, C and Rodríguez-Buritica, S and Armenteras, D},
title = {Author Correction: A policy-driven framework for conserving the best of Earth's remaining moist tropical forests.},
journal = {Nature ecology &amp; evolution},
volume = {8},
number = {12},
pages = {2336},
doi = {10.1038/s41559-024-02557-8},
pmid = {39271937},
issn = {2397-334X},
}
@article {pmid39273245,
year = {2024},
author = {Damarov, IS and Korbolina, EE and Rykova, EY and Merkulova, TI},
title = {Multi-Omics Analysis Revealed the rSNPs Potentially Involved in T2DM Pathogenic Mechanism and Metformin Response.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273245},
issn = {1422-0067},
support = {23-15-00113//Russian Science Foundation/ ; },
mesh = {Humans ; *Metformin/pharmacology/therapeutic use ; *Diabetes Mellitus, Type 2/genetics/drug therapy/metabolism ; *Polymorphism, Single Nucleotide ; *Genome-Wide Association Study ; Hypoglycemic Agents/therapeutic use/pharmacology ; Quantitative Trait Loci ; Computational Biology/methods ; Leukocytes, Mononuclear/metabolism/drug effects ; Gene Expression Regulation/drug effects ; Promoter Regions, Genetic ; Multiomics ; },
abstract = {The goal of our study was to identify and assess the functionally significant SNPs with potentially important roles in the development of type 2 diabetes mellitus (T2DM) and/or their effect on individual response to antihyperglycemic medication with metformin. We applied a bioinformatics approach to identify the regulatory SNPs (rSNPs) associated with allele-asymmetric binding and expression events in our paired ChIP-seq and RNA-seq data for peripheral blood mononuclear cells (PBMCs) of nine healthy individuals. The rSNP outcomes were analyzed using public data from the GWAS (Genome-Wide Association Studies) and Genotype-Tissue Expression (GTEx). The differentially expressed genes (DEGs) between healthy and T2DM individuals (GSE221521), including metformin responders and non-responders (GSE153315), were searched for in GEO RNA-seq data. The DEGs harboring rSNPs were analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 14,796 rSNPs in the promoters of 5132 genes of human PBMCs. We found 4280 rSNPs to associate with both phenotypic traits (GWAS) and expression quantitative trait loci (eQTLs) from GTEx. Between T2DM patients and controls, 3810 rSNPs were detected in the promoters of 1284 DEGs. Based on the protein-protein interaction (PPI) network, we identified 31 upregulated hub genes, including the genes involved in inflammation, obesity, and insulin resistance. The top-ranked 10 enriched KEGG pathways for these hubs included insulin, AMPK, and FoxO signaling pathways. Between metformin responders and non-responders, 367 rSNPs were found in the promoters of 131 DEGs. Genes encoding transcription factors and transcription regulators were the most widely represented group and many were shown to be involved in the T2DM pathogenesis. We have formed a list of human rSNPs that add functional interpretation to the T2DM-association signals identified in GWAS. The results suggest candidate causal regulatory variants for T2DM, with strong enrichment in the pathways related to glucose metabolism, inflammation, and the effects of metformin.},
}
@article {pmid39273837,
year = {2024},
author = {Gatina, E and Zinicovscaia, I and Yushin, N and Chaligava, O and Frontasyeva, M and Sharipova, A},
title = {Assessment of the Atmospheric Deposition of Potentially Toxic Elements Using Moss Pleurozium schreberi in an Urban Area: The Perm (Perm Region, Russia) Case Study.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {17},
pages = {},
pmid = {39273837},
issn = {2223-7747},
abstract = {Assessment of air quality in urban areas is very important because pollutants affect both the environment and human health. In Perm (Russia), a moss biomonitoring method was used to assess the level of air pollution. The concentrations of 15 elements in 87 samples of moss Pleurozium schreberi in the city territory were determined using a direct mercury analyzer and an inductively coupled plasma atomic emission spectroscopy. Using factor and correlation analyses, the grouping of elements and their relationship with emission sources were established. The main sources of emissions of potentially toxic elements are the transportation (road and rail), metallurgical, and chemical industries. The level of atmospheric air pollution was assessed by calculating the environmental risk index, pollutant load index, and pollution coefficient. Based on the values of the pollution index, the level of atmospheric air pollution in Perm varies from unpolluted to highly polluted, with moderate environmental risk.},
}
@article {pmid39274728,
year = {2024},
author = {Sąsiadek-Andrzejczak, E and Maras, P and Kozicki, M},
title = {Flexible and Ecological Cotton-Based Dosimeter for 2D UV Surface Dose Distribution Measurements.},
journal = {Materials (Basel, Switzerland)},
volume = {17},
number = {17},
pages = {},
pmid = {39274728},
issn = {1996-1944},
abstract = {This work presents a 2D radiochromic dosimeter for ultraviolet (UV) radiation measurements, based on cotton fabric volume-modified with nitroblue tetrazolium chloride (NBT) as a radiation-sensitive compound. The developed dosimeter is flexible, which allows it to adapt to various shapes and show a color change from yellowish to purple-brown during irradiation. The intensity of the color change depends on the type of UV radiation and is the highest for UVC (253.7 nm). It has been shown that the developed dosimeters (i) can be used for UVC radiation dose measurements in the range of up to 10 J/cm[2]; (ii) can be measured in 2D using a flatbed scanner; and (iii) can have the obtained images after scanning be filtered with a medium filter to improve their quality by reducing noise from the fabric structure. The developed cotton-NBT dosimeters can measure UVC-absorbed radiation doses on objects of various shapes, and when combined with a dedicated computer software package and a data processing method, they form a comprehensive system for measuring dose distributions for objects with complex shapes. The developed system can also serve as a comprehensive method for assessing the quality and control of UV radiation sources used in various industrial processes.},
}
@article {pmid39275913,
year = {2024},
author = {Takada, K and Nakagawa, S and Kryukov, K and Ozawa, M and Watanabe, T},
title = {Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan.},
journal = {FEBS open bio},
volume = {14},
number = {12},
pages = {1972-1984},
pmid = {39275913},
issn = {2211-5463},
support = {//Crane Conservation by the City of Izumi/ ; //Tokyo Biochemical Research Foundation/ ; JPMJCR20H6//Core Research for Evolutional Science and Technology/ ; //2020 Tokai University School of Medicine Research Aid/ ; 22gm1610010h0001//Japan Agency for Medical Research and Development/ ; JP223fa627002h//Japan Agency for Medical Research and Development/ ; //Takeda Science Foundation/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16H06434//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 19H04843//Japan Society for the Promotion of Science/ ; 19fk0108171//Japan Society for the Promotion of Science/ ; 21J01036//Japan Society for the Promotion of Science/ ; 22K15469//Japan Society for the Promotion of Science/ ; JP19fk0108113//Japan Society for the Promotion of Science/ ; JP22H02521//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; Japan ; *Gastrointestinal Microbiome/genetics ; *Birds/microbiology/virology ; *Metagenomics/methods ; Feces/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; },
abstract = {Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.},
}
@article {pmid39277496,
year = {2025},
author = {van der Feltz-Cornelis, CM and Turk, F and Sweetman, J and Khunti, K and Gabbay, M and Shepherd, J and Montgomery, H and Strain, WD and Lip, GYH and Wootton, D and Watkins, CL and Cuthbertson, DJ and Williams, N and Banerjee, A},
title = {Corrigendum to "Prevalence of mental health conditions and brain fog in people with long COVID: A systematic review and meta-analysis" [General Hospital Psychiatry volume 88 (2024)10-22 10.1016/j.genhosppsych.2024.02.009].},
journal = {General hospital psychiatry},
volume = {92},
number = {},
pages = {112},
doi = {10.1016/j.genhosppsych.2024.09.006},
pmid = {39277496},
issn = {1873-7714},
}
@article {pmid39283104,
year = {2024},
author = {Tedim, AP and Almeida-Santos, AC and Lanza, VF and Novais, C and Coque, TM and Freitas, AR and Peixe, L and , },
title = {Bacteriocin distribution patterns in Enterococcus faecium and Enterococcus lactis: bioinformatic analysis using a tailored genomics framework.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {10},
pages = {e0137624},
pmid = {39283104},
issn = {1098-5336},
support = {EXPL/SAU-INF/0261/2021, UIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020, UI/BD/151317/2021//MCTES | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; },
mesh = {*Bacteriocins/genetics/metabolism ; *Enterococcus faecium/genetics/metabolism/drug effects ; *Genomics ; *Computational Biology ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Enterococcus/genetics/metabolism/drug effects ; },
abstract = {UNLABELLED: Multidrug-resistant Enterococcus faecium strains represent a major concern due to their ability to thrive in diverse environments and cause life-threatening infections. While antimicrobial resistance and virulence mechanisms have been extensively studied, the contribution of bacteriocins to E. faecium's adaptability remains poorly explored. E. faecium, within the Bacillota phylum, is a prominent bacteriocin producer. Here, we developed a tailored database of 76 Bacillota bacteriocins (217 sequences, including 40 novel bacteriocins) and applied it to uncover bacteriocin distribution patterns in 997 quality-filtered E. faecium and Enterococcus lactis (former E. faecium clade B) genomes. Curated using computational pipelines and literature mining, our database demonstrates superior precision versus leading public tools in identifying diverse bacteriocins. Distinct bacteriocin profiles emerged between E. faecium and E. lactis, highlighting species-specific adaptations. E. faecium strains from hospitalized patients were significantly enriched in bacteriocins as enterocin A and bacteriocins 43 (or T8), AS5, and AS11. These bacteriocin genes were strongly associated with antibiotic resistance, particularly vancomycin and ampicillin, and Inc18 rep2_pRE25-derivative plasmids, classically associated with vancomycin resistance transposons. Such bacteriocin arsenal likely enhances the adaptability and competitive fitness of E. faecium in the nosocomial environment. By combining a novel tailored database, whole-genome sequencing, and epidemiological data, our work elucidates meaningful connections between bacteriocin determinants, antimicrobial resistance, mobile genetic elements, and ecological origins in E. faecium and provides a framework for elucidating bacteriocin landscapes in other organisms. Characterizing species- and strain-level differences in bacteriocin profiles may reveal determinants of ecological adaptation, and translating these discoveries could further inform strategies to exploit bacteriocins against high-risk clones.<br><br>IMPORTANCE: This work significantly expands the knowledge on the understudied bacteriocin diversity in opportunistic enterococci, revealing their contribution in the adaptation to different environments. It underscores the importance of placing increased emphasis on genetic platforms carrying bacteriocins as well as on cryptic plasmids that often exclusively harbor bacteriocins since bacteriocin production can significantly contribute to plasmid maintenance, potentially facilitating their stable transmission across generations. Further characterization of strain-level bacteriocin landscapes could inform strategies to combat high-risk clones. Overall, these insights provide a framework for unraveling the therapeutic and biotechnological potential of bacteriocins.},
}
@article {pmid39283951,
year = {2024},
author = {Amaral, AS and Devos, DP},
title = {The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012459},
pmid = {39283951},
issn = {1553-7358},
mesh = {*Proteome/metabolism ; Databases, Protein ; Computational Biology ; Proteins/metabolism/chemistry ; Humans ; Proteomics/methods ; Bacteria/metabolism/genetics ; Animals ; },
abstract = {An often-overlooked aspect of biology is formed by the outliers of the protein length distribution, specifically those proteins with more than 5000 amino acids, which we refer to as huge proteins (HPs). By examining UniprotKB, we discovered more than 41 000 HPs throughout the tree of life, with the majority found in eukaryotes. Notably, the phyla with the highest propensity for HPs are Apicomplexa and Fornicata. Moreover, we observed that certain bacteria, such as Elusimicrobiota or Planctomycetota, have a higher tendency for encoding HPs, even more than the average eukaryote. To investigate if these macro-polypeptides represent "real" proteins, we explored several indirect metrics. Additionally, orthology analyses reveals thousands of clusters of homologous sequences of HPs, revealing functional groups related to key cellular processes such as cytoskeleton organization and functioning as chaperones or as E3-ubiquitin ligases in eukaryotes. In the case of bacteria, the major clusters have functions related to non-ribosomomal peptide synthesis/polyketide synthesis, followed by pathogen-host attachment or recognition surface proteins. Further exploration of the annotations for each HPs supported the previously identified functional groups. These findings underscore the need for further investigation of the cellular and ecological roles of these HPs and their potential impact on biology and biotechnology.},
}
@article {pmid39287032,
year = {2024},
author = {Meaume, S and Senet, P and Thomé, B and Aragno, VA and Serge, B and Fortin, S and Boucley, I and Michon-Pasturel, U and Colboc, H},
title = {Impact of primary dressings on healing of venous leg ulcers: a French cohort study from the healthcare insurance database.},
journal = {Journal of wound care},
volume = {33},
number = {9},
pages = {678-686},
doi = {10.12968/jowc.2024.0189},
pmid = {39287032},
issn = {0969-0700},
mesh = {Humans ; Female ; Male ; *Wound Healing ; France ; *Varicose Ulcer/therapy/economics ; Aged ; *Bandages/economics ; Middle Aged ; Cohort Studies ; Databases, Factual ; Aged, 80 and over ; Insurance, Health/statistics &amp; numerical data ; Treatment Outcome ; Health Care Costs/statistics &amp; numerical data ; },
abstract = {OBJECTIVE: Multicomponent bandages (MCBs) are recommended by the French Authority for Health (Haute Autorité de Santé) as first-line treatment for venous leg ulcers (VLUs). A first analysis of the data collected from the French administrative healthcare database (Système National des Données de Santé (SNDS)) on 25,255 patients with a VLU supported superiority of MCBs versus short stretch bandages when considering the healing outcomes and costs associated with closure of these wounds. The aim of this study was to assess how beneficial the primary dressing (technology lipido-colloid nano-oligosaccharide factor (TLC NOSF) or control dressing group (CDG)) could be, when used in combination with MCBs in the treatment of VLUs.<br><br>METHOD: Data from the SNDS were collected for patients meeting the following inclusion criteria: treatment for a VLU with MCBs and with the same dressing type (TLC-NOSF or CDG) during the whole treatment period. Healing outcomes were documented on the global cohorts and propensity score-matched cohorts. The mean healthcare cost and the ecological impact were calculated for those patients healed within the study period.<br><br>RESULTS: In total, 12,507 patients met the criteria for treatment with both MCBs and TLC-NOSF dressings (n=1134) versus MCBs and CDG (n=11,373); with 1134 and 2268 patients per group following propensity score matching. Healing outcomes were favourable for the TLC-NOSF group in the global cohort and were enhanced in the propensity score-matched cohorts. At every point of the analysis, the adjusted healing rates were significantly higher in the TLC-NOSF group than in the CDG group (p<0.001). In the propensity score-matched cohorts (n=3402), the healing rate at three months was 52% in the TLC-NOSF group versus 37% in the CDG group (p<0.001). The median healing time was 87 days versus 125.5 days in the TLC-NOSF and CDG groups, respectively (p<0.0001). TLC-NOSF dressings significantly reduced the average treatment cost per healed ulcer (&#x20ac;2099) by 23.7% compared with dressings without TLC-NOSF (&#x20ac;2751) (p<0.001), as well as the resources used.<br><br>CONCLUSION: This SNDS analysis confirms, in the largest real-life study performed in VLU management, the superiority of the TLC-NOSF dressings versus those not impregnated with the NOSF compound. Better clinical outcomes associated with cost savings and a positive ecological impact support the combination of MCBs and TLC-NOSF dressings and should be considered as an optimal standard of care for the global management of VLUs. These outcomes reinforce the current positions of the international guidelines on the use of NOSF impregnated dressings (UrgoStart range; Laboratoires Urgo, France) in this pathology.},
}
@article {pmid39287883,
year = {2024},
author = {Stolz, BJ and Dhesi, J and Bull, JA and Harrington, HA and Byrne, HM and Yoon, IHR},
title = {Relational Persistent Homology for Multispecies Data with Application to the Tumor Microenvironment.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {11},
pages = {128},
pmid = {39287883},
issn = {1522-9602},
support = {EP/R018472/1//EPSRC/ ; EP/R018472/1, EP/K041096/1, EP/R005125/1, EP/T001968/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; RGF EA 201074, UF150238//Royal Society/ ; CTRQQR-2021/100002/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {*Tumor Microenvironment/immunology ; Humans ; *Mathematical Concepts ; *Models, Biological ; *Neoplasms/pathology/immunology ; Computer Simulation ; Computational Biology ; Macrophages/immunology/pathology ; },
abstract = {Topological data analysis (TDA) is an active field of mathematics for quantifying shape in complex data. Standard methods in TDA such as persistent homology (PH) are typically focused on the analysis of data consisting of a single entity (e.g., cells or molecular species). However, state-of-the-art data collection techniques now generate exquisitely detailed multispecies data, prompting a need for methods that can examine and quantify the relations among them. Such heterogeneous data types arise in many contexts, ranging from biomedical imaging, geospatial analysis, to species ecology. Here, we propose two methods for encoding spatial relations among different data types that are based on Dowker complexes and Witness complexes. We apply the methods to synthetic multispecies data of a tumor microenvironment and analyze topological features that capture relations between different cell types, e.g., blood vessels, macrophages, tumor cells, and necrotic cells. We demonstrate that relational topological features can extract biological insight, including the dominant immune cell phenotype (an important predictor of patient prognosis) and the parameter regimes of a data-generating model. The methods provide a quantitative perspective on the relational analysis of multispecies spatial data, overcome the limits of traditional PH, and are readily computable.},
}
@article {pmid39289538,
year = {2024},
author = {Mc Cartney, AM and Formenti, G and Mouton, A and De Panis, D and Marins, LS and Leitão, HG and Diedericks, G and Kirangwa, J and Morselli, M and Salces-Ortiz, J and Escudero, N and Iannucci, A and Natali, C and Svardal, H and Fernández, R and De Pooter, T and Joris, G and Strazisar, M and Wood, JMD and Herron, KE and Seehausen, O and Watts, PC and Shaw, F and Davey, RP and Minotto, A and Fernández, JM and Böhne, A and Alegria, C and Alioto, T and Alves, PC and Amorim, IR and Aury, JM and Backstrom, N and Baldrian, P and Baltrunaite, L and Barta, E and BedHom, B and Belser, C and Bergsten, J and Bertrand, L and Bilandija, H and Binzer-Panchal, M and Bista, I and Blaxter, M and Borges, PAV and Dias, GB and Bosse, M and Brown, T and Bruggmann, R and Buena-Atienza, E and Burgin, J and Buzan, E and Cariani, A and Casadei, N and Chiara, M and Chozas, S and Čiampor, F and Crottini, A and Cruaud, C and Cruz, F and Dalen, L and De Biase, A and Del Campo, J and Delic, T and Dennis, AB and Derks, MFL and Diroma, MA and Djan, M and Duprat, S and Eleftheriadi, K and Feulner, PGD and Flot, JF and Forni, G and Fosso, B and Fournier, P and Fournier-Chambrillon, C and Gabaldon, T and Garg, S and Gissi, C and Giupponi, L and Gomez-Garrido, J and González, J and Grilo, ML and Grüning, B and Guerin, T and Guiglielmoni, N and Gut, M and Haesler, MP and Hahn, C and Halpern, B and Harrison, PW and Heintz, J and Hindrikson, M and Höglund, J and Howe, K and Hughes, GM and Istace, B and Cock, MJ and Janžekovič, F and Jonsson, ZO and Joye-Dind, S and Koskimäki, JJ and Krystufek, B and Kubacka, J and Kuhl, H and Kusza, S and Labadie, K and Lähteenaro, M and Lantz, H and Lavrinienko, A and Leclère, L and Lopes, RJ and Madsen, O and Magdelenat, G and Magoga, G and Manousaki, T and Mappes, T and Marques, JP and Redondo, GIM and Maumus, F and McCarthy, SA and Megens, HJ and Melo-Ferreira, J and Mendes, SL and Montagna, M and Moreno, J and Mosbech, MB and Moura, M and Musilova, Z and Myers, E and Nash, WJ and Nater, A and Nicholson, P and Niell, M and Nijland, R and Noel, B and Noren, K and Oliveira, PH and Olsen, RA and Ometto, L and Oomen, RA and Ossowski, S and Palinauskas, V and Palsson, S and Panibe, JP and Pauperio, J and Pavlek, M and Payen, E and Pawlowska, J and Pellicer, J and Pesole, G and Pimenta, J and Pippel, M and Pirttilä, AM and Poulakakis, N and Rajan, J and M C Rego, R and Resendes, R and Resl, P and Riesgo, A and Rodin-Morch, P and Soares, AER and Fernandes, CR and Romeiras, MM and Roxo, G and Rüber, L and Ruiz-Lopez, MJ and Saarma, U and da Silva, LP and Sim-Sim, M and Soler, L and Sousa, VC and Santos, CS and Spada, A and Stefanovic, M and Steger, V and Stiller, J and Stöck, M and Struck, TH and Sudasinghe, H and Tapanainen, R and Tellgren-Roth, C and Trindade, H and Tukalenko, Y and Urso, I and Vacherie, B and Van Belleghem, SM and Van Oers, K and Vargas-Chavez, C and Velickovic, N and Vella, N and Vella, A and Vernesi, C and Vicente, S and Villa, S and Pettersson, OV and Volckaert, FAM and Voros, J and Wincker, P and Winkler, S and Ciofi, C and Waterhouse, RM and Mazzoni, CJ},
title = {The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.},
journal = {npj biodiversity},
volume = {3},
number = {1},
pages = {28},
pmid = {39289538},
issn = {2731-4243},
support = {/WT_/Wellcome Trust/United Kingdom ; P 32691/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.},
}
@article {pmid39290036,
year = {2024},
author = {Monreal-Di Bello, M and González-Bermejo, D and Castillo-Cano, B and Rodriguez-Pascual, A and Montero-Corominas, D},
title = {Impact of Regulatory Interventions on Ulipristal Acetate 5 mg (Esmya) Use in Spain: An Interrupted Time-Series Analysis.},
journal = {Pharmacoepidemiology and drug safety},
volume = {33},
number = {9},
pages = {e70004},
doi = {10.1002/pds.70004},
pmid = {39290036},
issn = {1099-1557},
support = {//Spanish Agency on Medicines and Medical Devices (AEMPS)/ ; },
mesh = {Humans ; Spain/epidemiology ; *Norpregnadienes/administration &amp; dosage/adverse effects/therapeutic use ; *Interrupted Time Series Analysis ; Female ; Databases, Factual ; Electronic Health Records/statistics &amp; numerical data ; Risk Evaluation and Mitigation ; Male ; Adult ; Middle Aged ; },
abstract = {PURPOSE: Since late 2017, the use of ulipristal acetate 5 mg (UPA; Proprietary name: Esmya) has been under review in the European Union, due to an emerging hepatic risk. In February 2018 and in July 2018, the Spanish Agency of Medicines and Medical Devices and the marketing authorization holder put two risk minimization measures (RMM) in place, in order to inform about new safety information and to mitigate this risk. This study aims to assess RMM effectiveness in Spain, by performing an interrupted time-series (ITS) analyses, between 2014 and 2019.<br><br>METHOD: Two quasi-experimental ITS analyses to examine the use of UPA before and after the RMM release were performed: (a) an ecological study using aggregated data from a drug consumption database; and (b) a study using primary healthcare data gathered from electronic clinical records.<br><br>RESULTS: Regulatory interventions were associated with an immediate and significant decrease level of DID (the number of DDD dispensed per 100&#x2009;000 inhabitants and day) and incidence. The DID was 70% less than expected 12&#x2009;months after the interventions. This value was 59% for the incidence. However, a change in the slope was not observed and the use started rising again in the last segment of the study period.<br><br>CONCLUSION: Despite RMM had an immediate strong impact on UPA use, the last segment upward trend in the long-term might have been affected by the lack of comparable therapeutic alternatives. Further studies should be performed to confirm the increase trend observed and analyze subsequent measures and additional data.},
}
@article {pmid39290364,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Red Chestnut moth, Cerastis rubricosa (Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {88},
pmid = {39290364},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Cerastis rubricosa (the Red Chestnut moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 678.7 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 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,784 protein coding genes.},
}
@article {pmid39290433,
year = {2024},
author = {Castrillo, M and Aguilar, F and García-Díaz, D},
title = {Dataset on sub-daily vertical profiles of physicochemical parameters and chlorophyll concentration in El Val reservoir, together with its daily meteorological data, storage state and downstream flow (2018-2022).},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110839},
pmid = {39290433},
issn = {2352-3409},
abstract = {The dataset addressed in this article contains parameters about El Val reservoir (province of Zaragoza, Spain). It includes physicochemical variables, the water level, the stored water volume, its meteorological conditions and the flow rate of its effluent, the Queiles River, a few metres downstream of the dam. The El Val reservoir stores water from the Val River, but it also receives water from the Queiles River through a pipeline and from several ravines. The dam releases on the Queiles River, which is a tributary of the Ebro River (the second one in Spain in length and discharge rate). A multiparametric probe (aquaDam, Adasa Systems), hanging from a structure located in the dam, every 6 h makes a vertical profile taking the measurements at each metre of depth from the surface to approximately 573 m above sea level (m.a.s.l.), in other words, between 2 and 3 m above the bottom outlet. This probe collects data of water temperature, pH, ORP, conductivity, dissolved oxygen, turbidity and chlorophyll concentration. Meteorological data are collected in the nearest weather station, located in the municipality of Los Fayos which is about 500 m downstream of the dam. These include daily accumulated precipitation, daily maximum and average solar irradiance, daily maximum, minimum and average air temperature and daily average wind speed. The water level and volume of stored water and the flow rate of the Queiles River are collected in the El Val monitoring station and the Queiles River gauge station respectively, and are also provided on a daily basis. These data are useful to feed deterministic, data driven or hybrid hydrological models with different purposes, like the identification of the impact of meteorological conditions on the physicochemical properties of the reservoir as well as the assessment of different management strategies in the reservoir. This is a data article that additionally supports the work published in Ecological Informatics [1] where the use of common and readily available open data is promoted through its use to feed data driven models, in particular to infer the depth of the thermocline in reservoirs that are periodically or permanently thermally stratified. In that article a dataset derived from the one presented in this article is used.},
}
@article {pmid39290666,
year = {2024},
author = {Guclu, C and Luk, CL and Ashton, LA and Abbas, S and Boyle, MJW},
title = {Beta diversity subcomponents of plant species turnover and nestedness reveal drivers of community assembly in a regenerating subtropical forest.},
journal = {Ecology and evolution},
volume = {14},
number = {9},
pages = {e70233},
pmid = {39290666},
issn = {2045-7758},
abstract = {Secondary forests represent a significant proportion of global forest cover, with over 70% of forests in East Asia classified as regenerating. While succession has been studied extensively in temperate systems, trajectories of subtropical succession remain poorly characterized in highly disturbed, urban-adjacent forests. Investigating the additive beta diversity components of turnover and nestedness may reveal community assembly mechanisms driving secondary succession. The present study investigates plant community assembly along a successional gradient from 7 to 70 years following the onset of succession in secondary subtropical forests in Hong Kong, China. Plant survey data for 28 plots were analysed, generating additive Simpsons turnover and nestedness beta diversity metrics. Dissimilarity matrices were generated and modelled as a function of environmental matrices including forest plant community age (years following onset of secondary succession), inter-community distance (metres), and soil moisture saturation (%) across three elevational bands using generalized dissimilarity models. Nonmetric multidimensional scaling of plant communities was conducted with Bray-Curtis dissimilarity matrices. Inter-community distance and successional age differentially influenced plant species turnover between lowland and Montane forest types. Models of nestedness found that plot age and soil moisture saturation were significant drivers of nestedness patterns in plant communities across elevational classes. Turnover represented a higher proportion of Sorensen beta diversity than nestedness, while ANOSIM found significant differentiation between plant communities at different successional stages. Turnover patterns suggest a deterministic model of community assembly, with strong patterns of species replacement between communities at fine spatial scales and successional stages, as well as clear compositional shifts between lowland and montane forest types. NMDS analysis and functional compositional assessments suggested a transition from early successional communities with a high proportion of shrub species, to later successional communities with a higher proportion of tree species, with an increase in species turnover with greater age dissimilarity.},
}
@article {pmid39292040,
year = {2024},
author = {Vasconcelos, NM and Bernal, RTI and Souza, JB and Bordoni, PHC and Stein, C and Coll, CVN and Murray, J and Malta, DC},
title = {Underreporting of violence against women: an analysis of two data sources.},
journal = {Ciencia &amp; saude coletiva},
volume = {29},
number = {10},
pages = {e07732023},
doi = {10.1590/1413-812320242910.07732023},
pmid = {39292040},
issn = {1678-4561},
mesh = {Humans ; Brazil/epidemiology ; Female ; Adult ; Young Adult ; Adolescent ; *Sex Offenses/statistics &amp; numerical data ; Middle Aged ; Health Surveys ; Gender-Based Violence/statistics &amp; numerical data ; Information Systems/statistics &amp; numerical data ; Information Sources ; },
abstract = {This article aims to estimate the underreporting of violence against women (VAW) in the Notifiable Diseases Information System (SINAN), based on data from the National Survey of Health (NSH), in Brazil and subnational units (SU). This work was an ecological study using SINAN and NSH, both from 2019. In SINAN, reports of sexual, physical, and psychological VAW, aged 18 years or older, were selected. In the NSH, women of the same age group who reported psychological, physical, or sexual violence, and who had sought health care due to consequences of the violence were selected. SINAN underreporting was calculated in reference to the NSH's estimated population, for Brazil and each SU. Underreporting of VAW in Brazil was 98.5%, 75.9%, and 89.4% for psychological, physical, and sexual violence, respectively. The North and Northeast states presented the lowest reporting rates among the states. VAW in Brazil is highly underreported by the health sector, showing the need for adequate training of health professionals to recognize situations of violence and raise awareness of the importance of reporting.},
}
@article {pmid39292164,
year = {2024},
author = {Sakai, K and Nagata, T and Mori, T and Inoue, S and Fujiwara, H and Odagami, K and Adi, NP and Tatemichi, M and Mori, K},
title = {Research topics in occupational medicine, 1990-2022: A text-mining-applied bibliometric study.},
journal = {Scandinavian journal of work, environment &amp; health},
volume = {50},
number = {7},
pages = {567-576},
pmid = {39292164},
issn = {1795-990X},
support = {240801-01//Industrial Disease Clinical Research Grants from the Ministry of Health, Labor and Welfare/ ; },
mesh = {*Bibliometrics ; *Data Mining ; Humans ; *Occupational Medicine ; Occupational Health ; },
abstract = {OBJECTIVE: Occupational health has been influenced by societal and industrial changes. This study aimed to clarify topic trends in occupational health research in 1990-2022.<br><br>METHODS: We conducted a text-mining-adjusted bibliometric study using research titles in occupational health. Data on research titles and the years of publication were collected from 26 peer-reviewed journals on PubMed. Using morphological and correspondence analyses in text mining, we structured research topics into multiple categories and visualized the relationship between all categories and publication years. Statistical analyses were conducted using the text mining software - KH Coder 3.0.<br><br>RESULTS: We obtained 48 645 articles containing 714 890 words in their titles. The research topics were classified into 4 categories and 17 subcategories, of which those of occupations; countries; non-intervention; psychosocial factors; lifestyle factors; safety; symptoms; therapy and care; and productivity have recently shown an increasing trend. In contrast, the subcategories of risk, chemical factors, disease, and organ damage showed decreasing trends. Chemical factors, which were the main topics in the 1990s, included risk, organ damage, and disease. Productivity, the main topic in the 2020s, co-occurred with lifestyle factors, symptoms, and intervention.<br><br>CONCLUSIONS: Focal areas in occupational-health research shift according to societal trends. Occupational-health research has primarily analyzed issues in developed countries with capitalist values and may not have sufficiently covered issues in developing countries. It is imperative for policymakers and public funding bodies to determine priorities for investigation in the field.},
}
@article {pmid39292721,
year = {2024},
author = {Bastien, GE and Cable, RN and Batterbee, C and Wing, AJ and Zaman, L and Duhaime, MB},
title = {Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1011649},
pmid = {39292721},
issn = {1553-7358},
mesh = {*Machine Learning ; Humans ; *Viruses/genetics ; *Computational Biology/methods ; *Host-Pathogen Interactions/genetics/physiology ; Host Microbial Interactions/genetics/physiology ; },
abstract = {Viruses of microbes are ubiquitous biological entities that reprogram their hosts' metabolisms during infection in order to produce viral progeny, impacting the ecology and evolution of microbiomes with broad implications for human and environmental health. Advances in genome sequencing have led to the discovery of millions of novel viruses and an appreciation for the great diversity of viruses on Earth. Yet, with knowledge of only "who is there?" we fall short in our ability to infer the impacts of viruses on microbes at population, community, and ecosystem-scales. To do this, we need a more explicit understanding "who do they infect?" Here, we developed a novel machine learning model (ML), Virus-Host Interaction Predictor (VHIP), to predict virus-host interactions (infection/non-infection) from input virus and host genomes. This ML model was trained and tested on a high-value manually curated set of 8849 virus-host pairs and their corresponding sequence data. The resulting dataset, 'Virus Host Range network' (VHRnet), is core to VHIP functionality. Each data point that underlies the VHIP training and testing represents a lab-tested virus-host pair in VHRnet, from which meaningful signals of viral adaptation to host were computed from genomic sequences. VHIP departs from existing virus-host prediction models in its ability to predict multiple interactions rather than predicting a single most likely host or host clade. As a result, VHIP is able to infer the complexity of virus-host networks in natural systems. VHIP has an 87.8% accuracy rate at predicting interactions between virus-host pairs at the species level and can be applied to novel viral and host population genomes reconstructed from metagenomic datasets.},
}
@article {pmid39294488,
year = {2024},
author = {Zhang, WH and Gao, JW and Lau, CC and Jiang, ZF and Yeong, YS and Mok, WJ and Zhou, W},
title = {Effects of different trophic conditions on total fatty acids, amino acids, pigment and gene expression profiles in Euglena gracilis.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {10},
pages = {325},
pmid = {39294488},
issn = {1573-0972},
support = {22zxbtsn00020//Tianjin Municipal Science and Technology Bureau/ ; },
mesh = {*Euglena gracilis/genetics/growth &amp; development/metabolism/ultrastructure ; *Gene Expression Profiling ; *Amino Acids/metabolism ; *Fatty Acids/metabolism ; *Pigments, Biological/metabolism ; Biomass ; Gene Ontology ; Gene Expression Regulation, Developmental ; Heterotrophic Processes ; },
abstract = {Euglena gracilis is a unique microalga that lacks a cell wall and is able to grow under different trophic culture conditions. In this study, cell growth, biomass production, and changes in the ultrastructure of E. gracilis cells cultivated photoautotrophically, mixotrophically, and under sequential-heterotrophy-photoinduction (SHP) were assessed. Mixotrophy induced the highest cell growth and biomass productivity (6.27 ± 0.59 mg/L/d) in E. gracilis, while the highest content of fatty acids, 2.69 ± 0.04% of dry cell weight (DCW) and amino acids, 38.16 ± 0.08% of DCW was obtained under SHP condition. E. gracilis also accumulated significantly higher saturated fatty acids and lower unsaturated fatty acids when cultivated under SHP condition. Transcriptomic analysis showed that the expression of photosynthetic genes (PsbA, PsbC, F-type ATPase alpha and beta) was lower, carbohydrate and protein synthetic genes (glnA, alg14 and fba) were expressed higher in SHP-culture cells when compared to other groups. Different trophic conditions also induced changes in the cell ultrastructure, where paramylon and starch granules were more abundant in SHP-cultured cells. The findings generated in this study illustrated that aerobic SHP cultivation of E. gracilis possesses great potential in human and animal feed applications.},
}
@article {pmid39294496,
year = {2024},
author = {Khaliq, AM and Rajamohan, M and Saeed, O and Mansouri, K and Adil, A and Zhang, C and Turk, A and Carstens, JL and House, M and Hayat, S and Nagaraju, GP and Pappas, SG and Wang, YA and Zyromski, NJ and Opyrchal, M and Lee, KP and O'Hagan, H and El Rayes, B and Masood, A},
title = {Spatial transcriptomic analysis of primary and metastatic pancreatic cancers highlights tumor microenvironmental heterogeneity.},
journal = {Nature genetics},
volume = {56},
number = {11},
pages = {2455-2465},
pmid = {39294496},
issn = {1546-1718},
mesh = {Humans ; *Tumor Microenvironment/genetics ; *Pancreatic Neoplasms/genetics/pathology ; *Carcinoma, Pancreatic Ductal/genetics/pathology ; *Transcriptome ; *Neoplasm Metastasis/genetics ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling/methods ; Female ; },
abstract = {Although the spatial, cellular and molecular landscapes of resected pancreatic ductal adenocarcinoma (PDAC) are well documented, the characteristics of its metastatic ecology remain elusive. By applying spatially resolved transcriptomics to matched primary and metastatic PDAC samples, we discovered a conserved continuum of fibrotic, metabolic and immunosuppressive spatial ecotypes across anatomical regions. We observed spatial tumor microenvironment heterogeneity spanning beyond that previously appreciated in PDAC. Through comparative analysis, we show that the spatial ecotypes exhibit distinct enrichment between primary and metastatic sites, implying adaptability to the local environment for survival and progression. The invasive border ecotype exhibits both pro-tumorigenic and anti-tumorigenic cell-type enrichment, suggesting a potential immunotherapy target. The ecotype heterogeneity across patients emphasizes the need to map individual patient landscapes to develop personalized treatment strategies. Collectively, our findings provide critical insights into metastatic PDAC biology and serve as a valuable resource for future therapeutic exploration and molecular investigations.},
}
@article {pmid39295890,
year = {2023},
author = {Boyes, D and Januszczak, I and , and , and , and , and , and , },
title = {The genome sequence of the Lunar-spotted Pinion, Cosmia pyralina (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {545},
pmid = {39295890},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Cosmia pyralina (the Lunar-spotted Pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 803.3 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 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,901 protein coding genes.},
}
@article {pmid39297890,
year = {2025},
author = {Daich Varela, M and Sanders Villa, A and Pontikos, N and Crossland, MD and Michaelides, M},
title = {Digital health and wearable devices for retinal disease monitoring.},
journal = {Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie},
volume = {263},
number = {2},
pages = {279-289},
pmid = {39297890},
issn = {1435-702X},
support = {/WT_/Wellcome Trust/United Kingdom ; 206619/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Wearable Electronic Devices ; *Retinal Diseases/diagnosis/physiopathology ; *Telemedicine/instrumentation ; Artificial Intelligence ; Monitoring, Physiologic/instrumentation ; Digital Health ; },
abstract = {Digital health is wielding a growing influence across all areas of healthcare, encompassing various facets such as telemedicine, artificial intelligence (AI), and electronic healthcare records. In Ophthalmology, digital health innovations can be broadly divided into four categories: (i) self-monitoring home devices and apps, (ii) virtual and augmented reality visual aids, (iii) AI software, and (iv) wearables. Wearable devices can work in the background, collecting large amounts of objective data while we do our day-to-day activities, which may be ecologically more valid and meaningful to patients than that acquired in traditional hospital settings. They can be a watch, wristband, piece of clothing, glasses, cane, smartphone in our pocket, earphones, or any other device with a sensor that we carry with us. Focusing on retinal diseases, a key challenge in developing novel therapeutics has been to prove a meaningful benefit in patients' lives and the creation of objective patient-centred endpoints in clinical trials. In this review, we will discuss wearable devices collecting different aspects of visual behaviour, visual field, central vision, and functional vision, as well as their potential implementation as outcome measures in research/clinical trial settings. The healthcare landscape is facing a paradigm shift. Clinicians have a key role of collaborating with the development and fine-tuning of digital health innovations, as well as identifying opportunities where they can be leveraged to enhance our understanding of retinal diseases and improve patient outcomes.},
}
@article {pmid39301440,
year = {2024},
author = {Morales, HE and Groombridge, JJ and Tollington, S and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Gilbert, MTP and , and , and , and , },
title = {The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton &amp; E. Newton, 1876).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {378},
pmid = {39301440},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Alexandrinus eques, formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.},
}
@article {pmid39303692,
year = {2024},
author = {Crits-Christoph, A and Levy, JI and Pekar, JE and Goldstein, SA and Singh, R and Hensel, Z and Gangavarapu, K and Rogers, MB and Moshiri, N and Garry, RF and Holmes, EC and Koopmans, MPG and Lemey, P and Peacock, TP and Popescu, S and Rambaut, A and Robertson, DL and Suchard, MA and Wertheim, JO and Rasmussen, AL and Andersen, KG and Worobey, M and Débarre, F},
title = {Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.},
journal = {Cell},
volume = {187},
number = {19},
pages = {5468-5482.e11},
pmid = {39303692},
issn = {1097-4172},
support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 AI151812/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *COVID-19/epidemiology/virology ; *SARS-CoV-2/genetics/isolation &amp; purification ; *Animals, Wild/virology ; *Phylogeny ; Humans ; Pandemics ; },
abstract = {Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.},
}
@article {pmid39304543,
year = {2024},
author = {Hossen, MF and Sultana, N},
title = {Landscape transition-induced ecological risk modeling using GIS and remote sensing techniques: a case of Saint Martin Island, Bangladesh.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {10},
pages = {964},
pmid = {39304543},
issn = {1573-2959},
mesh = {Bangladesh ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; *Geographic Information Systems ; *Conservation of Natural Resources ; *Islands ; *Ecosystem ; Risk Assessment/methods ; Humans ; Bayes Theorem ; },
abstract = {Uncontrolled human activity and nature are causing the deterioration of Saint Martin Island, Bangladesh's only tropical island, necessitating sustainable land use strategies and ecological practices. Therefore, the present study measures the land use/cover transition from 1974 to 2021, predicts 2032 and 2042, and constructs the spatiotemporal features of the Landscape Ecological Risk Index based on land use changes. The study utilized Maximum Likelihood Classification (MLC) on Landsat images from 1974, 1988, 2001, 2013, and Sentinel 2B in 2021, achieving ≥ 80% accuracy. The MLP-MC approach was also used to predict 2032 and 2042 LULC change patterns. The eco-risk index was developed using landscape disturbance and vulnerability indices, Bayesian Kriging interpolation, and spatial autocorrelations to indicate spatial clustering. The research found that settlements increased from 2.06 to 28.62 ha between 1974 and 2021 and would cover 41.22 ha in 2042, causing considerable losses in agricultural areas, waterbodies, sand, coral reefs, and vegetation. The area under study showed a more uniform and homogenous environment as Shannon's diversity and evenness scores decreased. The ecological risk of Saint Martin Island increased from 4.31 to 31.05 ha between 1974 and 2042 due to natural and human factors like erosion, tidal bores, population growth, coral mining, habitat destruction, and intensive agricultural practices and tourism, primarily in Nazrul Para, Galachipa, and Western Dakhin Para. The findings will benefit St. Martin Island stakeholders and policymakers by providing insights into current and potential landscape changes and land eco-management.},
}
@article {pmid39304763,
year = {2025},
author = {Pakkir Shah, AK and Walter, A and Ottosson, F and Russo, F and Navarro-Diaz, M and Boldt, J and Kalinski, JJ and Kontou, EE and Elofson, J and Polyzois, A and González-Marín, C and Farrell, S and Aggerbeck, MR and Pruksatrakul, T and Chan, N and Wang, Y and Pöchhacker, M and Brungs, C and Cámara, B and Caraballo-Rodríguez, AM and Cumsille, A and de Oliveira, F and Dührkop, K and El Abiead, Y and Geibel, C and Graves, LG and Hansen, M and Heuckeroth, S and Knoblauch, S and Kostenko, A and Kuijpers, MCM and Mildau, K and Papadopoulos Lambidis, S and Portal Gomes, PW and Schramm, T and Steuer-Lodd, K and Stincone, P and Tayyab, S and Vitale, GA and Wagner, BC and Xing, S and Yazzie, MT and Zuffa, S and de Kruijff, M and Beemelmanns, C and Link, H and Mayer, C and van der Hooft, JJJ and Damiani, T and Pluskal, T and Dorrestein, P and Stanstrup, J and Schmid, R and Wang, M and Aron, A and Ernst, M and Petras, D},
title = {Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data.},
journal = {Nature protocols},
volume = {20},
number = {1},
pages = {92-162},
pmid = {39304763},
issn = {1750-2799},
support = {EXC 2124//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; U24 DK133658/DK/NIDDK NIH HHS/United States ; R03 DE021437/DE/NIDCR NIH HHS/United States ; },
mesh = {Chromatography, Liquid/methods ; Data Interpretation, Statistical ; *Metabolomics/methods ; Software ; Tandem Mass Spectrometry/methods ; },
abstract = {Feature-based molecular networking (FBMN) is a popular analysis approach for liquid chromatography-tandem mass spectrometry-based non-targeted metabolomics data. While processing liquid chromatography-tandem mass spectrometry data through FBMN is fairly streamlined, downstream data handling and statistical interrogation are often a key bottleneck. Especially users new to statistical analysis struggle to effectively handle and analyze complex data matrices. Here we provide a comprehensive guide for the statistical analysis of FBMN results, focusing on the downstream analysis of the FBMN output table. We explain the data structure and principles of data cleanup and normalization, as well as uni- and multivariate statistical analysis of FBMN results. We provide explanations and code in two scripting languages (R and Python) as well as the QIIME2 framework for all protocol steps, from data clean-up to statistical analysis. All code is shared in the form of Jupyter Notebooks (https://github.com/Functional-Metabolomics-Lab/FBMN-STATS). Additionally, the protocol is accompanied by a web application with a graphical user interface (https://fbmn-statsguide.gnps2.org/) to lower the barrier of entry for new users and for educational purposes. Finally, we also show users how to integrate their statistical results into the molecular network using the Cytoscape visualization tool. Throughout the protocol, we use a previously published environmental metabolomics dataset for demonstration purposes. Together, the protocol, code and web application provide a complete guide and toolbox for FBMN data integration, cleanup and advanced statistical analysis, enabling new users to uncover molecular insights from their non-targeted metabolomics data. Our protocol is tailored for the seamless analysis of FBMN results from Global Natural Products Social Molecular Networking and can be easily adapted to other mass spectrometry feature detection, annotation and networking tools.},
}
@article {pmid39309222,
year = {2024},
author = {Boyes, D and Wawman, DC and , and , and , and , and , and , and , },
title = {The genome sequence of the Figure of Eighty moth Tethea ocularis Linnaeus, 1767.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {348},
pmid = {39309222},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Tethea ocularis (the Figure of Eighty; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 339.1 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 15.28 kilobases in length.},
}
@article {pmid39309224,
year = {2024},
author = {Boyes, D and Lees, DC and Wawman, DC and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Blue-bordered Carpet moth Plemyria rubiginata (Denis &amp; Schiffermüller) 1775.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {271},
pmid = {39309224},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Plemyria rubiginata (the Blue-bordered Carpet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 356.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.64 kilobases in length.},
}
@article {pmid39309423,
year = {2023},
author = {Boyes, D and Blaxter, ML and , and , and , and , and , and , },
title = {The genome sequence of the Beautiful Hook-tip, Laspeyria flexula (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {529},
pmid = {39309423},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Laspeyria flexula (the Beautiful Hook-tip; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 450.9 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 15.58 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,281 protein coding genes.},
}
@article {pmid39312537,
year = {2024},
author = {Malamud, J and Guloksuz, S and van Winkel, R and Delespaul, P and De Hert, MAF and Derom, C and Thiery, E and Jacobs, N and Rutten, BPF and Huys, QJM},
title = {Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012457},
pmid = {39312537},
issn = {1553-7358},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Affect/physiology ; *Depression/physiopathology ; *Computational Biology ; Algorithms ; Ecological Momentary Assessment ; Psychometrics/methods ; Male ; Female ; },
abstract = {BACKGROUND: Mood disorders involve a complex interplay between multifaceted internal emotional states, and complex external inputs. Dynamical systems theory suggests that this interplay between aspects of moods and environmental stimuli may hence determine key psychopathological features of mood disorders, including the stability of mood states, the response to external inputs, how controllable mood states are, and what interventions are most likely to be effective. However, a comprehensive computational approach to all these aspects has not yet been undertaken.<br><br>METHODS: Here, we argue that the combination of ecological momentary assessments (EMA) with a well-established dynamical systems framework-the humble Kalman filter-enables a comprehensive account of all these aspects. We first introduce the key features of the Kalman filter and optimal control theory and their relationship to aspects of psychopathology. We then examine the psychometric and inferential properties of combining EMA data with Kalman filtering across realistic scenarios. Finally, we apply the Kalman filter to a series of EMA datasets comprising over 700 participants with and without symptoms of depression.<br><br>RESULTS: The results show a naive Kalman filter approach performs favourably compared to the standard vector autoregressive approach frequently employed, capturing key aspects of the data better. Furthermore, it suggests that the depressed state involves alterations to interactions between moods; alterations to how moods responds to external inputs; and as a result an alteration in how controllable mood states are. We replicate these findings qualitatively across datasets and explore an extension to optimal control theory to guide therapeutic interventions.<br><br>CONCLUSIONS: Mood dynamics are richly and profoundly altered in depressed states. The humble Kalman filter is a well-established, rich framework to characterise mood dynamics. Its application to EMA data is valid; straightforward; and likely to result in substantial novel insights both into mechanisms and treatments.},
}
@article {pmid39313745,
year = {2024},
author = {Dabrowski, JK and Yang, EJ and Crofts, SJC and Hillary, RF and Simpson, DJ and McCartney, DL and Marioni, RE and Kirschner, K and Latorre-Crespo, E and Chandra, T},
title = {Probabilistic inference of epigenetic age acceleration from cellular dynamics.},
journal = {Nature aging},
volume = {4},
number = {10},
pages = {1493-1507},
pmid = {39313745},
issn = {2662-8465},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Epigenesis, Genetic ; *Aging/genetics ; *DNA Methylation ; CpG Islands/genetics ; Genome-Wide Association Study ; Aged ; Female ; Male ; Middle Aged ; Models, Statistical ; },
abstract = {The emergence of epigenetic predictors was a pivotal moment in geroscience, propelling the measurement and concept of biological aging into a quantitative era; however, while current epigenetic clocks show strong predictive power, they are data-driven in nature and are not based on the underlying biological mechanisms driving methylation dynamics. We show that predictions of these clocks are susceptible to several confounding non-age-related phenomena that make interpretation of these estimates and associations difficult. To address these limitations, we developed a probabilistic model describing methylation transitions at the cellular level. Our approach reveals two measurable components, acceleration and bias, which directly reflect perturbations of the underlying cellular dynamics. Acceleration is the proportional increase in the speed of methylation transitions across CpG sites, whereas bias corresponds to global changes in methylation levels. Using data from 15,900 participants from the Generation Scotland study, we develop a robust inference framework and show that these are two distinct processes confounding current epigenetic predictors. Our results show improved associations of acceleration and bias with physiological traits known to impact healthy aging, such as smoking and alcohol consumption, respectively. Furthermore, a genome-wide association study of epigenetic age acceleration identified seven genomic loci.},
}
@article {pmid39320588,
year = {2024},
author = {Oroud, IM},
title = {The implications of climate change on freshwater resources in the arid and semiarid Mediterranean environments using hydrological modeling, GIS tools, and remote sensing.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {10},
pages = {979},
pmid = {39320588},
issn = {1573-2959},
mesh = {*Climate Change ; *Environmental Monitoring/methods ; *Hydrology ; *Remote Sensing Technology ; *Geographic Information Systems ; Fresh Water/chemistry ; Groundwater/chemistry ; Models, Theoretical ; Mediterranean Region ; Desert Climate ; Water Resources ; },
abstract = {Precipitation partitioning in arid and semiarid environments is not well understood due to scanty precipitation, its temporal distribution, and the lack/absence of adequate measurements of the hydrometeorological components. Simulation methods have the potential to bridge the data gap, thereby providing a window to estimate the water balance components. The present investigation evaluates the water balance components of a typical watershed situated in the southeastern Mediterranean for the period 1979 through 2019 using daily meteorological data and a grid spacing of 250 m. Generated runoff results were commensurate with corresponding values obtained using the SWAT model. Computed groundwater recharge is also compatible with recharge values calculated using the chloride mass balance method. Results show that average runoff and groundwater recharge for the entire period was ⁓24 mm a[-1] and 19 mm a[-1], giving a precipitation ratio of 9.5% and 7.5%, respectively. Substantial interannual variability in the water balance components was observed during the study period which reflected the significant precipitation fluctuations typifying the Eastern Mediterranean. Results show that the period extending from 1998/1999 through 2018/2019 witnessed an 18% drop in annual precipitation, while surface runoff and groundwater recharge experienced a reduction of ⁓34% and ⁓67%, respectively. Although groundwater recharge is a complex function of numerous meteorological and geological factors, the NDVI can provide an excellent indicator of groundwater recharge in marginal Mediterranean environments. This is highly beneficial in areas where climate records are scanty or absent. The presented results emphasize the significant impacts of global warming and aridification on the future availability of water resources in the semiarid marginal climates in the Eastern Mediterranean and point out clearly that water resources in this area will become scarcer, leading to multiple security threats at national and regional levels.},
}
@article {pmid39321538,
year = {2024},
author = {Cao, J and Lei, Y and Li, W and Jiang, X and Li, M},
title = {Coupled digital visualization and multi-omics uncover neurobehavioral dysfunction in zebrafish induced by resorcinol bis(diphenylphosphate).},
journal = {Environment international},
volume = {192},
number = {},
pages = {109023},
doi = {10.1016/j.envint.2024.109023},
pmid = {39321538},
issn = {1873-6750},
mesh = {Animals ; *Zebrafish/physiology ; Water Pollutants, Chemical/toxicity ; Blood-Brain Barrier/drug effects ; Resorcinols/toxicity ; Brain/drug effects/metabolism ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Multiomics ; },
abstract = {Resorcinol bis(diphenylphosphate) (RDP) is an emerging pollutant that has been frequently detected in aquatic environments, although its toxicity is poorly characterized. To understand how RDP affects the neural system, two-month-old zebrafish were exposed to RDP at concentrations of 0.1 and 10 μg/L for 60 days. Following exposure, behavioral assessments were conducted, revealing the emergence of anxiety-like symptoms and memory deficits among the adult fish exposed to RDP, especially at the higher concentration. The increased blood-brain barrier (BBB) permeability (4.67-5.58-fold higher than the control group), reduced expression of tight junction proteins and the rapid brain RDP bioaccumulation (15.63 ± 2.34 ng/g wet weight) indicated the neurotoxicity of RDP. Excess reactive oxygen species synthesis (2.20-2.50-fold) was induced by RDP, leading to mitochondrial dysfunction and decreased production of neurotransmitters in the brain, specifically serotonin (5-HT; 16.3 %) and dopamine (DA; 18.1 %). Metabolomic analysis revealed that the low-toxicity RDP dose up-regulated lipid-related metabolites, while the high-toxicity dose up-regulated arachidonic acid metabolism and disrupted amino acid metabolism, including tryptophan and tyrosine metabolism related to dopaminergic and serotonergic pathways. The dysregulation of genes in various cellular processes was identified by transcriptomics, mainly involved in cell adhesion molecules and gap junctions, and oxidative phosphorylation, which were directly associated with BBB permeability and oxidative stress, respectively. Correlation analysis of microbiome-metabolite-host links built a mechanistic hypothesis for alterations in gut microbiota (Actinobacteriota and Proteobacteria) induced by high-dose RDP leading to the alteration of tryptophan, tyrosine, and arachidonic acid metabolism, decreasing the production of 5-HT and DA through the gut-brain axis. This study provides valuable insights into the mechanism underlying RDP-induced neurotoxicity in zebrafish, which can inform ecological risk assessments.},
}
@article {pmid39323166,
year = {2024},
author = {Lin, ML and Hu, ZQ and Peng, WH and Ye, WL and Zhang, CL and Huang, XR and Chen, S and Gui, HR},
title = {[Pollution Assessment and Source Apportionment of Heavy Metals in the Surrounding Soil of Typical Mining Areas in Tongling, Anhui Province].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {9},
pages = {5494-5505},
doi = {10.13227/j.hjkx.202307274},
pmid = {39323166},
issn = {0250-3301},
abstract = {To study the level of heavy metal pollution and ecological risks in the soil around typical mining areas in Tongling, a total of 150 soil samples were collected from the study area. The content characteristics of 10 elements, namely, As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, Fe, and Zn, in the soils were analyzed. Methods including enrichment factor, the geo-accumulation index, single-factor pollution index, Nemero comprehensive pollution index, and potential ecological risk index were used to evaluate the pollution status of heavy metals in the soil of the study area. The pollution sources of heavy metals in the soil were also analyzed using correlation analysis, cluster analysis, and principal component analysis. The results showed that except for Cr and Fe, the average contents of the other eight heavy metal elements were higher than the soil background values in the study area. Pb, Zn, As, Cu, and Cd had a high degree of variation and were significantly affected by external interference. The spatial distribution showed that both Cr and Ni showed a decreasing trend from the edge to the central region, whereas the other eight heavy metals showed a decreasing trend from the central region to the surrounding areas. The pollution level of Cd and Cu in the soil of the research area was relatively severe. The overall ecological risk was at a medium to low level. Cd and Hg were the main contributing factors. As, Cd, Cu, Fe, Mn, Pb, and Zn mainly came from agricultural, industrial, and transportation sources, whereas Cr and Ni were mainly from natural sources. However, the sources of Hg were relatively complex. The research results can provide a scientific basis for the prevention and control of soil heavy metal pollution in metal mining areas, as well as the remediation of mine pollution.},
}
@article {pmid39323974,
year = {2022},
author = {Boyes, D and Crowley, LM and , and , and , and , and , and Skojec, C and Plotkin, D and Kawahara, AY and , },
title = {The genome sequence of the 6-spot burnet, Zygaena filipendulae (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {197},
pmid = {39323974},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Zygaena filipendulae (6-spot burnet; Arthropoda; Insecta; Lepidoptera; Zygaenidae). The genome sequence is 365.9 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,493 protein coding genes.},
}
@article {pmid39325874,
year = {2024},
author = {Zhu, Y and Chen, G and Sun, Y},
title = {VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {10},
pages = {},
pmid = {39325874},
issn = {1367-4811},
support = {11206819//City University of Hong Kong, Hong Kong Research Grants Council/ ; //Hong Kong Innovation and Technology Fund/ ; },
mesh = {*RNA Viruses/genetics/classification ; *Software ; RNA, Viral/genetics ; Phylogeny ; Sequence Analysis, RNA/methods ; Genome, Viral ; Algorithms ; Computational Biology/methods ; },
abstract = {SUMMARY: RNA viruses are ubiquitous across a broad spectrum of ecosystems. Therefore, beyond their significant implications for public health, RNA viruses are also key players in ecological processes. High-through sequencing has accelerated the discovery of RNA viruses. Nevertheless, many of these viruses lack taxonomic annotation, posing a challenge to functional inference and evolutionary study. In particular, virus classification at the genus level remains difficult due to the limited reference data and ambiguous boundaries between some closely related genera. We introduce VirTAXA, a robust classification tool that combines remote homology search and tree-based validation to enhance the genus-level taxonomic classification of RNA viruses. VirTAXA is able to predict the genus label of an assembled viral contig and provide evidence type for each prediction. It achieves comparable accuracy to state-of-the-art methods while assigning genus labels to a greater number of sequences. Specifically, on the Global Ocean RNA metatranscriptomic data, VirTAXA can assign genus labels for 18% more contigs than the second-best classification tool. Furthermore, we demonstrated that VirTAXA can be conveniently extended to other types of viruses.<br><br>The source code and data of VirTAXA are available via https://github.com/JudithEllyn/VirTAXA.},
}
@article {pmid39326182,
year = {2024},
author = {Li, D and Ping, Q and Mo, R and Guo, W and Zhang, S and Wang, L and Li, Y},
title = {Revealing synergistic mechanisms of biochar-assisted microbial electrolysis cells in enhancing the anaerobic digestion performance of waste activated sludge: Extracellular polymeric substances characterization, enzyme activity assay, and multi-omics analysis.},
journal = {Water research},
volume = {267},
number = {},
pages = {122501},
doi = {10.1016/j.watres.2024.122501},
pmid = {39326182},
issn = {1879-2448},
mesh = {*Sewage/microbiology ; Anaerobiosis ; *Extracellular Polymeric Substance Matrix/metabolism ; Charcoal/chemistry ; Waste Disposal, Fluid/methods ; Electrolysis ; Methane/metabolism ; Multiomics ; },
abstract = {Although biochar (BC)-assisted microbial electrolysis cells (MEC) has been shown to improve anaerobic digestion (AD) performance of waste activated sludge (WAS), the underlying mechanisms remain unclear. This study conducted an in-depth investigation into the mechanism based on analyses of extracellular polymeric substances (EPS) characteristics, enzyme activities and multi-omics. The results showed that compared with the control group, methane production improved by 16.73 %, 21.32 %, and 29.37 % in the BC, MEC, and BC-assisted MEC (BC-MEC) groups, respectively. The reconfiguration of the protein secondary structure increased the hydrophobicity of the EPS, thereby promoting microbial aggregation. In addition, partial least-squares path modeling (PLS-PM) and mantel test based on the enzyme activity and multi-omics analyses revealed that the promotional effect of MEC on the hydrolysis of WAS was superior to that of BC, while BC was more advantageous in promoting electron transfer and biofilm formation regulated by quorum sensing. The synergistic effects of BC and MEC were exemplified in the BC-MEC group. g_norank_Aminicenantales responsible for the hydrolysis of WAS was enriched (29.6 %), and the activities of hydrolytic enzymes including α-glucosidases and proteases were increased by 29.1 % and 43.6 %, respectively. Further, the expressions of genes related to acyl homoserine lactones (AHLs) and diffusible signal factor (DSF) in quorum sensing systems, as well as the genes related to hydrogenase involved in electron transfer (mbhJKL, hyfB-JR, hypA-F, and hoxFHUY), were up-regulated in the BC-MEC group. This facilitated electron transfer and microbial communication, consequently enhancing methane production. This research significantly advances the understanding of the mechanism by which BC-assisted MEC enhances AD performance and provides valuable insights into strategies for improving energy recovery from WAS.},
}
@article {pmid39326744,
year = {2024},
author = {Wang, Y and Feng, Z and Ghani, MI and Wang, Q and Zeng, L and Yang, X and Zhang, X and Chen, C and Li, S and Cao, P and Chen, X and Cernava, T},
title = {Co-exposure to microplastics and soil pollutants significantly exacerbates toxicity to crops: Insights from a global meta and machine-learning analysis.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176490},
doi = {10.1016/j.scitotenv.2024.176490},
pmid = {39326744},
issn = {1879-1026},
mesh = {*Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Crops, Agricultural ; *Machine Learning ; Environmental Monitoring/methods ; Soil/chemistry ; Environmental Pollution/statistics &amp; numerical data ; },
abstract = {Environmental contamination of microplastics (MPs) is ubiquitous worldwide, and co-contamination of arable soils with MPs and other pollutants is of increasing concern, and may lead to unexpected consequences on crop production. However, the overall implications of this combined effect, whether beneficial or detrimental, remain a subject of current debate. Here, we conducted a global meta and machine-learning analysis to evaluate the effects of co-exposure to MPs and other pollutants on crops, utilizing 3346 biological endpoints derived from 68 different studies. Overall, compared with control groups that only exposure to conventional soil contaminants, co-exposure significantly exacerbated toxicity to crops, particularly with MPs intensifying adverse effects on crop morphology, oxidative damage, and photosynthetic efficiency. Interestingly, our analysis demonstrated a significant reduction in the accumulation of pollutants in the crop due to the presence of MPs. In addition, the results revealed that potential adverse effects were primarily associated with crop species, MPs mass concentration, and exposure duration. Our study reaffirms the substantial consequences of MPs as emerging pollutants on crops within the context of integrated pollution, providing novel insights into improving sustainability in agro-ecosystems.},
}
@article {pmid39328383,
year = {2023},
author = {Catalàn, N and Campo, RD and Talluto, L and Mendoza-Lera, C and Grandi, G and Bernal, S and Schiller, DV and Singer, G and Bertuzzo, E},
title = {Pulse, Shunt and Storage: Hydrological Contraction Shapes Processing and Export of Particulate Organic Matter in River Networks.},
journal = {Ecosystems (New York, N.Y.)},
volume = {26},
number = {4},
pages = {873-892},
pmid = {39328383},
issn = {1432-9840},
abstract = {UNLABELLED: Streams and rivers act as landscape-scale bioreactors processing large quantities of terrestrial particulate organic matter (POM). This function is linked to their flow regime, which governs residence times, shapes organic matter reactivity and controls the amount of carbon (C) exported to the atmosphere and coastal oceans. Climate change impacts flow regimes by increasing both flash floods and droughts. Here, we used a modelling approach to explore the consequences of lateral hydrological contraction, that is, the reduction of the wet portion of the streambed, for POM decomposition and transport at the river network scale. Our model integrates seasonal leaf litter input as generator of POM, transient storage of POM on wet and dry streambed portions with associated decomposition and ensuing changes in reactivity, and transport dynamics through a dendritic river network. Simulations showed that the amount of POM exported from the river network and its average reactivity increased with lateral hydrological contraction, due to the combination of (1) low processing of POM while stored on dry streambeds, and (2) large shunting during flashy events. The sensitivity analysis further supported that high lateral hydrological contraction leads to higher export of higher reactivity POM, regardless of transport coefficient values, average reactivity of fresh leaf litter and differences between POM reactivity under wet and dry conditions. Our study incorporates storage in dry streambed areas into the pulse-shunt concept (Raymond and others in Ecology 97(1):5-16, 2016. 10.1890/14-1684.1), providing a mechanistic framework and testable predictions about leaf litter storage, transport and decomposition in fluvial networks.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10021-022-00802-4.},
}
@article {pmid39328967,
year = {2024},
author = {Dey, B and Ferdous, J and Ahmed, R},
title = {Comprehensive stomata image dataset of Sundarbans Mangrove and Ratargul Swamp forest tree species in Bangladesh.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110908},
pmid = {39328967},
issn = {2352-3409},
abstract = {Plants' leaf stomata are crucial for various scientific research, including identifying species, studying ecology, conserving ecosystems, improving agriculture, and advancing the field of deep learning. This dataset, containing 1083 images, encompasses 11 species from two distinct locations in Bangladesh: nine from the Sundarbans mangrove forest and two from the Ratargul Swamp Forest. It is a valuable tool for refining machine learning algorithms that specialize in detecting stomata and categorizing species accurately. Researchers can explore a deeper understanding of plant physiology, adaptation mechanisms, and environmental interactions by employing pattern recognition, deep learning, and feature extraction techniques. Additionally, this dataset could be a potential tool for enhancing research in macroscopic metamaterials, extending its impact beyond traditional biological studies into interdisciplinary fields of technology and material science.},
}
@article {pmid39331576,
year = {2024},
author = {Qiao, B and Wang, S and Hou, M and Chen, H and Zhou, Z and Xie, X and Pang, S and Yang, C and Yang, F and Zou, Q and Sun, S},
title = {Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {10},
pages = {},
pmid = {39331576},
issn = {1367-4811},
support = {62273086//National Natural Science Foundation of China/ ; },
mesh = {*Deep Learning ; *NLR Proteins/metabolism ; *Computational Biology/methods ; Algorithms ; },
abstract = {MOTIVATION: Nucleotide-binding leucine-rich repeat (NLR) family is a class of immune receptors capable of detecting and defending against pathogen invasion. They have been widely used in crop breeding. Notably, the correspondence between NLRs and effectors (CNE) determines the applicability and effectiveness of NLRs. Unfortunately, CNE data is very scarce. In fact, we've found a substantial 91 291 NLRs confirmed via wet experiments and bioinformatics methods but only 387 CNEs are recognized, which greatly restricts the potential application of NLRs.<br><br>RESULTS: We propose a deep learning algorithm called ProNEP to identify NLR-effector pairs in a high-throughput manner. Specifically, we conceptualized the CNE prediction task as a protein-protein interaction (PPI) prediction task. Then, ProNEP predicts the interaction between NLRs and effectors by combining the transfer learning with a bilinear attention network. ProNEP achieves superior performance against state-of-the-art models designed for PPI predictions. Based on ProNEP, we conduct extensive identification of potential CNEs for 91&#xa0;291 NLRs. With the rapid accumulation of genomic data, we expect that this tool will be widely used to predict CNEs in new species, advancing biology, immunology, and breeding.<br><br>The ProNEP is available at http://nerrd.cn/#/prediction. The project code is available at https://github.com/QiaoYJYJ/ProNEP.},
}
@article {pmid39331660,
year = {2024},
author = {Pasqualini, J and Facchin, S and Rinaldo, A and Maritan, A and Savarino, E and Suweis, S},
title = {Emergent ecological patterns and modelling of gut microbiomes in health and in disease.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012482},
pmid = {39331660},
issn = {1553-7358},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Models, Biological ; Computational Biology ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Recent advancements in next-generation sequencing have revolutionized our understanding of the human microbiome. Despite this progress, challenges persist in comprehending the microbiome's influence on disease, hindered by technical complexities in species classification, abundance estimation, and data compositionality. At the same time, the existence of macroecological laws describing the variation and diversity in microbial communities irrespective of their environment has been recently proposed using 16s data and explained by a simple phenomenological model of population dynamics. We here investigate the relationship between dysbiosis, i.e. in unhealthy individuals there are deviations from the "regular" composition of the gut microbial community, and the existence of macro-ecological emergent law in microbial communities. We first quantitatively reconstruct these patterns at the species level using shotgun data, and addressing the consequences of sampling effects and statistical errors on ecological patterns. We then ask if such patterns can discriminate between healthy and unhealthy cohorts. Concomitantly, we evaluate the efficacy of different statistical generative models, which incorporate sampling and population dynamics, to describe such patterns and distinguish which are expected by chance, versus those that are potentially informative about disease states or other biological drivers. A critical aspect of our analysis is understanding the relationship between model parameters, which have clear ecological interpretations, and the state of the gut microbiome, thereby enabling the generation of synthetic compositional data that distinctively represent healthy and unhealthy individuals. Our approach, grounded in theoretical ecology and statistical physics, allows for a robust comparison of these models with empirical data, enhancing our understanding of the strengths and limitations of simple microbial models of population dynamics.},
}
@article {pmid39331699,
year = {2024},
author = {Yang, Z and Shan, Y and Liu, X and Chen, G and Pan, Y and Gou, Q and Zou, J and Chang, Z and Zeng, Q and Yang, C and Kong, J and Sun, Y and Li, S and Zhang, X and Wu, WC and Li, C and Peng, H and Holmes, EC and Guo, D and Shi, M},
title = {VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.},
journal = {Molecular biology and evolution},
volume = {41},
number = {10},
pages = {},
pmid = {39331699},
issn = {1537-1719},
support = {82341118//National Natural Science Foundation of China/ ; 2022A1515011854//Natural Science Foundation of Guangdong Province of China/ ; JCYJ20210324124414040//Shenzhen Science and Technology Program/ ; //Hong Kong Innovation and Technology Fund (ITF/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC (Australia) Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*RNA Viruses/genetics ; *Software ; *Metagenomics/methods ; *Phylogeny ; Humans ; RNA-Dependent RNA Polymerase/genetics ; Computational Biology/methods ; },
abstract = {RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.},
}
@article {pmid39332349,
year = {2024},
author = {Sun, Q and Zhang, Z and Ping, Q and Wang, L and Li, Y},
title = {Insight into using multi-omics analysis to elucidate nitrogen removal mechanisms in a novel improved constructed rapid infiltration system: Functional gene and metabolite signatures.},
journal = {Water research},
volume = {267},
number = {},
pages = {122502},
doi = {10.1016/j.watres.2024.122502},
pmid = {39332349},
issn = {1879-2448},
mesh = {*Nitrogen/metabolism ; *Wastewater/chemistry ; Waste Disposal, Fluid/methods ; Denitrification ; Nitrification ; Metabolomics ; Metagenomics ; Ammonium Compounds/metabolism ; Multiomics ; },
abstract = {In this study, a laboratory-scale improved constructed rapid infiltration (imCRI) system with non-saturated and saturated layers was constructed, and corn cobs as solid carbon source were added to the saturated layer to enhance the removal of nitrogen. Combined analyses of metagenomics and metabolomics were conducted to elucidate the nitrogen removal mechanism in the imCRI system. The results showed that the hydraulic load significantly influenced the treatment performance of the imCRI system, and a hydraulic load of 1.25 m[3]/(m[2]⋅d) was recommended. Under optimal conditions, the imCRI system using simulated wastewater achieved average removal efficiencies of 97.8 % for chemical oxygen demand, 85.7 % for total nitrogen (TN), and 97.6 % for ammonia nitrogen. Metagenomic and metabolomic analyses revealed that besides nitrification and denitrification, dissimilatory nitrate reduction to ammonium (DNRA), anammox, etc., are also involved in nitrogen metabolism in the imCRI system. Although nitrification was the predominant pathway in the non-saturated layer, aerobic denitrification also occurred, accounting for 22.59 % of the TN removal. In the saturated layer, nitrogen removal was attributed to synergistic effects of denitrification, DNRA and anammox. Moreover, correlation analysis among nitrogen removal, functional genes and metabolites suggested that metabolites related to the tricarboxylic acid cycle generated from the glycolysis of corn cobs provided sufficient energy for denitrification. Our results can offer a promising technology for decentralized wastewater treatment with stringent nitrogen removal requirements, and provide a foundation for understanding the underlying nitrogen transformation and removal mechanism.},
}
@article {pmid39337302,
year = {2024},
author = {Romano Spica, V and Volpini, V and Valeriani, F and Carotenuto, G and Arcieri, M and Platania, S and Castrignanò, T and Clementi, ME and Michetti, F},
title = {In Silico Predicting the Presence of the S100B Motif in Edible Plants and Detecting Its Immunoreactive Materials: Perspectives for Functional Foods, Dietary Supplements and Phytotherapies.},
journal = {International journal of molecular sciences},
volume = {25},
number = {18},
pages = {},
pmid = {39337302},
issn = {1422-0067},
mesh = {*Dietary Supplements ; *S100 Calcium Binding Protein beta Subunit/metabolism ; *Functional Food ; *Plants, Edible/chemistry ; Computer Simulation ; Amino Acid Motifs ; Phytotherapy/methods ; Computational Biology/methods ; Humans ; Fruit/chemistry/metabolism ; Phylogeny ; Plant Proteins/metabolism ; },
abstract = {The protein S100B is a part of the S100 protein family, which consists of at least 25 calcium-binding proteins. S100B is highly conserved across different species, supporting important biological functions. The protein was shown to play a role in gut microbiota eubiosis and is secreted in human breast milk, suggesting a physiological trophic function in newborn development. This study explores the possible presence of the S100B motif in plant genomes, and of S100B-like immunoreactive material in different plant extracts, opening up potential botanical uses for dietary supplementation. To explore the presence of the S100B motif in plants, a bioinformatic workflow was used. In addition, the immunoreactivity of S100B from vegetable and fruit samples was tested using an ELISA assay. The S100B motif was expected in silico in the genome of different edible plants belonging to the Viridiplantae clade, such as Durio zibethinus or Malus domestica and other medicinal species. S100B-like immunoreactive material was also detected in samples from fruits or leaves. The finding of S100B-like molecules in plants sheds new light on their role in phylogenesis and in the food chain. This study lays the foundation to elucidate the possible beneficial effects of plants or derivatives containing the S100B-like principle and their potential use in nutraceuticals.},
}
@article {pmid39340701,
year = {2024},
author = {Gang, J and Ping, Y and Du, C},
title = {Anti-Magnaporthe oryzae Activity of Streptomyces bikiniensis HD-087 In Vitro and Bioinformatics Analysis of Polyketide Synthase Gene pksL.},
journal = {Current microbiology},
volume = {81},
number = {11},
pages = {379},
pmid = {39340701},
issn = {1432-0991},
support = {32172468//National Natural Science Foundation of China/ ; },
mesh = {*Polyketide Synthases/genetics/metabolism ; *Streptomyces/genetics/metabolism/enzymology ; *Computational Biology ; *Multigene Family ; Bacterial Proteins/genetics/metabolism ; Erythromycin/pharmacology ; Antifungal Agents/pharmacology/metabolism ; Polyketides/metabolism/pharmacology ; Anti-Bacterial Agents/pharmacology ; Molecular Docking Simulation ; Ascomycota ; },
abstract = {Streptomyces bikiniensis HD-087 is capable of synthesizing various antimicrobial substances to counter the detrimental effects of hazardous microorganisms. To elucidate whether it produces polyketide antibiotics and the synthesis mechanism of antibiotic substances, the metabolites and related genes of S. bikiniensis HD-087 were analyzed through LC-MS, anti-Magnaporthe oryzae activity detection, and bioinformatics approaches. The result indicated that the strain HD-087 could produce erythromycin, a polyketide antibiotic. The inhibitory zones of the fermentation supernatant of strain HD-087 and methanol solution of erythromycin extract against M. oryzae were 40.84 ± 0.68 mm and 33.18 ± 0.81 mm, respectively. The IC50 value of erythromycin extract for inhibiting spore germination of erythromycin extract was 220.43 μg/mL. There are two polyketide synthesis gene clusters in the genome of strain HD-087, namely t1pks-nrps and t3pks-lantipeptide-t1pks-nrps. The key gene pksL in the t3pks-lantipeptide-t1pks-nrps gene cluster was predicted. The results suggested that it encodes a stable, hydrophilic, and acidic protein, mainly composed of α-helix and random coil. The PksL protein contains dehydrogenase (DH), ketone reductase (KR), acyl carrier protein (ACP), and ketone synthase (KS) domains. Moreover, it can form interaction networks with 11 proteins containing domains, such as polyketide synthase and ACP synthase. The molecular docking between PksL and acetyl-CoA is stable and strong, suggesting that PksL protein could catalyze the synthesis of polyketides with CoA as a substrate. This study provides a theoretical basis for further exploring the polyketides synthesis mechanism and developing antifungal metabolites in S. bikiniensis HD-087.},
}
@article {pmid39341239,
year = {2024},
author = {Adomako, MO and Jin, L and Li, C and Liu, J and Adu, D and Seshie, VI and Yu, FH},
title = {Mechanisms underpinning microplastic effects on the natural climate solutions of wetland ecosystems.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176491},
doi = {10.1016/j.scitotenv.2024.176491},
pmid = {39341239},
issn = {1879-1026},
abstract = {Wetland ecosystems are vital carbon dioxide (CO2) sinks, offering significant nature-based solutions for global climate mitigation. However, the recent influx of microplastic (MP) into wetlands substantially impacts key drivers (e.g., plants and microorganisms) underpinning these wetland functions. While MP-induced greenhouse gas (GHG) emissions and effects on soil organic carbon (SOC) mineralization potentially threaten the long-term wetland C-climate feedbacks, the exact mechanisms and linkage are unclear. This review provides a conceptual framework to elaborate on the interplay between MPs, wetland ecosystems, and the atmospheric milieu. We also summarize published studies that validate possible MP impacts on natural climate solutions of wetlands, as well as provide extensive elaboration on underlying mechanisms. We briefly highlight the relationships between MP influx, wetland degradation, and climate change and conclude by identifying key gaps for future research priorities. Globally, plastic production, MP entry into aquatic systems, and wetland degradation-related emissions are predicted to increase. This means that MP-related emissions and wetland-climate feedback should be addressed in the context of the UN Paris Climate Agreement on net-zero emissions by 2050. This overview serves as a wake-up call on the alarming impacts of MPs on wetland ecosystems and urges a global reconsideration of nature-based solutions in the context of climate mitigation.},
}
@article {pmid39343505,
year = {2024},
author = {Eneli, I and Heeren, FAN and Cason-Wilkerson, RL and Pratt, KJ},
title = {Metabolic and Bariatric Surgery for Adolescents.},
journal = {Pediatric clinics of North America},
volume = {71},
number = {5},
pages = {981-998},
doi = {10.1016/j.pcl.2024.06.007},
pmid = {39343505},
issn = {1557-8240},
mesh = {Humans ; Adolescent ; *Bariatric Surgery/methods ; *Pediatric Obesity/surgery ; Obesity, Morbid/surgery/psychology ; Gastrectomy/methods ; },
abstract = {Obesity is a chronic, complex, and multifactorial disease. Currently, approximately 6% have severe obesity with higher rates seen among racial/ethnic minority subgroups and in rural communities. Severe obesity is associated with cardiometabolic, psychologic, and musculoskeletal comorbidities. Metabolic and bariatric surgery is an effective treatment option for adolescents endorsed by major pediatric organizations. The most common procedure is the vertical sleeve gastrectomy. Pre-operative evaluation includes an in-depth medical, nutrition, physical activity and psychosocial assessment, with a care plan developed by a multidicplinary team with the adolescent and caregiver. The post-operative plan should include monitoring for surgical complications, weight regain, micronutrient deficiencies, psychologic challenges, and transition to adult care.},
}
@article {pmid39345343,
year = {2024},
author = {Halpern, B and Vörös, J and Mc Cartney, AM and Formenti, G and Mouton, A and , and , and , and , },
title = {The genome sequence of the Hungarian meadow viper, Vipera ursinii rakosiensis (Méhely, 1893).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {404},
pmid = {39345343},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Vipera ursinii rakosiensis (the Hungarian meadow viper; Chordata; Lepidosauria; Squamata; Viperidae). The genome sequence is 1,625.0 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.38 kilobases in length.},
}
@article {pmid39345378,
year = {2025},
author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Gooden, AA and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Behera, S and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Salas-González, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Bayabyan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, GL and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Krieger, G and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, A and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Bhakta, MS and Zachary Sanborn, J and Munding, EM and Wagner, J and Xiao, C and Liss, AS and Zook, JM},
title = {Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39345378},
issn = {2692-8205},
support = {OT2 OD034190/OD/NIH HHS/United States ; U01 CA253405/CA/NCI NIH HHS/United States ; R01 HG011274/HG/NHGRI NIH HHS/United States ; S10 OD028587/OD/NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; R35 GM133747/GM/NIGMS NIH HHS/United States ; R44 HG014126/HG/NHGRI NIH HHS/United States ; },
abstract = {The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, and Hi-C, and karyotyping. In future publications, these data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.},
}
@article {pmid39346055,
year = {2024},
author = {Knobloch, S and Salimi, F and Buaya, A and Ploch, S and Thines, M},
title = {RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17893},
pmid = {39346055},
issn = {2167-8359},
mesh = {*Nanopore Sequencing/methods ; Metagenomics/methods ; Plant Diseases/microbiology ; Bacteria/genetics/isolation &amp; purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation &amp; purification/classification ; Plants/microbiology ; Computational Biology/methods ; },
abstract = {Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de.},
}
@article {pmid39349447,
year = {2024},
author = {Zhou, L and Wu, S and Chen, Y and Huang, R and Cheng, B and Mao, Q and Liu, T and Liu, Y and Zhao, K and Pan, H and Yu, C and Gao, X and Luo, L and Zhang, Q},
title = {Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8469},
pmid = {39349447},
issn = {2041-1723},
mesh = {*Rosa/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; *Odorants/analysis ; *Genome, Plant ; *Gene Expression Regulation, Plant ; Gene Regulatory Networks ; Genomics/methods ; Eugenol/analogs &amp; derivatives/metabolism ; Plant Proteins/genetics/metabolism ; Pollination ; Multiomics ; },
abstract = {Rose is an important ornamental crop cultivated globally for perfume production. However, our understanding of the mechanisms underlying scent production and molecular breeding for fragrance is hindered by the lack of a reference genome for tea roses. We present the first complete telomere-to-telomere (T2T) genome of Rosa gigantea, with high quality (QV > 60), including detailed characterization of the structural features of repetitive regions. The expansion of genes associated with phenylpropanoid biosynthesis may account for the unique tea scent. We uncover the release rhythm of aromatic volatile organic compounds and their gene regulatory networks through comparative genomics and time-ordered gene co-expression networks. Analyzes of eugenol homologs demonstrate how plants attract pollinators using specialized phenylpropanoids in specific tissues. This study highlights the conservation and utilization of genetic diversity from wild endangered species through multi-omics approaches, providing a scientific foundation for enhancing rose fragrance via de novo domestication.},
}
@article {pmid39351031,
year = {2024},
author = {Wei, C and Cai, Y and Liu, J and Guo, Y and Wu, X and He, X and Hu, D},
title = {Factors influencing user's health information discernment abilities in online health communities: based on SEM and fsQCA.},
journal = {Frontiers in public health},
volume = {12},
number = {},
pages = {1379094},
pmid = {39351031},
issn = {2296-2565},
mesh = {Humans ; Surveys and Questionnaires ; Female ; Male ; Adult ; *Internet ; Consumer Health Information ; Latent Class Analysis ; Information Seeking Behavior ; Fuzzy Logic ; Young Adult ; Middle Aged ; },
abstract = {INTRODUCTION: Online health communities have become the main source for people to obtain health information. However, the existence of poor-quality health information, misinformation, and rumors in online health communities increases the challenges in governing information quality. It not only affects users' health decisions but also undermines social stability. It is of great significance to explore the factors that affect users' ability to discern information in online health communities.<br><br>METHODS: This study integrated the Stimulus-Organism-Response Theory, Information Ecology Theory and the Mindsponge Theory to constructed a model of factors influencing users' health information discernment abilities in online health communities. A questionnaire was designed based on the variables in the model, and data was collected. Utilizing Structural Equation Modeling (SEM) in conjunction with fuzzy-set Qualitative Comparative Analysis (fsQCA), the study analyzed the complex causal relationships among stimulus factors, user perception, and the health information discernment abilities.<br><br>RESULTS: The results revealed that the dimensions of information, information environment, information technology, and information people all positively influenced health information discernment abilities. Four distinct configurations were identified as triggers for users' health information discernment abilities. The core conditions included information source, informational support, technological security, technological facilitation, and perceived risk. It was also observed that information quality and emotional support can act as substitutes for one another, as can informational support and emotional support.<br><br>DISCUSSION: This study provides a new perspective to study the influencing factors of health information discernment abilities of online health community users. It can provide experiences and references for online health community information services, information resource construction and the development of users' health information discernment abilities.},
}
@article {pmid39351379,
year = {2024},
author = {Leavy, OC and Russell, RJ and Harrison, EM and Lone, NI and Kerr, S and Docherty, AB and Sheikh, A and Richardson, M and Elneima, O and Greening, NJ and Harris, VC and Houchen-Wolloff, L and McAuley, HJC and Saunders, RM and Sereno, M and Shikotra, A and Singapuri, A and Aul, R and Beirne, P and Bolton, CE and Brown, JS and Choudhury, G and Diar Bakerly, N and Easom, N and Echevarria, C and Fuld, J and Hart, N and Hurst, JR and Jones, M and Parekh, D and Pfeffer, P and Rahman, NM and Rowland-Jones, S and Shah, AM and Wootton, DG and Jolley, C and Thompson, AAR and Chalder, T and Davies, MJ and De Soyza, A and Geddes, JR and Greenhalf, W and Heller, S and Howard, L and Jacob, J and Jenkins, RG and Lord, JM and Man, WD and McCann, GP and Neubauer, S and Openshaw, PJM and Porter, J and Rowland, MJ and Scott, JT and Semple, MG and Singh, SJ and Thomas, D and Toshner, M and Lewis, K and Heaney, LG and Briggs, A and Zheng, B and Thorpe, M and Quint, JK and Chalmers, JD and Ho, LP and Horsley, A and Marks, M and Poinasamy, K and Raman, B and Wain, LV and Brightling, CE and Evans, RA},
title = {1-year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study.},
journal = {ERJ open research},
volume = {10},
number = {5},
pages = {},
pmid = {39351379},
issn = {2312-0541},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {BACKGROUND: In patients with coronavirus disease 2019 (COVID-19) requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) 1 year after discharge.<br><br>METHODS: Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies (Post-hospitalisation COVID-19 and the International Severe Acute Respiratory and emerging Infection Consortium). HRQoL, assessed by the EuroQol-Five Dimensions-Five Levels utility index (EQ-5D-5L UI), pre-hospital and 1 year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient-reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias.<br><br>FINDINGS: Of the 1888 participants included in the primary analysis, 1149 received corticosteroids. There was no between-group difference in EQ-5D-5L UI at 1 year (mean difference 0.004, 95% CI -0.026-0.034). A similar reduction in EQ-5D-5L UI was seen at 1 year between corticosteroid exposed and nonexposed groups (mean&#xb1;sd change -0.12&#xb1;0.22 versus -0.11&#xb1;0.22). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a cohort of 109&#x2009;318 patients admitted to hospital with COVID-19, EQ-5D-5L UI at 1 year remained similar between the two groups.<br><br>INTERPRETATION: Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL 1 year after hospital discharge. Treatments to address the persistent reduction in HRQoL are urgently needed.},
}
@article {pmid39352117,
year = {2024},
author = {Gu, S and Shao, Y and Rehm, K and Bigler, L and Zhang, D and He, R and Xu, R and Shao, J and Jousset, A and Friman, VP and Bian, X and Wei, Z and Kümmerli, R and Li, Z},
title = {Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39352117},
issn = {2050-084X},
support = {No. 2021YFF1200500//National Key Research and Development Program of China/ ; No. 42107140//National Natural Science Foundation of China/ ; No.41922053//National Natural Science Foundation of China/ ; No. 32071255//National Natural Science Foundation of China/ ; No. T2321001//National Natural Science Foundation of China/ ; No. BX2021012//National Postdoctoral Program for Innovative Talents/ ; no. 310030_212266/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Siderophores/metabolism/genetics ; *Genome, Bacterial ; *Pseudomonas/genetics/metabolism ; *Computational Biology/methods ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Oligopeptides/metabolism/genetics ; Secondary Metabolism/genetics ; Iron/metabolism ; },
abstract = {Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be predicted. Here, we developed a knowledge-guided bioinformatic pipeline to solve these issues. We analyzed 1928 genomes of Pseudomonas bacteria and focused on iron-scavenging pyoverdines as model metabolites. Our pipeline predicted 188 chemically different pyoverdines with nearly 100% structural accuracy and the presence of 94 distinct receptor groups required for the uptake of iron-loaded pyoverdines. Our pipeline unveils an enormous yet overlooked diversity of siderophores (151 new structures) and receptors (91 new groups). Our approach, combining feature sequence with phylogenetic approaches, is extendable to other metabolites and microbial genera, and thus emerges as powerful tool to reconstruct bacterial secondary metabolism pathways based on sequence data.},
}
@article {pmid39352141,
year = {2024},
author = {Coclet, C and Camargo, AP and Roux, S},
title = {MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0088824},
pmid = {39352141},
issn = {2379-5077},
mesh = {*Metagenome/genetics ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation &amp; purification ; Software ; Virome/genetics ; Computational Biology/methods ; Molecular Sequence Annotation ; },
abstract = {While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.},
}
@article {pmid39354608,
year = {2024},
author = {Navratilova, HF and Whetton, AD and Geifman, N},
title = {Artificial intelligence driven definition of food preference endotypes in UK Biobank volunteers is associated with distinctive health outcomes and blood based metabolomic and proteomic profiles.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {881},
pmid = {39354608},
issn = {1479-5876},
support = {202205080261//Lembaga Pengelola Dana Pendidikan/ ; },
mesh = {Humans ; *Food Preferences ; United Kingdom ; Male ; Female ; *Biological Specimen Banks ; Middle Aged ; *Proteomics/methods ; *Metabolomics ; *Artificial Intelligence ; Metabolome ; Adult ; Aged ; Surveys and Questionnaires ; Health ; UK Biobank ; },
abstract = {BACKGROUND: Specific food preferences can determine an individual's dietary patterns and therefore, may be associated with certain health risks and benefits.<br><br>METHODS: Using food preference questionnaire (FPQ) data from a subset comprising over 180,000 UK Biobank participants, we employed Latent Profile Analysis (LPA) approach to identify the main patterns or profiles among participants. blood biochemistry across groups/profiles was compared using the non-parametric Kruskal-Wallis test. We applied the Limma algorithm for differential abundance analysis on 168 metabolites and 2923 proteins, and utilized the Database for Annotation, Visualization and Integrated Discovery (DAVID) to identify enriched biological processes and pathways. Relative risks (RR) were calculated for chronic diseases and mental conditions per group, adjusting for sociodemographic factors.<br><br>RESULTS: Based on their food preferences, three profiles were termed: the putative Health-conscious group (low preference for animal-based or sweet foods, and high preference for vegetables and fruits), the Omnivore group (high preference for all foods), and the putative Sweet-tooth group (high preference for sweet foods and sweetened beverages). The Health-conscious group exhibited lower risk of heart failure (RR&#x2009;=&#x2009;0.86, 95%CI 0.79-0.93) and chronic kidney disease (RR&#x2009;=&#x2009;0.69, 95%CI 0.65-0.74) compared to the two other groups. The Sweet-tooth group had greater risk of depression (RR&#x2009;=&#x2009;1.27, 95%CI 1.21-1.34), diabetes (RR&#x2009;=&#x2009;1.15, 95%CI 1.01-1.31), and stroke (RR&#x2009;=&#x2009;1.22, 95%CI 1.15-1.31) compared to the other two groups. Cancer (overall) relative risk showed little difference across the Health-conscious, Omnivore, and Sweet-tooth groups with RR of 0.98 (95%CI 0.96-1.01), 1.00 (95%CI 0.98-1.03), and 1.01 (95%CI 0.98-1.04), respectively. The Health-conscious group was associated with lower levels of inflammatory biomarkers (e.g., C-reactive Protein) which are also known to be elevated in those with common metabolic diseases (e.g., cardiovascular disease). Other markers modulated in the Health-conscious group, ketone bodies, insulin-like growth factor-binding protein (IGFBP), and Growth Hormone 1 were more abundant, while leptin was less abundant. Further, the IGFBP pathway, which influences IGF1 activity, may be significantly enhanced by dietary choices.<br><br>CONCLUSIONS: These observations align with previous findings from studies focusing on weight loss interventions, which include a reduction in leptin levels. Overall, the Health-conscious group, with preference to healthier food options, has better health outcomes, compared to Sweet-tooth and Omnivore groups.},
}
@article {pmid39355992,
year = {2024},
author = {Auffret, AG and Ladouceur, E and Haussmann, NS and Daouti, E and Elumeeva, TG and Kačergytė, I and Knape, J and Kotowska, D and Low, M and Onipchenko, VG and Paquet, M and Rubene, D and Plue, J},
title = {A global database of soil seed bank richness, density, and abundance.},
journal = {Ecology},
volume = {105},
number = {11},
pages = {e4438},
doi = {10.1002/ecy.4438},
pmid = {39355992},
issn = {1939-9170},
mesh = {*Seed Bank ; *Soil ; *Databases, Factual ; *Biodiversity ; *Seeds ; Ecosystem ; Plants/classification ; },
abstract = {A soil seed bank is the collective name for viable seeds that are stored naturally in the soil. At the species or population level, the ability to form a seed bank represents a strategy for (re)colonization following a disturbance or other change in the local environmental conditions. At the community level, seed banks are thought to buffer local diversity during periods of environmental change and are often studied in relation to the potential for passive habitat restoration. The role that seed banks play in plant population and community dynamics, as well as their importance in the agricultural sector, means that they have been widely studied in ecological research. This database is the result of a comprehensive literature search, including all seed bank studies from the Web of Science from which data could be extracted, as well as an additional search of the Russian language literature. The database contains information on the species richness, seed density, and/or seed abundance in 3096 records from at least 1929 locations across the world's seven continents, extracted from 1442 studies published between 1940 and 2020. Records are grouped into five broad habitat categories (aquatic, arable, forest, grassland-including shrubland-and wetland), including information relating to habitat degradation from, or restoration to other habitats (total 14 combinations). Sampling protocols were also extracted for each record, and the database was extensively checked for errors. The location of each record was then used to extract summary climate data and biome classification from external published databases. The database has several potential uses. The large geographical spread relative to many other global biodiversity datasets is relevant for investigating patterns of diversity in biogeographical or macroecological contexts. Habitat type and status (intact, degraded, and restored) can be used to provide insights for biodiversity conservation, while the potential effects of sampling method and effort can be used to inform optimized data collection for future seed bank studies. This database is released under the CC-BY license.},
}
@article {pmid39359327,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Crescent Plume, Marasmarcha lunaedactyla (Haworth, 1811).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {431},
pmid = {39359327},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Marasmarcha lunaedactyla (the Crescent Plume; Arthropoda; Insecta; Lepidoptera; Pterophoridae). The genome sequence is 771.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,571 protein coding genes.},
}
@article {pmid39360250,
year = {2024},
author = {Soni, N and Eyre, MT and Souza, FN and Diggle, PJ and Ko, AI and Begon, M and Pickup, R and Childs, JE and Khalil, H and Carvalho-Pereira, TSA and Pertile, AC and Carvalho, M and de Oliveira, D and Nery, N and Giorgi, E and Costa, F},
title = {Disentangling the influence of reservoir abundance and pathogen shedding on zoonotic spillover of the Leptospira agent in urban informal settlements.},
journal = {Frontiers in public health},
volume = {12},
number = {},
pages = {1447592},
pmid = {39360250},
issn = {2296-2565},
support = {U01 AI088752/AI/NIAID NIH HHS/United States ; F31 AI114245/AI/NIAID NIH HHS/United States ; R01 TW009504/TW/FIC NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 AI052473/AI/NIAID NIH HHS/United States ; R25 TW009338/TW/FIC NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Leptospirosis/epidemiology/microbiology/transmission ; *Leptospira/isolation &amp; purification ; *Disease Reservoirs/microbiology ; Brazil/epidemiology ; Rats ; *Zoonoses/microbiology ; Male ; Female ; Adult ; Bacterial Shedding ; Longitudinal Studies ; Middle Aged ; Risk Factors ; Urban Population/statistics &amp; numerical data ; Adolescent ; Young Adult ; },
abstract = {Rats are major reservoirs for pathogenic Leptospira, the bacteria causing leptospirosis, particularly in urban informal settlements. However, the impact of variation in rat abundance and pathogen shedding rates on spillover transmission to humans remains unclear. This study aimed to investigate how spatial variation in reservoir abundance and pathogen pressure affect Leptospira spillover transmission to humans in a Brazilian urban informal settlement. A longitudinal eco-epidemiological study was conducted from 2013 to 2014 to characterize the spatial distribution of rat abundance and Leptospira shedding rates in rats and determine the association with human infection risk in a cohort of 2,206 community residents. Tracking plates and live-trapping were used to measure rat abundance and quantify rat shedding status and load. In parallel, four sequential biannual serosurveys were used to identify human Leptospira infections. To evaluate the role of shedding on human risk, we built three statistical models for: (1) the relative abundance of rats, (2) the shedding rate by individual rats, and (3) human Leptospira infection, in which "total shedding", obtained by multiplying the predictions from those two models, was used as a risk factor. We found that Leptospira shedding was associated with older and sexually mature rats and varied spatially and temporally-higher at valley bottoms and with seasonal rainfall (December to March). The point estimate for "total shedding" by rat populations was positive, i.e., Leptospira infection risk increased with total shedding, but the association was not significant [odds ratio (OR) = 1.1; 95% confidence interval (CI): 0.9, 1.4]. This positive trend was mainly driven by rat abundance, rather than individual rat shedding (OR = 1.8; 95% CI: 0.6, 5.4 vs. OR = 1.0; 95% CI: 0.7, 1.4]. Infection risk was higher in areas with more vegetative land cover (OR = 2.4; 95% CI: 1.2, 4.8), and when floodwater entered the house (OR = 2.4; 95% CI: 1.6, 3.4). Our findings indicate that environmental and hydrological factors play a more significant role in Leptospira spillover than rat associated factors. Furthermore, we developed a novel approach combining several models to elucidate complex links between animal reservoir abundance, pathogen shedding and environmental factors on zoonotic spillover in humans that can be extended to other environmentally transmitted diseases.},
}
@article {pmid39362167,
year = {2024},
author = {Fardullah, M and Hossain, MT and Islam, MS and Islam, MR and Rahman, MR and Akther, K and Uddin, A and Morshed, S and Sultana, N and Alam, MA and Bahadur, NM and Robel, FN},
title = {Occurrence and spatial distribution of microplastics in water and sediments of Hatiya Island, Bangladesh and their risk assessment.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122697},
doi = {10.1016/j.jenvman.2024.122697},
pmid = {39362167},
issn = {1095-8630},
mesh = {*Microplastics/analysis ; Risk Assessment ; Bangladesh ; *Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; Geologic Sediments/chemistry/analysis ; Islands ; },
abstract = {This research has evaluated the MPs distribution, characteristics, and potential threats of MPs in surface water and sediments from Hatiya Island. The results showed that the abundance of MPs was 139 ± 44 items/m[3] in surface water and 493 ± 80 items/kg dw in sediments, indicating higher levels of MPs contamination in sediment samples. Fibers were the predominant kind of microplastics, and microscopic sizes (0.3-1.5 mm) MPs were generally more frequent and largely present in both the surface water and sediments. Fourier-transform infrared spectroscopy (FTIR) confirmed that polyethylene terephthalate was the major polymer component of microplastics in surface water, whereas polyethylene was the most abundant polymer in sediments. MPs contamination risk was examined based on multiple risk assessment models. Nemerow pollution index (NPI) and pollutant load index (PLI) show minimal pollution levels of MPs. But potential hazard index (PHI), potential ecological risk factor (Er), and potential ecological risk index (RI), indicate severe MPs contamination due to the presence of polyurethane, polycarbonate, polyvinyl chloride, epoxy that were hazardous MPs and exhibited a critical concern for MPs risk. These statistics will help to understand the environmental difficulties generated by MPs and which hazard is waiting for mankind in the future.},
}
@article {pmid39362872,
year = {2024},
author = {Fu, SW and Feng, MC and Chi, PW and Ding, TS},
title = {Combining citizen science data and literature to build a traits dataset of Taiwan's birds.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1076},
pmid = {39362872},
issn = {2052-4463},
mesh = {Animals ; Taiwan ; *Birds ; *Citizen Science ; *Ecosystem ; Databases, Factual ; },
abstract = {Trait-based methodologies are gaining traction in the field of ecology, providing deeper insights into ecosystem structure and functions. To this end, trait databases tailored to specific taxonomic groups have become foundational. In Taiwan, the collaborative efforts of avian researchers and dedicated citizen scientists have led to the compilation of a vast array of data. This includes web-sourced images from social media, spatial distribution records from eBird, and morphological metrics from banded birds and specimens. Enriched by peer-reviewed literature, we have meticulously assembled a comprehensive trait dataset encompassing 454 bird species across 73 families. This dataset covers a wide range of traits, including foraging ecology, morphological characteristics, territorial behaviors, breeding attributes, and the roles of bird species in ecosystem regulation. As an invaluable resource, this dataset lays the foundation for in-depth exploration of functional diversity, trait-based community ecology, ecosystem function, and critical insights needed to shape conservation strategies.},
}
@article {pmid39363203,
year = {2024},
author = {Viana, PAB and Tschoeke, DA and de Moraes, L and Santos, LA and Barral-Netto, M and Khouri, R and Ramos, PIP and Meirelles, PM},
title = {Design and implementation of a metagenomic analytical pipeline for respiratory pathogen detection.},
journal = {BMC research notes},
volume = {17},
number = {1},
pages = {291},
pmid = {39363203},
issn = {1756-0500},
support = {2023-PPI-007//Rockefeller Foundation/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Respiratory Tract Infections/microbiology/diagnosis ; Metagenome/genetics ; Computational Biology/methods ; Reproducibility of Results ; Nasopharynx/microbiology/virology ; },
abstract = {OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment.<br><br>RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4&#xa0;min per sample (processing 1&#xa0;million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.},
}
@article {pmid39363544,
year = {2024},
author = {Panayi, P and Peters, E and Bentall, R and Hardy, A and Berry, K and Sellwood, W and Dudley, R and Longden, E and Underwood, R and Steel, C and Jafari, H and Emsley, R and Mason, L and Elliott, R and Varese, F},
title = {Complex PTSD symptoms predict positive symptoms of psychosis in the flow of daily life.},
journal = {Psychological medicine},
volume = {54},
number = {12},
pages = {3489-3500},
pmid = {39363544},
issn = {1469-8978},
support = {NIHR128623//Health Technology Assessment Programme/ ; NIHR130971//Efficacy and Mechanism Evaluation Programme/ ; N/A//NIHR Maudsley Biomedical Research Centre/ ; },
abstract = {BACKGROUND: Post-traumatic stress disorder (PTSD) has been shown to predict psychotic symptomology. However, few studies have examined the relative contribution of PTSD compared to broader post-traumatic sequelae in maintaining psychosis. Complex PTSD (cPTSD), operationalized using ICD-11 criteria, includes core PTSD (intrusions, avoidance, hyperarousal) as well as additional "disturbances of self-organisation" (DSO; emotional dysregulation, interpersonal difficulties, negative self-concept) symptoms, more likely to be associated with complex trauma histories. It was hypothesized that DSOs would be associated with positive psychotic symptoms (paranoia, voices, and visions) in daily life, over and above core PTSD symptoms.<br><br>METHODS: This study (N = 153) employed a baseline subsample of the Study of Trauma And Recovery (STAR), a clinical sample of participants with comorbid post-traumatic stress and psychosis symptoms. Core PTSD, DSO and psychosis symptoms were assessed up to 10 times per day at quasi-random intervals over six consecutive days using Experience Sampling Methodology.<br><br>RESULTS: DSOs within the preceding 90 min predicted paranoia, voices, and visions at subsequent moments. These relationships persisted when controlling for core PTSD symptoms within this timeframe, which were themselves significant. The associations between DSOs and paranoia but not voices or visions, were significantly stronger than those between psychosis and core PTSD symptoms.<br><br>CONCLUSIONS: Consistent with an affective pathway to psychosis, the findings suggest that DSOs may be more important than core PTSD symptoms in maintaining psychotic experiences in daily life among people with comorbid psychosis and cPTSD, and indicate the potential importance of addressing broad post-traumatic sequelae in trauma-focused psychosis interventions.},
}
@article {pmid39364368,
year = {2024},
author = {Bullion, CM and Bahlai, CA},
title = {Data gap or biodiversity gap? Evaluating apparent spatial biases in community science observations of Odonata in the east-central United States.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18115},
pmid = {39364368},
issn = {2167-8359},
mesh = {Animals ; *Biodiversity ; *Odonata ; Humans ; Bias ; United States ; Databases, Factual ; },
abstract = {Odonates (dragonflies and damselflies) have become popular study organisms for insect-based climate studies, due to the taxon's strong sensitivity to environmental conditions, and an enthusiastic following by community scientists due to their charismatic appearance and size. Where formal records of this taxon can be limited, public efforts have provided nearly 1,500,000 open-sourced odonate records through online databases, making real-time spatio-temporal monitoring more feasible. While these databases can be extensive, concerns regarding these public endeavors have arisen from a variety of sources: records may be biased by human factors (ex: density, technological access) which may cause erroneous interpretations. Indeed, records of odonates in the east-central US documented in the popular database iNaturalist bear striking patterns corresponding to political boundaries and other human activities. We conducted a 'ground-truthing' study using a structured sampling method to examine these patterns in an area where community science reports indicated variable abundance, richness, and diversity which appeared to be linked to observation biases. Our observations were largely consistent with patterns recorded by community scientists, suggesting these databases were indeed capturing representative biological trends and raising further questions about environmental drivers in the observed data gaps.},
}
@article {pmid39367017,
year = {2024},
author = {Zhou, M and Guo, F},
title = {Mechanism and spatial spillover effect of digital economy on common prosperity in the Yellow River Basin of China.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23086},
pmid = {39367017},
issn = {2045-2322},
support = {41801105//National Natural Science Foundation of China/ ; 2022RW040//Shandong Province Higher Education Youth Innovation Technology Support Program/ ; 23CGLJ15//Shandong Province Social Science Planning and Research Project/ ; },
abstract = {The digital economy has emerged as a new trend in economic development and has profoundly influenced the process of achieving common prosperity. However, current research on the correlation between the digital economy and common prosperity from the perspective of a river basin still needs to be strengthened. Based on this, the present study first theoretically elaborates the conceptual meanings of "digital economy" and "common prosperity", as well as the mechanism by which the digital economy empowers common prosperity. Subsequently, a scientifically-constructed performance evaluation index system for the digital economy and common prosperity is established. Considering the Yellow River Basin as an empirical case study area, this study investigates the mechanism and spatial spillover effects of the digital economy in empowering common prosperity from 2005 to 2020. The research findings reveal that: (1) The Yellow River Basin exhibits a basin characteristic with downstream > midstream > upstream areas regarding the level of common prosperity and digital economy. It indicates that a distinct spatial correlation exists between the two factors. However, the ongoing decrease in both high-level and very high-level areas reflects the lengthy and challenging journey of enhancing the quality and efficiency of the digital economy in empowering common prosperity. (2) The digital economy not only directly impacts common prosperity, but also fosters its development through spatial spillover effects. Among the control factors, informatization and housing levels have a major stimulating effect. (3) There exists a clear regional heterogeneity in how the digital economy affects common prosperity in the Yellow River Basin. Specifically, common prosperity of downstream cities is significantly impacted by the digital economy. The spatial spillover effects of the digital economy on common prosperity exhibit a pronounced "neighborhood as a moat" characteristic. (4) The digital economy facilitates the achievement of shared prosperity through the implementation of mechanisms centered on sharing, affluence, and sustainability. These research findings illuminate the empowering mechanisms and spatial spillover pathways of the digital economy in promoting shared prosperity, aligning with national strategies for ecological conservation and high-quality development in the Yellow River Basin.},
}
@article {pmid39367377,
year = {2024},
author = {Qiao, L and Zhang, C and Zhang, M and Jiang, H and Shi, Y and Zhang, W and Mei, Y and Li, Y and Wang, H},
title = {High-risk spatiotemporal patterns of leprosy in the southeastern region of Yunnan province from 2010 to 2022: an analysis at the township level.},
journal = {BMC public health},
volume = {24},
number = {1},
pages = {2707},
pmid = {39367377},
issn = {1471-2458},
support = {82103748//National Natural Science Foundation of China/ ; 81972950//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Leprosy/epidemiology ; China/epidemiology ; Female ; Male ; *Spatio-Temporal Analysis ; Adult ; Middle Aged ; *Geographic Information Systems ; Adolescent ; Young Adult ; Aged ; Child ; Risk Factors ; },
abstract = {BACKGROUND: Despite being preventable and curable, leprosy remains endemic in some undeveloped regions, including China. Wenshan Zhuang and Miao Autonomous Prefecture (Wenshan prefecture) currently bears the highest leprosy burden in China. In this ecological study, we aimed to analyze the epidemiological characteristics as well as identify and visualize the high-risk townships of Wenshan prefecture using the most updated leprosy data from 2010 to 2022.<br><br>METHODS: Geographical information system combined with spatial scan statistics was used for newly detected leprosy cases abstracted from the Leprosy Management Information System in China. Global Moran's I index was used to uncover the spatial pattern of leprosy at the township level. Spatial scan statistics, encompassing purely temporal, purely spatial, spatial variation in temporal trends, and space-time analysis, were implemented for detecting the risk clusters.<br><br>RESULTS: Between 2010 and 2022, Wenshan prefecture detected 532 new leprosy cases, comprising 352 (66.17%) males and 180 (33.83%) females. The aggregated time primarily occurred between October 2010 and March 2014. The distribution pattern of newly detected leprosy cases was spatially clustered. We identified four high-risk spatial clusters encompassing 54.51% of the new cases. Furthermore, spatial variation in temporal trends highlighted one cluster as a potential high-risk area. Finally, two space-time clusters were detected, and the most likely cluster was predominantly located in the central and northwest regions of Wenshan prefecture, spanning from January 2010 to September 2013.<br><br>CONCLUSIONS: In this ecology study, we characterized the epidemiological features and temporal and spatial patterns of leprosy in Wenshan prefecture using the most recent leprosy data between 2010 and 2022. Our findings offer scientific insights into the epidemiological profiles and spatiotemporal dynamics of leprosy in Wenshan prefecture. Clinicians and policymakers should pay particular attention to the identified clusters for the prevention and control of leprosy.},
}
@article {pmid39373052,
year = {2024},
author = {Xie, X and Gui, L and Qiao, B and Wang, G and Huang, S and Zhao, Y and Sun, S},
title = {Deep learning in template-free de novo biosynthetic pathway design of natural products.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
pmid = {39373052},
issn = {1477-4054},
support = {2572022BD04//Fundamental Research Funds for the Central Universities/ ; 62001088//National Natural Science Foundation of China/ ; },
mesh = {*Biological Products/metabolism ; *Deep Learning ; *Biosynthetic Pathways ; Algorithms ; Computational Biology/methods ; Humans ; },
abstract = {Natural products (NPs) are indispensable in drug development, particularly in combating infections, cancer, and neurodegenerative diseases. However, their limited availability poses significant challenges. Template-free de novo biosynthetic pathway design provides a strategic solution for NP production, with deep learning standing out as a powerful tool in this domain. This review delves into state-of-the-art deep learning algorithms in NP biosynthesis pathway design. It provides an in-depth discussion of databases like Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and UniProt, which are essential for model training, along with chemical databases such as Reaxys, SciFinder, and PubChem for transfer learning to expand models' understanding of the broader chemical space. It evaluates the potential and challenges of sequence-to-sequence and graph-to-graph translation models for accurate single-step prediction. Additionally, it discusses search algorithms for multistep prediction and deep learning algorithms for predicting enzyme function. The review also highlights the pivotal role of deep learning in improving catalytic efficiency through enzyme engineering, which is essential for enhancing NP production. Moreover, it examines the application of large language models in pathway design, enzyme discovery, and enzyme engineering. Finally, it addresses the challenges and prospects associated with template-free approaches, offering insights into potential advancements in NP biosynthesis pathway design.},
}
@article {pmid39373528,
year = {2024},
author = {Ros-Rocher, N},
title = {The evolution of multicellularity and cell differentiation symposium: bridging evolutionary cell biology and computational modelling using emerging model systems.},
journal = {Biology open},
volume = {13},
number = {10},
pages = {},
pmid = {39373528},
issn = {2046-6390},
support = {101106415//European Union's Horizon Europe research and innovation funding program/ ; //Institute Pasteur: Institut Pasteur; Baylor College of Medicine/ ; },
mesh = {*Cell Differentiation/genetics ; *Biological Evolution ; Animals ; Computational Biology/methods ; Humans ; Cell Biology ; Models, Biological ; Computer Simulation ; Genomics/methods ; },
abstract = {'The evolution of multicellularity and cell differentiation' symposium, organized as part of the EuroEvoDevo 2024 meeting on June 25-28th in Helsinki (Finland), addressed recent advances on the molecular and mechanistic basis for the evolution of multicellularity and cell differentiation in eukaryotes. The symposium involved over 100 participants and brought together 10 speakers at diverse career stages. Talks covered various topics at the interface of developmental biology, evolutionary cell biology, comparative genomics, computational biology, and ecology using animal, protist, algal and mathematical models. This symposium offered a unique opportunity for interdisciplinary dialog among researchers working on different systems, especially in promoting collaborations and aligning strategies for studying emerging model species. Moreover, it fostered opportunities to promote early career researchers in the field and opened discussions of ongoing work and unpublished results. In this Meeting Review, we aim to promote the research, capture the spirit of the meeting, and present key topics discussed within this dynamic, growing and open community.},
}
@article {pmid39373541,
year = {2025},
author = {Zuo, YW and Quan, MH and Liu, GH and Zhang, X and Long, NN and You, SQ and Peng, Y and Deng, HP},
title = {Multi-Omics Analysis Reveals Molecular Responses of Alkaloid Content Variations in Lycoris aurea Across Different Locations.},
journal = {Plant, cell &amp; environment},
volume = {48},
number = {2},
pages = {953-964},
doi = {10.1111/pce.15187},
pmid = {39373541},
issn = {1365-3040},
support = {//This study was supported by General Program of the Chongqing Natural Science Foundation and National Natural Science Foundation of China./ ; },
mesh = {*Lycoris/metabolism/genetics ; *Alkaloids/metabolism ; Gene Expression Regulation, Plant ; Metabolomics ; Transcriptome ; Soil Microbiology ; Protein Interaction Maps ; Gene Expression Profiling ; Photosynthesis ; Metabolome ; Genes, Plant ; Multiomics ; },
abstract = {Lycoris aurea, celebrated for its visually striking flowers and significant medicinal value due to the presence of alkaloids such as lycorine and galanthamine, has intricate yet poorly understood regulatory mechanisms. This study provides a detailed examination of the transcriptomic, metabolomic and ecological dynamics of L. aurea, aiming to elucidate the underlying molecular mechanisms of alkaloid biosynthesis. Our comparative analysis across different ecological settings highlighted key genes involved in alkaloid biosynthesis, such as genes encoding aldehyde dehydrogenase and norbelladine 4'-O-methyltransferase, which were distinctively increased in the high alkaloids-producing group. We identified a total of 6871 differentially expressed genes and 915 metabolites involved in pathways like terpenoid backbone biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis. Protein interaction network analysis revealed significant upregulation of photosynthesis, photosystem and photosynthetic membrane pathways in the alkaloids-producing region. Furthermore, our research delineated the interactions among soil microbial communities, genes and plant and soil biochemical properties, noting that bacterial populations correlate with soil properties that favour the activation of metabolic pathways essential for alkaloid production. Collectively, this study advances our understanding of the genetic and metabolic alkaloid biosynthesis pathways in L. aurea, shedding light on the complex interactions that govern alkaloid production.},
}
@article {pmid39373887,
year = {2024},
author = {Dittrich, SP and Adithya, S and Ajith, Y and Athira, N and Athira, KS and Safeer, MS and Preena, P and Aishwarya, A and Athira, K and Nisha, AR and Devi, G and Mäder, M and Beena, V and Jacob, SS},
title = {Parasite diversity among domestic goats of tropical monsoon climatic zone in India.},
journal = {Parasitology research},
volume = {123},
number = {10},
pages = {342},
pmid = {39373887},
issn = {1432-1955},
support = {IN-ME_BI-5550//Deutscher Akademischer Austauschdienst/ ; SRG/2022/000837//Science and Engineering Research Board/ ; SRG/2022/000837//Science and Engineering Research Board/ ; },
mesh = {Animals ; *Goats/parasitology ; India/epidemiology ; *Goat Diseases/parasitology/epidemiology ; *Tropical Climate ; Phylogeny ; Parasitic Diseases, Animal/parasitology/epidemiology ; Parasites/classification/isolation &amp; purification/genetics ; Biodiversity ; },
abstract = {Among different climatic zones in India, the tropical monsoon region comprises a diverse ecosystem characterized by the endemic nature of several parasites including certain emerging and re-emerging vector-borne pathogens of humans, whereas a systematic investigation of the occurrence of different parasites among domestic goats in this area is not yet explored. The goal of the present study is to explore the parasite diversity focusing on molecular identification of vector-borne hemoparasites and its health impacts on domestic goats reared in the tropical monsoon climate zone of Kerala, India. Among 227 goats presented to the Teaching Veterinary Clinical Complex (TVCC) in the monsoon months of 2023, thirty animals were recruited for the study. The animals were screened for the presence of different hemoparasites (Anaplasma spp., Theileria spp., and Babesia spp.), ectoparasites (ticks, lice, and fleas), and gastrointestinal (GI) parasites (hookworms, threadworms, tapeworms, whipworms, and coccidia). The isolated hemoparasites were further characterized by sequencing and phylogenetic analysis. The correlation studies to elucidate the association between the occurrence of different parasites and clinical manifestations (hyperthermia, pallor of mucous membrane, circulatory failure, respiratory signs, neurological instability, and GI signs), blood picture (anemia, leukopenia, thrombocytopenia), demographics (sex and age), and treatment history (hemoparasitic therapy, ectoparasiticidal application, and prophylactic deworming) were conducted. The co-infection status of these parasites was also evaluated. A substantial portion of the goats in the study group was found to be affected by vector-borne hemoparasitic diseases and their arthropod vectors or GI parasites or both. This can be attributed to the constantly warm and humid climate of the region, which is favorable for the survival and growth of different life cycle stages of these parasites and vectors. A strategic parasitic disease surveillance-cum-control program is the need of the hour for ensuring climate resilience and profitable goat farming in the region.},
}
@article {pmid39374677,
year = {2024},
author = {Ikeda, T and Cooray, U and Matsugaki, R and Suzuki, Y and Takagi, M and Muramatsu, K and Fushimi, K and Murakami, M and Osaka, K and Matsuda, S},
title = {Associations of hypothetical early intensive in-hospital rehabilitation with activities of daily living after hip fracture surgery in patients with and without dementia: emulating a randomized controlled trial using medical claims data.},
journal = {Journal of clinical epidemiology},
volume = {176},
number = {},
pages = {111550},
doi = {10.1016/j.jclinepi.2024.111550},
pmid = {39374677},
issn = {1878-5921},
mesh = {Humans ; *Hip Fractures/surgery/rehabilitation ; Female ; Male ; *Dementia/rehabilitation ; Aged ; *Activities of Daily Living ; Japan ; Aged, 80 and over ; Middle Aged ; Hospitalization/statistics &amp; numerical data ; Recovery of Function ; },
abstract = {OBJECTIVES: To investigate the impact of early intensive in-hospital rehabilitation, initiated within 2 days of surgery and lasting up to 7 days, on the recovery of activities of daily living in patients with and without dementia.<br><br>STUDY DESIGN AND SETTING: Medical claims data from 925 hospitals in Japan were analyzed. We enrolled patients aged &#x2265;50&#xa0;years who underwent hip fracture surgery within 2&#xa0;days of admission between April 1, 2018, and December 31, 2019. Low- (20&#xa0;minutes per day starting on day 2), highest- (60&#xa0;minutes per day starting on day 1), and gradually increasing (20&#xa0;minutes on day 1, 40&#xa0;minutes on days 2-4, and 60&#xa0;minutes per day thereafter) intensity regimens were used as exposures. The outcomes were Barthel Index (BI) scores at 14 and 30&#xa0;days postoperatively. For per-protocol analysis, a target trial emulation framework with the sequential doubly robust estimator was used.<br><br>RESULTS: Among patients without dementia (N&#xa0;=&#xa0;11,461), no significant differences in BI scores were observed at 14&#xa0;days postoperatively across regimens. At 30&#xa0;days postoperatively, significant differences in BI scores were noted between highest- and low-intensity regimens and between gradually increasing intensity and low-intensity regimens, with additive BI scores of 15.2 (95% CI, 10.7-19.7) and 14.7 (95% CI, 9.2-20.2), respectively. In patients with dementia (N&#xa0;=&#xa0;14,302), significant differences in BI scores were noted at 14&#xa0;days postoperatively between highest- and low-intensity regimens and between gradually increasing intensity and low-intensity regimens, with additive BI scores of 8.7 (95% CI, 5.2-12.2) and 10.7 (95% CI, 5.8-15.6), respectively. At 30&#xa0;days postoperatively, a significant difference in BI scores was observed between gradually increasing intensity and low-intensity regimens, with an additive BI score of 17.9 (95% CI, 11.3-24.5).<br><br>CONCLUSION: Early intensive in-hospital rehabilitation is highly relevant and beneficial for dementia patients.},
}
@article {pmid39376700,
year = {2024},
author = {Chelliah, DS and Ray, AE and Zhang, E and Terauds, A and Ferrari, BC},
title = {The Vestfold Hills are alive: characterising microbial and environmental dynamics in Old Wallow, eastern Antarctica.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1443491},
pmid = {39376700},
issn = {1664-302X},
abstract = {Old Wallow is an underexplored, hyper-arid coastal desert in Antarctica's Vestfold Hills. Situated near an elephant seal wallow, we examined how stochastic nutrient inputs from the seal wallow affect soil communities amid environmental changes along a spatially explicit sampling transect. We hypothesized that nutrient levels would be elevated due to proximity to the seal wallow, influencing community distributions. While the soil bacterial and eukaryotic communities at the phylum level were similar to other terrestrial environments, analysis at class and family levels revealed a dominance of unclassified taxa that are often linked to marine environments. Elevated nutrient concentrations (NO3 [-], SO4 [2-], SO3) were found at Old Wallow, with conductivity and Cl[-] levels up to 10-fold higher at the lowest elevation soils, correlating with significantly (p < 0.05) higher abundances of halophilic (Halomonadaceace) and uncultivated lineages (Ca Actinomarinales, unclassified Bacillariophyta and unclassified Opisthonkonta). An improved Gradient Forest model was used to quantify microbial responses to 26 soil gradients at OW, revealing variable responses to environmental predictors and identifying critical environmental thresholds or drivers of community turnover. Major tipping points were projected for eukaryotes with SO4 [2-], pH, and SO3, and for bacteria with moisture, Na2O, and Cl[-]. Thus, the Old Wallow ecosystem is primarily shaped by salt, sulphate, and moisture and is dominated by uncultivated taxa, which may be sensitive to environmental changes once critical tipping points are reached. This study provides critical baseline data for future regional monitoring under threats of environmental change.},
}
@article {pmid39379720,
year = {2024},
author = {Klopper, A},
title = {GPS tracking reveals how hares shape lynx populations.},
journal = {Nature},
volume = {634},
number = {8033},
pages = {301},
doi = {10.1038/d41586-024-03272-x},
pmid = {39379720},
issn = {1476-4687},
mesh = {Animals ; *Geographic Information Systems ; *Lynx/physiology ; Population Density ; Population Dynamics ; Alaska ; *Predatory Behavior ; *Hares/physiology ; },
}
@article {pmid39381069,
year = {2024},
author = {Boyes, D and Lees, DC and Sims, I and Phillips, D and Boyes, C and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Yellow-dotted Stilt, Euspilapteryx auroguttella Stephens, 1835.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {226},
pmid = {39381069},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Euspilapteryx auroguttella (the Yellow-dotted Stilt; Arthropoda; Insecta; Lepidoptera; Gracillariidae). The genome sequence is 331.9 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.94 kilobases in length.},
}
@article {pmid39385455,
year = {2024},
author = {Wu, H and Li, Q and Wu, JC},
title = {Bioinformatics-aided function exploration of GH29 fucosidases from human gut Parabacteroides.},
journal = {Glycobiology},
volume = {34},
number = {12},
pages = {},
doi = {10.1093/glycob/cwae086},
pmid = {39385455},
issn = {1460-2423},
support = {2023GDASZH-2023010102//GDAS' Project of Science and Technology Development/ ; SL2023A04J01435//Guangzhou Basic and Applied Basic Research Foundation/ ; 2022A1515110917//Guangdong Basic and Applied Basic Research Foundation/ ; 32302033//National Natural Science Foundation of China/ ; 2023A04J1494//Guangzhou Basic and Applied Basic Research Foundation/ ; 2022GDASZH-2022010110//GDAS' Project of Science and Technology Development/ ; },
mesh = {Humans ; *alpha-L-Fucosidase/metabolism/genetics/chemistry ; *Computational Biology ; Gastrointestinal Microbiome ; Bacteroidetes/enzymology/genetics ; Polysaccharides/metabolism/chemistry ; Substrate Specificity ; Mucins/metabolism/chemistry ; },
abstract = {Gut microbes produce α-l-fucosidases critical for utilizing human milk oligosaccharides, mucosal and dietary glycans. Although gut Parabacteroides have garnered attention for their impact on host health and disease, their CAZymes remain poorly studied. CAZome analysis of eleven gut Parabacteroides type strains revealed their capacity to degrade mucin O-glycans. Their abundance of GH29 fucosidases caught our attention, and we predicted the functional profiles of 46 GH29 fucosidases using in silico approaches. Our findings showed diverse linkages specificities and species-specific distributions, with over half of GH29 enzymes functioning as α1,3/4 fucosidases, essential for acting on Lewis antigen epitopes of mucin O-glycans. We further enzymatically validated 4 novel GH29 sequences from poorly characterized groups. PgoldGH29A (cluster37GH29BERT, GH29:75.1CUPP) does not act on tested natural substrates. PgoldGH29B (cluster1GH29BERT, GH29:84.1CUPP) functions as a strict α1,3/4 fucosidase. PgoldGH29C (cluster14GH29BERT, GH29:29.1CUPP) displays unprecedented substrate specificity for α1,2/3/4 disaccharides. PgoldGH29D (cluster4GH29BERT, GH29:6.2CUPP) acts on α1,2/3/4/6 linkages similar to enzymes from GH29:6.1CUPP but prefers disaccharides over trisaccharides. These results suggest that PgoldGH29B and PgoldGH29D can contribute to mucin O-glycan degradation via their α1,3/4 and α1,2 fucosidase activity, respectively, while the natural substrates of PgoldGH29A and PgoldGH29C may be irrelevant to host-glycans. These insights enhance our understanding of the ecological niches inhabited by gut Parabacteroides and may guide similar exploration in other intriguing gut microbial species.},
}
@article {pmid39386964,
year = {2024},
author = {Martin, SH and Lohse, K and Ebdon, S and Mackintosh, A and , and , and , and , and , },
title = {The genome sequence of the Pearl-bordered Fritillary, Boloria euphrosyne (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {267},
pmid = {39386964},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Boloria euphrosyne (the Pearl-bordered Fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 400.4 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 15.17 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,138 protein coding genes.},
}
@article {pmid39387871,
year = {2024},
author = {Smith, SJ and Cummins, SF and Motti, CA and Wang, T},
title = {A mass spectrometry database for the identification of marine animal saponin-related metabolites.},
journal = {Analytical and bioanalytical chemistry},
volume = {416},
number = {29},
pages = {6893-6907},
pmid = {39387871},
issn = {1618-2650},
mesh = {*Saponins/analysis/metabolism ; Animals ; *Aquatic Organisms/chemistry/metabolism ; *Mass Spectrometry/methods ; Databases, Factual ; },
abstract = {Saponins encompass a diverse group of naturally occurring glycoside molecules exhibiting amphiphilic properties and a broad range of biological activities. There is a resurgence of interest in those saponins produced by marine organisms based on their potential therapeutic benefits, application in food products and most recently their potential involvement in intra- and inter-species chemical communication. The continual advancements in liquid chromatography techniques and mass spectrometry technologies have allowed for greater detection rates, as well as improved isolation and elucidation of saponins. These factors have significantly contributed to the expansion in the catalogue of known saponin structures isolated from marine invertebrates; however, there currently exists no specific chemical library resource to accelerate the discovery process. In this study, a Marine Animal Saponin Database (MASD v1.0) has been developed to serve as a valuable chemical repository for known marine saponin-related data, including chemical formula, molecular mass and biological origin of nearly 1000 secondary metabolites associated with saponins produced by marine invertebrates. We demonstrate its application with an exemplar asteroid extract (Acanthaster cf. solaris, also known as crown-of-thorns starfish; COTS), identifying saponins from the MASD v1.0 that have been previously reported from COTS, as well as 21 saponins isolated from multiple other related asteroid species. This database will help facilitate future research endeavours, aiding researchers in exploring the vast chemical diversity of saponins produced by marine organisms and providing ecological insights, and the realisation of their potential for various applications, including as pharmaceuticals.},
}
@article {pmid39390511,
year = {2024},
author = {Li, Y and Thomas, GWC and Richards, S and Waterhouse, RM and Zhou, X and Pfrender, ME},
title = {Rapid evolution of mitochondrion-related genes in haplodiploid arthropods.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {229},
pmid = {39390511},
issn = {1741-7007},
mesh = {Animals ; *Evolution, Molecular ; *Arthropods/genetics ; *Genes, Mitochondrial/genetics ; Phylogeny ; Haploidy ; Diploidy ; Oxidative Phosphorylation ; Cell Nucleus/genetics ; },
abstract = {BACKGROUND: Mitochondrial genes and nuclear genes cooperate closely to maintain the functions of mitochondria, especially in the oxidative phosphorylation (OXPHOS) pathway. However, mitochondrial genes among arthropod lineages have dramatic evolutionary rate differences. Haplodiploid arthropods often show fast-evolving mitochondrial genes. One hypothesis predicts that the small effective population size of haplodiploid species could enhance the effect of genetic drift leading to higher substitution rates in mitochondrial and nuclear genes. Alternatively, positive selection or compensatory changes in nuclear OXPHOS genes could lead to the fast-evolving mitochondrial genes. However, due to the limited number of arthropod genomes, the rates of evolution for nuclear genes in haplodiploid species, besides hymenopterans, are largely unknown. To test these hypotheses, we used data from 76 arthropod genomes, including 5 independently evolved haplodiploid lineages, to estimate the evolutionary rates and patterns of gene family turnover of mitochondrial and nuclear genes.<br><br>RESULTS: We show that five haplodiploid lineages tested here have fast-evolving mitochondrial genes and fast-evolving nuclear genes related to mitochondrial functions, while nuclear genes not related to mitochondrion showed no significant evolutionary rate differences. Among hymenopterans, bees and ants show faster rates of molecular evolution in mitochondrial genes and mitochondrion-related nuclear genes than sawflies and wasps. With genome data, we also find gene family expansions and contractions in mitochondrion-related genes of bees and ants.<br><br>CONCLUSIONS: Our results reject the small population size hypothesis in haplodiploid species. A combination of positive selection and compensatory changes could lead to the observed patterns in haplodiploid species. The elevated evolutionary rates in OXPHOS complex 2 genes of bees and ants suggest a unique evolutionary history of social hymenopterans.},
}
@article {pmid39390673,
year = {2024},
author = {Udaondo, Z and Ramos, JL and Abram, K},
title = {Unraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms.},
journal = {FEMS microbiology reviews},
volume = {48},
number = {6},
pages = {},
pmid = {39390673},
issn = {1574-6976},
support = {PID2021-123469OB-I00//Plan Nacional sobre Drogas/ ; },
mesh = {*Pseudomonas putida/genetics/classification/drug effects ; *Genome, Bacterial/genetics ; *Genetic Variation ; Drug Resistance, Bacterial/genetics ; Genomics ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The genus Pseudomonas is characterized by its rich genetic diversity, with over 300 species been validly recognized. This reflects significant progress made through sequencing and computational methods. Pseudomonas putida group comprises highly adaptable species that thrive in diverse environments and play various ecological roles, from promoting plant growth to being pathogenic in immunocompromised individuals. By leveraging the GRUMPS computational pipeline, we scrutinized 26 363 genomes labeled as Pseudomonas in the NCBI GenBank, categorizing all Pseudomonas spp. genomes into 435 distinct species-level clusters or cliques. We identified 224 strains deposited under the taxonomic identifier "Pseudomonas putida" distributed within 31 of these species-level clusters, challenging prior classifications. Nine of these 31 cliques contained at least six genomes labeled as "Pseudomonas putida" and were analysed in depth, particularly clique_1 (P. alloputida) and clique_2 (P. putida). Pangenomic analysis of a set of 413 P. putida group strains revealed over 2.2 million proteins and more than 77 000 distinct protein families. The core genome of these 413 strains includes 2226 protein families involved in essential biological processes. Intraspecific genetic homogeneity was observed within each clique, each possessing a distinct genomic identity. These cliques exhibit distinct core genes and diverse subgroups, reflecting adaptation to specific environments. Contrary to traditional views, nosocomial infections by P. alloputida, P. putida, and P. monteilii have been reported, with strains showing varied antibiotic resistance profiles due to diverse mechanisms. This review enhances the taxonomic understanding of key P. putida group species using advanced population genomics approaches and provides a comprehensive understanding of their genetic diversity, ecological roles, interactions, and potential applications.},
}
@article {pmid39392918,
year = {2024},
author = {Kopania, EEK and Thomas, GWC and Hutter, CR and Mortimer, SME and Callahan, CM and Roycroft, E and Achmadi, AS and Breed, WG and Clark, NL and Esselstyn, JA and Rowe, KC and Good, JM},
title = {Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents.},
journal = {Evolution; international journal of organic evolution},
volume = {79},
number = {1},
pages = {11-27},
pmid = {39392918},
issn = {1558-5646},
support = {R01 HD094787/HD/NICHD NIH HHS/United States ; R01 HD073439/HD/NICHD NIH HHS/United States ; R01 HG009299/HG/NHGRI NIH HHS/United States ; DEB-1754096//National Science Foundation/ ; R01-HG009299/HG/NHGRI NIH HHS/United States ; R01-HD073439//National Institute of Child Health and Human Development/ ; },
mesh = {Animals ; Male ; *Spermatozoa/physiology ; Mice/genetics ; *Evolution, Molecular ; *Testis/anatomy &amp; histology ; Phylogeny ; Selection, Genetic ; Sexual Selection ; Spermatogenesis/genetics ; Murinae/genetics/physiology ; Rats ; Reproduction/genetics ; },
abstract = {It remains unclear how variation in the intensity of sperm competition shapes phenotypic and molecular evolution across clades. Mice and rats in the subfamily Murinae are a rapid radiation exhibiting incredible diversity in sperm morphology and production. We combined phenotypic and genomic data to perform phylogenetic comparisons of male reproductive traits and genes across 78 murine species. We identified several shifts towards smaller relative testes mass (RTM), presumably reflecting reduced sperm competition. Several sperm traits were associated with RTM, suggesting that mating system evolution selects for convergent suites of traits related to sperm competitive ability. We predicted that sperm competition would also drive more rapid molecular divergence in species with large testes. Contrary to this, we found that many spermatogenesis genes evolved more rapidly in species with smaller RTM due to relaxed purifying selection. While some reproductive genes evolved rapidly under recurrent positive selection, relaxed selection played a greater role in underlying rapid evolution in small testes species. Our work demonstrates that postcopulatory sexual selection can impose strong purifying selection shaping the evolution of male reproduction and that broad patterns of molecular evolution may help identify genes that contribute to male fertility.},
}
@article {pmid39395131,
year = {2024},
author = {Atesoglu, A and Ayyildiz, E and Karakaya, I and Bulut, FS and Serengil, Y},
title = {Land cover and drought risk assessment in Türkiye's mountain regions using neutrosophic decision support system.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {11},
pages = {1046},
pmid = {39395131},
issn = {1573-2959},
mesh = {*Droughts ; *Environmental Monitoring/methods ; *Climate Change ; Risk Assessment ; Ecosystem ; Turkey ; Decision Support Techniques ; Remote Sensing Technology ; Conservation of Natural Resources/methods ; },
abstract = {Earth observation (EO) provides dynamic scientific methods for tracking and defining ecological parameters in mountainous regions. Open-source platforms are frequently utilized in this context to efficiently collect and evaluate spatial data. In this study, we used Collect Earth (CE), an open-source land monitoring platform, to reveal and assess land cover, land cover change, and relevant ecological parameters such as drought risk. Mountain ecosystems were subject to an evaluation for the first time by combining remote sensing with a hybridization of Decision-Making Trial and Evaluation Laboratory (DEMATEL), analytic hierarchy process (AHP), and Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) for neutrosophic sets in risk assessment problems of several connected criteria. The high and dispersed high alpine environment of Türkiye accommodates land with relatively less human influence, making it suitable to observe climate change impacts. In the framework of the study, we evaluated more than two decades (2000-2022) of land use and land cover (LULC) changes in the mountain regions of the country. Using nine identified ecological parameters, we also evaluated drought risk. The parameters included were the LULC classes and their change, elevation, slope, aspect, precipitation, temperature, normalized difference vegetation index (NDVI), water deficit, and evapotranspiration (ET). The risk map we produced revealed a high to very high drought risk for almost throughout the Türkiye's mountainous areas. We concluded that integrating geospatial techniques with hybridization is promising for mapping drought risk, helping policymakers prepare effective drought mitigation measures to reasonably adapt to climate change impacts.},
}
@article {pmid39395210,
year = {2025},
author = {Pachade, S and Porwal, P and Kokare, M and Deshmukh, G and Sahasrabuddhe, V and Luo, Z and Han, F and Sun, Z and Qihan, L and Kamata, SI and Ho, E and Wang, E and Sivajohan, A and Youn, S and Lane, K and Chun, J and Wang, X and Gu, Y and Lu, S and Oh, YT and Park, H and Lee, CY and Yeh, H and Cheng, KW and Wang, H and Ye, J and He, J and Gu, L and Müller, D and Soto-Rey, I and Kramer, F and Arai, H and Ochi, Y and Okada, T and Giancardo, L and Quellec, G and Mériaudeau, F},
title = {RFMiD: Retinal Image Analysis for multi-Disease Detection challenge.},
journal = {Medical image analysis},
volume = {99},
number = {},
pages = {103365},
doi = {10.1016/j.media.2024.103365},
pmid = {39395210},
issn = {1361-8423},
mesh = {Humans ; *Retinal Diseases/diagnostic imaging ; Image Interpretation, Computer-Assisted/methods ; Deep Learning ; Fundus Oculi ; Datasets as Topic ; Diabetic Retinopathy/diagnostic imaging ; Databases, Factual ; },
abstract = {In the last decades, many publicly available large fundus image datasets have been collected for diabetic retinopathy, glaucoma, and age-related macular degeneration, and a few other frequent pathologies. These publicly available datasets were used to develop a computer-aided disease diagnosis system by training deep learning models to detect these frequent pathologies. One challenge limiting the adoption of a such system by the ophthalmologist is, computer-aided disease diagnosis system ignores sight-threatening rare pathologies such as central retinal artery occlusion or anterior ischemic optic neuropathy and others that ophthalmologists currently detect. Aiming to advance the state-of-the-art in automatic ocular disease classification of frequent diseases along with the rare pathologies, a grand challenge on "Retinal Image Analysis for multi-Disease Detection" was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI - 2021). This paper, reports the challenge organization, dataset, top-performing participants solutions, evaluation measures, and results based on a new "Retinal Fundus Multi-disease Image Dataset" (RFMiD). There were two principal sub-challenges: disease screening (i.e. presence versus absence of pathology - a binary classification problem) and disease/pathology classification (a 28-class multi-label classification problem). It received a positive response from the scientific community with 74 submissions by individuals/teams that effectively entered in this challenge. The top-performing methodologies utilized a blend of data-preprocessing, data augmentation, pre-trained model, and model ensembling. This multi-disease (frequent and rare pathologies) detection will enable the development of generalizable models for screening the retina, unlike the previous efforts that focused on the detection of specific diseases.},
}
@article {pmid39396151,
year = {2025},
author = {Burger, J and Gochfeld, M and Brown, KG and Cortes, M and Ng, K and Kosson, D},
title = {Using the National Land Cover Database as an indicator of shrub-steppe habitat: comparing two large United States federal lands with surrounding regions.},
journal = {Journal of toxicology and environmental health. Part A},
volume = {88},
number = {1},
pages = {1-19},
doi = {10.1080/15287394.2024.2412659},
pmid = {39396151},
issn = {2381-3504},
mesh = {*Ecosystem ; *Conservation of Natural Resources ; Idaho ; Washington ; Databases, Factual ; United States ; Grassland ; Environmental Monitoring/methods ; },
abstract = {There is a need to assess whether ecological resources are being protected on large, federal lands. The aim of this study was to present a methodology which consistently and transparently determines whether two large Department of Energy (U.S. DOE) facilities have protected valuable ecological lands on their sites compared to the surrounding region. The National Land Cover Database (2019) was used to examine the % shrub-scrub (shrub-steppe) and other habitats on the DOE's Hanford Site (HS, Washington) and on the Idaho National Laboratory (INL), compared to a 10-km and 30-km diameter band of land surrounding each site. On both sites, over 95% is in shrub-scrub or grassland, compared to the surrounding region. Approximately 70% of 10 km and 30-km bands around INL, and less than 50% of land surrounding HS is located in these two habitat types. INL has preserved a significantly higher % shrub/scrub habitat than HS, but INL allows grazing on 60% of its land. HS has preserved a significantly higher % grassland than INL but no grazing on site is present. The methodology presented may be used to compare key ecological habitat types such as grasslands, forest, and desert among sites in different parts of the country. This methodology enables managers, resource trustees, and the public to (1) make remediation decisions that protect resources, (2) assess whether landowners and managers have adequately characterized and protected environmental resources on their sites, and (3) whether landowners and managers have protected the integrity of that land as well as its climax vegetation.},
}
@article {pmid39398937,
year = {2024},
author = {Boyes, D and Crowley, LM and Morley, LM and , and , and , and , and , and , and , },
title = {The genome sequence of the Green Oak Leaf Roller, Tortrix viridana (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {260},
pmid = {39398937},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from a female Tortrix viridana (the Green Oak Leaf Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 456.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length.},
}
@article {pmid39398938,
year = {2024},
author = {Li, R and Li, J and Lemer, S and Lopez, JV and Oatley, G and Sinclair, E and Clayton-Lucey, IA 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 genome sequence of the heart cockle, Fragum sueziense (Issel, 1869).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {366},
pmid = {39398938},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual Fragum sueziense (the heart cockle; Mollusca; Bivalvia; Cardiida; Cardiidae). The genome sequence is 1,206.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 92.77 kilobases in length. Gene annotation of this assembly on Ensembl identified 70,309 protein-coding genes.},
}
@article {pmid39398940,
year = {2024},
author = {Boyes, D and Hutchinson, F and Crowley, LM and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Common Flat-body moth, Agonopterix heracliana Linnaeus, 1758.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {329},
pmid = {39398940},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Agonopterix heracliana (the Common Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 539.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length.},
}
@article {pmid39399250,
year = {2024},
author = {Arliyani, I and Noori, MT and Ammarullah, MI and Tangahu, BV and Mangkoedihardjo, S and Min, B},
title = {Constructed wetlands combined with microbial fuel cells (CW-MFCs) as a sustainable technology for leachate treatment and power generation.},
journal = {RSC advances},
volume = {14},
number = {44},
pages = {32073-32100},
pmid = {39399250},
issn = {2046-2069},
abstract = {The physical and chemical treatment processes of leachate are not only costly but can also possibly produce harmful by products. Constructed wetlands (CW) has been considered a promising alternative technology for leachate treatment due to less demand for energy, economic, ecological benefits, and simplicity of operations. Various trends and approaches for the application of CW for leachate treatment have been discussed in this review along with offering an informatics peek of the recent innovative developments in CW technology and its perspectives. In addition, coupling CW with microbial fuel cells (MFCs) has proven to produce renewable energy (electricity) while treating contaminants in leachate wastewaters (CW-MFC). The combination of CW-MFC is a promising bio electrochemical that plays symbiotic among plant microorganisms in the rhizosphere of an aquatic plant that convert sun electricity is transformed into bioelectricity with the aid of using the formation of radical secretions, as endogenous substrates, and microbial activity. Several researchers study and try to find out the application of CW-MFC for leachate treatment, along with this system and performance. Several key elements for the advancement of CW-MFC technology such as bioelectricity, reactor configurations, plant species, and electrode materials, has been comprehensively discussed and future research directions were suggested for further improving the performance. Overall, CW-MFC may offer an eco-friendly approach to protecting the aquatic environment and come with built-in advantages for visual appeal and animal habitats using natural materials such as gravel, soil, electroactive bacteria, and plants under controlled condition.},
}
@article {pmid39399683,
year = {2024},
author = {Martin, C and Gitter, A and Anantharaman, K},
title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {39399683},
issn = {2693-5015},
support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; },
abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.},
}
@article {pmid39401366,
year = {2024},
author = {Posch, BC and Bush, SE and Koepke, DF and Schuessler, A and Anderegg, LLD and Aparecido, LMT and Blonder, BW and Guo, JS and Kerr, KL and Moran, ME and Cooper, HF and Doughty, CE and Gehring, CA and Whitham, TG and Allan, GJ and Hultine, KR},
title = {Intensive leaf cooling promotes tree survival during a record heatwave.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {43},
pages = {e2408583121},
pmid = {39401366},
issn = {1091-6490},
support = {IOS-2140427//NSF (NSF)/ ; IOS-2140428//NSF (NSF)/ ; IOS-2140429//NSF (NSF)/ ; IOS-2003205//NSF (NSF)/ ; IOS-2216855//NSF (NSF)/ ; DEB-1340852//NSF (NSF)/ ; DEB-1340856//NSF (NSF)/ ; DEB-2017895//NSF (NSF)/ ; },
mesh = {*Plant Leaves/physiology ; *Populus/physiology/genetics ; *Trees/physiology/genetics ; *Water ; Soil ; Genotype ; Extreme Heat ; Hot Temperature ; Ecosystem ; },
abstract = {Increasing heatwaves are threatening forest ecosystems globally. Leaf thermal regulation and tolerance are important for plant survival during heatwaves, though the interaction between these processes and water availability is unclear. Genotypes of the widely distributed foundation tree species Populus fremontii were studied in a controlled common garden during a record summer heatwave-where air temperature exceeded 48 °C. When water was not limiting, all genotypes cooled leaves 2 to 5 °C below air temperatures. Homeothermic cooling was disrupted for weeks following a 72-h reduction in soil water, resulting in leaf temperatures rising 3 °C above air temperature and 1.3 °C above leaf thresholds for physiological damage, despite the water stress having little effect on leaf water potentials. Tradeoffs between leaf thermal safety and hydraulic safety emerged but, regardless of water use strategy, all genotypes experienced significant leaf mortality following water stress. Genotypes from warmer climates showed greater leaf cooling and less leaf mortality after water stress in comparison with genotypes from cooler climates. These results illustrate how brief soil water limitation disrupts leaf thermal regulation and potentially compromises plant survival during extreme heatwaves, thus providing insight into future scenarios in which ecosystems will be challenged with extreme heat and unreliable soil water access.},
}
@article {pmid39401552,
year = {2024},
author = {Yan, X and Zhao, Z and Feng, S and Zhang, Y and Wang, Z and Li, Z},
title = {Multi-omics analysis reveal the fall armyworm Spodoptera frugiperda tolerate high temperature by mediating chitin-related genes.},
journal = {Insect biochemistry and molecular biology},
volume = {174},
number = {},
pages = {104192},
doi = {10.1016/j.ibmb.2024.104192},
pmid = {39401552},
issn = {1879-0240},
mesh = {Animals ; *Spodoptera/genetics/growth &amp; development/metabolism/physiology ; *Chitin/metabolism ; Hot Temperature ; Larva/genetics/growth &amp; development/metabolism ; CRISPR-Cas Systems ; Insect Proteins/metabolism/genetics ; Thermotolerance ; Transcriptome ; RNA Interference ; Multiomics ; },
abstract = {Climate change facilitates the rapid invasion of agricultural pests, threatening global food security. The fall armyworm Spodoptera frugiperda is a highly polyphagous migratory pest tolerant to high temperatures, allowing its proliferation in harsh thermal environments. We aimed to demonstrate mechanisms of its high-temperature tolerance, particularly transcriptional and metabolic regulation, which are poorly understood. To achieve the aim, we examined the impact and mechanism of heat events on S. frugiperda by using multiple approaches: ecological measurements, transcriptomics, metabolomics, RNAi, and CRISPR/Cas9 technology. We observed that several physiological indices (larval survival rate, larval period, pupation rate, pupal weight, eclosion rate, and average fecundity) decreased as the temperature increased, with the 32 °C treatment displaying a significant difference from the control group at 26 °C. Significantly upregulated expression of genes encoding endochitinase and chitin deacetylase was observed in the chitin-binding, extracellular region, and carbohydrate metabolic process GO terms of hemolymph, fat body, and brain, exhibiting a tissue-specific pattern. Significantly enriched pathways (e.g., cutin, suberin, and wax biosynthesis; oxidative phosphorylation and cofactor biosynthesis; diverse amino acid biosynthesis and degradation; carbon metabolism; and energy metabolism), all of which are essential for S. frugiperda larvae to tolerate temperature, were found in metabolites that were expressed differently. Successful RNA interference targeting of the three chitin-related genes reduced gene expression levels and larval survival rate. Knockout of the endochitinase gene by using the CRISPR/Cas9 system significantly reduced the relative gene expression and increased sensitivity to high-temperature exposure. On the basis of our findings, theoretical foundations for understanding the high-temperature tolerance of S. frugiperda populations and latent genetic control strategies were established.},
}
@article {pmid39403309,
year = {2024},
author = {Sivell, O and Sivell, D and Webb, JA and Mitchell, R and Ashworth, M and , and , and , and , and , and , and , },
title = {The genome sequence of the acalyptrate fly Dryomyza anilis Fallén, 1820.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {440},
pmid = {39403309},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male acalyptrate fly Dryomyza anilis (Arthropoda; Insecta; Diptera; Dryomyzidae). The genome sequence has a total length of 656.60 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.48 kilobases in length.},
}
@article {pmid39403498,
year = {2024},
author = {Hung, RJ and Low, I and Yeh, HC and Wang, PY and Chen, YS and Chen, LF},
title = {Feedback matters: EEG correlates of empathy involved in the naturalistic communication of emotions.},
journal = {Heliyon},
volume = {10},
number = {19},
pages = {e38574},
pmid = {39403498},
issn = {2405-8440},
abstract = {Empathy involves the processing of complex information related to dynamic interactions between the empathizer and target. One neural signature of empathy is the suppression of electroencephalographic mu rhythm (8-13 Hz) over the sensorimotor region. It is important to consider that few researchers have studied the effects of empathizer feedback on empathy and its underlying neural mechanism, and most previous research has lacked ecological validity due to standardized emotional stimuli and constraints on the experiment environment. Our objective in this study was to investigate the means by which empathizer feedback influences one's own empathy in naturalistic social situations. Our results revealed that empathizer feedback decreases empathic accuracy but does not affect the emotional contagion nor the emotional intensity of the empathizer. We also found that the ability to accurately infer sadness is hindered by empathizer feedback. Empathizers presented lower alpha activity in the sensorimotor cortical areas only while receiving sad narratives and not providing feedback. This study contributes to the emerging research on the influence of empathizer feedback in naturalistic social settings.},
}
@article {pmid39404811,
year = {2024},
author = {Litavský, J and Majzlan, O and Langraf, V and Žarnovičan, H},
title = {Influence of habitat management and selected environmental parameters on the ground-living communities of harvestmen (Opiliones) in the historical park in Rusovce (Slovakia).},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {11},
pages = {1056},
pmid = {39404811},
issn = {1573-2959},
support = {No. 1/0007/21//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; No. 1/0007/21//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; No. 1/0255/23//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; },
mesh = {*Ecosystem ; *Parks, Recreational ; *Environmental Monitoring ; Animals ; Slovakia ; Biodiversity ; Arachnida ; Conservation of Natural Resources/methods ; Forests ; Microclimate ; },
abstract = {City parks serve as valuable refuges for invertebrates in the urban environment, which are constantly exposed to human influence caused by management practices in the parks. Many harvestman species are suitable bioindicators for monitoring ecological change; however, their effective use in environmental assessment necessitates to expand the insufficient knowledge of ecological environmental specificities of their communities. We studied the diversity and dynamics of harvestman (Opiliones) communities in the historical park in Rusovce, situated in the southwestern part of Bratislava (Slovakia). Seven study sites were investigated, representing areas subjected to different management practices. The research was conducted from March 2019 to April 2020, using pitfall traps. We evaluated the impact of microclimatic variables (soil and air temperature), environmental characteristics (plant diversity and cover of vegetation layers, age of forest stands, thickness of the litter layer), and management practices on the structure of harvestman communities. The study revealed the response of specific harvestman species to temperature variations, emphasizing the importance of microclimatic conditions. Environmental variables, such as the richness of plant species in the shrub layer, the cover of the herb and shrub vegetation layers, and the age of the forest stands, were identified as key factors that influence the dispersal of harvestman species. Furthermore, management practices, especially the presence of monoculture tree plantations, significantly affected the species composition of harvestmen. Examining the sensitivity of Opiliones, important bioindicators, to these factors is crucial for implementing effective conservation strategies in urban green spaces and anthropogenically influenced ecosystems.},
}
@article {pmid39407030,
year = {2024},
author = {Mc Cartney, AM and Formenti, G and Mouton, A and De Panis, D and Marins, LS and Leitão, HG and Diedericks, G and Kirangwa, J and Morselli, M and Salces-Ortiz, J and Escudero, N and Iannucci, A and Natali, C and Svardal, H and Fernández, R and De Pooter, T and Joris, G and Strazisar, M and Wood, JMD and Herron, KE and Seehausen, O and Watts, PC and Shaw, F and Davey, RP and Minotto, A and Fernández, JM and Böhne, A and Alegria, C and Alioto, T and Alves, PC and Amorim, IR and Aury, JM and Backstrom, N and Baldrian, P and Baltrunaite, L and Barta, E and BedHom, B and Belser, C and Bergsten, J and Bertrand, L and Bilandija, H and Binzer-Panchal, M and Bista, I and Blaxter, M and Borges, PAV and Dias, GB and Bosse, M and Brown, T and Bruggmann, R and Buena-Atienza, E and Burgin, J and Buzan, E and Cariani, A and Casadei, N and Chiara, M and Chozas, S and Čiampor, F and Crottini, A and Cruaud, C and Cruz, F and Dalen, L and De Biase, A and Del Campo, J and Delic, T and Dennis, AB and Derks, MFL and Diroma, MA and Djan, M and Duprat, S and Eleftheriadi, K and Feulner, PGD and Flot, JF and Forni, G and Fosso, B and Fournier, P and Fournier-Chambrillon, C and Gabaldon, T and Garg, S and Gissi, C and Giupponi, L and Gomez-Garrido, J and González, J and Grilo, ML and Grüning, B and Guerin, T and Guiglielmoni, N and Gut, M and Haesler, MP and Hahn, C and Halpern, B and Harrison, PW and Heintz, J and Hindrikson, M and Höglund, J and Howe, K and Hughes, GM and Istace, B and Cock, MJ and Janžekovič, F and Jonsson, ZO and Joye-Dind, S and Koskimäki, JJ and Krystufek, B and Kubacka, J and Kuhl, H and Kusza, S and Labadie, K and Lähteenaro, M and Lantz, H and Lavrinienko, A and Leclère, L and Lopes, RJ and Madsen, O and Magdelenat, G and Magoga, G and Manousaki, T and Mappes, T and Marques, JP and Redondo, GIM and Maumus, F and McCarthy, SA and Megens, HJ and Melo-Ferreira, J and Mendes, SL and Montagna, M and Moreno, J and Mosbech, MB and Moura, M and Musilova, Z and Myers, E and Nash, WJ and Nater, A and Nicholson, P and Niell, M and Nijland, R and Noel, B and Noren, K and Oliveira, PH and Olsen, RA and Ometto, L and Oomen, RA and Ossowski, S and Palinauskas, V and Palsson, S and Panibe, JP and Pauperio, J and Pavlek, M and Payen, E and Pawlowska, J and Pellicer, J and Pesole, G and Pimenta, J and Pippel, M and Pirttilä, AM and Poulakakis, N and Rajan, J and M C Rego, R and Resendes, R and Resl, P and Riesgo, A and Rodin-Morch, P and Soares, AER and Fernandes, CR and Romeiras, MM and Roxo, G and Rüber, L and Ruiz-Lopez, MJ and Saarma, U and da Silva, LP and Sim-Sim, M and Soler, L and Sousa, VC and Santos, CS and Spada, A and Stefanovic, M and Steger, V and Stiller, J and Stöck, M and Struck, TH and Sudasinghe, H and Tapanainen, R and Tellgren-Roth, C and Trindade, H and Tukalenko, Y and Urso, I and Vacherie, B and Van Belleghem, SM and Van Oers, K and Vargas-Chavez, C and Velickovic, N and Vella, N and Vella, A and Vernesi, C and Vicente, S and Villa, S and Pettersson, OV and Volckaert, FAM and Voros, J and Wincker, P and Winkler, S and Ciofi, C and Waterhouse, RM and Mazzoni, CJ},
title = {Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.},
journal = {npj biodiversity},
volume = {3},
number = {1},
pages = {31},
doi = {10.1038/s44185-024-00065-3},
pmid = {39407030},
issn = {2731-4243},
}
@article {pmid39409485,
year = {2024},
author = {Jechow, A and Bumberger, J and Palm, B and Remmler, P and Schreck, G and Ogashawara, I and Kiel, C and Kohnert, K and Grossart, HP and Singer, GA and Nejstgaard, JC and Wollrab, S and Berger, SA and Hölker, F},
title = {Characterizing and Implementing the Hamamatsu C12880MA Mini-Spectrometer for Near-Surface Reflectance Measurements of Inland Waters.},
journal = {Sensors (Basel, Switzerland)},
volume = {24},
number = {19},
pages = {},
pmid = {39409485},
issn = {1424-8220},
support = {Leibniz Competition No. K45/2017 (CONNECT-Connectivity and synchronization of lake ecosystems in space and time)//Leibniz Association/ ; IGB Frontiers project (2017)//Leibniz Institute of Freshwater Ecology and Inland Fisheries/ ; },
abstract = {In recent decades, inland water remote sensing has seen growing interest and very strong development. This includes improved spatial resolution, increased revisiting times, advanced multispectral sensors and recently even hyperspectral sensors. However, inland waters are more challenging than oceanic waters due to their higher complexity of optically active constituents and stronger adjacency effects due to their small size and nearby vegetation and built structures. Thus, bio-optical modeling of inland waters requires higher ground-truthing efforts. Large-scale ground-based sensor networks that are robust, self-sufficient, non-maintenance-intensive and low-cost could assist this otherwise labor-intensive task. Furthermore, most existing sensor systems are rather expensive, precluding their employability. Recently, low-cost mini-spectrometers have become widely available, which could potentially solve this issue. In this study, we analyze the characteristics of such a mini-spectrometer, the Hamamatsu C12880MA, and test it regarding its application in measuring water-leaving radiance near the surface. Overall, the measurements performed in the laboratory and in the field show that the system is very suitable for the targeted application.},
}
@article {pmid39414803,
year = {2024},
author = {Lončarević, N and Liu, U and Stefanaki, A and Carapeto, A and Ensslin, A and Meade, C and Metzing, D and Peci, D and Fantinato, E and Colling, G and Pankova, H and Akmane, I and Tsvetkov, IN and Sibik, J and Szitár, K and Van Meerbeek, K and Daco, L and Boudagher, M and Klisz, M and Walczak, M and Evju, M and Lužnik, M and Kiehn, M and Sarginci, M and Aksoy, N and Koçer, N and Barazani, O and Anastasiu, P and Stroh, P and Vit, P and Vergeer, P and Puchałka, R and Kahale, R and Godefroid, S and Lanfranco, S and Parpan, T and Kull, T and Rašomavičius, V and Fišer, &#x17d; and Glasnović, P},
title = {Database of European vascular plants red lists as a contribution to more coherent plant conservation.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1138},
pmid = {39414803},
issn = {2052-4463},
support = {R25 CA018201/CA/NCI NIH HHS/United States ; CA18201//European Cooperation in Science and Technology (COST)/ ; },
mesh = {Europe ; *Databases, Factual ; *Conservation of Natural Resources ; *Plants/classification ; Biodiversity ; },
abstract = {We introduce the database of European vascular plant red lists, a compilation of red list categories designated to taxa during in-country conservation assessments. Version 1.0 of the database is a standalone static dataset with open access in an end-user friendly format. Its aim is to fulfil the objectives of European Cooperation in Science and Technology (COST) Action 18201, ConservePlants. The database synthesizes data across 42 red lists from 41 countries, with participation of 39 out of a total of 44 European countries and two additional Mediterranean countries. The database contains 51,109 records representing 21,481 original taxonomic names with 37 different red list categories. During data harmonisation, 20,312 of the original taxonomic names were assigned to 17,873 unique accepted taxonomic names with scientific authorships across 184 families, 1650 genera and 15,593 species; and red list categories were standardised to 13 unique categories. We see this database as a source of information in diverse plant conservation activities and suitable for various stakeholders.},
}
@article {pmid39415784,
year = {2024},
author = {Lohse, K and Vila, R and Hayward, A and Laetsch, DR and Harnqvist, S and , and , and , and , and , },
title = {The genome sequence of the Essex Skipper butterfly, Thymelicus lineola (Ochsenheimer, 1808).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {452},
pmid = {39415784},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Essex Skipper butterfly, Thymelicus lineola (Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence spans 511.80 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.24 kilobases in length.},
}
@article {pmid39417330,
year = {2025},
author = {Kershenbaum, A and Akçay, &#xc7; and Babu-Saheer, L and Barnhill, A and Best, P and Cauzinille, J and Clink, D and Dassow, A and Dufourq, E and Growcott, J and Markham, A and Marti-Domken, B and Marxer, R and Muir, J and Reynolds, S and Root-Gutteridge, H and Sadhukhan, S and Schindler, L and Smith, BR and Stowell, D and Wascher, CAF and Dunn, JC},
title = {Automatic detection for bioacoustic research: a practical guide from and for biologists and computer scientists.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {100},
number = {2},
pages = {620-646},
pmid = {39417330},
issn = {1469-185X},
support = {//A*MIDEX/ ; //Cambridge Centre for Data-Driven Discovery/ ; //African Institute for Mathematical Sciences/ ; NE/W005468/1//Natural Environment Research Council/ ; //Global Affairs Canada/ ; ANR-20-CE23-0012-01 MIM//Agence Nationale de la Recherche/ ; ANR-20-CHIA-0014//Agence Nationale de la Recherche/ ; ANR-16-CONV-0002//Institute of Convergence ILCB/ ; //International Development Research Centre/ ; },
mesh = {*Acoustics ; Animals ; Machine Learning ; },
abstract = {Recent years have seen a dramatic rise in the use of passive acoustic monitoring (PAM) for biological and ecological applications, and a corresponding increase in the volume of data generated. However, data sets are often becoming so sizable that analysing them manually is increasingly burdensome and unrealistic. Fortunately, we have also seen a corresponding rise in computing power and the capability of machine learning algorithms, which offer the possibility of performing some of the analysis required for PAM automatically. Nonetheless, the field of automatic detection of acoustic events is still in its infancy in biology and ecology. In this review, we examine the trends in bioacoustic PAM applications, and their implications for the burgeoning amount of data that needs to be analysed. We explore the different methods of machine learning and other tools for scanning, analysing, and extracting acoustic events automatically from large volumes of recordings. We then provide a step-by-step practical guide for using automatic detection in bioacoustics. One of the biggest challenges for the greater use of automatic detection in bioacoustics is that there is often a gulf in expertise between the biological sciences and the field of machine learning and computer science. Therefore, this review first presents an overview of the requirements for automatic detection in bioacoustics, intended to familiarise those from a computer science background with the needs of the bioacoustics community, followed by an introduction to the key elements of machine learning and artificial intelligence that a biologist needs to understand to incorporate automatic detection into their research. We then provide a practical guide to building an automatic detection pipeline for bioacoustic data, and conclude with a discussion of possible future directions in this field.},
}
@article {pmid39417898,
year = {2024},
author = {Khalaf, SMH and Alqahtani, MSM and Ali, MRM and Abdelalim, ITI and Hodhod, MS},
title = {Modeling climate-related global risk maps of rice bacterial blight caused by Xanthomonas oryzae (Ishiyama 1922) using geographical information system (GIS).},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {11},
pages = {1064},
pmid = {39417898},
issn = {1573-2959},
mesh = {*Xanthomonas ; *Oryza/microbiology ; *Climate Change ; *Plant Diseases/microbiology/statistics &amp; numerical data ; *Geographic Information Systems ; Environmental Monitoring ; Climate ; },
abstract = {Rice is a critical staple crop that feeds more than half of the world's population. Still, its production confronts various biotic risks, notably the severe bacterial blight disease produced by Xanthomonas oryzae. Understanding the possible effects of climate change on the geographic distribution of this virus is critical to ensuring food security. This work used ecological niche modeling and the Maxent algorithm to create future risk maps for the range of X. oryzae under several climate change scenarios between 2050 and 2070. The model was trained using 93 occurrence records of X. oryzae and five critical bioclimatic variables. It has an excellent predictive performance, with an AUC of 0.889. The results show that X. oryzae's potential geographic range and habitat suitability are expected to increase significantly under low (RCP2.6) and high (RCP8.5) emission scenarios. Key climatic drivers allowing this development include increased yearly precipitation, precipitation during the wettest quarter, and the wettest quarter's mean temperature. These findings are consistent with broader research revealing that climate change is allowing many plant diseases and other dangerous microbes to spread across the globe. Integrating these spatial predictions with data on host susceptibility, agricultural practices, and socioeconomic vulnerabilities can help to improve targeted surveillance, preventative, and management methods for reducing the growing threat of bacterial blight to rice production. Proactive, multidisciplinary efforts to manage the changing disease dynamics caused by climate change will be critical to assuring global food security in the future decades.},
}
@article {pmid39419226,
year = {2024},
author = {Liu, J and Zhu, M and Shi, X and Hui, C and Sun, Y and Zhang, R and Jin, D and Li, Z and Chen, H and Zhao, Z},
title = {Cascading impacts of nitrogen deposition on soil microbiome and herbivore communities in desert steppes.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {176892},
doi = {10.1016/j.scitotenv.2024.176892},
pmid = {39419226},
issn = {1879-1026},
mesh = {*Nitrogen ; *Soil Microbiology ; *Microbiota/drug effects ; *Herbivory ; Animals ; *Insecta/physiology ; Desert Climate ; Soil/chemistry ; Biodiversity ; Grassland ; Ecosystem ; China ; },
abstract = {Human activities in the last century have intensified global nitrogen deposition, resulting in the degradation of ecosystem function and loss of biodiversity worldwide. Nitrogen addition is a crucial method for examining the effects of atmospheric nitrogen deposition on species composition and structure of soil microbiome and biotic community, as exogenous nitrogen inputs can trigger cascading effects on ecosystem functions. In a 6-year experiment, we evaluated the impact of nitrogen addition on soil microbial-plant-insect systems in desert steppes. Our results show that nitrogen addition significantly altered soil microbial composition and ecological function, leading to a decrease in nitrogen-fixing bacteria and an increase in saprophytic fungi. High levels of nitrogen addition increased total plant biomass while decreasing species diversity. Additionally, high nitrogen addition levels suppressed below-ground biomass of gramineae and legumes compared to low nitrogen addition. Nitrogen addition also increased herbivore abundance by altering insect community structure, particularly benefiting chewing pests over sucking pests, thus heightening the risk of biological disasters through trophic cascading effects. Consequently, excessive nitrogen addition may destabilize desert steppe ecosystems by disturbing soil microbial-plant-insect interactions, hindering the maintenance of biotic community diversity and steppe productivity.},
}
@article {pmid39420601,
year = {2024},
author = {Li, Z and Zhang, Y and Peng, B and Qin, S and Zhang, Q and Chen, Y and Chen, C and Bao, Y and Zhu, Y and Hong, Y and Liu, B and Liu, Q and Xu, L and Chen, X and Ma, X and Wang, H and Xie, L and Yao, Y and Deng, B and Li, J and De, B and Chen, Y and Wang, J and Li, T and Liu, R and Tang, Z and Cao, J and Zuo, E and Mei, C and Zhu, F and Shao, C and Wang, G and Sun, T and Wang, N and Liu, G and Ni, JQ and Liu, Y},
title = {A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.},
journal = {Nucleic acids research},
volume = {52},
number = {21},
pages = {13447-13468},
pmid = {39420601},
issn = {1362-4962},
support = {2021YFF1200500//China National Key R&amp;D Program/ ; 32070595//National Natural Science Foundation of China/ ; 20221250020//Ministry of Science and Technology/ ; 20181300988//National Natural Science Foundation of China/ ; },
mesh = {*Enhancer Elements, Genetic ; Animals ; *Deep Learning ; Drosophila melanogaster/genetics ; Drosophila/genetics ; Humans ; Computational Biology/methods ; Gene Expression Regulation ; },
abstract = {Enhancers play a critical role in dynamically regulating spatial-temporal gene expression and establishing cell identity, underscoring the significance of designing them with specific properties for applications in biosynthetic engineering and gene therapy. Despite numerous high-throughput methods facilitating genome-wide enhancer identification, deciphering the sequence determinants of their activity remains challenging. Here, we present the DREAM (DNA cis-Regulatory Elements with controllable Activity design platforM) framework, a novel deep learning-based approach for synthetic enhancer design. Proficient in uncovering subtle and intricate patterns within extensive enhancer screening data, DREAM achieves cutting-edge sequence-based enhancer activity prediction and highlights critical sequence features implicating strong enhancer activity. Leveraging DREAM, we have engineered enhancers that surpass the potency of the strongest enhancer within the Drosophila genome by approximately 3.6-fold. Remarkably, these synthetic enhancers exhibited conserved functionality across species that have diverged more than billion years, indicating that DREAM was able to learn highly conserved enhancer regulatory grammar. Additionally, we designed silencers and cell line-specific enhancers using DREAM, demonstrating its versatility. Overall, our study not only introduces an interpretable approach for enhancer design but also lays out a general framework applicable to the design of other types of cis-regulatory elements.},
}
@article {pmid39421415,
year = {2024},
author = {Ion, MC and Bloomer, CC and Bărăscu, TI and Oficialdegui, FJ and Shoobs, NF and Williams, BW and Scheers, K and Clavero, M and Grandjean, F and Collas, M and Baudry, T and Loughman, Z and Wright, JJ and Ruokonen, TJ and Chucholl, C and Guareschi, S and Koese, B and Banyai, ZM and Hodson, J and Hurt, M and Kaldre, K and Lipták, B and Fetzner, JW and Cancellario, T and Weiperth, A and Birzaks, J and Trichkova, T and Todorov, M and Balalaikins, M and Griffin, B and Petko, ON and Acevedo-Alonso, A and D'Elía, G and Śliwińska, K and Alekhnovich, A and Choong, H and South, J and Whiterod, N and Zorić, K and Haase, P and Soto, I and Brady, DJ and Haubrock, PJ and Torres, PJ and Şadrin, D and Vlach, P and Kaya, C and Woo Jung, S and Kim, JY and Vermeersch, XHC and Bonk, M and Guiaşu, R and Harlioğlu, MM and Devlin, J and Kurtul, I and Błońska, D and Boets, P and Masigol, H and Cabe, PR and Jussila, J and Vrålstad, T and Beresford, DV and Reid, SM and Patoka, J and Strand, DA and Tarkan, AS and Steen, F and Abeel, T and Harwood, M and Auer, S and Kelly, S and Giantsis, IA and Maciaszek, R and Alvanou, MV and Aksu, &#xd6; and Hayes, DM and Kawai, T and Tricarico, E and Chakandinakira, A and Barnett, ZC and Kudor, &#x15e;G and Beda, AE and Vîlcea, L and Mizeranschi, AE and Neagul, M and Licz, A and Cotoarbă, AD and Petrusek, A and Kouba, A and Taylor, CA and Pârvulescu, L},
title = {World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18229},
pmid = {39421415},
issn = {2167-8359},
mesh = {Animals ; *Astacoidea/microbiology ; *Fresh Water ; Aphanomyces ; Internet ; Ecosystem ; Databases, Factual ; },
abstract = {Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity.},
}
@article {pmid39423319,
year = {2025},
author = {Tian, Y and Yang, L and Ding, S and Zhang, D and Yuan, L and Liu, Z and Hu, QN},
title = {BioTRY: A Comprehensive Knowledge Base for Titer, Rate, and Yield of Biosynthesis.},
journal = {ACS synthetic biology},
volume = {14},
number = {1},
pages = {285-289},
doi = {10.1021/acssynbio.4c00347},
pmid = {39423319},
issn = {2161-5063},
mesh = {*Synthetic Biology/methods ; *Knowledge Bases ; *Computational Biology/methods ; Fermentation ; Databases, Factual ; },
abstract = {Synthetic biology is rapidly evolving into a data-intensive science that increasingly relies on massive data sets; one of its applications is the evaluation of the economic viability of fermentation processes. However, the key economic indicators, namely titer, rate, and yield (TRY), which respectively reflect the downstream processing, reactor size, and raw material costs, are not well captured in bioinformatics databases. In this paper, we present BioTRY, an intuitive and user-friendly tool that contains >5,000 biochemicals and >3,800 strains, along with over 52,000 corresponding TRY entries with original references. It is freely available at http://www.synbiohealth.cn/biotry. To our knowledge, BioTRY is the first available database on biosynthesis TRY data from original research. We anticipate that BioTRY will become a useful tool that aids researchers and decision-makers in understanding the current development state of biosynthesis and allows them to foresee potential prospects and applications for biosynthesis.},
}
@article {pmid39424895,
year = {2024},
author = {Melo, MS and Lima, SVMA and Dos Santos, AD and Ribeiro, CJN and Júnior, PAB and Silva, TKS and de Resende, LT and Corrêa, F and Migowski, A and Schiffman, M and Rodriguez, AC and Ribeiro, A and Raiol, T},
title = {Temporal trends, spatial and spatiotemporal clusters of cervical cancer mortality in Brazil from 2000 to 2021.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24436},
pmid = {39424895},
issn = {2045-2322},
support = {Grant number GEREB-Fiocruz/CNPq 440204/2019-4.//Oswaldo Cruz Foundation (Fiocruz) and National Council for Scientific and Technological Development (CNPq)/ ; },
mesh = {Humans ; Female ; Brazil/epidemiology ; *Uterine Cervical Neoplasms/mortality/epidemiology ; Adult ; Middle Aged ; *Spatio-Temporal Analysis ; Aged ; Young Adult ; Adolescent ; Mortality/trends ; },
abstract = {Cervical cancer, despite being preventable through primary and secondary prevention strategies, remains one of the leading causes of morbidity and mortality among women in Brazil. This study aimed to analyze the temporal, spatial, and space-time patterns of cervical cancer mortality in Brazil. An ecological study was conducted using temporal, spatial, and space-time analysis techniques, using death certificates with cervical cancer as the underlying cause or associated condition among females in Brazil from 2000 to 2021. Death certificate and population data were provided by the Department of Health Informatics of the Unified Health System (DATASUS) and the Brazilian Institute of Geography and Statistics (IBGE), respectively. A total of 123,306 deaths associated with cervical cancer among women were registered during the study period. A rising trend in mortality was detected since 2014 onwards, after 14 years of decline. Particularly, an increase in mortality was observed among the younger age groups, and in the North and Northeast regions regardless of age. Heterogeneity in the spatial distribution of cervical cancer mortality was observed, with high mortality clusters around the country, but mostly concentrated in the North and Northeast regions. These findings suggest a need and an opportunity to develop efficient and effective health policies targeting those regions and groups of women at higher risk which in turn will allow for fast and significant reductions in cervical cancer mortality in Brazil.},
}
@article {pmid39429632,
year = {2024},
author = {Li, R and Li, J and Lopez, JV and Oatley, G and Clayton-Lucey, IA 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 genome sequence of the smooth giant clam, Tridacna derasa Röding, 1798.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {375},
pmid = {39429632},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual Tridacna derasa (the smooth giant clam; Mollusca; Bivalvia;Cardiida; Cardiidae). The genome sequence is 1,060.2 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.95 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,638 protein coding genes.},
}
@article {pmid39429633,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Hebrew Character, Orthosia gothica (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {90},
pmid = {39429633},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Orthosia gothica (the Hebrew character; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 1,065.1 megabases in span. Most of the assembly is scaffolded into 37 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,691 protein coding genes.},
}
@article {pmid39430045,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Olive Pearl, Udea olivalis (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {238},
pmid = {39430045},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Udea olivalis (the Olive Pearl; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 624.4 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 15.3 kilobases in length.},
}
@article {pmid39430511,
year = {2024},
author = {Shamrat, FMJM and Idna Idris, MY and Zhou, X and Khalid, M and Sharmin, S and Sharmin, Z and Ahmed, K and Moni, MA},
title = {PollenNet: A novel architecture for high precision pollen grain classification through deep learning and explainable AI.},
journal = {Heliyon},
volume = {10},
number = {19},
pages = {e38596},
pmid = {39430511},
issn = {2405-8440},
abstract = {Pollen grains play a critical role in environmental, agricultural, and allergy research despite their tiny dimensions. The accurate classification of pollen grains remains a significant challenge, mainly attributable to their intricate structures and the extensive diversity of species. Traditional methods often lack accuracy and effectiveness, prompting the need for advanced solutions. This study introduces a novel deep learning framework, PollenNet, designed to tackle the intricate challenge of pollen grain image classification. The efficiency of PollenNet is thoroughly evaluated through stratified 5-fold cross-validation, comparing it with cutting-edge methods to demonstrate its superior performance. A comprehensive data preparation phase is conducted, including removing duplicates and low-quality images, applying Non-local Means Denoising for noise reduction, and Gamma correction to adjust image brightness. Furthermore, Explainable AI (XAI) is utilized to enhance the interpretability of the model, while Receiver Operating Characteristic (ROC) curve analysis serves as a quantitative method for evaluating the model's capabilities. PollenNet demonstrates superior performance when compared to existing models, with an accuracy of 98.45 %, precision of 98.20 %, specificity of 98.40 %, recall of 98.30 %, and f1-score of 98.25 %. The model also maintains low Mean Squared Error (0.03) and Mean Absolute Error (0.02) rates. The ROC curve analysis, the low False Positive Rate (0.016), and the False Negative Rate (0.017) highlight the reliability and dependability of the model. This study significantly improves the efficacy of classifying pollen grains, indicating an important advancement in the application of deep learning for ecological research.},
}
@article {pmid39432055,
year = {2025},
author = {Zhao, L and Henriksen, RA and Ramsøe, A and Nielsen, R and Korneliussen, TS},
title = {Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage.},
journal = {Molecular ecology resources},
volume = {25},
number = {1},
pages = {e14029},
pmid = {39432055},
issn = {1755-0998},
support = {R35 GM153400/GM/NIGMS NIH HHS/United States ; R302-2018-2155//Lundbeck Foundation/ ; CF19-0712//Carlsberg Foundation/ ; CF20-0071//Carlsberg Foundation/ ; },
mesh = {*DNA, Ancient/analysis ; DNA Damage ; Sequence Analysis, DNA/methods ; Likelihood Functions ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Humans ; },
abstract = {One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state-of-the-art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data.},
}
@article {pmid39434036,
year = {2024},
author = {Li, C and Zhang, X and Zhao, L and Liu, S},
title = {Multi-omics profiling reveals the molecular mechanisms of H2O2-induced detrimental effects on Thamnaconus septentrionalis.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {984},
pmid = {39434036},
issn = {1471-2164},
mesh = {Animals ; *Hydrogen Peroxide/metabolism ; Fishes/metabolism/genetics ; Transcriptome/drug effects ; Gene Expression Profiling ; Metabolomics ; Signal Transduction/drug effects ; Metabolome/drug effects ; Multiomics ; },
abstract = {BACKGROUND: Hydrogen peroxide (H2O2), a novel water treatment agent, can be used for disinfection, water quality adjustment, and disease prevention, while excessive H2O2 can injure farm animals, even leading to death. Hydrogen peroxide is a recommended disinfectant and bactericide for treating gill diseases and vibriosis in the greenfin horse-faced filefish Thamnaconus septentrionalis. However, its cumulative effect, toxic molecular mechanism and relevant signal transduction/metabolic networks in marine fishes are largely unknown.<br><br>RESULTS: We employed a multi-omics approach to investigate the detrimental effects of 50&#xa0;mg/L H2O2 exposure (2&#xa0;h/d) on filefish for 2 d, 4 d, and 6 d. Transcriptome sequencing showed that differentially expressed genes (DEGs) were mainly classified into functions such as signal transduction, nervous system, liver and bile acid metabolism, energy metabolism, cell adhesion and communication, inflammation and immune response. Metabolomic analysis found that the significantly changed metabolites (SCMs) were involved in phenylalanine metabolism, inflammatory mediator regulation, linoleic acid metabolism, and necroptosis. The main SCMs were cholic acid, carnitine C12:1, dimethylmalonic acid, glutamic acid, L-lactic acid, shikimic acid, 2-methylsuccinic acid, and others. Moreover, H2O2-induced oxidative stress also disturbs the balance of the gut microbiota, altering the microbial composition and affecting digestive processes.<br><br>CONCLUSIONS: Integrated multiomics analysis revealed that H2O2-induced detrimental impacts include mucosal damage, inflammatory and immune responses, altered energy metabolism, and gut microbiota disorders. These findings offer novel insights into the harmful effects and signal transduction/metabolic pathways triggered by H2O2 exposure in marine fishes.},
}
@article {pmid39435526,
year = {2025},
author = {Kan-Lingwood, NY and Sagi, L and Mazie, S and Shahar, N and Zecherle Bitton, L and Templeton, A and Rubenstein, D and Bouskila, A and Bar-David, S},
title = {Genotyping Error Detection and Customised Filtration for SNP Datasets.},
journal = {Molecular ecology resources},
volume = {25},
number = {1},
pages = {e14033},
doi = {10.1111/1755-0998.14033},
pmid = {39435526},
issn = {1755-0998},
support = {2011384//United States-Israel Binational Science Foundation/ ; },
mesh = {*Polymorphism, Single Nucleotide ; *Genotyping Techniques/methods ; Animals ; Genotype ; Computational Biology/methods ; },
abstract = {A major challenge in analysing single-nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses and misinterpret ecological and evolutionary processes. Here, we present a comprehensive method to estimate and minimise genotyping error rates (deviations from the 'true' genotype) in any SNP datasets using triplicates (three repeats of the same sample) in a four-step filtration pipeline. The approach involves: (1) SNP filtering by missing data; (2) SNP filtering by error rates; (3) sample filtering by missing data and (4) detection of recaptured individuals by using estimated SNP error rates. The modular pipeline is provided in an R script that allows customised adjustments. We demonstrate the applicability of the method using non-invasive sampling from the Asiatic wild ass (Equus hemionus) population in Israel. We genotyped 756 samples using 625 SNPs, of which 255 were triplicates of 85 samples. The average SNP error rate, calculated based on the number of mismatching genotypes across triplicates before filtration, was 0.0034 and was reduced to 0.00174 following filtration. Evaluating genetic distance (GD) and relatedness (r) between triplicates before and after filtration (expected to be at the minimum and maximum respectively) showed a significant reduction in the average GD, from 58.1 to 25.3 (p = 0.0002) and a significant increase in relatedness, from r = 0.98 to r = 0.991 (p = 0.00587). We demonstrate how error rate estimation enhances recapture detection and improves genotype quality.},
}
@article {pmid39436510,
year = {2024},
author = {Zinicovscaia, I and Chernyagina, O and Chaligava, O and Yushin, N and Devyatova, E and Grozov, D},
title = {Moss biomonitoring in areas affected by ashfalls of Shiveluch volcano (Kamchatka).},
journal = {Environmental science and pollution research international},
volume = {31},
number = {52},
pages = {61730-61739},
pmid = {39436510},
issn = {1614-7499},
mesh = {*Bryophyta/chemistry ; *Volcanic Eruptions ; *Environmental Monitoring/methods ; *Biological Monitoring ; Air Pollutants/analysis ; },
abstract = {The moss bag technique was applied on Kamchatka to assess the effect of Shiveluch volcano on the air quality. Moss bags were exposed in settlements located at different distances from the volcano and affected by ashfall to varying degrees. The inductively coupled plasma optical emission spectrometry was used for the determination of the content of Al, Ba, Co, Cd, Cr, Cu, Fe, Mn, P, Pb, Sr, S, V, and Zn in both exposed and unexposed moss samples. Relative accumulation factor revealed enrichment of mosses exposed in the area affected by ashfall with Al, Cr, V, and Zn. Correlation and principal component analysis allowed to identify elements of volcanogenic, geogenic, and anthropogenic origin. Ecological risk values less than 150 indicate low potential ecological risk in the region. Active moss biomonitoring can be considered a cheap and efficient tool for in-depth study of the influence of volcanic activity on air quality on the peninsula.},
}
@article {pmid39436938,
year = {2024},
author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP},
title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.},
journal = {PLoS computational biology},
volume = {20},
number = {10},
pages = {e1012530},
pmid = {39436938},
issn = {1553-7358},
mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Computer Simulation ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; },
abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.},
}
@article {pmid39438357,
year = {2024},
author = {Little, AJ and Matthee, CA and Ueckermann, EA and Horak, IG and Hui, C and Matthee, S},
title = {Host and habitat shape ectoparasite diversity on Mastomys natalensis and Mastomys coucha (Muridae).},
journal = {Parasitology},
volume = {151},
number = {8},
pages = {769-783},
pmid = {39438357},
issn = {1469-8161},
support = {R01 AI136832/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Rodent Diseases/parasitology/epidemiology ; *Ecosystem ; *Murinae/parasitology ; Male ; *Ectoparasitic Infestations/parasitology/veterinary ; Female ; Host-Parasite Interactions ; Mites/physiology/classification ; Siphonaptera/classification/physiology ; Biodiversity ; Ticks/classification/physiology ; },
abstract = {Mastomys natalensis and M. coucha are commensal rodent species endemic to Africa. A recent taxonomic revision within Mastomys leaves the parasite–host list of M. natalensis questionable and that of M. coucha incomplete. The current study aimed to develop a better understanding of the ectoparasite diversity associated with the 2 distinct but closely related rodent species and to explore the influence of host and habitat type on ectoparasite infestations. Between 2014 and 2020, 590 rodents were trapped in 3 habitat types (village, agriculture and natural) across a wildlife-human/domestic animal interface. In total 48 epifaunistic species (45 ectoparasitic and 3 predatory) represented by 29 genera from 4 taxonomic groups (fleas, lice, mites and ticks) were recorded. Only 50% of the epifauna were shared between the 2 rodent species, with mites the most speciose taxon in both host species. The abundance of epifaunistic individuals, and also those of mites and fleas, were significantly higher on male M. natalensis, while ticks were significantly higher on reproductively active M. natalensis. For both rodent species, infestations by most epifaunistic taxa (on M. natalensis) and some taxa (on M. coucha) were significantly lower in the village as opposed to the less disturbed agricultural and natural habitat types. The study highlights the importance of host life history, even in closely related rodent species, in shaping parasite profiles and a loss of parasite diversity in more extreme anthropogenic habitats.},
}
@article {pmid39439296,
year = {2025},
author = {Rosche, C and Broennimann, O and Novikov, A and Mrázová, V and Boiko, GV and Danihelka, J and Gastner, MT and Guisan, A and Kožić, K and Lehnert, M and Müller-Schärer, H and Nagy, DU and Remelgado, R and Ronikier, M and Selke, JA and Shiyan, NM and Suchan, T and Thoma, AE and Zdvořák, P and Mráz, P},
title = {Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe.},
journal = {The New phytologist},
volume = {245},
number = {1},
pages = {392-405},
pmid = {39439296},
issn = {1469-8137},
mesh = {*Centaurea/genetics/physiology ; Europe ; *Polyploidy ; *Introduced Species ; Phylogeography ; Ecosystem ; Diploidy ; },
abstract = {Numerous plant species are expanding their native ranges due to anthropogenic environmental change. Because cytotypes of polyploid complexes often show similar morphologies, there may be unnoticed range expansions (i.e. cryptic invasions) of one cytotype into regions where only the other cytotype is native. We critically revised herbarium specimens of diploid and tetraploid Centaurea stoebe, collected across Europe between 1790 and 2023. Based on their distribution in natural and relict habitats and phylogeographic data, we estimated the native ranges of both cytotypes. Diploids are native across their entire European range, whereas tetraploids are native only to South-Eastern Europe and have recently expanded their range toward Central Europe. The proportion of tetraploids has exponentially increased over time in their expanded but not in their native range. This cryptic invasion predominantly occurred in ruderal habitats and enlarged the climatic niche of tetraploids toward a more oceanic climate. We conclude that spatio-temporally explicit assessments of range shifts, habitat preferences and niche evolution can improve our understanding of cryptic invasions. We also emphasize the value of herbarium specimens for accurate estimation of species´ native ranges, with fundamental implications for the design of research studies and the assessment of biodiversity trends.},
}
@article {pmid39440963,
year = {2024},
author = {Wang, Y and Sun, Y and Huang, K and Gao, Y and Lin, Y and Yuan, B and Wang, X and Xu, G and Nussio, LG and Yang, F and Ni, K},
title = {Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.},
journal = {mSystems},
volume = {9},
number = {11},
pages = {e0068224},
pmid = {39440963},
issn = {2379-5077},
support = {32171686//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Medicago sativa/microbiology/metabolism ; *Silage/microbiology ; *Fermentation ; *Microbiota/genetics ; Animals ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Cattle ; Multiomics ; },
abstract = {UNLABELLED: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.<br><br>IMPORTANCE: Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.},
}
@article {pmid39441382,
year = {2025},
author = {Canzler, S and Schubert, K and Rolle-Kampczyk, UE and Wang, Z and Schreiber, S and Seitz, H and Mockly, S and Kamp, H and Haake, V and Huisinga, M and Bergen, MV and Buesen, R and Hackermüller, J},
title = {Evaluating the performance of multi-omics integration: a thyroid toxicity case study.},
journal = {Archives of toxicology},
volume = {99},
number = {1},
pages = {309-332},
pmid = {39441382},
issn = {1432-0738},
support = {C5 - XomeTox//European Chemical Industry Council/ ; 101057014//HORIZON EUROPE Framework Programme/ ; },
mesh = {Animals ; *Thyroid Gland/drug effects/pathology/metabolism ; Rats ; Risk Assessment ; Proteomics/methods ; Transcriptome/drug effects ; Male ; Metabolomics/methods ; *Genomics/methods ; Humans ; Toxicity Tests/methods ; Multiomics ; },
abstract = {Multi-omics data integration has been repeatedly discussed as the way forward to more comprehensively cover the molecular responses of cells or organisms to chemical exposure in systems toxicology and regulatory risk assessment. In Canzler et al. (Arch Toxicol 94(2):371-388. https://doi.org/10.1007/s00204-020-02656-y), we reviewed the state of the art in applying multi-omics approaches in toxicological research and chemical risk assessment. We developed best practices for the experimental design of multi-omics studies, omics data acquisition, and subsequent omics data integration. We found that multi-omics data sets for toxicological research questions were generally rare, with no data sets comprising more than two omics layers adhering to these best practices. Due to these limitations, we could not fully assess the benefits of different data integration approaches or quantitatively evaluate the contribution of various omics layers for toxicological research questions. Here, we report on a multi-omics study on thyroid toxicity that we conducted in compliance with these best practices. We induced direct and indirect thyroid toxicity through Propylthiouracil (PTU) and Phenytoin, respectively, in a 28-day plus 14-day recovery oral rat toxicity study. We collected clinical and histopathological data and six omics layers, including the long and short transcriptome, proteome, phosphoproteome, and metabolome from plasma, thyroid, and liver. We demonstrate that the multi-omics approach is superior to single-omics in detecting responses at the regulatory pathway level. We also show how combining omics data with clinical and histopathological parameters facilitates the interpretation of the data. Furthermore, we illustrate how multi-omics integration can hint at the involvement of non-coding RNAs in post-transcriptional regulation. Also, we show that multi-omics facilitates grouping, and we assess how much information individual and combinations of omics layers contribute to this approach.},
}
@article {pmid39442119,
year = {2024},
author = {Castro-Nunes, P and Palmieri, P and Bellas, H and Soares, A and Viana, J and Carvalho, PVR and Jatobá, A},
title = {Effects of pay for performance in primary care in an under-registration scenario.},
journal = {Revista de saude publica},
volume = {58},
number = {},
pages = {44},
pmid = {39442119},
issn = {1518-8787},
mesh = {Humans ; *Primary Health Care/economics ; Brazil ; *Reimbursement, Incentive/economics ; Female ; National Health Programs/economics ; },
abstract = {OBJECTIVE: To propose a method for detecting and analyzing under-registration and highlight its potential financial effect in view of the implementation of the Previne Brasil Program.<br><br>METHODS: An ecological study was carried out to analyze cytopathological exams in programmatic area 3.1 in the municipality of Rio de Janeiro. The data was collected from the Departamento de Inform&#xe1;tica do Sistema &#xda;nico de Sa&#xfa;de (DATASUS - Department of Informatics of the Unified Health System) database, including information on reports from outsourced cytopathology laboratories and those available in the Sistema de Informa&#xe7;&#xe3;o em Sa&#xfa;de para a Aten&#xe7;&#xe3;o B&#xe1;sica (SISAB - Health Information System for Primary Care) and the Sistema de Informa&#xe7;&#xe3;o do C&#xe2;ncer do Colo do &#xda;tero (SISCOLO - Cervical Cancer Information System) of DATASUS/Ministry of Health.<br><br>RESULTS: The estimated under-registrations per health unit totaled 108,511 exams in the last two years in the programmatic area 3.1 area, which corresponds to an estimated total of R$ 435,129.00 that would have been foregone if the Previne Brasil Program had been in place during the period studied.<br><br>CONCLUSION: The article's main contribution lies in the presentation of empirical evidence of the potential effects of under-registration on Primary Health Care financing. In addition, there are two other significant findings - firstly, it highlights weaknesses in the process of recording health information inherent to vulnerable regions; secondly, it indicates a vicious circle potentially fueled by sudden changes in Primary Health Care funding conditions, in addition to potential consequences for other levels of care.},
}
@article {pmid39445720,
year = {2025},
author = {Compton, ZT and Mellon, W and Harris, VK and Rupp, S and Mallo, D and Kapsetaki, SE and Wilmot, M and Kennington, R and Noble, K and Baciu, C and Ramirez, LN and Peraza, A and Martins, B and Sudhakar, S and Aksoy, S and Furukawa, G and Vincze, O and Giraudeau, M and Duke, EG and Spiro, S and Flach, E and Davidson, H and Li, CI and Zehnder, A and Graham, TA and Troan, BV and Harrison, TM and Tollis, M and Schiffman, JD and Aktipis, CA and Abegglen, LM and Maley, CC and Boddy, AM},
title = {Cancer Prevalence across Vertebrates.},
journal = {Cancer discovery},
volume = {15},
number = {1},
pages = {227-244},
pmid = {39445720},
issn = {2159-8290},
support = {T32 CA272303/CA/NCI NIH HHS/United States ; P01 CA091955/CA/NCI NIH HHS/United States ; OTKA K143421//Agence Nationale de la Recherche (ANR)/ ; COVER ANR-23-CE02-0019//Agence Nationale de la Recherche (ANR)/ ; U54 CA217376/CA/NCI NIH HHS/United States ; ADHS18-198847//Arizona Biomedical Research Commission (ABRC)/ ; U2C CA233254/CA/NCI NIH HHS/United States ; //Hyundai Hope On Wheels (Hope On Wheels)/ ; BC132057//Congressionally Directed Medical Research Programs (CDMRP)/ ; R01 CA140657/CA/NCI NIH HHS/United States ; R21 CA257980/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Neoplasms/epidemiology/genetics/veterinary ; Prevalence ; *Vertebrates ; Humans ; },
abstract = {Cancer is pervasive across multicellular species, but what explains the differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades of tetrapods (amphibians, sauropsids, and mammals), we found that neoplasia and malignancy prevalence increases with adult mass (contrary to Peto's paradox) and somatic mutation rate but decreases with gestation time. The relationship between adult mass and malignancy prevalence was only apparent when we controlled for gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%), the black-footed penguin (<0.4%), ferrets (63%), and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer. Significance: Evolution has discovered mechanisms for suppressing cancer in a wide variety of species. By analyzing veterinary necropsy records, we can identify species with exceptionally high or low cancer prevalence. Discovering the mechanisms of cancer susceptibility and resistance may help improve cancer prevention and explain cancer syndromes. See related commentary by Metzger, p. 14.},
}
@article {pmid39446479,
year = {2024},
author = {Oliveira, J and Aires Dias, J and Correia, R and Pinheiro, R and Reis, V and Sousa, D and Agostinho, D and Simões, M and Castelo-Branco, M},
title = {Exploring Immersive Multimodal Virtual Reality Training, Affective States, and Ecological Validity in Healthy Firefighters: Quasi-Experimental Study.},
journal = {JMIR serious games},
volume = {12},
number = {},
pages = {e53683},
pmid = {39446479},
issn = {2291-9279},
abstract = {BACKGROUND: Firefighters face stressful life-threatening events requiring fast decision-making. To better prepare for those situations, training is paramount, but errors in real-life training can be harmful. Virtual reality (VR) simulations provide the desired realism while enabling practice in a secure and controlled environment. Firefighters' affective states are also crucial as they are a higher-risk group.<br><br>OBJECTIVE: To assess the impact on affective states of 2 simulated immersive experiences in a sample of healthy firefighters (before, during, and after the simulation), we pursued a multivariate approach comprising cognitive performance, situational awareness, depression, anxiety, stress, number of previous adverse events experienced, posttraumatic stress disorder (PTSD) severity, and emotions. The efficacy and ecological validity of an innovative VR haptic system were also tested, exploring its impact on performance.<br><br>METHODS: In collaboration with the Portuguese National Fire Service School, we exposed 22 healthy firefighters to 2 immersive scenarios using the FLAIM Trainer VR system (neutral and arousing scenarios) while recording physiological data in a quasi-experimental study. Baseline cognitive performance, depression, anxiety, stress, number of adverse events, and severity of PTSD symptoms were evaluated. Positive and negative affective states were measured before, between, and after each scenario. Situational awareness, sense of presence, ecological validity, engagement, and negative effects resulting from VR immersion were tested.<br><br>RESULTS: Baseline positive affect score was high (mean 32.4, SD 7.2) and increased after the VR tasks (partial &#x3b7;[2]=0.52; Greenhouse-Geisser F1.82,32.78=19.73; P<.001). Contrarily, mean negative affect score remained low (range 11.0-11.9) throughout the study (partial &#x3b7;[2]=0.02; Greenhouse-Geisser F2.13,38.4=0.39; P=.69). Participants' feedback on the VR sense of presence was also positive, reporting a high sense of physical space (mean score 3.9, SD 0.8), ecological validity (mean score 3.8, SD 0.6), and engagement (mean score 3.8, SD 0.6). Engagement was related to the number of previously experienced adverse events (r=0.49; P=.02) and positive affect (after the last VR task; r=0.55; P=.02). Conversely, participants reported few negative effects (mean score 1.7, SD 0.6). The negative effects correlated positively with negative affect (after the last VR task; r=0.53; P=.03); and avoidance (r=0.73; P<.001), a PTSD symptom, controlling for relevant baseline variables. Performance related to situational awareness was positive (mean 46.4, SD 34.5), although no relation was found to metacognitively perceived situational awareness (r=-0.12; P=.59).<br><br>CONCLUSIONS: We show that VR is an effective alternative to in-person training as it was considered ecologically valid and engaging while promoting positive emotions, with few negative repercussions. This corroborates the use of VR to test firefighters' performance and situational awareness. Further research is needed to ascertain that firefighters with PTSD symptomatology are not negatively affected by VR. This study favors the use of VR training and provides new insights on its emotional and cognitive impact on the trainee.},
}
@article {pmid39448189,
year = {2024},
author = {Konečný, L and Peterková, K},
title = {Unveiling the peptidases of parasites from the office chair - The endothelin-converting enzyme case study.},
journal = {Advances in parasitology},
volume = {126},
number = {},
pages = {1-52},
doi = {10.1016/bs.apar.2024.05.003},
pmid = {39448189},
issn = {2163-6079},
mesh = {Animals ; *Computational Biology ; Endothelin-Converting Enzymes/genetics ; Schistosoma mansoni/enzymology/genetics ; Humans ; Peptide Hydrolases/genetics/metabolism ; Proteomics ; },
abstract = {The emergence of high-throughput methodologies such as next-generation sequencing and proteomics has necessitated significant advancements in biological databases and bioinformatic tools, therefore reshaping the landscape of research into parasitic peptidases. In this review we outline the development of these resources along the -omics technologies and their transformative impact on the field. Apart from extensive summary of general and specific databases and tools, we provide a general pipeline on how to use these resources effectively to identify candidate peptidases from these large datasets and how to gain as much information about them as possible without leaving the office chair. This pipeline is then applied in an illustrative case study on the endothelin-converting enzyme 1 homologue from Schistosoma mansoni and attempts to highlight the contemporary capabilities of bioinformatics. The case study demonstrate how such approach can aid to hypothesize enzyme functions and interactions through computational analysis alone effectively and emphasizes how such virtual investigations can guide and optimize subsequent wet lab experiments therefore potentially saving precious time and resources. Finally, by showing what can be achieved without traditional wet laboratory methods, this review provides a compelling narrative on the use of bioinformatics to bridge the gap between big data and practical research applications, highlighting the key role of these technologies in furthering our understanding of parasitic diseases.},
}
@article {pmid39449730,
year = {2021},
author = {Boyes, D and Crowley, LM and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of Svensson's copper underwing, Amphipyra berbera Rungs, 1949.},
journal = {Wellcome open research},
volume = {6},
number = {},
pages = {314},
pmid = {39449730},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Amphipyra berbera (Svensson's copper underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 582 megabases in span. The majority (99.97%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.},
}
@article {pmid39449983,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Currant Clearwing moth, Synanthedon tipuliformis (Clerck, 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {300},
pmid = {39449983},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Synanthedon tipuliformis (the Currant Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 295.8 megabases in span. Most of the assembly (99.98%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 27.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,878 protein-coding genes.},
}
@article {pmid39454020,
year = {2025},
author = {Wong, R and Matulewicz, RS and Talwar, R and Shoenbill, KA and Goldstein, AO and Bjurlin, MA},
title = {Increased Tobacco Taxation Associated With Decreased Consumption and Bladder Cancer Incidence.},
journal = {Urology practice},
volume = {12},
number = {2},
pages = {250-256},
pmid = {39454020},
issn = {2352-0787},
support = {K08 CA259452/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Taxes/statistics &amp; numerical data ; *Urinary Bladder Neoplasms/epidemiology/etiology ; Incidence ; United States/epidemiology ; *Tobacco Products/economics ; *Tobacco Use/epidemiology/economics ; Male ; Female ; },
abstract = {INTRODUCTION: The temporal relationship between smoking exposure and bladder cancer (BC) diagnosis remains ill defined. This study aims to cross-correlate and temporally associate changes in US tobacco tax and consumption with BC incidence.<br><br>METHODS: US tobacco consumption, tobacco tax data, and BC incidence rates from 1975 to 2019 were retrieved. A cross-correlation lag time for tobacco tax and consumption on BC incidence was calculated while controlling for national health expenditure. Proxied lag weighted semi-log linear models were used to determine the rate of change in BC incidence rates associated with a 1% change in tobacco tax percentages on a national and state level.<br><br>RESULTS: A 1% increase in tobacco tax was associated with a 1.77% decrease in BC incidence over a 6-year period (R[2] = 0.9687, P = .00044). Twenty-two states had a statistically significant decline in BC incidences correlated with increasing tobacco taxation. Reduction in BC incidence > 0.5% was observed in states along the western and eastern US borders. Montana, Utah, Nebraska, Arkansas, and Tennessee did not have decreasing BC incidences from tobacco tax increases. California had the most drastic decline in BC incidence (1.98%). Nationally, tobacco consumption decrease in 1 pack per capita was associated with a 0.47% decrease in BC incidence over a 28-year period (R[2] = 0.984, P = .00011).<br><br>CONCLUSIONS: Declining US tobacco consumption may indicate significant reduction in BC incidence through 2047. Primary prevention through adaptation of state-legislated tax changes may contribute to a reduction in BC incidence in states lying within the Central United States. A national tobacco tax initiative can be considered given the improvement in population health.},
}
@article {pmid39460811,
year = {2024},
author = {Hasan, A and Ibrahim, M and Alonazi, WB and Yu, R and Li, B},
title = {Pangenome analysis of five representative Tropheryma whipplei strains following multiepitope-based vaccine design via immunoinformatic approaches.},
journal = {Molecular genetics and genomics : MGG},
volume = {299},
number = {1},
pages = {101},
pmid = {39460811},
issn = {1617-4623},
mesh = {Humans ; *Tropheryma/genetics/immunology ; *Bacterial Vaccines/immunology/genetics ; Whipple Disease/immunology/microbiology/genetics ; Computational Biology/methods ; Bacterial Proteins/genetics/immunology ; Genome, Bacterial ; Epitopes/immunology/genetics ; Vaccine Development ; Immunodominant Epitopes/immunology/genetics ; Proteomics/methods ; Proteome/genetics/immunology ; },
abstract = {Whipple disease caused by Tropheryma whipplei a gram-positive bacterium is a systemic disorder that impacts not only the gastrointestinal tract but also the vascular system, joints, central nervous system, and cardiovascular system. Due to the lack of an approved vaccine, this study aimed to utilize immunoinformatic approaches to design multiepitope -based vaccine by utilizing the proteomes of five representative T. whipplei strains. The genomes initially comprised a total of 4,844 proteins ranging from 956 to 1012 proteins per strain. We collected 829 nonredundant lists of core proteins, that were shared among all the strains. Following subtractive proteomics, one extracellular protein, WP_033800108.1, a WhiB family transcriptional regulator, was selected for the chimeric-based multiepitope vaccine. Five immunodominant epitopes were retrieved from the WhiB family transcriptional regulator protein, indicating MHC-I and MHC-II with a global population coverage of 70.61%. The strong binding affinity, high solubility, nontoxicity, nonallergenic properties and high antigenicity scores make the selected epitopes more appropriate. Integration of the epitopes into a chimeric vaccine was carried out by applying appropriate adjuvant molecules and linkers, leading to the vaccine construct having enhanced immunogenicity and successfully eliciting both innate and adaptive immune responses. Moreover, the abilityof the vaccine to bind TLR4, a core innate immune receptor, was confirmed. Molecular dynamics simulations have also revealed the promising potential stability of the designed vaccine at 400 ns. In summary, we have designed a potential vaccine construct that has the ability not only to induce targeted immunogenicity for one strain but also for global T. whipplei strains. This study proposes a potential universal vaccine, reducing Whipple's disease risk and laying the groundwork for future research on multi-strain pathogens.},
}
@article {pmid39460934,
year = {2024},
author = {Frazer, SA and Baghbanzadeh, M and Rahnavard, A and Crandall, KA and Oakley, TH},
title = {Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD).},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {39460934},
issn = {2047-217X},
support = {DEB-2153773//National Science Foundation/ ; },
mesh = {*Machine Learning ; *Opsins/genetics/metabolism ; Animals ; *Phenotype ; *Databases, Genetic ; Genetic Association Studies ; Genotype ; Humans ; Mutation ; },
abstract = {BACKGROUND: Predicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking genetic changes to phenotypic changes has been a goal of decades of experimental work, especially for some model gene families, including light-sensitive opsin proteins. Opsins can be expressed in vitro to measure light absorption parameters, including λmax-the wavelength of maximum absorbance-which strongly affects organismal phenotypes like color vision. Despite extensive research on opsins, the data remain dispersed, uncompiled, and often challenging to access, thereby precluding systematic and comprehensive analyses of the intricate relationships between genotype and phenotype.<br><br>RESULTS: Here, we report a newly compiled database of all heterologously expressed opsin genes with &#x3bb;max phenotypes that we call the Visual Physiology Opsin Database (VPOD). VPOD_1.0 contains 864 unique opsin genotypes and corresponding &#x3bb;max phenotypes collected across all animals from 73 separate publications. We use VPOD data and deepBreaks to show regression-based machine learning (ML) models often reliably predict &#x3bb;max, account for nonadditive effects of mutations on function, and identify functionally critical amino acid sites.<br><br>CONCLUSION: The ability to reliably predict functions from gene sequences alone using ML will allow robust exploration of molecular-evolutionary patterns governing phenotype, will inform functional and evolutionary connections to an organism's ecological niche, and may be used more broadly for de novo protein design. Together, our database, phenotype predictions, and model comparisons lay the groundwork for future research applicable to families of genes with quantifiable and comparable phenotypes.},
}
@article {pmid39461044,
year = {2024},
author = {Wu, Y and Wei, C and Zhang, Y and Gu, C and Fang, Y},
title = {Investigating intrinsic and situational predictors of depression among older adults: An analysis of the CHARLS database.},
journal = {Asian journal of psychiatry},
volume = {102},
number = {},
pages = {104279},
doi = {10.1016/j.ajp.2024.104279},
pmid = {39461044},
issn = {1876-2026},
mesh = {Humans ; Female ; Male ; Aged ; Middle Aged ; Aged, 80 and over ; *Depression/epidemiology ; Databases, Factual ; China/epidemiology ; Risk Factors ; Follow-Up Studies ; Depressive Disorder/epidemiology ; Chronic Disease ; },
abstract = {BACKGROUND: This study aimed to investigate the intrinsic and situational predictors of depression under the health ecological model.<br><br>METHODS: Two waves (2011 and 2013) of survey data were collected from the CHARLS. A total of 5845 older adults (&#x2267;60) were included, and depression was defined as CESD-10 score &#x2267;10. Random forest combined with interpretable methods were utilized to select important predictors of depression. Multilevel logit model was used to examine the associations of intrinsic and situational predictors with depression.<br><br>RESULTS: After a 2-year follow up, 1822 individuals (31.17&#x202f;%) developed depression. Interpretable analyses showed that both intrinsic and situational variables were predictive for depression. Multilevel logit model showed that age, gender, number of chronic diseases, number of pain areas, life satisfaction, and toilet distance were significantly associated with depression.<br><br>CONCLUSION: Both intrinsic and situational factors were found to be associated with depression among community older population, highlighting their significance for early prevention from the perspective of public health.},
}
@article {pmid39464235,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Lewin, T and , },
title = {The genome sequence of the acorn piercer, Pammene fasciana (Linnaeus, 1761).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {258},
pmid = {39464235},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Pammene fasciana (acorn piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 564 megabases in span. Most of the assembly (99.94%) is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,224 protein-coding genes.},
}
@article {pmid39464503,
year = {2023},
author = {Weir, JC and , and , and , and , and , and , and Boyes, D},
title = {The genome sequence of the Vapourer moth, Orgyia antiqua (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {314},
pmid = {39464503},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Orgyia antiqua specimen (the Vapourer moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 480.1 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,475 protein coding genes.},
}
@article {pmid39466727,
year = {2024},
author = {Charniga, K and Park, SW and Akhmetzhanov, AR and Cori, A and Dushoff, J and Funk, S and Gostic, KM and Linton, NM and Lison, A and Overton, CE and Pulliam, JRC and Ward, T and Cauchemez, S and Abbott, S},
title = {Best practices for estimating and reporting epidemiological delay distributions of infectious diseases.},
journal = {PLoS computational biology},
volume = {20},
number = {10},
pages = {e1012520},
pmid = {39466727},
issn = {1553-7358},
support = {MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Communicable Diseases/epidemiology ; *Disease Outbreaks/statistics &amp; numerical data ; Models, Statistical ; Computational Biology/methods ; Epidemiological Models ; },
abstract = {Epidemiological delays are key quantities that inform public health policy and clinical practice. They are used as inputs for mathematical and statistical models, which in turn can guide control strategies. In recent work, we found that censoring, right truncation, and dynamical bias were rarely addressed correctly when estimating delays and that these biases were large enough to have knock-on impacts across a large number of use cases. Here, we formulate a checklist of best practices for estimating and reporting epidemiological delays. We also provide a flowchart to guide practitioners based on their data. Our examples are focused on the incubation period and serial interval due to their importance in outbreak response and modeling, but our recommendations are applicable to other delays. The recommendations, which are based on the literature and our experience estimating epidemiological delay distributions during outbreak responses, can help improve the robustness and utility of reported estimates and provide guidance for the evaluation of estimates for downstream use in transmission models or other analyses.},
}
@article {pmid39467848,
year = {2024},
author = {Büttiker, P and Boukherissa, A and Weissenberger, S and Ptacek, R and Anders, M and Raboch, J and Stefano, GB},
title = {Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods.},
journal = {Cellular and molecular neurobiology},
volume = {44},
number = {1},
pages = {72},
pmid = {39467848},
issn = {1573-6830},
mesh = {Humans ; *Molecular Mimicry ; Computational Biology/methods ; Cognition/physiology ; Protein Binding ; Amino Acid Sequence ; Viral Proteins/metabolism/chemistry ; Models, Molecular ; },
abstract = {Neurotropic pathogens, notably, herpesviruses, have been associated with significant neuropsychiatric effects. As a group, these pathogens can exploit molecular mimicry mechanisms to manipulate the host central nervous system to their advantage. Here, we present a systematic computational approach that may ultimately be used to unravel protein-protein interactions and molecular mimicry processes that have not yet been solved experimentally. Toward this end, we validate this approach by replicating a set of pre-existing experimental findings that document the structural and functional similarities shared by the human cytomegalovirus-encoded UL144 glycoprotein and human tumor necrosis factor receptor superfamily member 14 (TNFRSF14). We began with a thorough exploration of the Homo sapiens protein database using the Basic Local Alignment Search Tool (BLASTx) to identify proteins sharing sequence homology with UL144. Subsequently, we used AlphaFold2 to predict the independent three-dimensional structures of UL144 and TNFRSF14. This was followed by a comprehensive structural comparison facilitated by Distance-Matrix Alignment and Foldseek. Finally, we used AlphaFold-multimer and PPIscreenML to elucidate potential protein complexes and confirm the predicted binding activities of both UL144 and TNFRSF14. We then used our in silico approach to replicate the experimental finding that revealed TNFRSF14 binding to both B- and T-lymphocyte attenuator (BTLA) and glycoprotein domain and UL144 binding to BTLA alone. This computational framework offers promise in identifying structural similarities and interactions between pathogen-encoded proteins and their host counterparts. This information will provide valuable insights into the cognitive mechanisms underlying the neuropsychiatric effects of viral infections.},
}
@article {pmid39469049,
year = {2024},
author = {Chávez-Luzanía, RA and Ortega-Urquieta, ME and Aguilera-Ibarra, J and Morales-Sandoval, PH and Hernández-Coss, JA and González-Vázquez, LA and Jara-Morales, VB and Arredondo-Márquez, SH and Olea-Félix, MJ and de Los Santos-Villalobos, S},
title = {Transdisciplinary approaches for the study of cyanobacteria and cyanotoxins.},
journal = {Current research in microbial sciences},
volume = {7},
number = {},
pages = {100289},
pmid = {39469049},
issn = {2666-5174},
abstract = {Cyanobacteria, ancient aerobic and photoautotrophic prokaryotes, thrive in diverse ecosystems due to their extensive morphological and physiological adaptations. They play crucial roles in aquatic ecosystems as primary producers and resource providers but also pose significant ecological and health risks through blooms that produce harmful toxins, called cyanotoxins. The taxonomic affiliation of cyanobacteria has evolved from morphology-based methods to genomic analysis, which offers detailed structural and physiological insights that are essential for accurate taxonomic affiliation and monitoring. However, challenges posed by uncultured species have been extrapolated to the detection and quantification of cyanotoxins. Current advances in molecular biology and informatics improve the precision of monitoring and allow the analysis of groups of genes related to toxin production, providing crucial information for environmental biosafety and public health. Unfortunately, public genomic databases heavily underrepresent cyanobacteria, which limits the understanding of their diversity and metabolic capabilities. Despite the increasing availability of cyanobacterial genome sequences, research is still largely focused on a few model strains, narrowing the scope of genetic and metabolic studies. The challenges posed by cyanobacterial blooms and cyanotoxins necessitate improved molecular, cultivation, and polyphasic techniques for comprehensive classification and quantification, highlighting the need for advanced genomic approaches to better understand and manage cyanobacteria and toxins. This review explores the application of transdisciplinary approaches for the study of cyanobacteria and cyanotoxins focused on diversity analysis, population quantification, and cyanotoxin monitoring, emphasizing their genomic resources and their potential in the genomic mining of toxin-related genes.},
}
@article {pmid39469132,
year = {2024},
author = {Bernstein, JM and Bautista, JB and Clores, MA and Brown, RM and Ruane, S and Sanguila, MB and Alis-Besenio, MGJ and Pejo, CLF and Cuesta, MA},
title = {Using mangrove and field observation data to identify fine-scale species distributions: a case study in bockadams (Serpentes: Homalopsidae: Cerberus).},
journal = {Royal Society open science},
volume = {11},
number = {10},
pages = {240483},
pmid = {39469132},
issn = {2054-5703},
abstract = {Characterization of species distributions is a fundamental challenge in biodiversity science, with particular significance for downstream evolutionary studies, conservation efforts, field-based faunal studies and estimates of species diversity. Checklists and phylogenetic studies often focus on poorly known, rare taxa with limited ranges. However, studies of widely distributed, ecologically important species that are abundant in their preferred microhabitats are also important for systematics and local conservation efforts, but less often studied. We collected novel natural history data during fieldwork (2019-2023) for Philippine populations of bockadams (Homalopsidae: Cerberus), one of the most abundant vertebrates in Southeast Asian aquatic systems. Considered a coastal snake, many studies report Cerberus inland. We report the frequency of encounters of Cerberus schneiderii, and the IUCN data-deficient, Philippine-endemic Cerberus microlepis during six expeditions (62 days; 1041 person-hours). We report new occurrence data for 69 C. schneiderii and 6 C. microlepis for coastal and inland populations, water measurements and dietary observations. Regression analyses and ecological niche models show the importance of coastal and mangrove habitats for Cerberus. Our study is the most comprehensive assessment of Philippine Cerberus populations to date and provides critical baseline natural history data for downstream research on widespread and range-restricted species of Southeast Asian snakes.},
}
@article {pmid39470277,
year = {2024},
author = {Xie, J and Zhang, X and Cheng, L and Deng, Y and Ren, H and Mu, M and Zhao, L and Mu, C and Chen, J and Liu, K and Ma, R},
title = {Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0180824},
pmid = {39470277},
issn = {2165-0497},
support = {No. YNWR-MY-2020-044//Yunnan Provincial Health Commission/ ; No. 202102AA310002//Fuwai Yunnan Hospital,Chinese Academy of Medical Sciences/ ; },
mesh = {Humans ; Male ; Female ; *Heart Defects, Congenital/complications/microbiology ; Child ; Gastrointestinal Microbiome ; *Pulmonary Arterial Hypertension/microbiology ; Child, Preschool ; Lung/microbiology ; Metabolome ; *Microbiota ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Adolescent ; Multiomics ; },
abstract = {Dysregulation of immune and inflammatory cells around blood vessels and metabolic dysfunction are key mechanisms in the development of pulmonary arterial hypertension (PAH). The homeostasis of the human microbiome plays a crucial role in regulating immune responses and the progression of diseases. For pulmonary arterial hypertension associated with congenital heart disease involving body-lung shunt (PAH-CHD), the potential impact of the microbiome on the "gut-lung axis" remains underexplored. This study recruited 15 healthy individuals and 15 patients with pulmonary arterial hypertension due to congenital heart disease from Fuwai Yunnan Hospital, Chinese Academy of Medical Sciences, and Kunming Children's Hospital. We performed differential analyses of metabolites and microbiota from both the gut and lower respiratory tract for these two groups. The goal was to investigate the "gut-lung axis" microbiome and metabolome profiles in children with PAH-CHD and to analyze the interrelationships between these profiles. Ultimately, we aim to propose the potential value of these profiles in aiding diagnosis. The results indicated that the gut and pulmonary microbiota of children with PAH-CHD are characterized by an increased abundance of beneficial symbionts, which are closely linked to changes in the metabolome. Metabolite functional enrichment analysis revealed energy metabolism reprogramming in the PAH-CHD group, with active metabolic pathways associated with bile acid secretion and carnitine homeostasis. Moreover, the differential expression of metabolites was correlated with right heart function and growth development.IMPORTANCEPrevious studies have primarily focused on the relationship between the gut microbiome and PAH. However, the impact of microbial homeostasis on the progression of PAH-CHD from the perspective of the gut-lung axis has not been adequately elucidated. Our study utilizes an integrated multi-omics approach to report on the differential characteristics of gut and lung microbiota between children with PAH-CHD and reference subjects. We found that microbiota influence the pathological changes and disease manifestations of PAH-CHD through their metabolic activity. Additionally, alterations in metabolites impact the microbial ecological structure. Our findings suggest that modulating the microbiome composition may have positive implications for maintaining and regulating the immune environment and pathological progression of PAH-CHD.},
}
@article {pmid39470715,
year = {2025},
author = {Miao, Z and Ren, Y and Tarabini, A and Yang, L and Li, H and Ye, C and Liti, G and Fischer, G and Li, J and Yue, JX},
title = {ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D852-D863},
pmid = {39470715},
issn = {1362-4962},
support = {32070592//National Natural Science Foundation of China/ ; 2022A1515010717//Guangdong Basic and Applied Basic Research Foundation/ ; 2019QN01Y183//Guangdong Pearl River Talents Program/ ; YTP-SYSUCC-0042//Sun Yat-sen University Cancer Center/ ; 24qnpy293//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Saccharomyces cerevisiae/genetics/metabolism ; *Genome, Fungal ; *Databases, Genetic ; *Genomics/methods ; Telomere/genetics ; Molecular Sequence Annotation ; Proteomics ; Multiomics ; },
abstract = {As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tractability, serving as a long-standing classic model for both basic and applied studies. Recently, S. cerevisiae further emerged as a leading system for studying natural diversity of genome evolution and its associated functional implication at population scales. Having high-quality comparative and functional genomics data are critical for such efforts. Here, we exhaustively expanded the telomere-to-telomere (T2T) S. cerevisiae reference assembly panel (ScRAP) that we previously constructed for 142 strains to cover high-quality genome assemblies and annotations of 264 S. cerevisiae strains from diverse geographical and ecological niches and also 33 outgroup strains from all the other Saccharomyces species complex. We created a dedicated online database, ScRAPdb (https://www.evomicslab.org/db/ScRAPdb/), to host this expanded pangenome collection. Furthermore, ScRAPdb also integrates an array of population-scale pan-omics atlases (pantranscriptome, panproteome and panphenome) and extensive data exploration toolkits for intuitive genomics analyses. All curated data and downstream analysis results can be easily downloaded from ScRAPdb. We expect ScRAPdb to become a highly valuable platform for the yeast community and beyond, leading to a pan-omics understanding of the global genetic and phenotypic diversity.},
}
@article {pmid39470730,
year = {2025},
author = {Bağcı, C and Nuhamunada, M and Goyat, H and Ladanyi, C and Sehnal, L and Blin, K and Kautsar, SA and Tagirdzhanov, A and Gurevich, A and Mantri, S and von Mering, C and Udwary, D and Medema, MH and Weber, T and Ziemert, N},
title = {BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D618-D624},
pmid = {39470730},
issn = {1362-4962},
support = {161L0284C//Federal Ministry of Research and Education (BMBF)/ ; TTU09.716//German Centre for Infection Research (DZIF)/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; //Saarland University/ ; //National Agri-Food Biotechnology Institute/ ; 101064285//Horizon Europe-Research and Innovation Framework Programme/ ; //Office of Science/ ; DE-AC02-05CH11231//Department of Energy/ ; },
mesh = {*Genome, Bacterial/genetics ; *Internet ; *Multigene Family ; Databases, Genetic ; Bacteria/genetics/metabolism/classification ; Metagenomics/methods ; Metagenome/genetics ; Biosynthetic Pathways/genetics ; Secondary Metabolism/genetics ; Software ; },
abstract = {Secondary metabolites are compounds not essential for an organism's development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.},
}
@article {pmid39470965,
year = {2024},
author = {Sandin, P and Baard, P and Bülow, W and Helgesson, G},
title = {Authorship and Citizen Science: Seven Heuristic Rules.},
journal = {Science and engineering ethics},
volume = {30},
number = {6},
pages = {53},
pmid = {39470965},
issn = {1471-5546},
support = {2019-00548//Svenska Forskningsr&#xe5;det Formas/ ; },
mesh = {*Authorship/standards ; Humans ; *Citizen Science/ethics ; *Heuristics ; *Guidelines as Topic ; *Ethics, Research ; *Publishing/ethics/standards ; Editorial Policies ; Research Personnel/ethics ; Volunteers ; Social Responsibility ; },
abstract = {Citizen science (CS) is an umbrella term for research with a significant amount of contributions from volunteers. Those volunteers can occupy a hybrid role, being both 'researcher' and 'subject' at the same time. This has repercussions for questions about responsibility and credit, e.g. pertaining to the issue of authorship. In this paper, we first review some existing guidelines for authorship and their applicability to CS. Second, we assess the claim that the guidelines from the International Committee of Medical Journal Editors (ICMJE), known as 'the Vancouver guidelines', may lead to exclusion of deserving citizen scientists as authors. We maintain that the idea of including citizen scientists as authors is supported by at least two arguments: transparency and fairness. Third, we argue that it might be plausible to include groups as authors in CS. Fourth and finally, we offer a heuristic list of seven recommendations to be considered when deciding about whom to include as an author of a CS publication.},
}
@article {pmid39472185,
year = {2025},
author = {Orr, MC and Albert, G and Hughes, AC and Koludarov, I and Luo, A and Qiao, H and Wang, MQ and Chesters, D and Zhu, CD},
title = {Dark data limit the biological sciences.},
journal = {Science bulletin},
volume = {70},
number = {4},
pages = {452-453},
doi = {10.1016/j.scib.2024.10.021},
pmid = {39472185},
issn = {2095-9281},
}
@article {pmid39473051,
year = {2024},
author = {Wang, Y and Chen, J and Ni, Y and Liu, Y and Gao, X and Tse, MA and Panagiotou, G and Xu, A},
title = {Exercise-changed gut mycobiome as a potential contributor to metabolic benefits in diabetes prevention: an integrative multi-omics study.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2416928},
pmid = {39473051},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Exercise ; Middle Aged ; *Mycobiome ; *Fungi/classification/genetics/isolation &amp; purification ; *Feces/microbiology ; Proteomics ; Prediabetic State/microbiology/metabolism ; Metabolomics ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Adult ; Diabetes Mellitus, Type 2/microbiology/prevention &amp; control ; Metagenomics ; Multiomics ; },
abstract = {BACKGROUND: The importance of gut microbes in mediating the benefits of lifestyle intervention is increasingly recognized. However, compared to the bacterial microbiome, the role of intestinal fungi in exercise remains elusive. With our established randomized controlled trial of exercise intervention in Chinese males with prediabetes (n = 39, ClinicalTrials.gov:NCT03240978), we investigated the dynamics of human gut mycobiome and further interrogated their associations with exercise-elicited outcomes using multi-omics approaches.<br><br>METHODS: Clinical variations and biological samples were collected before and after training. Fecal fungal composition was analyzed using the internal transcribed spacer 2 (ITS2) sequencing and integrated with paired shotgun metagenomics, untargeted metabolomics, and Olink proteomics.<br><br>RESULTS: Twelve&#x2009;weeks of exercise training profoundly promoted fungal ecological diversity and intrakingdom connection. We further identified exercise-responsive genera with potential metabolic benefits, including Verticillium, Sarocladium, and Ceratocystis. Using multi-omics approaches, we elucidated comprehensive associations between changes in gut mycobiome and exercise-shaped metabolic phenotypes, bacterial microbiome, and circulating metabolomics and proteomics profiles. Furthermore, a machine-learning algorithm built using baseline microbial signatures and clinical characteristics predicted exercise responsiveness in improvements of insulin sensitivity, with an area under the receiver operating characteristic (AUROC) of 0.91 (95% CI: 0.85-0.97) in the discovery cohort and of 0.79 (95% CI: 0.74-0.86) in the independent validation cohort (n&#x2009;=&#x2009;30).<br><br>CONCLUSIONS: Our findings suggest that intense exercise training significantly remodels the human fungal microbiome composition. Changes in gut fungal composition are associated with the metabolic benefits of exercise, indicating gut mycobiome is a possible molecular transducer of exercise. Moreover, baseline gut fungal signatures predict exercise responsiveness for diabetes prevention, highlighting that targeting the gut mycobiome emerges as a prospective strategy in tailoring personalized training for diabetes prevention.},
}
@article {pmid39473806,
year = {2024},
author = {Ayadi, H and Elbéji, A and Despotovic, V and Fagherazzi, G},
title = {Digital Vocal Biomarker of Smoking Status Using Ecological Audio Recordings: Results from the Colive Voice Study.},
journal = {Digital biomarkers},
volume = {8},
number = {1},
pages = {159-170},
pmid = {39473806},
issn = {2504-110X},
abstract = {INTRODUCTION: The complex health, social, and economic consequences of tobacco smoking underscore the importance of incorporating reliable and scalable data collection on smoking status and habits into research across various disciplines. Given that smoking impacts voice production, we aimed to develop a gender and language-specific vocal biomarker of smoking status.<br><br>METHODS: Leveraging data from the Colive Voice study, we used statistical analysis methods to quantify the effects of smoking on voice characteristics. Various voice feature extraction methods combined with machine learning algorithms were then used to produce a gender and language-specific (English and French) digital vocal biomarker to differentiate smokers from never-smokers.<br><br>RESULTS: A total of 1,332&#x202c; participants were included after propensity score matching (mean age = 43.6 [13.65], 64.41% are female, 56.68% are English speakers, 50% are smokers and 50% are never-smokers). We observed differences in voice features distribution: for women, the fundamental frequency F0, the formants F1, F2, and F3 frequencies and the harmonics-to-noise ratio were lower in smokers compared to never-smokers (p < 0.05) while for men no significant disparities were noted between the two groups. The accuracy and AUC of smoking status prediction reached 0.71 and 0.76, respectively, for the female participants, and 0.65 and 0.68, respectively, for the male participants.<br><br>CONCLUSION: We have shown that voice features are impacted by smoking. We have developed a novel digital vocal biomarker that can be used in clinical and epidemiological research to assess smoking status in a rapid, scalable, and accurate manner using ecological audio recordings.},
}
@article {pmid39475188,
year = {2025},
author = {Kemmler, E and Lemfack, MC and Goede, A and Gallo, K and Toguem, SMT and Ahmed, W and Millberg, I and Preissner, S and Piechulla, B and Preissner, R},
title = {mVOC 4.0: a database of microbial volatiles.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D1692-D1696},
pmid = {39475188},
issn = {1362-4962},
support = {Pi153/36-1//German Research Foundation/ ; //University of Rostock/ ; 428445448//Food allergy and tolerance (FOOD@)/ ; },
mesh = {*Volatile Organic Compounds/metabolism/chemistry ; *Bacteria/metabolism/genetics ; Microbiota ; Metabolomics/methods ; Databases, Factual ; Humans ; Metabolome ; Terpenes/metabolism/chemistry ; Databases, Chemical ; },
abstract = {Metabolomic microbiome research has become an important topic for understanding agricultural, ecological as well as health correlations. Only the determination of both the non-volatile and the volatile organic compound (mVOC) production by microorganisms allows a holistic view for understanding the complete potential of metabolomes and metabolic capabilities of bacteria. In the recent past, more and more bacterial headspaces and culture media were analyzed, leading to an accumulation of about 3500 mVOCs in the updated mVOC 4.0 database, including compounds synthesized by the newly discovered non-canonical terpene pathway. Approximately 10% of all mVOCs can be assigned with a biological function, some mVOCs have the potential to impact agriculture in the future (e.g. eco-friendly pesticides) or animal and human health care. mVOC 4.0 offers various options for exploring extensively annotated mVOC data from different perspectives, including improved mass spectrometry matching. The mVOC 4.0 database includes literature searches with additional relevant keywords, making it the most up-to-date and comprehensive publicly available mVOC platform at: http://bioinformatics.charite.de/mvoc.},
}
@article {pmid39475336,
year = {2025},
author = {Menssen, M and Dammann, M and Fneish, F and Ellenberger, D and Schaarschmidt, F},
title = {Prediction Intervals for Overdispersed Poisson Data and Their Application in Medical and Pre-Clinical Quality Control.},
journal = {Pharmaceutical statistics},
volume = {24},
number = {2},
pages = {e2447},
pmid = {39475336},
issn = {1539-1612},
mesh = {Humans ; *Quality Control ; Poisson Distribution ; Monte Carlo Method ; Algorithms ; Computer Simulation ; Models, Statistical ; Multiple Sclerosis ; Data Interpretation, Statistical ; },
abstract = {In pre-clinical and medical quality control, it is of interest to assess the stability of the process under monitoring or to validate a current observation using historical control data. Classically, this is done by the application of historical control limits (HCL) graphically displayed in control charts. In many applications, HCL are applied to count data, for example, the number of revertant colonies (Ames assay) or the number of relapses per multiple sclerosis patient. Count data may be overdispersed, can be heavily right-skewed and clusters may differ in cluster size or other baseline quantities (e.g., number of petri dishes per control group or different length of monitoring times per patient). Based on the quasi-Poisson assumption or the negative-binomial distribution, we propose prediction intervals for overdispersed count data to be used as HCL. Variable baseline quantities are accounted for by offsets. Furthermore, we provide a bootstrap calibration algorithm that accounts for the skewed distribution and achieves equal tail probabilities. Comprehensive Monte-Carlo simulations assessing the coverage probabilities of eight different methods for HCL calculation reveal, that the bootstrap calibrated prediction intervals control the type-1-error best. Heuristics traditionally used in control charts (e.g., the limits in Shewhart c- or u-charts or the mean ± 2 SD) fail to control a pre-specified coverage probability. The application of HCL is demonstrated based on data from the Ames assay and for numbers of relapses of multiple sclerosis patients. The proposed prediction intervals and the algorithm for bootstrap calibration are publicly available via the R package predint.},
}
@article {pmid39475652,
year = {2024},
author = {Chala, D and Endresen, D and Demissew, S and Slaughter, LA and Johnsen, EB and Stenseth, NC},
title = {Stop using racist, unethical, and inappropriate names in taxonomy.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {45},
pages = {e2415490121},
pmid = {39475652},
issn = {1091-6490},
}
@article {pmid39477106,
year = {2024},
author = {Manzanedo, RD and Chin, ARO and Ettinger, AK and Pederson, N and Pradhan, K and Guiterman, CH and Su, J and Baumgarten, F and Hille Ris Lambers, J},
title = {Moving ecological tree-ring big data forwards: Limitations, data integration, and multidisciplinarity.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {177244},
doi = {10.1016/j.scitotenv.2024.177244},
pmid = {39477106},
issn = {1879-1026},
mesh = {*Ecology ; *Big Data ; *Trees ; *Databases, Factual ; Environmental Monitoring/methods ; Forests ; Ecosystem ; },
abstract = {In recent years, tree-ring databases have emerged as a remarkable resource for ecological research, allowing us to address ecological questions at unprecedented temporal and spatial scales. However, concerns regarding big tree-ring data limitations and risks have also surfaced, leading to questions about their potential to be representative of long-term forest responses. Here, we highlight three paths of action to improve on tree-ring databases in ecology: 1) Implementing consistent bias analyses in large dendroecological databases and promoting community-driven data to address data limitations, 2) Encouraging the integration of tree-ring data with other ecological datasets, and 3) Promoting theory-driven, mechanistic dendroecological research. These issues are increasingly important for tackling pressing cross-disciplinary research questions. Finally, although we focus here on tree ring databases, these points apply broadly across many aggregative databases in ecology.},
}
@article {pmid39480818,
year = {2024},
author = {Ramesh, S and Rapp, S and Tapias Gomez, J and Levine, B and Tapias-Gomez, D and Chung, D and Truong, Z},
title = {Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0309707},
pmid = {39480818},
issn = {1932-6203},
mesh = {*User-Computer Interface ; *Software ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Databases, Nucleic Acid ; Web Browser ; },
abstract = {Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.},
}
@article {pmid39480880,
year = {2024},
author = {Silva, GAA and Harder, AM and Kirksey, KB and Mathur, S and Willoughby, JR},
title = {Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history.},
journal = {PLoS computational biology},
volume = {20},
number = {10},
pages = {e1012566},
pmid = {39480880},
issn = {1553-7358},
mesh = {*Homozygote ; *Genetics, Population/methods ; *Inbreeding ; Animals ; Models, Genetic ; Computational Biology/methods ; Humans ; Computer Simulation ; Polymorphism, Single Nucleotide/genetics ; },
abstract = {Wild populations are increasingly threatened by human-mediated climate change and land use changes. As populations decline, the probability of inbreeding increases, along with the potential for negative effects on individual fitness. Detecting and characterizing runs of homozygosity (ROHs) is a popular strategy for assessing the extent of individual inbreeding present in a population and can also shed light on the genetic mechanisms contributing to inbreeding depression. Here, we analyze simulated and empirical datasets to demonstrate the downstream effects of program selection and long-term demographic history on ROH inference, leading to context-dependent biases in the results. Through a sensitivity analysis we evaluate how various parameter values impact ROH-calling results, highlighting its utility as a tool for parameter exploration. Our results indicate that ROH inferences are sensitive to factors such as sequencing depth and ROH length distribution, with bias direction and magnitude varying with demographic history and the programs used. Estimation biases are particularly pronounced at lower sequencing depths, potentially leading to either underestimation or overestimation of inbreeding. These results are particularly important for the management of endangered species, as underestimating inbreeding signals in the genome can substantially undermine conservation initiatives. We also found that small true ROHs can be incorrectly lumped together and called as longer ROHs, leading to erroneous inference of recent inbreeding. To address these challenges, we suggest using a combination of ROH detection tools and ROH length-specific inferences, along with sensitivity analysis, to generate robust and context-appropriate population inferences regarding inbreeding history. We outline these recommendations for ROH estimation at multiple levels of sequencing effort, which are typical of conservation genomics studies.},
}
@article {pmid39480949,
year = {2024},
author = {Goldshtein, A and Chen, X and Amichai, E and Boonman, A and Harten, L and Yinon, O and Orchan, Y and Nathan, R and Toledo, S and Couzin, ID and Yovel, Y},
title = {Acoustic cognitive map-based navigation in echolocating bats.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6721},
pages = {561-567},
doi = {10.1126/science.adn6269},
pmid = {39480949},
issn = {1095-9203},
mesh = {Animals ; Acoustics ; *Chiroptera/physiology ; *Cognition ; *Echolocation ; Geographic Information Systems ; Homing Behavior ; *Spatial Navigation ; },
abstract = {Bats are known for their ability to use echolocation for obstacle avoidance and orientation. However, the extent to which bats utilize their highly local and directional echolocation for kilometer-scale navigation is unknown. In this study, we translocated wild Kuhl's pipistrelle bats and tracked their homing abilities while manipulating their visual, magnetic, and olfactory sensing and accurately tracked them using a new reverse GPS system. We show that bats can identify their location after translocation and conduct several-kilometer map-based navigation using solely echolocation. This proposition was further supported by a large-scale echolocation model disclosing how bats use environmental acoustic information to perform acoustic cognitive map-based navigation. We also demonstrate that navigation is improved when using both echolocation and vision.},
}
@article {pmid39481332,
year = {2025},
author = {Yao, M and Ren, A and Yang, X and Chen, L and Wang, X and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M},
title = {Unveiling the influence of heating temperature on biofilm formation in shower hoses through multi-omics.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122704},
doi = {10.1016/j.watres.2024.122704},
pmid = {39481332},
issn = {1879-2448},
mesh = {*Biofilms ; Proteomics ; Heating ; Metagenomics ; Hot Temperature ; Metagenome ; Multiomics ; },
abstract = {Shower systems provide unique environments that are conducive to biofilm formation and the proliferation of pathogens. The water heating temperature is a delicate decision that can impact microbial growth, balancing safety and energy consumption. This study investigated the impact of different heating temperatures (39 °C, 45 °C, 51 °C and 58 °C) on the shower hose biofilm (exposed to a final water temperature of 39 °C) using controlled full-scale shower setups. Whole metagenome sequencing and metaproteomics were employed to unveil the microbial composition and protein expression profiles. Overall, the genes and enzymes associated with disinfectant resistance and biofilm formation appeared largely unaffected. However, metagenomic analysis revealed a sharp decline in the number of total (86,371 to 34,550) and unique genes (32,279 to 137) with the increase in hot water temperature, indicating a significant reduction of overall microbial complexity. None of the unique proteins were detected in the proteomics experiments, suggesting smaller variation among biofilms on the proteome level compared to genomic data. Furthermore, out of 43 pathogens detected by metagenomics, only 5 could actually be detected by metaproteomics. Most interestingly, our study indicates that 45 °C heating temperature may represent an optimal balance. It minimizes active biomass (ATP) and reduces the presence of pathogens while saving heating energy. Our study offered new insights into the impact of heating temperature on shower hose biofilm formation and proposed optimal parameters that ensure biosafety while conserving energy.},
}
@article {pmid39483086,
year = {2024},
author = {Behera, BP and Naik, H and Konkimalla, VB},
title = {Peptaloid: A Comprehensive Database for Exploring Peptide Alkaloid.},
journal = {Journal of chemical information and modeling},
volume = {64},
number = {22},
pages = {8387-8395},
doi = {10.1021/acs.jcim.4c01667},
pmid = {39483086},
issn = {1549-960X},
mesh = {*Peptides/chemistry ; *Alkaloids/chemistry/pharmacology ; Databases, Protein ; Machine Learning ; Databases, Factual ; Humans ; },
abstract = {Peptaloid is the first dedicated database for peptide alkaloid molecules, a unique class of naturally derived compounds known for their structural diversity and significant biological activities. Despite their promising potential in drug discovery and therapeutic development, research on peptide alkaloids has been limited by the absence of a comprehensive and centralized resource. Fragmented data across various sources have posed a significant challenge, underscoring the need for a specialized database to facilitate more efficient research and application. Peptaloid addresses this critical gap by providing a database with over 161,000 peptide alkaloid entries, each detailed with structural, physicochemical, and pharmacological properties. By leveraging advanced computational tools and machine learning, Peptaloid generates ADMET profiles, aiding in identifying and optimizing therapeutic candidates. Designed for versatility, the database supports various applications beyond drug discovery, including ecology and material sciences. Peptaloid (as a specialized database for peptide alkaloids) will play a crucial role in innovation and collaboration across scientific disciplines. Peptaloid is accessible at https://peptaloid.niser.ac.in.},
}
@article {pmid39488960,
year = {2024},
author = {Tayyab, M and Hussain, M and Zhang, J and Ullah, S and Tong, Z and Rahman, ZU and Al-Aizari, AR and Al-Shaibah, B},
title = {Leveraging GIS-based AHP, remote sensing, and machine learning for susceptibility assessment of different flood types in peshawar, Pakistan.},
journal = {Journal of environmental management},
volume = {371},
number = {},
pages = {123094},
doi = {10.1016/j.jenvman.2024.123094},
pmid = {39488960},
issn = {1095-8630},
mesh = {*Floods ; Pakistan ; *Machine Learning ; *Geographic Information Systems ; Algorithms ; Remote Sensing Technology ; },
abstract = {Due to its diverse topography, Pakistan faces different types of floods each year, which cause substantial physical, environmental, and socioeconomic damage. However, the susceptibility of specific regions to different flood types remains unexplored. To the best of our knowledge for the first time, this study employed an integrated approach by leveraging a GIS-based Analytical Hierarchy Process (AHP), remote sensing, and machine learning (ML) algorithms, to assess susceptibility to three different types of flooding in Peshawar, Pakistan. The study first evaluated the degree of susceptibility to riverine, urban, and flash floods using the GIS-based AHP technique, and then employed ML models, (i.e., specifically Random Forest [RF] and Extreme Gradient Boosting [XG-Boost] to analyze multi-type flood susceptibility in the study region. The performance of the ML models was also evaluated, and the XG-Boost model outperforms RF, demonstrating a higher correlation coefficient (R[2] = 0.561-0.922) and lower mean absolute error (MAE = 0.042-0.354), and root-mean-square error (RMSE = 0.119-0.415) for both training and testing datasets. The superior performance of the XG-Boost was further confirmed by the higher value of the area under the curve (AUC) values, which is relatively higher (0.87) than that of the AHP (0.70) and RF (0.86) models. Based on the relative best performance, the XG-Boost model was chosen for further susceptibility assessment of different types of floods, and the generated flood susceptibility maps revealed that 20.9% of the total area is susceptible to riverine flooding, while 30.27% and 48.68% of the total area is susceptible to urban and flash flooding, respectively. The study's findings are significant, offering valuable insights for relevant stakeholders in guiding future flood risk management and sustainable land use plans in the study area.},
}
@article {pmid39493638,
year = {2024},
author = {Reuken, PA and Besteher, B and Bleidorn, J and Brockmann, D and Finke, K and Freytag, A and Lehmann-Pohl, K and Lemhöfer, C and Mikolajczyk, R and Puta, C and Scherag, A and Wiedermann, M and Zippel-Schultz, B and Stallmach, A},
title = {Web-based telemedicine approach for treatment of post-COVID-19 in Thuringia (WATCH).},
journal = {Digital health},
volume = {10},
number = {},
pages = {20552076241291748},
pmid = {39493638},
issn = {2055-2076},
abstract = {OBJECTIVE: After infection with SARS-CoV-2, a substantial proportion of patients develop long-lasting sequelae. These sequelae include fatigue (potentially as severe as that seen in ME/CFS cases), cognitive dysfunction, and psychiatric symptoms. Because the pathophysiology of these sequelae remains unclear, existing therapeutic concepts address the symptoms through pacing strategies, cognitive training, and psychological therapy.<br><br>METHODS: Here, we present a protocol for a digital multimodal structured intervention addressing common symptoms through three intervention modules: BRAIN, BODY, and SOUL. This intervention includes an assessment conducted via a mobile "post-COVID-19 bus" near the patient's home, as well as the use of wearable devices and mobile applications to support pacing strategies and collection of data, including ecological momentary assessment.<br><br>RESULTS: We will focus on physical component subscore of the SF36 as Quality of Life parameter as the primary outcome parameter for WATCH to take into account the holistic approach that is necessary for care of post-COVID patients.<br><br>CONCLUSION: In the current project, we present a protocol for a holistic and multimodal structured therapeutic concept which is easily accessible, and scalable for post-COVID patients.},
}
@article {pmid39493766,
year = {2024},
author = {Chakraborty, H and Chakraborty, HJ and Das, BK and Maity, J},
title = {Age-specific changes in the serum proteome of female anadromous, hilsa Tenualosa ilisha: a comparative analysis across developmental stages.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1448627},
pmid = {39493766},
issn = {1664-3224},
mesh = {Female ; *Proteome ; Animals ; Proteomics/methods ; Tandem Mass Spectrometry ; Protein Interaction Maps ; Computational Biology/methods ; Age Factors ; Chromatography, Liquid ; Blood Proteins/metabolism ; Fishes/genetics/blood ; Aging/blood/immunology ; },
abstract = {INTRODUCTION: The proteome profile of the female Tenualosa ilisha (Hamilton, 1822), a species of great ecological and economic importance, across various age groups was investigated to comprehend the functional dynamics of the serum proteome for conservation and aquaculture, as well as sustain the population.<br><br>METHODS: Advanced liquid chromatography-tandem mass spectrometry LC-MS/MS-based proteomic data were analysed and submitted to the ProteomeXchange Consortium via PRIDE (PRoteomics IDEntifications database). Bioinformatics analysis of serum proteome have been done and it showed different proteins associated with GO Gene Ontology () terms, and the genes associated with enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways (such as phagosome, mTOR, Apelin signalling pathways, herpes simplex virus) implicated in immune responses.<br><br>RESULTS: The expression levels of important immunological proteins, such as those involved in cellular defence and inflammatory responses, were significantly different age-dependently. In this study, we annotated 952, 494, 415, and 282 proteins in year classes IV, III, II, and I Hilsa, respectively, and analysed their Protein-Protein Interaction (PPI) networks based on their functional characteristics. From year classes I to IV, new proteins appeared and were more than three-fold. Notably, class I hilsa displayed a lower abundance of proteins than class IV hilsa.<br><br>DISCUSSION: This is the first study, to the best of our knowledge, to report the analysis of the serum proteome of hilsa at different developmental stages, and the results can help improve the understanding of the mechanisms underlying the different changes in protein enrichment during migration in hilsa. This analysis also offers crucial insights into the immune system for hilsa conservation and management.},
}
@article {pmid39494195,
year = {2024},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Case-bearing Clothes moth, Tinea pellionella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {119},
pmid = {39494195},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Tinea pellionella (the Case-bearing Clothes moth; Arthropoda; Insecta; Lepidoptera; Tineidae). The genome sequence is 245.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 25.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,811 protein coding genes.},
}
@article {pmid39497067,
year = {2024},
author = {Moeller, AH and Dillard, BA and Goldman, SL and Real, MVF and Sprockett, DD},
title = {Removal of sequencing adapter contamination improves microbial genome databases.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1033},
pmid = {39497067},
issn = {1471-2164},
support = {R01 DK139214/DK/NIDDK NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Databases, Genetic ; DNA Contamination ; Genome, Microbial ; Humans ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Cattle ; Mice ; Swine ; },
abstract = {Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.},
}
@article {pmid39501271,
year = {2024},
author = {Sijm-Eeken, M and Ossebaard, HC and Čaluković, A and Temme, B and Peute, LW and Jaspers, MW},
title = {Linking theory and practice to advance sustainable healthcare: the development of maturity model version 1.0.},
journal = {BMC health services research},
volume = {24},
number = {1},
pages = {1350},
pmid = {39501271},
issn = {1472-6963},
mesh = {Humans ; *Delivery of Health Care/organization &amp; administration ; Climate Change ; Sustainable Development ; Conservation of Natural Resources/methods ; Models, Theoretical ; Models, Organizational ; },
abstract = {BACKGROUND: Climate change and increased awareness of planetary health have made reducing ecological footprints a priority for healthcare organizations. However, improving healthcare's environmental impact remains difficult. Numerous researchers argue these difficulties are caused by healthcare's environmental impact being multidimensional, influenced throughout the healthcare chain, and often has downstream consequences that are hard to identify or to measure. Even though existing research describes many successful approaches to reduce healthcare's environmental impact, a robust multidimensional framework to assess this impact is lacking. This research aims at developing a maturity model for sustainable healthcare that could be used for self-assessment by healthcare professionals to identify improvement actions and for sharing best practices in environmental sustainability.<br><br>METHODS: A design-oriented approach for maturity model development was combined with an expert panel and six case studies to develop, refine and expand the maturity model for environmentally sustainable healthcare.<br><br>RESULTS: A maturity model was developed containing four domains: 'Governance', 'Organization Structures', 'Processes', and 'Outcomes and Control'. Applying the model in real-world environments demonstrated the model's understandability, ease of use, usefulness, practicality and ability to identify improvement actions for environmental sustainability in healthcare organizations.<br><br>CONCLUSIONS: This study found that healthcare practitioners could apply the maturity model developed and tested in this study in several hours without training to help them gain valuable insights into the environment footprint of the healthcare setting they worked in. Systematically implementing the model developed in this study could help address the urgent need to mitigate the substantial environmental impact of healthcare. These implementations can help evaluate and improve the maturity model.},
}
@article {pmid39502585,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Small Phoenix, Ecliptopera silaceata (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {209},
pmid = {39502585},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Ecliptopera silaceata (the Small Phoenix; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 316.5 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,770 protein coding genes.},
}
@article {pmid39503522,
year = {2024},
author = {Campelo, F and de Oliveira, ALG and Reis-Cunha, J and Fraga, VG and Bastos, PH and Ashford, J and Ekárt, A and Adelino, TER and Silva, MVF and de Melo Iani, FC and de Jesus, ACP and Bartholomeu, DC and de Souza Trindade, G and Fujiwara, RT and Bueno, LL and Lobo, FP},
title = {Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
pmid = {39503522},
issn = {1477-4054},
support = {BIP-00123-23//FAPEMIG/ ; INCT-406441/2022-7//Brazilian National Institutes of Science and Technology/ ; RED-00067-23//Rede Mineira de Imunobiol&#xf3;gicos/ ; APQ-4035/17//State of Minas Gerais Research Support Foundation/ ; 310311/2023-3//National Council for Scientific and Technological Development/ ; 405249/2022-5//MCTI/Brazil/ ; MR/T016019/1//UK Medical Research Council/ ; //EPSRC/UK/ ; },
mesh = {*Phylogeny ; Humans ; *Epitopes, B-Lymphocyte/immunology ; Orthopoxvirus/immunology/genetics ; Computational Biology/methods ; Vaccinia virus/immunology/genetics ; Mpox, Monkeypox ; },
abstract = {We introduce a phylogeny-aware framework for predicting linear B-cell epitope (LBCE)-containing regions within proteins. Our approach leverages evolutionary information by using a taxonomic scaffold to build models trained on hierarchically structured data. The resulting models present performance equivalent or superior to generalist methods, despite using simpler features and a fraction of the data volume required by current state-of-the-art predictors. This allows the utilization of available data for major pathogen lineages to facilitate the prediction of LBCEs for emerging infectious agents. We demonstrate the efficacy of our approach by predicting new LBCEs in the monkeypox (MPXV) and vaccinia viruses. Experimental validation of selected targets using sera from infected patients confirms the presence of LBCEs, including candidates for the differential serodiagnosis of recent MPXV infections. These results point to the use of phylogeny-aware predictors as a useful strategy to facilitate the targeted development of immunodiagnostic tools.},
}
@article {pmid39507254,
year = {2024},
author = {Flores, M and Ho, E and Ly, C and Ceberio, N and Guardado, M and Felix, K and Thorner, HM and Paunovich, M and Godek, C and Kalaydjian, C and Rohlfs, RV},
title = {Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity.},
journal = {iScience},
volume = {27},
number = {11},
pages = {111067},
pmid = {39507254},
issn = {2589-0042},
support = {R25 GM059298/GM/NIGMS NIH HHS/United States ; T32 GM148332/GM/NIGMS NIH HHS/United States ; T34 GM008574/GM/NIGMS NIH HHS/United States ; },
abstract = {Forensic investigation of DNA samples from multiple contributors has become commonplace. These complex analyses use statistical frameworks accounting for multiple levels of uncertainty in allelic contributions from different individuals, particularly for samples containing few molecules of DNA. These methods have been thoroughly tested along some axes of variation, but less attention has been paid to accuracy across human genetic variation. Here, we quantify the accuracy of DNA mixture analysis over 83 human groups. We find higher false inclusion rates for mixtures with more contributors and for groups with lower genetic diversity. Even for three-contributor mixtures where two contributors are known and the reference group is correctly specified, false inclusion rates are 1e-5 or higher for 36 out of 83 groups. This means that, depending on multiple testing, some false inclusions may be expected. These false positives could be lessened with more selective and conservative use of DNA mixture analysis.},
}
@article {pmid39511491,
year = {2024},
author = {Tang, Y and Tian, C and Yao, D and Yang, S and Shi, L and Yi, L and Peng, Q},
title = {Community assembly and potential function analysis of the endophyte in Eucommia ulmoides.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {460},
pmid = {39511491},
issn = {1471-2180},
mesh = {*Endophytes/genetics/metabolism/classification/physiology/isolation &amp; purification ; *Eucommiaceae/microbiology ; *Ascomycota/genetics/growth &amp; development/physiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Iridoid Glucosides/metabolism ; Basidiomycota/genetics/physiology ; Symbiosis ; Fungi/classification/genetics/isolation &amp; purification/metabolism/physiology ; Computational Biology ; },
abstract = {Endophytes play a pivotal role in protecting host plants from both biotic and abiotic stresses, promoting the production of active components (AC) and plant growth. However, the succession of the endophyte community in Eucommia ulmoides (E. ulmoides), particularly the community assembly and function, has not been extensively investigated. In this study, we employed high-throughput sequencing and bioinformatics tools to analyze endophyte diversity across different tree ages, parts, and periods. We examined the population differences, correlations, community assembly mechanisms, and functional roles of these endophytes. Functional predictions via PICRUSt2 revealed that most endophytic fungal functions were linked to biosynthesis, with significant differences in biosynthetic functional abundance across parts and periods. In contrast, the metabolic activity of endophytic bacteria remained stable across different periods and parts. Correlation analysis further confirmed a strong positive relationship between ACs and certain endophytic fungi. Among them, the fungal phyla Ascomycota and Basidiomycota were identified as key contributors to the metabolism of chlorogenic acid (CA), while Aucubin was significantly positively correlated with several endophytic bacteria. These findings provide valuable insights into the functional roles and community assembly mechanism of E. ulmoides endophytes, as well as their symbiotic relationships.},
}
@article {pmid39512488,
year = {2024},
author = {Lewis, JH and Kojima, H and Suenaga, M and Petsopoulos, D and Fujisawa, Y and Truong, XL and Warren, DL},
title = {The era of cybertaxonomy: X-ray microtomography reveals cryptic diversity and concealed cuticular sculpture in Aphanerostethus Voss, 1957 (Coleoptera, Curculionidae).},
journal = {ZooKeys},
volume = {1217},
number = {},
pages = {1-45},
pmid = {39512488},
issn = {1313-2989},
abstract = {Weevils represent one of the most speciose and economically important animal clades, but remain poorly studied across much of the Oriental Region. Here, an integrative revision of the Oriental, flightless genus Aphanerostethus Voss, 1957 (Curculionidae: Molytinae) based on X-ray microtomography, multi-gene DNA barcoding (CO1, Cytb, 16S), and traditional morphological techniques (light microscopy, dissections) is presented. Twelve new species, namely, A.armatus Lewis &amp; Kojima, sp. nov., A.bifidus Kojima &amp; Lewis, sp. nov., A.darlingi Lewis, sp. nov., A.decoratus Lewis &amp; Kojima, sp. nov., A.falcatus Kojima, Lewis &amp; Fujisawa, sp. nov., A.incurvatus Kojima &amp; Lewis, sp. nov., A.japonicus Lewis &amp; Kojima, sp. nov., A.magnus Lewis &amp; Kojima, sp. nov., A.morimotoi Kojima &amp; Lewis, sp. nov., A.nudus Lewis &amp; Kojima, sp. nov., A.spinosus Lewis &amp; Kojima, sp. nov., and A.taiwanus Lewis, Fujisawa &amp; Kojima, sp. nov. are described from Japan, Taiwan, Vietnam, and Malaysia. A neotype is designated for A.vannideki Voss, 1957. The hitherto monotypic genus Darumazo Morimoto &amp; Miyakawa, 1985, syn. nov. is synonymized under Aphanerostethus based on new morphological data and Aphanerostethusdistinctus (Morimoto &amp; Miyakawa, 1985), comb. nov. is transferred accordingly. X-ray microtomography is successfully used to explore for stable interspecific differences in cuticular, internal and micro morphology. Remarkable species-specific sexual dimorphism in the metatibial uncus is described in seven of the newly described Aphanerostethus species and the evolution of this character is discussed.},
}
@article {pmid39513992,
year = {2025},
author = {Black, AN and Jeon, JY and Mularo, AJ and Allen, NM and Heenkenda, E and Buchanan-Schwanke, JC and Bickham, JW and Lowe, ZE and DeWoody, JA},
title = {Thematic Layers of Genomic Susceptibility for Conservation Monitoring.},
journal = {Molecular ecology},
volume = {34},
number = {23},
pages = {e17582},
doi = {10.1111/mec.17582},
pmid = {39513992},
issn = {1365-294X},
mesh = {*Conservation of Natural Resources/methods ; *Genetics, Population/methods ; *Genomics/methods ; Hybridization, Genetic ; Heterozygote ; Geographic Information Systems ; Homozygote ; },
abstract = {Population genomics has great potential to inform applied conservation management and associated policy. However, the bioinformatic analyses and interpretation of population genomic datasets can be daunting and difficult to convey to nonspecialists, including on-the-ground conservationists that work with many state, federal and international agencies. We think that individual population genomic metrics of interest can be interpolated and ultimately distilled into thematic GIS layers that represent spatiotemporal genomic potential (or conversely, susceptibility) in conservation monitoring. As examples relevant to ongoing conservation efforts, we use introgressive hybridisation and individual heterozygosity to illustrate a conceptual approach for mapping population genomic susceptibility. The general framework of thematic layers could be extended to integrate key genomic metrics (e.g., runs of homozygosity and genomic load) that are relevant to many conservation efforts.},
}
@article {pmid39516498,
year = {2024},
author = {Weistuch, C and Murgas, KA and Zhu, J and Norton, L and Dill, KA and Tannenbaum, AR and Deasy, JO},
title = {Normal tissue transcriptional signatures for tumor-type-agnostic phenotype prediction.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {27230},
pmid = {39516498},
issn = {2045-2322},
support = {BCRF-17-193//Breast Cancer Research Foundation/ ; W911NF2210292//Army Research Office/ ; P30 CA008748/CA/NCI NIH HHS/United States ; FA9550-20-1-0029//Air Force Office of Scientific Research/ ; R01-AG048769/GF/NIH HHS/United States ; R01 AG048769/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Transcriptome ; *Phenotype ; *Gene Expression Regulation, Neoplastic ; Female ; Neoplasms/genetics/pathology/metabolism ; Gene Expression Profiling ; Breast Neoplasms/genetics/pathology/metabolism ; },
abstract = {Cancer transcriptional patterns reflect both unique features and shared hallmarks across diverse cancer types, but whether differences in these patterns are sufficient to characterize the full breadth of tumor phenotype heterogeneity remains an open question. We hypothesized that these shared transcriptomic signatures reflect repurposed versions of functional tasks performed by normal tissues. Starting with normal tissue transcriptomic profiles, we use non-negative matrix factorization to derive six distinct transcriptomic phenotypes, called archetypes, which combine to describe both normal tissue patterns and variations across a broad spectrum of malignancies. We show that differential enrichment of these signatures correlates with key tumor characteristics, including overall patient survival and drug sensitivity, independent of clinically actionable DNA alterations. Additionally, we show that in HR+/HER2- breast cancers, metastatic tumors adopt transcriptomic signatures consistent with the invaded tissue. Broadly, our findings suggest that cancer often arrogates normal tissue transcriptomic characteristics as a component of both malignant progression and drug response. This quantitative framework provides a strategy for connecting the diversity of cancer phenotypes and could potentially help manage individual patients.},
}
@article {pmid39520764,
year = {2025},
author = {Rodriguez-Caturla, MY and Margalho, LP and Graça, JS and Pia, AKR and Xavier, VL and Noronha, MF and Cabral, L and Lemos-Junior, WJF and Castillo, CJC and SantˈAna, AS},
title = {Bacterial dynamics and volatile metabolome changes of vacuum-packaged beef with different pH during chilled storage.},
journal = {International journal of food microbiology},
volume = {427},
number = {},
pages = {110955},
doi = {10.1016/j.ijfoodmicro.2024.110955},
pmid = {39520764},
issn = {1879-3460},
mesh = {*Volatile Organic Compounds/analysis/metabolism ; Hydrogen-Ion Concentration ; Vacuum ; Cattle ; Animals ; *Red Meat/microbiology ; *Food Packaging/methods ; *Food Microbiology ; *Food Storage ; Bacteria/metabolism/growth &amp; development/classification/genetics/isolation &amp; purification ; Metabolome ; Brazil ; RNA, Ribosomal, 16S/genetics ; },
abstract = {This study aimed to assess the growth of spoilage bacteria in Brazilian vacuum-packed beef across different pH ranges (5.4-5.8, 5.8-6.1, ≥6.1) stored at temperatures of 0 °C, 4 °C, and 7 °C. Additionally, the research sought to identify predominant spoilage bacteria at the genus level using 16S rDNA gene sequencing and analyze the principal volatile organic compounds (VOCs) produced by this microbiota through HS-SPME/GC-MS. Lactic acid bacteria (LAB) consistently exhibited counts exceeding 6.0 Log CFU/g, regardless of temperature and pH conditions. The bacterial diversity in the meat samples reflected the influence of slaughterhouse environments, with Pseudomonas and Serratia remaining dominant across different cuts and pH levels. Post-storage, variations in pH and temperature modulated the initial bacterial diversity, leading to a reduction in diversity and an increase in LAB such as Lactobacillus, Lactococcus, Leuconostoc, and Carnobacterium. Notably, these changes were observed within pH ranges of 5.4-5.8 and 5.8-6.1, irrespective of beef cuts and storage temperatures. Based on high throughput sequencing and VOCS, correlation analysis revealed a relationship between the growth of specific spoilage microorganisms under vacuum conditions and the presence of VOCs such as alcohols (e.g., 1-propanol, 2-methyl-) and ketones (e.g., 2-nonanone, 2-octanone, 2-heptanone), identifying them as potential indicators of spoilage bacteria growth.},
}
@article {pmid39521320,
year = {2024},
author = {Coelho, LA and Gonzalez, CLR and Tammurello, C and Campus, C and Gori, M},
title = {Hand and foot overestimation in visually impaired human adults.},
journal = {Neuroscience},
volume = {563},
number = {},
pages = {74-83},
doi = {10.1016/j.neuroscience.2024.10.055},
pmid = {39521320},
issn = {1873-7544},
mesh = {Humans ; Female ; Male ; Adult ; *Hand ; *Foot ; Middle Aged ; *Blindness/physiopathology/psychology ; Persons with Visual Disabilities/psychology ; Body Image/psychology ; Young Adult ; Sex Characteristics ; },
abstract = {Previous research has shown that visual impairment results in reduced audio, tactile and proprioceptive ability. One hypothesis is that these issues arise from inaccurate body representations. Few studies have investigated metric body representations in a visually impaired population. We designed an ecologically valid behavioural task in which visually impaired adults haptically explored various sized gloves or shoes. They were asked to indicate if they perceived each clothing item as bigger than the size of their hand or foot. In the post-hoc analyses we fit psychometric curves to the data to extract the point of subjective equality. We then compared the results to age/sex matched controls. We hypothesized the blind participants body representations should be more distorted. Because previous research has shown that females are more likely to overestimate body size, we predicted sex differences in the sighted participants. However, because blind adults have no exposure to visual ideals of body size, we predicted that there would be no sex differences. Our results showed thatblind participants overestimated their hands and feetto a similar degree. Sighted controls overestimated their hands significantly more than their feet. Taken together, our results partially support our hypothesis and suggest that visual deprivation, even for short periods result in hand size overestimation.},
}
@article {pmid39526196,
year = {2024},
author = {Boyes, D and Crowley, LM and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Pale November moth, Epirrita christyi (Allen, 1906).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {540},
pmid = {39526196},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Pale November moth, Epirrita christyi (Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 474.20 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.99 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,983 protein-coding genes.},
}
@article {pmid39526854,
year = {2024},
author = {Tan, X and Xue, F and Zhang, C and Wang, T},
title = {mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
pmid = {39526854},
issn = {1477-4054},
support = {12331009//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; Computational Biology/methods ; Algorithms ; Gastrointestinal Microbiome ; },
abstract = {Alterations in human microbial communities are intricately linked to the onset and progression of diseases. Identifying the key microbes driving these community changes is crucial, as they may serve as valuable biomarkers for disease prevention, diagnosis, and treatment. However, there remains a need for further research to develop effective methods for addressing this critical task. This is primarily because defining the driver microbe requires consideration not only of each microbe's individual contributions but also their interactions. This paper introduces a novel framework, called mbDriver, for identifying driver microbes based on microbiome abundance data collected at discrete time points. mbDriver comprises three main components: (i) data preprocessing of time-series abundance data using smoothing splines based on the negative binomial distribution, (ii) parameter estimation for the generalized Lotka-Volterra (gLV) model using regularized least squares, and (iii) quantification of each microbe's contribution to the community's steady state by manipulating the causal graph implied by gLV equations. The performance of nonparametric spline-based denoising and regularized least squares estimation is comprehensively evaluated on simulated datasets, demonstrating superiority over existing methods. Furthermore, the practical applicability and effectiveness of mbDriver are showcased using a dietary fiber intervention dataset and an ulcerative colitis dataset. Notably, driver microbes identified in the dietary fiber intervention dataset exhibit significant effects on the abundances of short-chain fatty acids, while those identified in the ulcerative colitis dataset show a significant correlation with metabolism-related pathways.},
}
@article {pmid39530726,
year = {2024},
author = {Toledo, MJL and Zawadzki, MJ and Scott, SB and Johnson, JA and Marcusson-Clavertz, D and Kim, J and Lanza, S and Almeida, DM and Sliwinski, MJ and Smyth, JM},
title = {Exploring the Utility of a Real-Time Approach to Characterising Within-Person Fluctuations in Everyday Stress Responses.},
journal = {Stress and health : journal of the International Society for the Investigation of Stress},
volume = {40},
number = {6},
pages = {e3501},
pmid = {39530726},
issn = {1532-2998},
support = {/NH/NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; *Stress, Psychological/psychology ; Adult ; *Ecological Momentary Assessment ; Middle Aged ; Aged ; },
abstract = {Few studies have measured components of stress responses in real time-an essential step in designing just-in-time interventions targeting moments of risk. Using ecological momentary assessment (EMA), we characterised stress response components to everyday stressors, including reactivity (the response following a stressor), recovery (the return towards baseline), and pile-up (the accumulation of stressors) (RRPs) by quantifying the dynamics of response indicators (i.e., subjective stress, negative affect, and perseverative cognition). To determine the utility of these novel measures in capturing and characterising acute moments of the stress response, this study evaluated the proportion of variance in RRPs attributed to (1) between-person, (2) between-days, and (3) within-day (momentary) levels. Healthy adults (n = 123; aged 35-65, 79% women, 91% non-Hispanic White) participated in a 14-day study assessing stress response via EMA 6 times a day. RRPs were constructed from 10,065 EMA reports. Multilevel models with moments nested within days nested within persons were used to partition variance in the RRPs. Reactivity and recovery indicators captured the most variation within-days (i.e., across moments; range 76%-80% and 87%-89%, respectively), with small amounts of variance between-person. For pile-up, variation was mostly observed between-days (range 60%-63%) and between-persons (range 27%-31%). In contrast, raw measures of stress response reflected substantial between-person (range 32%-54%) and within-day (range 34%-53%) variance. These results demonstrated that a person-specific approach to measuring stress response components (i.e., RRPs) can capture the dynamic within-person variation in stress response, as it occurs in real time, making it well-suited for use in novel just-in-time interventions targeting moments of risk.},
}
@article {pmid39536049,
year = {2024},
author = {Zhao, Y and Cordero, OX and Tikhonov, M},
title = {Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function.},
journal = {PLoS computational biology},
volume = {20},
number = {11},
pages = {e1012590},
pmid = {39536049},
issn = {1553-7358},
mesh = {*Algorithms ; Linear Models ; *Ecosystem ; *Computational Biology/methods ; Models, Biological ; Microbiota/physiology ; Nonlinear Dynamics ; },
abstract = {Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species' contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the "correct" grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.},
}
@article {pmid39536186,
year = {2024},
author = {Corrêa-do-Nascimento, GS and Galvão, C and Leite, GR},
title = {Investigating the distribution of a rare Colombo-Venezuelan kissing bug, Rhodnius neivai, Lent, 1953, using geographical information system-based analyses.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {119},
number = {},
pages = {e240106},
pmid = {39536186},
issn = {1678-8060},
mesh = {Animals ; *Rhodnius ; *Geographic Information Systems ; Colombia ; *Insect Vectors/classification ; *Animal Distribution ; Venezuela ; Chagas Disease/transmission ; Ecosystem ; },
abstract = {BACKGROUND: Rhodnius neivai, a kissing bug found in the dry regions of Colombia and Venezuela, has limited documented occurrences. While it is not deemed a significant vector for Chagas disease, distributional and ecological studies are essential in monitoring species domiciliation and shedding light on the evolutionary aspects of the Rhodniini tribe.<br><br>OBJECTIVES: The study aims to provide a detailed revision of R. neivai distribution and evaluate general spatial data quality for ecological niche modelling (ENM). It will also provide the first published ENM for the species, which may aid species sampling and future analytical improvement.<br><br>METHODS: Registers and other spatial information were gathered by literature review; data georeferencing, preliminary geographical investigations, and model editing were conducted in GIS platforms; ENMs were built using R and explored the uncertainty of parameters and algorithms.<br><br>FINDINGS: Twenty four unique sites were identified, unearthing 17 previously uncovered records. Data lacks robust spatial and temporal precision; however, ENMs had acceptable validations. The models present some variation in suitability but with objective areas for sampling effort.<br><br>MAIN CONCLUSIONS: Rhodnius neivai distribution is better explained by conditions that characterise dry ecotypes, but further sampling is essential to improve modelling and advance with ecological and evolutive matters.},
}
@article {pmid39537340,
year = {2024},
author = {Di Battista, V and Danielsen, PH and Gajewicz-Skretna, A and Kedziorski, A and Seiffert, SB and Ma-Hock, L and Berthing, T and Mortensen, A and Sundermann, A and Skjolding, LM and Vogel, U and Baun, A and Wohlleben, W},
title = {Oxide-Perovskites for Automotive Catalysts Biotransform and Induce Multicomponent Clearance and Hazard.},
journal = {ACS nano},
volume = {18},
number = {47},
pages = {32672-32693},
pmid = {39537340},
issn = {1936-086X},
mesh = {*Oxides/chemistry ; Animals ; Catalysis ; *Lanthanum/chemistry ; Rats ; Mice ; Calcium Compounds/chemistry ; Titanium/chemistry ; Automobiles ; Male ; Biotransformation ; Surface Properties ; Lung/metabolism/drug effects ; },
abstract = {Oxide-perovskites designed for automotive catalysts contain multiple metal elements whose presence is crucial to achieving the targeted performance. They are highly stable in exhaust operating conditions; however, little is known about their stability under physiological conditions. As some of the metallic components are hazardous to humans and the environment, perovskite benefits in cleaner air must be balanced with risks in a Safe and Sustainable Design (SSbD) approach. New approach methodologies (NAMs), including in chemico and in silico methods, were used for testing hazards and benefits, including catalytic activity and tolerance for temporary excess of oxygen under dynamic driving conditions. The composition and surface properties of six different lanthanum-based oxide-perovskites compromised their stability under lung physiological conditions, influencing the oxidative damage of the particles and the bioacessibility of leaching metals. We found consistent biotransformation of the oxide-perovskite materials at pH 4.5. The leached lanthanum ions, but not other metals, respeciated into lanthanum phosphate nanoparticles, which increased the overall oxidative damage in additive synergy. The NAM results in the presented SSbD approach were challenged by in vivo studies in rats and mice, which confirmed multicomponent clearance from lungs into urine and supported the comparative ranking of effects against well-characterized spinel materials. Among the perovskites, the version with reduced nickel content and doped with palladium offered the best SSbD balance, despite not improving the conventional benchmark catalytic performance and related sustainability benefits. Redesign by industry may be necessary to better fulfill all SSbD dimensions.},
}
@article {pmid39537735,
year = {2024},
author = {Ki, J and Lee, JM and Lee, W and Kim, JH and Jin, H and Jung, S and Lee, J},
title = {Dual-encoder architecture for metal artifact reduction for kV-cone-beam CT images in head and neck cancer radiotherapy.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {27907},
pmid = {39537735},
issn = {2045-2322},
support = {NRF-2020R1F1A1073430//National Research Foundation of Korea/ ; NRF-2021R1F1A1057818//National Research Foundation of Korea/ ; HI21C1161//Korea Health Industry Development Institute/ ; RS-2020-II201336//Ministry of Science and ICT, South Korea/ ; },
mesh = {*Cone-Beam Computed Tomography/methods ; Humans ; *Head and Neck Neoplasms/radiotherapy/diagnostic imaging ; *Artifacts ; *Metals/chemistry ; Deep Learning ; Image Processing, Computer-Assisted/methods ; Radiotherapy Planning, Computer-Assisted/methods ; Radiotherapy Dosage ; Phantoms, Imaging ; },
abstract = {During a radiotherapy (RT) course, geometrical variations of target volumes, organs at risk, weight changes (loss/gain), tumor regression and/or progression can significantly affect the treatment outcome. Adaptive RT has become the effective methods along with technical advancements in imaging modalities including cone-beam computed tomography (CBCT). Planning CT (pCT) can be modified via deformable image registration (DIR), which is applied to the pair of pCT and CBCT. However, the artifact existed in both pCT and CBCT is a vulnerable factor in DIR. The dose calculation on CBCT is also suggested. Missing information due to the artifacts hinders the accurate dose calculation on CBCT. In this study, we aim to develop a deep learning-based metal artifact reduction (MAR) model to reduce the metal artifacts in CBCT for head and neck cancer RT. To train the proposed MAR model, we synthesized the kV-CBCT images including metallic implants, with and without metal artifacts (simulated image data pairs) through sinogram image handling process. We propose the deep learning architecture which focuses on both artifact removal and reconstruction of anatomic structure using a dual-encoder architecture. We designed four single-encoder models and three dual-encoder models based on UNet (for an artifact removal) and FusionNet (for a tissue restoration). Each single-encoder model contains either UNet or FusionNet, while the dual-encoder models have both UNet and FusionNet architectures. In the dual-encoder models, we implemented different feature fusion methods, including simple addition, spatial attention, and spatial/channel wise attention. Among the models, a dual-encoder model with spatial/channel wise attention showed the highest scores in terms of peak signal-to-noise ratio, mean squared error, structural similarity index, and Pearson correlation coefficient. CBCT images from 34 head and neck cancer patients were used to test the developed models. The dual-encoder model with spatial/channel wise attention showed the best results in terms of artifact index. By using the proposed model to CBCT, one can achieve more accurate synthetic pCT for head and neck patients as well as better tissue recognition and structure delineation for CBCT image itself.},
}
@article {pmid39537861,
year = {2025},
author = {Noria, SF and Pratt, KJ and Abdel-Rasoul, M and Diaz, K and Shalash, B and Abul-Khoudoud, D and Needleman, B and Magallanes, M},
title = {The impact of social determinants of health (SDOH) on completing bariatric surgery at a single academic institution.},
journal = {Surgical endoscopy},
volume = {39},
number = {2},
pages = {1234-1242},
pmid = {39537861},
issn = {1432-2218},
support = {UL1 TR002733/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; *Bariatric Surgery/statistics &amp; numerical data ; Male ; Female ; *Social Determinants of Health/statistics &amp; numerical data ; Middle Aged ; Adult ; *Obesity, Morbid/surgery ; Socioeconomic Factors ; Retrospective Studies ; },
abstract = {BACKGROUND: Underutilization of bariatric surgery is multifactorial. This study aimed to understand the association of SDOH on not achieving surgery.<br><br>METHODS: 1081 applications for primary MBS from January-December 2021 were stratified into those that completed surgery (COM; n&#x2009;=&#x2009;415), in progress&#x2009;>&#x2009;1-year (IP; n&#x2009;=&#x2009;107), dropped out (DO; n&#x2009;=&#x2009;379), and never started (NS; n&#x2009;=&#x2009;180). Using the American-Community-Survey results (2015-2020) and patient zip-codes, population differences in 4-domains of SDOH (demographic/social/housing/economic) were examined between COM versus the other groups. Additionally, using institutional MBSAQIP and EMR data, patient-specific differences in comorbidities were evaluated for COM versus IP/DO. Univariate analysis using Kruskal-Wallis, chi-squared/Fisher's exact tests were used for continuous and/or categorical variables. For patient-level analysis multinomial logistic regression was used to determine predictors of not achieving surgery. Hypothesis testing was conducted at an overall 5 percent type-I error rate (alpha&#x2009;=&#x2009;0.05) and Bonferroni's method was used to adjust for multiple comparisons.<br><br>RESULTS: Compared to COM, IP-patients resided in zip-codes characterized by fewer married people (43% vs 46%; p&#x2009;=&#x2009;0.019), lower education levels (49% vs 43%; p&#x2009;=&#x2009;0.048), more households where rent was&#x2009;>&#x2009;50% of household income (10% vs 8%, p&#x2009;=&#x2009;0.002), and households below the poverty line (17.6% vs 14.5%, p&#x2009;=&#x2009;0.017). At the patient-level, IP were more likely to be male (27.9% vs 14.9%; p&#x2009;=&#x2009;0.014), publicly insured (44.9% vs 28.4%; p&#x2009;=&#x2009;0.004), Black (35.5% vs 22.2%; p&#x2009;=&#x2009;0.006), an active smoker (8.9% vs 2.2%; p&#x2009;=&#x2009;0.018), have a higher BMI (49.6 vs 47.6; p&#x2009;=&#x2009;0.01), and coronary intervention (5.8% vs 1.7%, p&#x2009;=&#x2009;0.034). Comparison of COM vs DO was similar for both phases. Multinomial multivariable logistic regression demonstrated higher BMI (OR&#x2009;=&#x2009;1.03,[CI]:1.01-1.05, p&#x2009;=&#x2009;0.001), males (OR&#x2009;=&#x2009;1.9,[CI]:1.09-3.32, p&#x2009;=&#x2009;0.024), smoking (OR&#x2009;=&#x2009;4.58,[CI]:1.74-12.02, p&#x2009;=&#x2009;0.002), and Medicaid (OR&#x2009;=&#x2009;2.16,[CI]:1.33-3.49, p&#x2009;=&#x2009;0.002) independently predicted not achieving surgery.<br><br>CONCLUSION: Patient-level data demonstrated social not clinical factors predicted surgery completion. Given zip-codes characterizing the IP/DO groups had a greater prevalence of social risk, more attention needs to be directed patient-level social risks.},
}
@article {pmid39539549,
year = {2024},
author = {Pappa, T and Rivas, AL and Iandiorio, MJ and Hoogesteijn, AL and Fair, JM and Rojas Gil, AP and Burriel, AR and Bagos, PG and Chatzipanagiotou, S and Ioannidis, A},
title = {Personalized, disease-stage specific, rapid identification of immunosuppression in sepsis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1430972},
pmid = {39539549},
issn = {1664-3224},
mesh = {Humans ; *Sepsis/immunology/mortality/blood/diagnosis ; Male ; Female ; Middle Aged ; Aged ; *Precision Medicine ; Leukocyte Count ; Biomarkers/blood ; Aged, 80 and over ; Adult ; Immunosuppression Therapy ; },
abstract = {INTRODUCTION: Data overlapping of different biological conditions prevents personalized medical decision-making. For example, when the neutrophil percentages of surviving septic patients overlap with those of non-survivors, no individualized assessment is possible. To ameliorate this problem, an immunological method was explored in the context of sepsis.<br><br>METHODS: Blood leukocyte counts and relative percentages as well as the serum concentration of several proteins were investigated with 4072 longitudinal samples collected from 331 hospitalized patients classified as septic (n=286), non-septic (n=43), or not assigned (n=2). Two methodological approaches were evaluated: (i) a reductionist alternative, which analyzed variables in isolation; and (ii) a non-reductionist version, which examined interactions among six (leukocyte-, bacterial-, temporal-, personalized-, population-, and outcome-related) dimensions.<br><br>RESULTS: The reductionist approach did not distinguish outcomes: the leukocyte and serum protein data of survivors and non-survivors overlapped. In contrast, the non-reductionist alternative differentiated several data groups, of which at least one was only composed of survivors (a finding observable since hospitalization day 1). Hence, the non-reductionist approach promoted personalized medical practices: every patient classified within a subset associated with 100% survival subset was likely to survive. The non-reductionist method also revealed five inflammatory or disease-related stages (provisionally named 'early inflammation, early immunocompetence, intermediary immuno-suppression, late immuno-suppression, or other'). Mortality data validated these labels: both 'suppression' subsets revealed 100% mortality, the 'immunocompetence' group exhibited 100% survival, while the remaining sets reported two-digit mortality percentages. While the 'intermediary' suppression expressed an impaired monocyte-related function, the 'late' suppression displayed renal-related dysfunctions, as indicated by high concentrations of urea and creatinine.<br><br>DISCUSSION: The data-driven differentiation of five data groups may foster early and non-overlapping biomedical decision-making, both upon admission and throughout their hospitalization. This approach could evaluate therapies, at personalized level, earlier. To ascertain repeatability and investigate the dynamics of the 'other' group, additional studies are recommended.},
}
@article {pmid39541885,
year = {2024},
author = {Wang, G and Li, X and Deng, J and Cao, J and Meng, H and Dong, J and Zhang, H},
title = {Assessing soil cadmium quality standards for different land use types: A global synthesis.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136450},
doi = {10.1016/j.jhazmat.2024.136450},
pmid = {39541885},
issn = {1873-3336},
abstract = {The contamination of cadmium (Cd) in soil has become an increasingly serious issue worldwide, presenting significant risks to human health, crop safety, and ecosystems. Despite its importance, there is a lack of standardized soil threshold values for use in regulating exposure to Cd-contaminated surface soil. By synthesizing soil environmental standards for Cd from 61 countries and 75 regions, this study analyzed and categorized these standards by land use types. The distribution of Cd quality standards among various countries was determined, based on available data primarily from the United States, Canada, Europe, Australia, and China. The established soil Cd quality standards were also determined for different land types, including lands for agricultural, residential, industrial, construction, commercial uses, and parks/green spaces. Using the ecological environment criteria - species sensitivity distribution (ECC-SSD) model, Cd levels were analyzed across different land use types, and it was determined that a log-logistic distribution was the best fitted model. Our findings indicated that soil Cd quality standards ranged from 0.11 to 5.20 mg/kg for agricultural land, 1.25 to 171.51 mg/kg for residential land, and 2.58 to 1845.26 mg/kg for industrial land, all within the 5-95 % percentile range. The 5 % hazard concentration (HC5) value was recommended as the latest national quality standards for each land type. This comprehensive assessment of global soil Cd quality standards provides valuable insight for decision-makers tasked with effectively managing and mitigating Cd pollution in soil.},
}
@article {pmid39543483,
year = {2024},
author = {Rzehak, T and Praeg, N and Galla, G and Seeber, J and Hauffe, HC and Illmer, P},
title = {Comparison of commonly used software pipelines for analyzing fungal metabarcoding data.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1085},
pmid = {39543483},
issn = {1471-2164},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Fungi/genetics/classification ; *Software ; Animals ; Cattle ; Computational Biology/methods ; Feces/microbiology ; Soil Microbiology ; },
abstract = {BACKGROUND: Metabarcoding targeting the internal transcribed spacer (ITS) region is commonly used to characterize fungal communities of various environments. Given their size and complexity, raw ITS sequences are necessarily processed and quality-filtered with bioinformatic pipelines. However, such pipelines are not yet standardized, especially for fungal communities, and those available may produce contrasting results. While some pipelines cluster sequences based on a specified percentage of base pair similarity into operational taxonomic units (OTUs), others utilize denoising techniques to infer amplicon sequencing variants (ASVs). While ASVs are now considered a more accurate representation of taxonomic diversity for prokaryote communities based on 16S rRNA amplicon sequencing, the applicability of this method for fungal ITS sequences is still debated.<br><br>RESULTS: Here we compared the performance of two commonly used pipelines DADA2 (inferring ASVs) and mothur (clustering OTUs) on fungal metabarcoding sequences originating from two different environmental sample types (fresh bovine feces and pasture soil). At a 99% OTU similarity threshold, mothur consistently identified a higher fungal richness compared to DADA2. In addition, mothur generated homogenous relative abundances across multiple technical replicates (n&#x2009;=&#x2009;18), while DADA2 results for the same replicates were highly heterogeneous.<br><br>CONCLUSIONS: Our study highlights a potential pipeline-associated bias in fungal metabarcoding data analysis of environmental samples. Based on the homogeneity of relative abundances across replicates and the capacity to detect OTUs/ASVs, we suggest using OTU clustering with a similarity of 97% as the most appropriate option for processing fungal metabarcoding data.},
}
@article {pmid39543597,
year = {2024},
author = {Rajovic, N and Grubor, N and Cirkovic, A and Maheswaran, R and Bath, PA and Green, D and Bellantuono, I and Milicevic, O and Kanazir, S and Miljus, D and Zivkovic, S and Vidojevic, D and Mickovski, N and Rakocevic, I and Ivanovic, I and Mladenovic, A and Goyder, E and Milic, N},
title = {Insights into relationship of environmental inequalities and multimorbidity: a population-based study.},
journal = {Environmental health : a global access science source},
volume = {23},
number = {1},
pages = {99},
pmid = {39543597},
issn = {1476-069X},
support = {200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200007//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; 200007//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; 200110/WT_/Wellcome Trust/United Kingdom ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; },
mesh = {Humans ; Middle Aged ; *Multimorbidity ; Adult ; Male ; Female ; Serbia/epidemiology ; Aged ; Young Adult ; *Air Pollutants/analysis ; Adolescent ; Environmental Exposure/adverse effects ; Air Pollution/analysis/adverse effects ; Prevalence ; Water Quality ; Socioeconomic Factors ; },
abstract = {BACKGROUND: Substantial inequalities in the overall prevalence and patterns of multimorbidity have been widely reported, but the causal mechanisms are complex and not well understood. This study aimed to identify common patterns of multimorbidity in Serbia and assess their relationship with air pollutant concentrations and water quality indicators.<br><br>METHODS: This ecological study was conducted on a nationally representative sample of the Serbian population. Data were obtained from the European Health Interview (EHIS) Survey, a periodic study designed to assess population health using widely recognized standardized instruments. The study included 13,069 participants aged 15 and older, randomly selected through a multistage stratified sampling design. Multimorbidity was defined as having two or more self-reported diagnoses of chronic non-communicable diseases. Latent class analysis (LCA) was performed to identify clusters of multimorbidity. Concentrations of particulate matter (PM10), sulfur dioxide (SO2), nitrogen dioxide (NO2), carbon monoxide (CO), and ozone (O3), as well as water quality indicators, were obtained from the Serbian Environmental Protection Agency.<br><br>RESULTS: The overall prevalence of multimorbidity was 33.4% [32.6%-34.2%]. Six latent classes of multimorbidity were identified: Healthy, Multicondition, Cardiovascular, Metabolic syndrome, Respiratory, and Musculoskeletal. Annual increases in PM10 and SO2 concentrations, as well as daily increases in O3 concentrations, significantly raised the odds of having multimorbidity (OR&#x2009;=&#x2009;1.02, 95% CI 1.02-1.03; OR&#x2009;=&#x2009;1.01, 95% CI 1.00-1.02 and OR&#x2009;=&#x2009;1.03, 95% CI 1.02-1.03, respectively). A pattern of increased risk was observed with rising levels of water contamination. Exposure to physico-chemical, microbiological and combined contamination was associated with a 3.92%, 5.17% and 5.54% higher probability, respectively, of having multiple chronic conditions. There was strong evidence that air pollutants, as well as chemical and microbial water contamination, were significantly associated with higher odds of the most common clusters of multimorbidity identified by LCA.<br><br>CONCLUSION: There is compelling evidence of an association between multimorbidity and environmental pollution, suggesting that exposure to air pollutants and water contaminants may contribute to disease accumulation and help explain geographically and socioeconomically patterned inequalities. These findings underscore the need for extensive studies that simultaneously measure both multimorbidity and pollution to explore their complex interrelationships.},
}
@article {pmid39545367,
year = {2024},
author = {Heuck, MK and Powell, JR and Kath, J and Birnbaum, C and Frew, A},
title = {Evaluating the Usefulness of the C-S-R Framework for Understanding AM Fungal Responses to Climate Change in Agroecosystems.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17566},
doi = {10.1111/gcb.17566},
pmid = {39545367},
issn = {1365-2486},
support = {DE220100479//Australian Research Council (ARC) Discovery Early Career Researcher Award (DECRA)/ ; FT190100590//Australian Research Council Future Fellowship/ ; },
mesh = {*Climate Change ; *Mycorrhizae/physiology ; *Agriculture ; *Ecosystem ; Symbiosis ; },
abstract = {Arbuscular mycorrhizal (AM) fungi play a key role in terrestrial ecosystems by forming symbiotic relationships with plants and may confer benefits for sustainable agriculture, by reducing reliance on harmful fertiliser and pesticide inputs and enhancing plant resilience against insect herbivores. Despite their ecological importance, critical gaps in understanding AM fungal ecology limit predictions of their responses to global change in agroecosystems. However, predicting climate change impacts on AM fungi is important for maintaining crop productivity and ecosystem stability. Efforts to classify AM fungi based on functional traits, such as the competitor, stress-tolerator, ruderal (C-S-R) framework, aim to address these gaps but face challenges due to the obligate symbiotic nature of the fungi. As the framework is still widely used, we evaluate its applicability in predicting global change impacts on AM fungal communities in agroecosystems. Chagnon's adaptation of the C-S-R framework for AM fungi aligns with some study outcomes (e.g., under the context of water limitation) but faces challenges when used in complex climate change scenarios, varying agricultural conditions and/or extreme climatic conditions. The reliance on a limited dataset to classify AM fungal families further limits accurate predictions of AM fungal community dynamics. Trait data collection could support a nuanced understanding of AM fungi and leveraging AM fungal databases could streamline data management and analysis, enhancing efforts to clarify AM fungal responses to environmental change and guide ecosystem management practices. Thus, while the C-S-R framework holds promise, it requires additional AM fungal trait data for validation and improvement of its predictive power. Conclusively, before designing experiments based on life-history strategies and developing new frameworks tailored to AM fungi a critical first step is to gain a comprehensive understanding of their traits.},
}
@article {pmid39546825,
year = {2025},
author = {Meyer, A and Ndiaye, B and Larkins, A and Chaters, G and Gilbert, W and Huntington, B and Ilboudo, G and Dione, M and Jemberu, WT and Diouf, MN and Fall, AG and Fall, M and Lo, M and Rushton, J},
title = {Economic assessment of animal disease burden in Senegalese small ruminants.},
journal = {Preventive veterinary medicine},
volume = {234},
number = {},
pages = {106382},
doi = {10.1016/j.prevetmed.2024.106382},
pmid = {39546825},
issn = {1873-1716},
mesh = {Animals ; Senegal/epidemiology ; *Goat Diseases/economics/epidemiology ; *Goats ; Sheep ; *Sheep Diseases/economics/epidemiology ; Cost of Illness ; Animal Husbandry/economics/methods ; },
abstract = {Small ruminant production in sub-Saharan Africa is limited by a range of constraints, including animal health issues. This study aimed at estimating the impact of these issues on the small ruminant production in Senegal in a holistic manner, using an approach developed by the Global Burden of Animal Diseases (GBADs) programme. The estimation focused on the mixed crop-livestock system, representing a large proportion (>60 %) of the small ruminant population in the country. It was based on existing data collected via a systematic literature review, acquisition of secondary datasets from local stakeholders, and expert elicitation. A dynamic population model was used to calculate the gross margin of the sector under both the current health constraints and an ideal health state, where animals are not exposed to causes of morbidity and mortality. The difference between the current and ideal health scenarios, termed the Animal Health Loss Envelope (AHLE), provides a quantitative measure of the farm-level cost of disease in the system. The all-cause AHLE was estimated at 292 billion FCFA (468 million USD, with 95 % prediction interval 216 - 366 billion FCFA) per year for 2022, for a population of 8.8 million animals. The contribution of Peste des Petits Ruminants (PPR) was modelled separately, as an example of attributing part of the AHLE to a specific disease cause. PPR was estimated to contribute 5 % of the total AHLE. The animal disease burden experienced by Senegalese livestock keepers was largely due to loss in animals and production, with relatively small amounts of animal health expenditure. Implementation of this study contributed to the further development of the GBADs approach. Such estimates can support decision making at all levels, from investment decisions at the international level to local disease awareness campaigns targeting livestock keepers.},
}
@article {pmid39547957,
year = {2024},
author = {Kwon, EJ and Lee, H and Shin, U and Kim, ES and Myung, K and Kim, J and Park, JH and Kim, K and Lee, Y and Oh, CK and Kim, YH},
title = {Ionizing radiation inhibits zebrafish embryo hatching through induction of tissue inhibitors of metalloproteinases (TIMPs) expression.},
journal = {The FEBS journal},
volume = {291},
number = {24},
pages = {5470-5485},
doi = {10.1111/febs.17318},
pmid = {39547957},
issn = {1742-4658},
support = {IBS-R022-D1//Institute for Basic Science/ ; RS-2023-00223591//National Research Foundation of Korea/ ; RS-2023-00301938//National Research Foundation of Korea/ ; RS-2024-00439078//National Research Foundation of Korea/ ; //KREONET/ ; },
mesh = {Animals ; *Zebrafish/genetics/embryology/metabolism ; *Radiation, Ionizing ; *Tissue Inhibitor of Metalloproteinases/metabolism/genetics ; *Gene Expression Regulation, Developmental/radiation effects ; *Embryo, Nonmammalian/radiation effects/metabolism ; Zebrafish Proteins/genetics/metabolism ; },
abstract = {Ionizing radiation (IR) has garnered growing attention because of its biological effects on aquatic organisms and humans. Here, we identify the most impacted organs and uncover the molecular mechanisms causing the changes in the context of vertebrate development using single-cell RNA sequencing. Alterations in cellular composition and biological functions were explored using transcriptomic profiling of zebrafish embryos exposed to 5 Gy. Single-cell RNA sequencing analyses unveiled notable shifts in the proportions of brain/central nervous system and hatching gland clusters. Although IR exposure led to increased expression of hatching enzymes, a significant but mild delay in hatching was observed following 5 Gy IR exposure. Gene Ontology analysis showed an increased expression of tissue inhibitors of metalloproteinases (TIMPs), known as matrix metalloproteinase inhibitors, which was confirmed via whole-mount in situ hybridization. Correlation analysis linked TIMPs to transcription factors cebpb and cebpd, which were significantly correlated post-IR exposure. Although no morphological changes were observed in some organs, including the brain, the study reveals substantial alterations in developing vertebrates. Notably, despite increased hatching enzymes, elevated TIMPs in the hatching gland suggest a regulatory mechanism impacting hatching activity. This research contributes to comprehending the ecological repercussions of IR exposure, emphasizing the importance of safety measures for aquatic ecosystems and overall environmental health.},
}
@article {pmid39548060,
year = {2024},
author = {Conrad, RE and Brink, CE and Viver, T and Rodriguez-R, LM and Aldeguer-Riquelme, B and Hatt, JK and Venter, SN and Rossello-Mora, R and Amann, R and Konstantinidis, KT},
title = {Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9906},
pmid = {39548060},
issn = {2041-1723},
support = {1831582//NSF | BIO | Division of Environmental Biology (DEB)/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 2129823//U.S. National Science Foundation/ ; },
mesh = {*Homologous Recombination ; *Escherichia coli/genetics/classification ; Genome, Bacterial ; Microbiota/genetics ; Evolution, Molecular ; Gene Flow ; Phylogeny ; Computational Biology/methods ; },
abstract = {Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in both Salinibacter ruber, an environmental halophilic organism, and Escherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.},
}
@article {pmid39548719,
year = {2024},
author = {Chen, Y and Gao, Y and Zhang, Z and Zhan, A},
title = {Multi-Omics Inform Invasion Risks Under Global Climate Change.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17588},
doi = {10.1111/gcb.17588},
pmid = {39548719},
issn = {1365-2486},
support = {2022GDASZH-2022010106//GDAS Special Project of Science and Technology Development/ ; 2024A1515010914//Guangdong Basic and Applied Basic Research Foundation/ ; 42106098//National Natural Science Foundation of China/ ; 32061143012//National Natural Science Foundation of China/ ; 42276126//National Natural Science Foundation of China/ ; 32371753//National Natural Science Foundation of China/ ; },
mesh = {*Climate Change ; *Introduced Species ; *Genomics ; Urochordata/genetics ; Epigenomics ; Adaptation, Physiological/genetics ; Animals ; Multiomics ; },
abstract = {Global climate change is exacerbating biological invasions; however, the roles of genomic and epigenomic variations and their interactions in future climate adaptation remain underexplored. Using the model invasive ascidian Botryllus schlosseri across the Northern Hemisphere, we investigated genomic and epigenomic responses to future climates and developed a framework to assess future invasion risks. We employed generalized dissimilarity modeling and gradient forest analyses to assess genomic and epigenomic offsets under climate change. Our results showed that populations with genomic maladaptation did not geographically overlap with those experiencing epigenomic maladaptation, suggesting that genomic and epigenomic variations play complementary roles in adaptation to future climate conditions. By integrating genomic and epigenomic offsets into the genome-epigenomic index, we predicted that populations with lower index values were less maladapted, indicating a higher risk of future invasions. Native populations exhibited lower offsets than invasive populations, suggesting greater adaptive potentials and higher invasion risks under future climate change scenarios. These results highlight the importance of incorporating multi-omics data into predictive models to study future climate (mal)adaptation and assess invasion risks under global climate change.},
}
@article {pmid39549265,
year = {2025},
author = {Rayamajhi, N and Rivera-Colón, AG and Minhas, BF and Cheng, CHC and Catchen, JM},
title = {The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {1},
pages = {},
pmid = {39549265},
issn = {2160-1836},
support = {10-69157//NSF DGE/ ; //IGERT/ ; //AGR-C/ ; 1645087//NSF OPP/ ; //JC/ ; //C-HCC/ ; 11-42158//NSF ANT/ ; //C-HCC/ ; },
mesh = {Animals ; *Genome ; Antarctic Regions ; Synteny ; Molecular Sequence Annotation ; Chromosomes/genetics ; Female ; Perciformes/genetics ; Repetitive Sequences, Nucleic Acid ; Genomics/methods ; Phylogeny ; },
abstract = {The Antarctic bald notothen, Trematomus borchgrevinki (family Nototheniidae) occupies a high latitude, ice-laden environment and represents an extreme example of cold-specialization among fishes. We present the first, high-quality, chromosome-scale genome of a female T. borchgrevinki individual comprised of 23 putative chromosomes, the largest of which is 65 megabasepairs (Mbp) in length. The total length of the genome 935.13 Mbp, composed of 2,094 scaffolds, with a scaffold N50 of 42.67 Mbp. Annotation yielded 22,192 protein-coding genes while 54.75% of the genome was occupied by repetitive elements; an analysis of repeats demonstrated that an expansion occurred in recent time. Conserved synteny analysis revealed that the genome architecture of T. borchgrevinki is largely maintained with other members of the notothenioid clade, although several significant translocations and inversions are present, including the fusion of orthologous chromosomes 8 and 11 into a single element. This genome will serve as a cold-specialized model for comparisons to other members of the notothenioid adaptive radiation.},
}
@article {pmid39555185,
year = {2024},
author = {Yang, D and Hashizume, M and Tobías, A and Honda, Y and Roye, D and Oh, J and Dang, TN and Kim, Y and Abrutzky, R and Guo, Y and Tong, S and Coelho, MSZS and Saldiva, PHN and Lavigne, E and Correa, PM and Ortega, NV and Osorio, S and Kyselý, J and Urban, A and Orru, H and Indermitte, E and Jaakkola, J and Ryti, N and Pascal, M and Huber, V and Schneider, A and Katsouyanni, K and Analitis, A and Entezari, A and Mayvaneh, F and Goodman, P and Zeka, A and Michelozzi, P and de'Donato, F and Alahmad, B and Diaz, MH and la Cruz Valencia, C and Overcenco, A and Houthuijs, D and Ameling, C and Rao, S and Nunes, B and Madureira, J and Holo-Bâc, IH and Scovronick, N and Acquaotta, F and Kim, H and Lee, W and Íñiguez, C and Forsberg, B and Vicedo-Cabrera, AM and Ragettli, MS and Guo, YL and Pan, SC and Li, S and Sera, F and Zanobetti, A and Schwartz, J and Armstrong, B and Gasparrini, A and Chung, Y},
title = {Temporal change in minimum mortality temperature under changing climate: A multicountry multicommunity observational study spanning 1986-2015.},
journal = {Environmental epidemiology (Philadelphia, Pa.)},
volume = {8},
number = {5},
pages = {e334},
pmid = {39555185},
issn = {2474-7882},
support = {MR/R013349/1/MRC_/Medical Research Council/United Kingdom ; MR/V034162/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: The minimum mortality temperature (MMT) or MMT percentile (MMTP) is an indicator of population susceptibility to nonoptimum temperatures. MMT and MMTP change over time; however, the changing directions show region-wide heterogeneity. We examined the heterogeneity of temporal changes in MMT and MMTP across multiple communities and in multiple countries.<br><br>METHODS: Daily time-series data for mortality and ambient mean temperature for 699 communities in 34 countries spanning 1986-2015 were analyzed using a two-stage meta-analysis. First, a quasi-Poisson regression was employed to estimate MMT and MMTP for each community during the designated subperiods. Second, we pooled the community-specific temporally varying estimates using mixed-effects meta-regressions to examine temporal changes in MMT and MMTP in the entire study population, as well as by climate zone, geographical region, and country.<br><br>RESULTS: Temporal increases in MMT and MMTP from 19.5 &#xb0;C (17.9, 21.1) to 20.3 &#xb0;C (18.5, 22.0) and from the 74.5 (68.3, 80.6) to 75.0 (71.0, 78.9) percentiles in the entire population were found, respectively. Temporal change was significantly heterogeneous across geographical regions (P < 0.001). Temporal increases in MMT were observed in East Asia (linear slope [LS] = 0.91, P = 0.02) and South-East Asia (LS = 0.62, P = 0.05), whereas a temporal decrease in MMT was observed in South Europe (LS = -0.46, P = 0.05). MMTP decreased temporally in North Europe (LS = -3.45, P = 0.02) and South Europe (LS = -2.86, P = 0.05).<br><br>CONCLUSIONS: The temporal change in MMT or MMTP was largely heterogeneous. Population susceptibility in terms of optimum temperature may have changed under a warming climate, albeit with large region-dependent variations.},
}
@article {pmid39556417,
year = {2024},
author = {Helgeson, SA and Mudgalkar, RM and Jacobs, KA and Lee, AS and Sanghavi, D and Moreno Franco, P and Brooks, IS and , },
title = {Association Between X/Twitter and Prescribing Behavior During the COVID-19 Pandemic: Retrospective Ecological Study.},
journal = {JMIR infodemiology},
volume = {4},
number = {},
pages = {e56675},
pmid = {39556417},
issn = {2564-1891},
support = {U24 TR002306/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Retrospective Studies ; *Hydroxychloroquine/therapeutic use ; *Social Media ; United States/epidemiology ; *COVID-19/epidemiology ; *Practice Patterns, Physicians' ; Pandemics ; COVID-19 Drug Treatment ; Male ; Female ; Middle Aged ; SARS-CoV-2/drug effects ; },
abstract = {BACKGROUND: Social media has become a vital tool for health care providers to quickly share information. However, its lack of content curation and expertise poses risks of misinformation and premature dissemination of unvalidated data, potentially leading to widespread harmful effects due to the rapid and large-scale spread of incorrect information.<br><br>OBJECTIVE: We aim to determine whether social media had an undue association with the prescribing behavior of hydroxychloroquine, using the COVID-19 pandemic as the setting.<br><br>METHODS: In this retrospective study, we gathered the use of hydroxychloroquine in 48 hospitals in the United States between January and December 2020. Social media data from X/Twitter was collected using Brandwatch, a commercial aggregator with access to X/Twitter's data, and focused on mentions of "hydroxychloroquine" and "Plaquenil." Tweets were categorized by sentiment (positive, negative, or neutral) using Brandwatch's sentiment analysis tool, with results classified by date. Hydroxychloroquine prescription data from the National COVID Cohort Collaborative for 2020 was used. Granger causality and linear regression models were used to examine relationships between X/Twitter mentions and prescription trends, using optimum time lags determined via vector auto-regression.<br><br>RESULTS: A total of 581,748 patients with confirmed COVID-19 were identified. The median daily number of positive COVID-19 cases was 1318.5 (IQR 1005.75-1940.3). Before the first confirmed COVID-19 case, hydroxychloroquine was prescribed at a median rate of 559 (IQR 339.25-728.25) new prescriptions per day. A day-of-the-week effect was noted in both prescriptions and case counts. During the pandemic in 2020, hydroxychloroquine prescriptions increased significantly, with a median of 685.5 (IQR 459.75-897.25) per day, representing a 22.6% rise from baseline. The peak occurred on April 2, 2020, with 3411 prescriptions, a 397.6% increase. Hydroxychloroquine mentions on X/Twitter peaked at 254,770 per day on April 5, 2020, compared to a baseline of 9124 mentions per day before January 21, 2020. During this study's period, 3,823,595 total tweets were recorded, with 10.09% (n=386,115) positive, 37.87% (n=1,448,030) negative, and 52.03% (n=1,989,450) neutral sentiments. A 1-day lag was identified as the optimal time for causal association between tweets and hydroxychloroquine prescriptions. Univariate analysis showed significant associations across all sentiment types, with the largest impact from positive tweets. Multivariate analysis revealed only neutral and negative tweets significantly affected next-day prescription rates.<br><br>CONCLUSIONS: During the first year of the COVID-19 pandemic, there was a significant association between X/Twitter mentions and the number of prescriptions of hydroxychloroquine. This study showed that X/Twitter has an association with the prescribing behavior of hydroxychloroquine. Clinicians need to be vigilant about their potential unconscious exposure to social media as a source of medical knowledge, and health systems and organizations need to be more diligent in identifying expertise, source, and quality of evidence when shared on social media platforms.},
}
@article {pmid39558756,
year = {2025},
author = {Paris, JR and King, RA and Ferrer Obiol, J and Shaw, S and Lange, A and Bourret, V and Hamilton, PB and Rowe, D and Laing, LV and Farbos, A and Moore, K and Urbina, MA and van Aerle, R and Catchen, JM and Wilson, RW and Bury, NR and Santos, EM and Stevens, JR},
title = {The Genomic Signature and Transcriptional Response of Metal Tolerance in Brown Trout Inhabiting Metal-Polluted Rivers.},
journal = {Molecular ecology},
volume = {34},
number = {1},
pages = {e17591},
pmid = {39558756},
issn = {1365-294X},
support = {BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //University of Exeter/ ; WT097835MF/WT_/Wellcome Trust/United Kingdom ; Charityno.1135007,Companyno.06545646//Westcountry Rivers Trust, UK/ ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //Environment Agency, UK/ ; },
mesh = {*Genome ; *Transcription, Genetic/drug effects ; *Adaptation, Physiological/drug effects/genetics ; *Rivers ; *Water Pollutants, Chemical/toxicity ; *Salmon/genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; *Metals/toxicity ; United Kingdom ; Genetic Loci ; Gene Library ; Metagenomics ; Organ Specificity/drug effects ; Gene Ontology ; Animals ; },
abstract = {Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia, and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.},
}
@article {pmid39560426,
year = {2025},
author = {Zhu, H-H and Liu, M-M and Boekhout, T and Wang, Q-M},
title = {Improvement of a MALDI-TOF database for the reliable identification of Candidozyma auris (formally Candida auris) and related species.},
journal = {Microbiology spectrum},
volume = {13},
number = {1},
pages = {e0144424},
pmid = {39560426},
issn = {2165-0497},
mesh = {*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Humans ; *Candidiasis/microbiology/diagnosis ; Candida auris/chemistry/isolation &amp; purification/classification ; Databases, Factual ; Mycological Typing Techniques/methods ; Candida/classification/isolation &amp; purification/chemistry ; },
abstract = {UNLABELLED: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a promising technique for the rapid identification microorganisms. The aim of this study was to create a new database for the accurate identification of Candidozyma auris (formerly known as Candida auris) and 11 species of the Candidozyma haemuli species complex, including C. chanthaburiensis, C. duobushaemuli, C. haemuli, C. heveicola, C. khanbhai, C. konsanensis, C. metrosideri, C. ohialehuae, C. pseudohaemuli, C. ruelliae, and C. vulturna. Seventy-one Candidozyma isolates from different national institutions were studied. Thirty-seven strains were used to create a MALDI-TOF (microTyper MS) database using the formic acid extraction method. The validation of this database was performed with 34 other strains of the genus Candidozyma, and the result was compared with the identification results when using DBRs v1.0.0.4 (Tianrui, China). Our library allowed a 100% identification of the evaluated strains with all strains showing log scores of >2.0. Repeatability and reproducibility tests result showed a coefficient of variation of the log score values of less than 5%. The MALDI-TOF MS system can identify C. auris and related species quickly and accurately. This method will play a crucial role in accurately diagnosing infectious agents of the genus Candidozyma in clinical practice.<br><br>IMPORTANCE: Importance Candidozyma auris, also known as Candida auris, has quickly spread across the world, and prompt identification of C. auris from infected individuals is critical. However, a standard identification method is lacking for the identification of C. auris in clinical and public health laboratories. To make matters worse, its biochemical assimilation profile was found to be similar to that of closely related and even no-related species, leading to frequent misidentification. To improve diagnostics of this and closely related species, we created a database of reference mass spectra resulting in the efficient and correct identification of all Candidozyma species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Moreover, potential pathogenic species of Candidozyma can be effectively identified by MALDI-TOF MS, and differentiated from non-clinically relevant phylogenetic relatives. Thus, MALDI-TOF MS may help expedite laboratory diagnosis and treatment of C. auris and related species of clinical importance and help the clinician to decide on early treatment.},
}
@article {pmid39561196,
year = {2024},
author = {Konzen, E and Delahay, RJ and Hodgson, DJ and McDonald, RA and Brooks Pollock, E and Spencer, SEF and McKinley, TJ},
title = {Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers.},
journal = {PLoS computational biology},
volume = {20},
number = {11},
pages = {e1012592},
pmid = {39561196},
issn = {1553-7358},
mesh = {Animals ; *Mustelidae/microbiology ; *Tuberculosis, Bovine/epidemiology/transmission/diagnosis ; Cattle ; *Animals, Wild/microbiology ; United Kingdom/epidemiology ; Models, Biological ; Mycobacterium bovis ; Computational Biology/methods ; Disease Reservoirs/microbiology/veterinary ; Ireland/epidemiology ; },
abstract = {Bovine tuberculosis (bTB) has significant socio-economic and welfare impacts on the cattle industry in parts of the world. In the United Kingdom and Ireland, disease control is complicated by the presence of infection in wildlife, principally the European badger. Control strategies tend to be applied to whole populations, but better identification of key sources of transmission, whether individuals or groups, could help inform more efficient approaches. Mechanistic transmission models can be used to better understand key epidemiological drivers of disease spread and identify high-risk individuals and groups if they can be adequately fitted to observed data. However, this is a significant challenge, especially within wildlife populations, because monitoring relies on imperfect diagnostic test information, and even under systematic surveillance efforts (such as capture-mark-recapture sampling) epidemiological events are only partially observed. To this end we develop a stochastic compartmental model of bTB transmission, and fit this to individual-level data from a unique > 40-year longitudinal study of 2,391 badgers using a recently developed individual forward filtering backward sampling algorithm. Modelling challenges are further compounded by spatio-temporal meta-population structures and age-dependent mortality. We develop a novel estimator for the individual effective reproduction number that provides quantitative evidence for the presence of superspreader badgers, despite the population-level effective reproduction number being less than one. We also infer measures of the hidden burden of infection in the host population through time; the relative likelihoods of competing routes of transmission; effective and realised infectious periods; and longitudinal measures of diagnostic test performance. This modelling framework provides an efficient and generalisable way to fit state-space models to individual-level data in wildlife populations, which allows identification of high-risk individuals and exploration of important epidemiological questions about bTB and other wildlife diseases.},
}
@article {pmid39563229,
year = {2024},
author = {Toth, AL and Wyatt, CDR and Masonbrink, RE and Geist, KS and Fortune, R and Scott, SB and Favreau, E and Rehan, SM and Sumner, S and Gardiner, MM and Sivakoff, FS},
title = {New genomic resources inform transcriptomic responses to heavy metal toxins in the common Eastern bumble bee Bombus impatiens.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1106},
pmid = {39563229},
issn = {1471-2164},
support = {20176701326595//USDA National Institute of Food and Agriculture/ ; 1929239//NSF DEB-NERC/ ; },
mesh = {Animals ; Bees/genetics/drug effects ; *Metals, Heavy/toxicity ; *Transcriptome ; Genomics/methods ; Molecular Sequence Annotation ; Gene Expression Profiling ; Genome, Insect ; Toxins, Biological/genetics ; },
abstract = {BACKGROUND: The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression.<br><br>RESULTS: PacBio long-read sequencing resulted in 544x coverage of the genome, and HiC technology was used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high quality, chromosome-level assembly. The sequenced genome size is 266.6&#xa0;Mb and BRAKER3 annotation produced 13,938 annotated genes. The genome and annotation show high completeness, with &#x2265;&#x2009;96% of conserved Eukaryota and Hymenoptera genes present in both the assembly and annotated genes. RNA sequencing of heavy metal exposed workers revealed 603 brain and 34 fat body differentially expressed genes. In the brain, differentially expressed genes had biological functions related to chaperone activity and protein folding.<br><br>CONCLUSIONS: Our data represent a large improvement in genomic resources for this important model species-with 10% more genome coverage than previously available, and a high-quality assembly into 18 chromosomes, the expected karyotype for this species. The new gene annotation added 777 new genes. Altered gene expression in response to heavy metal exposure suggests a possible mechanism for how these urban toxins are negatively impacting bee health, specifically by altering protein folding in the brain. Overall, these data are useful as a general high quality genomic resource for this species, and provide insight into mechanisms underlying tissue-specific toxicological responses of bumble bees to heavy metals.},
}
@article {pmid39563951,
year = {2024},
author = {Sivell, O and Hawkes, WLS and , and , and , and , and , and , and , },
title = {The genome sequence of the silvery leafcutter bee, Megachile leachella Curtis, 1828.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {415},
pmid = {39563951},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Megachile leachella (the silvery leafcutter bee; Arthropoda; Insecta; Hymenoptera; Megachilidae). The genome sequence is 573.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.04 kilobases in length.},
}
@article {pmid39564491,
year = {2024},
author = {Zhang, Y and Wang, M and Huang, M and Zhao, J},
title = {Innovative strategies and challenges mosquito-borne disease control amidst climate change.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1488106},
pmid = {39564491},
issn = {1664-302X},
abstract = {The revival of the transmission dynamics of mosquito-borne diseases grants striking challenges to public health intensified by climate change worldwide. This inclusive review article examines multidimensional strategies and challenges linked to climate change and the epidemiology of mosquito-borne diseases such as malaria, dengue, Zika, chikungunya, and yellow fever. It delves into how the biology, pathogenic dynamics, and vector distribution of mosquitoes are influenced by continuously rising temperatures, modified rainfall patterns, and extreme climatic conditions. We also highlighted the high likelihood of malaria in Africa, dengue in Southeast Asia, and blowout of Aedes in North America and Europe. Modern predictive tools and developments in surveillance, including molecular gears, Geographic Information Systems (GIS), and remote sensing have boosted our capacity to predict epidemics. Integrated data management techniques and models based on climatic conditions provide a valuable understanding of public health planning. Based on recent data and expert ideas, the objective of this review is to provide a thoughtful understanding of existing landscape and upcoming directions in the control of mosquito-borne diseases regarding changing climate. This review determines emerging challenges and innovative vector control strategies in the changing climatic conditions to ensure public health.},
}
@article {pmid39567690,
year = {2025},
author = {Borton, MA and McGivern, BB and Willi, KR and Woodcroft, BJ and Mosier, AC and Singleton, DM and Bambakidis, T and Pelly, A and Daly, RA and Liu, F and Freiburger, A and Edirisinghe, JN and Faria, JP and Danczak, R and Leleiwi, I and Goldman, AE and Wilkins, MJ and Hall, EK and Pennacchio, C and Roux, S and Eloe-Fadrosh, EA and Good, SP and Sullivan, MB and Wood-Charlson, EM and Miller, CS and Ross, MRV and Henry, CS and Crump, BC and Stegen, JC and Wrighton, KC},
title = {A functional microbiome catalogue crowdsourced from North American rivers.},
journal = {Nature},
volume = {637},
number = {8044},
pages = {103-112},
pmid = {39567690},
issn = {1476-4687},
support = {P30 CA046934/CA/NCI NIH HHS/United States ; //US Department of Energy (DOE) Office of Science, Office of Biological and Environmental Research/ ; //US National Science Foundation/ ; //Environmental System Science (ESS) Program/ ; //US DOE, Office of Science, Office of Biological and Environmental Research/ ; },
mesh = {*Crowdsourcing ; *Microbiota/genetics ; *Rivers/microbiology ; United States ; Water Microbiology ; Transcriptome ; Carbon Cycle ; Metagenome ; Databases, Factual ; },
abstract = {Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept[1], we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures[2,3], so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.},
}
@article {pmid39568559,
year = {2024},
author = {Boyes, D and Hutchinson, F and Crowley, LM and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Silver-barred Sober moth, Aproaerema taeniolella (Zeller, 1839).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {500},
pmid = {39568559},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly of a female Silver-barred Sober moth Aproaerema taeniolella (Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence has a length of 636.60 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,274 protein-coding genes.},
}
@article {pmid39569448,
year = {2025},
author = {Yu, Y and Edelson, M and Pham, A and Pekar, JE and Johnson, B and Post, K and Kuo, TT},
title = {Distributed, immutable, and transparent biomedical limited data set request management on multi-capacity network.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {32},
number = {2},
pages = {296-307},
pmid = {39569448},
issn = {1527-974X},
support = {R01EB031030//U.S. National Institutes of Health/ ; R01EB031030/NH/NIH HHS/United States ; R01 HG011066/HG/NHGRI NIH HHS/United States ; //NIH/ ; T15LM011271/LM/NLM NIH HHS/United States ; //San Diego Biomedical Informatics Education &amp; Research/ ; T15 LM011271/LM/NLM NIH HHS/United States ; R01 EB031030/EB/NIBIB NIH HHS/United States ; },
mesh = {*Blockchain ; *Information Dissemination/methods ; Humans ; *Datasets as Topic ; *Computer Communication Networks ; },
abstract = {OBJECTIVE: Our study aimed to expedite data sharing requests of Limited Data Sets (LDS) through the development of a streamlined platform that allows distributed, immutable management of network activities, provides transparent and intuitive auditing of data access history, and systematically evaluated it on a multi-capacity network setting for meaningful efficiency metrics.<br><br>MATERIALS AND METHODS: We developed a blockchain-based system with six types of smart contracts to automate the LDS sharing process among major stakeholders. Our workflow included metadata initialization, access-request processing, and audit-log querying. We evaluated our system using synthetic data on three machines with varying specifications to emulate real-world scenarios. The data employed included &#x223c;1000 researcher requests and &#x223c;360&#xa0;000 log queries.<br><br>RESULTS: On average, it took &#x223c;2.5&#xa0;s to register and respond to a researcher access request. The average runtime for an audit-log query with non-empty output was &#x223c;3&#xa0;ms. The runtime metrics at each institution showed general trends affiliated with their computational capacity.<br><br>DISCUSSION: Our system can reduce the LDS sharing request time from potentially hours to seconds, while enhancing data access transparency in a multi-institutional setting. There were variations in performance across sites that could be attributed to differences in hardware specifications. The performance gains became marginal beyond certain hardware thresholds, pointing to the influence of external factors such as network speeds.<br><br>CONCLUSION: Our blockchain-based system can potentially accelerate clinical research by strengthening the data access process, expediting access and delivery of data links, increasing transparency with clear audit trails, and reinforcing trust in medical data management. Our smart contracts are available at: https://github.com/graceyufei/LDS-Request-Management.},
}
@article {pmid39569566,
year = {2025},
author = {Sung, ML and León, C and Reisman, JI and Gordon, KS and Kerns, RD and Li, W and Liu, W and Mitra, A and Yu, H and Becker, WC},
title = {Disparities in Receipt of Medications for Opioid Use Disorder Before and During the COVID-19 Pandemic in the US Veterans Health Administration.},
journal = {Substance use &amp; addiction journal},
volume = {46},
number = {2},
pages = {369-376},
doi = {10.1177/29767342241293334},
pmid = {39569566},
issn = {2976-7350},
support = {I01 HX003711/HX/HSRD VA/United States ; },
mesh = {Humans ; *COVID-19/epidemiology ; Male ; United States/epidemiology ; Female ; *Opioid-Related Disorders/drug therapy/epidemiology ; United States Department of Veterans Affairs ; Middle Aged ; *Healthcare Disparities/statistics &amp; numerical data ; *Veterans/statistics &amp; numerical data ; Adult ; Pandemics ; Cross-Sectional Studies ; *Opiate Substitution Treatment/statistics &amp; numerical data ; Comorbidity ; SARS-CoV-2 ; },
abstract = {BACKGROUND: Populations disproportionately impacted by the opioid epidemic are less likely to receive medications for opioid use disorder (MOUD; OUD). The COVID-19 pandemic exacerbated these disparities. We performed an ecological survey of subpopulations to compare differences in MOUD receipt among Veterans with OUD before versus during the pandemic.<br><br>METHODS: Using 2 cross-sections of 2 time periods of national Veterans Health Administration electronic health record data, we calculated proportions of Veterans with any MOUD receipt by demographics, Elixhauser comorbidity index, and natural language processing (NLP)-derived substance use and social determinants of health in each time period. We evaluated differences in MOUD receipt before and during the pandemic by patient characteristics using Chi-square and Cohen's h for effect size.<br><br>RESULTS: Among 62&#x2009;195 patients with OUD before the pandemic, the proportion prescribed MOUD increased from 46.5% before to 47.5% (P&#x2009;=&#x2009;.0003) during the pandemic. Statistically significant increased receipt of MOUD was observed for patients who were &#x2265;55&#x2009;years, men, White, with Elixhauser comorbidity indices of 2 and &#x2265;5, and with NLP-derived indicators of substance use. There was a decrease that did not achieve statistical significance in MOUD receipt from before to during the pandemic for patients who were women, Black, Latinx, and food insecure.<br><br>CONCLUSIONS: The proportions of patients with OUD prescribed MOUD increased from before to during the pandemic. However, Veterans who were women, Black, Latinx, and food insecure did not experience these increases. These patients may benefit from interventions such as targeted outreach efforts to improve MOUD engagement to reduce OUD harms.},
}
@article {pmid39570888,
year = {2024},
author = {Cuesta-Aguirre, DR and Malgosa, A and Santos, C},
title = {An easy-to-use pipeline to analyze amplicon-based Next Generation Sequencing results of human mitochondrial DNA from degraded samples.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0311115},
pmid = {39570888},
issn = {1932-6203},
mesh = {*DNA, Mitochondrial/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Forensic Genetics/methods ; DNA, Ancient/analysis ; },
abstract = {Genome and transcriptome examinations have become more common due to Next-Generation Sequencing (NGS), which significantly increases throughput and depth coverage while reducing costs and time. Mitochondrial DNA (mtDNA) is often the marker of choice in degraded samples from archaeological and forensic contexts, as its higher number of copies can improve the success of the experiment. Among other sequencing strategies, amplicon-based NGS techniques are currently being used to obtain enough data to be analyzed. There are some pipelines designed for the analysis of ancient mtDNA samples and others for the analysis of amplicon data. However, these pipelines pose a challenge for non-expert users and cannot often address both ancient and forensic DNA particularities and amplicon-based sequencing simultaneously. To overcome these challenges, a user-friendly bioinformatic tool was developed to analyze the non-coding region of human mtDNA from degraded samples recovered in archaeological and forensic contexts. The tool can be easily modified to fit the specifications of other amplicon-based NGS experiments. A comparative analysis between two tools, MarkDuplicates from Picard and dedup parameter from fastp, both designed for duplicate removal was conducted. Additionally, various thresholds of PMDtools, a specialized tool designed for extracting reads affected by post-mortem damage, were used. Finally, the depth coverage of each amplicon was correlated with its level of damage. The results obtained indicated that, for removing duplicates, dedup is a better tool since retains more non-repeated reads, that are removed by MarkDuplicates. On the other hand, a PMDS = 1 in PMDtools was the threshold that allowed better differentiation between present-day and ancient samples, in terms of damage, without losing too many reads in the process. These two bioinformatic tools were added to a pipeline designed to obtain both haplotype and haplogroup of mtDNA. Furthermore, the pipeline presented in the present study generates information about the quality and possible contamination of the sample. This pipeline is designed to automatize mtDNA analysis, however, particularly for ancient samples, some manual analyses may be required to fully validate results since the amplicons that used to be more easily recovered were the ones that had fewer reads with damage, indicating that special care must be taken for poor recovered samples.},
}
@article {pmid39570994,
year = {2024},
author = {Madden, WG and Jin, W and Lopman, B and Zufle, A and Dalziel, B and E Metcalf, CJ and Grenfell, BT and Lau, MSY},
title = {Deep neural networks for endemic measles dynamics: Comparative analysis and integration with mechanistic models.},
journal = {PLoS computational biology},
volume = {20},
number = {11},
pages = {e1012616},
pmid = {39570994},
issn = {1553-7358},
mesh = {*Measles/epidemiology ; Humans ; *Neural Networks, Computer ; *Disease Outbreaks/statistics &amp; numerical data ; *Endemic Diseases/statistics &amp; numerical data ; England/epidemiology ; Wales/epidemiology ; Computational Biology ; Forecasting/methods ; Epidemiological Models ; },
abstract = {Measles is an important infectious disease system both for its burden on public health and as an opportunity for studying nonlinear spatio-temporal disease dynamics. Traditional mechanistic models often struggle to fully capture the complex nonlinear spatio-temporal dynamics inherent in measles outbreaks. In this paper, we first develop a high-dimensional feed-forward neural network model with spatial features (SFNN) to forecast endemic measles outbreaks and systematically compare its predictive power with that of a classical mechanistic model (TSIR). We illustrate the utility of our model using England and Wales measles data from 1944-1965. These data present multiple modeling challenges due to the interplay between metapopulations, seasonal trends, and nonlinear dynamics related to demographic changes. Our results show that while the TSIR model yields similarly performant short-term (1 to 2 biweeks ahead) forecasts for highly populous cities, our neural network model (SFNN) consistently achieves lower root mean squared error (RMSE) across other forecasting windows. Furthermore, we show that our spatial-feature neural network model, without imposing mechanistic assumptions a priori, can uncover gravity-model-like spatial hierarchy of measles spread in which major cities play an important role in driving regional outbreaks. We then turn our attention to integrative approaches that combine mechanistic and machine learning models. Specifically, we investigate how the TSIR can be utilized to improve a state-of-the-art approach known as Physics-Informed-Neural-Networks (PINN) which explicitly combines compartmental models and neural networks. Our results show that the TSIR can facilitate the reconstruction of latent susceptible dynamics, thereby enhancing both forecasts in terms of mean absolute error (MAE) and parameter inference of measles dynamics within the PINN. In summary, our results show that appropriately designed neural network-based models can outperform traditional mechanistic models for short to long-term forecasts, while simultaneously providing mechanistic interpretability. Our work also provides valuable insights into more effectively integrating machine learning models with mechanistic models to enhance public health responses to measles and similar infectious disease systems.},
}
@article {pmid39576832,
year = {2024},
author = {Devadhasan, A and Kolodny, O and Carja, O},
title = {Competition for resources can reshape the evolutionary properties of spatial structure.},
journal = {PLoS computational biology},
volume = {20},
number = {11},
pages = {e1012542},
pmid = {39576832},
issn = {1553-7358},
support = {R35 GM147445/GM/NIGMS NIH HHS/United States ; T32 EB009403/EB/NIBIB NIH HHS/United States ; },
mesh = {*Ecosystem ; Humans ; *Biological Evolution ; Computational Biology ; Mutation ; Models, Biological ; Computer Simulation ; },
abstract = {Many evolving ecosystems have spatial structures that can be conceptualized as networks, with nodes representing individuals or homogeneous subpopulations and links the patterns of spread between them. Prior models of evolution on networks do not take ecological niche differences and eco-evolutionary interplay into account. Here, we combine a resource competition model with evolutionary graph theory to study how heterogeneous topological structure shapes evolutionary dynamics under global frequency-dependent ecological interactions. We find that the addition of ecological competition for resources can produce a reversal of roles between amplifier and suppressor networks for deleterious mutants entering the population. We show that this effect is a nonlinear function of ecological niche overlap and discuss intuition for the observed dynamics using simulations and analytical approximations. We use these theoretical results together with spatial representations from imaging data to show that, for ductal carcinoma, where tumor growth is highly spatially constrained, with cells confined to a tree-like network of ducts, the topological structure can lead to higher rates of deleterious mutant hitchhiking with metabolic driver mutations, compared to tumors characterized by different spatial topologies.},
}
@article {pmid39578727,
year = {2024},
author = {Ang'ang'o, LM and Herren, JK and Tastan Bishop, &#xd6;},
title = {Bioinformatics analysis of the Microsporidia sp. MB genome: a malaria transmission-blocking symbiont of the Anopheles arabiensis mosquito.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1132},
pmid = {39578727},
issn = {1471-2164},
mesh = {*Anopheles/microbiology/parasitology/genetics ; Animals ; *Microsporidia/genetics ; *Symbiosis ; *Computational Biology/methods ; *Genome, Fungal ; Malaria/transmission ; Phylogeny ; Mosquito Vectors/microbiology/genetics ; Genomics/methods ; RNA Interference ; },
abstract = {BACKGROUND: The use of microsporidia as a disease-transmission-blocking tool has garnered significant attention. Microsporidia sp. MB, known for its ability to block malaria development in mosquitoes, is an optimal candidate for supplementing malaria vector control methods. This symbiont, found in Anopheles mosquitoes, can be transmitted both vertically and horizontally with minimal effects on its mosquito host. Its genome, recently sequenced from An. arabiensis, comprises a compact 5.9 Mbp.<br><br>RESULTS: Here, we analyze the Microsporidia sp. MB genome, highlighting its major genomic features, gene content, and protein function. The genome contains 2247 genes, predominantly encoding enzymes. Unlike other members of the Enterocytozoonida group, Microsporidia sp. MB has retained most of the genes in the glycolytic pathway. Genes involved in RNA interference (RNAi) were also identified, suggesting a mechanism for host immune suppression. Importantly, meiosis-related genes (MRG) were detected, indicating potential for sexual reproduction in this organism. Comparative analyses revealed similarities with its closest relative, Vittaforma corneae, despite key differences in host interactions.<br><br>CONCLUSION: This study provides an in-depth analysis of the newly sequenced Microsporidia sp. MB genome, uncovering its unique adaptations for intracellular parasitism, including retention of essential metabolic pathways and RNAi machinery. The identification of MRGs suggests the possibility of sexual reproduction, offering insights into the symbiont's evolutionary strategies. Establishing a reference genome for Microsporidia sp. MB sets the foundation for future studies on its role in malaria transmission dynamics and host-parasite interactions.},
}
@article {pmid39580513,
year = {2024},
author = {Li, J and Weckwerth, W and Waldherr, S},
title = {Network structure and fluctuation data improve inference of metabolic interaction strengths with the inverse Jacobian.},
journal = {NPJ systems biology and applications},
volume = {10},
number = {1},
pages = {137},
pmid = {39580513},
issn = {2056-7189},
support = {201806010428//China Scholarship Council (CSC)/ ; },
mesh = {Humans ; *Algorithms ; *Metabolic Networks and Pathways/genetics ; *Breast Neoplasms/metabolism/genetics ; *Metabolomics/methods ; Cell Line, Tumor ; Models, Biological ; Computational Biology/methods ; Female ; Systems Biology/methods ; },
abstract = {Based on high-throughput metabolomics data, the recently introduced inverse differential Jacobian algorithm can infer regulatory factors and molecular causality within metabolic networks close to steady-state. However, these studies assumed perturbations acting independently on each metabolite, corresponding to metabolic system fluctuations. In contrast, emerging evidence puts forward internal network fluctuations, particularly from gene expression fluctuations, leading to correlated perturbations on metabolites. Here, we propose a novel approach that exploits these correlations to quantify relevant metabolic interactions. By integrating enzyme-related fluctuations in the construction of an appropriate fluctuation matrix, we are able to exploit the underlying reaction network structure for the inverse Jacobian algorithm. We applied this approach to a model-based artificial dataset for validation, and to an experimental breast cancer dataset with two different cell lines. By highlighting metabolic interactions with significantly changed interaction strengths, the inverse Jacobian approach identified critical dynamic regulation points which are confirming previous breast cancer studies.},
}
@article {pmid39581005,
year = {2024},
author = {Tinsley, E and Froidevaux, JSP and Jones, G},
title = {The location of solar farms within England's ecological landscape: Implications for biodiversity conservation.},
journal = {Journal of environmental management},
volume = {372},
number = {},
pages = {123372},
doi = {10.1016/j.jenvman.2024.123372},
pmid = {39581005},
issn = {1095-8630},
mesh = {*Biodiversity ; England ; *Conservation of Natural Resources ; *Ecosystem ; Solar Energy ; Farms ; Geographic Information Systems ; Ecology ; Agriculture ; },
abstract = {A global energy transition to using sustainable renewable sources is being driven by global agreements. Simultaneously there is a call for increased biodiversity conservation. This creates a green-green dilemma, where the expansion of renewables could lead to the demise of biodiversity if not carefully assessed, managed and monitored. Recognition of the dilemma is central to the development of Sustainable Development Goals. It is therefore important to understand whether renewable energy sources such as solar farms are being sited in areas where they have minimal impact on biodiversity. If solar farms were sited with minimal impacts on biodiversity, we hypothesised that they would be less likely to be sited close to ecologically sensitive areas than near random points. We used Geographic Information System methods to explore the density of solar photovoltaic (PV) farms in England and assessed their siting relative to sensitive ecological features, including priority habitat types, designated sites, and land conservation initiatives. We compared the area of 25 sensitive ecological features around solar farms and random points across three spatial scales (100 m, 1000 m, and 6000 m radius scales). Solar farms were distributed throughout England, with the highest concentration in South West England. Solar sites were primarily surrounded by habitats with anthropogenic influences, such as agricultural and urban settings. Priority habitats, such as woodland, grassland, wetland and heathland, were more extensive around random points across spatial scales (except for woodland at the largest scale). Most designated sites were significantly more extensive around random points. We conclude that, under current planning regulations, solar sites in England are being placed appropriately with regard to sensitive ecological habitats, and are often sited in areas already impacted by farming and development. Adaptive planning should be implemented to ensure that the evolving research around biodiversity and solar farms is incorporated into decision making, and monitoring is completed across the lifespan of solar farms to assess impacts and effective mitigation.},
}
@article {pmid39583330,
year = {2024},
author = {Hakkenberg, CR and Clark, ML and Bailey, T and Burns, P and Goetz, SJ},
title = {Ladder fuels rather than canopy volumes consistently predict wildfire severity even in extreme topographic-weather conditions.},
journal = {Communications earth &amp; environment},
volume = {5},
number = {1},
pages = {721},
pmid = {39583330},
issn = {2662-4435},
abstract = {Drivers of forest wildfire severity include fuels, topography and weather. However, because only fuels can be actively managed, quantifying their effects on severity has become an urgent research priority. Here we employed GEDI spaceborne lidar to consistently assess how pre-fire forest fuel structure affected wildfire severity across 42 California wildfires between 2019-2021. Using a spatial-hierarchical modeling framework, we found a positive concave-down relationship between GEDI-derived fuel structure and wildfire severity, marked by increasing severity with greater fuel loads until a decline in severity in the tallest and most voluminous forest canopies. Critically, indicators of canopy fuel volumes (like biomass and height) became decoupled from severity patterns in extreme topographic and weather conditions (slopes >20°; winds > 9.3 m/s). On the other hand, vertical continuity metrics like layering and ladder fuels more consistently predicted severity in extreme conditions - especially ladder fuels, where sparse understories were uniformly associated with lower severity levels. These results confirm that GEDI-derived fuel estimates can overcome limitations of optical imagery and airborne lidar for quantifying the interactive drivers of wildfire severity. Furthermore, these findings have direct implications for designing treatment interventions that target ladder fuels versus entire canopies and for delineating wildfire risk across topographic and weather conditions.},
}
@article {pmid39584487,
year = {2025},
author = {Daru, BH},
title = {A global database of butterfly species native distributions.},
journal = {Ecology},
volume = {106},
number = {1},
pages = {e4462},
doi = {10.1002/ecy.4462},
pmid = {39584487},
issn = {1939-9170},
support = {2345994//National Science Foundation/ ; 2416314//National Science Foundation/ ; },
mesh = {*Butterflies/physiology ; Animals ; *Animal Distribution ; *Databases, Factual ; Ecosystem ; Species Specificity ; },
abstract = {Butterflies represent a diverse group of insects, playing key ecosystem roles such as pollination and their larval form engage in herbivory. Despite their importance, comprehensive global distribution data for butterfly species are lacking. This lack of comprehensive global data has hindered many large-scale questions in ecology, evolutionary biology, and conservation at the regional and global scales. Here, I use an integrative workflow that combines occurrence records, alpha hull polygons, species' dispersal capacity, and natural habitat and environmental variables within a framework of species distribution models to generate species-level native distributions for butterflies at a global scale in the contemporary period. The database releases native range maps for 10,372 extant species of butterflies at a spatial grain resolution of 5 arcmin (~10 km). This database has the potential to allow unprecedented large-scale analyses in ecology, biogeography, and conservation of butterflies. The maps are available in the WGS84 coordinate reference system (EPSG:4326 code) and stored as vector polygons in the GEOPACKAGE format for maximum compression, allowing easy data manipulation using a standard computer. I additionally provide each species' spatial raster. All maps and R scripts are open access and available for download in Dryad and Zenodo, respectively, and are guided by FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. By making these data available to the scientific community, I aim to advance the sharing of biological data to stimulate more comprehensive research in ecology, biogeography, and conservation of butterflies.},
}
@article {pmid39585479,
year = {2024},
author = {Sahak, AS and Karsli, F and Saraj, MA},
title = {Evaluating the impact of urban sprawl on the urban ecological status using GIS and remote sensing from 2000 to 2021: a case study of Herat City, Afghanistan.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {12},
pages = {1246},
pmid = {39585479},
issn = {1573-2959},
mesh = {*Geographic Information Systems ; *Remote Sensing Technology ; *Environmental Monitoring/methods ; *Urbanization ; *Cities ; Afghanistan ; Conservation of Natural Resources/methods ; Ecosystem ; },
abstract = {Urbanization often incurs environmental costs, as fertile agricultural and forested lands are converted into urban areas. Herat City is currently undergoing significant urban transformation. This research aims to assess the impact of urban sprawl on Herat City's urban ecological status during 2000, 2013, and 2021, using GIS and remote sensing. The urban expansion intensity index was used to measure urban sprawl. The Mean Remote Sensing Ecological Index (MRSEI), integrating known granulation entropy (KGE) and comprehensive distance-based ranking (COBRA) algorithms, was utilized to evaluate urban ecological status. The random forest (RF) supervised machine learning-based algorithm was used to classify the study area into four categories (Built-up, Bare-land, Water, and Vegetation). Findings indicate rapid development from 2000 to 2013, followed by moderate expansion until 2021. Urban ecological quality degradation is observed in various directions over time, with the southeast consistently demonstrating excellent status. Interestingly, while good and excellent urban ecological status decreases over two decades, poor and very poor conditions improve. The research underscores an inverse relationship between urban expansion intensity and ecological status, highlighting the need for improved strategies to mitigate environmental decline. These findings will inform Afghan governmental bodies and international organizations, enabling them to better address resource consumption, ecological disruptions, social inequalities, and foster sustainable development.},
}
@article {pmid39585857,
year = {2024},
author = {Adderley-Heron, K and Chow-Fraser, P},
title = {Unsupervised classification of Blanding's turtle (Emydoidea blandingii) behavioural states from multi-sensor biologger data.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0314291},
pmid = {39585857},
issn = {1932-6203},
mesh = {Animals ; *Turtles/physiology/classification ; Female ; Male ; *Behavior, Animal/physiology ; Accelerometry ; Markov Chains ; Geographic Information Systems ; Nesting Behavior/physiology ; },
abstract = {Classifying animal behaviors in their natural environments is both challenging and ecologically important, but the use of biologgers with multiple sensors has significantly advanced this research beyond the capabilities of traditional methods alone. Here, we show how biologgers containing an integrated tri-axial accelerometer, GPS logger and immersion sensor were used to infer behavioural states of a cryptic, freshwater turtle, the Blanding's turtle (Emydoidea blandingii). Biologgers were attached to three males and five females that reside in two undisturbed coastal marshes in northeastern Georgian Bay (Ontario, Canada) between May and July 2023. Raw acceleration values were separated into static and dynamic acceleration and subsequently used to calculate overall dynamic body acceleration (ODBA) and pitch. The unsupervised Hidden Markov Model (HMM) successfully differentiated five behavioural states as follows: active in water, resting in water, active out of water, resting in water, and nesting. Overall accuracy of the classification was 93.8%, and except for nesting (79%), all other behaviours were above 92%. There were significant differences in daily activity budgets between male and female turtles, with females spending a greater proportion of time active out of water, and inactive out of the water, while males spent a greater proportion of time active in water. These differences were likely a result of large seasonal life-history requirements such as nesting and mate finding. Accurate classification of behavioural states is important for researchers to understand fine-scale activities carried out during the active season and how environmental variables may influence the behaviours of turtles in their natural habitats.},
}
@article {pmid39586901,
year = {2025},
author = {Ma, Y and Xu, L and Zhuang, H and Abd-Eldaim, FA and Tang, Z and Dewer, Y and Wang, H},
title = {Evaluation of Skin Color Supervision Genes in Chickpea Seeds by Multiomics.},
journal = {Molecular biotechnology},
volume = {67},
number = {11},
pages = {4280-4288},
pmid = {39586901},
issn = {1559-0305},
support = {NICGR2019-029//National Infrastructure for Crop Germplasm Resources of China/ ; PT2030//Xinjiang Uygur Autonomous Region Science and Technology Innovation Base Construction/ ; 2017E01023-1//Xinjiang Uygur Autonomous Region Regional Collaborative Innovation Project/ ; },
mesh = {*Seeds/genetics/metabolism ; Gene Expression Regulation, Plant ; *Cicer/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Flavonoids/metabolism ; Gene Expression Profiling ; Transcriptome ; *Pigmentation/genetics ; Metabolome ; Genes, Plant ; Multiomics ; },
abstract = {Seed samples of two types of chickpea (Cicer arietinum Linn.), including variety A (NRCGR-4452) and variety B (local varieties), with different seed colors, were collected every five days for a total of four times during the seed development period. Non-targeted metabolome and transcriptome sequencing were conducted to identify differentially expressed genes and metabolites associated with chickpea seed coat color. The results indicated that the relative quercetin, pelargonidin, luteolin, rutin, myricetin, kaempferol, glycitin, and naringin contents were higher in variety A than in variety B, and that carbohydrate and amino acid metabolites had a greater impact on flavonoid metabolites. Quercetin, luteolin, and kaempferol were most significantly associated with seed color differences, the associated enzyme genes were LOC101491583 (callose synthase 5-like), LOC101503703 (flavonoid 3',5'-hydroxylase), LOC101514158 (callose synthase 5), LOC101497872 (UDP-glycosyltransferase 74F1-like), LOC101500232 (callose synthase 7 isoform X1), LOC101511206 (UDP-glycosyltransferase 73C3-like), LOC101502065 (galactoside 2-alpha-L-fucosyltransferase), LOC101492791 (sulfoquinovosyl transferase SQD2), and LOC101509377 (flavonol synthase). Additionally, the gene transcription factor MYB44 may regulate UDP-glycosyltransferase 73C3 to affect seed color differences.},
}
@article {pmid39586965,
year = {2024},
author = {Gianicolo, E and Russo, A and Di Staso, R and Ronckers, CM and Schmidtmann, I and Wollschläger, D and Blettner, M},
title = {A municipality-specific analysis to investigate persistent increased incidence rates of childhood leukaemia near the nuclear power plant of Krümmel in Germany.},
journal = {European journal of epidemiology},
volume = {39},
number = {12},
pages = {1373-1378},
pmid = {39586965},
issn = {1573-7284},
mesh = {Humans ; Germany/epidemiology ; Child ; *Nuclear Power Plants ; Incidence ; Male ; Child, Preschool ; Female ; *Leukemia/epidemiology ; Adolescent ; Infant ; *Registries ; Leukemia, Radiation-Induced/epidemiology ; Infant, Newborn ; Cities/epidemiology ; Environmental Exposure/adverse effects/statistics &amp; numerical data ; Risk Factors ; },
abstract = {Increased incidence rates for childhood leukaemia have been reported in municipalities close to the nuclear power plant (NPP) Krümmel (Geesthacht, Germany). Methodological challenges arise when analysing this association at ecological level. They include the use of an appropriate reference population, unstable estimates of standardised incidence ratios (SIRs), and the potential role of prevailing winds. The aim of our study is to address these challenges. The German Childhood Cancer Registry provided data on leukaemia in children under 15 years (2004-2019). The German Federal Statistical Office provided the population data. The study region included all municipalities with ≥ 75% surface area within 50 kms from the Krümmel NPP. We calculated SIRs using national and regional reference rates. Smoothed incidence relative rates (IRRs) were calculated and mapped to check for potential patterns associated with prevailing winds. Overall 356 cases of childhood leukaemia were observed in the study region (321 municipalities) during 2004-2019. SIRs based on national reference rates show nearly no difference to those calculated using the regional rates as reference. Increased SIR and IRR were observed in Geesthacht (observed-cases = eight; SIR = 2.29; 95% confidence interval: 0.99-4.51. IRR = 1.80; 95% credibility interval: 0.88-2.79). The analysis of the IRR map does not show patterns associated with prevailing winds. Using a regional population as the reference, we found evidence that there may still be an increased risk for childhood leukaemia in Geesthacht. However, IRR estimates are uncertain and credibility intervals are compatible with the absence of elevated risk. The persistent evidence of risk of childhood leukaemia in Geesthacht warrants further epidemiological surveillance.},
}
@article {pmid39589804,
year = {2025},
author = {Arias, M and Behrendt, L and Dreßler, L and Raka, A and Perrier, C and Elias, M and Gomez, D and Renoult, JP and Tedore, C},
title = {Testing the equivalency of human "predators" and deep neural networks in the detection of cryptic moths.},
journal = {Journal of evolutionary biology},
volume = {38},
number = {2},
pages = {214-224},
doi = {10.1093/jeb/voae146},
pmid = {39589804},
issn = {1420-9101},
support = {ANR-16-CE02-0012//Clearwing ANR/ ; ANR-10-LABX-04-01//LabEx CeMEB/ ; },
mesh = {Animals ; *Moths/physiology/anatomy &amp; histology ; *Neural Networks, Computer ; Humans ; *Biological Mimicry ; *Predatory Behavior ; },
abstract = {Researchers have shown growing interest in using deep neural networks (DNNs) to efficiently test the effects of perceptual processes on the evolution of colour patterns and morphologies. Whether this is a valid approach remains unclear, as it is unknown whether the relative detectability of ecologically relevant stimuli to DNNs actually matches that of biological neural networks. To test this, we compare image classification performance by humans and 6 DNNs (AlexNet, VGG-16, VGG-19, ResNet-18, SqueezeNet, and GoogLeNet) trained to detect artificial moths on tree trunks. Moths varied in their degree of crypsis, conferred by different sizes and spatial configurations of transparent wing elements. Like humans, four of six DNN architectures found moths with larger transparent elements harder to detect. However, humans and only one DNN architecture (GoogLeNet) found moths with transparent elements touching one side of the moth's outline harder to detect than moths with untouched outlines. When moths took up a smaller proportion of the image (i.e., were viewed from further away), the camouflaging effect of transparent elements touching the moth's outline was reduced for DNNs but enhanced for humans. Viewing distance can thus interact with camouflage type in opposing directions in humans and DNNs, which warrants a deeper investigation of viewing distance/size interactions with a broader range of stimuli. Overall, our results suggest that human and DNN responses had some similarities, but not enough to justify widespread use of DNNs for studies of camouflage.},
}
@article {pmid39591213,
year = {2024},
author = {Roman-Ramos, H and Ho, PL},
title = {Current Technologies in Snake Venom Analysis and Applications.},
journal = {Toxins},
volume = {16},
number = {11},
pages = {},
pmid = {39591213},
issn = {2072-6651},
support = {2017/18398-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 309741/2023-8//National Council for Scientific and Technological Development/ ; },
mesh = {*Snake Venoms/chemistry ; Animals ; *Proteomics ; Humans ; Genomics ; Computational Biology ; Snakes ; },
abstract = {This comprehensive review explores the cutting-edge advancements in snake venom research, focusing on the integration of proteomics, genomics, transcriptomics, and bioinformatics. Highlighting the transformative impact of these technologies, the review delves into the genetic and ecological factors driving venom evolution, the complex molecular composition of venoms, and the regulatory mechanisms underlying toxin production. The application of synthetic biology and multi-omics approaches, collectively known as venomics, has revolutionized the field, providing deeper insights into venom function and its therapeutic potential. Despite significant progress, challenges such as the functional characterization of toxins and the development of cost-effective antivenoms remain. This review also discusses the future directions of venom research, emphasizing the need for interdisciplinary collaborations and new technologies (mRNAs, cryo-electron microscopy for structural determinations of toxin complexes, synthetic biology, and other technologies) to fully harness the biomedical potential of venoms and toxins from snakes and other animals.},
}
@article {pmid39591252,
year = {2024},
author = {Baradaran, M and Salabi, F and Mahdavinia, M and Mohammadi, E and Vazirianzadeh, B and Avella, I and Kazemi, SM and Lüddecke, T},
title = {ScorpDb: A Novel Open-Access Database for Integrative Scorpion Toxinology.},
journal = {Toxins},
volume = {16},
number = {11},
pages = {},
pmid = {39591252},
issn = {2072-6651},
mesh = {*Scorpion Venoms/chemistry ; *Scorpions ; Animals ; Humans ; Databases, Factual ; Scorpion Stings/drug therapy ; Databases, Protein ; },
abstract = {Scorpion stings are a significant public health concern globally, particularly in tropical and subtropical regions. Scorpion venoms contain a diverse array of bioactive peptides, and different scorpion species around the world typically exhibit varying venom profiles, resulting in a wide range of envenomation symptoms. Despite their harmful effects, scorpion venom peptides hold immense potential for drug development due to their unique characteristics. Therefore, the establishment of a comprehensive database that catalogs scorpions along with their known venom peptides and proteins is imperative in furthering research efforts in this research area. We hereby present ScorpDb, a novel database that offers convenient access to data related to different scorpion species, the peptides and proteins found in their venoms, and the symptoms they can cause. To this end, the ScorpDb database has been primarily advanced to accommodate data on the Iranian scorpion fauna. From there, we propose future community efforts to include a larger diversity of scorpions and scorpion venom components. ScorpDb holds the promise to become a valuable resource for different professionals from a variety of research fields, like toxinologists, arachnologists, and pharmacologists. The database is available at https://www.scorpdb.com/.},
}
@article {pmid39592922,
year = {2024},
author = {Das, VA and Gautam, B and Yadav, PK and Varadwaj, PK and Wadhwa, G and Singh, S},
title = {Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1127},
pmid = {39592922},
issn = {1471-2229},
mesh = {*Bacillus/genetics/physiology ; *Malus/microbiology/genetics ; *Genome, Bacterial ; Genetic Fitness ; Genomics/methods ; Genomic Islands ; Computational Biology/methods ; },
abstract = {A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.},
}
@article {pmid39594004,
year = {2024},
author = {Alrhmoun, M and Sulaiman, N and Haq, SM and Abidullah, S and Prakofjewa, J and Krigas, N and Pieroni, A and Sõukand, R},
title = {Is Boiling Bitter Greens a Legacy of Ancient Crete? Contemporary Foraging in the Minoan Refugium of the Lasithi Plateau.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {22},
pages = {},
pmid = {39594004},
issn = {2304-8158},
support = {N/A//University of Gastronomic Sciences, Pollenzo, Italy/ ; N/A//Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari Uni-versity of Venice, Italy/ ; },
abstract = {Wild greens (WGs) play a significant role in Mediterranean diets (MDs), reflecting botanical and cultural diversities, mainly influenced by a complex conglomerate of local human ecologies. This study investigates local ecological knowledge (LEK) linked to traditional gathering and consumption of WGs in the Lasithi Plateau of eastern Crete, where human genetic studies one decade ago showed very peculiar patterns, hypothesising that the Minoan civilisation took refuge there before it disappeared. A field ethnobotanical study was conducted to document the diversity of WGs and their detailed local culinary uses in the Lasithi area by interviewing 31 study participants. Fifty-nine folk taxa (species and subspecies) were recorded, corresponding to fifty-eight botanical taxa. A quotation index was measured to assess the cultural significance of WGs in the study areas; logistic regression analysis was adopted to understand the impact of sensory classifications of WGs and their local cooking methods. Lasithi's foraging showed a notable prevalence of bitter-tasting WGs, which play a central role in local cognition and culinary practices. This bitterness aspect of WGs, potentially influenced by cultural preferences and genetic factors, probably suggests a connection to the ancient Lasithi's inhabitants, i.e., Minoan dietary habits. We found that bitterness is the predominant sensory attribute in Lasithi, characterising 45.76% of the WGs. These findings underscore the complex interplay between local ecologies and biodiversity, LEK, and dietary traditions, highlighting the importance of WGs in understanding the evolution of foraging and plant culinary diversities across the Mediterranean.},
}
@article {pmid39595758,
year = {2024},
author = {Aras, SG and Runyon, JR and Kazman, JB and Thayer, JF and Sternberg, EM and Deuster, PA},
title = {Is Greener Better? Quantifying the Impact of a Nature Walk on Stress Reduction Using HRV and Saliva Cortisol Biomarkers.},
journal = {International journal of environmental research and public health},
volume = {21},
number = {11},
pages = {},
pmid = {39595758},
issn = {1660-4601},
support = {XX//The Institute for Integrative Health and Nature Sacred/ ; },
mesh = {Humans ; *Hydrocortisone/analysis/metabolism ; *Saliva/chemistry ; *Walking/physiology ; *Heart Rate/physiology ; Male ; Adult ; Female ; *Biomarkers/analysis/metabolism ; Stress, Psychological/metabolism/physiopathology ; Affect/physiology ; Stress, Physiological/physiology ; Young Adult ; Nature ; Middle Aged ; },
abstract = {The physiological impact of walking in nature was quantified via continuous heart rate variability (HRV), pre- and post-walk saliva cortisol measures, and self-reported mood and mindfulness scores for N = 17 participants who walked "The Green Road" at Walter Reed National Military Medical Center in Bethesda, Maryland. For N = 15 of the participants, HRV analysis revealed two main groups: group one individuals had a 104% increase (mean) in the root mean square standard deviation (RMSSD) and a 47% increase (mean) in the standard deviation of NN values (SDNN), indicating an overall reduction in physiological stress from walking the Green Road, and group two individuals had a decrease (mean) of 42% and 31% in these respective HRV metrics, signaling an increase in physiological stresses. Post-walk self-reported scores for vigor and mood disturbance were more robust for the Green Road than for a comparable urban road corridor and showed that a higher HRV during the walk was associated with improved overall mood. Saliva cortisol was lower after taking a walk for all participants, and it showed that walking the Green Road elicited a significantly larger reduction in cortisol of 53%, on average, when compared with 37% of walking along an urban road. It was also observed that the order in which individuals walked the Green Road and urban road also impacted their cortisol responses, with those walking the urban road before the Green Road showing a substantial reduction in cortisol, suggesting a possible attenuation effect of walking the Green Road first. These findings provide quantitative data demonstrating the stress-reducing effects of being in nature, thus supporting the health benefit value of providing access to nature more broadly in many settings.},
}
@article {pmid39596552,
year = {2024},
author = {Signore, IA and Donoso, G and Bocchieri, P and Tobar-Calfucoy, EA and Yáñez, CE and Carvajal-Silva, L and Silva, AX and Otth, C and Cappelli, C and Valenzuela Jorquera, H and Zapata-Contreras, D and Espinosa-Parrilla, Y and Zúñiga-Pacheco, P and Fuentes-Guajardo, M and Monardes-Ramírez, VA and Kochifas Velasquez, P and Muñoz, CA and Dorador, C and García-Araya, J and Campillay-Véliz, CP and Echeverria, C and Santander, RA and Cerpa, LC and Martínez, MF and Quiñones, LA and Lamoza Galleguillos, ER and Saez Hidalgo, J and Nova-Lamperti, E and Sanhueza, S and Giacaman, A and Acosta-Jamett, G and Verdugo, C and Plaza, A and Verdugo, C and Selman, C and Verdugo, RA and Colombo, A},
title = {The Chilean COVID-19 Genomics Network Biorepository: A Resource for Multi-Omics Studies of COVID-19 and Long COVID in a Latin American Population.},
journal = {Genes},
volume = {15},
number = {11},
pages = {},
pmid = {39596552},
issn = {2073-4425},
support = {ANID COVID0961, ANID COVID0789, ANID COVID1005, ANID COVID0585, ACT210085, FONDECYT 1170446, FONDECYT 1211480//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; MAG1995//Ministry of Education/ ; RED21193//Interuniversity Center for Healthy Aging/ ; VRID220.085.041-INI//University of Concepci&#xf3;n/ ; },
mesh = {Humans ; *COVID-19/genetics/virology/epidemiology ; Chile ; *Biological Specimen Banks ; *Genomics/methods ; *SARS-CoV-2/genetics ; Male ; Female ; Adult ; Middle Aged ; Aged ; Latin America ; Multiomics ; },
abstract = {Although a lack of diversity in genetic studies is an acknowledged obstacle for personalized medicine and precision public health, Latin American populations remain particularly understudied despite their heterogeneity and mixed ancestry. This gap extends to COVID-19 despite its variability in susceptibility and clinical course, where ethnic background appears to influence disease severity, with non-Europeans facing higher hospitalization rates. In addition, access to high-quality samples and data is a critical issue for personalized and precision medicine, and it has become clear that the solution lies in biobanks. The creation of the Chilean COVID-19 Biorepository reported here addresses these gaps, representing the first nationwide multicentric Chilean initiative. It operates under rigorous biobanking standards and serves as one of South America's largest COVID cohorts. A centralized harmonization strategy was chosen and included unified standard operating procedures, a sampling coding system, and biobanking staff training. Adults with confirmed SARS-CoV-2 infection provided broad informed consent. Samples were collected to preserve blood, plasma, buffy coat, and DNA. Quality controls included adherence to the standard preanalytical code, incident reporting, and DNA concentration and absorbance ratio 260/280 assessments. Detailed sociodemographic, health, medication, and preexisting condition data were gathered. In five months, 2262 participants were enrolled, pseudonymized, and sorted by disease severity. The average Amerindian ancestry considering all participant was 44.0% [SD 15.5%], and this value increased to 61.2% [SD 19.5%] among those who self-identified as Native South Americans. Notably, 279 participants self-identified with one of 12 ethnic groups. High compliance (>90%) in all assessed quality controls was achieved. Looking ahead, our team founded the COVID-19 Genomics Network (C19-GenoNet) focused on identifying genetic factors influencing SARS-CoV-2 outcomes. In conclusion, this bottom-up collaborative effort aims to promote the integration of Latin American populations into global genetic research and welcomes collaborations supporting this endeavor. Interested parties are invited to explore collaboration opportunities through our catalog, accessible online.},
}
@article {pmid39597377,
year = {2024},
author = {Maślanka, P and Korycki, R},
title = {Material, Aerodynamic, and Operational Aspects of Single-Skin Paraglider.},
journal = {Materials (Basel, Switzerland)},
volume = {17},
number = {22},
pages = {},
pmid = {39597377},
issn = {1996-1944},
abstract = {The operating comfort of a paraglider is created by the aerodynamic parameters as well as the mass and packing volume of the wing. A classic paraglider has upper and lower covers. To reduce the material and manufacturing costs as well as protect the environment, it is possible to introduce a single-skin wing. This article conducts an analysis of a single-skin paraglider covered only with upper panels, whereas the lower cover is applied only at the leading and trailing edges. The analysis is theoretically oriented; aerodynamic and structural calculations were performed using the ANSYS environment. The single-skin structure was evaluated in terms of the predicted behavior during flight and the material's deformation under the influence of a specified pressure and the overloads acting on it. The results show that developing these structures may influence the creation of models with comparable aerodynamic characteristics to traditional ones. Additionally, the reduced masses and packing volumes of difficult-to-degrade materials are strongly correlated with saving costs and an ecological approach. No corresponding studies were found in the available literature. Thus, this presented analysis may result in a greater understanding and application of this paraglider type.},
}
@article {pmid39599286,
year = {2024},
author = {Toghan, A and Alduaij, OK and Sanad, MMS and Elessawy, NA},
title = {Scalable Engineering of 3D Printing Filaments Derived from Recycling of Plastic Drinking Water Bottle and Glass Waste.},
journal = {Polymers},
volume = {16},
number = {22},
pages = {},
pmid = {39599286},
issn = {2073-4360},
support = {IMSIU-RG23086//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University/ ; },
abstract = {The most significant challenge that the world is currently facing is the development of beneficial industrial applications for solid waste. A novel strategy was implemented to produce a composite with varying loadings of glass waste nanoparticles (GWNP) in 5, 10, and 15 wt.% with recycled polyethylene terephthalate drinking water bottle waste (RPET). This strategy was based on glass and drinking water bottle waste. An analysis was conducted to evaluate the performance of the composite as filaments for 3D printer applications. This study evaluated the effect of GWNP addition on the chemical structure, thermal and mechanical characteristics of the composite. The Fourier Transform Infrared (FTIR) spectra of the filament composites and RPET composites exhibited similarities. However, the mechanical strength and thermal stability of the filament composites were enhanced due to the increased GWNP content. Furthermore, the results indicated that the filament developed could be utilized for 3D printing, as demonstrated by the successful fabrication of the filament composite, including 5 wt.% GWNP, using a 3D printer pen. The production of filaments using GWNP and RPET matrix presents a cost-effective, high-yield, and ecologically beneficial alternative. The present study may pave the way for the future advancement and utilization of 3D printing filaments by treating hazardous waste and using more ecologically friendly materials in design applications.},
}
@article {pmid39600916,
year = {2021},
author = {Boyes, D and Crowley, LM and , and , and , and , and , and , },
title = {The genome sequence of the harlequin ladybird, Harmonia axyridis (Pallas, 1773).},
journal = {Wellcome open research},
volume = {6},
number = {},
pages = {300},
pmid = {39600916},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Harmonia axyridis (the harlequin ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 426 megabases in span. The majority (99.98%) of the assembly is scaffolded into 8 chromosomal pseudomolecules, with the X sex chromosome assembled.},
}
@article {pmid39602490,
year = {2024},
author = {Soares, R and Azevedo, L and Vasconcelos, V and Pratas, D and Sousa, SF and Carneiro, J},
title = {Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds: A Resource for Therapeutics and Bioremediation.},
journal = {Journal of chemical information and modeling},
volume = {64},
number = {24},
pages = {9576-9593},
doi = {10.1021/acs.jcim.4c00995},
pmid = {39602490},
issn = {1549-960X},
mesh = {*Cyanobacteria/metabolism ; *Machine Learning ; *Biodegradation, Environmental ; *Drug Discovery ; Molecular Docking Simulation ; Databases, Factual ; Databases, Chemical ; Humans ; Software ; },
abstract = {Cyanobacteria strains have the potential to produce bioactive compounds that can be used in therapeutics and bioremediation. Therefore, compiling all information about these compounds to consider their value as bioresources for industrial and research applications is essential. In this study, a searchable, updated, curated, and downloadable database of cyanobacteria bioactive compounds was designed, along with a machine-learning model to predict the compounds' targets of newly discovered molecules. A Python programming protocol obtained 3431 cyanobacteria bioactive compounds, 373 unique protein targets, and 3027 molecular descriptors. PaDEL-descriptor, Mordred, and Drugtax software were used to calculate the chemical descriptors for each bioactive compound database record. The biochemical descriptors were then used to determine the most promising protein targets for human therapeutic approaches and environmental bioremediation using the best machine learning (ML) model. The creation of our database, coupled with the integration of computational docking protocols, represents an innovative approach to understanding the potential of cyanobacteria bioactive compounds. This resource, adhering to the findability, accessibility, interoperability, and reuse of digital assets (FAIR) principles, is an excellent tool for pharmaceutical and bioremediation researchers. Moreover, its capacity to facilitate the exploration of specific compounds' interactions with environmental pollutants is a significant advancement, aligning with the increasing reliance on data science and machine learning to address environmental challenges. This study is a notable step forward in leveraging cyanobacteria for both therapeutic and ecological sustainability.},
}
@article {pmid39606930,
year = {2024},
author = {Whyte, M and Wambui, KM and Musenge, E},
title = {Nigeria's malaria prevalence in 2015: a geospatial, exploratory district-level approach.},
journal = {Geospatial health},
volume = {19},
number = {2},
pages = {},
doi = {10.4081/gh.2024.1243},
pmid = {39606930},
issn = {1970-7096},
mesh = {Humans ; Nigeria/epidemiology ; *Malaria/epidemiology ; Prevalence ; Child, Preschool ; Infant ; *Spatial Analysis ; Female ; Male ; *Geographic Information Systems ; Socioeconomic Factors ; Adult ; Adolescent ; Child ; Middle Aged ; Young Adult ; },
abstract = {This study used data from the second Nigeria Malaria Indicator Survey (NMIS) conducted in 2015 to investigate the spatial distribution of malaria prevalence in the country and identify its associated factors. Nigeria is divided into 36 states with 109 senatorial districts, most of which are affected by malaria, a major cause of morbidity and mortality in children under five years of age. We carried out an ecological study with analysis at the senatorial district level. A malaria prevalence map was produced combining geographic information systems data from the Nigeria Malaria Indicator Survey (NMIS) of 2015 with shape files from an open data-sharing platform. Spatial autoregressive models were fitted using a set of key covariates. Malaria prevalence in children under-five was highest in Kebbi South senatorial district (70.6%). It was found that poorest wealth index (β = 0.10 (95% CI: 0.01, 0.20), p = 0.04), mothers having only secondary level of education (β = 0.78 (95% CI: 0.05, 1.51), p = 0.04) and households without mosquito bed nets (β = 0.21 (95% CI: 0.02, 0.39), p = 0.03) were all significantly associated with higher malaria prevalence. Moran's I (54.81, p<0.001) showed spatial dependence of malaria prevalence across contiguous districts and spatial autoregressive modelling demonstrated significant spill-over effect of malaria prevalence. Maps produced in this study provide a useful graphical representation of the spatial distribution of malaria prevalence based on NMIS-2015 data. Clustering of malaria prevalence in certain areas further highlights the need for sustained malaria elimination interventions across affected regions in order to break the chain of transmission.},
}
@article {pmid39609363,
year = {2025},
author = {Xu, S and Akhatayeva, Z and Liu, J and Feng, X and Yu, Y and Badaoui, B and Esmailizadeh, A and Kantanen, J and Amills, M and Lenstra, JA and Johansson, AM and Coltman, DW and Liu, GE and Curik, I and Orozco-terWengel, P and Paiva, SR and Zinovieva, NA and Zhang, L and Yang, J and Liu, Z and Wang, Y and Yu, Y and Li, M},
title = {Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations.},
journal = {Science China. Life sciences},
volume = {68},
number = {4},
pages = {934-960},
pmid = {39609363},
issn = {1869-1889},
mesh = {Animals ; *Livestock/genetics ; *Genomics/methods ; *Breeding/methods ; *Ruminants/genetics ; *Genome ; Phenotype ; Multiomics ; },
abstract = {Ruminant livestock provide a rich source of products, such as meat, milk, and wool, and play a critical role in global food security and nutrition. Over the past few decades, genomic studies of ruminant livestock have provided valuable insights into their domestication and the genetic basis of economically important traits, facilitating the breeding of elite varieties. In this review, we summarize the main advancements for domestic ruminants in reference genome assemblies, population genomics, and the identification of functional genes or variants for phenotypic traits. These traits include meat and carcass quality, reproduction, milk production, feed efficiency, wool and cashmere yield, horn development, tail type, coat color, environmental adaptation, and disease resistance. Functional genomic research is entering a new era with the advancements of graphical pangenomics and telomere-to-telomere (T2T) gap-free genome assembly. These advancements promise to improve our understanding of domestication and the molecular mechanisms underlying economically important traits in ruminant livestock. Finally, we provide new perspectives and future directions for genomic research on ruminant genomes. We suggest how ever-increasing multiomics datasets will facilitate future studies and molecular breeding in livestock, including the potential to uncover novel genetic mechanisms underlying phenotypic traits, to enable more accurate genomic prediction models, and to accelerate genetic improvement programs.},
}
@article {pmid39609505,
year = {2024},
author = {Alvarez-Mamani, E and Buettner, F and Beltran-Castanon, CA and Ibanez, AJ},
title = {Exploratory analysis of metabolic changes using mass spectrometry data and graph embeddings.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {29570},
pmid = {39609505},
issn = {2045-2322},
support = {No. 174-2020-FONDECYT "Doctoral Programs in Peruvian Universities"//Consejo Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Tecnol&#xf3;gica (CONCYTEC), and Fondo Nacional de Desarrollo Cient&#xed;fico, Tecnol&#xf3;gico y de Innovaci&#xf3;n Tecnol&#xf3;gica (FONDECYT)/ ; "The Max Planck Partner Group" (Max Planck Institute for Chemical Ecology-Jena)//Max-Planck-Gesellschaft/ ; "The Max Planck Partner Group" (Max Planck Institute for Chemical Ecology-Jena)//Max-Planck-Gesellschaft/ ; N&#xba; PE501086715-2024- PROCIENCIA)//CONCYTEC-Prociencia convocatoria E041-2024-01/ ; },
mesh = {*Metabolomics/methods ; *Mass Spectrometry/methods ; *Algorithms ; *Data Mining/methods ; Humans ; Deep Learning ; Metabolic Networks and Pathways ; Metabolome ; },
abstract = {Mass spectrometry (MS)-based metabolomics analysis is a powerful tool, but it comes with its own set of challenges. The MS workflow involves multiple steps before its interpretation in what is denominate data mining. Data mining consists of a two-step process. First, the MS data is ordered, arranged, and presented for filtering before being analyzed. Second, the filtered and reduced data are analyzed using statistics to remove further variability. This holds true particularly for MS-based untargeted metabolomics studies, which focused on understanding fold changes in metabolic networks. Since the task of filtering and identifying changes from a large dataset is challenging, automated techniques for mining untargeted MS-based metabolomic data are needed. The traditional statistics-based approach tends to overfilter raw data, which may result in the removal of relevant data and lead to the identification of fewer metabolomic changes. This limitation of the traditional approach underscores the need for a new method. In this work, we present a novel deep learning approach using node embeddings (powered by GNNs), edge embeddings, and anomaly detection algorithm to analyze the data generated by mass spectrometry (MS)-based metabolomics called GEMNA (Graph Embedding-based Metabolomics Network Analysis), for example for an untargeted volatile study on Mentos candy, the data clusters produced by GEMNA were better than the ones used traditional tools, i.e., GEMNA has [Formula: see text], vs. the traditional approach has [Formula: see text].},
}
@article {pmid39611246,
year = {2025},
author = {Armstrong, EE and Li, C and Campana, MG and Ferrari, T and Kelley, JL and Petrov, DA and Solari, KA and Mooney, JA},
title = {A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14048},
pmid = {39611246},
issn = {1755-0998},
support = {R35 GM118165/GM/NIGMS NIH HHS/United States ; },
mesh = {*Polymorphism, Single Nucleotide ; *Genetics, Population/methods ; *Computational Biology/methods ; *Genotyping Techniques/methods ; },
abstract = {Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user-friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for a diploid species of conservation concern.},
}
@article {pmid39611775,
year = {2025},
author = {Andorf, CM and Ross-Ibarra, J and Seetharam, AS and Hufford, MB and Woodhouse, MR},
title = {A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {2},
pages = {},
pmid = {39611775},
issn = {2160-1836},
support = {5030-21000-072-00-D//US. Department of Agriculture, Agricultural Research Service/ ; //Corn Insects and Crop Genetics Research Unit in Ames, Iowa/ ; //Iowa State University/ ; //SCINet/ ; 0201-88888-003-000D//AI Center of Excellence of the USDA Agricultural Research Service/ ; CA-D-PLS-2066-H//USDA/ ; },
mesh = {*Zea mays/genetics ; *Genome, Plant ; *Genomics/methods ; Polymorphism, Single Nucleotide ; *Databases, Genetic ; Software ; Genotype ; Genetic Variation ; Molecular Sequence Annotation ; Linkage Disequilibrium ; },
abstract = {Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Genetics and Genomics Database has collaborated with maize researchers to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, completeness, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool, SNPversity 2.0, to filter, visualize, and download genotype sets based on genomic locations and accessions of interest, and added external datasets to demonstrate SNPversity 2.0's broad usage. MaizeGDB plans to host annual updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.},
}
@article {pmid39612036,
year = {2024},
author = {Ma, D and Huang, Q and Wang, Q and Xu, H and Yan, Y},
title = {Detection of spatiotemporal changes in eco-environmental quality based on RSEI and SG filtering and its driving force analysis: a case study in Sichuan Province, China.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {12},
pages = {1274},
pmid = {39612036},
issn = {1573-2959},
support = {ZR2020MD025//Natural Science Foundation of Shandong Province/ ; 42171435//National Natural Science Foundation of China/ ; },
mesh = {China ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; Forests ; Ecosystem ; Grassland ; Conservation of Natural Resources/methods ; },
abstract = {Landsat images were extracted using Google Earth Engine (GEE) platform and optimized by Savitzky-Golay (SG) filtering. The Remote Sensing Ecological Index (RSEI) method was used to analyze the eco-environmental quality in Sichuan Province in recent 20 years. In addition, Theil-Sen median method and Mann-Kendall (MK) test were used to test the change trend of eco-environmental quality. Furthermore, drivers were evaluated by partial correlation analysis, 2D scatter plots, and t tests. The results showed that (1) in the past 20 years, the eco-environmental quality of Sichuan Province was on the rise, and the eco-environmental quality in the western region was better than that in the eastern region. The eco-environmental quality was positively correlated with forest and grassland types, and negatively correlated with cultivated land and urban and rural construction land types. (2) The eco-environmental quality of Sichuan Province is linearly correlated with the digital elevation model, but poorly correlated with slope and slope direction. In the range of slope 0° ~ 9° and southeast direction, the eco-environmental quality is the worst. (3) The eco-environmental quality of Sichuan Province was most significantly affected by soil moisture and sunshine hours. The study can help us to understand and assess the health of ecosystems in Sichuan Province, provide a scientific basis for protecting and improving the environment, and guide the formulation and implementation of environmental protection policies.},
}
@article {pmid39615103,
year = {2025},
author = {Sha, J and Liu, X and Wang, H and Song, X and Bao, M and Yu, Q and Wen, G and Wei, M},
title = {Status and habitat suitability evaluation: A case study of the typical temperate seagrass beds in the Bohai Sea, China.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106873},
doi = {10.1016/j.marenvres.2024.106873},
pmid = {39615103},
issn = {1879-0291},
mesh = {China ; *Ecosystem ; *Environmental Monitoring/methods ; Conservation of Natural Resources ; Geographic Information Systems ; Oceans and Seas ; },
abstract = {Seagrass beds serve crucial ecological functions, yet they are facing a severe decline necessitating immediate conservation and restoration efforts. Current assessments of seagrass habitat suitability are insufficient, thus hindering the restoration effects. This study used a combination of field surveys and satellite remote sensing to conduct a three-year monitoring of typical temperate seagrass beds in the Caofeidian and Xingcheng areas of the Bohai Sea. The relationships between seagrass community factors and environmental factors were investigated using Spearman correlation analysis, BIOENV analysis, and redundancy analysis (RDA). Subsequently, the weights of each environmental factor were determined using the Analytic Hierarchy Process (AHP), leading to the development of the Habitat Suitability Index (HSI). Seagrass habitat suitability maps for Caofeidian and Xingcheng areas were then generated using Geographic Information System (GIS). The results indicate that both seagrass ecosystems degraded during the study period, which coincided with a decreasing trend in habitat suitability shown by the suitability maps. This study provides a methodology for seagrass bed habitat suitability assessment, thereby contributing to the conservation and restoration of these vital ecosystems.},
}
@article {pmid39616400,
year = {2024},
author = {Asaaga, FA and Shakeer, I and Sriram, A and Chhotaria, K and Dutta, S and Narayanaswamy, D and Amankwaa, G and Chanda, MM and Hoti, SL and Young, JC and Purse, BV},
title = {Ties that bind: understanding One Health networks and participation for zoonoses prevention and control in India.},
journal = {One health outlook},
volume = {6},
number = {1},
pages = {24},
pmid = {39616400},
issn = {2524-4655},
abstract = {BACKGROUND: Cross-sectoral collaborations as exemplified by the One Health approach, are widely endorsed as pragmatic avenues for addressing zoonotic diseases, but operationalisation remain limited in low-and-middle income countries (LMICs). Complexities and competing interests and agendas of key stakeholders and the underlying politico-administrative context can all shape outcomes of collaborative arrangements. Evidence is building that organised collaborations are complex political initiatives where different objectives; individual and institutional agendas need to be reconciled to incentivise collaborations.<br><br>METHODS: Drawing on a qualitative network analysis of published sources on 'One Health' stakeholders supplemented with 26 multi-scale (national-state-district level) key-informant interviews (including policymakers, disease managers and public health experts), this paper characterises the fragmented and complex characteristics of institutional networks involved in zoonoses prevention and control in India.<br><br>RESULTS: Our results highlight how the local socio-political and institutional contexts interact to modulate how and when collaborations occur (or not), the associated contingencies and stakeholder innovations in circumventing existing barriers (e.g. competing interests, distrust between actors, departmental bureaucracy) to cross-sector collaborations and zoonoses management. Aside from principal actors negotiating common ground in some instance, they also capitalised on political/institutional pressure to subtly 'manipulate' their subordinates as a way of fostering collaboration, especially in instances when the institutional and political stakes are high.<br><br>CONCLUSION: Altogether our findings suggest that cross-sectoral collaborations are by-product of political and institutional tinkering as long as individual actors and institutional interests converge and these dynamics must be embraced to embed meaningful and sustainable collaborations in local socio-political and administrative contexts.},
}
@article {pmid39618809,
year = {2024},
author = {Boyes, D and Young, MR and , and , and , and , and , and , and , },
title = {The genome sequence of the Straw Grass-veneer moth, Agriphila straminella (Denis &amp; Schiffermüller), 1775.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {433},
pmid = {39618809},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Straw Grass-veneer moth, Agriphila straminella (Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a length of 511.50 megabases. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,087 protein-coding genes.},
}
@article {pmid39621775,
year = {2024},
author = {Osiecka, AN and Bryndza, P and Briefer, EF and Wojczulanis-Jakubas, K},
title = {Long distance calls: Negligible information loss of little auk social vocalisations due to high frequency propagation losses.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1011961},
pmid = {39621775},
issn = {1553-7358},
mesh = {Animals ; *Vocalization, Animal/physiology ; Sound Spectrography/methods ; Computational Biology ; Acoustics ; Social Behavior ; },
abstract = {How well does the information contained in vocal signals travel through the environment? To assess the efficiency of information transfer in little auk (Alle alle, an Arctic seabird) calls over distance, we selected two of the social call types with the highest potential for individuality coding. Using available recordings of known individuals, we calculated the apparent source levels, with apparent maximum peak sound pressure level (ASPL) of 63 dB re 20 μPa at 1 m for both call types. Further, we created a sound attenuation model using meteorological data collected in the vicinity of the little auk colony in Hornsund, Spitsbergen. Using this model, we modelled the calls to reflect higher frequency filtering and sound level loss occurring during spherical spreading in perfect local conditions, down to the putative hearing threshold of the species, calculated to equal ASPL of signals "propagated" to roughly one kilometre. Those modelled calls were then used in a permuted discriminant function analysis, support vector machine models, and linear models of Beecher's information statistic, to investigate whether transmission loss will affect the retention of individual information of the signal. Calls could be correctly classified to individuals above chance level independently of the distance, down to and over the putative physiological hearing threshold. Interestingly, the information capacity of the signal did not decrease with its filtering and attenuation. While this study touches on signal properties purely and cannot provide evidence of the actual use by the animals, it shows that little auk signals can theoretically travel long distances with negligible information loss, and supports the hypothesis that vocalisations could facilitate long-distance communication in the species.},
}
@article {pmid39621910,
year = {2024},
author = {Alfaro-Sánchez, R and Richardson, AD and Smith, SL and Johnstone, JF and Turetsky, MR and Cumming, SG and Le Moine, JM and Baltzer, JL},
title = {Permafrost instability negates the positive impact of warming temperatures on boreal radial growth.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {50},
pages = {e2411721121},
pmid = {39621910},
issn = {1091-6490},
support = {15879//Aurora Research Institute (ARI)/ ; permafrost monitoring in the Mackenzie River Valley//Canadian Government | Natural Resources Canada (NRCan)/ ; MZ2021//Mar&#xed;a Zambrano program/ ; Small Research 2021 - SR21/1291//British Ecological Society (BES)/ ; Environmental Studies Research Fund and Cumulative Impacts Monitoring Program (Project 170)//Environment and Natural Resources, Northwest Territories (ENR, NWT)/ ; Discovery Grant support//Canadian Government | NSERC | RES'EAU-WaterNET/ ; Bonanza Creek LTER DEB-2224776//National Science Foundation (NSF)/ ; },
mesh = {*Permafrost ; *Trees/growth &amp; development ; Temperature ; Taiga ; Global Warming ; Climate Change ; Forests ; },
abstract = {Climate warming can alleviate temperature and nutrient constraints on tree growth in boreal regions, potentially enhancing boreal productivity. However, in permafrost environments, warming also disrupts the physical foundation on which trees grow, leading to leaning trees or "drunken" forests. Tree leaning might reduce radial growth, undermining potential benefits of warming. Here, we found widespread radial growth reductions in southern latitude boreal forests since the 1980s. At mid latitudes, radial growth increased from ~1980 to ~2000 but showed recent signs of decline afterward. Increased growth was evident since the 1980 s at higher latitudes, where radial growth appears to be temperature limited. However, recent changes in permafrost stability, and the associated increased frequency of tree leaning events, emerged as a significant stressor, leading to reduced radial growth in boreal trees at the highest latitudes, where permafrost is extensive. We showed that trees growing in unstable permafrost sites allocated more nonstructural carbohydrate reserves to offset leaning which compromised radial growth and potential carbon uptake benefits of warming. This higher allocation of resources in drunken trees is needed to build the high-density reaction wood, rich in lignin, that is required to maintain a vertical position. With continued climate warming, we anticipate widespread reductions in radial growth in boreal forests, leading to lower carbon sequestration. These findings enhance our understanding of how climate warming and indirect effects, such as ground instability caused by warming permafrost, will affect boreal forest productivity in the future.},
}
@article {pmid39622351,
year = {2025},
author = {Nishimura, H and Nawa, N and Ogawa, T and Fushimi, K and Schwartz, BS and Fujiwara, T},
title = {Projections of future heat-related emergency hospitalizations for asthma under climate and demographic change scenarios: A Japanese nationwide time-series analysis.},
journal = {Environmental research},
volume = {266},
number = {},
pages = {120498},
doi = {10.1016/j.envres.2024.120498},
pmid = {39622351},
issn = {1096-0953},
mesh = {Japan/epidemiology ; *Asthma/epidemiology/etiology ; Humans ; *Hospitalization/statistics &amp; numerical data ; *Climate Change ; Child ; *Hot Temperature/adverse effects ; Infant ; Child, Preschool ; Adolescent ; Infant, Newborn ; Adult ; Young Adult ; Middle Aged ; Female ; Male ; Aged ; Forecasting ; East Asian People ; },
abstract = {BACKGROUND: There is growing concern about climate impacts on human health. However, empirical evidence is lacking regarding future projections of heat-related asthma hospitalizations. This study aimed to project excess emergency hospitalizations for heat-related asthma exacerbation in Japan.<br><br>METHODS: Using Japanese nationwide administrative data from 2011 to 2019, we conducted an ecological time-series quasi-Poisson regression analysis to estimate the heat-related relative risk of emergency hospitalization for asthma over a lag of 0-3 days during the warm season (June to September). Heat exposure was defined as the region-specific daily mean temperature exceeding the locally defined minimum morbidity temperature percentile (MMP). Heat-related excess hospitalizations for asthma were projected under future climate and demographic change scenarios based on Shared Socioeconomic Pathways (SSPs).<br><br>RESULTS: We identified 75,829 emergency hospitalizations for asthma. The heat-related relative risk of hospitalization was 1.22 (95% confidence interval (CI): 1.12-1.33) at the 99th percentile temperature relative to the MMP, with the highest estimates for cases aged 0-14 years. Heat-related excess hospitalizations were projected to increase by 6.78 (95%CI: 5.84-7.67) times in 2091-2099 versus 2011-2019 along SSP5-8.5 when constant population structure was assumed. The increasing trend persisted even when the future population decline was considered (4.19 (95%CI: 3.53-4.85) times in 2091-2099 versus 2011-2019 under SSP5-8.5).<br><br>CONCLUSION: Future heat-related impacts on asthma exacerbation are expected to increase in Japan toward the end of this century, even when the future demographic change is considered. Our projections will contribute to resilient health systems adapting to ongoing climate change.},
}
@article {pmid39622813,
year = {2024},
author = {Monadjem, A and Montauban, C and Webala, PW and Laverty, TM and Bakwo-Fils, EM and Torrent, L and Tanshi, I and Kane, A and Rutrough, AL and Waldien, DL and Taylor, PJ},
title = {African bat database: curated data of occurrences, distributions and conservation metrics for sub-Saharan bats.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1309},
pmid = {39622813},
issn = {2052-4463},
mesh = {*Chiroptera/classification/physiology ; Animals ; Africa South of the Sahara ; *Conservation of Natural Resources ; *Databases, Factual ; Ecosystem ; Animal Distribution ; },
abstract = {Accurate knowledge of species distributions is foundational for effective conservation efforts. Bats are a diverse group of mammals, with important roles in ecosystem functioning. However, our understanding of bats and their ecological importance is hindered by poorly defined ranges, mostly as a result of under-recording. This issue is exacerbated in Africa by the ongoing rapid discovery of new species, both de novo and splits of existing species, and by inaccessibility to museum specimens that are mostly hosted outside of the continent. Here we present the African bat database - a curated set of 17,285 unique locality records of all 266 species of bats from sub-Saharan Africa, vouched for by specimens and/or genetic sequencing, and aligned with current taxonomy. Based on these records, we also present Maxent-based distribution models and calculate the IUCN Red List metrics for Extent of Occurrence and Area of Occupancy. This database and online visualization tool provide an important open-source resource and is expected to significantly advance studies in ecology, and aid in bat conservation.},
}
@article {pmid39622961,
year = {2024},
author = {Jeong, D and Hyun, JY and Marchenkova, T and Matiukhina, D and Cho, S and Lee, J and Kim, DY and Li, Y and Darman, Y and Min, MS and Bardyuk, V and Lee, Y and Pandey, P and Lee, H},
title = {Genetic insights and conservation strategies for Amur tigers in Southwest Primorye Russia.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {29985},
pmid = {39622961},
issn = {2045-2322},
support = {550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; },
mesh = {Animals ; *Tigers/genetics ; *Conservation of Natural Resources ; *Genetic Variation ; *Microsatellite Repeats/genetics ; Male ; Female ; *DNA, Mitochondrial/genetics ; Russia ; Genetics, Population ; Population Density ; },
abstract = {Southwest Primorye hosts approximately 9% of the remaining wild Amur tiger population and represents hope for the revival of tigers in Northeast China and the Korean peninsula. Decades of conservation efforts have led to a significant increase in population size, from less than 10 individuals surviving in the region in 1996 to multiple folds today. However, while the population size has recovered since the mid-1900s, the effects of genetic depletion on evolutionary potential are not easily reversed. In this study, a non-invasive genetic analysis of the Amur tiger subpopulation in Southwest Primorye was conducted using microsatellite loci and mitochondrial genes to estimate genetic diversity, relatedness, and determine the impact of historical demographic dynamics. A total of 32 individuals (16 males, 15 females, and 1 unidentified sex) were identified, and signs of bottlenecks were detected, reflecting past demographic events. Low genetic variation observed in mitochondrial DNA also revealed genetic depletion within the population. Most individuals were found to be closely related to each other, raising concerns about inbreeding given the small population size and somewhat isolated environment from the main population in Sikhote-Alin. These findings emphasize the urgent need to establish ecological corridors to neighboring areas to restore genetic diversity and ensure the conservation of the Amur tiger population in Southwest Primorye.},
}
@article {pmid39624726,
year = {2024},
author = {Tian, T and Zhang, X and Zhang, F and Huang, X and Li, M and Quan, Z and Wang, W and Lei, J and Wang, Y and Liu, Y and Wang, JH},
title = {Harnessing AI for advancing pathogenic microbiology: a bibliometric and topic modeling approach.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1510139},
pmid = {39624726},
issn = {1664-302X},
abstract = {INTRODUCTION: The integration of artificial intelligence (AI) in pathogenic microbiology has accelerated research and innovation. This study aims to explore the evolution and trends of AI applications in this domain, providing insights into how AI is transforming research and practice in pathogenic microbiology.<br><br>METHODS: We employed bibliometric analysis and topic modeling to examine 27,420 publications from the Web of Science Core Collection, covering the period from 2010 to 2024. These methods enabled us to identify key trends, research areas, and the geographical distribution of research efforts.<br><br>RESULTS: Since 2016, there has been an exponential increase in AI-related publications, with significant contributions from China and the USA. Our analysis identified eight major AI application areas: pathogen detection, antibiotic resistance prediction, transmission modeling, genomic analysis, therapeutic optimization, ecological profiling, vaccine development, and data management systems. Notably, we found significant lexical overlaps between these areas, especially between drug resistance and vaccine development, suggesting an interconnected research landscape.<br><br>DISCUSSION: AI is increasingly moving from laboratory research to clinical applications, enhancing hospital operations and public health strategies. It plays a vital role in optimizing pathogen detection, improving diagnostic speed, treatment efficacy, and disease control, particularly through advancements in rapid antibiotic susceptibility testing and COVID-19 vaccine development. This study highlights the current status, progress, and challenges of AI in pathogenic microbiology, guiding future research directions, resource allocation, and policy-making.},
}
@article {pmid39627652,
year = {2025},
author = {Peltier, DMP and Carbone, MS and Ogle, K and Koch, GW and Richardson, AD},
title = {Decades-old carbon reserves are widespread among tree species, constrained only by sapwood longevity.},
journal = {The New phytologist},
volume = {245},
number = {4},
pages = {1468-1480},
doi = {10.1111/nph.20310},
pmid = {39627652},
issn = {1469-8137},
support = {149//Save the Redwoods League/ ; 1936205//Division of Integrative Organismal Systems/ ; 2053337//Division of Integrative Organismal Systems/ ; 1832218//Division of Environmental Biology/ ; 2213599//Division of Environmental Biology/ ; },
mesh = {*Carbon/metabolism ; *Trees/physiology/metabolism ; *Wood/physiology ; Species Specificity ; *Longevity ; Time Factors ; Droughts ; Carbon Isotopes ; Photosynthesis ; Plant Stems/physiology ; Fires ; Models, Biological ; },
abstract = {Carbon reserves are distributed throughout plant cells allowing past photosynthesis to fuel current metabolism. In trees, comparing the radiocarbon (Δ[14]C) of reserves to the atmospheric bomb spike can trace reserve ages. We synthesized Δ[14]C observations of stem reserves in nine tree species, fitting a new process model of reserve building. We asked how the distribution, mixing, and turnover of reserves vary across trees and species. We also explored how stress (drought and aridity) and disturbance (fire and bark beetles) perturb reserves. Given sufficient sapwood, young (< 1 yr) and old (20-60+ yr) reserves were simultaneously present in single trees, including 'prebomb' reserves in two conifers. The process model suggested that most reserves are deeply mixed (30.2 ± 21.7 rings) and then respired (2.7 ± 3.5-yr turnover time). Disturbance strongly increased Δ[14]C mean ages of reserves (+15-35 yr), while drought and aridity effects on mixing and turnover were species-dependent. Fire recovery in Sequoia sempervirens also appears to involve previously unobserved outward mixing of old reserves. Deep mixing and rapid turnover indicate most photosynthate is rapidly metabolized. Yet ecological variation in reserve ages is enormous, perhaps driven by stress and disturbance. Across species, maximum reserve ages appear primarily constrained by sapwood longevity, and thus old reserves are probably widespread.},
}
@article {pmid39627996,
year = {2025},
author = {Rodman, KC and Bradford, JB and Formanack, AM and Fulé, PZ and Huffman, DW and Kolb, TE and Miller-Ter Kuile, AT and Normandin, DP and Ogle, K and Pedersen, RJ and Schlaepfer, DR and Stoddard, MT and Waltz, AEM},
title = {Restoration treatments enhance tree growth and alter climatic constraints during extreme drought.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {35},
number = {1},
pages = {e3072},
pmid = {39627996},
issn = {1939-5582},
support = {22-DG-11030000-012//U.S. Forest Service/ ; },
mesh = {*Droughts ; *Pinus ponderosa/growth &amp; development/physiology ; *Trees/growth &amp; development ; *Climate Change ; *Forestry/methods ; Forests ; *Pinus/growth &amp; development ; *Environmental Restoration and Remediation/methods ; },
abstract = {The frequency and severity of drought events are predicted to increase due to anthropogenic climate change, with cascading effects across forested ecosystems. Management activities such as forest thinning and prescribed burning, which are often intended to mitigate fire hazard and restore ecosystem processes, may also help promote tree resistance to drought. However, it is unclear whether these treatments remain effective during the most severe drought conditions or whether their impacts differ across environmental gradients. We used tree-ring data from a system of replicated, long-term (>20 years) experiments in the southwestern United States to evaluate the effects of forest restoration treatments (i.e., evidence-based thinning and burning) on annual growth rates (i.e., basal area increment; BAI) of ponderosa pine (Pinus ponderosa), a broadly distributed and heavily managed species in western North America. The study sites were established at the onset of the most extreme drought event in at least 1200 years and span much of the climatic niche of Rocky Mountain ponderosa pine. Across sites, tree-level BAI increased due to treatment, where trees in treated units grew 133.1% faster than trees in paired, untreated units. Likewise, trees in treated units grew an average of 85.6% faster than their pre-treatment baseline levels (1985 to ca. 2000), despite warm, dry conditions in the post-treatment period (ca. 2000-2018). Variation in the local competitive environment promoted variation in BAI, and larger trees were the fastest-growing individuals, irrespective of treatment. Tree thinning and prescribed fire altered the climatic constraints on growth, decreasing the effects of belowground moisture availability and increasing the effects of atmospheric evaporative demand over multi-year timescales. Our results illustrate that restoration treatments can enhance tree-level growth across sites spanning ponderosa pine's climatic niche, even during recent, extreme drought events. However, shifting climatic constraints, combined with predicted increases in evaporative demand in the southwestern United States, suggest that the beneficial effects of such treatments on tree growth may wane over the upcoming decades.},
}
@article {pmid39631859,
year = {2025},
author = {Suzuki, T and Nagasu, H and Ebara, T and Kagiyama, N and Kishi, T and Yano, Y and Kario, K and Nishiyama, A and Arima, H and Kawai, F and Shibata, S and Node, K and Mizuno, A},
title = {Unraveling the Implications of Digit Bias in Digital Health - A Literature Review.},
journal = {Internal medicine (Tokyo, Japan)},
volume = {64},
number = {14},
pages = {2090-2099},
pmid = {39631859},
issn = {1349-7235},
mesh = {Humans ; Bias ; *Digital Technology ; Digital Health ; },
abstract = {Digital health, which encompasses digital medicine and therapy, integrates advanced technologies across healthcare. Central to this transformation is 'digitization,' which converts continuous analog data into a discrete digital form. However, this process is challenging. First, digitization inherently has the potential to introduce information loss, thereby diminishing the richness and complexity of data. Second, "digit bias," a cognitive distortion, emerges in the interpretation phase, where individuals' perceptions of and reactions to digital data are intrinsically skewed. There exist two major cognitive biases during digitization process: "digit preferences," where healthcare providers prioritize specific numbers, and "left digit bias" where continuous variables are disproportionately estimated by focusing on the leftmost digit. Although information loss and cognitive biases can cause significant distortions in healthcare, the effects of this "digitization" process have not been adequately quantified, and the accumulation of further evidence in this field is anticipated.},
}
@article {pmid39635120,
year = {2024},
author = {Qiu, Y and He, Z and Yu, X and Jia, G and Wang, Y},
title = {Analysis of factors influencing groundwater drought in the Loess zone of China.},
journal = {iScience},
volume = {27},
number = {10},
pages = {110929},
pmid = {39635120},
issn = {2589-0042},
abstract = {Understanding the characteristics and factors influencing groundwater resources is important for regional water resources management. The Gravity Recovery and Climate Experiment (GRACE)-based groundwater conditions were used to analyze the spatiotemporal characteristics of and the factors influencing groundwater storage (GWS) distribution in the Loess zone of the Yellow River Basin. The results revealed that the spatiotemporal distribution of GWS anomalies in the Loess zone of China was best explained by the first three components of the empirical orthogonal function (EOF), representing 85.6% of the total variance. The normalized difference vegetation index (NDVI) was significantly correlated with groundwater drought (p < 0.05). In addition, NDVI and evapotranspiration (ET) were the dominant factors influencing groundwater drought. NDVI was the dominant influencing factor in 67% and 80% of the total study area between 2002-2014 and 2015-2021, respectively. This study provides important guidance for a future ecological restoration plan in the Loess zone.},
}
@article {pmid39636475,
year = {2024},
author = {Ganie, PA and Posti, R and Bharti, VS and Sehgal, VK and Sarma, D and Pandey, PK},
title = {Erosion landscape characterization in the Himalayan basin: insights from geospatial data and multi-criteria evaluation.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {1},
pages = {29},
pmid = {39636475},
issn = {1573-2959},
mesh = {India ; *Environmental Monitoring ; *Rivers/chemistry ; *Geographic Information Systems ; Soil Erosion ; Conservation of Natural Resources ; Hydrology ; },
abstract = {In regions characterized by mountainous landscapes, such as watersheds with high elevations, steep inclines, and rugged terrains, there exists an inherent susceptibility to water-induced soil erosion. This susceptibility underscores the importance of identifying areas prone to erosion to mitigate the loss of valuable natural resources and ensure their preservation over time. In response to this need, the current research employed a combination of four multi-criteria decision-making (MCDM) models, namely TOPSIS-AHP, VIKOR-AHP, ARAS-AHP, and CODAS-AHP, for the identification of areas susceptible to soil erosion within the Himalayan River basin of Nandakini, Uttarakhand, India. This identification was facilitated through the utilization of remote sensing and geospatial technologies. The study considered a total of 19 prioritization parameters that included morphological, topo-hydrological, climatic, and environmental factors specific to the Nandakini catchment for the purpose of prioritization modeling. The adoption of morphometric parameters in depicting the geological structures and hydrodynamic behavior of the river basin proves to be a crucial approach in locales where hydrological data may be scarce. The investigation delineated twenty watersheds within the catchment by employing SRTM DEM, SOI toposheets, and Geographic Information Systems (GIS), calculating the catchment's total area to be approximately 540.98 km[2]. The analysis determined that the catchment is classified as a 6th-order catchment, exhibiting mainly a sub-dendritic to dendritic drainage pattern. It was identified that the catchment is vulnerable to flooding and subsequent gully erosion due to the slow movement of surface runoff. Furthermore, the catchment's elongated shape and the compactness coefficient suggest a delayed peak runoff. The drainage texture ranged from very coarse to coarse, and the relief characteristics highlighted that the watersheds within the catchment possess a high relief ratio, thereby increasing their erosion vulnerability. Topo-hydrological indices revealed significant topographic variability and spatial differences in water availability and erosion potential across the basin. The efficacy of the MCDM models was evaluated through the Spearman's correlation coefficient test, alongside indices of intensity and percentage of change, to validate the findings. The ARAS-AHP and CODAS-AHP models were found to exhibit superior efficiency and higher accuracy relative to the other methods assessed. The insights gained from the ARAS-AHP and CODAS-AHP models are instrumental in the development of strategies for sustainable catchment management plans and inform decision-making processes regarding water resources management within the catchment.},
}
@article {pmid39638881,
year = {2024},
author = {Vojteková, J and Janizadeh, S and Vojtek, M and Tirpáková, A and Ruttkay, M and Petrovič, F},
title = {Prediction of potential occurrence of historical objects with defensive function in Slovakia using machine learning approach.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {30350},
pmid = {39638881},
issn = {2045-2322},
support = {033UKF-4/2023//Kult&#xfa;rna a Edukacn&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR/ ; },
abstract = {In this article, we aim at the prediction of possible locations of already defunct historical objects with a defensive function (HODFs) in Slovakia, which have not been found and documented so far, using three machine learning methods. Specifically, we used the support vector machine, k-nearest neighbors, and random forest algorithms, which were trained based on the following five factors influencing the possible occurrence of HODFs: elevation, distance from a river, distance from a settlement, lithological rock type, and type of representative geoecosystems. Training and testing datasets were based on a database of already documented 605 HODFs, which were divided into 70% of training samples and 30% of testing samples. All of the three models reached the AUC-ROC value over 0.74 based on the testing dataset. The best performance was recorded by the random forest predictive model with the AUC-ROC value equal to 0.79. The results of the random forest model were also validated with the recently documented HODFs via the archeological research.},
}
@article {pmid39642168,
year = {2024},
author = {Champion, C and Momal, R and Le Chatelier, E and Sola, M and Mariadassou, M and Berland, M},
title = {OneNet-One network to rule them all: Consensus network inference from microbiome data.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012627},
pmid = {39642168},
issn = {1553-7358},
mesh = {*Computational Biology/methods ; Humans ; *Microbiota/physiology ; *Algorithms ; *Gastrointestinal Microbiome/physiology ; Microbial Interactions/physiology ; },
abstract = {Modeling microbial interactions as sparse and reproducible networks is a major challenge in microbial ecology. Direct interactions between the microbial species of a biome can help to understand the mechanisms through which microbial communities influence the system. Most state-of-the art methods reconstruct networks from abundance data using Gaussian Graphical Models, for which several statistically grounded and computationnally efficient inference approaches are available. However, the multiplicity of existing methods, when applied to the same dataset, generates very different networks. In this article, we present OneNet, a consensus network inference method that combines seven methods based on stability selection. This resampling procedure is used to tune a regularization parameter by computing how often edges are selected in the networks. We modified the stability selection framework to use edge selection frequencies directly and combine them in the inferred network to ensure that only reproducible edges are included in the consensus. We demonstrated on synthetic data that our method generally led to slightly sparser networks while achieving much higher precision than any single method. We further applied the method to gut microbiome data from liver-cirrothic patients and demonstrated that the resulting network exhibited a microbial guild that was meaningful in terms of human health.},
}
@article {pmid39642189,
year = {2024},
author = {Graham, AL and Regoes, RR},
title = {Dose-dependent interaction of parasites with tiers of host defense predicts "wormholes" that prolong infection at intermediate inoculum sizes.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012652},
pmid = {39642189},
issn = {1553-7358},
mesh = {*Host-Parasite Interactions/immunology ; Animals ; Computational Biology ; Parasites/physiology/immunology ; Immunity, Innate ; Models, Biological ; },
abstract = {Immune responses are induced by parasite exposure and can in turn reduce parasite burden. Despite such apparently simple rules of engagement, key drivers of within-host dynamics, including dose-dependence of defense and infection duration, have proven difficult to predict. Here, we model how varied inoculating doses interact with multi-tiered host defenses at a site of inoculation, by confronting barrier, innate, and adaptive tiers with replicating and non-replicating parasites across multiple orders of magnitude of dose. We find that, in general, intermediate parasite doses generate infections of longest duration because they are sufficient in number to breach barrier defenses, but insufficient to strongly induce subsequent tiers of defense. These doses reveal "wormholes" in defense from which parasites might profit: Deviation from the hypothesis of independent action, which postulates that each parasite has an independent probability of establishing infection, may therefore be widespread. Interestingly, our model predicts local maxima of duration at two doses-one for each tier transition. While some empirical evidence is consistent with nonlinear dose-dependencies, testing the predicted dynamics will require finer-scale dose variation than experiments usually incorporate. Our results help explain varied infection establishment and duration among differentially-exposed hosts and elucidate evolutionary pressures that shape both virulence and defense.},
}
@article {pmid39642364,
year = {2024},
author = {Lee, TY and Chen, CH and Chen, IM and Chen, HC and Liu, CM and Wu, SI and Hsiao, CK and Kuo, PH},
title = {Dynamic Bidirectional Associations Between Global Positioning System Mobility and Ecological Momentary Assessment of Mood Symptoms in Mood Disorders: Prospective Cohort Study.},
journal = {Journal of medical Internet research},
volume = {26},
number = {},
pages = {e55635},
pmid = {39642364},
issn = {1438-8871},
mesh = {Humans ; *Geographic Information Systems ; *Ecological Momentary Assessment ; Prospective Studies ; Male ; Adult ; Female ; Middle Aged ; *Mood Disorders/psychology ; Smartphone/statistics &amp; numerical data ; Affect ; Mobile Applications ; },
abstract = {BACKGROUND: Although significant research has explored the digital phenotype in mood disorders, the time-lagged and bidirectional relationship between mood and global positioning system (GPS) mobility remains relatively unexplored. Leveraging the widespread use of smartphones, we examined correlations between mood and behavioral changes, which could inform future scalable interventions and personalized mental health monitoring.<br><br>OBJECTIVE: This study aims to investigate the bidirectional time lag relationships between passive GPS data and active ecological momentary assessment (EMA) data collected via smartphone app technology.<br><br>METHODS: Between March 2020 and May 2022, we recruited 45 participants (mean age 42.3 years, SD 12.1 years) who were followed up for 6 months: 35 individuals diagnosed with mood disorders referred by psychiatrists and 10 healthy control participants. This resulted in a total of 5248 person-days of data. Over 6 months, we collected 2 types of smartphone data: passive data on movement patterns with nearly 100,000 GPS data points per individual and active data through EMA capturing daily mood levels, including fatigue, irritability, depressed, and manic mood. Our study is limited to Android users due to operating system constraints.<br><br>RESULTS: Our findings revealed a significant negative correlation between normalized entropy (r=-0.353; P=.04) and weekly depressed mood as well as between location variance (r=-0.364; P=.03) and depressed mood. In participants with mood disorders, we observed bidirectional time-lagged associations. Specifically, changes in homestay were positively associated with fatigue (&#x3b2;=0.256; P=.03), depressed mood (&#x3b2;=0.235; P=.01), and irritability (&#x3b2;=0.149; P=.03). A decrease in location variance was significantly associated with higher depressed mood the following day (&#x3b2;=-0.015; P=.009). Conversely, an increase in depressed mood was significantly associated with reduced location variance the next day (&#x3b2;=-0.869; P<.001). These findings suggest a dynamic interplay between mood symptoms and mobility patterns.<br><br>CONCLUSIONS: This study demonstrates the potential of utilizing active EMA data to assess mood levels and passive GPS data to analyze mobility behaviors, with implications for managing disease progression in patients. Monitoring location variance and homestay can provide valuable insights into this process. The daily use of smartphones has proven to be a convenient method for monitoring patients' conditions. Interventions should prioritize promoting physical movement while discouraging prolonged periods of staying at home.},
}
@article {pmid39642727,
year = {2025},
author = {Mendrik, F and Hackney, CR and Cumming, VM and Waller, C and Hak, D and Dorrell, R and Hung, NN and Parsons, DR},
title = {The transport and vertical distribution of microplastics in the Mekong River, SE Asia.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136762},
doi = {10.1016/j.jhazmat.2024.136762},
pmid = {39642727},
issn = {1873-3336},
abstract = {Rivers are primary vectors of plastic debris to oceans, but sources, transport mechanisms, and fate of fluvial microplastics (<5 mm) remain poorly understood, impeding accurate predictions of microplastic flux, ecological risk and socio-economic impacts. We report on microplastic concentrations, characteristics and dynamics in the Mekong River, one of the world's largest and polluting rivers, in Cambodia and Vietnam. Sampling throughout the water column at multiple localities detected an average of 24 microplastics m[-3] (0.073 mg l[-1]). Concentrations increased downstream from rural Kampi, Cambodia (344 km from river mouth; 2 microplastics m[-3,] 0.006 mg l[-1]), to Can Tho, Vietnam (83 km from river mouth; 64 microplastics m[-3], 0.182 mg l[-1]) with most microplastics being fibres (53 %), followed by fragments (44 %) and the most common polymer being polyethylene terephthalate (PET) or polyester. Pathways of microplastic pollution are expected to be from urban wastewater highlighting the need for improved wastewater treatment in this region. On average, 86 % of microplastics are transported within the water column and consequently we identified an optimum sampling depth capturing a representative flux value, highlighting that sampling only the water surface substantially biases microplastic concentration predictions. Additionally, microplastic abundance does not linearly follow discharge changes during annual monsoonal floods or mirror siliciclastic sediment transport, as microplastic concentrations decrease rapidly during higher monsoon flows. The findings reveal complex microplastic transport in large rivers and call for improved sampling methods and predictive models to better assess environmental risk and guide policy.},
}
@article {pmid39643871,
year = {2024},
author = {Zhang, W and Jin, Z and Huang, R and Huang, W and Li, L and He, Y and Zhou, J and Tian, C and Xiao, L and Li, P and Quan, M and Zhang, D and Du, Q},
title = {Multi-omics analysis reveals genetic architecture and local adaptation of coumarins metabolites in Populus.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1170},
pmid = {39643871},
issn = {1471-2229},
support = {No. 2021ZD0008//Major Science and Technology project of Inner Mongolia Autonomous Region/ ; No. 2021ZD0008//Major Science and Technology project of Inner Mongolia Autonomous Region/ ; No. 6212021//Project of the Natural Science Foundation of Beijing Municipality/ ; QNTD202305//Fundamental Research Funds for Central Universities of the Central South University/ ; },
mesh = {*Populus/genetics/metabolism ; *Coumarins/metabolism ; *Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Adaptation, Physiological/genetics ; Gene Expression Regulation, Plant ; Genes, Plant ; Multiomics ; },
abstract = {BACKGROUND: Accumulation of coumarins plays key roles in response to immune and abiotic stress in plants, but the genetic adaptation basis of controlling coumarins in perennial woody plants remain unclear.<br><br>RESULTS: We detected 792 SNPs within 334 genes that were significantly associated with the phenotypic variations of 15 single-metabolic traits and multiple comprehensive index, such as principal components (PCs) of coumarins metabolites. Expression quantitative trait locus mapping uncovered that 337 eQTLs associated with the expression levels of 132 associated genes. Selective sweep revealed 55 candidate genes have potential selective signature among three geographical populations, highlighting that the coumarins biosynthesis have been encountered forceful local adaptation. Furthermore, we constructed a genetic network of seven candidate genes that coordinately regulate coumarins biosynthesis, revealing the multiple regulatory patterns affecting coumarins accumulation in Populus tomentosa. Validation of candidate gene variations in a drought-tolerated population and DUF538 heterologous transformation experiments verified the function of candidate genes and their roles in adapting to the different geographical conditions in poplar.<br><br>CONCLUSIONS: Our study uncovered the genetic regulation of the coumarins metabolic biosynthesis of Populus, and offered potential clues for drought-tolerance evaluation and regional improvement in woody plants.},
}
@article {pmid39644634,
year = {2025},
author = {Xie, Y and Guo, J and Fan, Q and Huang, S and Qi, W and Cao, X and Peng, J and Chen, Y and Chen, M},
title = {High-density sampling reveals the occurrence, levels and transport flux of 15 polycyclic aromatic hydrocarbons derivatives (PAHs-d) along the Yangtze River.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {177907},
doi = {10.1016/j.scitotenv.2024.177907},
pmid = {39644634},
issn = {1879-1026},
abstract = {Polycyclic aromatic hydrocarbons derivatives (PAHs-d) have higher toxicity levels compared to its parent polycyclic aromatic hydrocarbons (PPAHs). Their partitioning in different media and large-scale transport patterns in rivers remain largely unknown. This study investigated the occurrence of 15 PAHs-d and 19 PPAHs in water and suspended particulate matter (SPM) of the Yangtze River between 2019 and 2020. The range of Σ15PAHs-d concentrations was 20.54 to 2010.03 ng·L[-1] in water and 0.62 to 29.80 μg·g[-1] in SPM. The primary PAHs-d components were 2,6-dimethylnaphthalene, 2-methylnaphthalene, and anthraquinone. The range of Σ19PPAHs concentrations in water and SPM was 34.89 to 739.53 ng·L[-1] and 0.37 to 204.62 μg·g[-1], respectively. And low-ring PAHs-d and PPAHs were more prevalent in water than SPM. Partitioning behaviors indicated that PAHs-d and PPAHs were more readily partitioned into water and SPM during normal and dry periods, respectively. The concentrations of PAHs-d saw significant changes in their spatial distribution, which rose in water and reduced in SPM in downstream of the Three Gorges Dam. This is due to the dam's blocking effect on sediment transport. Positive matrix factorization source analysis revealed biomass combustion upstream and vehicle emissions downstream as primary sources, shaped by the evolving energy consumption patterns of urban areas situated around the Yangtze River. The annual fluxes of PAHs-d in water and SPM of the Yangtze River were 90.40 t·yr[-1] and 11.95 t·yr[-1], representing 88.3 % and 11.7 % of the overall PAHs-d fluxes, respectively. The total fluxes of PAHs-d and PPAHs in water and SPM tended to increase spatially along the river, with growth rates exceeding 76 and 24 times, respectively. Interception within the Three Gorges Reservoir area has resulted in the differences in the concentration and transport distribution of PAHs-d and PPAHs upstream and downstream, which play important roles in reducing PAHs-d and PPAHs entry into the sea. Future studies on PAHs-d in Yangtze River basin tributaries and estuaries are essential.},
}
@article {pmid39647412,
year = {2024},
author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD},
title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.},
journal = {Environment international},
volume = {194},
number = {},
pages = {109155},
doi = {10.1016/j.envint.2024.109155},
pmid = {39647412},
issn = {1873-6750},
mesh = {*Bacteriophages/genetics ; *Particulate Matter ; China ; *Bacteria/genetics/drug effects ; *Seasons ; Humans ; Air Microbiology ; Cities ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Air Pollutants/analysis ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Microbiota ; },
abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.},
}
@article {pmid39648557,
year = {2025},
author = {Huang, Y and Wang, T and Li, Y and Wang, Z and Cai, X and Chen, J and Li, R and Li, X},
title = {In Vitro-to-In Vivo Extrapolation on Lung Toxicity Induced by Metal Oxide Nanoparticles via Data-Mining.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {3},
pages = {1673-1682},
doi = {10.1021/acs.est.4c06186},
pmid = {39648557},
issn = {1520-5851},
mesh = {Animals ; *Lung/drug effects ; Mice ; *Metal Nanoparticles/toxicity ; Data Mining ; Humans ; Oxides/toxicity ; },
abstract = {While in silico analyses are commonly employed for chemical risk assessments, predicting chronic lung toxicity induced by engineered nanoparticles (ENMs) in vivo still faces many challenges due to complex interactions at multiple nanobio interfaces. In this study, we developed a rigorous method to compile published evidence on the in vivo lung toxicity of metal oxide nanoparticles (MeONPs) and revealed previously overlooked in vitro-to-in vivo extrapolation (IVIVE) relationships. A comprehensive multidimensional data set containing 1102 in vivo data points, 75 pulmonary toxicological biomarkers, and 20 features (covering in vitro effects, physicochemical properties, and exposure conditions) was constructed. An IVIVE approach that related effects at the cellular level to in vivo lung toxicity in rodent model was established with prediction accuracy reaching 89 and 80% in training and test sets. Experimental validation was conducted by testing chronic lung fibrosis of 8 new MeONPs in 32 independent mice, with prediction accuracy reaching 88%. The IVIVE model indicated that the proinflammatory cytokine IL-1β in THP-1 cells could serve as an in vitro marker to predict lung toxicity. The IVIVE model showed great promise for minimizing unnecessary animal tests and understanding toxicological mechanisms.},
}
@article {pmid39649625,
year = {2024},
author = {Boyes, D and Crowley, LC and Hutchinson, F and Wawman, DC and , and , and , and , and , and , and , },
title = {The genome sequence of the Broad-barred Knot-horn, Acrobasis consociella (Hübner, 1813).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {429},
pmid = {39649625},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from one female Acrobasis consociella (the Broad-barred Knot-horn; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 598.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.22 kilobases in length.},
}
@article {pmid39652754,
year = {2024},
author = {Pillay, R and Watson, JEM and Hansen, AJ and Burns, P and Virnig, ALS and Supples, C and Armenteras, D and González-Del-Pliego, P and Aragon-Osejo, J and A Jantz, P and Ervin, J and Goetz, SJ and Venter, O},
title = {Global rarity of high-integrity tropical rainforests for threatened and declining terrestrial vertebrates.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {51},
pages = {e2413325121},
pmid = {39652754},
issn = {1091-6490},
support = {NNX17AG51G/NASA/NASA/United States ; NNL15AA03/NASA/NASA/United States ; 80NSSC18K0338/NASA/NASA/United States ; },
mesh = {*Rainforest ; Animals ; *Biodiversity ; *Vertebrates/physiology ; *Conservation of Natural Resources/methods ; Tropical Climate ; Endangered Species ; Ecosystem ; },
abstract = {Structurally intact native forests free from major human pressures are vitally important habitats for the persistence of forest biodiversity. However, the extent of such high-integrity forest habitats remaining for biodiversity is unknown. Here, we quantify the amount of high-integrity tropical rainforests, as a fraction of total forest cover, within the geographic ranges of 16,396 species of terrestrial vertebrates worldwide. We found up to 90% of the humid tropical ranges of forest-dependent vertebrates was encompassed by forest cover. Concerningly, however, merely 25% of these remaining rainforests are of high integrity. Forest-dependent species that are threatened and declining and species with small geographic ranges have disproportionately low proportions of high-integrity forest habitat left. Our work brings much needed attention to the poor quality of much of the forest estate remaining for biodiversity across the humid tropics. The targeted preservation of the world's remaining high-integrity tropical rainforests that are currently unprotected is a critical conservation priority that may help alleviate the biodiversity crisis in these hyperdiverse and irreplaceable ecosystems. Enhanced efforts worldwide to preserve tropical rainforest integrity are essential to meet the targets of the Convention on Biological Diversity's 2022 Kunming-Montreal Global Biodiversity Framework which aims to achieve near zero loss of high biodiversity importance areas (including ecosystems of high integrity) by 2030.},
}
@article {pmid39652873,
year = {2025},
author = {Naderian, M and Norland, K and Schaid, DJ and Kullo, IJ},
title = {Development and Evaluation of a Comprehensive Prediction Model for Incident Coronary Heart Disease Using Genetic, Social, and Lifestyle-Psychological Factors: A Prospective Analysis of the UK Biobank.},
journal = {Annals of internal medicine},
volume = {178},
number = {1},
pages = {1-10},
pmid = {39652873},
issn = {1539-3704},
support = {R35 GM140487/GM/NIGMS NIH HHS/United States ; U01 HG006379/HG/NHGRI NIH HHS/United States ; U01 HG011710/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; Male ; Female ; *Coronary Disease/genetics/epidemiology/psychology ; Middle Aged ; United Kingdom/epidemiology ; Prospective Studies ; Risk Assessment/methods ; *Life Style ; Incidence ; Machine Learning ; Aged ; Biological Specimen Banks ; Multifactorial Inheritance ; Adult ; UK Biobank ; },
abstract = {BACKGROUND: Clinical risk calculators for coronary heart disease (CHD) do not include genetic, social, and lifestyle-psychological risk factors.<br><br>OBJECTIVE: To improve CHD risk prediction by developing and evaluating a prediction model that incorporated a polygenic risk score (PRS) and a polysocial score (PSS), the latter including social determinants of health and lifestyle-psychological factors.<br><br>DESIGN: Cohort study.<br><br>SETTING: United Kingdom.<br><br>PARTICIPANTS: UK Biobank participants recruited between 2006 and 2010.<br><br>MEASUREMENTS: Incident CHD (myocardial infarction and/or coronary revascularization); 10-year clinical risk based on pooled cohort equations (PCE), Predicting Risk of cardiovascular disease EVENTs (PREVENT), and QRISK3; PRS (Polygenic Score Catalog identification: PGS000018) for CHD (PRSCHD); and PSSCHD from 100 related covariates. Machine-learning and time-to-event analyses and model performance indices.<br><br>RESULTS: In 388&#x2009;224 participants (age, 55.5 [SD, 8.1] years; 42.5% men; 94.9% White), the hazard ratio for 1 SD increase in PSSCHD for incident CHD was 1.43 (95% CI, 1.38 to 1.49; P&#x2009;<&#x2009;0.001) and for 1 SD increase in PRSCHD was 1.59 (CI, 1.53 to 1.66, P&#x2009;<&#x2009;0.001). Non-White persons had higher PSSCHD than White persons. The effects of PSSCHD and PRSCHD on CHD were independent and additive. At a 10-year CHD risk threshold of 7.5%, adding PSSCHD and PRSCHD to PCE reclassified 12% of participants, with 1.86 times higher CHD risk in the up- versus down-reclassified persons and showed superior performance compared with PCE as reflected by improved net benefit while maintaining good calibration relative to the clinical risk calculators. Similar results were seen when incorporating PSSCHD and PRSCHD into PREVENT and QRISK3.<br><br>LIMITATION: A predominantly White cohort; possible healthy participant effect and ecological fallacy.<br><br>CONCLUSION: A PSSCHD was associated with incident CHD and its joint modeling with PRSCHD improved the performance of clinical risk calculators.<br><br>PRIMARY FUNDING SOURCE: National Human Genome Research Institute.},
}
@article {pmid39653494,
year = {2024},
author = {Lee, HB and Nguyen, TTT and Noh, SJ and Kim, DH and Kang, KH and Kim, SJ and Kirk, PM and Avery, SV and Medina, A and Hallsworth, JE},
title = {Aspergillus ullungdoensis sp. nov., Penicillium jeongsukae sp. nov., and other fungi from Korea.},
journal = {Fungal biology},
volume = {128},
number = {8 Pt B},
pages = {2479-2492},
doi = {10.1016/j.funbio.2024.05.014},
pmid = {39653494},
issn = {1878-6146},
mesh = {Republic of Korea ; *Phylogeny ; *Penicillium/isolation &amp; purification/classification/genetics ; DNA, Fungal/genetics ; Soil Microbiology ; Aspergillus/isolation &amp; purification/classification/genetics ; Sequence Analysis, DNA ; Cluster Analysis ; DNA, Ribosomal Spacer/genetics/chemistry ; },
abstract = {Eurotiales fungi are thought to be distributed worldwide but there is a paucity of information about their occurrence on diverse substrates or hosts and at specific localities. Some of the Eurotiales, including Aspergillus and Penicillium species, produce an array of secondary metabolites of use for agricultural, medicinal, and pharmaceutical applications. Here, we carried out a survey of the Eurotiales in South Korea, focusing on soil, freshwater, and plants (dried persimmon fruits and seeds of Perilla frutescens, known commonly as shiso). We obtained 11 species that-based on morphology, physiology, and multi-locus (ITS, BenA, CaM, and RPB2) phylogenetic analyses-include two new species, Aspergillus ullungdoensis sp. nov. and Penicillium jeongsukae sp. nov., and nine species that were known, but previously not described in South Korea, Aspergillus aculeatinus, Aspergillus aurantiacoflavus, Aspergillus croceiaffinis, Aspergillus pseudoviridinutans, Aspergillus uvarum, Penicillium ferraniaense, Penicillium glaucoroseum, Penicillium sajarovii, and one, Penicillium charlesii, that was isolated from previously unknown host, woodlouse (Porcellio scaber). We believe that biodiversity survey and identifying new species can contribute to set a baseline for future changes in the context of humanitarian crises such as climate change.},
}
@article {pmid39656857,
year = {2024},
author = {Alvarado, M and Gómez-Navajas, JA and Blázquez-Muñoz, MT and Gómez-Molero, E and Fernández-Sánchez, S and Eraso, E and Munro, CA and Valentín, E and Mateo, E and de Groot, PWJ},
title = {The good, the bad, and the hazardous: comparative genomic analysis unveils cell wall features in the pathogen Candidozyma auris typical for both baker's yeast and Candida.},
journal = {FEMS yeast research},
volume = {24},
number = {},
pages = {},
pmid = {39656857},
issn = {1567-1364},
support = {PID2020-117983RB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; SBPLY/23/180225/000029//UCLM/ ; //European Regional Development Fund/ ; JDC2023-051226-I//European Social Fund Plus/ ; },
mesh = {*Cell Wall/metabolism ; *Saccharomyces cerevisiae/genetics/metabolism ; Computational Biology ; Genomics ; Candida auris/genetics/metabolism/drug effects ; beta-Glucans/metabolism ; Genome, Fungal ; Fungal Proteins/genetics/metabolism ; Glycosylphosphatidylinositols/metabolism/genetics ; Candida albicans/genetics/pathogenicity ; Candida/genetics/metabolism/pathogenicity ; },
abstract = {The drug-resistant pathogenic yeast Candidozyma auris (formerly named Candida auris) is considered a critical health problem of global importance. As the cell wall plays a crucial role in pathobiology, here we performed a detailed bioinformatic analysis of its biosynthesis in C. auris and related Candidozyma haemuli complex species using Candida albicans and Saccharomyces cerevisiae as references. Our data indicate that the cell wall architecture described for these reference yeasts is largely conserved in Candidozyma spp.; however, expansions or reductions in gene families point to subtle alterations, particularly with respect to β--1,3--glucan synthesis and remodeling, phosphomannosylation, β-mannosylation, and glycosylphosphatidylinositol (GPI) proteins. In several aspects, C. auris holds a position in between C. albicans and S. cerevisiae, consistent with being classified in a separate genus. Strikingly, among the identified putative GPI proteins in C. auris are adhesins typical for both Candida (Als and Hyr/Iff) and Saccharomyces (Flo11 and Flo5-like flocculins). Further, 26 putative C. auris GPI proteins lack homologs in Candida genus species. Phenotypic analysis of one such gene, QG37_05701, showed mild phenotypes implicating a role associated with cell wall β-1,3-glucan. Altogether, our study uncovered a wealth of information relevant for the pathogenicity of C. auris as well as targets for follow-up studies.},
}
@article {pmid39656924,
year = {2025},
author = {Bastian, FB and Cammarata, AB and Carsanaro, S and Detering, H and Huang, WT and Joye, S and Niknejad, A and Nyamari, M and Mendes de Farias, T and Moretti, S and Tzivanopoulou, M and Wollbrett, J and Robinson-Rechavi, M},
title = {Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D878-D885},
pmid = {39656924},
issn = {1362-4962},
support = {//University of Lausanne/ ; U01CA215010/GF/NIH HHS/United States ; //Service de la Sant&#xe9; Publique, Canton de Vaud/ ; U01 CA215010/CA/NCI NIH HHS/United States ; 31003A_173048/SNSF_/Swiss National Science Foundation/Switzerland ; 863410//Horizon 2020 - Research and Innovation Framework Programme/ ; //swissuniversities Programme Open Science/ ; //SIB Swiss Institute of Bioinformatics/ ; },
mesh = {Animals ; *Single-Cell Analysis/methods ; *RNA-Seq/methods ; *Software ; *Databases, Genetic ; Humans ; Internet ; Molecular Sequence Annotation ; Gene Expression Profiling/methods ; Data Curation ; Single-Cell Gene Expression Analysis ; },
abstract = {Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species. Expression data are integrated and made comparable between species thanks to consistent data annotation and processing. In the past years, we have integrated single-cell RNA-sequencing expression data into Bgee through careful curation of public datasets in multiple species. We have fully integrated this new technology along with the wealth of other data existing in Bgee. As a result, Bgee can now provide one definitive answer all the way to the cell resolution about a gene's expression pattern, comparable between species. We have updated our programmatic access tools to adapt to these changes accordingly. We have introduced a new web interface, providing detailed access to our annotations and expression data. It enables users to retrieve data, e.g. for specific organs, cell types or developmental stages, and leverages ontology reasoning to build powerful queries. Finally, we have expanded our species count from 29 to 52, emphasizing fish species critical for vertebrate genome studies, species of agronomic and veterinary importance and nonhuman primates.},
}
@article {pmid39657789,
year = {2025},
author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, &#xc1;T and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH},
title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D678-D690},
pmid = {39657789},
issn = {1362-4962},
support = {//Conahcyt Mexico International PhD Studentship/ ; 32170080//National Natural Science Foundation of China/ ; 547394769//German Research Foundation/ ; 101066127//European Union/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; //Swedish Pharmaceutical Society PostDoc/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; //Werner Siemens Foundation/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; PROYEXCEL_00012//Spanish "Junta de Andaluc&#xed;a"/ ; 1347411//CONAHCYT/ ; IM230100154//Australian Research Council Industry Fellowship/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01 GM146224/GM/NIGMS NIH HHS/United States ; //Swiss Federal Government/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; //NWO Merian/ ; R01 GM097142/GM/NIGMS NIH HHS/United States ; 024.004.014//MiCRop Consortium/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP230102668//Australian Research Council Discovery Project/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //Delta Stewardship Council Delta Science Program/ ; T32 GM136629/GM/NIGMS NIH HHS/United States ; //Basic Science Research Program/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; AUFF-E-2022-9-42//AUFF/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; CBET-2032243//U.S. National Science Foundation/ ; //University of Illinois/ ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Horizon Europe Marie Sk&#x142;odowska-Curie Actions Postdoctoral Fellowship/ ; NE/T010959/1//Signals in the Soil/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; DNRF137//Danish National Research Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; BB/V005723/2//BBSRC/ ; 101087181//EU/ ; 101000392//Horizon 2020/ ; 101072485//European Union's Horizon/ ; 10.55776/P 34036//Austrian Science Fund/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 23/01956-2//S&#xe3;o Paulo Research Foundation/ ; //Department of Biotechnology/ ; 222676//USDA Evans-Allen Research/ ; //Saarland University/ ; 102022750//SINTEF/ ; //Hans Fischer Society/ ; 21K06336//KAKENHI/ ; CF22-1239//Carlsberg Foundation/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; 495740318//German Research Foundation/ ; 802736//European Union Horizon 2020/ ; //Strathclyde University Global Research Scholarship/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 101099528//European Innovation Council/ ; GNT2021638//National Health and Medical Research Council/ ; 757173//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; NA22NOS4200050//NERRS/ ; 865738/ERC_/European Research Council/International ; DGE 2241144//NSF GRFP/ ; //National Research Fund of Ukraine/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 102029187//SEP AGREE/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; F31 ES036421/ES/NIEHS NIH HHS/United States ; KICH1.LWV04.21.013//NWO/ ; DM60066//Italian Ministry of Research/ ; 101117891-MeDiSyn//ERC Starting/ ; //European Union's Horizon 2020 Research/ ; R01 GM123998/GM/NIGMS NIH HHS/United States ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; PS00349981//Fulbright/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 735867//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 3141-00013A//Innovation Fund Denmark/ ; CFB 2.0//Novo Nordisk Foundation/ ; 21/07038-0//S&#xe3;o Paulo Research Foundation/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; 101072485//European Union's Horizon Europe/ ; OCENW.XL21.XL21.088//NWO-XL/ ; //University Grants Commission/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; //European Regional Development Fund/ ; 101072485//Horizon Europe Marie Sk&#x142;odowska-Curie/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; 802736//European Union's Horizon 2020/ ; //Alexander von Humboldt-Stiftung/ ; //UK Government Department for Environment, Food &amp; Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 102024676-14//POS BIOINFO 2024/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101106349//Marie Sklodowska-Curie/ ; T32-GM136629//Chemical-Biology Interface Training/ ; //University of Sydney/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 101130799//European Union's Horizon/ ; 852600//Innovation Program ERC St/ ; //National Agri-Food Biotechnology Institute/ ; //German Academic Scholarship Foundation/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; F32 AT011475/AT/NCCIH NIH HHS/United States ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; K445/2022//Leibniz Association/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; VI.Veni.202.130//NWO Talent/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; T32GM136583/NH/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy/ ; },
mesh = {*Multigene Family ; *Databases, Genetic ; Biosynthetic Pathways/genetics ; Molecular Sequence Annotation ; Biological Products/metabolism/chemistry ; Data Curation ; },
abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.},
}
@article {pmid39660611,
year = {2024},
author = {Mortzfeld, BM and Bhattarai, SK and Bucci, V},
title = {Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39660611},
issn = {2050-084X},
support = {R01 AG075283/AG/NIA NIH HHS/United States ; 457837076//Deutsche Forschungsgemeinschaft/ ; W81XWH2020013//Congressionally Directed Medical Research Programs/ ; 1R01AG075283-01A1/NH/NIH HHS/United States ; },
mesh = {*Bacteriocins/pharmacology/genetics/metabolism ; *Enterobacteriaceae/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Gram-Negative Bacteria/drug effects/genetics ; Plant Diseases/microbiology ; Microbial Sensitivity Tests ; },
abstract = {Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered 12 previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella. Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e., Acinetobacter baumannii or Pseudomonas aeruginosa, providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.},
}
@article {pmid39660842,
year = {2025},
author = {Xu, C and Song, LY and Li, J and Zhang, LD and Guo, ZJ and Ma, DN and Dai, MJ and Li, QH and Liu, JY and Zheng, HL},
title = {MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data.},
journal = {Plant, cell &amp; environment},
volume = {48},
number = {5},
pages = {2950-2962},
doi = {10.1111/pce.15318},
pmid = {39660842},
issn = {1365-3040},
support = {//This work was supported by the Natural Science Foundation of China (NSFC) (32171740, 31870581); the National Key Research and Development Program of China (2017YFC0506102)/ ; },
mesh = {*Databases, Genetic ; Transcriptome/genetics ; Genomics ; *Wetlands ; Computational Biology/methods ; Gene Expression Profiling ; Internet ; *Avicennia/genetics ; Genome, Plant/genetics ; *Rhizophoraceae/genetics ; Multiomics ; },
abstract = {Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets.},
}
@article {pmid39663400,
year = {2025},
author = {Carter, KR and Cavaleri, MA and Atkin, OK and Bahar, NHA and Cheesman, AW and Choury, Z and Crous, KY and Doughty, CE and Dusenge, ME and Ely, KS and Evans, JR and Fonseca da Silva, J and Mau, AC and Medlyn, BE and Meir, P and Norby, RJ and Read, J and Reed, SC and Reich, PB and Rogers, A and Serbin, SP and Slot, M and Schwartz, EC and Tribuzy, ES and Uddling, J and Vårhammar, A and Walker, AP and Winter, K and Wood, TE and Wu, J},
title = {Photosynthetic responses to temperature across the tropics: a meta-analytic approach.},
journal = {Annals of botany},
volume = {135},
number = {7},
pages = {1293-1310},
pmid = {39663400},
issn = {1095-8290},
support = {DE-SC-0012000, DE-SC-0011806, DE-SC-0018942, 89243018S-SC-000014 and 89243018S-SC-000017//United States Department of Energy Office of Science/ ; 31922090//National Natural Science Foundation of China/ ; },
mesh = {*Photosynthesis/physiology ; Tropical Climate ; Temperature ; Climate Change ; Plant Leaves/physiology ; Carbon Dioxide/metabolism ; },
abstract = {BACKGROUND AND AIMS: Tropical forests exchange more carbon dioxide (CO2) with the atmosphere than any other terrestrial biome. Yet, uncertainty in the projected carbon balance over the next century is roughly three times greater for the tropics than other for ecosystems. Our limited knowledge of tropical plant physiological responses, including photosynthetic, to climate change is a substantial source of uncertainty in our ability to forecast the global terrestrial carbon sink.<br><br>METHODS: We used a meta-analytic approach, focusing on tropical photosynthetic temperature responses, to address this knowledge gap. Our dataset, gleaned from 18 independent studies, included leaf-level light-saturated photosynthetic (Asat) temperature responses from 108 woody species, with additional temperature parameters (35 species) and rates (250 species) of both maximum rates of electron transport (Jmax) and Rubisco carboxylation (Vcmax). We investigated how these parameters responded to mean annual temperature (MAT), temperature variability, aridity and elevation, as well as also how responses differed among successional strategy, leaf habit and light environment.<br><br>KEY RESULTS: Optimum temperatures for Asat (ToptA) and Jmax (ToptJ) increased with MAT but not for Vcmax (ToptV). Although photosynthetic rates were higher for 'light' than 'shaded' leaves, light conditions did not generate differences in temperature response parameters. ToptA did not differ with successional strategy, but early successional species had ~4 &#xb0;C wider thermal niches than mid/late species. Semi-deciduous species had ~1 &#xb0;C higher ToptA than broadleaf evergreen species. Most global modelling efforts consider all tropical forests as a single 'broadleaf evergreen' functional type, but our data show that tropical species with different leaf habits display distinct temperature responses that should be included in modelling efforts.<br><br>CONCLUSIONS: This novel research will inform modelling efforts to quantify tropical ecosystem carbon cycling and provide more accurate representations of how these key ecosystems will respond to altered temperature patterns in the face of climate warming.},
}
@article {pmid39664717,
year = {2024},
author = {Baker, KS and Millerand, F},
title = {The Incremental Growth of Data Infrastructure in Ecology (1980-2020).},
journal = {Ecology and evolution},
volume = {14},
number = {12},
pages = {e70444},
pmid = {39664717},
issn = {2045-7758},
abstract = {After decades of growth, a research community's network information system and data repository were transformed to become a national data management office and a major element of data infrastructure for ecology and the environmental sciences. Developing functional data infrastructures is key to the support of ongoing Open Science and Open Data efforts. This example of data infrastructure growth contrasts with the top-down development typical of many digital initiatives. The trajectory of this network information system evolved within a collaborative, long-term ecological research community. This particular community is funded to conduct ecological research while collective data management is also carried out across its geographically dispersed study sites. From this longitudinal ethnography, we describe an Incremental Growth Model that includes a sequence of six relatively stable phases where each phase is initiated by a rapid response to a major pivotal event. Exploring these phases and the roles of data workers provides insight into major characteristics of digital growth. Further, a transformation in assumptions about data management is reported for each phase. Investigating the growth of a community information system over four decades as it becomes data infrastructure reveals details of its social, technical, and institutional dynamics. In addition to addressing how digital data infrastructure characteristics change, this study also considers when the growth of data infrastructure begins.},
}
@article {pmid39664868,
year = {2024},
author = {Boyes, D and Zilli, A and , and , and , and , and , and , and , },
title = {The genome sequence of the Grey Shoulder-knot, Lithophane ornitopus (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {214},
pmid = {39664868},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Lithophane ornitopus (the Grey Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 508.6 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 15.33 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,397 protein coding genes.},
}
@article {pmid39670410,
year = {2025},
author = {Alipio, K and García-Colón, J and Boscarino, N and Fox, K},
title = {Indigenous Data Sovereignty, Circular Systems, and Solarpunk Solutions for a Sustainable Future.},
journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing},
volume = {30},
number = {},
pages = {717-733},
doi = {10.1142/9789819807024_0054},
pmid = {39670410},
issn = {2335-6936},
mesh = {*Artificial Intelligence ; *Computational Biology ; Humans ; Cloud Computing/statistics &amp; numerical data ; Sustainable Development ; Indigenous Peoples/statistics &amp; numerical data ; Conservation of Natural Resources ; },
abstract = {Recent advancements in Artificial Intelligence (AI) and data center infrastructure have brought the global cloud computing market to the forefront of conversations about sustainability and energy use. Current policy and infrastructure for data centers prioritize economic gain and resource extraction, inherently unsustainable models which generate massive amounts of energy and heat waste. Our team proposes the formation of policy around earth-friendly computation practices rooted in Indigenous models of circular systems of sustainability. By looking to alternative systems of sustainability rooted in Indigenous values of aloha 'āina, or love for the land, we find examples of traditional ecological knowledge (TEK) that can be imagined alongside Solarpunk visions for a more sustainable future. One in which technology works with the environment, reusing electronic waste (e-waste) and improving data life cycles.},
}
@article {pmid39671336,
year = {2024},
author = {Karim, AAJ and Mahmud, MZ and Khan, R},
title = {Advanced vision transformers and open-set learning for robust mosquito classification: A novel approach to entomological studies.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012654},
pmid = {39671336},
issn = {1553-7358},
mesh = {Animals ; *Culicidae/classification ; *Deep Learning ; *Computational Biology/methods ; Entomology/methods ; Mosquito Vectors/classification ; Humans ; Algorithms ; Neural Networks, Computer ; },
abstract = {Mosquito-related diseases pose a significant threat to global public health, necessitating efficient and accurate mosquito classification for effective surveillance and control. This work presents an innovative approach to mosquito classification by leveraging state-of-the-art vision transformers and open-set learning techniques. A novel framework has been introduced that integrates Transformer-based deep learning models with comprehensive data augmentation and preprocessing methods, enabling robust and precise identification of ten mosquito species. The Swin Transformer model achieves the best performance for traditional closed-set learning with 99.60% accuracy and 0.996 F1 score. The lightweight MobileViT technique attains an almost equivalent accuracy of 98.90% with significantly reduced parameters and model complexities. Next, the applied deep learning models' adaptability and generalizability in a static environment have been enhanced by using new classes of data samples during the inference stage that have not been included in the training set. The proposed framework's ability to handle unseen classes like insects similar to mosquitoes, even humans, through open-set learning further enhances its practical applicability employing the OpenMax technique and Weibull distribution. The traditional CNN model, Xception, outperforms the latest transformer with higher accuracy and F1 score for open-set learning. The study's findings highlight the transformative potential of advanced deep-learning architectures in entomology, providing a strong groundwork for future research and development in mosquito surveillance and vector control. The implications of this work extend beyond mosquito classification, offering valuable insights for broader ecological and environmental monitoring applications.},
}
@article {pmid39671449,
year = {2024},
author = {Celiker, E and Woodrow, C and Guadayol, &#xd2; and Davranoglou, LR and Schlepütz, CM and Mortimer, B and Taylor, GK and Humphries, S and Montealegre-Z, F},
title = {Mechanical network equivalence between the katydid and mammalian inner ears.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012641},
pmid = {39671449},
issn = {1553-7358},
mesh = {Animals ; *Ear, Inner/anatomy &amp; histology/physiology ; *Mammals/physiology ; *Hearing/physiology ; Computer Simulation ; Insecta/physiology ; Computational Biology ; Models, Biological ; Cochlea/physiology/anatomy &amp; histology ; X-Ray Microtomography ; },
abstract = {Mammalian hearing operates on three basic steps: 1) sound capturing, 2) impedance conversion, and 3) frequency analysis. While these canonical steps are vital for acoustic communication and survival in mammals, they are not unique to them. An equivalent mechanism has been described for katydids (Insecta), and it is unique to this group among invertebrates. The katydid inner ear resembles an uncoiled cochlea, and has a length less than 1 mm. Their inner ears contain the crista acustica, which holds tonotopically arranged sensory cells for frequency mapping via travelling waves. The crista acustica is located on a curved triangular surface formed by the dorsal wall of the ear canal. While empirical recordings show tonotopic vibrations in the katydid inner ear for frequency analysis, the biophysical mechanism leading to tonotopy remains elusive due to the small size and complexity of the hearing organ. In this study, robust numerical simulations are developed for an in silico investigation of this process. Simulations are based on the precise katydid inner ear geometry obtained by synchrotron-based micro-computed tomography, and empirically determined inner ear fluid properties for an accurate representation of the underlying mechanism. We demonstrate that the triangular structure below the hearing organ drives the tonotopy and travelling waves in the inner ear, and thus has an equivalent role to the mammalian basilar membrane. This reveals a stronger analogy between the inner ear basic mechanical networks of two organisms with ancient evolutionary differences and independent phylogenetic histories.},
}
@article {pmid39671935,
year = {2025},
author = {Paulukonis, EA and Purucker, ST},
title = {Spatiotemporally derived agricultural field delineations for species effects assessments and environmental decision support.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {177967},
doi = {10.1016/j.scitotenv.2024.177967},
pmid = {39671935},
issn = {1879-1026},
mesh = {*Agriculture/methods ; *Environmental Monitoring/methods ; Pesticides ; Risk Assessment/methods ; *Decision Support Techniques ; Crops, Agricultural ; United States ; Geographic Information Systems ; Endangered Species ; },
abstract = {Rural landscapes are strongly defined by the spatial distribution of agricultural fields. GIS layers that capture this information have much utility in many decision support contexts, particularly with regards to the intersection of agricultural pesticide use and endangered species habitat. The United States Department of Agriculture's Cropland Data Layer (CDL) is a georeferenced, annual resource that often serves a crucial role in pesticide risk-related decision support applications. However, CDL agriculture timeseries data are not mapped to explicit field boundaries, contributing to increased uncertainty regarding differentiated crop type spatial homogeneity and geographic extent, inherently adding complexity to multi-temporal crop monitoring and analyses efforts. We describe the development and testing of an approach for field delineation based on timeseries information from the 2008-2021 CDL at spatial scales relevant for endangered species risk assessment. We validate and test the approach against quantitative crop information and contextualize the outputs as part of a case study reconstructing past agricultural pesticide exposures to non-target species to demonstrate the utility of the method for ecological risk assessment decision support. The approach resulted in delineated field unit boundaries that effectively incorporated the unmodified CDL crop type generalized spatial distribution patterns; derived metrics closely corresponded with reported crop metrics for landscapes with proportionally significant agriculture use. When modified to reflect areas of mixed/small crop acreages, the method can provide a useful framework for large-scale field delineation of the CDL, which can complement ongoing environmental risk assessment and conservation efforts in agricultural landscapes.},
}
@article {pmid39675288,
year = {2025},
author = {Mu, X and Chen, C and Fan, Q and Zhang, W and Liu, F and Guo, J and Qi, W and Liu, H},
title = {Removal and ecological impact of sulfamethoxazole and N-acetyl sulfamethoxazole in mesocosmic wetlands dominated by submerged plants: Plant tolerance, microbial response, and nitrogen transformation.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {178034},
doi = {10.1016/j.scitotenv.2024.178034},
pmid = {39675288},
issn = {1879-1026},
mesh = {*Wetlands ; *Sulfamethoxazole/metabolism/analysis ; *Water Pollutants, Chemical/metabolism/analysis ; Nitrogen/metabolism ; Biodegradation, Environmental ; *Waste Disposal, Fluid/methods ; },
abstract = {Sulfamethoxazole (SMX) and its human metabolite N-acetylsulfamethoxazole (N-SMX) are frequently detected in aquatic environments, posing potential threats to freshwater ecosystem health. Constructed wetlands are pivotal for wastewater treatment, with plant species serving as key determinants of pollutant removal efficiency. In this study, wetlands dominated by three submerged plants (Myriophyllum verticillatum, Vallisneria spiralis, Hydrilla verticillata) were respectively constructed to investigate the removal of SMX and N-SMX, and the impact on wetland ecology regarding plant tolerance, microbial response, and nitrogen transformation. Results showed that wetlands removed N-SMX (82.3-99.8 %) more effectively than SMX (54.3-80.2 %), with the wetland dominated by Myriophyllum verticillatum showing the highest removal efficiency. However, high concentrations (5 mg/L) of SMX and N-SMX significantly reduced NH4[+]-N and TN removal (p < 0.05), accompanied by shifts in microbial communities, especially a decreased abundance of Proteobacteria and key nitrogen-transforming genes. A total of 22 different ARGs (antibiotic resistance genes) were detected. SMX significantly increased the relative abundance of sulfonamide resistance genes (sul1, sul2) (p < 0.05), while major denitrifying genera, such as Thiobacillus, which were not the primary hosts of these genes, showed a significant negative correlation with sul1 and sul2 (p < 0.05). This study provides a reference for ecological remediation of wetlands in response to antibiotic contamination.},
}
@article {pmid39679384,
year = {2024},
author = {Khosravi, M and Mojtabaeian, SM and Sarvestani, MA},
title = {A Systematic Review on the Outcomes of Climate Change in the Middle-Eastern Countries: The Catastrophes of Yemen and Syria.},
journal = {Environmental health insights},
volume = {18},
number = {},
pages = {11786302241302270},
pmid = {39679384},
issn = {1178-6302},
abstract = {The Middle East is facing serious climate change challenges, rendering it as one of the most affected regions worldwide. This paper aimed to investigate the outcomes of climate change in the Middle East. In 2024, a qualitative study was conducted employing a methodology that integrated systematic review for data collection and thematic analysis for data analysis. Such integration of the approaches provided valuable insights into the findings within the literature in a comprehensive and categorized format. PubMed, Scopus, ProQuest, and the Cochrane Database of Systematic Reviews were searched for relevant studies published between 2000 and 2024. The quality of these studies was assessed using the AACODS (Accuracy, Coverage, Objectivity, Date, Significance) checklist. The data extracted from the included studies underwent a thematic analysis utilizing Braun and Clarke's methodology. After completing the screening process, a total of 93 papers were deemed suitable for inclusion in the study. The quality assessment of these selected studies demonstrated a notably high standard, particularly in terms of authority, accuracy, coverage, objectivity, and significance. Moreover, minimal levels of bias were observed within the included studies. Subsequent thematic analysis of the findings from the systematic review identified 6 overarching themes: "Human Health Outcomes," "Animal Health Outcomes," "Plant Health Outcomes," "Ecological Outcomes," "Economic Outcomes," and "Political Outcomes." The study revealed ecological outcomes as the most prevalent consequences of climate change in the Middle East, including alterations in habitat distribution, temperature increase, water scarcity, and more. The outcomes seemed to be interconnected, exacerbating each other. Yemen and Syria had faced severe consequences, leading to political unrest and humanitarian crises in which Yemen ranking among the most water-stressed nations globally, while Syria contending with millions of displaced individuals living in dire conditions.},
}
@article {pmid39683090,
year = {2024},
author = {Chaligava, O and Zinicovscaia, I and Peshkova, A and Yushin, N and Frontasyeva, M and Vergel, K and Nurkassimova, M and Cepoi, L},
title = {Major and Trace Airborne Elements and Ecological Risk Assessment: Georgia Moss Survey 2019-2023.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {23},
pages = {},
pmid = {39683090},
issn = {2223-7747},
abstract = {The study, carried out as part of the International Cooperative Program on Effects of Air Pollution on Natural Vegetation and Crops, involved collecting 95 moss samples across the territory of Georgia during the period from 2019 to 2023. Primarily samples of Hypnum cupressiforme were selected, with supplementary samples of Abietinella abietina, Pleurozium schreberi, and Hylocomium splendens in cases of the former's absence. The content of 14 elements (Al, Ba, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, S, Sr, V, and Zn) was detected using Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES), while the Hg content was determined using a Direct Mercury Analyzer. To identify any relationships between chemical elements and to depict their sources, multivariate statistics was applied. Principal component analysis identified three main components: PC1 (geogenic, 43.4%), PC2 (anthropogenic, 13.3%), and PC3 (local anomalies, 8.5%). The results were compared with the first moss survey conducted in Georgia in the period from 2014 to 2017, offering insights into temporal trends of air quality. Utilizing GIS, a spatial map illustrating pollution levels across Georgia, based on the Pollution Load Index, was generated. The Potential Environmental Risk Index emphasized significant risks associated with mercury and cadmium at several locations. The study highlights the utility of moss biomonitoring in assessing air pollution and identifying hotspots of contamination. The findings from this study could be beneficial for future biomonitoring research in areas with varying physical and geographical conditions.},
}
@article {pmid39684378,
year = {2024},
author = {Zhang, KL and Leng, YN and Hao, RR and Zhang, WY and Li, HF and Chen, MX and Zhu, FY},
title = {Adaptation of High-Altitude Plants to Harsh Environments: Application of Phenotypic-Variation-Related Methods and Multi-Omics Techniques.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684378},
issn = {1422-0067},
support = {KYCX24_1376//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; 2023ZD0405602//STI 2030&#xff0d;Major Projects/ ; CX (21)2023//Jiangsu Agricultural Science and Technology Innovation Fund/ ; BK20240668//Basic Research Program of Jiangsu Province/ ; },
mesh = {*Altitude ; *Metabolomics/methods ; *Plants/metabolism/genetics ; *Proteomics/methods ; *Adaptation, Physiological ; *Genomics/methods ; *Phenotype ; Plant Physiological Phenomena ; Acclimatization ; Transcriptome ; Multiomics ; },
abstract = {High-altitude plants face extreme environments such as low temperature, low oxygen, low nutrient levels, and strong ultraviolet radiation, causing them to adopt complex adaptation mechanisms. Phenotypic variation is the core manifestation of ecological adaptation and evolution. Many plants have developed a series of adaptive strategies through long-term natural selection and evolution, enabling them to survive and reproduce under such harsh conditions. This article reviews the techniques and methods used in recent years to study the adaptive evolution of high-altitude plants, including transplantation techniques, genomics, transcriptomics, proteomics, and metabolomics techniques, and their applications in high-altitude plant adaptive evolution. Transplantation technology focuses on phenotypic variation, which refers to natural variations in morphological, physiological, and biochemical characteristics, exploring their key roles in nutrient utilization, photosynthesis optimization, and stress-resistance protection. Multiple omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revealed genes, regulatory pathways, and metabolic networks associated with phenotypic variations at the genetic and molecular levels. At the same time, the limitations and deficiencies of current technologies used to study plant adaptation to high-altitude environments were discussed. In addition, we propose future improvements to existing technologies and advocate for the integration of different technologies at multiple levels to study the molecular mechanisms of plant adaptation to high-altitude environments, thus providing insights for future research in this field.},
}
@article {pmid39684926,
year = {2024},
author = {Liu, R and Zhang, P and Bai, J and Zhong, Z and Shan, Y and Cheng, Z and Zhang, Q and Guo, Q and Zhang, H and Zhang, B},
title = {Integrated Transcriptomic and Proteomic Analyses of Antler Growth and Ossification Mechanisms.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684926},
issn = {1422-0067},
support = {23CB063 and 24CE-BGS-09//Beijing Academy of Science and Technology Financial Support Projects/ ; },
mesh = {*Antlers/growth &amp; development/metabolism ; Animals ; *Osteogenesis/genetics ; *Deer/genetics/growth &amp; development ; *Transcriptome ; *Proteomics/methods ; Proteome/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Computational Biology/methods ; },
abstract = {Antlers are the sole mammalian organs capable of continuous regeneration. This distinctive feature has evolved into various biomedical models. Research on mechanisms of antler growth, development, and ossification provides valuable insights for limb regeneration, cartilage-related diseases, and cancer mechanisms. Here, ribonucleic acid sequencing (RNA-seq) and four-dimensional data-independent acquisition (4D DIA) technologies were employed to examine gene and protein expression differences among four tissue layers of the Chinese milu deer antler: reserve mesenchyme (RM), precartilage (PC), transition zone (TZ), cartilage (CA). Overall, 4611 differentially expressed genes (DEGs) and 2388 differentially expressed proteins (DEPs) were identified in the transcriptome and proteome, respectively. Among the 828 DEGs common to both omics approaches, genes from the collagen, integrin, and solute carrier families, and signaling molecules were emphasized for their roles in the regulation of antler growth, development, and ossification. Bioinformatics analysis revealed that in addition to being regulated by vascular and nerve regeneration pathways, antler growth and development are significantly influenced by numerous cancer-related signaling pathways. This indicates that antler growth mechanisms may be similar to those of cancer cell proliferation and development. This study lays a foundation for future research on the mechanisms underlying the rapid growth and ossification of antlers.},
}
@article {pmid39688289,
year = {2025},
author = {Bao, Y and Jia, F and Geng, Y and Song, G and Xu, R and Wang, H and Mu, Y and Tong, HHY and Zhang, F and Guo, J},
title = {Uncovering the Differed Susceptibility of Fusarium oxysporum (Fo32931 and FocII5) to Fungicide Phenamacril: From Computational and Experimental Perspectives.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {1},
pages = {189-201},
doi = {10.1021/acs.jafc.4c07865},
pmid = {39688289},
issn = {1520-5118},
mesh = {*Fusarium/drug effects/genetics/metabolism ; *Fungicides, Industrial/pharmacology/chemistry ; *Fungal Proteins/genetics/metabolism/chemistry ; *Drug Resistance, Fungal/genetics ; Plant Diseases/microbiology ; },
abstract = {Fo32931 and FoCII5 are two subtypes of Fusarium oxysporum (Fo), a pathogenic filamentous fungus. Phenamacril (PHA), a Fusarium-specific fungicide that targets myosin I, exhibits significant hyphal growth inhibition in Fo32931 but shows weak resistance in FocII5, despite only two amino acid differences in the PHA-binding pocket of myosin I. In this study, we aim to elucidate the molecular basis for the differential sensitivity ofF. oxysporum myosin I variants (FoMyoI[32931] and FoMyoI[cII5]) to phenamacril through computational methods and biochemical validation. The results suggest that phenamacril functions as an allosteric inhibitor for FoMyoI[32931], inhibiting the large oscillation of the converter lever domain (CLD) upon ATP binding and promoting the opening of the outer cleft, further impairing protein function. PHA significantly reduced the coupling between the CLD, especially the converter, and the catalytic center, diminishing the response of the CLD to the motor domain in FoMyoI[32931]. From the residue mutation experiment, we found that the S418T substitution in FoMyoI[cII5] is the key to the reduced phenamacril sensitivity of FocII5. According to the microscale thermophoresis (MST) assay and pocket conformation analysis, the S418T mutation disturbs the orientation of pocket residues, especially Lys537, leading to a looser pocket and reduced interaction between Lys537 and phenamacril, which lowers the binding affinity of FoMyoI[cII5] for phenamacril. These findings provide deeper insights into the reasons for the lower sensitivity of FoCII5 to phenamacril from both molecular and structural perspectives and will also guide the design of novel inhibitors against resistant Fusarium spp., like FoCII5.},
}
@article {pmid39689059,
year = {2024},
author = {Bernadou, A and Jeanson, R},
title = {Randomness as a driver of inactivity in social groups.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012668},
pmid = {39689059},
issn = {1553-7358},
mesh = {Animals ; *Ants/physiology ; Bees/physiology ; Behavior, Animal/physiology ; Computational Biology ; Computer Simulation ; Models, Biological ; *Social Behavior ; },
abstract = {Social insects, such as ants and bees, are known for their highly efficient and structured colonies. Division of labour, in which each member of the colony has a specific role, is considered to be one major driver of their ecological success. However, empirical evidence has accumulated showing that many workers, sometimes more than half, remain idle in insect societies. Several hypotheses have been put forward to explain these patterns, but none provides a consensual explanation. Task specialisation exploits inter-individual variations, which are mainly influenced by genetic factors beyond the control of the colony. As a result, individuals may also differ in the efficiency with which they perform tasks. In this context, we aimed to test the hypothesis that colonies generate a large number of individuals in order to recruit only the most efficient to perform tasks, at the cost of producing and maintaining a fraction of workers that remain inactive. We developed a model to explore the conditions under which variations in the scaling of workers' production and maintenance costs, along with activity costs, allow colonies to sustain a fraction of inactive workers. We sampled individual performances according to different random distributions in order to simulate the variability associated with worker efficiency. Our results show that the inactivity of part of the workforce can be beneficial for a wide range of parameters if it allows colonies to select the most efficient workers. In decentralised systems such as insect societies, we suggest that inactivity is a by-product of the random processes associated with the generation of individuals whose performance levels cannot be controlled.},
}
@article {pmid39689854,
year = {2024},
author = {Radice, VZ and Hernández-Agreda, A and Pérez-Rosales, G and Booker, R and Bellworthy, J and Broadribb, M and Carpenter, GE and Diaz, C and Eckert, RJ and Foster, NL and Gijsbers, JC and Gress, E and Laverick, JH and Micaroni, V and Pierotti, M and Rouzé, H and Stevenson, A and Sturm, AB and Bongaerts, P},
title = {Recent trends and biases in mesophotic ecosystem research.},
journal = {Biology letters},
volume = {20},
number = {12},
pages = {20240465},
pmid = {39689854},
issn = {1744-957X},
mesh = {*Ecosystem ; Animals ; Oceans and Seas ; Research/trends ; Anthozoa/physiology ; Bias ; Databases, Factual ; },
abstract = {Mesophotic ecosystems (approx. 30-150 m) represent a significant proportion of the world's oceans yet have long remained understudied due to challenges in accessing these deeper depths. Owing to advances in underwater technologies and a growing scientific and management interest, there has been a major expansion in research of both (sub)tropical mesophotic coral ecosystems and temperate mesophotic ecosystems. Here, we characterize the recent global trends in mesophotic research through an updated release of the 'mesophotic.org' database (www.mesophotic.org) where we reviewed and catalogued 1500 scientific publications. In doing so, we shed light on four major research biases: a gross imbalance in (a) the geographical spread of research efforts, differences in (b) the focal depth range and (c) research fields associated with study organisms and research platforms, and (d) the lack of temporal studies. Overall, we are optimistic about the future of mesophotic research and hope that by highlighting current trends and imbalances, we can raise awareness and stimulate discussion on the future directions of this emerging field.},
}
@article {pmid39689860,
year = {2025},
author = {Wu, Z and Huang, Z and Tang, N and Wang, K and Bian, C and Li, D and Kuraki, V and Schmid, F},
title = {Research on Sports Injury Rehabilitation Detection Based on IoT Models for Digital Health Care.},
journal = {Big data},
volume = {13},
number = {2},
pages = {144-160},
doi = {10.1089/big.2023.0134},
pmid = {39689860},
issn = {2167-647X},
mesh = {Humans ; *Internet of Things ; *Athletic Injuries/rehabilitation/diagnosis ; Delivery of Health Care ; Telemedicine ; Digital Health ; },
abstract = {Physical therapists specializing in sports rehabilitation detection help injured athletes recover from their wounds and avoid further harm. Sports rehabilitators treat not just commonplace sports injuries but also work-related musculoskeletal injuries, discomfort, and disorders. Sensor-equipped Internet of Things (IoT) monitors the real-time location of medical equipment such as scooters, cardioverters, nebulizer treatments, oxygenation pumps, or other monitor gear. Analysis of medicine deployment across sites is possible in real time. Health care delivery based on digital technology to improve access, affordability, and sustainability of medical treatment is known as digital health care. The challenging characteristics of such sports injury rehabilitation for digital health care are playing position, game strategies, and cybersecurity. Hence, in this research, health care IoT-enabled body area networks (HIoT-BAN) have been designed to improve sports injury rehabilitation detection for digital health care. The health care sector may benefit significantly from IoT adoption since it allows for enhanced patient safety; health care investment management includes controlling the hospital's pharmaceutical stock and monitoring the heat and humidity levels. Digital health describes a group of programmers made to aid health care delivery, whether by assisting with clinical decision-making or streamlining back-end operations in health care institutions. A HIoT-BAN effectively predicts the rise in sports injury rehabilitation detection with faster digital health care based on IoT. The research concludes that the HIoT-BAN effectively indicates sports injury rehabilitation detection for digital health care. The experimental analysis of HIoT-BAN outperforms the IoT method in terms of performance, accuracy, prediction ratio, and mean square error rate.},
}
@article {pmid39691468,
year = {2024},
author = {Winders, S and Yoo, L and Heitkemper, M and Kamp, K},
title = {Multilevel Factors and Sleep in Adults With Inflammatory Bowel Disease: A Qualitative Study.},
journal = {Crohn's &amp; colitis 360},
volume = {6},
number = {4},
pages = {otae075},
pmid = {39691468},
issn = {2631-827X},
abstract = {BACKGROUND: This study aimed to describe the patient-reported factors that impact sleep among individuals with inflammatory bowel disease (IBD), aligning with the Social Ecological Model of Sleep. This addresses the gap in IBD sleep research, which predominantly focuses on individual-level factors and their impact on sleep.<br><br>METHODS: Adults (ages 18-65) with IBD were recruited online through ResearchMatch in June 2023. Participants filled out survey questions on their demographic characteristics, health history, sleep, and IBD-related symptoms. Content analysis was conducted on 2 open-ended questions about factors that impacted their sleep.<br><br>RESULTS: This analysis included 163 adults with IBD (M&#x2005;=&#x2005;39 years of age, 76.7% White, 91.4% non-Hispanic or Latino, 66.9% female, and 83.4% active IBD) who answered open-ended questions with comments about their sleep. Most participants indicated an individual-level factor impacted their sleep quality (85.3%, n&#x2005;=&#x2005;139), categorized into 5 subthemes: Mental health, health, behavior and choices, physiology, and attitudes. Additionally, participants (43.6%, n&#x2005;=&#x2005;71) mentioned social-level factors divided into 7 subthemes: Family, work, home, neighborhood, social network, and school. A smaller group of participants (17.2%, n&#x2005;=&#x2005;28) mentioned societal-level factors designated into 4 subthemes: Natural environment and geography, technology, 24/7 society, and economics.<br><br>CONCLUSIONS: This study highlights the need for tailored sleep interventions for those with IBD that consider not only disease activity but also mental health, family, work, and the natural environment. IBD clinics should prioritize sleep health using an interdisciplinary approach to holistically address the unique needs of those with IBD.},
}
@article {pmid39692459,
year = {2024},
author = {Shitindo, M},
title = {Interactions between wild pigs and the spread of disease.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39692459},
issn = {2050-084X},
mesh = {Animals ; *Animals, Wild ; Swine ; Swine Diseases ; Geographic Information Systems ; Humans ; },
abstract = {Tracking wild pigs with GPS devices reveals how their social interactions could influence the spread of disease, offering new strategies for protecting agriculture, wildlife, and human health.},
}
@article {pmid39694720,
year = {2025},
author = {Reynolds, SA and Beery, S and Burgess, N and Burgman, M and Butchart, SHM and Cooke, SJ and Coomes, D and Danielsen, F and Di Minin, E and Durán, AP and Gassert, F and Hinsley, A and Jaffer, S and Jones, JPG and Li, BV and Mac Aodha, O and Madhavapeddy, A and O'Donnell, SAL and Oxbury, WM and Peck, L and Pettorelli, N and Rodríguez, JP and Shuckburgh, E and Strassburg, B and Yamashita, H and Miao, Z and Sutherland, WJ},
title = {The potential for AI to revolutionize conservation: a horizon scan.},
journal = {Trends in ecology &amp; evolution},
volume = {40},
number = {2},
pages = {191-207},
doi = {10.1016/j.tree.2024.11.013},
pmid = {39694720},
issn = {1872-8383},
mesh = {*Conservation of Natural Resources/methods ; *Biodiversity ; *Artificial Intelligence ; Animals ; },
abstract = {Artificial Intelligence (AI) is an emerging tool that could be leveraged to identify the effective conservation solutions demanded by the urgent biodiversity crisis. We present the results of our horizon scan of AI applications likely to significantly benefit biological conservation. An international panel of conservation scientists and AI experts identified 21 key ideas. These included species recognition to uncover 'dark diversity', multimodal models to improve biodiversity loss predictions, monitoring wildlife trade, and addressing human-wildlife conflict. We consider the potential negative impacts of AI adoption, such as AI colonialism and loss of essential conservation skills, and suggest how the conservation field might adapt to harness the benefits of AI while mitigating its risks.},
}
@article {pmid39695260,
year = {2024},
author = {Ma, X and Zheng, G and Xu, C and Moskal, LM and Gong, P and Guo, Q and Huang, H and Li, X and Liang, X and Pang, Y and Wang, C and Xie, H and Yu, B and Zhao, B and Zhou, Y},
title = {A global product of 150-m urban building height based on spaceborne lidar.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1387},
pmid = {39695260},
issn = {2052-4463},
support = {42171340//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Urban building height, as a fundamental 3D urban structural feature, has far-reaching applications. However, creating readily available datasets of recent urban building heights with fine spatial resolutions and global coverage remains a challenging task. Here, we provide a 150-m global urban building heights dataset around 2020 by combining the spaceborne lidar (Global Ecosystem Dynamics Investigation, GEDI), multi-sourced data (Landsat-8, Sentinel-2, and Sentinel-1), and topographic data. The validation results revealed that the GEDI-estimated building height samples were effective compared to the reference data (Pearson's r = 0.81, RMSE = 3.58 m). The mapping product also demonstrated good performance, as indicated by its strong correlation with the reference data (Pearson's r = 0.71, RMSE = 4.73 m). Compared with the currently existing datasets, it holds the ability to provide a spatial resolution (150 m) with a great level of inherent details about the spatial heterogeneity and flexibility of updating using the GEDI samples as inputs. This product will boost future urban studies across many fields, including environmental, ecological, and social sciences.},
}
@article {pmid39695923,
year = {2024},
author = {Zhang, Z and Li, Q and Li, H and Wei, S and Yu, W and Peng, Z and Wei, F and Zhou, W},
title = {Integrative multi-omics analysis reveals the contribution of neoVTX genes to venom diversity of Synanceia verrucosa.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1210},
pmid = {39695923},
issn = {1471-2164},
support = {2023YFF1304900//Ministry of Science and Technology of the People's Republic of China/ ; 2024A1515013196//Science and Technology Department of Guangdong Province/ ; SLYJ2023B4004//Guangdong Forestry Administration/ ; GML2020GD0804//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; GML2022GD0804//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 32222014//National Natural Science Foundation of China/ ; 2021YFF0502804//Ministry of Science and Technology of China/ ; },
mesh = {Animals ; *Transcriptome ; Fish Venoms/genetics/chemistry ; Genomics/methods ; Proteomics ; Proteome ; Alternative Splicing ; Fishes/genetics ; Phylogeny ; Gene Expression Profiling ; Multiomics ; },
abstract = {BACKGROUND: Animal venom systems are considered as valuable model for investigating the molecular mechanisms underlying phenotypic evolution. Stonefish are the most venomous and dangerous fish because of severe human envenomation and occasionally fatalities, whereas the genomic background of their venom has not been fully explored compared with that in other venomous animals.<br><br>RESULTS: In this study, we followed modern venomic pipelines to decode the Synanceia verrucosa venom components. A catalog of 478 toxin genes was annotated based on our assembled chromosome-level genome. Integrative analysis of the high-quality genome, the transcriptome of the venom gland, and the proteome of crude venom revealed mechanisms underlying the venom complexity in S. verrucosa. Six tandem-duplicated neoVTX subunit genes were identified as the major source for the neoVTX protein production. Further isoform sequencing revealed massive alternative splicing events with a total of 411 isoforms demonstrated by the six genes, which further contributed to the venom diversity. We then characterized 12 dominantly expressed toxin genes in the venom gland, and 11 of which were evidenced to produce the venom protein components, with the neoVTX proteins as the most abundant. Other major venom proteins included a presumed CRVP, Kuntiz-type serine protease inhibitor, calglandulin protein, and hyaluronidase. Besides, a few of highly abundant non-toxin proteins were also characterized and they were hypothesized to function in housekeeping or hemostasis maintaining roles in the venom gland. Notably, gastrotropin like non-toxin proteins were the second highest abundant proteins in the venom, which have not been reported in other venomous animals and contribute to the unique venom properties of S. verrucosa.<br><br>CONCLUSIONS: The results identified the major venom composition of S. verrucosa, and highlighted the contribution of neoVTX genes to the diversity of venom composition through tandem-duplication and alternative splicing. The diverse neoVTX proteins in the venom as lethal particles are important for understanding the adaptive evolution of S. verrucosa. Further functional studies are encouraged to exploit the venom components of S. verrucosa for pharmaceutical innovation.},
}
@article {pmid39700412,
year = {2024},
author = {Duan, HN and Hearne, G and Polikar, R and Rosen, GL},
title = {The Naïve Bayes classifier++ for metagenomic taxonomic classification-query evaluation.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {1},
pages = {},
pmid = {39700412},
issn = {1367-4811},
support = {1936791//National Science Foundation/ ; },
mesh = {*Metagenomics/methods ; Bayes Theorem ; *Software ; Algorithms ; Databases, Genetic ; },
abstract = {MOTIVATION: This study examines the query performance of the NBC++ (Incremental Naive Bayes Classifier) program for variations in canonicality, k-mer size, databases, and input sample data size. We demonstrate that both NBC++ and Kraken2 are influenced by database depth, with macro measures improving as depth increases. However, fully capturing the diversity of life, especially viruses, remains a challenge.<br><br>RESULTS: NBC++ can competitively profile the superkingdom content of metagenomic samples using a small training database. NBC++ spends less time training and can use a fraction of the memory than Kraken2 but at the cost of long querying time. Major NBC++ enhancements include accommodating canonical k-mer storage (leading to significant storage savings) and adaptable and optimized memory allocation that accelerates query analysis and enables the software to be run on nearly any system. Additionally, the output now includes log-likelihood values for each training genome, providing users with valuable confidence information.<br><br>Source code and Dockerfile are available at http://github.com/EESI/Naive_Bayes.},
}
@article {pmid39700981,
year = {2025},
author = {Wong, SY and Machado-de-Lima, NM and Wilkins, D and Zhang, E and Ferrari, BC},
title = {Fine-scale landscape heterogeneity drives microbial community structure at Robinson Ridge, East Antarctica.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {177964},
doi = {10.1016/j.scitotenv.2024.177964},
pmid = {39700981},
issn = {1879-1026},
mesh = {Antarctic Regions ; *Soil Microbiology ; *Microbiota ; *Environmental Monitoring ; Soil/chemistry ; Biodiversity ; Ecosystem ; },
abstract = {Life at Robinson Ridge, located in the Windmill Islands region of East Antarctica, is susceptible to a changing climate. At this site, responses of the vegetation communities and moss-beds have been well researched, but corresponding information for microbial counterparts is still lacking. To bridge this knowledge gap, we established baseline data for monitoring the environmental drivers shaping the soil microbial community on the local 'hillslope' scale. Using triplicate 300-m long transects encompassing a hillslope with wind-exposed arid soils near the top, and snowmelt-sustained-moss beds at the bottom, we assessed the fine-scale heterogeneity of the soil environmental and microbial properties. Moist, low-lying, and vegetated soils exhibited higher soil fertility and unique biodiversity, with taxa adapted to thrive in moist conditions (i.e., Tardigrada, Phragmoplastophyta, Chloroflexi) and those that have previously demonstrated strong specificity for moss species (i.e., Fibrobacterota, Mucoromycota and Cyanobacteria) dominating. In contrast, elevated soils with limited moisture and nutrients were dominated by metabolically diverse phyla like Actinobacteriota and Ascomycota. Significant differences in microbial communities were observed at both hillslope (50-300 m) and fine spatial scales, as small as 0.1 m. Vertical heterogeneity was observed with higher abundances of Cyanobacteria and micro-algae in surfaces compared to subsoil, potentially indicating early biocrust formation. Stochastic and deterministic processes governing phylogenetic assembly were linked to soil positional groups and microbial domains rather than soil depth. Gradient Forest modeling identified critical environmental thresholds, such as ammonia, manganese, and sulphur, responsible for drastic community changes following level alterations. This reinforces the existence of strong niche preferences and distinct distribution patterns within the local microbial communities. This study highlights the need for finer-scale investigations considering site topography to better understand the relationship between environmental drivers and local microbiota. Ultimately, these insights enable us to understand environmental drivers and predict Antarctic ecosystem responses, helping safeguard this fragile environment.},
}
@article {pmid39701966,
year = {2024},
author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L},
title = {Unraveling the ancient fungal DNA from the Iceman gut.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1225},
pmid = {39701966},
issn = {1471-2164},
mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; },
abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).<br><br>METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.<br><br>RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.<br><br>CONCLUSION: We suggest that &#xd6;tzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.},
}
@article {pmid39703500,
year = {2024},
author = {Townsend, HA and Rosenberger, KJ and Vanderlinden, LA and Inamo, J and Zhang, F},
title = {Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1454263},
pmid = {39703500},
issn = {1664-3224},
support = {T15 LM009451/LM/NLM NIH HHS/United States ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; *Genome-Wide Association Study ; Inflammation/genetics ; Arthritis, Rheumatoid/genetics/immunology ; Polymorphism, Single Nucleotide ; Genetic Predisposition to Disease ; Colitis, Ulcerative/genetics/immunology ; Algorithms ; Sequence Analysis, RNA/methods ; },
abstract = {BACKGROUND: Understanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible.<br><br>METHODS: We present a 3-step robust benchmarking analysis of integrating GWAS and scRNA-seq to identify genetically relevant cell states and genes in inflammatory diseases. First, we applied and compared the results of three recent algorithms, based on pathways (scGWAS), single-cell disease scores (scDRS), or both (scPagwas), according to accuracy/sensitivity and interpretability. While previous studies focused on coarse cell types, we used disease-specific, fine-grained single-cell atlases (183,742 and 228,211 cells) and GWAS data (Ns of 97,173 and 45,975) for rheumatoid arthritis (RA) and ulcerative colitis (UC). Second, given the lack of scRNA-seq for many diseases with GWAS, we further tested the tools' resolution limits by differentiating between similar diseases with only one fine-grained scRNA-seq atlas. Lastly, we provide a novel evaluation of noncoding SNP incorporation methods by testing which enabled the highest sensitivity/accuracy of known cell-state calls.<br><br>RESULTS: We first found that single-cell based tools scDRS and scPagwas called superior numbers of supported cell states that were overlooked by scGWAS. While scGWAS and scPagwas were advantageous for gene exploration, scDRS effectively accounted for batch effect and captured cellular heterogeneity of disease-relevance without single-cell genotyping. For noncoding SNP integration, we found a key trade-off between statistical power and confidence with positional (e.g. MAGMA) and non-positional approaches (e.g. chromatin-interaction, eQTL). Even when directly incorporating noncoding SNPs through 5' scRNA-seq measures of regulatory elements, non disease-specific atlases gave misleading results by not containing disease-tissue specific transcriptomic patterns. Despite this criticality of tissue-specific scRNA-seq, we showed that scDRS enabled deconvolution of two similar diseases with a single fine-grained scRNA-seq atlas and separate GWAS. Indeed, we identified supported and novel genetic-phenotype linkages separating RA and ankylosing spondylitis, and UC and crohn's disease. Overall, while noting evolving single-cell technologies, our study provides key findings for integrating expanding fine-grained scRNA-seq, GWAS, and noncoding SNP resources to unravel the complexities of inflammatory diseases.},
}
@article {pmid39705088,
year = {2025},
author = {Deuker, A and Wittkugel, J and Dublin, Y and Braunstein, B and Rein, R and Davids, K and Vogt, T},
title = {Beyond the Pitch: Unveiling the Concave Hull as Soccer's Ecological Niche in Practice Design.},
journal = {Research quarterly for exercise and sport},
volume = {96},
number = {3},
pages = {463-474},
doi = {10.1080/02701367.2024.2434155},
pmid = {39705088},
issn = {2168-3824},
mesh = {*Soccer/physiology/psychology ; Humans ; *Athletic Performance/physiology/psychology ; Cross-Over Studies ; Geographic Information Systems ; Male ; Young Adult ; *Environment Design ; Adult ; },
abstract = {An ecological niche is a field in a landscape of affordances, rich in information inviting its inhabitants to develop functionality and effectiveness of their behavior. This idea means that, in sports like soccer, the playing area encapsulates an ecological niche, replete with affordances inviting collective and individual technical-tactical actions, contextualized with associated psychological and physical demands. To examine the co-adaptive relationships framing players' actions in their ecological niche, the present study employed a crossover design with repeated measures to compare the players' transactions within 11 vs. 11 training games across four different field dimensions (from official size to a small-sided game). Player transactions with the performance environment were analyzed across 40 game sequences, using 10Hz GPS positional data. Metrics such as convex hull dimensions, field occupancy, and proximity to opponents were derived. Repeated-measures ANOVA revealed significant differences between tendencies for forming synergies constrained by field dimensions scaling. When field size was reduced, the convex hull dimension significantly decreased. Additionally, relative field occupancy and distance to nearest opponent exhibited significant changes, especially when contrasted with performance transactions emerging on the official size field. These observations underline the essential functional relationship between the playing field dimension and emergent player actions. Such findings underscore the need for soccer coaches and training designers to integrate the specificity of field dimension scaling in training designs to represent competitive performance contexts. Data analytics deriving spatial constraint values from competitive matches may help researchers and practitioners improve task representativeness in practice and performance preparation, supporting the optimality of training niches in soccer.},
}
@article {pmid39707199,
year = {2024},
author = {Zhang, M and Sun, Y and Lan, Y and Cheng, L and Lv, Z and Han, M and Yang, L},
title = {Multiomics joint analysis reveals the potential mechanism of differences in the taproot thickening between cultivated ginseng and mountain-cultivated ginseng.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1228},
pmid = {39707199},
issn = {1471-2164},
support = {20230204001YY//the Key Research and Development Projects of Jilin Province Science and Technology Development Plan/ ; 20200504002YY//the Major Projects of Jilin Province Science and Technology Development Plan/ ; CARS-21//the National Modern Agricultural Industrial Technology System Fund Project/ ; },
mesh = {*Panax/genetics/growth &amp; development/metabolism ; *Plant Roots/genetics/growth &amp; development/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Transcriptome ; Metabolomics ; Starch/metabolism ; Sucrose/metabolism ; Phenotype ; Genomics ; Multiomics ; },
abstract = {Panax ginseng is an important medicinal plant in China and is classified into two types: cultivated ginseng (CFCG) and mountain-cultivated ginseng (MCG). The two types of genetic varieties are the same, but the growth environments and management practices are different, resulting in substantial differences in their taproot morphology. Currently, there is a paucity of research on the internal mechanisms that regulate the phenotypic differences between cultivated ginseng and mountain-cultivated ginseng. In this study, we explored the potential mechanisms underlying their phenotypic differences using transcriptomic and metabolomic techniques. The results indicate that the taproot thickening of CFCG was significantly greater than that of MCG. Compared with MCG-4, MCG-10, and MCG-18, the diameters of the taproots of CFCG-4 increased by 158.96, 81.57, and 43.21%, respectively. Additionally, the contents of sucrose and starch in the taproot, as well as TRA and DHZR, were markedly elevated. Transcriptome analysis revealed that compared with MCG of different age groups, genes associated with starch and sucrose metabolism pathways (PgSUS1, PgSPS1, PgSPS3, and PgglgC1) were significantly upregulated in CFCG-4, whereas genes involved in the phenylpropanoid biosynthesis pathway (PgPER3, PgPER51, and PgPER12) were significantly downregulated in CFCG-4. This imbalance in the metabolic pathways suggests that these genes play crucial roles in ginseng taproot thickening. PgbHLH130 and PgARF18 may be key regulators of transcriptional changes in these pathways. These findings elucidate the molecular mechanisms governing ginseng taproot thickening, and have important implications for enhancing the overall quality and value of ginseng.},
}
@article {pmid39709502,
year = {2024},
author = {Jakobsson, M and Mohammad, R and Karlsson, M and Salas-Romero, S and Vacek, F and Heinze, F and Bringensparr, C and Castro, CF and Johnson, P and Kinney, J and Cardigos, S and Bogonko, M and Accettella, D and Amblas, D and An, L and Bohan, A and Brandt, A and Bünz, S and Canals, M and Casamor, JL and Coakley, B and Cornish, N and Danielson, S and Demarte, M and Di Franco, D and Dickson, ML and Dorschel, B and Dowdeswell, JA and Dreutter, S and Fremand, AC and Hall, JK and Hally, B and Holland, D and Hong, JK and Ivaldi, R and Knutz, PC and Krawczyk, DW and Kristofferson, Y and Lastras, G and Leck, C and Lucchi, RG and Masetti, G and Morlighem, M and Muchowski, J and Nielsen, T and Noormets, R and Plaza-Faverola, A and Prescott, MM and Purser, A and Rasmussen, TL and Rebesco, M and Rignot, E and Rysgaard, S and Silyakova, A and Snoeijs-Leijonmalm, P and Sørensen, A and Straneo, F and Sutherland, DA and Tate, AJ and Travaglini, P and Trenholm, N and van Wijk, E and Wallace, L and Willis, JK and Wood, M and Zimmermann, M and Zinglersen, KB and Mayer, L},
title = {The International Bathymetric Chart of the Arctic Ocean Version 5.0.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1420},
pmid = {39709502},
issn = {2052-4463},
abstract = {Knowledge about seafloor depth, or bathymetry, is crucial for various marine activities, including scientific research, offshore industry, safety of navigation, and ocean exploration. Mapping the central Arctic Ocean is challenging due to the presence of perennial sea ice, which limits data collection to icebreakers, submarines, and drifting ice stations. The International Bathymetric Chart of the Arctic Ocean (IBCAO) was initiated in 1997 with the goal of updating the Arctic Ocean bathymetric portrayal. The project team has since released four versions, each improving resolution and accuracy. Here, we present IBCAO Version 5.0, which offers a resolution four times as high as Version 4.0, with 100 × 100 m grid cells compared to 200 × 200 m. Over 25% of the Arctic Ocean is now mapped with individual depth soundings, based on a criterion that considers water depth. Version 5.0 also represents significant advancements in data compilation and computing techniques. Despite these improvements, challenges such as sea-ice cover and political dynamics still hinder comprehensive mapping.},
}
@article {pmid39709508,
year = {2024},
author = {De Wint, FC and Nicholson, S and Koid, QQ and Zahra, S and Chestney-Claassen, G and Seelan, JSS and Xie, J and Xing, S and Fayle, TM and Haelewaters, D},
title = {Introducing a global database of entomopathogenic fungi and their host associations.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1418},
pmid = {39709508},
issn = {2052-4463},
support = {2023 Student Mobility Grant to F.C.D.W.//EC | Erasmus+/ ; Senior Postdoctoral Fellowship 1206024N to D.H.//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
mesh = {Animals ; Biodiversity ; *Databases, Factual ; Host Specificity ; *Hypocreales ; *Insecta/microbiology ; *Internationality ; *Host Microbial Interactions ; },
abstract = {Pathogens significantly influence natural and agricultural ecosystems, playing a crucial role in the regulation of species populations and maintaining biodiversity. Entomopathogenic fungi (EF), particularly within the Hypocreales order, exemplify understudied pathogens that infect insects and other arthropods globally. Despite their ecological importance, comprehensive data on EF host specificity and geographical distribution are lacking. To address this, we present EntomoFun 1.0, an open-access database centralizing global records of EF-insect associations in Hypocreales. This database includes 1,791 records detailing EF species, insect host taxa, countries of occurrence, life stages of hosts, and information sources. EntomoFun 1.0 is constructed based on 600 literature sources, as well as herbarium specimens of the Royal Botanical Gardens, Kew. This database is intended to test hypotheses, identify knowledge gaps, and stimulate future research. Contents of the EntomoFun 1.0 database are visualized with a global map, taxonomic chart, bipartite community network, and graphs.},
}
@article {pmid39710433,
year = {2024},
author = {Yuan, H and Hicks, P and Ahmadian, M and Johnson, KA and Valtadoros, L and Krishnan, A},
title = {Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39710433},
issn = {1477-4054},
support = {2328140//National Science Foundation/ ; },
mesh = {*Metadata ; *Natural Language Processing ; *Machine Learning ; Humans ; Computational Biology/methods ; Proteomics/methods ; Vocabulary, Controlled ; },
abstract = {Reusing massive collections of publicly available biomedical data can significantly impact knowledge discovery. However, these public samples and studies are typically described using unstructured plain text, hindering the findability and further reuse of the data. To combat this problem, we propose txt2onto 2.0, a general-purpose method based on natural language processing and machine learning for annotating biomedical unstructured metadata to controlled vocabularies of diseases and tissues. Compared to the previous version (txt2onto 1.0), which uses numerical embeddings as features, this new version uses words as features, resulting in improved interpretability and performance, especially when few positive training instances are available. Txt2onto 2.0 uses embeddings from a large language model during prediction to deal with unseen-yet-relevant words related to each disease and tissue term being predicted from the input text, thereby explaining the basis of every annotation. We demonstrate the generalizability of txt2onto 2.0 by accurately predicting disease annotations for studies from independent datasets, using proteomics and clinical trials as examples. Overall, our approach can annotate biomedical text regardless of experimental types or sources. Code, data, and trained models are available at https://github.com/krishnanlab/txt2onto2.0.},
}
@article {pmid39713561,
year = {2024},
author = {Blair, ME and Noguera-Urbano, EA and Ochoa-Quintero, JM and Paz, A and Lopez-Gallego, C and Echeverry-Galvis, M&#xc1; and Zuloaga, J and Rodríguez, P and Lemus-Mejia, L and Ersts, P and López-Lozano, DF and Aiello-Lammens, ME and Arango, HM and Buitrago, L and Chang Triguero, S and Cruz-Rodríguez, CA and Díaz-Nieto, JF and Escobar, D and Grisales-Betancur, V and Johnson, BA and Kass, JM and Londoño-Murcia, MC and Merow, C and Muñoz-Rodríguez, CJ and Olaya-Rodríguez, MH and Parra, JL and Pinilla-Buitrago, GE and Roach, NS and Rojas-Soto, O and Roncancio-Duque, N and Suárez-Valencia, E and Urbina-Cardona, JN and Velásquez-Tibatá, J and Zapata-Martinez, CA and Anderson, RP},
title = {Software codesign between end users and developers to enhance utility for biodiversity conservation.},
journal = {Bioscience},
volume = {74},
number = {12},
pages = {867-873},
pmid = {39713561},
issn = {0006-3568},
abstract = {Creating software tools that address the needs of a wide range of decision-makers requires the inclusion of differing perspectives throughout the development process. Software tools for biodiversity conservation often fall short in this regard, partly because broad decision-maker needs may exceed the toolkits of single research groups or even institutions. We show that participatory, collaborative codesign enhances the utility of software tools for better decision-making in biodiversity conservation planning, as demonstrated by our experiences developing a set of integrated tools in Colombia. Specifically, we undertook an interdisciplinary, multi-institutional collaboration of ecological modelers, software engineers, and a diverse profile of potential end users, including decision-makers, conservation practitioners, and biodiversity experts. We leveraged and modified common paradigms of software production, including codesign and agile development, to facilitate collaboration through all stages (including conceptualization, development, testing, and feedback) to ensure the accessibility and applicability of the new tools to inform decision-making for biodiversity conservation planning.},
}
@article {pmid39716000,
year = {2025},
author = {Chunduri, JR and Sagar, SP},
title = {Insect Brain Proteomics: A Case Study of Periplaneta americana.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2884},
number = {},
pages = {99-118},
pmid = {39716000},
issn = {1940-6029},
mesh = {Animals ; *Periplaneta/metabolism ; *Proteomics/methods ; *Brain/metabolism ; *Insect Proteins/metabolism/analysis ; *Proteome ; Chromatography, Liquid/methods ; Mass Spectrometry/methods ; Computational Biology/methods ; },
abstract = {Insects are known invertebrate species with economic, ecological, pathological, and medicinal value, as well as closely associated with human populations. Entomophagy and entomotherapy are future promising prospects largely attributable to the abundant availability, high protein content, and climatic sustainability of insects. In particular, the insect brain is an important system with a secluded, compact, and protective exoskeleton. It is immunologically privileged and capable of producing a robust immune response against pathogens. It is also a source of materials that initiate key activity throughout the body. Proteomic interrogation of Periplaneta americana enables understanding the role of this insect in the fields of food and pharmacology. Proximate analyses of P. americana highlights its richness in proteins. Here we perform a simple proteomic analysis to study the brain proteome of P. americana. The processes applied during the study include gel-based isolation and separation of proteins, followed by NanoLC-MS (Orbitrap) analyses and bioinformatic interrogation of the data. The results demonstrated that this insect proteome comprises antimicrobial proteins, allergens, and proteins required for metabolic processes.},
}
@article {pmid39716198,
year = {2024},
author = {Mendoza, JN and Prūse, B and Ciriaco, A and Mendoza, A and Ciriaco, H and Buen, C and Pua, JJ and Primavera, F and Mattalia, G and Sõukand, R},
title = {Fishery and ecology-related knowledge about plants among fishing communities along Laguna Lake, Philippines.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {20},
number = {1},
pages = {108},
pmid = {39716198},
issn = {1746-4269},
mesh = {*Fisheries ; Philippines ; *Ethnobotany ; Humans ; *Knowledge ; *Conservation of Natural Resources ; *Lakes ; Ecosystem ; Fishes ; Animals ; Ecology ; Female ; Male ; Middle Aged ; Adult ; Plants ; },
abstract = {BACKGROUND: Ethnobotanical knowledge about plant roles in fisheries is crucial for sustainable resource management. Local ecological knowledge helps understand dynamics of the lake ecosystem. Fishers use plants based on availability and characteristics while adapting to the changes in the environment. Studying fishery related uses of plants and algae and the challenges interconnected with them from local perspectives can provide insights into their beneficial uses and impacts to the ecosystem.<br><br>METHODS: The study investigates the botanical knowledge of three fishing villages in Laguna Lake or Laguna de Bay (LB), Philippines, including Buhangin, Sampiruhan, and Mabato-Azufre, each with varying degrees of industrialization. The ethnobotanical study, which gathered 27 interviews between June 2022 and July 2024, included plant collection with the help of local collaborators, including local fishers as research guides.<br><br>RESULTS: Fishers in LB highlighted positive and negative plant-fishing interactions. The most frequently mentioned plant applications were fish habitat and fish hiding places. Fish food, spawning sites, conservation, and a number of challenges such as navigational concerns and aquaculture fish deaths had been previously reported in local use reports. The remaining observations provide new insights into plant-fishing interactions, including indicators of food quality and food sources for fish, the decrease in the action of waves, and how plants help in improving the quality of the water.<br><br>CONCLUSION: These results highlight that the knowledge of fishers regarding the ecosystem in which they conduct their fishing activities provides baseline information about the positive and negative relationships between plants and fishing activities in the region, which is vital for further understanding its biodiversity and ecosystem interactions. It is crucial to consider fisher knowledge and involve them as equal partners in conservation efforts of LB.},
}
@article {pmid39717508,
year = {2025},
author = {Wang, T and Campbell, C and Stockdale, AJ and Todd, S and McIntyre, K and Frankland, A and Jaworski, J and Glampson, B and Papadimitriou, D and Mercuri, L and Mayer, E and Jones, CR and Salih, H and Roadknight, G and Little, S and Noble, T and Várnai, KA and Davis, C and Heinson, AI and George, M and Borca, F and English, L and Romão, L and Ramlakhan, D and , and Woods, K and Davies, J and Nastouli, E and Khakoo, SI and Gelson, W and Cooke, GS and Barnes, E and Matthews, PC},
title = {Distinct virologic trajectories in chronic hepatitis B identify heterogeneity in response to nucleos(t)ide analogue therapy.},
journal = {JHEP reports : innovation in hepatology},
volume = {7},
number = {1},
pages = {101229},
pmid = {39717508},
issn = {2589-5559},
abstract = {BACKGROUND &amp; AIMS: The dynamics of HBV viral load (VL) in patients with chronic hepatitis B (CHB) on nucleos(t)ide analogue (NA) treatment and its relationship with liver disease are poorly understood. We aimed to study longitudinal VL patterns and their associations with CHB clinical outcomes.<br><br>METHODS: Utilising large scale, routinely collected electronic health records from six centres in England, collated by the National Institute for Health and Care Research Health Informatics Collaborative (NIHR HIC), we applied latent class mixed models to investigate VL trajectory patterns in adults receiving NA treatment. We assessed associations of VL trajectory with alanine transaminase, and with liver fibrosis/cirrhosis.<br><br>RESULTS: We retrieved data from 1,885 adults on NA treatment (median follow-up 6.2 years, IQR 3.7-9.3 years), with 21,691 VL measurements (median 10 per patient, IQR 5-17). Five VL classes were identified from the derivation cohort (n&#xa0;= 1,367, discrimination: 0.93, entropy: 0.90): class 1 'long term suppression' (n&#xa0;= 827, 60.5%), class 2 'timely virological suppression' (n&#xa0;= 254, 18.6%), class 3 'persistent moderate viraemia' (n&#xa0;= 140, 10.2%), class 4 'persistent high-level viraemia' (n&#xa0;= 44, 3.2%), and class 5 'slow virological suppression' (n&#xa0;= 102, 7.5%). The model demonstrated a discrimination of 0.93 and entropy of 0.88 for the validation cohort (n&#xa0;= 518). Alanine transaminase decreased variably over time in VL-suppressed groups (classes 1, 2, 5; all p <0.001), but did not significantly improve in those with persistent viraemia (classes 3, 4). Patients in class 5 had twofold increased hazards of fibrosis/cirrhosis compared with class 1 (adjusted hazard ratio, 2.00; 95% CI, 1.33-3.02).<br><br>CONCLUSIONS: Heterogeneity exists in virological response to NA therapy in CHB patients, with over 20% showing potentially suboptimal responses. Slow virological suppression is associated with liver disease progression.<br><br>IMPACT AND IMPLICATIONS: Treatment recommendations for people living with chronic hepatitis B virus (HBV) infection are becoming less stringent, meaning that more of the population will be eligible to receive therapy with nucleos(t)ide analogue agents. We explored outcomes of HBV treatment in a large UK dataset, describing different responses to treatment, and showing that the viral load is not completely suppressed after 1 year in about one in five cases, associated with an increased risk of liver complications. As treatment is rolled out more widely, patients and clinicians need to be aware of the potential for incomplete virologic responses. The findings can support the identification of high-risk individuals, improve early fibrosis and cirrhosis prediction, guide monitoring and preventive interventions, and support public health elimination goals.},
}
@article {pmid39717656,
year = {2024},
author = {Nguyen, TTT and de A Santiago, ALCM and Hallsworth, JE and Cordeiro, TRL and Voigt, K and Kirk, PM and Crous, PW and Júnior, MAM and Elsztein, C and Lee, HB},
title = {New Mucorales from opposite ends of the world.},
journal = {Studies in mycology},
volume = {109},
number = {},
pages = {273-321},
pmid = {39717656},
issn = {0166-0616},
abstract = {The Mucorales is a group of ancient fungi with global distribution. In the current study we accessed mucoralean fungi isolated from two countries on opposite sides of the Earth and in different hemispheres: South Korea and Brazil. Mucorales isolates were obtained from freshwater, soil, invertebrates, and fruit seeds and identified using phenotypic techniques combined with the DNA sequence data. These analyses revealed 15 new species including one that we affiliated to a newly proposed genus, Neofennellomyces. Names proposed for these 15 new species are Absidia cheongyangensis, A. fluvii, A. kunryangriensis, A. paracylindrospora, A. tarda, A. variiprojecta, A. variispora, Backusella varians, Mucor albicolonia, M. aurantiacus, M. cryophilus, M. glutinatus, M. paraorantomantidis, M. timomeni, and Neofennellomyces jeongsukae. Of these new species, 12 were isolated from South Korea: A. cheongyangensis, A. fluvii, A. kunryangriensis, A. paracylindrospora, B. varians, M. albicolonia, M. aurantiacus, M. cryophilus, M. glutinatus, M. paraorantomantidis, M. timomeni, and N. jeongsukae, and three from Brazil: A. tarda, A. variiprojecta, and A. variispora. Niche specificity of these fungi is discussed including newly recorded invertebrate hosts and a new geographic distribution for species of Backusella, Circinella, Cunninghamella, and Mucor. Given these findings, we provide an inventory of Mucorales. Taxonomic novelties: New genus: Neofennellomyces Hyang B. Lee &amp; T.T.T. Nguyen. New species: Absidia cheongyangensis Hyang B. Lee &amp; T.T.T. Nguyen, Absidia fluvii Hyang B. Lee, A.L. Santiago, P.M. Kirk, K. Voigt &amp; T.T.T. Nguyen, Absidia kunryangriensis Hyang B. Lee &amp; T.T.T. Nguyen, Absidia paracylindrospora Hyang B. Lee &amp; T.T.T. Nguyen, Absidia tarda T.R.L. Cordeiro, Hyang B. Lee &amp; A.L. Santiago, Absidia variiprojecta T.R.L. Cordeiro &amp; A.L. Santiago, Absidia variispora T.R.L. Cordeiro &amp; A.L. Santiago, Backusella varians Hyang B. Lee &amp; T.T.T. Nguyen, Mucor aurantiacus Hyang B. Lee &amp; T.T.T. Nguyen, Mucor cryophilus Hyang B. Lee &amp; T.T.T. Nguyen, Mucor albicolonia Hyang B. Lee &amp; T.T.T. Nguyen, Mucor glutinatus Hyang B. Lee &amp; T.T.T. Nguyen, Mucor paraorantomantidis Hyang B. Lee &amp; T.T.T. Nguyen, Mucor timomeni Hyang B. Lee &amp; T.T.T. Nguyen, Neofennellomyces jeongsukae Hyang B. Lee &amp; T.T.T. Nguyen. Citation: Nguyen TTT, de A. Santiago ALCM, Hallsworth JE, Cordeiro TRL, Voigt K, Kirk PM, Crous PW, Júnior MAM, Elsztein C, Lee HB (2024). New Mucorales from opposite ends of the world. Studies in Mycology 109: 273-321. doi: 10.3114/sim.2024.109.04.},
}
@article {pmid39718830,
year = {2024},
author = {Kicsiny, R and Hufnagel, L and Lóczi, L and Székely, L and Varga, Z},
title = {Modeling the Mutation and Competition of Certain Nutrient-Producing Protocells by Means of Specific Turing Machines.},
journal = {Artificial life},
volume = {31},
number = {1},
pages = {2-30},
doi = {10.1162/artl_a_00463},
pmid = {39718830},
issn = {1530-9185},
mesh = {*Mutation ; *Artificial Cells/metabolism ; *Models, Biological ; *Nutrients/metabolism ; },
abstract = {It is very important to model the behavior of protocells as basic lifelike artificial organisms more and more accurately from the level of genomes to the level of populations. A better understanding of basic protocell communities may help us in describing more complex ecological systems accurately. In this article, we propose a new comprehensive, bilevel mathematical model of a community of three protocell species (one generalist and two specialists). The aim is to achieve a model that is as basic/fundamental as possible while already displaying mutation, selection, and complex population dynamics phenomena (like competitive exclusion and keystone species). At the microlevel of genetic codes, the protocells and their mutations are modeled with Turing machines (TMs). The specialists arise from the generalist by means of mutation. Then the species are put into a common habitat, where, at the macrolevel of populations, they have to compete for the available nutrients, a part of which they themselves can produce. Because of different kinds of mutations, the running times of the species as TMs (algorithms) are different. This feature is passed on to the macrolevel as different reproduction times. At the macrolevel, a discrete-time dynamic model describes the competition. The model displays complex lifelike behavior known from population ecology, including the so-called competitive exclusion principle and the effect of keystone species. In future works, the bilevel model will have a good chance of serving as a simple and useful tool for studying more lifelike phenomena (like evolution) in their pure/abstract form.},
}
@article {pmid39719706,
year = {2025},
author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ},
title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.},
journal = {Cell genomics},
volume = {5},
number = {1},
pages = {100725},
pmid = {39719706},
issn = {2666-979X},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems/genetics ; Gene Transfer, Horizontal/genetics ; Bacteriophages/genetics ; Bifidobacterium longum/genetics ; Metagenome/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genome, Bacterial/genetics ; },
abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.},
}
@article {pmid39720717,
year = {2024},
author = {Luo, Z and Zhou, F and Jiang, S and Huang, J and Yang, L and Yang, Q and Shi, J and Li, E and Ma, Z and Li, Y},
title = {Immune and physiological responses in Penaeus monodon to ammonia-N stress: a multi-omics approach.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1510887},
pmid = {39720717},
issn = {1664-3224},
mesh = {Animals ; *Penaeidae/immunology ; *Ammonia/metabolism ; *Stress, Physiological/immunology ; *Oxidative Stress ; Transcriptome ; Metabolomics ; Immunity, Innate ; Gene Expression Profiling ; Nitrogen/metabolism ; Aquaculture ; Biomarkers ; Hepatopancreas/immunology/metabolism ; Multiomics ; },
abstract = {Ammonia-N stress is a significant environmental factor that adversely affects the health and productivity of aquaculture species. This study investigates the effects of ammonia-N stress on the shrimp Penaeus monodon through a combination of biochemical, histological, transcriptomic, and metabolomic analyses. Shrimp were exposed to ammonia-N stress for 12 and 96 hours, and key markers of oxidative stress, nitrogen metabolism, immune response, and overall health were assessed. The results showed that prolonged ammonia-N exposure causes significant hepatopancreatic damage, including atrophy and deformation. Transcriptomic analysis revealed significant changes in gene expression related to apoptosis, immune response, and key metabolic pathways, with particular emphasis on the disruption of innate immune signaling and defense mechanisms. Metabolomic analysis identified disruptions in nucleotide turnover, antioxidant defenses, and fundamental metabolic processes. These findings suggest that ammonia-N stress induces a multifaceted stress response in shrimp, involving oxidative stress, immune activation, and metabolic disturbances. Understanding these immune-related and metabolic mechanisms provides valuable insights into the molecular responses of crustaceans to environmental stress, laying the foundation for assessing the ecological risk of ammonia-N and identifying potential immunological biomarkers for monitoring and mitigating its adverse effects in aquaculture systems.},
}
@article {pmid39724139,
year = {2024},
author = {Stephens, JL and Fraga, LAO and Ferreira, JA and De Mondesert, L and Kitron, U and Clennon, JA and Fairley, JK},
title = {Spatial associations of Hansen's disease and schistosomiasis in endemic regions of Minas Gerais, Brazil.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {12},
pages = {e0012682},
pmid = {39724139},
issn = {1935-2735},
mesh = {Humans ; Brazil/epidemiology ; *Leprosy/epidemiology ; *Endemic Diseases ; Female ; Male ; Spatial Analysis ; Adult ; Incidence ; Adolescent ; Middle Aged ; Young Adult ; Child ; Geographic Information Systems ; Animals ; *Schistosomiasis mansoni/epidemiology ; *Schistosomiasis/epidemiology ; Child, Preschool ; Aged ; },
abstract = {BACKGROUND: Brazil has the second highest case count of Hansen's disease (leprosy, HD), but factors contributing to transmission in highly endemic areas of the country remain unclear. Recent studies have shown associations of helminth infection and leprosy, supporting a biological plausibility for increased leprosy transmission in areas with helminths. However, spatial analyses of the overlap of these infections are limited. Therefore, we aimed to spatially analyze these two diseases in a co-endemic area of Minas Gerais, Brazil, in order to identify potential epidemiologic associations.<br><br>METHODS: An ecological study using public health surveillance records and census data was conducted to investigate whether the occurrence of HD -and specifically multibacillary (MB) disease- was associated with the presence of schistosomiasis in a community of 41 municipalities in eastern Minas Gerais, Brazil from 2011 to 2015. Multivariate logistic regression and spatial cluster analyses using geographic information systems (GIS) were performed.<br><br>RESULTS: The average annual incidence of HD in the study area was 35.3 per 100,000 while Schistosoma mansoni average annual incidence was 26 per 100,000. Both HD and schistosomiasis were spatially distributed showing significant clustering across the study area. Schistosomiasis was present in 10.4% of the tracts with HD and thirteen high-high clusters of local bivariate autocorrelation for HD and schistosomiasis cases were identified. A multivariate non-spatial analysis found that census tracts with MB disease were more likely to have schistosomiasis when adjusted for population density, household density, and household income (aOR = 1.7, 95% CI 1.0, 2.7). This remained significant when accounting for spatial correlation (aOR = 1.1, 95% CI (1.0, 1.2)).<br><br>CONCLUSION: We found clustering of both HD and schistosomiasis in this area with some statistically significant overlap of multibacillary HD with S. mansoni infection. Not only did we provide an effective approach to study the epidemiology of two endemic neglected tropical diseases with geographic spatial analyses, we highlight the need for further clinical and translational studies to study the potential epidemiologic associations uncovered.},
}
@article {pmid39724715,
year = {2025},
author = {Zhang, L and Du, Y and Li, Y and Wang, T and Pan, Y and Xue, X and Mu, X and Qiu, J and Qian, Y},
title = {Mitochondrial mechanism of florfenicol-induced nonalcoholic fatty liver disease in zebrafish using multi-omics technology.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {136958},
doi = {10.1016/j.jhazmat.2024.136958},
pmid = {39724715},
issn = {1873-3336},
mesh = {Animals ; Zebrafish ; *Thiamphenicol/analogs &amp; derivatives/toxicity ; *Non-alcoholic Fatty Liver Disease/chemically induced/metabolism/pathology ; *Anti-Bacterial Agents/toxicity ; *Mitochondria/drug effects/metabolism ; *Water Pollutants, Chemical/toxicity ; Oxidative Stress/drug effects ; Liver/drug effects/metabolism/pathology ; Metabolomics ; Multiomics ; },
abstract = {Florfenicol (FF), a third-generation chloramphenicol antibiotic widely used in food-producing animals, has become a "pseudopersistent" environmental contaminant, raising concerns about its potential ecological and human health impacts. However, its bioaccumulation behavior and hepatotoxic mechanisms remain poorly understood. This study aims to address these gaps with a 28-day exposure experiment in adult zebrafish at 0.05 and 0.5 mg/L FF. Multiomic analyses (metabolomics, lipidomics, and transcriptomics), combined with histological and mitochondrial function assessments, were employed. Higher bioaccumulation was observed at 0.05 mg/L, potentially due to metabolic saturation at higher concentrations. Histological analysis revealed significant hepatic steatosis (>5 % steatosis area), indicative of moderate nonalcoholic fatty liver disease (NAFLD). Multiomic data demonstrated global dysregulation in energy metabolism, including marked alterations in lipids (accumulation of toxic sphingolipids, excessive fatty acids, and acylglycerol), amino acids, tricarboxylic acid cycle intermediates, and nucleotides. Crucially, mitochondrial dysfunction was identified as a central mechanism, with impaired respiratory chain activities, adenosine triphosphate depletion, elevated reactive oxygen species, and oxidative stress promoting NAFLD progression. These findings highlight mitochondrial impairment and oxidative stress as key drivers of FF-induced hepatotoxicity, providing novel insights into its toxicological mechanisms and emphasizing the ecological risks posed by antibiotic pollution in aquatic systems.},
}
@article {pmid39727130,
year = {2024},
author = {Jia, J and Su, X and Zhang, J and Lu, CL and Zhang, MY and Li, X and Dong, YG and Ren, HC},
title = {[Land use changes and driving forces of landslide area in Tongwei County, Gansu Province, Northwest China from 1985 to 2020.].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {10},
pages = {2833-2841},
doi = {10.13287/j.1001-9332.202410.020},
pmid = {39727130},
issn = {1001-9332},
mesh = {China ; *Landslides ; *Conservation of Natural Resources ; *Crops, Agricultural/growth &amp; development ; Ecosystem ; Trees/growth &amp; development ; Forests ; Grassland ; Environmental Monitoring/methods ; Disasters ; Geographic Information Systems ; Poaceae/growth &amp; development ; },
abstract = {Accurately analyzing the type of land use and change characteristics of disaster damage in landslide areas is of great significance to scientifically promote the optimization of regional land use pattern and disaster prevention and mitigation. We analyzed the characteristic parameters of landslides as well as the characteristics and driving factors of land use change from 1985 to 2020 in Tongwei County, Gansu Province, using ALOS DEM data and 1985-2020 land use data, GIS spatial analysis, land-use dynamic attitude, transfer matrix, and Geodetector. The results showed that a total of 1012 landslide samples were identified, characterized by medium elevation, gentle gradient, low elevation difference, short length, and small size. During 1985-2020, landslide area land use types were cropland, woodland, grassland, bare land and impervious surface, dominated by grassland and cropland. During 2015-2020, each category of single land use dynamic attitude reached the largest, with the value of cropland, grassland, woodland, bare land, and the combined land use being 3.1%, 3.0%, 10.9%, 20.0%, 1.5%, respectively. During the study period, land use change was dominated by cropland and grassland, with a total reduction of 4.39 km[2] in cultivated land area, which was converted into grassland and forest. There was no change in bare land and impervious surfaces. We investigated the driving factors of land use change across 2000-2005 and 2015-2020. Slope and normalized difference vegetation index had a stronger explanatory power for land use change during 2000-2005, while slope, population density and total population had a stronger explanatory power during 2015-2020. The land use mode of regional individual landslide tended to be unified, and the increase of grassland enhanced the vegetation cover of the region. The findings would provide a scientific basis for the development and reuse of disaster damaged land and ecological restoration.},
}
@article {pmid39727132,
year = {2024},
author = {Xin, PY and Tian, T and Zhang, ML and Han, WZ and Song, YT},
title = {[Assessment of habitat quality changes and driving factors in Jilin Province based on InVEST model and geodetector].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {10},
pages = {2853-2860},
doi = {10.13287/j.1001-9332.202410.026},
pmid = {39727132},
issn = {1001-9332},
mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; *Models, Theoretical ; Environmental Monitoring ; Forests ; Trees/growth &amp; development ; Geographic Information Systems ; },
abstract = {Jilin Province is an important ecological security barrier in Northeast China as it is located at the junction of the Northeast forest belts and the northern sand prevention belts. In recent years, Jilin Province has actively carried out ecological protection and restoration projects, resulting in a continuous improvement trend for the overall ecological environment. However, the evolution patterns and mechanisms of habitat quality are largely unkown. We applied the InVEST model and geographic detector method to analyze the changes in habitat quality and evaluate the main driving factors from 2000 to 2020. The results showed that the average habitat quality in Jilin Province showed a slight downward trend, and that the spatial heterogeneity characteristics of habitat quality in east and west gradually increased. The degree of habitat degradation presented a single nuclear radiation pattern centered on Changchun City. Vegetation factors and terrain factors were the first and secondary causes of spatial heterogeneity of habitat quality, respectively. The average habitat quality within the eco-redline of Jilin Province was showing an increasing trend year by year, which was consistent with the overall distribution of regions with extremely high habitat quality levels. There was a local spatial dislocation (the phenomenon of extremely high habitat quality levels not within the eco-redline) in the eastern part of Jilin Province. Our results could provide reference basis for ecosystem protection and the spatial pattern optimization.},
}
@article {pmid39729740,
year = {2025},
author = {Gupta, AK and Ravikumar, K and Gopal, V and Begum, N and Tabassum, and Sangeetha, S and Narendran, P and Shankar, D},
title = {A trans-disciplinary agro-ecology strategy to grow medicinal plants.},
journal = {Journal of Ayurveda and integrative medicine},
volume = {16},
number = {1},
pages = {100985},
pmid = {39729740},
issn = {0975-9476},
abstract = {The scope of the emerging field of Ayurvedic-biology visualized thus far is confined to studies on dimensions pertaining to clinical and experimental pharmacology, basic trans-disciplinary science and drug design. However, given the multiple facets of classical Ayurveda knowledge system, its application in the field of organic agriculture perhaps also needs to be urgently explored. The urgency is due to the growing public acceptance of Ayurveda as a preferred clinical choice for well-being and disease management. The turnover of the sector across manufacturing and health services is estimated to be around Rs.1,00,000 crores per annum. Medicinal plants today and in the coming decade will therefore be required in large volumes and given that their applications are solely for enhancing health of humans, livestock (Pashu Ayurveda) and crops (Vriksh Ayurveda), it is imperative that they be cultivated in an organic manner employing the fusion of best available inter-cultural knowledge. The Ayurvedic subjects relevant for organic agriculture are Desh vichar, Dravya guna Shastra and Vriksh Ayurveda. From the perspective of modern biology subjects like soil micro biome, genetics, plant physiology and the natural geographical distribution of species are relevant. It must be stated at the very outset that this article is largely theoretical. While experiments in Vriksh Ayurveda have been attempted on a small scale, the fusion of Ayurveda and biology for improving organic agriculture of medicinal plants has thus far not been systematically explored.},
}
@article {pmid39730187,
year = {2025},
author = {Yan, M and Andersen, TO and Pope, PB and Yu, Z},
title = {Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.},
journal = {Genome research},
volume = {35},
number = {2},
pages = {368-378},
pmid = {39730187},
issn = {1549-5469},
mesh = {Animals ; *Ruminants/microbiology/parasitology/genetics ; *Metagenomics/methods ; Metagenome ; *Deep Learning ; *Databases, Protein ; Rumen/microbiology ; Fungi/genetics/classification ; Computational Biology/methods ; *Eukaryota/genetics/classification ; *Gastrointestinal Microbiome/genetics ; },
abstract = {Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.},
}
@article {pmid39730727,
year = {2024},
author = {Kato, H},
title = {Daily walking time effects of the opening of a multifunctional facility "ONIKURU" using propensity score matching and GPS tracking techniques.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {31047},
pmid = {39730727},
issn = {2045-2322},
support = {24K17421//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; Female ; *Walking/physiology ; Male ; Adult ; *Geographic Information Systems ; *Propensity Score ; Middle Aged ; Young Adult ; Exercise/physiology ; Adolescent ; Environment Design ; Time Factors ; Smartphone ; },
abstract = {Urban design focused on improving walkability has received attention as a method of increasing physical activity among the population. However, only a few studies have examined the effect of walking time of opening multifunctional facilities as an architecture-scale intervention. This study aimed to clarify the effect of opening a multifunctional facility on residents' daily walking time. In addition, this study analyzed the gender and age subgroups. The natural experiment was conducted using the case of the Ibaraki City Cultural and Childcare Complex "ONIKURU," a public multifunctional facility. This study used GPS-trajectory data based on GPS tracking techniques, which is anonymized location data for smartphone users. The causal relationship was analyzed using propensity score matching and difference-in-differences analysis. The results showed that the opening of ONIKURU significantly increased the average walking time of visitors to 3.165 [- 1.697, 8.027] min/day compared with that of non-visitors. Specifically, visitors' average daily walking time improved to a level comparable to that of non-visitors after the opening of ONIKURU. In addition, opening ONIKURU significantly increased female young adults' average walking time to 3.385 [- 4.906, 11.676] min/day. Therefore, this study provides theoretical contributions to a health-promoting built environment significantly affecting walking at an architecture-scale intervention.},
}
@article {pmid39736019,
year = {2024},
author = {Kobzeva, K and Ivenkov, M and Gromov, R and Bushueva, O},
title = {HSP90 Family Members, Their Regulators and Ischemic Stroke Risk: A Comprehensive Molecular-Genetics and Bioinformatics Analysis.},
journal = {Frontiers in bioscience (Scholar edition)},
volume = {16},
number = {4},
pages = {19},
doi = {10.31083/j.fbs1604019},
pmid = {39736019},
issn = {1945-0524},
support = {22-15-00288//Russian Science Foundation/ ; },
mesh = {Humans ; *Polymorphism, Single Nucleotide ; *HSP90 Heat-Shock Proteins/genetics/metabolism ; *Ischemic Stroke/genetics ; Male ; Female ; Middle Aged ; *Computational Biology ; Aged ; *Genetic Predisposition to Disease ; Russia/epidemiology ; Risk Factors ; Case-Control Studies ; Heat Shock Transcription Factors/genetics/metabolism ; },
abstract = {BACKGROUND: Disruptions in proteostasis are recognized as key drivers in cerebro- and cardiovascular disease progression. Heat shock proteins (HSPs), essential for maintaining protein stability and cellular homeostasis, are pivotal in neuroperotection. Consequently, deepening the understanding the role of HSPs in ischemic stroke (IS) risk is crucial for identifying novel therapeutic targets and advancing neuroprotective strategies.<br><br>AIM: Our objective was to examine the potential correlation between single nucleotide polymorphisms (SNPs) in genes that encode members of the Heat shock protein 90 (HSP90), small heat shock proteins (HSPB), and heat shock factors (HSF) families, and the risk and clinical characteristics of IS.<br><br>METHODS: 953 IS patients and 1265 controls from Central Russia were genotyped for nine SNPs in genes encoding HSP90AA1, HSFs, and HSPBs using the MassArray-4 system and probe-based polymerase chain reaction (PCR).<br><br>RESULTS: In smokers, SNP rs1133026 HSPB8 increased the risk of IS (risk allele A, odds ratio (OR) = 1.43, 95% Confidence Interval (CI) 1.02-2.02, p = 0.035), and rs556439 HSF2 increased the brain infarct size (risk allele A, p = 0.02). In non-smokers, SNPs rs4279640 HSF1 (protective allele T, OR = 0.58, 95% CI 0.37-0.92, p = 0.02) and rs4264324 HSP90AA1 (protective allele C, OR = 0.11, 95% CI 0.01-0.78, p = 0.001) lowered the risk of recurrent stroke; SNP rs7303637 HSPB8 increased the age of onset of IS (protective allele T, p = 0.04). In patients with body mass index (BMI) &#x2265;25, SNPs rs556439 HSF2 (risk allele A, OR = 1.33, 95% CI 1.04-1.69, p = 0.02) and rs549302 HSF2 (risk allele G, OR = 1.34, 95% CI 1.02-1.75, p = 0.03) were linked to a higher risk of IS.<br><br>CONCLUSIONS: The primary molecular mechanisms through which the studied SNPs contribute to IS pathogenesis were found to be the regulation of cell death, inflammatory and oxidative stress responses.},
}
@article {pmid39739202,
year = {2025},
author = {Bard, NW and Davies, TJ and Cronk, QCB},
title = {Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14056},
pmid = {39739202},
issn = {1755-0998},
support = {RGPIN-2019-04041//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04439//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Fungi/classification/genetics/isolation &amp; purification ; *Plants/microbiology ; DNA, Ribosomal Spacer/genetics/chemistry ; *Computational Biology/methods ; DNA, Fungal/genetics/chemistry ; *DNA Barcoding, Taxonomic/methods ; *Genome, Plant ; Endophytes/classification/genetics ; *Biodiversity ; Sequence Analysis, DNA ; },
abstract = {Relatively little is known of the host associations and compatibility of fungal plant pathogens and endophytes. Publicly available plant genomic DNA can be mined to detect incidental fungal DNA, but taxonomic assignment can be challenging due to short lengths and variable discriminative power among different genomic regions and taxa. Here, we introduce a computationally lightweight and accessible Snakemake pipeline for rapid detection and classification (identification and assignment to taxonomic rank) of pathogenic and endophytic fungi (and other fungi associated with plants) that targets the internal transcribed spacer (ITS) region, a fungal barcode standard. We include methods for maximising query sequence length, which gives higher support for ITS1 and ITS2 taxonomic classifications by extending to other fragments of the ITS region and providing taxon-specific local cut-off and confidence scores. We demonstrate our pipeline with a case study using public genomic sequence data for six diverse plant species, including four species within Betula, an ecologically and economically important broadleaved forest tree genus, a shrub and a grass. Our pipeline classified fungi within minutes to a few hours per host individual, with 204 different fungal genera identified at high confidence (≥ 70%). Our pipeline detected and classified pathogenic and endophytic genera known to associate with Betula, and many others with no prior record of association. Our pipeline, leveraging existing sequence data, has several potential applications, including detecting cryptic fungal pathogens and helping characterise the endophytic fungal microbiome, bioprospecting commercially useful fungal species, and determining the plant host range of fungi.},
}
@article {pmid39742640,
year = {2025},
author = {Zhang, H and Dong, S and Shan, H and Yang, C and Wang, F},
title = {Application of the DEB-TKTD model with multi-omics data: Prediction of life history traits of Chinese mitten crab (Eriocheir sinensis) under different salinities.},
journal = {Ecotoxicology and environmental safety},
volume = {290},
number = {},
pages = {117635},
doi = {10.1016/j.ecoenv.2024.117635},
pmid = {39742640},
issn = {1090-2414},
mesh = {Animals ; *Brachyura/physiology/growth &amp; development ; *Salinity ; *Life History Traits ; Aquaculture ; Female ; Water Pollutants, Chemical/toxicity ; Metabolomics ; Multiomics ; },
abstract = {Saline-alkaline aquaculture plays a crucial role in the ecological restoration of saline soils, yet high water salinity can significantly restrict the growth of cultured organisms. The Chinese mitten crab (Eriocheir sinensis) is typically farmed in freshwater, to evaluate the effects of salinity stress on these crabs, this study conducted laboratory aquaculture experiments at salinities of ≤ 0.5 (freshwater), 6, 12, and 18 ‰. Regular data on crab survival and growth were collected over 35 days. Subsequently, tissues including the eyestalk, posterior gill, hepatopancreas, and ovary were sampled from crabs in both the freshwater control group and the 18 ‰ salinity treatment group for transcriptional and metabolomic analysis. The omics data were used to ascertain the physiological mode of action (pMoA) affected by salinity in the crabs. A dynamic energy budget toxicokinetic-toxicodynamic (DEB-TKTD) model was built based on these pMoAs to predict the life history traits of crabs across different salinities, including survival, growth, and reproduction. The omics results indicated that at 18 ‰, the osmoregulatory capacity and oxidative stress resistance were enhanced, and vitellogenin synthesis was stimulated. This suggests that the two pMoAs involved increasing maintenance costs and reallocating energy between soma and reproduction. DEB-TKTD model predictions fit well with the observed data, with high R[2] values (0.9704 for survival, 0.9842 for carapace width, and 0.9283 for reproduction) and low NRMSE (0.0093, 0.1175, and 0.0778, respectively). The predictions indicate that after 60 days, survival rates under salinities of 6, 12, and 18 ‰ decreased by 35.7 %, 56.7 %, and 66.2 %, respectively, compared to freshwater conditions. Growth in carapace width was similarly affected, with reductions of 21.5 %, 42.3 %, and 62.5 %, respectively. The maturation process was accelerated for crabs in saline conditions, with puberty achieved at 45, 36, and 31 days, compared to the freshwater group that had not matured. Furthermore, the LC50 for salinity decreased from 9.07 ‰ (95 % CI: 7.33-10.15 ‰) at 35 days to 4.59 ‰ (95 % CI: 3.12-5.83 ‰) at 60 days. The findings of this study indicate the significant impact of salinity on the survival, growth, and maturation of Chinese mitten crabs by altering maintenance costs and energy allocation. The DEB-TKTD model, informed by omics data, accurately predicts the life history traits of crabs under saline stress. This approach provides an innovative tool for ecological toxicological research in the aquaculture environment.},
}
@article {pmid39742992,
year = {2025},
author = {Kim, DH and Kim, Y},
title = {Factors Associated With Habitual Drug Use Among Adolescents: A Secondary Data Analysis.},
journal = {Asian nursing research},
volume = {19},
number = {1},
pages = {78-85},
doi = {10.1016/j.anr.2024.12.006},
pmid = {39742992},
issn = {2093-7482},
mesh = {Humans ; Adolescent ; Male ; Female ; *Substance-Related Disorders/epidemiology/psychology ; Republic of Korea/epidemiology ; *Adolescent Behavior/psychology ; Risk Factors ; Prevalence ; Risk-Taking ; Students/psychology/statistics &amp; numerical data ; Cross-Sectional Studies ; Surveys and Questionnaires ; Secondary Data Analysis ; },
abstract = {PURPOSE: Drug use during adolescence can have lasting health consequences, and understanding the factors that contribute to drug use is essential for effective prevention. This study aimed to identify the factors influencing habitual drug use among South Korean adolescents. It employed Bronfenbrenner's ecological model to examine personal, familial, school-related, and social factors.<br><br>METHODS: The study analyzed data from the 19th Korea Youth Risk Behavior Survey for 41,928 students from 1st grade of middle school to 3rd grade of high school. Data analysis involved cross-tabulation and logistic regression for complex samples.<br><br>RESULTS: The prevalence of habitual drug use was 1.4%. Significant personal factors included smoking [adjusted odds ratio (aOR)&#xa0;=&#xa0;2.61], alcohol consumption (aOR&#xa0;=&#xa0;1.55), sexual intercourse (aOR&#xa0;=&#xa0;1.45), smartphone overdependence (high-risk group aOR&#xa0;=&#xa0;2.04, potential risk group aOR&#xa0;=&#xa0;1.31), suicidal ideation (aOR&#xa0;=&#xa0;2.66), depressed mood (aOR&#xa0;=&#xa0;1.87), and loneliness (aOR&#xa0;=&#xa0;1.88). Significant family factors included non-cohabitation with family (aOR&#xa0;=&#xa0;1.86) and both parents being foreign-born (aOR&#xa0;=&#xa0;3.36). Experience of violence (aOR&#xa0;=&#xa0;2.95) was also a significant factor.<br><br>CONCLUSION: This study highlights the need for an integrated approach to prevent adolescent drug use by addressing adolescents' personal behaviors, family dynamics, and school environments. Prevention programs should account for the influence of multiple systems on habitual drug use. School and community nurses should adopt a comprehensive, multi-dimensional strategy that involves families, schools, and communities to prevent adolescent drug use. Additionally, there is a need to develop family-centered and culturally sensitive drug prevention programs for adolescents.},
}
@article {pmid39745426,
year = {2025},
author = {Gulyaeva, A and Liu, L and Garmaeva, S and Kruk, M and Weersma, RK and Harmsen, HJM and Zhernakova, A},
title = {Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements.},
journal = {Microbiology spectrum},
volume = {13},
number = {2},
pages = {e0106624},
pmid = {39745426},
issn = {2165-0497},
mesh = {*Prophages/genetics/isolation &amp; purification/classification ; *Retroelements/genetics ; Humans ; Genome, Viral ; Gastrointestinal Microbiome/genetics ; Metagenomics ; Host Specificity ; Computational Biology/methods ; Virome ; Feces/microbiology ; },
abstract = {Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.},
}
@article {pmid39746011,
year = {2025},
author = {Wohltjen, S and Colón, YI and Zhu, Z and Miller, K and Huang, WC and Mutlu, B and Li, Y and Niedenthal, PM},
title = {Uniting theory and data: the promise and challenge of creating an honest model of facial expression.},
journal = {Cognition &amp; emotion},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/02699931.2024.2446945},
pmid = {39746011},
issn = {1464-0600},
abstract = {People routinely use facial expressions to communicate successfully and to regulate other's behaviour, yet modelling the form and meaning of these facial behaviours has proven surprisingly complex. One reason for this difficulty may lie in an over-reliance on the assumptions inherent in existing theories of facial expression - specifically that (1) there is a putative set of facial expressions that signal an internal state of emotion, (2) patterns of facial movement have been empirically linked to the prototypical emotions in this set, and (3) static, non-social, posed images from convenience samples are adequate to validate the first two assumptions. These assumptions have guided the creation of datasets, which are then used to train unrepresentative computational models of facial expression. In this article, we discuss existing theories of facial expression and review how they have shaped current facial expression recognition tools. We then discuss the resources that are available to help researchers build a more ecologically valid model of facial expressions.},
}
@article {pmid39747514,
year = {2025},
author = {Liu, X and Tan, Y and Dong, J and Wu, J and Wang, X and Sun, Z},
title = {Assessing habitat selection parameters of Arabica coffee using BWM and BCM methods based on GIS.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8},
pmid = {39747514},
issn = {2045-2322},
support = {51979133//National Natural Science Foundation of China/ ; 202301AS070030//Yunnan Fundamental Research Projects/ ; 202302AE090024//Yunnan Major Science and Technology Special Plan/ ; },
mesh = {*Ecosystem ; *Geographic Information Systems ; *Coffea/growth &amp; development ; China ; Coffee ; Climate ; Decision Making ; Conservation of Natural Resources/methods ; Soil/chemistry ; },
abstract = {Arabica coffee, as one of the world's three native coffee species, requires rational planning for its growing areas to ensure ecological and sustainable agricultural development. This study aims to establish a decision-making framework using Geographic Information Systems (GIS) and Multi-Criteria Decision-Making (MCDM), with a focus on assessing the habitat suitability of Arabica coffee in Yunnan Province, China. The impacts of climate, topography, soil, and socio-economic factors were considered by selecting 13 criteria through correlation analysis. Indicator weights were determined using the Best-Worst Method (BWM), while weighted processing was conducted using the Base-Criterion Method (BCM). Sensitivity analysis was performed to verify the accuracy and stability of the model. Additionally, several decision models were evaluated to investigate regionalizing Arabica coffee habitats in Yunnan. The results highlighted that minimum temperature during the coldest month is crucial for evaluation purposes. The BWM-GIS model identified suitable areas comprising 13.55% of the total area as most suitable, 27.46% as suitable, and 59.00% as unsuitable, whereas corresponding values for the BCM-GIS model were 9.97%, 30.43%, and 59.59%. Despite employing different decision-making methods, both models yielded similar and consistent results. The suitable areas mainly encompass Dehong, Pu'er, Lincang, Xishuangbanna, Baoshan, southern Chuxiong, eastern Honghe, southern Yuxi, and parts of Wenshan. BWM-GIS achieved an area under curve (AUC) value of 0.891, while BCM-GIS obtained an AUC value of 0.890, indicating the stability and reliability of the models. Among them, the evaluation process of BCM-GIS was simpler and more realistic. Therefore, it has high feasibility and practical value in practical application. The findings from this study provide a significant scientific foundation for optimizing Yunnan Province.},
}
@article {pmid39747897,
year = {2025},
author = {Petrovic, M and Salovic, B and Tomic, A and Jesic-Petrovic, T and Matejic, A and Radovic, I and Babic, S and Korugic, A and Jelovac, D and Mikovic, N and Jakovljevic, S and Pelemis, S and Dimitrijevic, M and Milovanovic, J and Jotic, A and Trivic, A and Dimitrijevic, A and Bulatovic, S and Dudvarski, Z and Soldatovic, I and Ilic-Zivojinovic, J},
title = {Functional assessment of cancer therapy - head &amp; neck (FACT-HN) translation and validation in Serbian.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {298},
pmid = {39747897},
issn = {2045-2322},
mesh = {Humans ; *Head and Neck Neoplasms/therapy/psychology ; Male ; Serbia ; Female ; *Quality of Life ; Middle Aged ; *Psychometrics/methods ; Surveys and Questionnaires ; Aged ; Reproducibility of Results ; Adult ; Translations ; },
abstract = {This study aimed to translate and validate the Functional Assessment of Cancer Therapy - Head &amp; Neck (FACT-HN) in a Serbian-speaking population, assessing its psychometric properties and utility in evaluating the quality of life in head and neck cancer patients. The research focuses on determining the translated questionnaire's reliability, validity, and cultural relevance. A total of 106 Serbian-speaking head and neck cancer patients completed the translated FACT-HN, along with other validated instruments, including the EORTC QLQ-C30, EORTC QLQ-HN43, CES-D, and GAD-7. The translation followed a standard internationally accepted procedure. Psychometric analyses were conducted using confirmatory and exploratory factor analysis, Pearson correlations, and reliability measures such as Cronbach's alpha and intraclass correlation coefficients. The Serbian version of the FACT-HN showed excellent internal consistency across all subscales, with Cronbach's alpha ranging from 0.70 to 0.89. Confirmatory factor analysis confirmed the five-factor structure. Strong correlations were observed between the FACT-HN and other validated QoL measures, particularly with the EORTC QLQ-C30 and EORTC QLQ-HN43. Convergent validity was satisfactory for all components except the Social Well-Being component. The Serbian version of the FACT-HN is a valid and reliable tool for assessing the quality of life in head and neck cancer patients. It provides a comprehensive assessment of physical, social, emotional, and functional well-being, making it valuable for clinical and research applications in Serbian-speaking populations. Further research is needed to assess its sensitivity to longitudinal treatment-related changes.},
}
@article {pmid39749403,
year = {2025},
author = {Bougiouri, K},
title = {Mind the Gap: A Neural Network Framework for Imputing Genotypes in Non-Model Species.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14066},
doi = {10.1111/1755-0998.14066},
pmid = {39749403},
issn = {1755-0998},
mesh = {*Genotype ; *Neural Networks, Computer ; Haplotypes ; *Computational Biology/methods ; Machine Learning ; },
abstract = {Reduced representation sequencing (RRS) has proven to be a cost-effective solution for sequencing subsets of the genome in non-model species for large-scale studies. However, the targeted nature of RRS approaches commonly introduces large amounts of missing data, leading to reduced statistical power and biased estimates in downstream analyses. Genotype imputation, the statistical inference of missing sites across the genome, is a powerful alternative to overcome the caveats associated with missing sites. Typically, genotype imputation requires the presence of a reference panel of haplotypes, however, this is not always feasible for non-model species. In this issue of Molecular Ecology Resources, Mora-Márquez et al. (2024) develop gtImputation, an unsupervised machine learning imputation tool with an interactive GUI, which leverages information from the underlying data structure itself, without the need for a reference panel. They showcase that their method performs equally well and even surpasses existing haplotype-clustering and unsupervised machine learning algorithms, particularly for sites with low minor allele frequency (MAF) and for data sets with strong underlying population structure. This innovative framework adds to the ongoing efforts to expand the applicability of imputation to non-model species, offering the opportunity to apply varied types of analyses requiring dense sets of markers, while also maintaining lower sequencing costs.},
}
@article {pmid39749768,
year = {2025},
author = {Fifield, K and Veerakanjana, K and Hodsoll, J and Kuntsi, J and Tye, C and Simblett, S},
title = {Completion Rates of Smart Technology Ecological Momentary Assessment (EMA) in Populations With a Higher Likelihood of Cognitive Impairment: A Systematic Review and Meta-Analysis.},
journal = {Assessment},
volume = {32},
number = {8},
pages = {1175-1194},
pmid = {39749768},
issn = {1552-3489},
mesh = {Humans ; *Ecological Momentary Assessment ; *Cognitive Dysfunction/diagnosis/psychology ; *Smartphone ; },
abstract = {Ecological Momentary Assessment using smartphone technology (smart EMA) has grown substantially over the last decade. However, little is known about the factors associated with completion rates in populations who have a higher likelihood of cognitive impairment. A systematic review of Smart EMA studies in populations who have a higher likelihood of cognitive impairment was carried out (PROSPERO; ref no CRD42022375829). Smartphone EMA studies in neurological, neurodevelopmental and neurogenetic conditions were included. Six databases were searched, and bias was assessed using Egger's test. Completion rates and moderators were analyzed using meta-regression. Fifty-five cohorts were included with 18 cohorts reporting confirmed cognitive impairment. In the overall cohort, the completion rate was 74.4% and EMA protocol characteristics moderated completion rates. Participants with cognitive impairment had significantly lower completion rates compared with those without (p = .021). There were no significant moderators in the cognitive impairment group. Limitations included significant methodological issues in reporting of completion rates, sample characteristics, and associations with completion and dropout rates. These findings conclude that smart EMA is feasible for people with cognitive impairment. Future research should focus on the efficacy of using smart EMA within populations with cognitive impairment to develop an appropriate methodological evidence base.},
}
@article {pmid39750058,
year = {2024},
author = {Jain, S and Srinivasan, R and Helton, TJ and Karthikeyan, R},
title = {TXSELECT: a web-based decision support system for regional assessment of potential E. coli loads using a spatially explicit approach.},
journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering},
volume = {59},
number = {10},
pages = {550-561},
doi = {10.1080/10934529.2024.2445953},
pmid = {39750058},
issn = {1532-4117},
mesh = {*Escherichia coli/isolation &amp; purification ; Texas ; *Internet ; Environmental Monitoring/methods ; Water Microbiology ; Decision Support Techniques ; },
abstract = {Bacterial source characterization and allocation are imperative to watershed planning and identifying best management practices. The Spatially Explicit Load Enrichment Calculation Tool (SELECT) has been extensively utilized in watershed protection plans to evaluate the potential bacteria loads and sources in impaired watersheds. However, collecting data, compiling inputs, and spatially mapping sources can be arduous, time-intensive, expensive, and iterative until potential bacteria loads are appropriately allocated to sources based on stakeholder recommendations. We developed a web-based decision support system (DSS), TXSELECT (https://tx.select.tamu.edu), providing a user-friendly interface to run the SELECT model on Texas watersheds. The DSS includes pre-determined watershed-specific inputs that can be readily adjusted within the interface based on user preference and stakeholder recommendations, obviating the necessity for expensive GIS tools and data extraction. To illustrate the applications of TXSELECT, we implemented it in the entire coverage area to identify the potential hotspots and source contributions for Escherichia coli at a regional scale. Median potential E. coli loads were significantly higher in subwatersheds not supporting recreation use. Overall, the large-scale application of SELECT has the potential to aid in prioritizing management measures in watersheds that are less frequently monitored but could have an elevated risk of impairment.},
}
@article {pmid39752826,
year = {2025},
author = {Zhao, X and Jiang, WY and Liu, JJ and Yan, WJ and Zhang, YH and Zhang, Z and Zhang, PD},
title = {Unraveling the impact of PFOA toxicity on Zostera marina using a multi-omics approach: Insights from growth, physiological, transcriptomic, and metabolomic signatures.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {137024},
doi = {10.1016/j.jhazmat.2024.137024},
pmid = {39752826},
issn = {1873-3336},
mesh = {*Fluorocarbons/toxicity ; Transcriptome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Zosteraceae/drug effects/growth &amp; development/metabolism/genetics ; *Caprylates/toxicity ; Metabolomics ; Gene Expression Profiling ; Metabolome/drug effects ; Multiomics ; },
abstract = {Perfluorooctanoic acid (PFOA), an anthropogenic organic pollutant known for its persistence, resistance to degradation, and toxicity, has raised significant concerns about its potential ecological impacts. Zostera marina, a common submerged seagrass species in temperate offshore areas, is highly vulnerable to pollutant stressors. However, the impact of PFOA on Z. marina remains unclear. In this study, Z. marina was exposed to different concentrations of PFOA (0, 0.5, 1, 5, 10, and 20 μg/L) for 14 days. We subsequently assessed survival rates, growth patterns, physiological indices, transcriptomic profiles, and metabolomic characteristics. The results revealed dose-dependent PFOA accumulation in Z. marina tissues and significant growth inhibition. Furthermore, exposure to PFOA resulted in a significant reduction in photosynthetic pigment content (IBRv2 indices: 2.78-10.29) and elevated enzyme activity (IBRv2 indices: 2.90-8.96). Transcriptomic analysis identified 1511 differentially expressed genes associated with 11 KEGG pathways predominantly affected by PFOA exposure. Weighted gene co-expression network analysis highlighted the crucial role of the hydroxyphenylpyruvate reductase (hppr) gene in antioxidant defense mechanisms and detoxification processes against PFOA-induced stress. Metabolomics identified 412 differentially expressed metabolites, mainly consisting of flavonoids, organic acids, and lipids. In summary, PFOA exposure resulted in the down-regulation of gene expression related to photosynthesis and energy metabolism while also affecting metabolite synthesis. The response of Z. marina to PFOA stress involves modulation of the cytoskeletal dynamics and signal transduction pathways, as well as activation of a suite of genes and metabolites to initiate defense mechanisms.},
}
@article {pmid39753264,
year = {2025},
author = {Aguirre Vergara, F and Pinker, I and Fischer, A and Seuring, T and Tichomirowa, MA and de Beaufort, C and Kamp, SM and Fagherazzi, G and Aguayo, GA},
title = {Readiness of adults with type 1 diabetes and diabetes caregivers for diabetes distress monitoring using a voice-based digital health solution: insights from the PsyVoice mixed methods study.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e088424},
pmid = {39753264},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 1/therapy/psychology ; Female ; Male ; Adult ; *Caregivers/psychology ; Middle Aged ; *Qualitative Research ; Telemedicine ; Young Adult ; Surveys and Questionnaires ; Interviews as Topic ; Stress, Psychological/etiology ; Digital Health ; },
abstract = {OBJECTIVES: Diabetes distress can negatively affect the well-being of individuals with type 1 diabetes (T1D). Voice-based (VB) technology can be used to develop inexpensive and ecological tools for managing diabetes distress. This study explored the competencies to engage with digital health services, needs and preferences of individuals with T1D or caring for a child with this condition regarding VB technology to inform the tailoring of a co-designed tool for supporting diabetes distress management.<br><br>DESIGN: We used a mixed methods design. We performed a qualitative reflexive thematic analysis of semistructured interviews of people living with T1D or caring for a child with T1D, complemented by quantitative analysis (descriptive statistics).<br><br>SETTING: 12 adults living with T1D who attended diabetes centres or cared for a child with this condition participated in semistructured interviews to collect opinions about voice technology. They also responded to three questionnaires on sociodemographics and diabetes management, diabetes distress and e-health literacy.<br><br>OUTCOME MEASURES: Main: Patient experiences and perceptions derived from the coded transcriptions of interview data. Secondary: Quantitative data generated from Socio-Demographic and Diabetes Management questionnaire; Problem Areas in Diabetes Scale and e-Health Literacy Questionnaire.<br><br>RESULTS: Five major themes were generated from the participants' interview responses: (1) Experience of T1D, (2) Barriers to VB technology use, (3) Facilitators of VB technology, (4) Expectations of VB technology management in T1D, (5) Role of healthcare professionals in implementing VB technology for T1D. Most participants expressed a favourable view of voice technology for diabetes distress management. Trust in technology and healthcare professionals emerged as the predominant sentiment, with participants' current device type impacting anticipated barriers to adopting new technologies.<br><br>CONCLUSION: The results highlighted positive participant views towards VB technology. Device use, previous experience and health professional endorsement were influential facilitators of novel VB digital health solutions. Further research involving younger people with T1D could further contribute to the successful development of these tools.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov, NCT05517772.},
}
@article {pmid39753746,
year = {2025},
author = {Allegretti, E and D'Innocenzo, G and Coco, MI},
title = {The Visual Integration of Semantic and Spatial Information of Objects in Naturalistic Scenes (VISIONS) database: attentional, conceptual, and perceptual norms.},
journal = {Behavior research methods},
volume = {57},
number = {1},
pages = {42},
pmid = {39753746},
issn = {1554-3528},
support = {PTDC/PSI-ESP/30958/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LISBOA-01-0145-FEDER-0309//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Humans ; *Semantics ; *Attention/physiology ; Female ; Adult ; Male ; Young Adult ; *Space Perception/physiology ; *Visual Perception/physiology ; Databases, Factual ; Eye-Tracking Technology ; Adolescent ; },
abstract = {The complex interplay between low- and high-level mechanisms governing our visual system can only be fully understood within ecologically valid naturalistic contexts. For this reason, in recent years, substantial efforts have been devoted to equipping the scientific community with datasets of realistic images normed on semantic or spatial features. Here, we introduce VISIONS, an extensive database of 1136 naturalistic scenes normed on a wide range of perceptual and conceptual norms by 185 English speakers across three levels of granularity: isolated object, whole scene, and object-in-scene. Each naturalistic scene contains a critical object systematically manipulated and normed regarding its semantic consistency (e.g., a toothbrush vs. a flashlight in a bathroom) and spatial position (i.e., left, right). Normative data are also available for low- (i.e., clarity, visual complexity) and high-level (i.e., name agreement, confidence, familiarity, prototypicality, manipulability) features of the critical object and its embedding scene context. Eye-tracking data during a free-viewing task further confirms the experimental validity of our manipulations while theoretically demonstrating that object semantics is acquired in extra-foveal vision and used to guide early overt attention. To our knowledge, VISIONS is the first database exhaustively covering norms about integrating objects in scenes and providing several perceptual and conceptual norms of the two as independently taken. We expect VISIONS to become an invaluable image dataset to examine and answer timely questions above and beyond vision science, where a diversity of perceptual, attentive, mnemonic, or linguistic processes could be explored as they develop, age, or become neuropathological.},
}
@article {pmid39753915,
year = {2025},
author = {Davidson, SC and Cagnacci, F and Newman, P and Dettki, H and Urbano, F and Desmet, P and Bajona, L and Bryant, E and Carneiro, APB and Dias, MP and Fujioka, E and Gambin, D and Hoenner, X and Hunter, C and Kato, A and Kot, CY and Kranstauber, B and Lam, CH and Lepage, D and Naik, H and Pye, JD and Sequeira, AMM and Tsontos, VM and van Loon, E and Vo, D and Rutz, C},
title = {Establishing bio-logging data collections as dynamic archives of animal life on Earth.},
journal = {Nature ecology &amp; evolution},
volume = {9},
number = {2},
pages = {204-213},
pmid = {39753915},
issn = {2397-334X},
support = {80NSSC21K1182//National Aeronautics and Space Administration (NASA)/ ; Fellowship at Fondation Im&#xe9;RA//Institut de Recherche pour le D&#xe9;veloppement (French Research Institute for Development)/ ; CN00000033//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca (Ministry of Education, University and Research)/ ; LifeWatch//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; DP210103091//Department of Education and Training | Australian Research Council (ARC)/ ; GBMF9881//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; NGS-82515R-20//National Geographic Society/ ; },
mesh = {Animals ; *Data Collection/methods ; *Natural History/methods ; *Biodiversity ; *Conservation of Natural Resources/methods ; Archives ; },
abstract = {Rapid growth in bio-logging-the use of animal-borne electronic tags to document the movements, behaviour, physiology and environments of wildlife-offers opportunities to mitigate biodiversity threats and expand digital natural history archives. Here we present a vision to achieve such benefits by accounting for the heterogeneity inherent to bio-logging data and the concerns of those who collect and use them. First, we can enable data integration through standard vocabularies, transfer protocols and aggregation protocols, and drive their wide adoption. Second, we need to develop integrated data collections on standardized data platforms that support data preservation through public archiving and strategies that ensure long-term access. We outline pathways to reach these goals, highlighting the need for resources to govern community data standards and guide data mobilization efforts. We propose the launch of a community-led coordinating body and provide recommendations for how stakeholders-including government data centres, museums and those who fund, permit and publish bio-logging work-can support these efforts.},
}
@article {pmid39760247,
year = {2025},
author = {Lee, CE and Messer, LF and Wattiez, R and Matallana-Surget, S},
title = {Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms.},
journal = {Proteomics},
volume = {25},
number = {7},
pages = {e202400208},
pmid = {39760247},
issn = {1615-9861},
support = {//Joint UKRI Natural Environment Research Council (NERC) and National Research Foundation (NRF) Singapore/ ; NE/V009621/1//UKRI NERC/NRF/ ; NRF-SEAP-2020-0001//UKRI NERC/NRF/ ; NE/S007342/1//NERC Scottish Universities Partnership for Environmental Research (SUPER) Doctoral Training Partnership (DTP)/ ; },
mesh = {*Biofilms/growth &amp; development ; *Proteomics/methods ; *Plastics ; *Bacterial Proteins/metabolism/genetics ; Pseudomonas/genetics/metabolism ; Metagenomics/methods ; *Proteome/metabolism ; *Bacteria/metabolism/genetics ; Metagenome ; Multiomics ; },
abstract = {Marine plastispheres represent dynamic microhabitats where microorganisms colonise plastic debris and interact. Metaproteomics has provided novel insights into the metabolic processes within these communities; however, the early metabolic interactions driving the plastisphere formation remain unclear. This study utilised metaproteomic and metagenomic approaches to explore early plastisphere formation on low-density polyethylene (LDPE) over 3 (D3) and 7 (D7) days, focusing on microbial diversity, activity and biofilm development. In total, 2948 proteins were analysed, revealing dominant proteomes from Pseudomonas and Marinomonas, with near-complete metagenome-assembled genomes (MAGs). Pseudomonas dominated at D3, whilst at D7, Marinomonas, along with Acinetobacter, Vibrio and other genera became more prevalent. Pseudomonas and Marinomonas showed high expression of reactive oxygen species (ROS) suppression proteins, associated with oxidative stress regulation, whilst granule formation, and alternative carbon utilisation enzymes, also indicated nutrient limitations. Interestingly, 13 alkanes and other xenobiotic degradation enzymes were expressed by five genera. The expression of toxins, several type VI secretion system (TVISS) proteins, and biofilm formation proteins by Pseudomonas indicated their competitive advantage against other taxa. Upregulated metabolic pathways relating to substrate transport also suggested enhanced nutrient cross-feeding within the more diverse biofilm community. These insights enhance our understanding of plastisphere ecology and its potential for biotechnological applications.},
}
@article {pmid39761073,
year = {2026},
author = {Sangeetha, S and Sajeev, S and Hamza, MK and Shome, BR and Raisen, C and Holmes, MA and Sivaraman, GK},
title = {Whole-Genome Sequencing of Antimicrobial Resistant Klebsiella quasipneumoniae, a Novel Sequence Type 5655 from Retail Fish Market, Assam, India.},
journal = {Foodborne pathogens and disease},
volume = {23},
number = {1},
pages = {29-37},
doi = {10.1089/fpd.2023.0017},
pmid = {39761073},
issn = {1556-7125},
mesh = {*Klebsiella/genetics/isolation &amp; purification/drug effects/classification ; India ; Animals ; Whole Genome Sequencing ; Fishes/microbiology ; Klebsiella pneumoniae/genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Genome, Bacterial ; Microbial Sensitivity Tests ; *Seafood/microbiology ; Food Microbiology ; Phylogeny ; },
abstract = {Klebsiella quasipneumoniae is a recently described species that can be differentiated from Klebsiella pneumoniae. However, in clinical settings, they are frequently misidentified as K. pneumoniae. In this study, our objective was to conduct genomic characterization and bioinformatics analysis of K. quasipneumoniae subsp. quasipneumoniae (KpII-A) isolated from a sample obtained from a retail fish market in Assam, India. Notably, this particular isolate was identified as K. pneumoniae when identified using BD Pheonix™ M50 (BD Difco, USA). This represents a serious pitfall of conventional microbiological methods for distinguishing between K. pneumoniae and K. quasipneumoniae. In this connection, identifying differences in nuclear gene content is key to avoid misidentification. The isolate was confirmed to be KpII-A using species identification by Mash Screen and whole-genome sequencing by the Illumina platform. We report the draft genome sequence of this strain, comprising of 53 contigs with an average GC content of 58.11%. The annotation revealed 5,095 protein coding sequences, 69 tRNA genes, and 4 rRNA genes. The isolated strain acknowledges the presence of oqxA, oqxB, fosA, and blaOKP-A-3 antimicrobial resistance genes (ARGs). Additionally two phage genomes were detected in contigs 3 and 19 of the bacterial genome. Based on the multilocus sequence typing and genome sequencing, the isolate was identified as a novel sequence type, ST5655, within the species K. quasipneumoniae under the phylogroup KpII-A. The presence of antimicrobial resistance genes in KpII-A, isolated from retail fish samples, raises concerns regarding transmission across barriers in ecological niches and possible transmission to consumers. Given that fish may serve as a potential vehicle for ARG transmission, our findings are highly relevant and paramount to human health. Moreover, our study supports the robustness of the sequence-based microbial identification.},
}
@article {pmid39761773,
year = {2025},
author = {Banakar, SN and Karan, R and Prasannakumar, MK and Venkateshbabu, G and Harish, J and Patil, SS and Chandrashekar, BS and Mahesh, HB and Devanna, P and Manjunatha, C and Vamsidharreddy, N and Pallavi, KN and Sarangi, AN and Vaidya, K and Guru Murthy, DS},
title = {Unveiling Fusarium falciforme: Genome sequencing of a Novel wilt causing pathogen in subabul (Leucaena leucocephala L.) in India.},
journal = {Microbial pathogenesis},
volume = {200},
number = {},
pages = {107281},
doi = {10.1016/j.micpath.2025.107281},
pmid = {39761773},
issn = {1096-1208},
mesh = {*Fusarium/genetics/isolation &amp; purification/pathogenicity/classification ; *Plant Diseases/microbiology ; Phylogeny ; India ; *Genome, Fungal ; *Fabaceae/microbiology ; Virulence Factors/genetics ; Whole Genome Sequencing ; Sequence Analysis, DNA ; Host Specificity ; Cicer/microbiology ; DNA, Fungal/genetics ; Glycine max/microbiology ; Fungal Proteins/genetics ; },
abstract = {Subabul (Leucaena leucocephala L.) is a leguminous species often referred to as the "miracle tree," it provides numerous ecosystem services and exhibits robust ecological characteristics. However, the infection caused by phytopathogenic fungi is poorly understood in Subabul. Therefore, this study provides comprehensive insights into the molecular and genomic characteristics of Fusarium falciforme, the causal agent of wilt disease in Subabul (Leucaena leucocephala). Pathogen isolation from infected samples, followed by morpho-molecular characterization through DNA sequencing of key markers (ITS, LSU, TEF1α) and phylogenetic analysis, confirmed the identity of F. falciforme. Host range analysis demonstrated the pathogen's ability to infect additional leguminous crops, including chickpea (Cicer arietinum) and soybean (Glycine max). A complete genome assembly revealed a genome size of 59.19 Mb, comprising 18,853 protein-coding genes. Comparative genomic analysis elucidated evolutionary relationships with other Fusarium species, while functional annotation identified critical virulence factors, such as polyketide synthases, ABC transporters, and secretory proteins, which facilitate host tissue invasion. These findings enhance the understanding of F. falciforme pathogenicity, enabling improved diagnostic tools and management strategies for controlling wilt disease in Subabul and related legumes.},
}
@article {pmid39763978,
year = {2024},
author = {Palma-Martínez, MJ and Posadas-García, YS and López-Ángeles, BE and Quiroz-López, C and Lewis, ACF and Bird, KA and Lasisi, T and Zaidi, AA and Sohail, M},
title = {The multi-scale complexity of human genetic variation beyond continental groups.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39763978},
issn = {2692-8205},
support = {K99 HG012809/HG/NHGRI NIH HHS/United States ; R00 GM137076/GM/NIGMS NIH HHS/United States ; },
abstract = {Traditional clustering and visualization approaches in human genetics often operate under frameworks that assume inherent, discrete groupings[1,2]. These methods can inadvertently simplify multifaceted relationships, functioning to entrench the idea of typological groups[3]. We introduce a network-based pipeline and visualization tool grounded in relational thinking[4], which constructs networks from a variety of genetic similarity metrics. We identify communities at multiple resolutions, departing from typological models of analysis and interpretation that categorize individuals into a (predefined) number of sets. We applied our pipeline to a dataset merged from the 1000 Genomes and Human Genome Diversity Project[5], revealing the limitations of traditional groupings and capturing the complexities introduced by demographic events and evolutionary processes. This method embraces the context-specificity of genetic similarities that are salient depending on the question, markers of interest, and study individuals. Different numbers of communities are revealed depending on the resolution chosen and metric used, underscoring a fluid spectrum of genetic relationships and challenging the notion of universal categorization. We provide a web application (https://sohail-lab.shinyapps.io/GG-NC/) for interactive visualization and engagement with these intricate genetic landscapes.},
}
@article {pmid39771200,
year = {2024},
author = {Sedmáková, D and Jaloviar, P and Mišíková, O and Šumichrast, L and Slováčková, B and Kucbel, S and Vencurik, J and Bosela, M and Sedmák, R},
title = {Small Gap Dynamics in High Mountain Central European Spruce Forests-The Role of Standing Dead Trees in Gap Formation.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {24},
pages = {},
pmid = {39771200},
issn = {2223-7747},
support = {APVV-21-0199//Slovak Research and Development Agency/ ; APVV-19-0183//Slovak Research and Development Agency/ ; APVV-20-0408//Slovak Research and Development Agency/ ; 1/0515/23//The Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; },
abstract = {Gap dynamics are driving many important processes in the development of temperate forest ecosystems. What remains largely unknown is how often the regeneration processes initialized by endogenous mortality of dominant and co-dominant canopy trees take place. We conducted a study in the high mountain forests of the Central Western Carpathians, naturally dominated by the Norway spruce. Based on the repeated forest inventories in two localities, we quantified the structure and amount of deadwood, as well as the associated mortality of standing dead canopy trees. We determined the basic specific gravity of wood and anatomical changes in the initial phase of wood decomposition. The approach for estimating the rate of gap formation and the number of canopy trees per unit area needed for intentional gap formation was formulated based on residence time analysis of three localities. The initial phase of gap formation (standing dead tree in the first decay class) had a narrow range of residence values, with a 90-95% probability that gap age was less than 10 or 13 years. Correspondingly, a relatively constant absolute number of 12 and 13 canopy spruce trees per hectare died standing in 10 years, with a mean diameter reaching 50-58 cm. Maximum diameters trees (70-80 cm) were represented by 1-4 stems per hectare. The values of the wood-specific gravity of standing trees were around 0.370-0.380 g.cm[-3], and varied from 0.302 to 0.523 g.cm[-3]. Microscopically, our results point out that gap formation is a continuous long-lasting process, starting while canopy trees are living. We observed early signs of wood degradation and bacteria, possibly associated with bark beetles, that induce a strong effect when attacking living trees with vigorous defenses. New information about the initial phase of gap formation has provided a basis for the objective proposal of intervals and intensities of interventions, designed to promote a diversified structure and the long-term ecological stability of the mountain spruce stands in changing climate conditions.},
}
@article {pmid39776261,
year = {2025},
author = {Nolasco, M and Balzarini, M},
title = {Assessment of temporal aggregation of Sentinel-2 images on seasonal land cover mapping and its impact on landscape metrics.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {2},
pages = {142},
pmid = {39776261},
issn = {1573-2959},
mesh = {*Environmental Monitoring/methods ; *Ecosystem ; *Seasons ; Satellite Imagery ; Geographic Information Systems ; },
abstract = {Landscape metrics (LM) play a crucial role in fields such as urban planning, ecology, and environmental research, providing insights into the ecological and functional dynamics of ecosystems. However, in dynamic systems, generating thematic maps for LM analysis poses challenges due to the substantial data volume required and issues such as cloud cover interruptions. The aim of this study was to compare the accuracy of land cover maps produced by three temporal aggregation methods: median reflectance, maximum normalised difference vegetation index (NDVI), and a two-date image stack using Sentinel-2 (S2) and then to analyse their implications for LM calculation. The Google Earth Engine platform facilitated data filtering, image selection, and aggregation. A random forest algorithm was employed to classify five land cover classes across ten sites, with classification accuracy assessed using global measurements and the Kappa index. LM were then quantified. The analysis revealed that S2 data provided a high-quality, cloud-free dataset suitable for analysis, ensuring a minimum of 25 cloud-free pixels over the study period. The two-date and median methods exhibited superior land cover classification accuracy compared to the max NDVI method. In particular, the two-date method resulted in lower fragmentation-heterogeneity and complexity metrics in the resulting maps compared to the median and max NDVI methods. Nevertheless, the median method holds promise for integration into operational land cover mapping programmes, particularly for larger study areas exceeding the width of S2 swath coverage. We find patch density combined with conditional entropy to be particularly useful metrics for assessing fragmentation and configuration complexity.},
}
@article {pmid39776539,
year = {2024},
author = {Chandel, N and Maile, A and Shrivastava, S and Verma, AK and Thakur, V},
title = {Establishment and perturbation of human gut microbiome: common trends and variations between Indian and global populations.},
journal = {Gut microbiome (Cambridge, England)},
volume = {5},
number = {},
pages = {e8},
pmid = {39776539},
issn = {2632-2897},
abstract = {Human gut microbial species are crucial for dietary metabolism and biosynthesis of micronutrients. Digested products are utilised by the host as well as several gut bacterial species. These species are influenced by various factors such as diet, age, geographical location, and ethnicity. India is home to the largest human population in the world. It is spread across diverse ecological and geographical locations. With variable dietary habits and lifestyles, Indians have unique gut microbial composition. This review captures contrasting and common trends of gut bacterial community establishment in infants (born through different modes of delivery), and how that bacterial community manifests itself along infancy, through old age between Indian and global populations. Because dysbiosis of the gut community structure is associated with various diseases, this review also highlights the common and unique bacterial species associated with various communicable as well as noncommunicable diseases such as diarrhoea, amoebiasis, malnutrition, type 2 diabetes, obesity, colorectal cancer, inflammatory bowel disease, and gut inflammation and damage to the brain in the global and Indian population.},
}
@article {pmid39777935,
year = {2025},
author = {Mond, L and Geyer, S and Tetzlaff, J and Weißenborn, K and Schneider, J and Epping, J},
title = {More Drugs and Fewer Strokes? Time Trends in CVD Medication and Incidence of Stroke With German Health Insurance Data.},
journal = {Pharmacoepidemiology and drug safety},
volume = {34},
number = {1},
pages = {e70077},
pmid = {39777935},
issn = {1099-1557},
support = {//Allgemeine Ortskrankenkasse Niedersachsen/ ; GE 1167/15-1//Deutsche Forschungsgemeinschaft/ ; GE 1167/19-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; Germany/epidemiology ; Female ; Male ; Incidence ; Middle Aged ; Aged ; *Stroke/epidemiology/prevention &amp; control ; Adult ; Aged, 80 and over ; *Cardiovascular Diseases/epidemiology/prevention &amp; control ; Young Adult ; Adolescent ; *Insurance, Health/statistics &amp; numerical data ; Prevalence ; Cardiovascular Agents/therapeutic use/adverse effects ; Age Factors ; Time Factors ; Databases, Factual ; },
abstract = {BACKGROUND: Successful prevention of cardiovascular diseases (CVD) may reduce the burden of diseases. Preventive medication is an important measure to decrease the risks of cardiovascular events, in particular myocardial infarction and stroke. The aim of this study is to analyze the prevalence of CVD preventive medication in Germany over time with respect to sex and age and to compare it with the temporal development of strokes.<br><br>METHODS: The study is based on statutory health insurance claims data from the AOK Niedersachsen (AOKN) covering the years 2005-2018. The study population comprises all AOKN insured persons aged 18&#x2009;years and older (N&#x2009;=&#x2009;2&#x2009;088&#x2009;495). Age-standardized time trends of the prevalence of CVD preventive medication and incidence of stroke were calculated for men and women in different age groups. After that, the relationship of both measures was examined in an ecological correlation.<br><br>RESULTS: We found a clear increase in medication prevalence over time. In 2018, about 35% of the total population and about 85% of those over 85&#x2009;years of age received CVD preventive medication. At the same time, age-standardized incidence rates of ischemic stroke were decreasing slightly. The ecological correlation showed a negative association between medication prevalence and stroke incidence especially in the higher age groups.<br><br>CONCLUSION: High correlation coefficients indicate that higher medication prevalence could be linked to better population health. Further research is needed to draw conclusions about the effects of increasing medicalization, including adverse risks and side effects at the population level.},
}
@article {pmid39778451,
year = {2025},
author = {Lausch, A and Selsam, P and Heege, T and von Trentini, F and Almeroth, A and Borg, E and Klenke, R and Bumberger, J},
title = {Monitoring and modelling landscape structure, land use intensity and landscape change as drivers of water quality using remote sensing.},
journal = {The Science of the total environment},
volume = {960},
number = {},
pages = {178347},
doi = {10.1016/j.scitotenv.2024.178347},
pmid = {39778451},
issn = {1879-1026},
abstract = {The interactions between landscape structure, land use intensity (LUI), climate change, and ecological processes significantly impact hydrological processes, affecting water quality. Monitoring these factors is crucial for understanding their influence on water quality. Remote sensing (RS) provides a continuous, standardized approach to capture landscape structures, LUI, and landscape changes over long-term time series. In this study, RS-based indicators from Landsat data (2018-2021) were used to assess landscape structure, LUI, and land use change for a study area in northern Germany, applying the ESIS/Imalys tool. These indicators were then used to model and predict water quality (Chla) in 119 standing waters. Various machine learning methods, including Generalised Linear Models, Support Vector Machines, Deep Learning, Decision Trees, Random Forest, and Gradient Boosted Trees, were tested. The Random Forest model performed best, with a correlation of 0.744 ± 0.11. Indicators related to landscape structure, such as diversity_mean (0.376) and relation_mean (0.292), had the highest global correlation weights, while LUI and land use change indicators like NirV2_mean (0.369) and NirV_regme (0.284) were also significant. All indicators and their effects on water quality (Chla) are discussed in detail. The study highlights the potential of the ESIS/Imalys tool for quantifying landscape structure, LUI, and land use change with RS to model and predict water quality and suggests directions for future model improvements by incorporating additional influencing factors.},
}
@article {pmid39787194,
year = {2025},
author = {Bantie, GM and Tadege, M and Nigussie, TZ and Woya, AA and Tekile, AK and Melese, AA and Ayalew, S and Beyene, BB and Wubetu, GY},
title = {Regional disparities of full pentavalent vaccine uptake and the determinants in Ethiopia: Mapping and spatial analysis using the EDHS data.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0312514},
pmid = {39787194},
issn = {1932-6203},
mesh = {Humans ; Ethiopia ; Infant ; Female ; Adult ; *Spatial Analysis ; Male ; *Vaccination/statistics &amp; numerical data ; Diphtheria-Tetanus-Pertussis Vaccine/administration &amp; dosage ; Hepatitis B Vaccines/administration &amp; dosage ; Young Adult ; Immunization Programs/statistics &amp; numerical data ; Middle Aged ; Haemophilus Vaccines ; Adolescent ; Vaccination Coverage/statistics &amp; numerical data ; Vaccines, Combined ; },
abstract = {BACKGROUND: The full pentavalent (DPT-HepB-Hib) vaccination is the main strategy to prevent five communicable diseases in early childhood, especially in countries with huge communicable disease burdens like Ethiopia. Exploring spatial distributions and determinants of full pentavalent vaccination status in minor ecological areas in Ethiopia is crucial for creating targeted immunization campaigns and monitoring the advancement of accomplishing sustainable development goals. This study aimed to investigate the spatial disparities and determinants of full pentavalent vaccination among 12-23-month-old children in Ethiopia.<br><br>METHOD: The data on pentavalent vaccine uptake was found in the Ethiopian Health and Demographic Survey (EDHS, 2019). A two-stage cluster sampling method was applied to collect the EDHS data. The enumeration area was the primary sample unit while the household served as the secondary sampling unit. The geographical variations of full pentavalent vaccine uptake were explored using Quantum Geographic Information System (QGIS) software. The significant predictors of full pentavalent vaccination were identified using a simple logistic regression model through R version 4.1 software.<br><br>RESULT: The national full pentavalent vaccine uptake was 59.2%. The spatial distribution of full pentavalent vaccine uptake was not uniform in Ethiopia. Spatial cluster analysis revealed that most of low coverage regions for full pentavalent vaccine uptake were Afar, Somali, and Harari. The regions with the highest and lowest rates of vaccine uptake were Tigray and Harari region, respectively. Maternal age of 35-49 years (AOR = 3.42; 95% CI: 1.99, 5.87), and 25-34 years (AOR = 1.55; 95% CI: 1.17, 2.19), primary education attended (AOR = 1.51; 95%CI: 1.07, 2.11), richness wealth index (AOR = 1.96; 95% CI: 1.40, 2.75), birth order of 1-3 (AOR = 1.88; 95% CI: 1.19, 2.96), and delivery in the health facility (AOR = 3.41: 95% CI: 2.52, 4.61) were the determinants of full pentavalent vaccine uptake in Ethiopia.<br><br>CONCLUSION: Ethiopia's full pentavalent vaccine uptake was far lower than the global target. Older maternal age, maternal education, wealth index, birth order, and giving birth in a health facility were the determinants of full pentavalent vaccine uptake. Special attention should be given to Afar, Somali, and Harari regions, to strengthen the vaccine uptake. Moreover, improved socioeconomic status and getting maternal health services during delivery are necessary to enhance vaccine uptake.},
}
@article {pmid39787642,
year = {2025},
author = {Aanes, H and Vigeland, MD and Star, B and Gilfillan, GD and Mattingsdal, M and Trøan, S and Strand, M and Eide, LM and Hanssen, EN},
title = {Heating up three cold cases in Norway using investigative genetic genealogy.},
journal = {Forensic science international. Genetics},
volume = {76},
number = {},
pages = {103217},
doi = {10.1016/j.fsigen.2024.103217},
pmid = {39787642},
issn = {1878-0326},
mesh = {Humans ; Databases, Nucleic Acid ; DNA/genetics/isolation &amp; purification ; *DNA Fingerprinting/methods ; Forensic Genetics/methods ; Microsatellite Repeats ; Norway ; *Pedigree ; },
abstract = {With the advent of commercial DNA databases, investigative genetic genealogy (IGG) has emerged as a powerful forensic tool, rivalling the impact of STR analyses, introduced four decades ago. IGG has been frequently applied in the US and tested in other countries, but never in Norway. Here, we apply IGG to three cold criminal cases and successfully identify the donor of the DNA in two of these cases. Our findings suggest that when combined with phenotypic prediction and case information, IGG holds substantial potential for resolving both active and cold cases in Norway. This potential is amplified by the digitalization of archives and the transparent and structured nature of society in Norway. Additionally, the databases exhibit sufficient representation to yield matches with distant relatives. Moreover, this work has uncovered a series of lingering research questions spanning the entire workflow from DNA extraction to genealogy research. Finally, we highlight the possibility that more insights can be gleaned from genetic profiles, for instance using an accurate age prediction method. The results show that IGG can be successfully applied in Norway, having reached a level of maturity that enables identification of unknown individuals in cases where DNA is accessible.},
}
@article {pmid39788970,
year = {2025},
author = {Sánchez-Jardón, L and Hernández de Diego, A and Mackenzie, R and Villodre, M and Arnaiz-Schmitz, C and Schmitz, MF and Acosta-Gallo, B},
title = {Bryophyte literature records database of Aysén, Chilean sub-Antarctic ecoregion.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {36},
pmid = {39788970},
issn = {2052-4463},
mesh = {*Bryophyta ; Chile ; *Biodiversity ; Antarctic Regions ; Ecosystem ; Databases, Factual ; },
abstract = {The Chilean sub-Antarctic ecoregion hosts the largest expanse of temperate forests, wetlands and peatlands, as well as the largest proportion of protected areas in the southern hemisphere. Bryophytes are highly diverse and ecologically essential in sub-Antarctic ecosystems and are considered as biodiversity loss indicators caused by the current socio-ecological crisis. However, knowledge about their biodiversity is rather limited. Integrating the available information on bryophyte diversity in regional platforms such as SIB-Aysén can be useful to acknowledge their ecological importance and remarkable biodiversity. This article integrates 345 records of 273 bryophyte taxa known in the region of Aysén and emphasizes the need to include citizen science as a tool to increase observations in lesser-known taxonomic groups.},
}
@article {pmid39789035,
year = {2025},
author = {Li, F and Xia, H and Miao, J and Yang, J},
title = {Changes of the ecological environment status in villages under the background of traditional village preservation: a case study in Enshi Tujia and Miao Autonomous Prefecture.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1504},
pmid = {39789035},
issn = {2045-2322},
support = {42271318//National Natural Science Foundation of China/ ; },
mesh = {*Conservation of Natural Resources/methods ; *Ecosystem ; China ; Humans ; Rural Population ; Geographic Information Systems ; },
abstract = {The preservation of Chinese traditional villages plays a crucial role in promoting the sustainable development of rural natural, cultural, and ecological environments. It is also a key strategy for achieving rural revitalization. Current research on traditional villages predominantly focuses on the realm of cultural landscapes, with an emphasis on preserving the cultural ecological value of these communities. In comparison, discussions on the quality of the ecological environment of villages from the perspectives of natural environment, economic environment, and the social organizational environment within regional development are relatively scarce. Our study employed GIS and RS technology and refers to the Technical Criterion for Ecosystem Status Evaluation. Several sub-indices of the ecological environment status, including the biological richness index, vegetation coverage index, water network density index, and land stress index, were selected to construct an ecological environment assessment model. This model was used to analyze the spatial-temporal changes in the ecological environment status of each county, county-level city, and traditional village within the jurisdiction of Enshi Tujia and Miao Autonomous Prefecture and its surrounding areas from 2010 to 2020. The study quantitatively evaluated the ecological environment status of each county, county-level city, and village in Enshi before and after the implementation of traditional village preservation policies. Through comparative analysis, the study revealed the impact of these policies on the natural ecological environment of the study area. The results indicated the following: (1) From 2010 to 2020, the ecological index (EI) values in the villages of Enshi Prefecture exhibited a similar trend to the EI values in the respective counties and county-level cities they are located in, although significant differences in magnitude of change were observed. (2) The EI values in the counties, county-level cities, and villages demonstrated greater variation in the latter five years of the decade (2015-2020) compared to the previous five years (2010-2015). (3) In 2020, the EI value of the villages experienced more significant changes compared to 2010, whereas the overall EI value of the counties and county-level cities showed less pronounced changes. The findings of this study suggest that the traditional village preservation policies implemented in Enshi Prefecture have both positive and negative impacts on the ecological environment of the surrounding areas of protected villages, and these impacts become increasingly evident over time. By comparing and analyzing the ecological changes in the surrounding areas of traditional villages in Enshi Prefecture with the overall ecological changes in the respective counties and county-level cities, our study employs quantitative analytical methods to delve into the impact of traditional village conservation policies on the natural ecological environment. It assesses the effects of policy implementation on the natural ecological environment of traditional villages, analyzing both the positive and negative impacts brought about by the execution of these policies, with the aim of effectively guiding the natural ecological conditions of traditional villages towards a more healthy trajectory of development.},
}
@article {pmid39789290,
year = {2025},
author = {Sağlam, S and Özdemir, E and Özden, &#xd6; and Makineci, E and Özkan, UY and Bingöl, D and Güzelçimen, F},
title = {The effects of some chemical compounds on the sound absorbing ability of tree bark.},
journal = {Biologia futura},
volume = {76},
number = {1},
pages = {49-57},
pmid = {39789290},
issn = {2676-8607},
mesh = {*Plant Bark/chemistry ; *Trees/chemistry ; *Sound ; Pinus/chemistry ; },
abstract = {Tree bark is an important natural polymer for sound absorption. The main components in the bark of different tree species are polymers with high molecular weight such as cellulose, hemicellulose, and lignin. The aim of this study is to determine the noise reduction coefficient (NRC), lignin, alcohol-benzene solubility (ABS), carbon (C), and nitrogen (N) contents in samples taken from the bark of different tree species-black locust (Robinia pseudoacacia), narrow-leaved ash (Fraxinus angustifolia), stone pine (Pinus pinea), silver lime (Tilia tomentosa), sweet chestnut (Castanea sativa), sessile oak (Quercus petraea), and maritime pine (Pinus pinaster) and to investigate the relationship between these chemical properties and sound absorption measurements. Tree species showed a statistically significant difference in terms of all measured variables. In the correlation matrix obtained as a result of the analysis, only ABS showed a significant and the highest positive correlation with the NRC, with a correlation coefficient of r = 0.812. ABS in bark is seen as the most important chemical factor regarding sound retention, indicating the abundance of extractives in barks of different tree species. An investigation into the relationship between sound retention and different extractive substance and contents of different extractive substances in bark is recommended for further studies.},
}
@article {pmid39792790,
year = {2025},
author = {Kherroubi Garcia, I and Erdmann, C and Gesing, S and Barton, M and Cadwallader, L and Hengeveld, G and Kirkpatrick, CR and Knight, K and Lemmen, C and Ringuette, R and Zhan, Q and Harrison, M and Mac Gabhann, F and Meyers, N and Osborne, C and Till, C and Brenner, P and Buys, M and Chen, M and Lee, A and Papin, J and Rao, Y},
title = {Ten simple rules for good model-sharing practices.},
journal = {PLoS computational biology},
volume = {21},
number = {1},
pages = {e1012702},
pmid = {39792790},
issn = {1553-7358},
mesh = {*Information Dissemination/methods ; Humans ; *Computational Biology ; Computer Simulation ; },
abstract = {Computational models are complex scientific constructs that have become essential for us to better understand the world. Many models are valuable for peers within and beyond disciplinary boundaries. However, there are no widely agreed-upon standards for sharing models. This paper suggests 10 simple rules for you to both (i) ensure you share models in a way that is at least "good enough," and (ii) enable others to lead the change towards better model-sharing practices.},
}
@article {pmid39792995,
year = {2025},
author = {Soeishi, T and Nakata, A and Nagata, T and Akutsu, S and Tondokoro, T and Inoue, Y and Katsumura, F and Kikunaga, K},
title = {Predicting Depressive Symptoms and Psychological Distress by Circulating Inflammatory Mediators: A 16-Month Prospective Study in Japanese White-Collar Employees.},
journal = {Journal of occupational and environmental medicine},
volume = {67},
number = {4},
pages = {235-244},
doi = {10.1097/JOM.0000000000003307},
pmid = {39792995},
issn = {1536-5948},
mesh = {Humans ; Female ; Male ; Prospective Studies ; *Depression/blood/diagnosis ; Adult ; Middle Aged ; *Psychological Distress ; Japan ; Sex Factors ; *Inflammation Mediators/blood ; Tumor Necrosis Factor-alpha/blood ; Interferon-gamma/blood ; *Stress, Psychological/blood ; Psychiatric Status Rating Scales ; East Asian People ; },
abstract = {OBJECTIVE: Although increasing evidence suggests that depression/distress involves inflammatory processes, its potential sex differences and the temporal directions for this association remain elusive.<br><br>METHODS: We examined the temporal association between serum inflammatory mediators and depression/distress as measured by the Center for Epidemiologic Studies Depression Scale (CES-D) and the Kessler Psychological Distress Scale (K6), in nondepressed working men and women (n = 61 and 43, respectively) by a 16-month prospective design.<br><br>RESULTS: Fully adjusted partial correlation analyses revealed that, in men, a lower IFN-&#x3b3; predicted subsequent increases in CES-D and K6 scores, whereas a higher TNF-&#x3b1; predicted increased K6 scores. In women, a higher IFN-&#x3b3; predicted a subsequent increase in the CES-D score. CES-D and K6 scores did not predict inflammatory mediators at follow-up.<br><br>CONCLUSIONS: The finding suggests that inflammatory activation precedes depression/distress with distinct sex differences.},
}
@article {pmid39793033,
year = {2025},
author = {Clauss, M and Roller, M and Bertelsen, MF and Rudolf von Rohr, C and Müller, DWH and Schiffmann, C and Kummrow, M and Encke, D and Ferreira, S and Duvall, ES and Maré, C and Abraham, AJ},
title = {Zoos must embrace animal death for education and conservation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {1},
pages = {e2414565121},
pmid = {39793033},
issn = {1091-6490},
support = {101062339//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; },
}
@article {pmid39793648,
year = {2025},
author = {Ji, G and Wang, Y and Lu, Z and Long, G and Xu, C},
title = {Associations between ambient benzene and stroke, and the mediating role of accelerated biological aging: Findings from the UK biobank.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {367},
number = {},
pages = {125656},
doi = {10.1016/j.envpol.2025.125656},
pmid = {39793648},
issn = {1873-6424},
mesh = {*Benzene/analysis ; Humans ; United Kingdom/epidemiology ; *Stroke/epidemiology ; Male ; Female ; *Environmental Exposure/statistics &amp; numerical data ; Middle Aged ; Aged ; *Air Pollutants ; *Aging ; Biological Specimen Banks ; Cohort Studies ; UK Biobank ; },
abstract = {Benzene can cause respiratory diseases. However, the associations between benzene and stroke are unclear. A total of 13,116 patients with stroke and 377,120 controls from the UK Biobank were included. The benzene exposure concentrations were matched on the basis of the address information of each participant via a data form from the UK Department for Environment, Food and Rural Affairs. Weighted Cox regression was used to investigate the association between benzene and stroke risk. The polygenic risk score (PRS) was used to observe the joint effects of benzene exposure and genetic factors on stroke risk. We conducted a mediation analysis to investigate the mediating role of accelerated biological aging in this cohort study. After adjusting for covariates, every 1 μg/m[3] increase in benzene exposure increased the risk of stroke by 70%, which may be mediated by accelerated biological aging. The population with high benzene exposure concentrations and high PRSs had a 44% greater risk of stroke than did those with low benzene exposure concentrations and low PRSs. Benzene exposure and the PRS have joint effects on the risk of stroke. Benzene exposure was associated with stroke risk, possibly through increased biological aging, and the PRS modified this association.},
}
@article {pmid39794649,
year = {2025},
author = {Mohammad, L and Bandyopadhyay, J and Mondal, I and Altuwaijri, HA and Khatun, S and Hossain, SKA and Juliev, M},
title = {Assessing cropping system dynamics over three decades: remote sensing and GIS insights in Murshidabad-Jiaganj Block.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {2},
pages = {164},
pmid = {39794649},
issn = {1573-2959},
mesh = {*Remote Sensing Technology ; *Agriculture/methods/statistics &amp; numerical data ; *Environmental Monitoring/methods ; *Geographic Information Systems ; China ; Crops, Agricultural/growth &amp; development ; },
abstract = {Agriculture is a significant contributor to the country's economic development. We used multiple Landsat images from 1990 to 2021 in the Murshidabad-Jiaganj Block to assess changes in the agricultural system and their underlying causes. The Rabi season saw a 10.99% growth in agrarian regions from 1990 to 2000 and an 8.86% increase in 2010, yet it declined by 28.12% in 2021. During the summer, the cultivated lands diminished by 26.63%, 19.43%, and 19.64%, while in the Kharif season, they declined by 21.78%, 15.68%, and 11.99% from 1990 in the years 2000, 2010, and 2021, respectively. The agricultural area had 36.82%, 34.16%, and 19.01% increases between 1990 and 2021, respectively. Regarding direction, farmland acreage decreased in all zones except the SSE, which had a 0.95% increase. Mono-, double-, and triple-cropping systems have decreased in area, while multi-cropping systems have experienced increases of 43.51%, 4.50%, and 18.49% in 1990-2021, respectively. The multi-cropping system has a good correlation with all agroclimatic factors. The reduction of irrigated lands post-2009 significantly affected the agriculture system. The fall in agricultural employment in recent decades is attributable to migration seeking higher-paying occupations. The advancement of accurate remote sensing-based modeling is crucial for mitigating food security risks, particularly those posed by climate change, and informing policy decisions.},
}
@article {pmid39794678,
year = {2025},
author = {Sasia, I and Bueno, G and Etxano, I},
title = {Amalur EIS: a system for calculating the environmental impacts of industrial sites from E-PRTR records.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {2},
pages = {163},
pmid = {39794678},
issn = {1573-2959},
support = {IT 1567-22 Ekopol Research Group&#xa0;(UPV/EHU)//Department of Education of the Basque Government/ ; },
mesh = {*Environmental Monitoring/methods ; *Environmental Pollutants/analysis ; Europe ; *Industry/statistics &amp; numerical data ; *Environmental Pollution/statistics &amp; numerical data ; Databases, Factual ; Climate Change ; },
abstract = {This article presents Amalur EIS (https://www.amalur-eis.eus/), an Environmental Information System that estimates environmental impacts using data sourced from the European Pollutant Release and Transfer Register database (E-PRTR). The system uses data on the releases into land, air and water of 31,556 European industrial facilities for the period 2007-2021. Amalur EIS calculates environmental impacts of industrial releases using 31 life cycle impact assessment methods (LCIA) and covering 78 of the 91 pollutants regulated by the PRTR Protocol. The system has been constructed using a two-layer software infrastructure: (i) a data layer supported by a relational database built in Postgres and (ii) a presentation layer built in Tableau, so it provides user-friendly access to the information. For an illustrative analysis of the tool, the EF 3.0 LCIA method recommended by the European Commission was used, including normalisation and weighting steps for a better comparison. The analysis concludes that the climate change impact category contributes the most (68.6%) to the total impacts, while the largest contributor from an economic activity perspective is the energy sector (59.5%). Geographically, both elements coincide in the German regions of Düsseldorf, Köln and Brandenburg, resulting in the concentration of the largest impacts at the European regional level. In fact, Germany is the country with the highest impact (20.3% of total). Beyond this analysis, Amalur EIS is poised to be a valuable tool for tracking the transition towards sustainability, particularly in Europe.},
}
@article {pmid39798660,
year = {2025},
author = {Li, J and Lu, Y and Chen, X and Wang, L and Cao, Z and Lei, H and Zhang, Z and Wang, P and Sun, B},
title = {Seasonal variation of microbial community and diversity in the Taiwan Strait sediments.},
journal = {Environmental research},
volume = {268},
number = {},
pages = {120809},
doi = {10.1016/j.envres.2025.120809},
pmid = {39798660},
issn = {1096-0953},
mesh = {*Seasons ; Taiwan ; *Geologic Sediments/microbiology ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Biodiversity ; *Microbiota ; Archaea/genetics ; },
abstract = {Human activities and ocean currents in the Taiwan Strait exhibit significant seasonal variation, yet the response of marine microbes to ocean changes under anthropogenic and climatic stress remains unclear. Using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics and functional variations of microbial communities in sediment samples. Our findings revealed distinct seasonal patterns in microbial diversity and composition. Proteobacteria, Desulfobacterota, and Crenarchaeota dominated at the phylum level, while Candidatus Nitrosopumilus, Woeseia, and Subgroup 10 were prevalent at the genus level. Iron concentrations, heavy metals and C/N ratio were primary factors influencing microbial communities during specific seasons, whereas sulfur content, temperature fluctuations, and heavy metals shaped the entire microbial structure and diversity. Core microbial groups, including Desulfobulbus, Subgroup 10, Unidentified Latescibacterota, and Sumerlaea, played essential roles in regulating community structure and functional transitions. Marker species, such as Aliidiomarina sanyensis, Spirulina platensis, Croceimarina litoralis and Sulfuriflexus mobilis, acted as seasonal indicators. Bacteria exhibited survival strategy akin to higher organisms, encompassing process of synthesis, growth, dormancy, and disease resistance throughout the seasonal cycle. Core microbial groups and marker species in specific seasons can serve as indicators for monitoring and assessing the health of the Taiwan Strait ecosystem.},
}
@article {pmid39799926,
year = {2025},
author = {Fridman, M and Krasko, O and Veyalkin, I},
title = {The incidence trends of papillary thyroid carcinoma in Belarus during the post-Chernobyl epoch.},
journal = {Cancer epidemiology},
volume = {95},
number = {},
pages = {102745},
doi = {10.1016/j.canep.2025.102745},
pmid = {39799926},
issn = {1877-783X},
mesh = {Humans ; Republic of Belarus/epidemiology ; *Chernobyl Nuclear Accident ; Incidence ; *Thyroid Neoplasms/epidemiology/etiology ; Adolescent ; Male ; *Thyroid Cancer, Papillary/epidemiology/etiology ; Female ; Adult ; Child ; Young Adult ; *Neoplasms, Radiation-Induced/epidemiology ; Registries/statistics &amp; numerical data ; Middle Aged ; Child, Preschool ; Infant ; Iodine Radioisotopes/adverse effects ; },
abstract = {BACKGROUND: The increase of papillary thyroid cancer (PTC) rate among children who were exposed to post-Chernobyl 131-I release was reported only four years after the accident, first in Belarus where the heaviest fallout happened. The evolution of the occurrence of thyroid carcinoma based on the age-period-cohort analysis and the effects of age, period, and birth cohort on time trends aimed to reveal if post-Chernobyl follicular cells irradiation still has been impacting on incidence rate of papillary thyroid carcinoma nowadays.<br><br>METHODS: The Belarusian Cancer Registry was used to identify patients with PTC diagnosed during the years 1980-2019. The incidence trends were analysed using Join-point regression software.<br><br>RESULTS: The highest peak of age-specific incidence curve was shown during the years 1980-2001 in the age group of 15-19 years old that was associated also with short-latency cases of post-Chernobyl PTC. This is the same age group that demonstrated significant growth of the incidence rate during the years 2006-2019, largely because of the increasing number of non-exposed patients with PTC (p&#x202f;<&#x202f;0.001). Influence of post-Chernobyl exposure also can be seen in the young adults age-groups of patients (for 20-24 years old during the years 1980-2003 and 2013-2019, p&#x202f;<&#x202f;0.001; for 25-29 years old during the years 1980-1999 and 1999-2011, p&#x202f;<&#x202f;0.001).<br><br>CONCLUSION: After the Chernobyl accident, epidemiological waves that reflect the age shift of the group of children exposed to 131-I have consistently emerged. Currently, the incidence rate continues to increase only in the cohort of patients aged 20-44 years.},
}
@article {pmid39801085,
year = {2025},
author = {Anderson, EC and Giglio, RM and DeSaix, MG and Smyser, TJ},
title = {gscramble: Simulation of Admixed Individuals Without Reuse of Genetic Material.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14069},
pmid = {39801085},
issn = {1755-0998},
support = {//National Wildlife Research Center/ ; //Southwest Fisheries Science Center/ ; },
mesh = {*Computer Simulation ; *Computational Biology/methods ; *Genetics, Population/methods ; Genotype ; *Software ; },
abstract = {While a best practice for evaluating the behaviour of genetic clustering algorithms on empirical data is to conduct parallel analyses on simulated data, these types of simulation techniques often involve sampling genetic data with replacement. In this paper we demonstrate that sampling with replacement, especially with large marker sets, inflates the perceived statistical power to correctly assign individuals (or the alleles that they carry) back to source populations-a phenomenon we refer to as resampling-induced, spurious power inflation (RISPI). To address this issue, we present gscramble, a simulation approach in R for creating biologically informed individual genotypes from empirical data that: (1) samples alleles from populations without replacement and (2) segregates alleles based on species-specific recombination rates. This framework makes it possible to simulate admixed individuals in a way that respects the physical linkage between markers on the same chromosome and which does not suffer from RISPI. This is achieved in gscramble by allowing users to specify pedigrees of varying complexity in order to simulate admixed genotypes, segregating and tracking haplotype blocks from different source populations through those pedigrees, and then sampling-using a variety of permutation schemes-alleles from empirical data into those haplotype blocks. We demonstrate the functionality of gscramble with both simulated and empirical data sets and highlight additional uses of the package that users may find valuable.},
}
@article {pmid39805953,
year = {2025},
author = {Daruka, L and Czikkely, MS and Szili, P and Farkas, Z and Balogh, D and Grézal, G and Maharramov, E and Vu, TH and Sipos, L and Juhász, S and Dunai, A and Daraba, A and Számel, M and Sári, T and Stirling, T and Vásárhelyi, BM and Ari, E and Christodoulou, C and Manczinger, M and Enyedi, MZ and Jaksa, G and Kovács, K and van Houte, S and Pursey, E and Pintér, L and Haracska, L and Kintses, B and Papp, B and Pál, C},
title = {ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro.},
journal = {Nature microbiology},
volume = {10},
number = {2},
pages = {313-331},
pmid = {39805953},
issn = {2058-5276},
mesh = {*Anti-Bacterial Agents/pharmacology ; Humans ; Microbial Sensitivity Tests ; *Drug Resistance, Bacterial/genetics ; Klebsiella pneumoniae/drug effects/genetics ; Pseudomonas aeruginosa/drug effects/genetics ; Acinetobacter baumannii/drug effects/genetics ; Escherichia coli/drug effects/genetics ; *Bacteria/drug effects/genetics ; Mutation ; Gastrointestinal Microbiome/genetics ; Metagenomics ; *Gram-Negative Bacteria/drug effects/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of antibiotic exposure in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, priority Gram-negative ESKAPE pathogens. Resistance mutations are already present in natural populations of pathogens, indicating that resistance in nature can emerge through selection of pre-existing bacterial variants. Functional metagenomics showed that mobile resistance genes to antibiotic candidates are prevalent in clinical bacterial isolates, soil and human gut microbiomes. Overall, antibiotic candidates show similar susceptibility to resistance development as antibiotics currently in use, and the corresponding resistance mechanisms overlap. However, certain combinations of antibiotics and bacterial strains were less prone to developing resistance, revealing potential narrow-spectrum antibacterial therapies that could remain effective. Finally, we develop criteria to guide efforts in developing effective antibiotic candidates.},
}
@article {pmid39806613,
year = {2024},
author = {Shen, A and Ye, J and Zhao, H and Qiang, W and Zhao, H and Huang, Y and Zhou, Y and Wang, Y and Li, X and Zhang, Z and Bian, J and Zhang, L and Wu, P and Wang, Y and Lu, Q},
title = {Risk factors and prediction model of breast cancer-related lymphoedema in a Chinese cancer centre: a prospective cohort study protocol.},
journal = {BMJ open},
volume = {14},
number = {12},
pages = {e089769},
pmid = {39806613},
issn = {2044-6055},
mesh = {Adult ; Female ; Humans ; Middle Aged ; *Breast Cancer Lymphedema/epidemiology/etiology ; *Breast Neoplasms/surgery/complications ; China/epidemiology ; Incidence ; *Lymphedema/epidemiology/etiology ; Observational Studies as Topic ; Prospective Studies ; Risk Assessment ; Risk Factors ; East Asian People ; },
abstract = {INTRODUCTION: Lymphoedema is a distressing and long-term complication for breast cancer survivors. However, the reported incidence of lymphoedema varies, and its risk factors remain underexplored. Currently, a well-established risk prediction model is still lacking. This study aims to describe the rationale, objectives, protocol and baseline characteristics of a prospective cohort study focused on examining the incidence and risk factors of breast cancer-related lymphoedema (BCRL), as well as developing a risk prediction model.<br><br>METHODS AND ANALYSIS: This study is an ongoing single-centre prospective observational cohort study recruiting 1967 patients with breast cancer scheduled for surgery treatment in northern China between 15 February 2022 and 21 June 2023. Assessments will be conducted presurgery and at 1, 3, 6, 12, 18, 24, 30 and 36 months postsurgery. Bilateral limb circumferences will be measured by patients at home or by researchers at the outpatient clinics during follow-up visits. The diagnosis of lymphoedema is based on a relative limb volume increase of &#x2265;10% from the preoperative assessment. Self-reported symptoms will be assessed to assist in diagnosis. Potential risk factors are classified into innate personal traits, behavioural lifestyle, interpersonal networks, socioeconomic status and macroenvironmental factors, based on health ecology model. Data collection, storage and management were conducted using the online 'H6WORLD' data management platform. Survival analysis using the Kaplan-Meier estimate will determine the incidence of BCRL. Risk factors of BCRL will be analysed using log-rank test and COX-LASSO regression. Traditional COX regression analysis and seven common survival analysis machine learning algorithms (COX, CARST, RSF, GBSM, XGBS, SSVM and SANN) will be employed for model construction and validation.<br><br>ETHICS AND DISSEMINATION: The study protocol was approved by the Biomedical Ethics Committee of Peking University (IRB00001052-21124) and the Research Ethics Committee of Tianjin Medical University Cancer Institute and Hospital (bc2023013). The results of this study will be published in peer-reviewed journals and will be presented at several research conferences.<br><br>TRIAL REGISTRATION NUMBER: ChiCTR2200057083.},
}
@article {pmid39807382,
year = {2024},
author = {Smith, SD and Geraghty, EM and Rivas, AL and Fasina, FO and Kosoy, M and Malania, L and Hoogesteijn, AL and Fair, JM},
title = {Multidimensional perspectives of geo-epidemiology: from interdisciplinary learning and research to cost-benefit oriented decision-making.},
journal = {Frontiers in public health},
volume = {12},
number = {},
pages = {1492426},
pmid = {39807382},
issn = {2296-2565},
mesh = {Humans ; *Cost-Benefit Analysis ; *Decision Making ; *Epidemiology/education ; Geographic Information Systems ; Interdisciplinary Research ; },
abstract = {Research typically promotes two types of outcomes (inventions and discoveries), which induce a virtuous cycle: something suspected or desired (not previously demonstrated) may become known or feasible once a new tool or procedure is invented and, later, the use of this invention may discover new knowledge. Research also promotes the opposite sequence-from new knowledge to new inventions. This bidirectional process is observed in geo-referenced epidemiology-a field that relates to but may also differ from spatial epidemiology. Geo-epidemiology encompasses several theories and technologies that promote inter/transdisciplinary knowledge integration, education, and research in population health. Based on visual examples derived from geo-referenced studies on epidemics and epizootics, this report demonstrates that this field may extract more (geographically related) information than simple spatial analyses, which then supports more effective and/or less costly interventions. Actual (not simulated) bio-geo-temporal interactions (never captured before the emergence of technologies that analyze geo-referenced data, such as geographical information systems) can now address research questions that relate to several fields, such as Network Theory. Thus, a new opportunity arises before us, which exceeds research: it also demands knowledge integration across disciplines as well as novel educational programs which, to be biomedically and socially justified, should demonstrate cost-effectiveness. Grounded on many bio-temporal-georeferenced examples, this report reviews the literature that supports this hypothesis: novel educational programs that focus on geo-referenced epidemic data may help generate cost-effective policies that prevent or control disease dissemination.},
}
@article {pmid39808116,
year = {2024},
author = {Zárate, A and Díaz-González, L and Taboada, B},
title = {VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39808116},
issn = {1477-4054},
mesh = {Humans ; Artificial Intelligence ; Computational Biology/methods ; *Convolutional Neural Networks ; *Eukaryota/virology ; Genome, Viral ; Metagenome ; *Metagenomics/methods ; *Viral Proteins/genetics ; *Viruses/genetics ; },
abstract = {This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus identification often face limitations due to the diversity and rapid evolution of viral genomes. In response, recent efforts have focused on leveraging artificial intelligence (AI) techniques to enhance accuracy and efficiency in virus detection. However, existing AI-based approaches are primarily binary classifiers, lacking specificity in identifying viral types and reliant on nucleotide sequences. To address these limitations, VirDetect-AI, a novel tool specifically designed for the identification of eukaryotic viruses within metagenomic datasets, is introduced. The VirDetect-AI model employs a combination of convolutional neural networks and residual neural networks to effectively extract hierarchical features and detailed patterns from complex amino acid genomic data. The results demonstrated that the model has outstanding results in all metrics, with a sensitivity of 0.97, a precision of 0.98, and an F1-score of 0.98. VirDetect-AI improves our comprehension of viral ecology and can accurately classify metagenomic sequences into 980 viral protein classes, hence enabling the identification of new viruses. These classes encompass an extensive array of viral genera and families, as well as protein functions and hosts.},
}
@article {pmid39808665,
year = {2025},
author = {Fonseca, LL and Böttcher, L and Mehrad, B and Laubenbacher, RC},
title = {Optimal control of agent-based models via surrogate modeling.},
journal = {PLoS computational biology},
volume = {21},
number = {1},
pages = {e1012138},
pmid = {39808665},
issn = {1553-7358},
support = {R01 AI135128/AI/NIAID NIH HHS/United States ; R01 GM127909/GM/NIGMS NIH HHS/United States ; R01 HL169974/HL/NHLBI NIH HHS/United States ; },
mesh = {*Algorithms ; Humans ; Computational Biology/methods ; Computer Simulation ; *Models, Biological ; },
abstract = {This paper describes and validates an algorithm to solve optimal control problems for agent-based models (ABMs). For a given ABM and a given optimal control problem, the algorithm derives a surrogate model, typically lower-dimensional, in the form of a system of ordinary differential equations (ODEs), solves the control problem for the surrogate model, and then transfers the solution back to the original ABM. It applies to quite general ABMs and offers several options for the ODE structure, depending on what information about the ABM is to be used. There is a broad range of applications for such an algorithm, since ABMs are used widely in the life sciences, such as ecology, epidemiology, and biomedicine and healthcare, areas where optimal control is an important purpose for modeling, such as for medical digital twin technology.},
}
@article {pmid39809329,
year = {2025},
author = {Amino, K and Hirakawa, T and Yago, M and Matsuo, T},
title = {Dorsoventral comparison of intraspecific variation in the butterfly wing pattern using a convolutional neural network.},
journal = {Biology letters},
volume = {21},
number = {1},
pages = {20240446},
pmid = {39809329},
issn = {1744-957X},
support = {//ACT-X/ ; //Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; Female ; Male ; *Butterflies/anatomy &amp; histology ; *Convolutional Neural Networks ; Sex Characteristics ; Species Specificity ; *Wings, Animal/anatomy &amp; histology ; },
abstract = {Butterfly wing patterns exhibit notable differences between the dorsal and ventral surfaces, and morphological analyses of them have provided insights into the ecological and behavioural characteristics of wing patterns. Conventional methods for dorsoventral comparisons are constrained by the need for homologous patches or shared features between two surfaces, limiting their applicability across species. We used a convolutional neural network (CNN)-based analysis, which can compare images of the two surfaces without focusing on homologous patches or features, to detect dorsoventral bias in two types of intraspecific variation: sexual dimorphism and mimetic polymorphism. Using specimen images of 29 species, we first showed that the level of sexual dimorphism calculated by CNN-based analysis corresponded well with traditional assessments of sexual dissimilarity, demonstrating the validity of the method. Dorsal biases were widely detected in sexual dimorphism, suggesting that the conventional hypothesis of dorsally biased sexual selection can be supported in a broader range of species. In contrast, mimetic polymorphism showed no such bias, indicating the importance of both surfaces in mimicry. Our study demonstrates the potential versatility of CNN in comparing wing patterns between the two surfaces, while elucidating the relationship between dorsoventrally different selections and dorsoventral biases in intraspecific variations.},
}
@article {pmid39809974,
year = {2025},
author = {Jia, W and Chan, JC and Wong, TY and Fisher, EB},
title = {Diabetes in China: epidemiology, pathophysiology and multi-omics.},
journal = {Nature metabolism},
volume = {7},
number = {1},
pages = {16-34},
pmid = {39809974},
issn = {2522-5812},
mesh = {Humans ; China/epidemiology ; *Diabetes Mellitus/epidemiology/physiopathology/genetics ; Metabolomics ; Risk Factors ; Prevalence ; Multiomics ; },
abstract = {Although diabetes is now a global epidemic, China has the highest number of affected people, presenting profound public health and socioeconomic challenges. In China, rapid ecological and lifestyle shifts have dramatically altered diabetes epidemiology and risk factors. In this Review, we summarize the epidemiological trends and the impact of traditional and emerging risk factors on Chinese diabetes prevalence. We also explore recent genetic, metagenomic and metabolomic studies of diabetes in Chinese, highlighting their role in pathogenesis and clinical management. Although heterogeneity across these multidimensional areas poses major analytic challenges in classifying patterns or features, they have also provided an opportunity to increase the accuracy and specificity of diagnosis for personalized treatment and prevention. National strategies and ongoing research are essential for improving diabetes detection, prevention and control, and for personalizing care to alleviate societal impacts and maintain quality of life.},
}
@article {pmid39810621,
year = {2025},
author = {Gottlieb, E and Gupta, S and Gahan, L and Raymann, RJ and Watson, NF},
title = {Social jetlag decreases across the lifespan: A prospective big data analysis of objective sleep metrics.},
journal = {Journal of sleep research},
volume = {34},
number = {4},
pages = {e14433},
doi = {10.1111/jsr.14433},
pmid = {39810621},
issn = {1365-2869},
mesh = {Humans ; Female ; Male ; Middle Aged ; *Jet Lag Syndrome/physiopathology ; Adult ; *Sleep/physiology ; Prospective Studies ; Big Data ; Polysomnography ; Aged ; Longitudinal Studies ; Self Report ; Retirement ; Caffeine ; Age Factors ; Circadian Rhythm/physiology ; Cross-Sectional Studies ; },
abstract = {Changes in social zeitgebers across the lifespan affect the interaction between biological and social clocks, potentially contributing to social jetlag. Extant literature suggests a reduction in social jetlag given declining social obligations occurring after retirement, but is limited to self-reported methods and cross-sectional designs. Leveraging longitudinal and ecologically valid data from consumer sleep technology, we analysed objective sleep data from 2439 users of the polysomnography-validated SleepScore mobile application, encompassing 500,415 total nights recorded. We examined the relationship between age as a continuous variable, age as a proxy for retirement status, and social jetlag. Additional linear models were employed to assess the effect of self-reported chronotype, average reported daily caffeine, alcohol and stress on social jetlag. There was a significant negative association between overall age and social jetlag (β = -0.64, t = -9.90, p < 0.001, effect size = 0.040), such that every 1-year increase in age corresponded with a 0.64-min reduction in social jetlag. The inclusion of self-reported chronotype, stress, caffeine and alcohol increased the explanatory power of our models slightly, but the effect of age remained consistent (β = -0.642, t = -8.91, p < 0.001, effect size = 0.046). Retirement-aged individuals exhibited nearly 50% less reduction in social jetlag than pre-retirement (30.6 ± 48.2 min versus post-retirement: 15.8 ± 41.6 min, p < 0.0001). While social jetlag after retirement was most pronounced for strong evening chronotypes (β = -0.41, t = -2.876, p = 0.004, effect size = -0.4276), pairwise comparisons revealed no statistically significant differences in the slopes between chronotypes (p > 0.05). Thus, social jetlag decreases across the lifespan, and its reduction appears to be amplified post-retirement even after accounting for behavioural factors.},
}
@article {pmid39813347,
year = {2025},
author = {Gu, S and Shao, Z and Qu, Z and Zhu, S and Shao, Y and Zhang, D and Allen, R and He, R and Shao, J and Xiong, G and Jousset, A and Friman, VP and Wei, Z and Kümmerli, R and Li, Z},
title = {Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq5038},
pmid = {39813347},
issn = {2375-2548},
mesh = {*Siderophores/metabolism/genetics ; *Iron/metabolism ; *Ecosystem ; *Evolution, Molecular ; Microbial Interactions ; Humans ; *Pseudomonas/genetics/metabolism ; *Bacteria/metabolism/genetics ; Computational Biology/methods ; *Bacterial Proteins/genetics/metabolism ; },
abstract = {Bacterial social interactions play crucial roles in various ecological, medical, and biotechnological contexts. However, predicting these interactions from genome sequences is notoriously difficult. Here, we developed bioinformatic tools to predict whether secreted iron-scavenging siderophores stimulate or inhibit the growth of community members. Siderophores are chemically diverse and can be stimulatory or inhibitory depending on whether bacteria have or lack corresponding uptake receptors. We focused on 1928 representative Pseudomonas genomes and developed an experimentally validated coevolution algorithm to match encoded siderophore synthetases to corresponding receptor groups. We derived community-level iron interaction networks to show that siderophore-mediated interactions differ across habitats and lifestyles. Specifically, dense networks of siderophore sharing and competition were observed among environmental and nonpathogenic species, while small, fragmented networks occurred among human-associated and pathogenic species. Together, our sequence-to-ecology approach empowers the analyses of social interactions among thousands of bacterial strains and offers opportunities for targeted intervention to microbial communities.},
}
@article {pmid39813804,
year = {2025},
author = {Ahmad, S and Peng, X and Ashraf, A and Yin, D and Chen, Z and Ahmed, R and Israr, M and Jia, H},
title = {Building resilient urban drainage systems by integrated flood risk index for evidence-based planning.},
journal = {Journal of environmental management},
volume = {374},
number = {},
pages = {124130},
doi = {10.1016/j.jenvman.2025.124130},
pmid = {39813804},
issn = {1095-8630},
mesh = {*Drainage, Sanitary/methods/statistics &amp; numerical data ; Cities/statistics &amp; numerical data ; *Floods/statistics &amp; numerical data ; *City Planning/methods ; Urbanization ; Climate Change ; *Risk Management/methods ; Geographic Information Systems ; Water Movements ; Risk Assessment ; Pakistan ; },
abstract = {Urban flooding poses a significant risk to cities worldwide, exacerbated by increasing urbanization and climate change. Effective flood risk management requires comprehensive assessments considering the complex interaction of social, economic, and environmental factors. This study developed an innovative Urban Flood Risk Index (FRI) to quantify and assess flood risk at the sub-catchment level, providing a tool for evidence-based planning and resilient infrastructure development. This study integrates Geographic Information System (GIS), Storm Water Management Model (SWMM), Analytic Hierarchy Process (AHP), and the Pressure-State-Response (PSR) framework. The FRI incorporates seven pressure and state indicators and three response indicators weighted by expert judgment. The FRI was calculated by combining the weighted sub-indices, classifying flood risk into five levels. Results showed that 51% of the study area experienced high pressure, with 26% facing very-high pressure. The state index indicated that 55% of the area falls under a moderate state, while 21% exhibits a high state. Importantly, the response index highlighted the effectiveness of Low Impact Development (LID) practices, with 20% of the area showing high to very-high response levels. The integrated FRI demonstrated an overall moderate flood risk level for maximum sub-catchments, emphasizing the positive impact of LID practices in mitigating flood risk despite existing pressures and system limitations. This evidence-based assessment provides a valuable tool for sub-catchment level flood risk assessment. It empowers decision-makers to prioritize investments, target interventions, and develop adaptive strategies to enhance urban resilience in a changing climate.},
}
@article {pmid39813953,
year = {2025},
author = {Knight, ME and Farkas, K and Wade, M and Webster, G and Pass, DA and Perry, W and Kille, P and Singer, A and Jones, DL},
title = {Wastewater-based analysis of antimicrobial resistance at UK airports: Evaluating the potential opportunities and challenges.},
journal = {Environment international},
volume = {195},
number = {},
pages = {109260},
doi = {10.1016/j.envint.2025.109260},
pmid = {39813953},
issn = {1873-6750},
mesh = {*Wastewater/microbiology ; *Airports ; United Kingdom ; *Drug Resistance, Microbial/genetics ; Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; },
abstract = {With 40 million annual passenger flights, airports are key hubs for microbial communities from diverse geographic origins to converge, mix, and distribute. Wastewater derived from airports and aircraft represent both a potential route for the global dispersion of antimicrobial resistant (AMR) organisms and an under-utilised resource for strengthening global AMR surveillance. This study investigates the abundance and diversity of antimicrobial resistance genes (ARGs) in wastewater samples collected from airport terminals (n = 132), aircraft (n = 25), and a connected wastewater treatment plant (n = 11) at three international airports in the UK (London Heathrow, Edinburgh and Bristol). A total of 76 ARGs were quantified using high throughput qPCR (HT-qPCR) while a subset of samples (n = 30) was further analysed by metagenomic sequencing. Our findings reveal that aircraft wastewater resistomes were compositionally distinct from those observed at airport terminals, despite their similar diversity. Notably, flights originating from Asia and Africa carried a higher number of unique ARGs compared to those from Europe and North America. However, clustering of the ARG profile displayed no overall association with geography. Edinburgh terminal and pumping station wastewater had compositionally comparable resistomes to that of the connected urban wastewater treatment plant, though further research is needed to determine the relative contributions of the local population and international travellers. This study provides the first comprehensive investigation of AMR in wastewater from both aircraft and terminals across multiple international airports. Our results highlight aircraft wastewater as a potential route for cross-border AMR transmission and a valuable tool for global AMR surveillance. However, the findings also underscore the limitations and need for standardised approaches for AMR monitoring in airport environments, to effectively mitigate the global spread of AMR and enhance public health surveillance strategies.},
}
@article {pmid39814778,
year = {2025},
author = {Gómez-Gras, D and Linares, C and Viladrich, N and Zentner, Y and Grinyó, J and Gori, A and McFadden, CS and Fabricius, KE and Madin, JS},
title = {The Octocoral Trait Database: a global database of trait information for octocoral species.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {82},
pmid = {39814778},
issn = {2052-4463},
mesh = {*Anthozoa ; Animals ; *Databases, Factual ; Coral Reefs ; Biodiversity ; Ecosystem ; },
abstract = {Trait-based approaches are revolutionizing our understanding of high-diversity ecosystems by providing insights into the principles underlying key ecological processes, such as community assembly, species distribution, resilience, and the relationship between biodiversity and ecosystem functioning. In 2016, the Coral Trait Database advanced coral reef science by centralizing trait information for stony corals (i.e., Subphylum Anthozoa, Class Hexacorallia, Order Scleractinia). However, the absence of trait data for soft corals, gorgonians, and sea pens (i.e., Class Octocorallia) limits our understanding of ecosystems where these organisms are significant members and play pivotal roles. To address this gap, we introduce the Octocoral Trait Database, a global, open-source database of curated trait data for octocorals. This database houses species- and individual-level data, complemented by contextual information that provides a relevant framework for analyses. The inaugural dataset, OctocoralTraits v2.2, contains over 97,500 global trait observations across 98 traits and over 3,500 species. The database aims to evolve into a steadily growing, community-led resource that advances future marine science, with a particular emphasis on coral reef research.},
}
@article {pmid39817434,
year = {2025},
author = {Blum, J and Brüll, M and Hengstler, JG and Dietrich, DR and Gruber, AJ and Dipalo, M and Kraushaar, U and Mangas, I and Terron, A and Fritsche, E and Marx-Stoelting, P and Hardy, B and Schepky, A and Escher, S and Hartung, T and Landsiedel, R and Odermatt, A and Sachana, M and Koch, K and Dönmez, A and Masjosthusmann, S and Bothe, K and Schildknecht, S and Beilmann, M and Beltman, JB and Fitzpatrick, S and Mangerich, A and Rehm, M and Tangianu, S and Zickgraf, FM and Kamp, H and Burger, G and van de Water, B and Kleinstreuer, N and White, A and Leist, M},
title = {The long way from raw data to NAM-based information: Overview on data layers and processing steps.},
journal = {ALTEX},
volume = {42},
number = {1},
pages = {167-180},
doi = {10.14573/altex.2412171},
pmid = {39817434},
issn = {1868-8551},
mesh = {Animals ; Humans ; *Animal Testing Alternatives/methods ; Risk Assessment ; *Toxicity Tests/methods ; },
abstract = {Toxicological test methods generate raw data and provide instructions on how to use these to determine a final outcome such as a classification of test compounds as hits or non-hits. The data processing pipeline provided in the test method description is often highly complex. Usually, multiple layers of data, ranging from a machine-generated output to the final hit definition, are considered. Transition between each of these layers often requires several data processing steps. As changes in any of these processing steps can impact the final output of new approach methods (NAMs), the processing pipeline is an essential part of a NAM description and should be included in reporting templates such as the ToxTemp. The same raw data, processed in different ways, may result in different final outcomes that may affect the readiness status and regulatory acceptance of the NAM, as an altered output can affect robustness, performance, and relevance. Data management, pro­cessing, and interpretation are therefore important elements of a comprehensive NAM definition. We aim to give an overview of the most important data levels to be considered during the devel­opment and application of a NAM. In addition, we illustrate data processing and evaluation steps between these data levels. As NAMs are increasingly standard components of the spectrum of toxi­cological test methods used for risk assessment, awareness of the significance of data processing steps in NAMs is crucial for building trust, ensuring acceptance, and fostering the reproducibility of NAM outcomes.},
}
@article {pmid39821365,
year = {2025},
author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y},
title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.},
journal = {Drug development research},
volume = {86},
number = {1},
pages = {e70045},
doi = {10.1002/ddr.70045},
pmid = {39821365},
issn = {1098-2299},
support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; },
mesh = {Humans ; *Pharmacovigilance ; *Adverse Drug Reaction Reporting Systems/statistics &amp; numerical data ; *Histamine H2 Antagonists/adverse effects/administration &amp; dosage ; United States ; United States Food and Drug Administration ; *Famotidine/adverse effects/administration &amp; dosage ; Female ; Male ; Middle Aged ; Adult ; Aged ; Young Adult ; Adolescent ; Databases, Factual ; Child ; },
abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.},
}
@article {pmid39822261,
year = {2025},
author = {Proença Neto, MA and De Sousa, MPA},
title = {Pytaxon: A Python software for resolving and correcting taxonomic names in biodiversity data.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e138257},
pmid = {39822261},
issn = {1314-2828},
abstract = {BACKGROUND: The standardisation and correction of taxonomic names in large biodiversity databases remain persistent challenges for researchers, as errors in species names can compromise ecological analyses, land-use planning and conservation efforts, particularly when inaccurate data are shared on global biodiversity portals.<br><br>NEW INFORMATION: We present pytaxon, a Python software designed to resolve and correct taxonomic names in biodiversity data by leveraging the Global Names Verifier (GNV) API and employing fuzzy matching techniques to suggest corrections for discrepancies and nomenclatural inconsistencies. The pytaxon offers both a Command Line Interface (CLI) and a Graphical User Interface (GUI), ensuring accessibility to users with different levels of computing expertise. Tests on spreadsheets derived from datasets published in the Global Biodiversity Information Facility (GBIF) demonstrated its effectiveness in identifying and resolving taxonomic errors. By mitigating the propagation of inaccuracies from researchers' datasets to global biodiversity databases, pytaxon supports more reliable conservation decisions and robust scientific investigations. Its contributions enhance data integrity and promote informed biodiversity management in a rapidly evolving global environment.},
}
@article {pmid39822595,
year = {2024},
author = {Boyes, D and , and , and , and , and , and , and , },
title = {The genome sequence of the Poplar Grey moth, Subacronicta megacephala (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {696},
pmid = {39822595},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Subacronicta megacephala (Poplar Grey moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 424.20 megabases. Most of the assembly (99.02%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,189 protein-coding genes.},
}
@article {pmid39823671,
year = {2025},
author = {Liu, T and Wang, M and Wang, M and Xiong, Q and Jia, L and Ma, W and Sui, S and Wu, W and Guo, X},
title = {Identification of the primary pollution sources and dominant influencing factors of soil heavy metals using a random forest model optimized by genetic algorithm coupled with geodetector.},
journal = {Ecotoxicology and environmental safety},
volume = {290},
number = {},
pages = {117731},
doi = {10.1016/j.ecoenv.2025.117731},
pmid = {39823671},
issn = {1090-2414},
mesh = {*Metals, Heavy/analysis ; *Soil Pollutants/analysis ; China ; *Environmental Monitoring/methods ; Soil/chemistry ; Algorithms ; Geographic Information Systems ; *Environmental Pollution/analysis/statistics &amp; numerical data ; Risk Assessment ; Monte Carlo Method ; Principal Component Analysis ; Genetic Algorithms ; Random Forest ; },
abstract = {Identifying and quantifying the dominant factors influencing heavy metal (HM) pollution sources are essential for maintaining soil ecological health and implementing effective pollution control measures. This study analyzed soil HM samples from 53 different land use types in Jiaozuo City, Henan Province, China. Pollution sources were identified using Absolute Principal Component Score (APCS), with 8 anthropogenic factors, 9 natural factors, and 4 soil physicochemical properties mapped using Geographic Information System (GIS) kernel density estimation. Geodetector and a genetic algorithm optimized random forest model (GA-RF) were employed to quantify the dominant factors and precisely identify pollution sources. A Monte Carlo model was further applied to assess source-oriented health risk probabilities across age groups in the study area. The results revealed three principal components representing pollution sources, with contribution rates of 47.2 %, 33.3 %, and 19.5 %, respectively. For pollution source 1, industrial activities were dominant, with factory density (27.7 %) and distance from the factory (36.3 %) identified as the main factors. Cr, Cu, Mn, and Ni had high loads in this source. Pollution source 2, a combination of natural and transportation influences, was primarily affected by the normalized difference vegetation index (NDVI, 37.8 %), road network density (16.8 %), and proximity to roads (15.3 %). Pollution source 3 was linked to agricultural activities, with cultivated land density (CLD) contributing 39.1 %. As exhibited a high load (91.1 %) in this source, with an exceedance rate of 93 % in cultivated soil, a moderate enrichment factor of 2.33, and a strong ecological risk index of 615.72, making it the most polluted metal in the area. The source-oriented Health Risk Assessment (HRA) showed that agricultural activities contributed 88.7 % to the carcinogenic risk from As in cultivated land. Overall, 99.3 % of the population faced an acceptable cancer risk level. Unlike traditional source apportionment methods, the GA-RF model effectively quantified the contributions of specific influencing factors (e.g., factory density) to pollution sources, rather than merely estimating the percentage contributions of the sources themselves. This approach provides a novel perspective for HM source apportionment under complex environmental conditions.},
}
@article {pmid39823836,
year = {2025},
author = {Li, Z and Meng, C and Azad, MAK and Zhu, Q and Lin, W and Cui, Y and Lan, W and He, Q and Kong, X},
title = {Effects of the Salvia miltiorrhiza, Ligustrum lucidum, and Taraxacum mongolicum ultra-fine powder formula on meat quality of aged layers by multi-omics.},
journal = {Poultry science},
volume = {104},
number = {2},
pages = {104783},
pmid = {39823836},
issn = {1525-3171},
mesh = {Animals ; *Ligustrum/chemistry ; *Salvia miltiorrhiza/chemistry ; Dietary Supplements/analysis ; Animal Feed/analysis ; *Meat/analysis ; *Taraxacum/chemistry ; *Chickens/physiology ; Diet/veterinary ; *Drugs, Chinese Herbal/administration &amp; dosage/metabolism ; Female ; Powders ; Antioxidants/metabolism ; Random Allocation ; Multiomics ; },
abstract = {This study was aimed to identify the targets of 1% ultra-fine Chinese medicine formula (UCMF, 0.5% Salvia miltiorrhiza Bge. + 0.25% Ligustrum lucidum Ait. + 0.25% Taraxacum mongolicum Hand.-Mazz.) in delaying aging and explore its impacts on meat quality of aged layers. The effective components of the above three Chinese herbs were screened, and the network pharmacology analysis identified 91 common targets and enriched pathways between herbs and aging. The results showed that cellular response to chemical stimulus, response to oxidative stress, and response to oxygen-containing compound pathways were crucial for UCMF to resist aging. Further in vivo analyses confirmed that UCMF supplementation enhanced the antioxidant function in breast muscles of aged layers by upregulating (P < 0.05) the SOD2 gene expression. Meanwhile, UCMF supplementation reduced (P < 0.05) yellowness (b* value) and drip loss while enhancing (P < 0.05) cooked meat percentage of aged layers. For the health lipid indices in breast muscles, UCMF supplementation increased (P < 0.05) polyunsaturated fatty acids/saturated fatty acids and hypocholesterolemic/hypercholesterolemic ratios and decreased (P < 0.05) the thrombogenic index. The UCMF supplementation optimized the cecal microbiota of aged layers by enhancing the relative abundance of Firmicutes and reducing the relative abundances of Bacteroidetes and Spirochaetes (P < 0.05), which may be related to improving meat quality. In conclusion, dietary UCMF supplementation may be an effective strategy for improving antioxidant function and the meat quality of aged layers.},
}
@article {pmid39825388,
year = {2025},
author = {Burthe, SJ and Kumbar, B and Schäfer, SM and Purse, BV and Vanak, AT and Balakrishnan, N and Hassall, R and Hoti, SL and Narayanaswamy, D and Potadar, S and Rahman, M and Chanda, MM},
title = {First evidence of transovarial transmission of Kyasanur Forest disease virus in Haemaphysalis and Rhipicephalus ticks in the wild.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {14},
pmid = {39825388},
issn = {1756-3305},
support = {MR/T029846/1//Global Challenges Research Fund/ ; MR/P024335/1//Global Challenges Research Fund/ ; },
mesh = {Animals ; *Encephalitis Viruses, Tick-Borne/isolation &amp; purification/genetics/physiology ; Female ; India/epidemiology ; *Rhipicephalus/virology ; *Kyasanur Forest Disease/transmission/virology ; Larva/virology ; *Ixodidae/virology ; Animals, Wild/virology ; *Arachnid Vectors/virology ; },
abstract = {BACKGROUND: Kyasanur forest disease virus (KFDV) is a tick-borne flavivirus causing debilitating and potentially fatal disease in people in the Western Ghats region of India. The transmission cycle is complex, involving multiple vector and host species, but there are significant gaps in ecological knowledge. Empirical data on pathogen-vector-host interactions and incrimination have not been updated since the last century, despite significant local changes in land use and the expansion of KFD to new areas. Mathematical models predict that transovarial transmission, whereby adult female ticks pass KFDV infections to their offspring, plays an important role in the persistence of KFD, but this has not been shown in the wild. Here we set out to establish whether transovarial transmission of KFDV was occurring under natural field conditions by assessing whether host-seeking larvae were positive for KFDV.<br><br>METHODS: Ticks were sampled by dragging and flagging across a broad range of habitats within the agro-forest matrix at 49 sites in two districts: Shivamogga, Karnataka and Wayanad, Kerala (September 2018-March 2019), and larvae were tested for KFDV by PCR.<br><br>RESULTS: In total, larval ticks from 7 of the 49 sites sampled tested positive for KFDV, indicating that transovarial transmission is occurring. Of the 13 KFDV-positive larval samples, 3 came from around houses and gardens, 5 from crops (3 from harvested rice paddy and 2 from areca plantation), 1 from teak plantation and 4 (2 from 1 transect) from forests. Five different tick species were found to have KFDV-positive larvae: Haemaphysalis spinigera, H. bispinosa, Rhipicephalus annulatus, R. microplus and an unidentifiable species of Haemaphysalis (no close match in GenBank).<br><br>CONCLUSIONS: Our empirical confirmation of transovarial transmission has important implications for understanding and predicting KFD dynamics, suggesting that ticks may act as a reservoir for KFDV. Moreover, small mammals and cattle may play crucial roles in transmission if small mammals are the main hosts for larvae infected via transovarial transmission, and cattle support large numbers of infected female adult ticks. This first report of transovarial transmission of KFDV, and within a hitherto undescribed range of vectors and habitats, will help disease managers improve KFD surveillance and mitigation strategies, ultimately leading to communities becoming more resilient to the risk of this tick-transmitted disease.},
}
@article {pmid39826720,
year = {2025},
author = {Akhoon, BA and Qiao, Q and Stewart, A and Chen, J and Rodriguez Lopez, CM and Corbin, KR},
title = {Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.},
journal = {International journal of biological macromolecules},
volume = {298},
number = {},
pages = {139980},
doi = {10.1016/j.ijbiomac.2025.139980},
pmid = {39826720},
issn = {1879-0003},
mesh = {*Cellulose/biosynthesis ; Phylogeny ; *Genome, Bacterial ; *Genomics/methods ; *Acetobacteraceae/genetics/metabolism ; Multigene Family ; Genetic Variation ; },
abstract = {Bacterial cellulose holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges related to bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters, including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.},
}
@article {pmid39830079,
year = {2024},
author = {Couch, J and Arnaout, R and Arnaout, R},
title = {Beyond Size and Class Balance: Alpha as a New Dataset Quality Metric for Deep Learning.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {39830079},
issn = {2331-8422},
support = {R01 AI148747/AI/NIAID NIH HHS/United States ; R01 HL150394/HL/NHLBI NIH HHS/United States ; },
abstract = {In deep learning, achieving high performance on image classification tasks requires diverse training sets. However, the current best practice-maximizing dataset size and class balance-does not guarantee dataset diversity. We hypothesized that, for a given model architecture, model performance can be improved by maximizing diversity more directly. To test this hypothesis, we introduce a comprehensive framework of diversity measures from ecology that generalizes familiar quantities like Shannon entropy by accounting for similarities among images. (Size and class balance emerge as special cases.) Analyzing thousands of subsets from seven medical datasets showed that the best correlates of performance were not size or class balance but A -"big alpha"-a set of generalized entropy measures interpreted as the effective number of image-class pairs in the dataset, after accounting for image similarities. One of these, A 0 , explained 67% of the variance in balanced accuracy, vs. 54% for class balance and just 39% for size. The best pair of measures was size-plus- A 1 (79%), which outperformed size-plus-class-balance (74%). Subsets with the largest A 0 performed up to 16% better than those with the largest size (median improvement, 8%). We propose maximizing A as a way to improve deep learning performance in medical imaging.},
}
@article {pmid39830091,
year = {2023},
author = {Boyes, D and Eljounaidi, K and , and , and , and , and , and , },
title = {The genome sequence of the Beautiful Golden Y, Autographa pulchrina (Haworth, 1809).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {375},
pmid = {39830091},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Autographa pulchrina (the Beautiful Golden Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 426.2 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 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,916 protein coding genes.},
}
@article {pmid39830898,
year = {2025},
author = {Gartler, S and Scheer, J and Meyer, A and Abass, K and Bartsch, A and Doloisio, N and Falardeau, J and Hugelius, G and Irrgang, A and Haukur Ingimundarson, J and Jungsberg, L and Lantuit, H and Nymand Larsen, J and Lodi, R and Martin, VS and Mercer, L and Nielsen, D and Overduin, P and Povoroznyuk, O and Rautio, A and Schweitzer, P and Speetjens, NJ and Tomaškovičová, S and Timlin, U and Vanderlinden, JP and Vonk, J and Westerveld, L and Ingeman-Nielsen, T},
title = {A transdisciplinary, comparative analysis reveals key risks from Arctic permafrost thaw.},
journal = {Communications earth &amp; environment},
volume = {6},
number = {1},
pages = {21},
pmid = {39830898},
issn = {2662-4435},
abstract = {Permafrost thaw poses diverse risks to Arctic environments and livelihoods. Understanding the effects of permafrost thaw is vital for informed policymaking and adaptation efforts. Here, we present the consolidated findings of a risk analysis spanning four study regions: Longyearbyen (Svalbard, Norway), the Avannaata municipality (Greenland), the Beaufort Sea region and the Mackenzie River Delta (Canada) and the Bulunskiy District of the Sakha Republic (Russia). Local stakeholders' and scientists' perceptions shaped our understanding of the risks as dynamic, socionatural phenomena involving physical processes, key hazards, and societal consequences. Through an inter- and transdisciplinary risk analysis based on multidirectional knowledge exchanges and thematic network analysis, we identified five key hazards of permafrost thaw. These include infrastructure failure, disruption of mobility and supplies, decreased water quality, challenges for food security, and exposure to diseases and contaminants. The study's novelty resides in the comparative approach spanning different disciplines, environmental and societal contexts, and the transdisciplinary synthesis considering various risk perceptions.},
}
@article {pmid39832137,
year = {2025},
author = {Iobbi, V and Parisi, V and Giacomini, M and De Riccardis, F and Brun, P and Núñez-Pons, L and Drava, G and Giordani, P and Monti, MC and Poggi, R and Murgia, Y and De Tommasi, N and Bisio, A},
title = {Sesterterpenoids: sources, structural diversity, biological activity, and data management.},
journal = {Natural product reports},
volume = {42},
number = {3},
pages = {443-481},
doi = {10.1039/d4np00041b},
pmid = {39832137},
issn = {1460-4752},
mesh = {*Sesterterpenes/chemistry/pharmacology/isolation &amp; purification ; Molecular Structure ; Biological Products/chemistry/pharmacology ; Data Management ; Humans ; },
abstract = {Reviewing the literature published up to October 2024.Sesterterpenoids are one of the most chemically diverse and biologically promising subgroup of terpenoids, the largest family of secondary metabolites. The present review article summarizes more than seven decades of studies on isolation and characterization of more than 1600 structurally novel sesterterpenoids, supplemented by biological, pharmacological, ecological, and geographic distribution data. All the information have been implemented in eight tables available on the web and a relational database https://sesterterpenoids.unige.net/. The interface has two sections, one open to the public for reading only and the other, protected by an authentication mechanism, for timely updating of published results.},
}
@article {pmid39832144,
year = {2024},
author = {Ištoňová, M and Dorko, E and Knap, V and Stehlíková, B and Murgová, A and Ondová, P and Rimárová, K},
title = {Assessment of depressive disorders and states of anxiety in patients following cerebrovascular accidents in connection with health care provision.},
journal = {Central European journal of public health},
volume = {32},
number = {Supplement},
pages = {18-24},
pmid = {39832144},
issn = {1210-7778},
mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; Aged, 80 and over ; *Stroke/psychology/complications ; Slovakia/epidemiology ; *Anxiety Disorders/epidemiology/etiology ; *Depressive Disorder/epidemiology/etiology ; *Anxiety/epidemiology ; Depression/epidemiology ; Surveys and Questionnaires ; },
abstract = {OBJECTIVE: Anxiety and depression in patients following cerebrovascular accidents are among frequently occurring complications of the medical condition. The consequences affect personal, family, professional, and social life. They cause severe functional and cognitive impairments, limit the ability to perform normal daily activities, which can result in complete disability. The aim of the study was to monitor the occurrence of anxiety and depression in patients following cerebrovascular accidents hospitalized in neurological departments in the region of eastern Slovakia.<br><br>METHODS: A total of 101 patients following cerebrovascular accidents, aged from 48-86 years, were included in the descriptive study. Demographic and clinical data were obtained from patients and from medical records. We determined the occurrence of anxiety disorders, depression and emotional distress in patients following cerebrovascular accidents using a standardized Hospital Anxiety and Depression Scale (HADS) questionnaire.<br><br>RESULTS: Data analysis confirms a high incidence of anxiety in the HADS-A subscale (9.23 &#xb1; 4.13) and depression in the HADS-D subscale (9.09 &#xb1; 4.43) during the hospitalization phase of the disease. It demonstrates the pathological occurrence of anxiety states in 37%, depression in 36%, emotional distress in 36%, and a serious degree of combination of pathological values of the anxiety subscale and the depression subscale in 27% of patients. The existence of a strong positive correlation between anxiety and depression indicators was confirmed.<br><br>CONCLUSION: The results confirm a high prevalence of anxiety and depression in the acute phase of the disease. The findings indicate that patients recovering from cerebrovascular accidents not only face physical difficulties and loss of independence but also struggle with anxiety and depression, which can negatively impact and slow their recovery. Given the high frequency of these psychological conditions, further research is needed to enhance the quality and effectiveness of care provided to patients with cerebrovascular accidents.},
}
@article {pmid39832988,
year = {2025},
author = {Shimels, T and Kantelhardt, EJ and Assefa, M and Fenta, TG},
title = {Spatiotemporal dynamics and prevention strategies of cervical cancer incidence in Addis Ababa, Ethiopia: an ecological study.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e089521},
pmid = {39832988},
issn = {2044-6055},
mesh = {Humans ; Ethiopia/epidemiology ; Female ; *Uterine Cervical Neoplasms/epidemiology/prevention &amp; control ; Incidence ; Middle Aged ; Adult ; Spatio-Temporal Analysis ; Young Adult ; Aged ; Adolescent ; Bayes Theorem ; },
abstract = {OBJECTIVE: This study analysed the spatial and temporal patterns of cervical cancer incidence in Addis Ababa from 2012 to 2021.<br><br>DESIGN: An ecological study was conducted from 1 September to 30 November 2023 to examine the spatiotemporal trends of cervical cancer incidence.<br><br>SETTING: The research was conducted in Addis Ababa, the capital city of Ethiopia.<br><br>PARTICIPANTS: Included were all patients with clinically and/or histopathologically confirmed diagnoses of cervical cancer.<br><br>DATA ANALYSIS: The study employed advanced analytical tools including R programming, Quantum Geographic Information System V.3.36.0, GeoDa V.1.2.2 and System for Automated Geoscientific Analyses GIS V.9.3.2. Techniques such as Bayesian empirical testing with a block weighting matrix for hotspot identification, Global Moran's I for spatial autocorrelation, nearest neighbour imputation and universal Kriging interpolation were used to manage data gaps. Joinpoint trend analysis and direct age-standardised incidence rate (ASIR) using the Segi's World standard population was applied to compare trends across subcities. A statistical significance threshold was set at p<0.05.<br><br>RESULTS: Between 2012 and 2021, a total of 2435 new cervical cancer cases were recorded in the Addis Ababa City Population-based Cancer Registry, with significant spatial clustering observed in Nifas Silk Lafto, Bole, Kirkos as well as parts of Gulele and Yeka sub cities (z score>1.96) in 2018. The citywide age-standardised incidence rate varied from 19 to 26 cases per 100&#x2009;000&#x2009;women-years during 2013 and 2016, respectively. Subcity trends varied significantly, with increases and decreases noted in Akaki Kality and Kolfe Keraniyo over different periods while Bole subcity showed modest increase at 4.2% APC (95% CI: 0.6% to 7.9%; p=0.026).<br><br>CONCLUSION: The study highlights substantial fluctuations in ASIR and significant geographic disparities in cervical cancer throughout Addis Ababa. To address these challenges, the implementation of school-based human papillomavirus vaccination programmes, alongside targeted interventions, active campaigns and sustained surveillance, is critical. These strategies are essential to effectively reduce the cervical cancer burden and improve health outcomes in the community.},
}
@article {pmid39833104,
year = {2024},
author = {Liu, F and Zhao, Z and Liu, Y},
title = {PHPGAT: predicting phage hosts based on multimodal heterogeneous knowledge graph with graph attention network.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39833104},
issn = {1477-4054},
support = {62303193//National Natural Science Foundation of China/ ; 20230101064JC//Natural Science Foundation of Jilin Province, China/ ; },
mesh = {*Bacteriophages/physiology ; *Computational Biology/methods ; *Bacteria/virology ; },
abstract = {Antibiotic resistance poses a significant threat to global health, making the development of alternative strategies to combat bacterial pathogens increasingly urgent. One such promising approach is the strategic use of bacteriophages (or phages) to specifically target and eradicate antibiotic-resistant bacteria. Phages, being among the most prevalent life forms on Earth, play a critical role in maintaining ecological balance by regulating bacterial communities and driving genetic diversity. Accurate prediction of phage hosts is essential for successfully applying phage therapy. However, existing prediction models may not fully encapsulate the complex dynamics of phage-host interactions in diverse microbial environments, indicating a need for improved accuracy through more sophisticated modeling techniques. In response to this challenge, this study introduces a novel phage-host prediction model, PHPGAT, which leverages a multimodal heterogeneous knowledge graph with the advanced GATv2 (Graph Attention Network v2) framework. The model first constructs a multimodal heterogeneous knowledge graph by integrating phage-phage, host-host, and phage-host interactions to capture the intricate connections between biological entities. GATv2 is then employed to extract deep node features and learn dynamic interdependencies, generating context-aware embeddings. Finally, an inner product decoder is designed to compute the likelihood of interaction between a phage and host pair based on the embedding vectors produced by GATv2. Evaluation results using two datasets demonstrate that PHPGAT achieves precise phage host predictions and outperforms other models. PHPGAT is available at https://github.com/ZhaoZMer/PHPGAT.},
}
@article {pmid39833389,
year = {2025},
author = {Schroeder, MW and Frumkin, MR and Mace, RA},
title = {Proof-of-concept for integrating multimodal digital health assessments into lifestyle interventions for older adults with dementia risk factors.},
journal = {Journal of behavioral medicine},
volume = {48},
number = {2},
pages = {373-384},
pmid = {39833389},
issn = {1573-3521},
support = {1 K23 AG075257-01/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; Aged ; Female ; Male ; *Dementia/prevention &amp; control ; Actigraphy ; *Ecological Momentary Assessment ; Pilot Projects ; Mindfulness ; Middle Aged ; *Life Style ; Proof of Concept Study ; Risk Factors ; Sleep ; Cognitive Dysfunction ; Patient Compliance ; Aged, 80 and over ; Digital Health ; },
abstract = {Multimodal digital health assessments overcome the limitations of patient-reported outcomes by allowing for continuous and passive monitoring but remain underutilized in older adult lifestyle interventions for brain health. Therefore, we aim to (1) report ecological momentary assessment (EMA) and ActiGraph adherence among older adults during a lifestyle intervention; and (2) use dynamic data collected via EMA and ActiGraph to examine person-specific patterns of mindfulness, steps, and sleep throughout the intervention. We analyzed EMA and ActiGraph data from a pilot study of the 8-week My Healthy Brain program (N = 10) lifestyle group for older adults (60+) with subjective cognitive decline. EMA adherence metrics included proportion of EMA completed and the proportion of days with at least 10 mindfulness minutes. ActiGraph GT9X adherence metrics included the number of valid wear days (≥ 7 h) and the number of days participants achieved their step goal. We used linear mixed-effects models to examine person-specific patterns of step count, sleep efficiency, and mindfulness practice. On average, participants completed 39 of the 49 possible EMAs (80%) during the program. ActiGraph adherence was slightly higher than EMA (M = 61.40 days, 87.71%). Participants achieved the daily mindfulness goal (10 min/day) and step goal on 46.32% and 55.10% of days, respectively. Dynamic data revealed that on average, participant step counts increased by approximately 16.5 steps per day (b = 16.495, p = 0.002). However, some participants exhibited no changes while improvements made by other participants returned to baseline levels of activity. There was substantial heterogeneity in trajectories of mindfulness practice and sleep efficiency. EMA and ActiGraph are feasible for older adults enrolled in dementia risk reduction lifestyle interventions. Future studies are needed to better understand how mechanisms of lifestyle behaviors captured by EMA and ActiGraph are related to cognitive outcomes in older adults.},
}
@article {pmid39833495,
year = {2025},
author = {Akar, SE and Nwachukwu, W and Adewuyi, OS and Ahumibe, AA and Akanimo, I and Okunromade, O and Babatunde, O and Ihekweazu, C and Hitachi, M and Kato, K and Takamatsu, Y and Hirayama, K and Kaneko, S},
title = {Epidemiology of Yellow Fever in Nigeria: Analysis of Climatic, Ecological, Socio-Demographic, and Clinical Factors Associated with Viral Positivity Among Suspected Cases Using National Surveillance Data, 2017-2023.},
journal = {Journal of epidemiology and global health},
volume = {15},
number = {1},
pages = {2},
pmid = {39833495},
issn = {2210-6014},
mesh = {Humans ; Nigeria/epidemiology ; *Yellow Fever/epidemiology/prevention &amp; control ; Female ; Male ; Retrospective Studies ; Adolescent ; Adult ; Middle Aged ; Child ; Young Adult ; Child, Preschool ; Infant ; Climate ; Population Surveillance ; Socioeconomic Factors ; Risk Factors ; Disease Outbreaks ; Aged ; Yellow fever virus/isolation &amp; purification ; },
abstract = {BACKGROUND: Since its resurgence in 2017, Yellow fever (YF) outbreaks have continued to occur in Nigeria despite routine immunization and the implementation of several reactive mass vaccinations. Nigeria, Africa's most populous endemic country, is considered a high-priority country for implementing the End Yellow fever Epidemics strategy.<br><br>METHODS: This retrospective analysis described the epidemiological profile, trends, and factors associated with Yellow fever viral positivity in Nigeria. We conducted a multivariable binary logistic regression analysis to identify factors associated with YF viral positivity.<br><br>RESULTS: Of 16,777 suspected cases, 8532(50.9%) had laboratory confirmation with an overall positivity rate of 6.9%(585). Predictors of YFV positivity were the Jos Plateau, Derived/Guinea Savanah, and the Freshwater/Lowland rainforest compared to the Sahel/Sudan Savannah; dry season compared to rainy season; the hot dry or humid compared to the temperate, dry cool/humid climatic zone; 2019, 2020, 2021, 2022, and 2023 epidemic years compared to compared to 2017; first, third, and fourth quarters compared to the second; male sex compared to female; age group&#x2009;>&#x2009;=&#x2009;15 years compared to <&#x2009;15 years; working in outdoor compared to indoor settings; having traveled within the last two weeks; being of unknown vaccination status compared to being vaccinated; and vomiting.<br><br>CONCLUSION: Ecological, climatic, and socio-demographic characteristics are drivers of YF outbreaks in Nigeria, and public health interventions need to target these factors to halt local epidemics and reduce the risk of international spread. Inadequate vaccination coverage alone may not account for the recurrent outbreaks of YF in Nigeria.},
}
@article {pmid39834325,
year = {2025},
author = {Chen, L and Xu, Z and He, Y and Zhang, X and Li, L and Zhu, R and Zhang, Z and Lin, H and Hong, G},
title = {Multiomics Analysis Reveals Key Targeted Metabolic Pathways Underlying the Hormesis and Detrimental Effects of Enrofloxacin on Rice Plants.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {4},
pages = {2678-2695},
doi = {10.1021/acs.jafc.4c09001},
pmid = {39834325},
issn = {1520-5118},
mesh = {*Oryza/metabolism/drug effects/genetics/growth &amp; development ; Hormesis ; *Anti-Bacterial Agents/pharmacology/toxicity ; *Enrofloxacin/toxicity/pharmacology ; Metabolic Networks and Pathways/drug effects ; *Plant Proteins/metabolism/genetics ; Plant Growth Regulators/metabolism ; Gene Expression Regulation, Plant/drug effects ; Antioxidants/metabolism ; Metabolomics ; Reactive Oxygen Species/metabolism ; Multiomics ; },
abstract = {Fluoroquinolone antibiotic enrofloxacin (ENR) is frequently detected in agricultural environments. The hormesis and detrimental effects of ENR on crops have been extensively observed. However, the molecular mechanisms underlying these crops' responses to ENR remain limited. Here, integrated physiological, transcriptomic, and metabolomic analysis revealed the key metabolic pathway responses underlying the ENR-induced effects on rice. The results showed that ENR mainly affected three metabolic pathways: 'biosynthesis of amino acids', "tryptophan metabolism", and 'phenylpropanoid/flavonoid biosynthesis'. A low level of ENR treatment promoted root elongation and enhanced the antioxidant capacity by increasing the phytohormone gibberellin A3 and the flavonol quercetin-3-O-neohesperidoside, respectively. However, the high dose of ENR significantly stimulated ROS production, inhibited photosynthesis, and ultimately impaired plant growth. In response to high ENR toxicity, plants accumulated more quercetin derivatives as antioxidants and produced defense-related substances, such as N-hydroxytryptamine, indole-3-acetonitrile, and jasmonic acid, to combat biotic stress. In conclusion, this study provides new insights into the molecular mechanism accounting for the ecological effects of antibiotic pollution in farmland.},
}
@article {pmid39838963,
year = {2024},
author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y},
title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39838963},
issn = {1477-4054},
support = {11209823//City University of Hong Kong/ ; },
mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Viral Proteins/genetics/metabolism/chemistry ; *Molecular Sequence Annotation/methods ; Genomics/methods ; Computational Biology/methods ; },
abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.},
}
@article {pmid39840283,
year = {2024},
author = {Yan, B and Nam, Y and Li, L and Deek, RA and Li, H and Ma, S},
title = {Recent advances in deep learning and language models for studying the microbiome.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1494474},
pmid = {39840283},
issn = {1664-8021},
support = {R01 GM123056/GM/NIGMS NIH HHS/United States ; U24 OD035523/OD/NIH HHS/United States ; },
abstract = {Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.},
}
@article {pmid39841777,
year = {2025},
author = {Cardoso, ADRO and Ferreira, ACG and Rabahi, MF},
title = {Asthma-related deaths in Brazil: data from an ecological study.},
journal = {Jornal brasileiro de pneumologia : publicacao oficial da Sociedade Brasileira de Pneumologia e Tisilogia},
volume = {50},
number = {6},
pages = {e20240296},
pmid = {39841777},
issn = {1806-3756},
mesh = {Humans ; Brazil/epidemiology ; *Asthma/mortality ; Female ; Male ; Middle Aged ; Adult ; *Hospitalization/statistics &amp; numerical data/trends ; Aged ; Sex Distribution ; Young Adult ; Age Distribution ; Adolescent ; Child ; Child, Preschool ; Sex Factors ; Infant ; Age Factors ; },
abstract = {OBJECTIVE: The aim of this study was to present epidemiological data on hospitalizations and deaths related to asthma in Brazil over the past 11 years.<br><br>METHODS: An ecological study was conducted on asthma-related hospitalizations and mortality in Brazil from 2013 to 2023, using data extracted from the Department of Informatics of the Brazilian Unified Health System and the Mortality Information System.<br><br>RESULTS: Asthma-related deaths showed an increasing trend during the analyzed period. A surge in deaths was observed in 2022 compared to 2014 (difference between means = 56.08 &#xb1; 19.7; 95% CI = 15.2-96.9). The mean number of deaths was higher among females, with their rate remaining stable, while the rate for males increased. Individuals aged >60 years accounted for approximately 65% of all asthma-related deaths from 2013 to 2023, with a strong direct correlation observed between age and the number of deaths, regardless of sex. During the same period, the total number of asthma-related hospitalizations in Brazil showed a declining trend, decreasing from 134,322 in 2013 to 87,707 in 2023.<br><br>CONCLUSION: Over the past 11 years, asthma-related deaths have increased in Brazil, with the majority occurring among females. Older individuals accounted for most asthma-related deaths, and a positive correlation was observed between age and the number of deaths.},
}
@article {pmid39842565,
year = {2025},
author = {Zheng, JY and Jiang, G and Gao, FH and Ren, SN and Zhu, CY and Xie, J and Li, Z and Yin, W and Xia, X and Li, Y and Wang, HL},
title = {MCTASmRNA: A deep learning framework for alternative splicing events classification.},
journal = {International journal of biological macromolecules},
volume = {300},
number = {},
pages = {139941},
doi = {10.1016/j.ijbiomac.2025.139941},
pmid = {39842565},
issn = {1879-0003},
mesh = {*Deep Learning ; *Alternative Splicing/genetics ; Humans ; RNA, Messenger/genetics ; *Computational Biology/methods ; Animals ; },
abstract = {Alternative splicing (AS) plays crucial post-transcriptional gene function regulation roles in eukaryotic. Despite progress in studying AS at the RNA level, existing methods for AS event identification face challenges such as inefficiency, lengthy processing times, and limitations in capturing the complexity of RNA sequences. To overcome these challenges, we evaluated 10 AS detection tools and selected rMATS for dataset construction. We then developed a multi-scale convolutional and Transformer-based model (MCTASmRNA) to classify AS events in mRNA sequences without relying on a reference genome. To handle the problem of large intra-class and small inter-class difference in AS event sequences, we incorporated an efficient channel attention mechanism and designed a new joint loss function to optimize MCTASmRNA training. MCTASmRNA outperformed baseline models, with an accuracy improvement and exhibited enhanced cross-species generalizability. This model provides valuable support for AS research across different organisms. Future work will focus on optimizing and expanding the model to further explore the complex mechanisms underlying AS.},
}
@article {pmid39843543,
year = {2025},
author = {Gioiosa, S and Gasparini, S and Presutti, C and Rinaldi, A and Castrignanò, T and Mannironi, C},
title = {Integrated gene expression and alternative splicing analysis in human and mouse models of Rett syndrome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2778},
pmid = {39843543},
issn = {2045-2322},
support = {GJC22071//Cariplo Telethon Alliance/ ; },
mesh = {*Rett Syndrome/genetics ; Animals ; Humans ; *Alternative Splicing ; Mice ; Disease Models, Animal ; *Methyl-CpG-Binding Protein 2/genetics ; Gene Expression Profiling ; Computational Biology/methods ; Gene Expression Regulation ; Mutation ; Transcriptome ; },
abstract = {Mutations of the MECP2 gene lead to Rett syndrome (RTT), a rare developmental disease causing severe intellectual and physical disability. How the loss or defective function of MeCP2 mediates RTT is still poorly understood. MeCP2 is a global gene expression regulator, acting at transcriptional and post-transcriptional levels. Little attention has been given so far to the contribution of alternative splicing (AS) dysregulation to RTT pathophysiology. To perform a comparative analysis of publicly available RNA sequencing (RNA-seq) studies and generate novel data resources for AS, we explored 100 human datasets and 130 mouse datasets from Mecp2-mutant models, processing data for gene expression and alternative splicing. Our comparative analysis across studies indicates common species-specific differentially expressed genes (DEGs) and differentially alternatively spliced (DAS) genes. Human and mouse dysregulated genes are involved in two main functional categories: cell-extracellular matrix adhesion regulation and synaptic functions, the first category more significantly enriched in human datasets. Our extensive bioinformatics study indicates, for the first time, a significant dysregulation of AS in human RTT datasets, suggesting the crucial contribution of altered RNA processing to the pathophysiology of RTT.},
}
@article {pmid39848196,
year = {2025},
author = {Wang, S and Liping, Y and Arif, M},
title = {Evolutionary analysis of ecological-production-living space-carrying capacity in tourism-centric traditional villages in Guangxi, China.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124182},
doi = {10.1016/j.jenvman.2025.124182},
pmid = {39848196},
issn = {1095-8630},
mesh = {China ; *Tourism ; Humans ; Geographic Information Systems ; *Conservation of Natural Resources ; },
abstract = {The carrying capacity of ecological-production-living space (EPLS) is pivotal to the development of traditional villages and the optimization of their tourism industries. However, research on tourism-centric traditional villages in China remains limited. This study addresses this gap by examining EPLS carrying capacity in tourism-focused villages in Guangxi, China. Using remote sensing imagery of Chengyang Bazhai (CYBZ) along with data on local tourism and socio-economic development, the study classifies different types of EPLS and establishes a comprehensive indicator system. Geographic information system spatial analysis, combined with grey correlation analysis, was employed to assess the evolution of EPLS carrying capacity and its influencing factors in CYBZ. The findings indicate that between 2006 and 2015, the overall carrying capacity of EPLS experienced a decline. While the carrying capacity of production spaces remained relatively stable, ecological and living spaces saw notable decreases. However, from 2015 to 2021, EPLS carrying capacity increased substantially. The most substantial growth was observed in Pingyan Village, followed by Chengyang Village, with Pingfu Village exhibiting the smallest improvement. The expansion of the tourism industry has significantly influenced the evolution of EPLS carrying capacity in CYBZ, creating a greater need for strategic future planning. Optimal EPLS and durable tourism development require continuous enhancements in EPLS capacity, reductions in negative interactions between carrying capacity and tourism growth, as well as ecological revitalization. This study contributes to the existing literature by enhancing EPLS carrying capacity understanding. It offers theoretical guidance for its optimization in Chengyang and practical insights into sustainable tourism development in similar regions.},
}
@article {pmid39849009,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K},
title = {The influence of depth on the global deep-sea plasmidome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2959},
pmid = {39849009},
issn = {2045-2322},
support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; },
mesh = {*Plasmids/genetics ; *Metagenome ; *Seawater/microbiology ; Ecosystem ; Gammaproteobacteria/genetics ; Alphaproteobacteria/genetics ; Oceans and Seas ; Bacteria/genetics ; Computational Biology/methods ; Indian Ocean ; },
abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.},
}
@article {pmid39852552,
year = {2025},
author = {Yang, H and Luo, X and Shang, Z and Li, K and Cai, J and Chen, Y and Xin, L and Ju, J},
title = {Metabolic Blockade-Based Genome Mining of Malbranchea circinata SDU050: Discovery of Diverse Secondary Metabolites.},
journal = {Marine drugs},
volume = {23},
number = {1},
pages = {},
pmid = {39852552},
issn = {1660-3397},
support = {U2106207//National Natural Science Foundation of China/ ; 2022YFC2804100//National Key Research and Development Program of China/ ; 22037006//National Natural Science Foundation of China/ ; SYS202205//Shandong Laboratory Program/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology/isolation &amp; purification ; *Secondary Metabolism/genetics ; Multigene Family ; Polyketide Synthases/genetics/metabolism ; Biosynthetic Pathways/genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects ; Genome, Fungal ; Microbial Sensitivity Tests ; Gram-Positive Bacteria/drug effects ; Staphylococcus aureus/drug effects ; Bacillus subtilis/drug effects ; *Ascomycota/genetics/metabolism ; Isocoumarins/pharmacology ; Computational Biology ; Geologic Sediments/microbiology ; },
abstract = {Malbranchea circinata SDU050, a fungus derived from deep-sea sediment, is a prolific producer of diverse secondary metabolites. Genome sequencing revealed the presence of at least 69 biosynthetic gene clusters (BGCs), including 30 encoding type I polyketide synthases (PKSs). This study reports the isolation and identification of four classes of secondary metabolites from wild-type M. circinata SDU050, alongside five additional metabolite classes, including three novel cytochalasins (7-9), obtained from a mutant strain through the metabolic blockade strategy. Furthermore, bioinformatic analysis of the BGC associated with the isocoumarin sclerin (1) enabled the deduction of its biosynthetic pathway based on gene function predictions. Bioactivity assays demonstrated that sclerin (1) and (-)-mycousnine (10) exhibited weak antibacterial activity against Gram-positive bacteria such as Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), and Bacillus subtilis. These findings underscore the chemical diversity and biosynthetic potential of M. circinata SDU050 and highlight an effective strategy for exploring marine fungal metabolites.},
}
@article {pmid39853577,
year = {2025},
author = {Pierrat, ZA and Magney, TS and Richardson, WP and Runkle, BRK and Diehl, JL and Yang, X and Woodgate, W and Smith, WK and Johnston, MR and Ginting, YRS and Koren, G and Albert, LP and Kibler, CL and Morgan, BE and Barnes, M and Uscanga, A and Devine, C and Javadian, M and Meza, K and Julitta, T and Tagliabue, G and Dannenberg, MP and Antala, M and Wong, CYS and Santos, ALD and Hufkens, K and Marrs, JK and Stovall, AEL and Liu, Y and Fisher, JB and Gamon, JA and Cawse-Nicholson, K},
title = {Proximal remote sensing: an essential tool for bridging the gap between high-resolution ecosystem monitoring and global ecology.},
journal = {The New phytologist},
volume = {246},
number = {2},
pages = {419-436},
pmid = {39853577},
issn = {1469-8137},
support = {//National Research Council Postdoctoral Research Associateship Program/ ; 2020/37/B/ST10/01213//National Science Centre of Poland/ ; //TVL E-13 work contract at the Climate Monitoring Group of the University of Bonn/ ; //The LEMONTREE project by E. Schmidt and W. Schmidt/ ; 1926090//National Science Foundation/ ; 2044818//National Science Foundation/ ; 2131853//National Science Foundation/ ; IOS-2005574 OPP-2023205//National Science Foundation/ ; 80NSSC20K1805/NASA/NASA/United States ; 80NSSC21K1002/NASA/NASA/United States ; 80NSSC21K1639/NASA/NASA/United States ; 80NSSC21K1707/NASA/NASA/United States ; 80NSSC23K0109/NASA/NASA/United States ; 80NSSC23K0309/NASA/NASA/United States ; 80NSSC24K0135/NASA/NASA/United States ; NNH20ZDA001N-BIODIV/NASA/NASA/United States ; DE190101182//Australian Research Council/ ; },
mesh = {*Remote Sensing Technology/methods ; *Ecosystem ; *Ecology/methods ; *Environmental Monitoring/methods ; *Internationality ; },
abstract = {A new proliferation of optical instruments that can be attached to towers over or within ecosystems, or 'proximal' remote sensing, enables a comprehensive characterization of terrestrial ecosystem structure, function, and fluxes of energy, water, and carbon. Proximal remote sensing can bridge the gap between individual plants, site-level eddy-covariance fluxes, and airborne and spaceborne remote sensing by providing continuous data at a high-spatiotemporal resolution. Here, we review recent advances in proximal remote sensing for improving our mechanistic understanding of plant and ecosystem processes, model development, and validation of current and upcoming satellite missions. We provide current best practices for data availability and metadata for proximal remote sensing: spectral reflectance, solar-induced fluorescence, thermal infrared radiation, microwave backscatter, and LiDAR. Our paper outlines the steps necessary for making these data streams more widespread, accessible, interoperable, and information-rich, enabling us to address key ecological questions unanswerable from space-based observations alone and, ultimately, to demonstrate the feasibility of these technologies to address critical questions in local and global ecology.},
}
@article {pmid39854538,
year = {2025},
author = {Katchali, M and Richard, E and Tonnang, HEZ and Tanga, CM and Beesigamukama, D and Senagi, K},
title = {Mathematical and computational modeling for organic and insect frass fertilizer production: A systematic review.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0292418},
pmid = {39854538},
issn = {1932-6203},
support = {INV-032416/GATES/Gates Foundation/United States ; },
mesh = {*Fertilizers ; Animals ; *Computer Simulation ; *Models, Theoretical ; *Insecta ; Agriculture/methods ; },
abstract = {Organic fertilizers have been identified as a sustainable agricultural practice that can enhance productivity and reduce environmental impact. Recently, the European Union defined and accepted insect frass as an innovative and emerging organic fertilizer. In the wider domain of organic fertilizers, mathematical and computational models have been developed to optimize their production and application conditions. However, with the advancement in policies and regulations, modelling has shifted towards efficiencies in the deployment of these technologies. Therefore, this paper reviews and critically analyzes the recent developments in the mathematical and computation modeling that have promoted various organic fertilizer products including insect frass. We reviewed a total of 35 studies and discussed the methodologies, benefits, and challenges associated with the use of these models. The results show that mathematical and computational modeling can improve the efficiency and effectiveness of organic fertilizer production, leading to improved agricultural productivity and reduced environmental impact. Mathematical models such as simulation, regression, dynamics, and kinetics have been applied while computational data driven machine learning models such as random forest, support vector machines, gradient boosting, and artificial neural networks have also been applied as well. These models have been used in quantifying nutrients concentration/release, effects of nutrients in agro-production, and fertilizer treatment. This paper also discusses prospects for the use of these models, including the development of more comprehensive and accurate models and integration with emerging technologies such as Internet of Things.},
}
@article {pmid39854555,
year = {2025},
author = {Zhou, J and Johnson, VC and Shi, J and Tan, ML and Zhang, F},
title = {Multi-scenario land use change simulation and spatial-temporal evolution of carbon storage in the Yangtze River Delta region based on the PLUS-InVEST model.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0316255},
pmid = {39854555},
issn = {1932-6203},
mesh = {*Rivers/chemistry ; China ; *Conservation of Natural Resources ; *Carbon Sequestration ; *Carbon/analysis ; *Models, Theoretical ; Spatio-Temporal Analysis ; Urbanization ; Computer Simulation ; Ecosystem ; Humans ; },
abstract = {Influenced by urban expansion, population growth, and various socio-economic activities, land use in the Yangtze River Delta (YRD) area has undergone prominent changes. Modifications in land use have resulted in adjustments to ecological structures, leading to subsequent fluctuations in carbon storage. This study focuses on YRD region and analyzes the characteristics of land use changes in the area using land use data from 2000 to 2020, with a 10-year interval. Utilizing InVEST Model's Carbon Storage module in combination with PLUS model (patch-generating land use simulation), we simulated and projected future land use patterns and carbon storage across YRD region under five scenarios including natural development (ND), urban development (UD), ecological protection (EP), cropland protection (CP), and balanced development (BD). Upon comparing carbon storage levels predicted for 2030 under the five scenarios with those in 2020, carbon stocks decrease in the initial four scenarios and then increase in the fifth scenario. In the initial four declining scenarios, CP scenario had the least reduction in carbon storage, followed by EP scenario. The implementation of policies aimed at safeguarding cropland and preserving ecological integrity can efficaciously curtail the expansion of developed land into woodland and cropland, enhance the structure of land use, and mitigate the loss of carbon storage.},
}
@article {pmid39854567,
year = {2025},
author = {Moody, NM and Williams, CM and Ramachandran, S and Fuxjager, MJ},
title = {Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense.},
journal = {PLoS computational biology},
volume = {21},
number = {1},
pages = {e1012740},
pmid = {39854567},
issn = {1553-7358},
support = {R35 GM139628/GM/NIGMS NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Female ; Male ; *Aggression/physiology ; *Territoriality ; *Birds/physiology ; Social Behavior ; Behavior, Animal/physiology ; Computational Biology ; Sexual Behavior, Animal/physiology ; },
abstract = {Negotiating social dynamics among allies and enemies is a complex problem that often requires individuals to tailor their behavioral approach to a specific situation based on environmental and/or social factors. One way to make these contextual adjustments is by arranging behavioral output into intentional patterns. Yet, few studies explore how behavioral patterns vary across a wide range of contexts, or how allies might interlace their behavior to produce a coordinated response. Here, we investigate the possibility that resident female and male downy woodpeckers guard their breeding territories from conspecific intruders by deploying defensive behavior in context-specific patterns. To study whether this is the case, we use correlation networks to reveal how suites of agonistic behavior are interrelated. We find that residents do organize their defense into definable patterns, with female and male social mates deploying their behaviors non-randomly in a correlated fashion. We then employ spectral clustering analyses to further distill these responses into distinct behavioral motifs. Our results show that this population of woodpeckers adjusts the defensive motifs deployed according to threat context. When we combine this approach with behavioral transition analyses, our results reveal that pair coordination is a common feature of territory defense in this species. However, if simulated intruders are less threatening, residents are more likely to defend solo, where only one bird deploys defensive behaviors. Overall, our study supports the hypothesis that nonhuman animals can pattern their behavior in a strategic and coordinated manner, while demonstrating the power of systems approaches for analyzing multiagent behavioral dynamics.},
}
@article {pmid39856257,
year = {2025},
author = {Gulakhmadov, A and Chen, X and Gulahmadov, N and Rizwan, M and Gulakhmadov, M and Nadeem, MU and Rakhimova, M and Liu, T},
title = {Modeling of historical and future changes in temperature and precipitation in the Panj River Basin in Central Asia under the CMIP5 RCP and CMIP6 SSP scenarios.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3037},
pmid = {39856257},
issn = {2045-2322},
support = {42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; },
abstract = {This study examines the complexities of climate modeling, specifically in the Panj River Basin (PRB) in Central Asia, to evaluate the transition from CMIP5 to CMIP6 models. The research aimed to identify differences in historical simulations and future predictions of rainfall and temperature, examining the accuracy of eight General Circulation Models (GCMs) used in both CMIP5 (RCP4.5 and 8.5) and CMIP6 (SSP2-4.5 and 5-8.5). The evaluation metrics demonstrated that the GCMs have a high level of accuracy in reproducing maximum temperature (Tmax) with a correlation coefficient of 0.96. The models also performed well in replicating minimum temperature (Tmin) with a correlation coefficient of 0.94. This suggests that the models have improved modeling capabilities in both CMIPs. The performance of Max Plank Institute (MPI) across all variables in CMIP6 models was exceptional. Within the CMIP5 domain, Geophysical Fluid Dynamics (GFDL) demonstrated outstanding skill in reproducing maximum temperature (Tmax) and precipitation (KGE 0.58 and 0.34, respectively), while (Institute for Numerical Mathematics) INMCM excelled in replicating minimum temperature (Tmin) (KGE 0.28). The uncertainty analysis revealed a significant improvement in the CMIP6 precipitation bias bands, resulting in a more precise depiction of diverse climate zones compared to CMIP5. Both CMIPs consistently tended to underestimate Tmax in the Csa zone and overestimate it in the Bwk zone throughout all months. Nevertheless, the CMIP6 models demonstrated a significant decrease in uncertainty, especially in ensemble simulations, suggesting improvements in forecasting PRB climate dynamics. The projections revealed a complex story, as the CMIP6 models predict a relatively small increase in temperature and a simultaneous drop in precipitation. This indicates a trend towards more uniform temperature patterns across different areas. Nevertheless, the precipitation forecasts exhibited increased variability, highlighting the intricate interaction of climate dynamics in the PRB area under the impact of global warming scenarios. Hydrological components in global climate models can be further improved and developed with the theoretical reference provided by this study.},
}
@article {pmid39856573,
year = {2025},
author = {Sun, Z and Zhang, F and Zhong, N and Zhou, K and Tang, J},
title = {Genome sequence resources for three strains of the genus Clonostachys.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {8},
pmid = {39856573},
issn = {2730-6844},
support = {No. 2022AH051346 and No. KJ2021A0676//the Key Natural Science Research Projects in Anhui Universities/ ; No. KJTS2022002; No. KJTS2022003//Science and Technology Innovation Capability Enhancement Projects in Fuyang National Agricultural Sci-Tech Park/ ; No. 2022AH020081//Natural Science Foundation of Universities of Anhui Province for Distinguished Young Project/ ; No. 2020KYQD0023//The Fuyang Normal University Research Project/ ; [2023]13//Biological and Medical Sciences of Applied Summit Nurturing Disciplines in Anhui Province, Anhui Education Secretary Department/ ; },
mesh = {*Ascomycota/classification/genetics ; Datasets as Topic ; Genome, Fungal ; Molecular Sequence Annotation ; Biological Control Agents ; },
abstract = {OBJECTIVE: Clonostachys, a genus with rich morphological and ecological diversity in Bionectriaceae, has a wide distribution among diverse habitats. Several studies have reported Clonostachys fungi as effective biological agents against multiple fungal plant pathogens. To clarify the diversity and biocontrol mechanisms of the Clonostachys fungi, this study was undertaken to sequence and assemble the genomes of two C. chloroleuca and one C. rhizophaga.<br><br>DATA DESCRIPTION: Here, we performed genomic sequencing of three strains of genus Clonostachys collected from the China General Microbiological Culture Collection Center (CGMCC) using Illumina HiSeq 2500 sequencing technology. Whole genome analysis indicated that their genomes consist of 58,484,224&#xa0;bp with a GC content of 48.58%, 58,114,960&#xa0;bp with a GC content of 47.74% and 58,450,453&#xa0;bp with a GC content of 48.58%, respectively. BUSCO analysis of the genome assembly indicated that the completeness of these genomes was at least 98%. In summary, these datasets provide a valuable resource for ongoing studies that include further exploration of biological function, marker development, enhanced biological control ability of Clonostachys fungi, and population diversity.},
}
@article {pmid39860723,
year = {2025},
author = {Dewmini, H and Meedeniya, D and Perera, C},
title = {Elephant Sound Classification Using Deep Learning Optimization.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {2},
pages = {},
pmid = {39860723},
issn = {1424-8220},
mesh = {*Deep Learning ; Animals ; *Elephants/physiology ; *Vocalization, Animal/physiology/classification ; Bayes Theorem ; Sound ; Sound Spectrography ; },
abstract = {Elephant sound identification is crucial in wildlife conservation and ecological research. The identification of elephant vocalizations provides insights into the behavior, social dynamics, and emotional expressions, leading to elephant conservation. This study addresses elephant sound classification utilizing raw audio processing. Our focus lies on exploring lightweight models suitable for deployment on resource-costrained edge devices, including MobileNet, YAMNET, and RawNet, alongside introducing a novel model termed ElephantCallerNet. Notably, our investigation reveals that the proposed ElephantCallerNet achieves an impressive accuracy of 89% in classifying raw audio directly without converting it to spectrograms. Leveraging Bayesian optimization techniques, we fine-tuned crucial parameters such as learning rate, dropout, and kernel size, thereby enhancing the model's performance. Moreover, we scrutinized the efficacy of spectrogram-based training, a prevalent approach in animal sound classification. Through comparative analysis, the raw audio processing outperforms spectrogram-based methods. In contrast to other models in the literature that primarily focus on a single caller type or binary classification that identifies whether a sound is an elephant voice or not, our solution is designed to classify three distinct caller-types namely roar, rumble, and trumpet.},
}
@article {pmid39865039,
year = {2024},
author = {Alekseeva, AO and Zolotovskaia, MA and Sorokin, MI and Suntsova, MV and Zakharova, GS and Pugacheva, PA and Tinkov, AA and Korobeinikova, TV and Sekacheva, MI and Poddubskaya, EV and Skalny, AV and Kushlinskii, NE and Buzdin, AA},
title = {The First Multiomics Association Study of Trace Element and Mineral Concentration and RNA Sequencing Profiles in Human Cancers.},
journal = {Biochemistry. Biokhimiia},
volume = {89},
number = {12},
pages = {2274-2286},
doi = {10.1134/S0006297924120150},
pmid = {39865039},
issn = {1608-3040},
mesh = {Humans ; *Trace Elements/analysis/metabolism ; Sequence Analysis, RNA ; *Neoplasms/metabolism/genetics ; *Minerals/analysis/metabolism ; Gene Expression Profiling ; Female ; Multiomics ; },
abstract = {Integration of various types of omics data is an important trend in contemporary molecular oncology. In this regard, high-throughput analysis of trace and essential elements in cancer biosamples is an emerging field that has not yet been sufficiently addressed. For the first time, we simultaneously obtained gene expression profiles (RNA sequencing) and essential and trace element profiles (inductively coupled plasma mass spectrometry) for a set of human cancer samples. The biosamples were formalin-fixed, paraffin-embedded primary tumor tissue blocks: 67 for colorectal cancer patients and 18 for other solid cancer types (16 types). Mass spectrometry profiles were obtained for 45 chemical elements: Ag, Al, As, Au, B, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Fe, Ga, Ge, Hg, I, K, La, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Pd, Pt, Rb, Sb, Sc, Se, Si, Sn, Sr, Te, Ti, Tl, Zn, U, V, W, and Zr. The expression levels were profiled for 36,596 known human genes, and the activation levels were assessed for 10,520 human intracellular molecular pathways. For the concentrations of essential elements Ca, Cu, Fe, K, Mg, Na, P, and Zn we detected statistically significant correlations on both gene expression and pathway activation levels for both colorectal cancer samples and at the pan-cancer level. In total, 222/137, 122/220, 1/0, 239/186, 71/44, 1/0, 354/294, 69/82 gene/pathway biomarkers were detected for Ca, Cu, Fe, K, Mg, Na, P, and Zn, respectively. We believe that this first-in-class database provided here will be valuable for multiomics cancer research.},
}
@article {pmid39866757,
year = {2023},
author = {Gudelj Rakić, J and Maksimović, M and Vlajinac, H and Janković, J and Vukašinović, D and Marinković, J},
title = {TRENDS IN OVERWEIGHT AND OBESITY AMONG SERBIAN ADULT POPULATION 2000-2013.},
journal = {Acta clinica Croatica},
volume = {62},
number = {4},
pages = {605-614},
pmid = {39866757},
issn = {1333-9451},
mesh = {Humans ; Serbia/epidemiology ; Female ; Male ; Adult ; *Obesity/epidemiology ; Prevalence ; *Overweight/epidemiology ; Cross-Sectional Studies ; Middle Aged ; Body Mass Index ; Young Adult ; Health Surveys ; },
abstract = {The aim of the study was to determine changes in body mass index (BMI) and in the prevalence of overweight and obesity in Serbian adult population. Data for this study were obtained from three National Health Interview Surveys, carried out as cross-sectional, nationally representative surveys in 2000, 2006 and 2013. The values of p for trends of sociodemographic and health related behavioral characteristics, of BMI distribution, and of overweight and obesity prevalence were determined by univariate and multivariate linear and logistic regression analyses, with year of survey as a continuous variable. The mean values of BMI and standard deviations in surveys were 26.09±3.92, 26.28±4.02 and 26.87±4.33 in men, and 25.91±5.25, 25.77±5.22 and 26.35±5.58 in women, respectively (trend p<0.001 both). The prevalence of obesity was 14.3%, 16.5% and 21.4% in men, and 20.0%, 19.7% and 23.3% in women, respectively (trend p<0.001 both). The prevalence of overweight did not change significantly during the observed period. In conclusion, the prevalence of obesity showed an increasing trend in both men and women, demanding targeted public health interventions.},
}
@article {pmid39868965,
year = {2025},
author = {Grikscheit, K and Berger, A and Rabenau, H and Kohmer, N and Appel, KS and Scherer, M and Bals, R and Blaschke, S and Hamprecht, A and Hopff, SM and Krefting, D and Meybohm, P and Nürnberger, C and Heuschmann, P and Pley, C and Nunes de Miranda, SM and Dahl, E and Jensen, B and Illig, T and Anton, G and Vehreschild, JJ and Ciesek, S},
title = {Occurrence and clinical correlates of SARS-CoV-2 viremia in two German patient cohorts.},
journal = {Emerging microbes &amp; infections},
volume = {14},
number = {1},
pages = {2459137},
pmid = {39868965},
issn = {2222-1751},
mesh = {Humans ; *COVID-19/epidemiology/virology/blood/diagnosis ; *Viremia/epidemiology/virology ; Germany/epidemiology ; Male ; Female ; Middle Aged ; *SARS-CoV-2/genetics/isolation &amp; purification/immunology ; Aged ; Cross-Sectional Studies ; Antibodies, Viral/blood ; Adult ; RNA, Viral/blood ; Cohort Studies ; Antibodies, Neutralizing/blood ; Severity of Illness Index ; Aged, 80 and over ; },
abstract = {Viremia defined as detectable SARS-CoV-2 RNA in the blood is a potential marker of disease severity and prognosis in COVID-19 patients. Here, we determined the frequency of viremia in serum of two independent COVID-19 patient cohorts within the German National Pandemic Cohort Network (German: Nationales Pandemie Kohorten Netzwerk, NAPKON) with diagnostic RT-PCR against SARS-CoV-2. A cross-sectional cohort with 1122 COVID-19 patients (German: Sektorenuebergreifende Platform, SUEP) and 299 patients recruited in a high-resolution platform with patients at high risk to develop severe courses (German: Hochaufloesende Plattform, HAP) were tested for viremia. Our study also involved a comprehensive analysis and association of serological, diagnostic, and clinical parameters of the NAPKON medical dataset. Prevalence of viremia at the recruitment visit was 12.8% (SUEP) and 13% (HAP), respectively. Serological analysis revealed that viremic patients had lower levels of SARS-CoV-2 specific antibodies as well as lower neutralizing antibodies compared to aviremic patients. Viremia was associated with severity (<0.0001 SUEP; 0.002 HAP) and mortality of COVID-19 (both cohorts <0.0001) compared to aviremic patients. While rare, viremia was also detected in patients with mild disease (0.7%). In patients of the SUEP cohort with acute kidney disease (p = 0.0099) and hematooncological conditions (p = 0.0091), viremia was detected more frequently. Compared to the aviremic group, treatment with immunomodulating drugs as well as elevated levels of inflammatory markers in the blood was more frequent in the viremic group. In conclusion, our analysis revealed that detectable viremia correlates with hyperinflammatory conditions and higher risk for severe COVID-19 disease.},
}
@article {pmid39869900,
year = {2025},
author = {Yeom, JW and Kim, H and Pack, SP and Lee, HJ and Cheong, T and Cho, CH},
title = {Exploring the Psychological and Physiological Insights Through Digital Phenotyping by Analyzing the Discrepancies Between Subjective Insomnia Severity and Activity-Based Objective Sleep Measures: Observational Cohort Study.},
journal = {JMIR mental health},
volume = {12},
number = {},
pages = {e67478},
pmid = {39869900},
issn = {2368-7959},
mesh = {Humans ; *Sleep Initiation and Maintenance Disorders/physiopathology/psychology/diagnosis ; Middle Aged ; Male ; Female ; Adult ; Severity of Illness Index ; Aged ; Young Adult ; Cohort Studies ; *Sleep/physiology ; Exercise/physiology ; Wearable Electronic Devices ; Surveys and Questionnaires ; Ecological Momentary Assessment ; },
abstract = {BACKGROUND: Insomnia is a prevalent sleep disorder affecting millions worldwide, with significant impacts on daily functioning and quality of life. While traditionally assessed through subjective measures such as the Insomnia Severity Index (ISI), the advent of wearable technology has enabled continuous, objective sleep monitoring in natural environments. However, the relationship between subjective insomnia severity and objective sleep parameters remains unclear.<br><br>OBJECTIVE: This study aims to (1) explore the relationship between subjective insomnia severity, as measured by ISI scores, and activity-based objective sleep parameters obtained through wearable devices; (2) determine whether subjective perceptions of insomnia align with objective measures of sleep; and (3) identify key psychological and physiological factors contributing to the severity of subjective insomnia complaints.<br><br>METHODS: A total of 250 participants, including both individuals with and without insomnia aged 19-70 years, were recruited from March 2023 to November 2023. Participants were grouped based on ISI scores: no insomnia, mild, moderate, and severe insomnia. Data collection involved subjective assessments through self-reported questionnaires and objective measurements using wearable devices (Fitbit Inspire 3) that monitored sleep parameters, physical activity, and heart rate. The participants also used a smartphone app for ecological momentary assessment, recording daily alcohol consumption, caffeine intake, exercise, and stress. Statistical analyses were used to compare groups on subjective and objective measures.<br><br>RESULTS: Results indicated no significant differences in general sleep structure (eg, total sleep time, rapid eye movement sleep time, and light sleep time) among the insomnia groups (mild, moderate, and severe) as classified by ISI scores (all P>.05). Interestingly, the no insomnia group had longer total awake times and lower sleep quality compared with the insomnia groups. Among the insomnia groups, no significant differences were observed regarding sleep structure (all P>.05), suggesting similar sleep patterns regardless of subjective insomnia severity. There were significant differences among the insomnia groups in stress levels, dysfunctional beliefs about sleep, and symptoms of restless leg syndrome (all P&#x2264;.001), with higher severity associated with higher scores in these factors. Contrary to expectations, no significant differences were observed in caffeine intake (P=.42) and alcohol consumption (P=.07) between the groups.<br><br>CONCLUSIONS: The findings demonstrate a discrepancy between subjective perceptions of insomnia severity and activity-based objective sleep parameters, suggesting that factors beyond sleep duration and quality may contribute to subjective sleep complaints. Psychological factors, such as stress, dysfunctional sleep beliefs, and symptoms of restless legs syndrome, appear to play significant roles in the perception of insomnia severity. These results highlight the importance of considering both subjective and objective assessments in the evaluation and treatment of insomnia and suggest potential avenues for personalized treatment strategies that address both psychological and physiological aspects of sleep disturbances.<br><br>TRIAL REGISTRATION: Clinical Research Information Service KCT0009175; https://cris.nih.go.kr/cris/search/detailSearch.do?seq=26133.},
}
@article {pmid39870652,
year = {2025},
author = {Koizumi, T and Suzuki, K and Mizuki, I and Kumaishi, K and Ichihashi, Y},
title = {A quantitative prediction method utilizing whole omics data for biosensing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1928},
pmid = {39870652},
issn = {2045-2322},
support = {21J00762//Japan Society for the Promotion of Science/ ; Technologies for Smart Bio-industry and Agriculture//the Cabinet Office, Goverment of Japan/ ; },
mesh = {Transcriptome ; Biomarkers/analysis ; *Biosensing Techniques/methods ; Humans ; Metabolome ; *Computational Biology/methods ; Microbiota ; Gene Expression Profiling ; Algorithms ; *Genomics/methods ; },
abstract = {Omics data provide a plethora of quantifiable information that can potentially be used to identify biomarkers targeting the physiological processes and ecological phenomena of organisms. However, omics data have not been fully utilized because current prediction methods in biomarker construction are susceptible to data multidimensionality and noise. We developed OmicSense, a quantitative prediction method that uses a mixture of Gaussian distributions as the probability distribution, yielding the most likely objective variable predicted for each biomarker. Our benchmark test using a transcriptome dataset revealed that OmicSense achieves accurate and robust prediction against background noise without overfitting. Weighted gene co-expression network analysis revealed that OmicSense preferentially utilized hub nodes of the network, indicating the interpretability of the method. Application of OmicSense to single-cell transcriptome, metabolome, and microbiome datasets confirmed high prediction performance (r > 0.8), suggesting applicability to diverse scientific fields. Given the recent rapidly expanding availability of omics data, the developed prediction tool OmicSense, can accelerate the use of omics data as a "biosensor" based on an assemblage of potential biomarkers.},
}
@article {pmid39870942,
year = {2025},
author = {Lazaro, A and Tiago, I and Mendes, J and Ribeiro, J and Bernardes, A and Oliveira, F and Regateiro, F and Caramelo, F and Silva, H},
title = {Sleeve Gastrectomy and Gastric Bypass Impact in Patient's Metabolic, Gut Microbiome, and Immuno-inflammatory Profiles-A Comparative Study.},
journal = {Obesity surgery},
volume = {35},
number = {3},
pages = {733-745},
pmid = {39870942},
issn = {1708-0428},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Gastric Bypass ; *Gastrectomy/methods ; Female ; *Obesity, Morbid/surgery/microbiology/immunology/metabolism ; Prospective Studies ; Male ; Adult ; Middle Aged ; Weight Loss ; *Metabolic Syndrome/metabolism ; Treatment Outcome ; },
abstract = {BACKGROUND: Bariatric surgery is the most long-term effective treatment option for severe obesity. The role of gut microbiome (GM) in either the development of obesity or in response to obesity management strategies has been a matter of debate. This study aims to compare the impact of two of the most popular procedures, sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (GB), on metabolic syndrome parameters and gut bacterial microbiome and in systemic immuno-inflammatory response.<br><br>METHODS: A prospective observational study enrolled 24 patients with severe obesity, 14 underwent SG and 10&#xa0;GB. Evaluations before (0&#xa0;M) and 6&#xa0;months (6&#xa0;M) after surgical procedures included clinical and biochemical parameters, expression of 17 immuno-inflammatory genes in peripheral blood leukocytes, and assessment of gut microbiome profile using 16&#xa0;s rRNA next-generation sequencing approach. Statistical significance was set to a p value&#x2009;<&#x2009;0.05 with an FDR&#x2009;<&#x2009;0.1.<br><br>RESULTS: A significant and similar decrease in weight-associated parameters and for most metabolic markers was achieved with both surgeries. Considering the gut microbiome in the whole study population, there was an increase in alpha diversity at family-level taxa. Beta diversity between SG and GB at 6&#xa0;M showed near significant differences (p&#x2009;=&#x2009;0.042) at genus levels. Analysis of the relative abundance of individual taxonomic groups highlighted differences between pre- and post-surgical treatment and between both approaches, namely, a higher representation of family Enterobacteriaceae and genera Veillonella and Enterobacteriaceae_unclassified after GB. Increased expression of immune-inflammatory genes was observed mainly for SG patients.<br><br>CONCLUSIONS: We conclude that SG and GB have similar clinical and metabolic outcomes but different impacts in the gut bacterial microbiome. Results also suggest reactivation of immune response after bariatric surgery.},
}
@article {pmid39871100,
year = {2025},
author = {Terauds, A and Lee, JR and Wauchope, HS and Raymond, B and Bergstrom, DM and Convey, P and Mason, C and Patterson, CR and Robinson, SA and Van de Putte, A and Watts, D and Chown, SL},
title = {The biodiversity of ice-free Antarctica database.},
journal = {Ecology},
volume = {106},
number = {1},
pages = {e70000},
pmid = {39871100},
issn = {1939-9170},
support = {n&#xb0;FR/36/AN1/AntaBIS(EU-LifeWatch)//Belgian Science Policy Office/ ; n&#xb0;RT/23/ADVANCE//Belgian Science Policy Office/ ; //Royal Commission for the Exhibition of 1851 Research Fellowship/ ; SRIEAS-SR200100005//Australian Research Council/ ; //Securing Antarctica's Environmental Future/ ; AAS 4296//Australian Antarctic Division/ ; AAS 4297//Australian Antarctic Division/ ; },
mesh = {Antarctic Regions ; *Biodiversity ; *Databases, Factual ; Animals ; Conservation of Natural Resources ; },
abstract = {Antarctica is one of Earth's most untouched, inhospitable, and poorly known regions. Although knowledge of its biodiversity has increased over recent decades, a diverse, wide-ranging, and spatially explicit compilation of the biodiversity that inhabits Antarctica's permanently ice-free areas is unavailable. This absence hinders both Antarctic biodiversity research and the integration of Antarctica in global biodiversity-related studies. Fundamental and applied research on biodiversity patterns, ecological structure and function, and options for conservation are reliant on spatially resolved, taxonomically consistent observations. Such information is especially important for modern, data-driven biodiversity science, in both Antarctica and globally, and forms the backbone of biodiversity informatics, reflected, for example, in the Darwin Core Standard used by the Global Biodiversity Information Facility. Biodiversity data are also essential to fulfill the conservation requirements for Antarctica, as set out in the Protocol on Environmental Protection to the Antarctic Treaty and inform the design of systematic surveys to address biodiversity and ecological knowledge gaps, for both specific taxa and ecosystems. Such surveys are key requirements for understanding and mitigating the impacts of environmental change on the region's biodiversity. Here, we address these requirements through the public release of The Biodiversity of Ice-free Antarctica Database. In 2008, we extracted a subset of biodiversity records only from terrestrial ice-free areas from the Scientific Committee on Antarctic Research (SCAR) Antarctic Biodiversity Database. We have subsequently added thousands of records from a range of sources: checking, and where necessary (and possible), correcting the spatial location, clarifying, cross-referencing, and harmonizing taxonomy with globally recognized sources, and documenting the original source of records. The Biodiversity of Ice-free Antarctica Database spans the early 1800s to 2019 (with most records collected after 1950) and represents the most comprehensive consolidation of Antarctic ice-free biodiversity occurrence data yet compiled into a single database. The Biodiversity of Ice-free Antarctica Database contains 35,654 records of 1890 species in over 800 genera across six kingdoms and spans all Antarctic Conservation Biogeographic Regions. These data are released under a CC BY Attribution License (http://creativecommons.org/licenses/by/4.0/).},
}
@article {pmid39871222,
year = {2025},
author = {Diongue, FB and Faye, A and Loucoubar, C and Sougou, NM and Sy, I and Tall, A and Ndiaye, Y and Sarr, SC},
title = {Situational analysis of the quality of maternal, child, and adolescent health data in the health districts of Thiès, Mbour, Kédougou, and Saraya in Senegal.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {337},
pmid = {39871222},
issn = {1471-2458},
mesh = {Senegal ; Humans ; Adolescent ; Female ; *Data Accuracy ; Child ; *Health Information Systems/standards ; *Child Health/statistics &amp; numerical data ; *Adolescent Health/statistics &amp; numerical data ; Qualitative Research ; Lot Quality Assurance Sampling ; *Maternal Health ; },
abstract = {INTRODUCTION: In Senegal, the Routine Health Information System (RHIS) captures the majority of data from the Ministry of Health and Social Action (MHSA) public structures and very little health data from the private sector and other ministerial departments. Quality data strengthens the validity and reliability of research results. Common areas of data quality include accuracy, completeness, consistency, credibility, and timeliness. The work aims to assess the quality of routine maternal, child, and adolescent health data in Senegal.<br><br>MATERIALS AND METHODS: A mixed quantitative and qualitative design was chosen in four health districts, including Thi&#xe8;s, Mbour, K&#xe9;dougou, and Saraya. The study included functional health structures that produce maternal, child, and adolescent health data. For the quantitative part, a descriptive and analytical study was carried out. Lot Quality Assurance Sampling (LQAS) was used as the sampling method. Data were collected using Performance of Routine Information Systems Management (PRISM) data collection tools and the ODK application and analyzed (univariate and bivariate) using R and Stata with an alpha risk of 5%. The following data quality indicators (accuracy, completeness, and promptness) were estimated. An exploratory case study and purposive sampling supported the qualitative part by implementing individual interviews.<br><br>RESULTS: The study showed an accuracy ratio of 1 in the intervention districts, a difference in the control districts, and a disparity in the transmission of guidelines between districts (inter- and intra-region). The average level of completeness was 0.64 (+/- 0.44) for all regions combined, with no significant difference between districts. The promptness rate for K&#xe9;dougou, Saraya, Thi&#xe8;s, and Mbour districts was 81%, 75.9%, 72.2%, and 86.7%, respectively. Between 40% and 60% of facilities in each district carried out self-assessments. Data collection tools were considered to be numerous. A large number of tools were easy to use. The recording space was appreciated. On the other hand, the length of the forms was little or not appreciated by the providers. Few of the providers in the 4 districts had been trained to record data in DHIS2.<br><br>CONCLUSION: Assessment of data quality in the districts studied shows shortcomings in terms of completeness and timeliness. Many factors influence the SMEA data quality situation, including knowledge or application of RHIS policies, standards, and protocols, perception of the importance of RHIS, ease of use of data collection tools, training of providers, and diversity of data production sources.},
}
@article {pmid39874571,
year = {2025},
author = {Sahandi Far, M and Fischer, JM and Senge, S and Rathmakers, R and Meissner, T and Schneble, D and Narava, M and Eickhoff, SB and Dukart, J},
title = {Cross-Platform Ecological Momentary Assessment App (JTrack-EMA+): Development and Usability Study.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e51689},
pmid = {39874571},
issn = {1438-8871},
mesh = {*Mobile Applications/standards ; *Software/standards ; *Self Report ; Pilot Projects ; *Patient Compliance/statistics &amp; numerical data ; Humans ; Infant, Newborn ; Adult ; Parents ; *Clinical Studies as Topic/instrumentation ; },
abstract = {BACKGROUND: Traditional in-clinic methods of collecting self-reported information are costly, time-consuming, subjective, and often limited in the quality and quantity of observation. However, smartphone-based ecological momentary assessments (EMAs) provide complementary information to in-clinic visits by collecting real-time, frequent, and longitudinal data that are ecologically valid. While these methods are promising, they are often prone to various technical obstacles. However, despite the potential of smartphone-based EMAs, they face technical obstacles that impact adaptability, availability, and interoperability across devices and operating systems. Deficiencies in these areas can contribute to selection bias by excluding participants with unsupported devices or limited digital literacy, increase development and maintenance costs, and extend deployment timelines. Moreover, these limitations not only impede the configurability of existing solutions but also hinder their adoption for addressing diverse clinical challenges.<br><br>OBJECTIVE: The primary aim of this research was to develop a cross-platform EMA app that ensures a uniform user experience and core features across various operating systems. Emphasis was placed on maximizing the integration and adaptability to various study designs, all while maintaining strict adherence to security and privacy protocols. JTrack-EMA+ was designed and implemented per the FAIR (findable, accessible, interpretable, and reusable) principles in both its architecture and data management layers, thereby reducing the burden of integration for clinicians and researchers.<br><br>METHODS: JTrack-EMA+ was built using the Flutter framework, enabling it to run seamlessly across different platforms. This platform comprises two main components. JDash (Research Centre J&#xfc;lich, Institute of Neuroscience and Medicine, Brain and Behaviour [INM-7]) is an online management tool created using Python (Python Software Foundation) with the Django (Django Software Foundation) framework. This online dashboard offers comprehensive study management tools, including assessment design, user administration, data quality control, and a reminder casting center. The JTrack-EMA+ app supports a wide range of question types, allowing flexibility in assessment design. It also has configurable assessment logic and the ability to include supplementary materials for a richer user experience. It strongly commits to security and privacy and complies with the General Data Protection Regulations to safeguard user data and ensure confidentiality.<br><br>RESULTS: We investigated our platform in a pilot study with 480 days of follow-up to assess participants' compliance. The 6-month average compliance was 49.3%, significantly declining (P=.004) from 66.7% in the first month to 42% in the sixth month.<br><br>CONCLUSIONS: The JTrack-EMA+ platform prioritizes platform-independent architecture, providing an easy entry point for clinical researchers to deploy EMA in their respective clinical studies. Remote and home-based assessments of EMA using this platform can provide valuable insights into patients' daily lives, particularly in a population with limited mobility or inconsistent access to health care services.},
}
@article {pmid39880083,
year = {2025},
author = {Vande Moortele, T and Verschaffelt, P and Huang, Q and Doncheva, NT and Holstein, T and Jachmann, C and Dawyndt, P and Martens, L and Mesuere, B and Van Den Bossche, T},
title = {PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.},
journal = {Molecular &amp; cellular proteomics : MCP},
volume = {24},
number = {3},
pages = {100918},
pmid = {39880083},
issn = {1535-9484},
mesh = {*Software ; *Metabolic Networks and Pathways ; Humans ; *Proteomics/methods ; Gastrointestinal Microbiome ; User-Computer Interface ; Proteome/metabolism ; *Computational Biology/methods ; Caloric Restriction ; },
abstract = {Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with the potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.},
}
@article {pmid39882857,
year = {2025},
author = {Grettenberger, C and Gold, DA and Brown, CT},
title = {Distribution of early-branching Cyanobacteriia and the potential habitats that gave rise to the earliest oxygenic phototrophs.},
journal = {mSphere},
volume = {10},
number = {2},
pages = {e0101324},
pmid = {39882857},
issn = {2379-5042},
mesh = {*Cyanobacteria/genetics/classification/metabolism ; *Ecosystem ; Photosynthesis ; Phylogeny ; *Oxygen/metabolism ; *Phototrophic Processes ; Computational Biology ; Metagenome ; Biological Evolution ; },
abstract = {The evolution of oxygenic photosynthesis in the Cyanobacteria was one of the most transformative events in Earth history, eventually leading to the oxygenation of Earth's atmosphere. However, it is difficult to understand how the earliest Cyanobacteria functioned or evolved on early Earth in part because we do not understand their ecology, including the environments in which they lived. Here, we use a cutting-edge bioinformatics tool to survey nearly 500,000 metagenomes for relatives of the taxa that likely bookended the evolution of oxygenic photosynthesis to identify the modern environments in which these organisms live. Ancestral state reconstruction suggests that the common ancestors of these organisms lived in terrestrial (soil and/or freshwater) environments. This restricted distribution may have increased the lag between the evolution of oxygenic photosynthesis and the oxygenation of Earth's atmosphere.IMPORTANCECyanobacteria generate oxygen as part of their metabolism and are responsible for the rise of oxygen in Earth's atmosphere over two billion years ago. However, we do not know how long this process may have taken. To help constrain how long this process would have taken, it is necessary to understand where the earliest Cyanobacteria may have lived. Here, we use a cutting-edge bioinformatics tool called branch water to examine the environments where modern Cyanobacteria and their relatives live to constrain those inhabited by the earliest Cyanobacteria. We find that these species likely lived in non-marine environments. This indicates that the rise of oxygen may have taken longer than previously believed.},
}
@article {pmid39888239,
year = {2025},
author = {Giles, EC and González, VL and Carimán, P and Leiva, C and Suescún, AV and Lemer, S and Guillemin, ML and Ortiz-Barrientos, D and Saenz-Agudelo, P},
title = {Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14075},
doi = {10.1111/1755-0998.14075},
pmid = {39888239},
issn = {1755-0998},
support = {2190878//BECA CONICYT-PCHA/Doctorado Nacional Chile/2019/ ; 1190710//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; OIA-1946352//National Science Foundation NSF-EPSCoR/ ; },
mesh = {Animals ; *Gastropoda/genetics/classification ; *Genomics ; *Genetic Variation ; *Evolution, Molecular ; *Genome ; Transcriptome ; Ecosystem ; },
abstract = {Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high-quality annotated genomes for intertidal species and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species (Scurria scurra, Scurria viridula and Scurria zebrina). Comparative analysis using these genomic resources suggest that and recently diverging lineages (10-20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species-specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus Scurria aligns with their unique ecological characteristics. Overall, the resources presented here will be valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.},
}
@article {pmid39889380,
year = {2025},
author = {Weeks, F and Myerson, R and Gangnon, R and Dykema, J and Cornelius, C and Green, T},
title = {Racial disparities in intrapartum care experiences and birth hospital characteristics.},
journal = {Social science &amp; medicine (1982)},
volume = {367},
number = {},
pages = {117720},
doi = {10.1016/j.socscimed.2025.117720},
pmid = {39889380},
issn = {1873-5347},
mesh = {Humans ; Female ; Adult ; Pregnancy ; *Healthcare Disparities/ethnology/statistics &amp; numerical data ; Wisconsin ; *Hospitals/statistics &amp; numerical data/standards ; Surveys and Questionnaires ; *Racial Groups/statistics &amp; numerical data/ethnology ; Black or African American/statistics &amp; numerical data ; Patient-Centered Care ; Logistic Models ; White ; },
abstract = {Policymakers and researchers have posited intrapartum care as a potential mediator of racial inequities in perinatal outcomes. However, few studies have measured patient-centered quality of intrapartum care or explored differences by race. To address this gap, we developed a survey supplement using cognitive interviewing and administered it to a probability-based race-stratified random sample of people who recently gave birth in Wisconsin in 2020, including oversamples of non-Hispanic Black and Indigenous birthing people. We estimate overall and race-specific prevalences of intrapartum care experiences and use survey-weighted mixed effects ordinal and logistic regression to estimate differences in intrapartum care experiences by race/ethnicity and hospital characteristics. We find significant racial differences in the population prevalence of negative experiences of intrapartum care providers, including disrespect, lack of responsiveness, inclusion in decision-making about care, and pressure to use epidural analgesia. In unadjusted models, both non-Hispanic Indigenous (American Indian/Alaska Native) and non-Hispanic Black respondents had higher odds (than non-Hispanic White birthing people) of reporting several negative intrapartum experiences, including feeling disrespected by providers and experiencing a lower level of care team responsiveness. In adjusted models, Indigenous respondents had significantly higher odds of reporting that intrapartum care providers withheld information, showed disrespect, and were less responsive. Giving birth at a low birth-volume hospital was associated with higher odds of reporting greater participation in decision-making. CONCLUSION: While all birthing people are entitled to respectful and person-centered care, in practice, Indigenous and Black birthing persons are more likely than their white counterparts to endure negative intrapartum experiences including disrespect and lack of responsiveness to their needs. Equitable implementation of person-centered care principles will require concerted efforts to institutionalize practices that preserve patient dignity and autonomy.},
}
@article {pmid39889433,
year = {2025},
author = {Shukla, S and Khan, R and Chrzanowski, &#x141; and Vagliasindi, FGA and Roccaro, P},
title = {Advancing sustainable agriculture through multi-omics profiling of biosolids for safe application: A review.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124292},
doi = {10.1016/j.jenvman.2025.124292},
pmid = {39889433},
issn = {1095-8630},
mesh = {*Agriculture/methods ; Soil ; Multiomics ; },
abstract = {Biosolids, derived from wastewater treatment processes, are valuable resources for soil amendment in agriculture due to their nutrient-rich composition. However, various contaminants of concern (CEC) such as pharmaceuticals, per-and poly-fluoroalkyl substances, endocrine disruptive chemicals, surfactants, pathogens, nanoplastics, and microplastics, are also reported in biosolids. The use of biosolids for agriculture may introduce these CEC into the soil, which raises concerns about their environmental and human health impacts. Moreover, the presence of pathogens (Escherichia coli, Salmonella sp., Shigella, Giardia, Rotavirus, etc.) even after treatment calls for microbial profiling of biosolids, especially in developing countries. Multi-omics approaches can be used as powerful tools for characterizing microbial communities and highlighting metabolic pathways. Moreover, these approaches also help in predicting the ecological and agronomic effects of biosolids application in agricultural soils. This review discusses the advantages and challenges of using biosolids in agriculture, considering the range of different CEC reported in biosolids. Moreover, the current legislation for the use of biosolids in agriculture is also presented, highlighting the limitations with respect to guidelines for emerging contaminants in biosolids. Furthermore, the role of the multi-omics approach in biosolids management, focusing on genomics, transcriptomics, proteomics, and metabolomics is also assessed. Multi-omics also allows for real-time monitoring, ensuring continuous optimization of biosolids towards changing environmental conditions. This dynamic approach not only enhances the safe use, but also enhances the sustainability of waste management practices, minimizing the negative effects. Finally, the future research directions for integrating the multi-omics approach into biosolid management practices are also suggested. The need for updating the legislative framework, continued innovation to promote sustainable and robust agricultural systems, bringing the process closer to the principles of a circular bioeconomy is also empahasized.},
}
@article {pmid39890763,
year = {2025},
author = {Kuru, A and Yüzer, MA and Yüzer, A&#x15e; and Güney, BG and Yüzer, ME},
title = {Integrated site selection model for industrial areas: case study for İnegöl furniture industry.},
journal = {Environmental science and pollution research international},
volume = {32},
number = {8},
pages = {4771-4793},
pmid = {39890763},
issn = {1614-7499},
mesh = {*Interior Design and Furnishings ; *Industry ; Noise ; Odorants/analysis ; Environmental Monitoring ; Socioeconomic Factors ; Geographic Information Systems ; *Environment ; },
abstract = {Industrial activities in the central area have adverse effects such as noise, odor, and traffic congestion. Simultaneously, due to changing technological and economic advances, existing industrial areas cannot meet the needs, spatial inadequacies obstruct competition, and production capacity decreases. Decentralizing industrial activities from urban centers are ecologically and economically necessary. Various elements on a macro and micro scale need to be considered to select suitable sites for new industrial areas. Natural, socioeconomic, and built environment features must be examined to ensure sustainability. The objective of this study is to develop an integrated industrial site location model that considers the needs of authorities and industrial stakeholders, as well as economic and ecological sustainability for the İnegöl district, one of Turkey's leading settlements in the furniture industry. Thirty-seven criteria were evaluated using GIS based multi-criteria decision making methods. The criteria were defined through spatial analysis, expert opinions, and in-depth interviews with industry and local government representatives. Using weighted linear combination process the five sub-regions exhibiting the lowest economic costs and the least environmental degradation have been identified. Advantages and disadvantages were identified through the use of sketches and comparisons between the sub-regions. A decision support system was developed for local and central government institutions to be used in industrial site selection processes.},
}
@article {pmid39891349,
year = {2025},
author = {Wang, Y and Li, J and Chiu, TP and Gompel, N and Rohs, R},
title = {DNAdesign: feature-aware in silico design of synthetic DNA through mutation.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {2},
pages = {},
pmid = {39891349},
issn = {1367-4811},
support = {R35 GM130376/GM/NIGMS NIH HHS/United States ; RGP0021/2018//Human Frontier Science Program/ ; },
mesh = {*DNA/chemistry/genetics ; *Software ; *Mutation ; Nucleic Acid Conformation ; Computer Simulation ; *Computational Biology/methods ; Binding Sites ; Sequence Analysis, DNA/methods ; Base Sequence ; Synthetic Biology/methods ; },
abstract = {MOTIVATION: DNA sequence and shape readout represent different modes of protein-DNA recognition. Current tools lack the functionality to simultaneously consider alterations in different readout modes caused by sequence mutations. DNAdesign is a web-based tool to compare and design mutations based on both DNA sequence and shape characteristics. Users input a wild-type sequence, select sites to introduce mutations and choose a set of DNA shape parameters for mutation design.<br><br>RESULTS: DNAdesign utilizes Deep DNAshape to provide ultra-fast predictions of DNA shape based on extended k-mers and offers multiple encoding methods for nucleotide sequences, including the physicochemical encoding of DNA through their functional groups in the major and minor groove. DNAdesign provides all mutation candidates along the sequence and shape dimensions, with interactive visualization comparing each candidate with the wild-type DNA molecule. DNAdesign provides an approach to studying gene regulation and applications in synthetic biology, such as the design of synthetic enhancers and transcription factor binding sites.<br><br>The DNAdesign webserver and documentation are freely accessible at https://dnadesign.usc.edu.},
}
@article {pmid39892263,
year = {2025},
author = {Yang, W and Liu, Y and Shao, H and Iravani, M and Yu, Z and Weber, M},
title = {Developing a cloud-based WebGIS tool for communicating integrated ecosystem services assessment modeling to conservation stakeholders.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124372},
doi = {10.1016/j.jenvman.2025.124372},
pmid = {39892263},
issn = {1095-8630},
mesh = {*Cloud Computing ; *Geographic Information Systems ; Ecosystem ; *Agriculture/economics/methods/statistics &amp; numerical data ; *Conservation of Natural Resources/economics/methods/statistics &amp; numerical data ; Environmental Monitoring ; Models, Statistical ; Farms/economics/statistics &amp; numerical data ; Cost-Effectiveness Analysis ; Alberta ; Agroecology/economics/methods/statistics &amp; numerical data ; Stakeholder Participation ; Hydrology ; },
abstract = {Various modeling efforts have been conducted to evaluate ecosystem services (ES) of agricultural conservation practices but typically these models are too complex for conservation stakeholders to use. This research developed a cloud-based WebGIS tool for communicating integrated ES modeling to conservation stakeholders. The integrated ES modeling was developed by linking farm economic, watershed hydrologic, and soil carbon modeling within a spatial optimization framework for identifying conservation practices to minimize economic costs subject to multiple ES targets including water quality and soil carbon improvement benefits. The WebGIS tool, named "Ecosystem Services Assessment Tool" (ESAT), has a suite of functions to visualize watershed characteristics, summarize the effectiveness of existing agricultural conservation practices, examine the cost, effectiveness, and cost-effectiveness of future agricultural conservation practices, and further, identify optimal sets of conservation practices for achieving cost-effectiveness. The study area for the integrated ES modeling and WebGIS tool development was the 4,820-km[2] Modeste watershed in Alberta, Canada. The ESAT application demonstrated its functionalities to support decision making, particularly in identifying cost-effective conservation practices for achieving sediment, phosphorus or nitrogen reduction, or soil carbon increase target. In the research, conservation stakeholders including municipal and provincial governments, conservation management agencies, and NGOs were actively engaged in data collection, modeling development, WebGIS tool development, and training for the use of the WebGIS tool. Conservation stakeholders assessed that the ESAT is a very useful tool for supporting decision making in agri-environmental programs. However, the WebGIS tool can be further simplified and streamlined to improve the user-friendliness of the ESAT.},
}
@article {pmid39897501,
year = {2025},
author = {Fuster-Calvo, A and Valentin, S and Tamayo, WC and Gravel, D},
title = {Evaluating the feasibility of automating dataset retrieval for biodiversity monitoring.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18853},
pmid = {39897501},
issn = {2167-8359},
mesh = {*Biodiversity ; *Databases, Factual ; *Information Storage and Retrieval/methods ; Algorithms ; Feasibility Studies ; *Conservation of Natural Resources/methods ; Quebec ; },
abstract = {AIM: Effective management strategies for conserving biodiversity and mitigating the impacts of global change rely on access to comprehensive and up-to-date biodiversity data. However, manual search, retrieval, evaluation, and integration of this information into databases present a significant challenge to keeping pace with the rapid influx of large amounts of data, hindering its utility in contemporary decision-making processes. Automating these tasks through advanced algorithms holds immense potential to revolutionize biodiversity monitoring.<br><br>INNOVATION: In this study, we investigate the potential for automating the retrieval and evaluation of biodiversity data from Dryad and Zenodo repositories. We have designed an evaluation system based on various criteria, including the type of data provided and its spatio-temporal range, and applied it to manually assess the relevance for biodiversity monitoring of datasets retrieved through an application programming interface (API). We evaluated a supervised classification to identify potentially relevant datasets and investigate the feasibility of automatically ranking the relevance. Additionally, we applied the same appraoch on a scientific literature source, using data from Semantic Scholar for reference. Our evaluation centers on the database utilized by a national biodiversity monitoring system in Quebec, Canada.<br><br>MAIN CONCLUSIONS: We retrieved 89 (55%) relevant datasets for our database, showing the value of automated dataset search in repositories. Additionally, we find that scientific publication sources offer broader temporal coverage and can serve as conduits guiding researchers toward other valuable data sources. Our automated classification system showed moderate performance in detecting relevant datasets (with an F-score up to 0.68) and signs of overfitting, emphasizing the need for further refinement. A key challenge identified in our manual evaluation is the scarcity and uneven distribution of metadata in the texts, especially pertaining to spatial and temporal extents. Our evaluative framework, based on predefined criteria, can be adopted by automated algorithms for streamlined prioritization, and we make our manually evaluated data publicly available, serving as a benchmark for improving classification techniques.},
}
@article {pmid39897809,
year = {2025},
author = {Milling, M and Rampp, SDN and Triantafyllopoulos, A and Plaza, MP and Brunner, JO and Traidl-Hoffmann, C and Schuller, BW and Damialis, A},
title = {Automating airborne pollen classification: Identifying and interpreting hard samples for classifiers.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41656},
pmid = {39897809},
issn = {2405-8440},
abstract = {Deep-learning-based classification of pollen grains has been a major driver towards automatic monitoring of airborne pollen. Yet, despite an abundance of available datasets, little effort has been spent to investigate which aspects pose the biggest challenges to the (often black-box- resembling) pollen classification approaches. To shed some light on this issue, we conducted a sample-level difficulty analysis based on the likelihood for one of the largest automatically-generated datasets of pollen grains on microscopy images and investigated the reason for which certain airborne samples and specific pollen taxa pose particular problems to deep learning algorithms. It is here concluded that the main challenges lie in A) the (partly) co-occurring of multiple pollen grains in a single image, B) the occlusion of specific markers through the 2D capturing of microscopy images, and C) for some taxa, a general lack of salient, unique features. Our code is publicly available under https://github.com/millinma/SDPollen.},
}
@article {pmid39897842,
year = {2025},
author = {Loukili, I and Laamrani, A and El Ghorfi, M and El Moutak, S and Ghafiri, A},
title = {Monitoring land changes at an open mine site using remote sensing and multi-spectral indices.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41845},
pmid = {39897842},
issn = {2405-8440},
abstract = {This study investigates the growth of mining activities in Benguerir, one of Morocco's largest and fastest-growing phosphate mines and a global leader in phosphate production, using remote sensing and ancillary data. The study examines spatio-temporal changes in land use and land cover (LULC) within this phosphate mining city to analyze the impacts of mining on agricultural areas, built-up lands, and water bodies over time. A series of images from 1984 to 2021 were processed in to assess patterns of change within the city. Five LULC maps were generated using supervised classification with the maximum likelihood method, providing detailed insights into both urban and non-urban transformations during the study period. Classification quality was evaluated using accuracy assessment and the Kappa index. Additionally, multi-spectral indices, including the Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI), and Normalized Difference Built-up Index (NDBI), were simulated and analyzed across four intervals. The results reveal significant variations in LULC and ecological indices over time, which are associated with mining activities, water stress, urban sprawl, and socio-economic changes in the region.These results provide a valuable means for decision-makers and planners to effectively manage the spaces and lands in the future.},
}
@article {pmid39897903,
year = {2025},
author = {Doshi, P and Klas, M and Kyzek, S and Zahoranová, A and Šerá, B},
title = {Investigating the effect of plasma activated water on entomopathogenic nematodes under laboratory conditions.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e42038},
pmid = {39897903},
issn = {2405-8440},
abstract = {Entomopathogenic nematodes are currently being tested for their efficiency in controlling several insect pests. In recent years, non-thermal plasma has been investigated as a state-of-the-art technology for its disinfection/decontamination properties on the seed surface. In addition, it is also used to induce seed germination. In this investigation, the effect of plasma activated water (PAW) was tested on three EPN species, namely Steinernema feltiae Filipjev (1934), S. carpocapsae Weiser (1955), and Heterorhabditis bacteriophora Poinar (1976). Seven different PAW prepared at different treatment times, that is, (1s, 3s, 5s, 10s, 20s, 60s, 90s) were tested directly on the three selected nematode species. Distilled water was used as a control treatment (0s). In the case of H. bacteriophora, significantly higher mortality was observed in PAW preparation times of 5, 10, 20, 60 and 90s compared to the control. In the case of S. feltiae, significantly high mortality was observed for PAW preparation times of 10, 20, 60 and 90s. However, S. carpocapsae was found to have the least sensitivity against all PAW treatments, with a maximum mortality of 14 % (<20 %), indicating the potential synergy between PAW and EPNs. The possibility of combined treatments in the context of integrated pest management is presented and discussed.},
}
@article {pmid39899595,
year = {2025},
author = {McKenzie-Smith, GC and Wolf, SW and Ayroles, JF and Shaevitz, JW},
title = {Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data.},
journal = {PLoS computational biology},
volume = {21},
number = {2},
pages = {e1012753},
pmid = {39899595},
issn = {1553-7358},
support = {R01 ES029929/ES/NIEHS NIH HHS/United States ; R35 GM124881/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Drosophila melanogaster/physiology ; *Behavior, Animal/physiology ; Locomotion/physiology ; Circadian Rhythm/physiology ; *Posture/physiology ; Computational Biology ; Female ; Grooming/physiology ; },
abstract = {Animal behavior spans many timescales, from short, seconds-scale actions to daily rhythms over many hours to life-long changes during aging. To access longer timescales of behavior, we continuously recorded individual Drosophila melanogaster at 100 frames per second for up to 7 days at a time in featureless arenas on sucrose-agarose media. We use the deep learning framework SLEAP to produce a full-body postural dataset for 47 individuals resulting in nearly 2 billion pose instances. We identify stereotyped behaviors such as grooming, proboscis extension, and locomotion and use the resulting ethograms to explore how the flies' behavior varies across time of day and days in the experiment. We find distinct daily patterns in all stereotyped behaviors, adding specific information about trends in different grooming modalities, proboscis extension duration, and locomotion speed to what is known about the D. melanogaster circadian cycle. Using our holistic measurements of behavior, we find that the hour after dawn is a unique time point in the flies' daily pattern of behavior, and that the behavioral composition of this hour tracks well with other indicators of health such as locomotion speed and the fraction of time spend moving vs. resting. The method, data, and analysis presented here give us a new and clearer picture of D. melanogaster behavior across timescales, revealing novel features that hint at unexplored underlying biological mechanisms.},
}
@article {pmid39899630,
year = {2025},
author = {Sheen, JK and Kennedy-Shaffer, L and Levy, MZ and Metcalf, CJE},
title = {Design of field trials for the evaluation of transmissible vaccines in animal populations.},
journal = {PLoS computational biology},
volume = {21},
number = {2},
pages = {e1012779},
pmid = {39899630},
issn = {1553-7358},
mesh = {Animals ; *Vaccines/immunology ; *Vaccination/veterinary ; Computational Biology ; Research Design ; },
abstract = {Vaccines which can transmit from vaccinated to unvaccinated animals may be especially useful for increasing immunity in hard to reach populations or in populations where achieving high coverage is logistically infeasible. However, gauging the public health utility for future use of such transmissible vaccines and assessing their risk-benefit tradeoff, given their potential for unintended evolution, hinges on accurate estimates of their indirect protective effect. Here, we establish the conditions under which a two-stage randomized field trial can characterize the protective effects of a transmissible vaccine relative to a traditional vaccine. We contrast the sample sizes required to adequately power these trials when the vaccine is weakly and strongly transmissible. We also identify how required sample sizes change based on the characteristics of host ecology such as the overdispersion of the contact structure of the population, as well as the efficacy of the vaccine and timing of vaccination. Our results indicate the range of scenarios where two-stage randomized field trial designs are feasible and appropriate to capture the protective effects of transmissible vaccines. Our estimates identify the protective benefit of using transmissible vaccines compared to traditional vaccines, and thus can be used to weigh against evolutionary risks.},
}
@article {pmid39899643,
year = {2025},
author = {Hozé, N and Pons-Salort, M and Metcalf, CJE and White, M and Salje, H and Cauchemez, S},
title = {RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies.},
journal = {PLoS computational biology},
volume = {21},
number = {2},
pages = {e1012777},
pmid = {39899643},
issn = {1553-7358},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI175941/AI/NIAID NIH HHS/United States ; U01 AI151758/AI/NIAID NIH HHS/United States ; },
mesh = {Seroepidemiologic Studies ; Humans ; Bayes Theorem ; *Software ; *Computational Biology/methods ; Computer Simulation ; Disease Outbreaks/statistics &amp; numerical data ; Epidemiological Models ; },
abstract = {Population-based serological surveys are a key tool in epidemiology to characterize the level of population immunity and reconstruct the past circulation of pathogens. A variety of serocatalytic models have been developed to estimate the force of infection (FOI) (i.e., the rate at which susceptible individuals become infected) from age-stratified seroprevalence data. However, few tool currently exists to easily implement, combine, and compare these models. Here, we introduce an R package, Rsero, that implements a series of serocatalytic models and estimates the FOI from age-stratified seroprevalence data using Bayesian methods. The package also contains a series of features to perform model comparison and visualise model fit. We introduce new serocatalytic models of successive outbreaks and extend existing models of seroreversion to any transmission model. The different features of the package are illustrated with simulated and real-life data. We show we can identify the correct epidemiological scenario and recover model parameters in different epidemiological settings. We also show how the package can support serosurvey study design in a variety of epidemic situations. This package provides a standard framework to epidemiologists and modellers to study the dynamics of past pathogen circulation from cross-sectional serological survey data.},
}
@article {pmid39900590,
year = {2025},
author = {Chen, Y and Zheng, L and Ma, J and Zhu, H and Gan, Y},
title = {The Mediating Role of Meaning-Making in the Relationship Between Mental Time Travel and Positive Emotions in Stress-Related Blogs: Big Data Text Analysis Research.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e63407},
pmid = {39900590},
issn = {1438-8871},
mesh = {Humans ; *Emotions ; *Stress, Psychological/psychology ; *Big Data ; *Blogging ; },
abstract = {BACKGROUND: Given the ubiquity of stress, a key focus of stress research is exploring how to better coexist with stress.<br><br>OBJECTIVE: This study conducted text analysis on stress-related Weibo posts using a web crawler to investigate whether these posts contained positive emotions, as well as elements of mental time travel and meaning-making. A mediation model of mental time travel, meaning-making, and positive emotions was constructed to examine whether meaning-making triggered by mental time travel can foster positive emotions under stress.<br><br>METHODS: Using Python 3.8, the original public data from active Weibo users were crawled, yielding 331,711 stress-related posts. To avoid false positives, these posts were randomly divided into two large samples for cross-validation (sample 1: n=165,374; sample 2: n=166,337). Google's natural language processing application programming interface was used for word segmentation, followed by text and mediation analysis using the Chinese psychological analysis system "Wenxin." A mini-meta-analysis of the mediation path coefficients was conducted. Text analysis identified mental time travel words, meaning-making words, and positive emotion words in stress-related posts.<br><br>RESULTS: The constructed mediation model of mental time travel words (time words), meaning-making words (causal and insightful words), and positive poststress emotions validated positive adaptation following stress. A mini-meta-analysis of two different mediation models constructed in the two subsamples indicated a stable mediation effect across the 2 random subsamples. The combined effect size (B) obtained was .013 (SE 0.003, 95% CI 0.007-0.018; P<.001), demonstrating that meaning-making triggered by mental time travel in stress-related blog posts can predict positive emotions under stress.<br><br>CONCLUSIONS: Individuals can adapt positively to stress by engaging in meaning-making processes that are triggered by mental time travel and reflected in their social media posts. The study's mediation model confirmed that mental time travel leads to meaning-making, which fosters positive emotional responses to stress. Mental time travel serves as a psychological strategy to facilitate positive adaptation to stressful situations.},
}
@article {pmid39903189,
year = {2025},
author = {Gallardo García Freire, P and Matías, E and Malizia, A and Monmany-Garzia, AC and Galindo-Cardona, A},
title = {Pollution risk assessment in sub-basins of an open dump using drones and geographic information systems.},
journal = {Waste management &amp; research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA},
volume = {43},
number = {9},
pages = {1425-1433},
doi = {10.1177/0734242X251314180},
pmid = {39903189},
issn = {1096-3669},
mesh = {*Geographic Information Systems ; Risk Assessment ; Argentina ; *Environmental Monitoring/methods ; *Unmanned Aerial Devices ; *Refuse Disposal/methods ; Satellite Imagery ; *Solid Waste/analysis ; *Environmental Pollution/analysis ; },
abstract = {The sustainable management of municipal solid waste (MSW) presents a pressing global challenge. This study introduces an innovative methodology for analysing open dumps in Tucumán, Argentina, using unmanned aerial vehicles (UAVs) and DroneDeploy software for data collection, coupled with QGIS for estimating contamination risk at the sub-basin level. By integrating satellite imagery, ground surveys, high-resolution UAV imagery and a multi-criteria decision analysis within geographic information system, we provide a comprehensive overview of dumpsite conditions at one open dump. Commercial drone flights facilitate the rapid and cost-effective creation of digital elevation models and digital terrain models, along with orthomosaic imagery, from which waste footprints are delineated using artificial intelligence to enhance the understanding of geospatial issues. Approaching data layers, such as leachate pools, riverbanks and solar radiation, supports informed decision-making in MSW management through a replicable methodology. Field validation and the inclusion of subsurface and groundwater processes are recommended for future research to improve accuracy and maximize socio-ecological benefits.},
}
@article {pmid39903560,
year = {2025},
author = {Thomas, GWC and Hughes, JJ and Kumon, T and Berv, JS and Nordgren, CE and Lampson, M and Levine, M and Searle, JB and Good, JM},
title = {The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents.},
journal = {Genome biology and evolution},
volume = {17},
number = {2},
pages = {},
pmid = {39903560},
issn = {1759-6653},
support = {RRID:SCR_021757//Cornell University Biotechnology Resource Center BioHPC/ ; //Cornell Center for Vertebrate Genomics/ ; //University of Michigan Museum of Zoology/ ; R35 GM124684/GM/NIGMS NIH HHS/United States ; DEB-1754096//National Science Foundation/ ; CC-2018112//University of Montana Griz Shared Computing Cluster/ ; MRI-2215705//University of California Riverside HPCC/ ; //Jean Wright Cohn Endowment Fund/ ; //University of Michigan Life Sciences Fellows Program/ ; S10 OD016290/OD/NIH HHS/United States ; R01 HD094787/HD/NICHD NIH HHS/United States ; //Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01-HD094787/NH/NIH HHS/United States ; },
mesh = {Animals ; *Phylogeny ; Mice/genetics ; *Genome ; Rats/genetics ; Evolution, Molecular ; Rodentia/genetics ; Genomics ; Conserved Sequence ; Selection, Genetic ; Recombination, Genetic ; },
abstract = {A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents-a large and ecologically diverse group that gave rise to the laboratory mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultraconserved elements (UCEs) to infer a robust time-calibrated species tree. We then used whole genomes to examine finer-scale patterns of discordance across ∼12 million years of divergence. We found that proximate chromosomal regions tended to have more similar phylogenetic histories. There was no clear relationship between local tree similarity and recombination rates in house mice, but we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to appreciably less discordance. Finally, we show that assuming a single species tree can result in substantial deviation from the results with gene trees when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.},
}
@article {pmid39904391,
year = {2025},
author = {Mihaljevic, JR and Páez, DJ},
title = {Systematic shifts in the variation among host individuals must be considered in climate-disease theory.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2040},
pages = {20242515},
pmid = {39904391},
issn = {1471-2954},
support = {//Exxon Valdez Oil Spill Trustee Council/ ; //Division of Environmental Biology/ ; },
mesh = {*Climate Change ; Temperature ; *Host-Pathogen Interactions ; Animals ; Population Dynamics ; Models, Biological ; Disease Susceptibility ; },
abstract = {To make more informed predictions of host-pathogen interactions under climate change, studies have incorporated the thermal performance of host, vector and pathogen traits into disease models to quantify effects on average transmission rates. However, this body of work has omitted the fact that variation in susceptibility among individual hosts affects disease spread and long-term patterns of host population dynamics. Furthermore, and especially for ectothermic host species, variation in susceptibility is likely to be plastic, influenced by variables such as environmental temperature. For example, as host individuals respond idiosyncratically to temperature, this could affect the population-level variation in susceptibility, such that there may be predictable functional relationships between variation in susceptibility and temperature. Quantifying the relationship between temperature and among-host trait variation will therefore be critical for predicting how climate change and disease will interact to influence host-pathogen population dynamics. Here, we use a model to demonstrate how short-term effects of temperature on the distribution of host susceptibility can drive epidemic characteristics, fluctuations in host population sizes and probabilities of host extinction. Our results emphasize that more research is needed in disease ecology and climate biology to understand the mechanisms that shape individual trait variation, not just trait averages.},
}
@article {pmid39906497,
year = {2025},
author = {Palande, S and Arsenault, J and Basurto-Lozada, P and Bleich, A and Brown, BNI and Buysse, SF and Connors, NA and Das Adhikari, S and Dobson, KC and Guerra-Castillo, FX and Guerrero-Carrillo, MF and Harlow, S and Herrera-Orozco, H and Hightower, AT and Izquierdo, P and Jacobs, M and Johnson, NA and Leuenberger, W and Lopez-Hernandez, A and Luckie-Duque, A and Martínez-Avila, C and Mendoza-Galindo, EJ and Plancarte, DC and Schuster, JM and Shomer, H and Sitar, SC and Steensma, AK and Thomson, JE and Villaseñor-Amador, D and Waterman, R and Webster, BM and Whyte, M and Zorilla-Azcué, S and Montgomery, BL and Husbands, AY and Krishnan, A and Percival, S and Munch, E and VanBuren, R and Chitwood, DH and Rougon-Cardoso, A},
title = {Expression-based machine learning models for predicting plant tissue identity.},
journal = {Applications in plant sciences},
volume = {13},
number = {1},
pages = {e11621},
pmid = {39906497},
issn = {2168-0450},
abstract = {PREMISE: The selection of Arabidopsis as a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural- or ecological-based model species were rejected, in favor of building knowledge in a species that would facilitate genome-enabled research.<br><br>METHODS: Here, we examine the ability of models based on Arabidopsis gene expression data to predict tissue identity in other flowering plants. Comparing different machine learning algorithms, models trained and tested on Arabidopsis data achieved near perfect precision and recall values, whereas when tissue identity is predicted across the flowering plants using models trained on Arabidopsis data, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64.<br><br>RESULTS: The identity of belowground tissue can be predicted more accurately than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance from Arabidopsis. k-nearest neighbors is the most successful algorithm, suggesting that gene expression signatures, rather than marker genes, are more valuable to create models for tissue and cell type prediction in plants.<br><br>DISCUSSION: Our data-driven results highlight that the assertion that knowledge from Arabidopsis is translatable to other plants is not always true. Considering the current landscape of abundant sequencing data, we should reevaluate the scientific emphasis on Arabidopsis and prioritize plant diversity.},
}
@article {pmid39907430,
year = {2025},
author = {Hebert, JD and Tang, YJ and Szamecz, M and Andrejka, L and Lopez, SS and Petrov, DA and Boross, G and Winslow, MM},
title = {Combinatorial In Vivo Genome Editing Identifies Widespread Epistasis and an Accessible Fitness Landscape During Lung Tumorigenesis.},
journal = {Molecular biology and evolution},
volume = {42},
number = {2},
pages = {},
pmid = {39907430},
issn = {1537-1719},
support = {P30 CA124435/CA/NCI NIH HHS/United States ; R01 CA230025/CA/NCI NIH HHS/United States ; R01 CA231253/CA/NCI NIH HHS/United States ; R01 CA234349/CA/NCI NIH HHS/United States ; },
mesh = {*Epistasis, Genetic ; Animals ; Mice ; *Lung Neoplasms/genetics ; *Carcinogenesis/genetics ; *Gene Editing ; Genetic Fitness ; *Adenocarcinoma of Lung/genetics ; },
abstract = {Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable the evolution of cancer in vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and quantitative manner. Here, we employed a novel platform to generate tumors with inactivation of pairs of ten diverse tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. Sign epistasis was extremely rare, suggesting a surprisingly accessible fitness landscape during lung tumorigenesis. These findings expand our understanding of the interactions that drive tumorigenesis in vivo.},
}
@article {pmid39909332,
year = {2025},
author = {Cheng, Z and He, Y and Wang, N and Wu, L and Xu, J and Shi, J},
title = {Uncovering soil amendment-induced genomic and functional divergence in soybean rhizosphere microbiomes during cadmium-contaminated soil remediation: Novel insights from field multi-omics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {368},
number = {},
pages = {125787},
doi = {10.1016/j.envpol.2025.125787},
pmid = {39909332},
issn = {1873-6424},
mesh = {*Cadmium/analysis ; *Rhizosphere ; *Soil Pollutants/analysis ; *Glycine max/microbiology ; *Soil Microbiology ; *Microbiota ; Soil/chemistry ; Biodegradation, Environmental ; *Environmental Restoration and Remediation/methods ; Multiomics ; },
abstract = {Soil amendments exhibit great potential in reducing cadmium (Cd) bioavailability and its accumulation in crop grains, but their practical implications on microbial characteristics (genomic traits and ecological functions) remain unclear. The objective of this study was to combine metagenomics and metatranscriptomics to track the dynamics of bacterial and viral communities in the soybean rhizosphere during the remediation of Cd-contaminated soil using a commercial Mg-Ca-Si conditioner (CMC), applied at low and high (975 kg ha[-1] and 1950 kg ha[-1]) rates under field conditions. Application of CMC increased the average size and decreased the guanine-cytosine (GC) content of microbial genomes, which were strongly shaped by soil pH and available Cd (ACd). Gene and transcript abundances analysis indicated that CMC promoted the enrichment of Alphaproteobacterial metagenome-assembled genomes (MAGs) carrying czcC gene encoding Cd efflux and dsbB gene encoding disulfide bond oxidoreductase. These genes are closely related to Cd resistance and exhibited notable (p < 0.05) increased expression in CMC-treated soils. Additionally, low and high CMC addition significantly increased viral alpha diversity by 5.7% and 9.6%, and viral activity by 3.3% and 7.8%, respectively, in comparison to the control. Temperate viruses were predicted as the major group (64%) and actively linked to the dominant host, and CMC amendment increased host metabolism and adaptability by enhancing (p < 0.05) the abundance and transcriptional activity of virus-encoded auxiliary metabolic genes (AMGs) involved in heavy metal resistance (ABC transport), sulfur cycling (cysH), and host metabolism (galE and queD) through "piggyback-the-winner" strategy. Structural equation modeling further revealed that CMC application influences Cd accumulation in soybean grains through its direct and indirect effects on soil properties and rhizosphere microbiomes, and highlighted the potential role of rhizosphere viruses in agricultural soil remediation.},
}
@article {pmid39910401,
year = {2025},
author = {Fatima, M and Butt, I and MohammadEbrahimi, S and Kiani, B and Gruebner, O},
title = {Spatiotemporal clusters of acute respiratory infections associated with socioeconomic, meteorological, and air pollution factors in South Punjab, Pakistan.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {469},
pmid = {39910401},
issn = {1471-2458},
mesh = {Pakistan/epidemiology ; Humans ; Socioeconomic Factors ; *Respiratory Tract Infections/epidemiology ; *Air Pollution/adverse effects/statistics &amp; numerical data ; Spatio-Temporal Analysis ; Incidence ; *Meteorological Concepts ; Acute Disease ; Weather ; Female ; Male ; Risk Factors ; },
abstract = {BACKGROUND: In Pakistan, acute respiratory infections (ARI) continue to be a major public health problem. However, there is still a lack of scholarly work regarding different environmental and socioeconomic influencing factors and how they interact with respiratory infections. Furthermore, we do not know much about geographic variation in this context. Therefore, our study examines the ecological-level spatial and temporal patterns of acute respiratory infection incidence (ARI) and their geographic relationship with selected socio-economic, meteorological, and air pollution factors in Pakistan.<br><br>METHODS: We applied the spatiotemporal scan statistics to examine the purely temporal, spatial, and spatiotemporal clusters of ARI in South Punjab, Pakistan for five years (2016-2020). Generalized Linear Model (GLM) and geographically weighted regression (GWR) were also applied to model the linear and non-linear spatial relationships between selected variables and ARI.<br><br>RESULTS: Our results indicate that in the central and northern regions of Pakistan, two spatial clusters of ARI were present, accounting for 28.5% of the total cases. A spatiotemporal cluster with a relative risk of 1.57 was discovered in the northeastern area. The results obtained from the season-based GLM highlighted the significance of climatic factors (temperature, fog, dust storms) and air pollutants (NO2) in influencing ARI incidence, while socio-economic variables (rural population, literacy) had limited impact. In addition, GWR revealed that the relationships between predictors and ARI incidence varied across locations, emphasizing the importance of considering local settings. Season-based non-stationary GLM revealed a multifaceted interaction among socio-economic, meteorological, and air pollution factors.<br><br>CONCLUSIONS: Our study provides evidence about environmental and socio-economic factors significantly associated with ARI incidence. In addition, this study provides the first baseline of ARI cases in Pakistan to plan for intervention and adaptation strategies and may be replicated in other regions of comparable settings worldwide.},
}
@article {pmid39915771,
year = {2025},
author = {Gould, E and Fraser, HS and Parker, TH and Nakagawa, S and Griffith, SC and Vesk, PA and Fidler, F and Hamilton, DG and Abbey-Lee, RN and Abbott, JK and Aguirre, LA and Alcaraz, C and Aloni, I and Altschul, D and Arekar, K and Atkins, JW and Atkinson, J and Baker, CM and Barrett, M and Bell, K and Bello, SK and Beltrán, I and Berauer, BJ and Bertram, MG and Billman, PD and Blake, CK and Blake, S and Bliard, L and Bonisoli-Alquati, A and Bonnet, T and Bordes, CNM and Bose, APH and Botterill-James, T and Boyd, MA and Boyle, SA and Bradfer-Lawrence, T and Bradham, J and Brand, JA and Brengdahl, MI and Bulla, M and Bussière, L and Camerlenghi, E and Campbell, SE and Campos, LLF and Caravaggi, A and Cardoso, P and Carroll, CJW and Catanach, TA and Chen, X and Chik, HYJ and Choy, ES and Christie, AP and Chuang, A and Chunco, AJ and Clark, BL and Contina, A and Covernton, GA and Cox, MP and Cressman, KA and Crotti, M and Crouch, CD and D'Amelio, PB and de Sousa, AA and Döbert, TF and Dobler, R and Dobson, AJ and Doherty, TS and Drobniak, SM and Duffy, AG and Duncan, AB and Dunn, RP and Dunning, J and Dutta, T and Eberhart-Hertel, L and Elmore, JA and Elsherif, MM and English, HM and Ensminger, DC and Ernst, UR and Ferguson, SM and Fernandez-Juricic, E and Ferreira-Arruda, T and Fieberg, J and Finch, EA and Fiorenza, EA and Fisher, DN and Fontaine, A and Forstmeier, W and Fourcade, Y and Frank, GS and Freund, CA and Fuentes-Lillo, E and Gandy, SL and Gannon, DG and García-Cervigón, AI and Garretson, AC and Ge, X and Geary, WL and Géron, C and Gilles, M and Girndt, A and Gliksman, D and Goldspiel, HB and Gomes, DGE and Good, MK and Goslee, SC and Gosnell, JS and Grames, EM and Gratton, P and Grebe, NM and Greenler, SM and Griffioen, M and Griffith, DM and Griffith, FJ and Grossman, JJ and Güncan, A and Haesen, S and Hagan, JG and Hager, HA and Harris, JP and Harrison, ND and Hasnain, SS and Havird, JC and Heaton, AJ and Herrera-Chaustre, ML and Howard, TJ and Hsu, BY and Iannarilli, F and Iranzo, EC and Iverson, ENK and Jimoh, SO and Johnson, DH and Johnsson, M and Jorna, J and Jucker, T and Jung, M and Kačergytė, I and Kaltz, O and Ke, A and Kelly, CD and Keogan, K and Keppeler, FW and Killion, AK and Kim, D and Kochan, DP and Korsten, P and Kothari, S and Kuppler, J and Kusch, JM and Lagisz, M and Lalla, KM and Larkin, DJ and Larson, CL and Lauck, KS and Lauterbur, ME and Law, A and Léandri-Breton, DJ and Lembrechts, JJ and L'Herpiniere, K and Lievens, EJP and de Lima, DO and Lindsay, S and Luquet, M and MacLeod, R and Macphie, KH and Magellan, K and Mair, MM and Malm, LE and Mammola, S and Mandeville, CP and Manhart, M and Manrique-Garzon, LM and Mäntylä, E and Marchand, P and Marshall, BM and Martin, CA and Martin, DA and Martin, JM and Martinig, AR and McCallum, ES and McCauley, M and McNew, SM and Meiners, SJ and Merkling, T and Michelangeli, M and Moiron, M and Moreira, B and Mortensen, J and Mos, B and Muraina, TO and Murphy, PW and Nelli, L and Niemelä, P and Nightingale, J and Nilsonne, G and Nolazco, S and Nooten, SS and Novotny, JL and Olin, AB and Organ, CL and Ostevik, KL and Palacio, FX and Paquet, M and Parker, DJ and Pascall, DJ and Pasquarella, VJ and Paterson, JH and Payo-Payo, A and Pedersen, KM and Perez, G and Perry, KI and Pottier, P and Proulx, MJ and Proulx, R and Pruett, JL and Ramananjato, V and Randimbiarison, FT and Razafindratsima, OH and Rennison, DJ and Riva, F and Riyahi, S and Roast, MJ and Rocha, FP and Roche, DG and Román-Palacios, C and Rosenberg, MS and Ross, J and Rowland, FE and Rugemalila, D and Russell, AL and Ruuskanen, S and Saccone, P and Sadeh, A and Salazar, SM and Sales, K and Salmón, P and Sánchez-Tójar, A and Santos, LP and Santostefano, F and Schilling, HT and Schmidt, M and Schmoll, T and Schneider, AC and Schrock, AE and Schroeder, J and Schtickzelle, N and Schultz, NL and Scott, DA and Scroggie, MP and Shapiro, JT and Sharma, N and Shearer, CL and Simón, D and Sitvarin, MI and Skupien, FL and Slinn, HL and Smith, GP and Smith, JA and Sollmann, R and Whitney, KS and Still, SM and Stuber, EF and Sutton, GF and Swallow, B and Taff, CC and Takola, E and Tanentzap, AJ and Tarjuelo, R and Telford, RJ and Thawley, CJ and Thierry, H and Thomson, J and Tidau, S and Tompkins, EM and Tortorelli, CM and Trlica, A and Turnell, BR and Urban, L and Van de Vondel, S and van der Wal, JEM and Van Eeckhoven, J and van Oordt, F and Vanderwel, KM and Vanderwel, MC and Vanderwolf, KJ and Vélez, J and Vergara-Florez, DC and Verrelli, BC and Vieira, MV and Villamil, N and Vitali, V and Vollering, J and Walker, J and Walker, XJ and Walter, JA and Waryszak, P and Weaver, RJ and Wedegärtner, REM and Weller, DL and Whelan, S and White, RL and Wolfson, DW and Wood, A and Yanco, SW and Yen, JDL and Youngflesh, C and Zilio, G and Zimmer, C and Zimmerman, GM and Zitomer, RA},
title = {Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {35},
pmid = {39915771},
issn = {1741-7007},
mesh = {Animals ; *Ecology/methods ; *Biological Evolution ; Eucalyptus/growth &amp; development ; },
abstract = {Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small "many analyst" study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.},
}
@article {pmid39917311,
year = {2025},
author = {Lysholm, S and Chaters, GL and Di Bari, C and Hughes, EC and Huntington, B and Rushton, J and Thomas, L},
title = {A framework for quantifying the multisectoral burden of animal disease to support decision making.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1476505},
pmid = {39917311},
issn = {2297-1769},
abstract = {Animal diseases have wide-ranging impacts in multiple societal arenas, including agriculture, public health and the environment. These diseases cause significant economic losses for farmers, disrupt food security and present zoonotic risks to human populations. Additionally, they contribute to antimicrobial resistance and a range of environmental issues such as greenhouse gas emissions. The societal and ecological costs of livestock diseases are frequently underrepresented or unaddressed in policy decisions and resource allocations. Social cost-benefit analysis (SCBA) offers a comprehensive framework to evaluate the broad impacts of animal diseases across different sectors. This approach aligns with the One Health concept, which seeks to integrate and optimize the health of humans, animals and the environment. Traditional economic evaluations often focus narrowly on profit maximization within the livestock sector, neglecting wider externalities such as public health and environmental impacts. In contrast, SCBA takes a multi-sectoral whole-system view, considering multiple factors to guide public and private sector investments toward maximizing societal benefits. This paper discusses three separate sector specific (Animal health, Human health, Environmental health) methodologies for quantifying the burden of animal diseases. It then discusses how these estimates can be combined to generate multisectoral estimates of the impacts of animal diseases on human societies and the environment using monetary values. Finally this paper explores how this framework can support the evaluation of interventions from a One Health perspective though SCBA. This integrated assessment framework supports informed decision-making and resource allocation, ultimately contributing to improved public health outcomes, enhanced animal welfare, and greater environmental sustainability.},
}
@article {pmid39918865,
year = {2025},
author = {Astill Wright, L and Moore, M and Reeves, S and Vallejos, EP and Morriss, R},
title = {Improving the Utility, Safety, and Ethical Use of a Passive Mood-Tracking App for People With Bipolar Disorder Using Coproduction: Qualitative Focus Group Study.},
journal = {JMIR formative research},
volume = {9},
number = {},
pages = {e65140},
pmid = {39918865},
issn = {2561-326X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Bipolar Disorder/psychology/therapy ; Male ; Female ; *Mobile Applications/ethics ; Focus Groups ; Adult ; Middle Aged ; Qualitative Research ; *Affect ; Telemedicine ; },
abstract = {BACKGROUND: Coproduction with users of new digital technology, such as passive mood monitoring, is likely to improve its utility, safety, and successful implementation via improved design and consideration of how such technology fits with their daily lives. Mood-monitoring interventions are commonly used by people with bipolar disorder (BD) and have promising potential for digitization using novel technological methods.<br><br>OBJECTIVE: This study aims to explore how a passive behavioral monitoring platform, Remote Assessment of Disease and Relapse, would meet the needs of people with BD by specifically considering purpose and function, diversity of need, personal preference, essential components and potential risks, and harms and mitigation strategies through an iterative coproduction process.<br><br>METHODS: A total of 17 people with BD were recruited via national charities. We conducted 3 web-based focus groups as a part of an iterative coproduction process in line with responsible research and innovation principles and with consideration of clinical challenges associated with BD. Data were analyzed thematically. Results were cross-checked by someone with lived experience of BD.<br><br>RESULTS: Focus groups were transcribed and analyzed using thematic analysis. Six themes were identified as follows: (1) the purpose of using the app, (2) desired features, (3) when to use the app, (4) risks of using the app, (5) sharing with family and friends, and (6) sharing with health care professionals.<br><br>CONCLUSIONS: People with BD who are interested in using passive technology to monitor their mood wish to do so for a wide variety of purposes, identifying several preferences and potential risks. Principally, people with BD wished to use this novel technology to aid them in self-managing their BD with greater insight and a better understanding of potential triggers. We discuss key features that may aid this functionality and purpose, including crisis plans and sharing with others. Future development of passive mood-monitoring technologies should not assume that the involvement of formal mental health services is desired.},
}
@article {pmid39921816,
year = {2025},
author = {Asuako, PAG and Stojan, R and Bock, O and Mack, M and Voelcker-Rehage, C},
title = {Multitasking: does task-switching add to the effect of dual-tasking on everyday-like driving behavior?.},
journal = {Cognitive research: principles and implications},
volume = {10},
number = {1},
pages = {5},
pmid = {39921816},
issn = {2365-7464},
support = {SPP 1772//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; Female ; Male ; Young Adult ; Adult ; Adolescent ; *Automobile Driving/psychology ; *Psychomotor Performance/physiology ; *Executive Function/physiology ; *Multitasking Behavior/physiology ; Reaction Time/physiology ; *Attention/physiology ; },
abstract = {It is well established that performing multiple tasks simultaneously (dual-tasking) or sequentially (task-switching) degrades performance on one or both tasks. However, it is unknown whether task-switching adds to the effects of dual-tasking in a single setup. We investigated this in a simulated everyday-like car driving scenario. We expected an additive effect of task-switching on dual-tasking, leading to a stronger deterioration of driving performance due to the increased cognitive load required to handle multiple task-sets. Forty-five young adults aged 18 to 30 years (age: 23.62 ± 2.51, 28 females) were instructed to follow a lead car driving at a constant speed of 70 km/h through a rural landscape while concurrently performing additional tasks. The additional tasks were typing and arguing, in response to stimuli presented visually or auditorily. The tasks were presented either in separate blocks or in intermixed order (conditions: repetitive vs. switching). Driving performance was assessed by use of the average velocity and the standard deviation of lateral position, and performance in the additional tasks was assessed by reaction time. Linear-mixed effect models revealed better performance in the repetitive, compared to the switch condition only for the standard deviation of the lateral lane position while performing the additional typing task. This provides limited evidence for the view that task-switching adds to the challenges of dual-tasking. We therefore posit that already dual-tasking alone involves processing demands that are not substantially increased by adding switching demands.},
}
@article {pmid39923291,
year = {2025},
author = {de Melo, LRS and Dos Santos Pereira, J and Melo, MS and Andrade, LA and Bezerra-Santos, M and Lima, CA and Dos Santos, AD},
title = {Spatial and temporal dynamic of colorectal cancer mortality in Brazil: A nationwide population-based study of four decades (1980-2021).},
journal = {Cancer epidemiology},
volume = {95},
number = {},
pages = {102766},
doi = {10.1016/j.canep.2025.102766},
pmid = {39923291},
issn = {1877-783X},
mesh = {Humans ; Brazil/epidemiology ; *Colorectal Neoplasms/mortality ; Female ; Male ; Middle Aged ; Aged ; Adult ; Spatio-Temporal Analysis ; Mortality/trends ; Aged, 80 and over ; },
abstract = {BACKGROUND: Regardless of being preventable through screening strategies and prompt diagnosis, deaths from colorectal cancer (CRC) still represent a serious public health concern in Brazil, with more than 20 thousand deaths annually. Herein, we aimed to assess the temporal trends and spatiotemporal patterns of CRC mortality in all Brazilian states.<br><br>METHODS: An ecological study using temporal and spatial analysis techniques on deaths due to CRC as the underlying cause in Brazil from 1980 to 2021 was conducted. Death certificate and population data were provided by the Department of Informatics of the Unified Health System (DATASUS) and by the Brazilian Institute of Geography and Statistics (IBGE), respectively.<br><br>RESULTS: A total of 395,782 deaths from CRC were recorded in this period and most of them were in female (205,479; 51.92&#x202f;%), &#x2265;&#x202f;65 years old (233,059; 58.89&#x202f;%), diagnosed with malignant neoplasm of the colon (212,277; 53.63&#x202f;%), with 1-7 years of education (157.564; 39.81&#x202f;%), married (192.276; 48.58&#x202f;%), hospital as place of death (331.393; 83.73&#x202f;%) and white (212.666; 65.07&#x202f;%). Moreover, there was an increasing temporal trend in the Northeast region (APC: 2.6; p&#x202f;<&#x202f;0.05), men (APC: 1.5; p&#x202f;<&#x202f;0.05) and 45-64 years old (APC: 1.2; p&#x202f;<&#x202f;0.05). Also, the spatial analysis showed positive spatial autocorrelation in all periods, with the South and Southeast regions presenting the highest concentration of high-risk clusters CRC deaths. Nevertheless, high-risk clusters were also observed in capitals and municipalities in metropolitan regions in the Northeast region.<br><br>CONCLUSIONS: In general, a temporal and spatial expansion of CRC mortality has been observed in Brazil over the last few decades.},
}
@article {pmid39923474,
year = {2025},
author = {Lucca, E and Kofinas, D and Avellán, T and Kleemann, J and Mooren, CE and Blicharska, M and Teutschbein, C and Sperotto, A and Sušnik, J and Milliken, S and Fader, M and Đorđević, D and Dašić, T and Vasilić, V and Taiwo, B and Baubekova, A and Pineda-Martos, R and Spyropoulou, A and Baganz, GFM and El Jeitany, J and Oral, HV and Merheb, M and Castelli, G and Pagano, A and Sambo, B and Suškevičs, M and Arnold, M and Rađenović, T and Psomas, A and Masia, S and La Jeunesse, I and Amorocho-Daza, H and Das, SS and Bresci, E and Munaretto, S and Brouwer, F and Laspidou, C},
title = {Integrating "nature" in the water-energy-food Nexus: Current perspectives and future directions.},
journal = {The Science of the total environment},
volume = {966},
number = {},
pages = {178600},
doi = {10.1016/j.scitotenv.2025.178600},
pmid = {39923474},
issn = {1879-1026},
abstract = {Integrated approaches for managing natural resources are said to meet increasing demand for water, energy, and food, while maintaining the integrity of ecosystems, and ensuring equitable access to resources. The Water-Energy-Food (WEF) Nexus has been proposed as a cross-sectoral approach to manage trade-offs and exploit synergies that arise among these sectors. Although not initially included as a component of the Nexus, the role of nature in sustaining the water, energy, and food sectors and in regulating their interrelationships is increasingly recognised by Nexus researchers and practitioners. To converge existing approaches that integrate nature into the WEF Nexus and suggest a common framework, we - an interdisciplinary group of natural resources management researchers and systems thinkers from the European research network NEXUSNET COST Action - followed a collaborative process of knowledge creation combining literature review, elicitation of expert opinion and collaborative writing. Our results reveal a multiplicity of concepts utilised in the literature to represent, partially or fully, "nature" in the Nexus, such as "environment", "ecosystems", "ecosystem services", "social-ecological systems", and "biodiversity". Disparity was also found in the role attributed to nature, represented by three key paradigms: (1) ecosystems as the fourth component of an expanded Nexus, i.e., the WEF-Ecosystems (WEFE) Nexus; (2) ecosystems as a foundational layer to the Nexus; and (3) the WEF Nexus as a central component of social-ecological systems (SES). By creating a hybrid approach that brings together the benefits of the respective paradigms, we present a forward-looking WEFE Nexus conceptualisation. This paradigm expands the mutual interlinkages among water, energy and food to the entirety of SES, thus acknowledging the social-ecological processes that are affected by and affect the WEF Nexus. The results of this collaborative research effort intend to provide researchers and stakeholders with means to better understand and ultimately manage Nexus issues towards a transformative change.},
}
@article {pmid39925235,
year = {2025},
author = {Shi, T and Gao, Z and Zhang, Y and Rausher, MD and Chen, J},
title = {A Strategy of Assessing Gene Copy Number Differentiation Between Populations Using Ultra-Fast De Novo Assembly of Next-Generation Sequencing Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14080},
doi = {10.1111/1755-0998.14080},
pmid = {39925235},
issn = {1755-0998},
support = {31570220//National Natural Science Foundation of China/ ; 31870208//National Natural Science Foundation of China/ ; 32170240//National Natural Science Foundation of China/ ; KFJ-BRP-007-009//Biological Resources Program, CAS/ ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *DNA Copy Number Variations ; *Computational Biology/methods ; *Genetics, Population/methods ; *Gene Dosage ; Sequence Analysis, DNA/methods ; },
abstract = {Gene duplication and loss play pivotal roles in the evolutionary dynamics of genomes, contributing to species phenotypic diversity and adaptation. However, detecting copy number variations (CNVs) in homoploid populations and newly-diverged species using short reads from next-generation sequencing (NGS) with traditional methods can often be challenging due to uneven read coverage caused by variations in GC content and the presence of repetitive sequences. To address these challenges, we developed a novel pipeline, ST4gCNV, which leverages ultra-fast de novo assemblies of NGS data to detect gene-specific CNVs between populations. The pipeline effectively reduces the variance of read coverage due to technical factors such as GC bias, providing a reliable CNV detection with a minimum sequencing depth of 10. We successfully apply ST4gCNV to the resequencing analysis of homoploid species Nelumbo nucifera and Nelumbo lutea (lotus). We reveal significant CNV-driven differentiation between these species, particularly in genes related to petal colour diversity such as those involved in the anthocyanin pathway. By highlighting the extensive gene duplication and loss events in Nelumbo, our study demonstrates the utility of ST4gCNV in population genomics and underscores its potential of integrating genomic CNV analysis with traditional SNP-based resequencing analysis.},
}
@article {pmid39928107,
year = {2025},
author = {Güneri, FD and Karaarslan, F and Özen, H and Odabaşi, E},
title = {Medical mud-pack treatment with different temperatures in patients with knee osteoarthritis.},
journal = {International journal of biometeorology},
volume = {69},
number = {9},
pages = {2071-2080},
pmid = {39928107},
issn = {1432-1254},
mesh = {Humans ; *Osteoarthritis, Knee/therapy ; Male ; Female ; Middle Aged ; Aged ; *Mud Therapy/methods ; Temperature ; Pain Measurement ; Treatment Outcome ; },
abstract = {To compare the effects of medical mud-pack (MMP) treatments applied at different temperatures on the pain and joint functions of patients with knee osteoarthritis (KOA). Kellgren Lawrence (KL) stage 3 or 4 KOA patients were included and randomized into three groups. Patients in groups 1, 2, and 3 took MMP treatment to both knees at 39 °C, 42 °C, and 45 °C, respectively. The treatment was performed for 12 days (only weekdays) and was 30 min long per day. The same blinded physician evaluated the patients at baseline and at the end of the treatment. The assessments were done before and after the intervention. The primary outcome was to achieve a minimal clinically important improvement (MCII) for KOA (decrease of at least 19 mm (-40.8%) on the VAS for pain, a decrease of 18.3 mm (-39%) on the patient's global assessment (PGA), and/or a decrease of at least 9.1 points (-26%) on the Western Ontario and McMaster Universities Osteoarthritis Index function subscale (WOMAC-FS). Secondary outcomes were pain (VAS), patient's global assessment (VAS), physician's global assessment (VAS), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Patient's health state, Patient Acceptable Symptom State (PASS). 217 patients were analyzed. Groups 1, 2, and 3 had 68, 81,68 patients, respectively. The MCII measurement revealed that MMP treatment did not show a significant difference between groups 2 and 3 (p > 0.05). Also, it was observed that more patients in groups 2 and 3 reached the MCII compared to group 1 (p < 0.001). For the secondary outcomes, significant improvements were observed within-group evaluations for each of the three groups (p < 0.001). Between groups comparisons, the improvements at the end of the treatment were found to be superior for group 2 and group 3 compared to group 1 (p < 0.001). There was no statistically significant difference between groups 2 and 3 for any parameters (p > 0.05). The number of patients who achieved the PASS was statistically lower for group 1 compared to groups 2 and 3 (p < 0.001). We observed significant improvements in all groups after treatment. The main result, as measured by MCII, suggests that MMP treatments at 42-45 °C is more effective than at 39 °C in managing severe KOA patients' pain and functional status. We found no significant difference in pain and joint function improvement between 42 °C and 45 °C after MMP.},
}
@article {pmid39929026,
year = {2025},
author = {Song, J and Zhou, S and Kwan, MP and Song, G and Long, J and Song, W},
title = {The time-lagged effect of noise exposure on noise annoyance: The role of temporal, spatial and social contexts.},
journal = {Social science &amp; medicine (1982)},
volume = {368},
number = {},
pages = {117817},
doi = {10.1016/j.socscimed.2025.117817},
pmid = {39929026},
issn = {1873-5347},
mesh = {Humans ; Male ; Female ; Ecological Momentary Assessment ; *Noise/adverse effects ; Adult ; *Environmental Exposure/adverse effects ; Time Factors ; Middle Aged ; },
abstract = {While some research has examined the time-lagged effect of restorative soundscape in specific contexts (e.g., parks), how the time-lagged effect of noise annoyance during people's daily activities may vary across different temporal, spatial, and social contexts remains largely unknown. To address this research gap, we utilized Ecological Momentary Assessment (EMA) data to measure people's real-time noise annoyance and activity diary data to assess their time-lagged noise annoyance. Real-time noise exposure was captured by portable noise sensors. We employed fixed effects ordered panel logistic regression to examine the effects of different thresholds of noise levels on people's time-lagged noise annoyance, and how it varied across different temporal, spatial, and social contexts. The results indicated that: (1) there were significant time-lagged effects between participants' real-time noise exposure and their time-lagged noise annoyance; (2) participants' time-lagged noise annoyance associated with an activity was influenced by its temporal, spatial, and social contexts, particularly on weekdays; (3) participants' time-lagged noise annoyance was significantly associated with measured noise levels, with the highest coefficient for 65 dB, followed by 70 dB; and (4) there were significant interaction effects between noise levels and temporal-spatial-social contexts on participants' time-lagged noise annoyance (particularly when noise levels exceeded 70 dB). These findings enhance our understanding and have crucial implications for the implementation of noise control policies, which should consider not only noise levels but also the time-lagged effects of noise, particularly on weekdays, at outdoor recreational activity sites, as well as the potential vulnerabilities of individuals experiencing noise exposure in isolation.},
}
@article {pmid39931107,
year = {2024},
author = {Boyes, D and Murray, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Bird-cherry Ermine moth, Yponomeuta evonymella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {618},
pmid = {39931107},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Yponomeuta evonymella (the Bird-cherry Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence has a total length of 572.70 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the trivalent sex chromosomes Z 1, Z 2 and W. The mitochondrial genome has also been assembled and is 16.16 kilobases in length.},
}
@article {pmid39934908,
year = {2025},
author = {Wang, L and Simopoulos, CMA and Serrana, JM and Ning, Z and Li, Y and Sun, B and Yuan, J and Figeys, D and Li, L},
title = {PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {50},
pmid = {39934908},
issn = {2049-2618},
support = {201906015034//China Scholarship Council/ ; TECHNOMISE Program//Natural Sciences and Engineering Research Council of Canada/ ; 32370050//National Natural Science Foundation of China/ ; },
mesh = {*Phylogeny ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; *Proteomics/methods ; Humans ; *Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate. A more informative functional distance metric that incorporates evolutionary relatedness is needed to better understand microbiome functional dissimilarities.<br><br>RESULTS: Here, we introduce PhyloFunc, a novel functional beta-diversity metric that incorporates microbiome phylogeny to inform on metaproteomic functional distance. Leveraging the phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths to weigh between-sample functional distances for each taxon, rather than differences in taxonomic abundance as in weighted UniFrac. Proof of concept using a simulated toy dataset and a real dataset from mouse inoculated with a synthetic gut microbiome and fed different diets show that PhyloFunc successfully captured functional compensatory effects between phylogenetically related taxa. We further tested a third dataset of complex human gut microbiomes treated with five different drugs to compare PhyloFunc's performance with other traditional distance methods. PCoA and machine learning-based classification algorithms revealed higher sensitivity of PhyloFunc in microbiome responses to paracetamol. We provide PhyloFunc as an open-source Python package (available at https://pypi.org/project/phylofunc/), enabling efficient calculation of functional beta-diversity distances between a pair of samples or the generation of a distance matrix for all samples within a dataset.<br><br>CONCLUSIONS: Unlike traditional approaches that consider metaproteomics features as independent and unrelated, PhyloFunc acknowledges the role of phylogenetic context in shaping the functional landscape in metaproteomes. In particular, we report that PhyloFunc accounts for the functional compensatory effect of taxonomically related species. Its effectiveness, ecological relevance, and enhanced sensitivity in distinguishing group variations are demonstrated through the specific applications presented in this study. Video Abstract.},
}
@article {pmid39934999,
year = {2025},
author = {De Moor, D and Skelton, M and , and Amici, F and Arlet, ME and Balasubramaniam, KN and Ballesta, S and Berghänel, A and Berman, CM and Bernstein, SK and Bhattacharjee, D and Bliss-Moreau, E and Brotcorne, F and Butovskaya, M and Campbell, LAD and Carosi, M and Chatterjee, M and Cooper, MA and Cowl, VB and De la O, C and De Marco, A and Dettmer, AM and Dhawale, AK and Erinjery, JJ and Evans, CL and Fischer, J and García-Nisa, I and Giraud, G and Hammer, R and Hansen, MF and Holzner, A and Kaburu, S and Konečná, M and Kumara, HN and Larrivaz, M and Leca, JB and Legrand, M and Lehmann, J and Li, JH and Lezé, AS and MacIntosh, A and Majolo, B and Maréchal, L and Marty, PR and Massen, JJM and Maulany, RI and McCowan, B and McFarland, R and Merieau, P and Meunier, H and Micheletta, J and Mishra, PS and Sah, SAM and Molesti, S and Morrow, KS and Müller-Klein, N and Ngakan, PO and Palagi, E and Petit, O and Pflüger, LS and di Sorrentino, EP and Raghaven, R and Raimbault, G and Ram, S and Reichard, UH and Riley, EP and Rincon, AV and Ruppert, N and Sadoughi, B and Santhosh, K and Schino, G and Sheeran, LK and Silk, JB and Singh, M and Sinha, A and Sosa, S and Stribos, MS and Sueur, C and Tiddi, B and Tkaczynski, PJ and Trebouet, F and Widdig, A and Whitehouse, J and Wooddell, LJ and Xia, DP and von Fersen, L and Young, C and Schülke, O and Ostner, J and Neumann, C and Duboscq, J and Brent, LJN},
title = {MacaqueNet: Advancing comparative behavioural research through large-scale collaboration.},
journal = {The Journal of animal ecology},
volume = {94},
number = {4},
pages = {519-534},
pmid = {39934999},
issn = {1365-2656},
support = {864461//H2020 European Research Council/ ; LSC-AF2023_03//Leibniz ScienceCampus EEGA/ ; },
mesh = {Animals ; *Databases, Factual ; *Behavior, Animal ; *Social Behavior ; *Macaca ; *Behavioral Research ; Cooperative Behavior ; },
abstract = {There is a vast and ever-accumulating amount of behavioural data on individually recognised animals, an incredible resource to shed light on the ecological and evolutionary drivers of variation in animal behaviour. Yet, the full potential of such data lies in comparative research across taxa with distinct life histories and ecologies. Substantial challenges impede systematic comparisons, one of which is the lack of persistent, accessible and standardised databases. Big-team approaches to building standardised databases offer a solution to facilitating reliable cross-species comparisons. By sharing both data and expertise among researchers, these approaches ensure that valuable data, which might otherwise go unused, become easier to discover, repurpose and synthesise. Additionally, such large-scale collaborations promote a culture of sharing within the research community, incentivising researchers to contribute their data by ensuring their interests are considered through clear sharing guidelines. Active communication with the data contributors during the standardisation process also helps avoid misinterpretation of the data, ultimately improving the reliability of comparative databases. Here, we introduce MacaqueNet, a global collaboration of over 100 researchers (https://macaquenet.github.io/) aimed at unlocking the wealth of cross-species data for research on macaque social behaviour. The MacaqueNet database encompasses data from 1981 to the present on 61 populations across 14 species and is the first publicly searchable and standardised database on affiliative and agonistic animal social behaviour. We describe the establishment of MacaqueNet, from the steps we took to start a large-scale collective, to the creation of a cross-species collaborative database and the implementation of data entry and retrieval protocols. We share MacaqueNet's component resources: an R package for data standardisation, website code, the relational database structure, a glossary and data sharing terms of use. With all these components openly accessible, MacaqueNet can act as a fully replicable template for future endeavours establishing large-scale collaborative comparative databases.},
}
@article {pmid39936183,
year = {2025},
author = {Brait, N and Hackl, T and Lequime, S},
title = {detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14083},
pmid = {39936183},
issn = {1755-0998},
mesh = {*Computational Biology/methods ; *Genomics/methods ; *Software ; Genome, Viral ; *Viruses/genetics ; Sensitivity and Specificity ; },
abstract = {Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.},
}
@article {pmid39936843,
year = {2025},
author = {Kim, KK and Backonja, U},
title = {Digital health equity frameworks and key concepts: a scoping review.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {32},
number = {5},
pages = {932-944},
pmid = {39936843},
issn = {1527-974X},
support = {//The MITRE Innovation Program/ ; //MITRE Corporation/ ; //MITRE Innovation Program/ ; },
mesh = {*Health Equity ; Humans ; *Telemedicine ; Digital Health ; },
abstract = {OBJECTIVES: Digital health equity, the opportunity for all to engage with digital health tools to support good health outcomes, is an emerging priority across the world. The field of digital health equity would benefit from a comprehensive and systematic understanding of digital health, digital equity, and health equity, with a focus on real-world applications. We conducted a scoping review to identify and describe published frameworks and concepts relevant to digital health equity interventions.<br><br>MATERIALS AND METHODS: We conducted a scoping review of published peer-reviewed literature guided by the PRISMA Extension for Scoping Reviews. We searched 5 databases for frameworks related to or applied to digital health or equity interventions. Using deductive and inductive approaches, we analyzed frameworks and concepts based on the socio-ecological model.<br><br>RESULTS: Of the 910 publications initially identified, we included 44 (4.8%) publications in our review that described 42 frameworks that sought to explain the ecosystem of digital and/or health equity, but none were comprehensive. From the frameworks we identified 243 concepts grouped into 43 categories including characteristics of individuals, communities, and organizations; societal context; perceived value of the intervention by and impacts on individuals, community members, and the organization; partnerships; and access to digital health services, in-person services, digital services, and data and information, among others.<br><br>DISCUSSION: We suggest a consolidated definition of digital health equity, highlight illustrative frameworks, and suggest concepts that may be needed to enhance digital health equity intervention development and evaluation.<br><br>CONCLUSION: The expanded understanding of frameworks and relevant concepts resulting from this study may inform communities and stakeholders who seek to achieve digital inclusion and digital health equity.},
}
@article {pmid39937595,
year = {2025},
author = {Royaux, C and Mihoub, JB and Jossé, M and Pelletier, D and Norvez, O and Reecht, Y and Fouilloux, A and Rasche, H and Hiltemann, S and Batut, B and Marc, E and Seguineau, P and Massé, G and Amossé, A and Bissery, C and Lorrilliere, R and Martin, A and Bas, Y and Virgoulay, T and Chambon, V and Arnaud, E and Michon, E and Urfer, C and Trigodet, E and Delannoy, M and Loïs, G and Julliard, R and Grüning, B and Le Bras, Y and , },
title = {Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {39937595},
issn = {2047-217X},
support = {2020-1-NL01-KA203-064717//European Union/ ; //Agence Nationale de la Recherche/ ; //Mus&#xe9;um National d'Histoire Naturelle/ ; //Ministry of Higher Education and Research/ ; },
mesh = {*Ecology/methods/standards ; *Software ; *Data Analysis ; Reproducibility of Results ; *Computational Biology/methods/standards ; },
abstract = {Numerous conceptual frameworks exist for best practices in research data and analysis (e.g., Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology. Here, we propose a practical and operational framework for researchers and experts in ecology to achieve best practices for building analytical procedures from individual research projects to production-level analytical pipelines. We introduce the concept of atomization to identify analytical steps that support generalization by allowing us to go beyond single analyses. The term atomization is employed to convey the idea of single analytical steps as "atoms" composing an analytical procedure. When generalized, "atoms" can be used in more than a single case analysis. These guidelines were established during the development of the Galaxy-Ecology initiative, a web platform dedicated to data analysis in ecology. Galaxy-Ecology allows us to demonstrate a way to reach higher levels of reproducibility in ecological sciences by increasing the accessibility and reusability of analytical workflows once atomized and generalized.},
}
@article {pmid39938295,
year = {2025},
author = {Zhuo, W and Wu, N and Shi, R and Cui, Y and Zhang, C and Liu, S and Zhu, F and Zhang, B and Liu, P},
title = {Assessing the impacts of reclamation and invasion on ecological dynamics of coastal wetland vegetation in the Yangtze Estuary from 1985 to 2019:A case study of Chongming Island, China.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124505},
doi = {10.1016/j.jenvman.2025.124505},
pmid = {39938295},
issn = {1095-8630},
mesh = {*Wetlands ; China ; *Estuaries ; *Introduced Species ; Ecosystem ; *Conservation of Natural Resources ; Humans ; Climate Change ; },
abstract = {The distribution of coastal wetland vegetation is influenced by biological invasions, human reclamations and climate changes, which continually reshape vegetation structures. However, limited attention has been given to the impact of biological invasion on native vegetation and tidal wetlands. This study focuses on the wetlands of Chongming Island, employing a multi-feature dataset combining spectral, phenological, and temporal information on the Google Earth Engine (GEE) platform. Using the Random Forest (RF) classification method, we analyzed annual vegetation distribution changes and examined the distinct effects of natural and anthropogenic factors. The research results indicate that: (1) From 1985 to 2019, the total area of Chongming Island expanded, while wetland vegetation decreased due to embankment construction and island connection projects. (2) The total area of wetland vegetation on Chongming Island dropped to its lowest point in 2002 (3812.76 ha), and then gradually recovered. (3) Human reclamation was the primary driver of vegetation changes from 1985 to 1995. (4) Vegetation distribution in Dongtan was influenced by both human and natural factors, whereas Beiliuyao affected by the invasion and expansion of the S. alterniflor. These findings provide valuable insights into the drivers of long-term vegetation distribution changes, offering essential data and theoretical support for sustainable development and management of Chongming Island's ecosystems.},
}
@article {pmid39938845,
year = {2025},
author = {Rakkannan, G and Mohanty, AK and Das, II and Nayak, S and Sahoo, L and Kumar, R and Rasal, A and Rather, MA and Ahmad, I and Sundaray, JK},
title = {Triflumezopyrim induced oxidative stress, DNA damage and apoptosis on Labeo rohita: Insights from Bioinformatics, Histopathological and Molecular approaches.},
journal = {International journal of biological macromolecules},
volume = {304},
number = {Pt 2},
pages = {140911},
doi = {10.1016/j.ijbiomac.2025.140911},
pmid = {39938845},
issn = {1879-0003},
mesh = {Animals ; *Oxidative Stress/drug effects ; *DNA Damage/drug effects ; *Apoptosis/drug effects ; *Computational Biology/methods ; Molecular Docking Simulation ; *Carps/metabolism/genetics ; Liver/drug effects/pathology/metabolism ; Cyprinidae ; 8-Hydroxy-2'-Deoxyguanosine ; Water Pollutants, Chemical/toxicity ; },
abstract = {Triflumezopyrim is a novel mesoionic pesticide used in Asian rice fields to control brown plant hopper, which can reach aquatic environments through drift during application or surface runoff. Thus, this study aimed to investigate the effect of chronic exposure of sub-lethal concentrations of triflumezopyrim (2.468 ppm, 1.480 ppm, and 0.740 ppm) on freshwater carp, Labeo rohita.This study encompassed a multi-pronged approach, including molecular docking studies to elucidate the interactions between triflumezopyrim and selected proteins, an assessment of 8-OHdG (8-hydroxy-2-deoxyguanosine) activity to gauge DNA damage, histopathological examinations to identify cellular alterations, and expression of genes involved in oxidative stress, DNA repair, and apoptosis in L. rohita. We observed dose-dependent responses in 8-OHdG activity and the expression of select genes, with higher concentrations of triflumezopyrim yielding more pronounced transcriptional alterations. Notably, histopathological examinations of liver and brain tissues vividly portrayed the impact of triflumezopyrim on L. rohita. These findings contribute to the assessment of biological toxicity and the environmental footprint left by chemical pollutants such as triflumezopyrim. The study emphasizes the crucial role of monitoring histopathological alterations, 8-OHdG activity and gene expression changes as potential biomarkers for assessing exposures to triflumezopyrim. This research provides valuable insights into the ecological implications of triflumezopyrim in aquatic ecosystems.},
}
@article {pmid39943576,
year = {2025},
author = {Cleveland, P and Morrison, A},
title = {Sông Sài Gòn: Extreme Plastic Pollution Pathways in Riparian Waterways.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {3},
pages = {},
pmid = {39943576},
issn = {1424-8220},
support = {2023//Annual Award, School of Future Environments, Auckland University of Techolology/ ; },
mesh = {*Plastics/analysis ; *Rivers/chemistry ; *Environmental Monitoring/methods ; Vietnam ; Geographic Information Systems ; *Water Pollutants, Chemical/analysis ; },
abstract = {Plastic pollution in waterways poses a significant global challenge, largely stemming from land-based sources and subsequently transported by rivers to marine environments. With a substantial percentage of marine plastic waste originating from land-based sources, comprehending the trajectory and temporal experience of single-use plastic bottles assumes paramount importance. This project designed, developed, and released a plastic pollution tracking device, coinciding with Vietnam's annual Plastic Awareness Month. By mapping the plastic tracker's journey through the Saigon River, this study generated high-fidelity data for comprehensive analysis and bolstered public awareness through regular updates on the Re-Think Plastics Vietnam website. The device, equipped with technologies such as drone flight controller, open-source software, embedded computing, and cellular networking effectively captured GPS position, track, and localized conditions experienced by the plastic bottle tracker on its journey. This amalgamation of data contributes to the understanding of plastic pollution behaviors and serves as a data set for future initiatives aimed at plastic prevention in the ecologically sensitive Mekong Delta. By illuminating the transportation of single-use plastic bottles in the riparian waterways of Ho Chi Minh City and beyond, this study plays a role in collective efforts to understand plastic pollution and preserve aquatic ecosystems. By deploying a GPS-enabled plastic tracker, this study provides novel, high-resolution empirical data on plastic transport in urban tidal systems. These findings contribute to improving waste interception strategies and informing environmental policies aimed at reducing plastic accumulation in critical retention zones.},
}
@article {pmid39945053,
year = {2025},
author = {Tittes, S and Lorant, A and McGinty, SP and Holland, JB and de Jesus Sánchez-González, J and Seetharam, A and Tenaillon, M and Ross-Ibarra, J},
title = {The population genetics of convergent adaptation in maize and teosinte is not locally restricted.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {39945053},
issn = {2050-084X},
support = {1822330//National Science Foundation/ ; 1238014//National Science Foundation/ ; CA-D-PLS-2066-H 548//U.S. Department of Agriculture/ ; },
mesh = {*Genetics, Population ; *Zea mays/genetics ; *Adaptation, Physiological/genetics ; Gene Flow ; Genetic Variation ; Inbreeding ; Mutation ; Selection, Genetic ; Sympatry/genetics ; },
abstract = {What is the genetic architecture of local adaptation and what is the geographic scale over which it operates? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea mays subsp. parviglumis). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are also frequently shared by several populations, and often between subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations but smaller than the species range.},
}
@article {pmid39948527,
year = {2025},
author = {Rakshasa-Loots, AM and Steyn, C and Swiffen, D and Marwick, KFM and Semple, RK and Reynolds, RM and Burgess, K and Lawrie, SM and Lightman, SL and Luz, S and Smith, DJ},
title = {Metabolic biomarkers of clinical outcomes in severe mental illness (METPSY): protocol for a prospective observational study in the Hub for metabolic psychiatry.},
journal = {BMC psychiatry},
volume = {25},
number = {1},
pages = {122},
pmid = {39948527},
issn = {1471-244X},
support = {MR/Z503563/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Young Adult ; Biomarkers/blood ; *Bipolar Disorder/metabolism/blood ; *Major Depressive Disorder/metabolism/blood ; Metabolomics ; Prospective Studies ; *Schizophrenia/metabolism/blood ; Scotland ; Observational Studies as Topic ; },
abstract = {People with severe mental illness have high rates of obesity, type 2 diabetes, and cardiovascular disease. Emerging evidence suggests that metabolic dysfunction may be causally linked to the risk of severe mental illness. However, more research is needed to identify reliable metabolic markers which may have an impact on mental health outcomes, and to determine the mechanisms behind their impact. In the METPSY research study, we will investigate the relationship between metabolic markers and clinical outcomes of severe mental illness in young adults. We will recruit 120 young adults aged 16-25 years living in Scotland with major depressive disorder, bipolar disorder, schizophrenia, or no severe mental illness (controls) for a prospective observational study. We will assess clinical symptoms at three in-person visits (baseline, 6 months, and 12 months) using the Structured Clinical Interview for DSM-5, and collect blood samples at each of these visits for agnostic profiling of metabolic biomarkers through an untargeted metabolomic screen, using the rapid hydrophilic interaction liquid chromatography ion mobility mass spectrometry method (RHIMMS). Participants will also complete remote assessments at 3 and 9 months after the baseline visit: Ecological Momentary Assessments to measure mental health, wrist actigraphy to measure rhythms of rest and activity, and continuous glucose monitoring to measure metabolic changes. Throughout the 12-month enrolment period, we will also measure objective markers of sleep using a radar sleep monitor (Somnofy). Using advanced statistical techniques and machine learning analysis, we will seek to better understand the mechanisms linking metabolic health with mental health in young adults with schizophrenia, bipolar disorder, and severe depression. Clinical trial number: Not applicable.},
}
@article {pmid39949385,
year = {2023},
author = {Lohse, K and , and , and , and Vila, R and , },
title = {The genome sequence of the Common Blue, Polyommatus icarus (Rottemburg, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {72},
pmid = {39949385},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Polyommatus icarus (the Common Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 512 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the assembled Z chromosome. The mitochondrial genome has also been assembled and is 15.6 kilobases long. Gene annotation of this assembly on Ensembl identified 13,350 protein-coding genes.},
}
@article {pmid39952461,
year = {2025},
author = {Shi, W and Lu, P and Yang, H and Han, J and Wang, Q},
title = {Quantifying the relative importance of natural and human factors on vegetation dynamics in China's western frontiers during 2010-2021.},
journal = {Environmental research},
volume = {271},
number = {},
pages = {121120},
doi = {10.1016/j.envres.2025.121120},
pmid = {39952461},
issn = {1096-0953},
mesh = {China ; *Conservation of Natural Resources ; Humans ; *Ecosystem ; *Environmental Monitoring ; *Plant Development ; },
abstract = {Vegetation is a core component of terrestrial ecosystems, thus understanding the drivers of its dynamics is crucial for ecological conservation and management, especially in regions rich in natural resources but ecologically fragile. Here, we examined vegetation cover changes in China's western frontiers and quantified the relative importance of key drivers of vegetation dynamics. First, we employed the Dimidiate Pixel Model (DPM) via Google Earth Engine (GEE) to estimate fractional vegetation cover (FVC), followed by trend analysis using the Theil-Sen median and Mann-Kendall methods to examine FVC dynamics from 2010 to 2021. Next, we applied the optimal parameter-based geographic detector (OPGD) to further assess the impact of natural (ie., temperature, precipitation, and elevation) and human (ie., land use and population density) factors on FVC. Our results revealed that approximately 61.26% of the vegetation-covered regions in China's western frontiers have shown improvement. In Xinjiang, population density, land use, and precipitation were the primary drivers of FVC changes, with Q values exceeding 0.20. In Xizang, precipitation, elevation, temperature, and land use changes were the dominant drivers, with Q values greater than 0.30. Furthermore, interactions between natural and human factors significantly influenced FVC variation. Our findings have the potential to provide references for promoting sustainable vegetation management in western China.},
}
@article {pmid39952543,
year = {2025},
author = {Chaemsaithong, P and Romero, R and Pongchaikul, P and Warintaksa, P and Mongkolsuk, P and Bhuwapathanapun, M and Kotchompoo, K and Nimsamer, P and Kruasuwan, W and Amnuaykiatlert, O and Vivithanaporn, P and Meyyazhagan, A and Awonuga, A and Settacomkul, R and Singhsnaeh, A and Laolerd, W and Santanirand, P and Thaipisuttikul, I and Wongsurawat, T and Jenjaroenpun, P},
title = {The rapid diagnosis of intraamniotic infection with nanopore sequencing.},
journal = {American journal of obstetrics and gynecology},
volume = {233},
number = {3},
pages = {193.e1-193.e18},
doi = {10.1016/j.ajog.2025.02.011},
pmid = {39952543},
issn = {1097-6868},
mesh = {Humans ; Pregnancy ; Female ; *Amniotic Fluid/microbiology/chemistry ; *Chorioamnionitis/diagnosis/microbiology ; Prospective Studies ; Adult ; RNA, Ribosomal, 16S/genetics ; *Nanopore Sequencing ; Interleukin-6/analysis/metabolism ; Premature Rupture of Fetal Membranes/microbiology ; Obstetric Labor, Premature/microbiology ; Polymerase Chain Reaction ; *Pregnancy Complications, Infectious/diagnosis/microbiology ; },
abstract = {BACKGROUND: Intraamniotic infection (defined as intraamniotic inflammation with microorganisms) is an important cause of the preterm labor syndrome. Methods for the detection of microorganisms in amniotic fluid are culture and/or polymerase chain reaction assay. However, both methods take time, and the results are rarely available for clinical decision-making. Nanopore sequencing technology offers real-time, long-read sequencing that can produce rapid results.<br><br>OBJECTIVE: To determine 1) the diagnostic performance of the 16S rDNA nanopore sequencing method for the identification of microorganisms in patients with intraamniotic inflammation and 2) the relationship between microbial burden and the intensity of the amniotic fluid inflammatory response.<br><br>STUDY DESIGN: We performed a prospective cohort study that included singleton pregnancies presenting with symptoms of preterm labor with intact membranes or of preterm prelabor rupture of the membranes. Amniotic fluid samples were obtained for the evaluation of bacteria in the amniotic cavity using cultivation and polymerase chain reaction-based 16S Sanger sequencing methods. Participants were classified into 4 groups according to the results of an amniotic fluid culture, 16S Sanger sequencing, and an amniotic fluid interleukin 6 concentration: 1) no intraamniotic infection and intraamniotic inflammation (interleukin 6 <2.6 ng/mL, and no microorganisms in the amniotic cavity, as determined by culture or 16S Sanger sequencing); 2) microbial invasion of the amniotic cavity without intraamniotic inflammation, defined by the presence of bacteria detected by culture or 16S Sanger sequencing; 3) sterile intraamniotic inflammation (interleukin 6 &#x2265;2.6 ng/mL without microbial invasion of the amniotic cavity); and 4) intraamniotic infection (interkeukin 6 &#x2265;2.6 ng/mL with microbial invasion of the amniotic cavity). Patients who underwent a mid-trimester amniocentesis, had no intraamniotic infection or intraamniotic inflammation, and delivered at term represented the control group. 16S rDNA nanopore sequencing was performed and the diagnostic indices for the identification of intraamniotic infection were determined. Bioinformatic analysis was carried out to identify microorganisms, and a read count of at least 100 or a read count exceeding that of the background species from the control group, along with a relative abundance of no less than 1%, was used.<br><br>RESULTS: 1) The 16S nanopore sequencing had a sensitivity of 88.9% (8/9), specificity of 95.4% (41/43), positive predictive value of 80.0% (8/10), negative predictive value of 97.6% (41/42), positive likelihood ratio of 19.1 (95% confidence interval, 4.8-75.4), negative likelihood ratio of 0.1 (95% confidence interval, 0.02-0.7), and an accuracy of 94.2% (49/52) for the identification of intraamniotic infection (prevalence, 17% [9/52]); 2) the microbial load determined by the 16S nanopore sequencing had a strong positive correlation with the intensity of an intraamniotic inflammatory response (amniotic fluid interleukin 6 concentration; Spearman's correlation 0.9; P=.002); and 3) a subgroup of patients with intraamniotic inflammation did not have bacteria determined by culture, Sanger sequencing, or nanopore 16S, thus confirming the existence of sterile intraamniotic inflammation.<br><br>CONCLUSION: The 16S nanopore sequencing has high diagnostic indices, predictive values, likelihood ratios, and accuracy in the diagnosis of intraamniotic infection.},
}
@article {pmid39952648,
year = {2025},
author = {Siddiqui, JA and Fan, R and Liu, Y and Syed, AH and Benlin, Y and Chu, Q and Ding, Z and Ghani, MI and Liu, X and Wakil, W and Liu, DD and Chen, X and Cernava, T and Smagghe, G},
title = {The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure.},
journal = {Insect molecular biology},
volume = {34},
number = {3},
pages = {452-469},
doi = {10.1111/imb.12983},
pmid = {39952648},
issn = {1365-2583},
support = {32360705//National Natural Science Foundation of China/ ; 31960555//National Natural Science Foundation of China/ ; GCC[2023]070//Guizhou Provincial Science and Technology Program/ ; HZJD[2022]001//Guizhou Provincial Science and Technology Program/ ; 2019-1410//Guizhou Provincial Science and Technology Program/ ; [2023]1-4//Guiyang Science and Technology Program/ ; D20023//Program for Introducing Talents to Chinese Universities/ ; },
mesh = {Animals ; *Spodoptera/microbiology/growth &amp; development/drug effects ; *Gastrointestinal Microbiome/drug effects ; Larva/microbiology/drug effects/growth &amp; development ; *Insecticides/pharmacology ; *Bacteria/drug effects/genetics/classification/metabolism/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.},
}
@article {pmid39955351,
year = {2025},
author = {Yang, Y and Yang, Y and Yang, S and Zhang, J},
title = {Pollution control mechanism of national water network with water quality differences based on differential game and case study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5588},
pmid = {39955351},
issn = {2045-2322},
support = {51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; },
abstract = {The construction of the national water network optimizes water resource allocation but also causes a redistribution of pollutants due to water quality differences, posing urgent challenges for water pollution management. Taking the South-to-North Water Diversion Project and Yangtze-to-Hanjiang River Water Diversion Project (YHRWDP) as an example and considering the pressure brought by the redistribution of pollutants to the polluting enterprises (PE) and water diversion enterprises (WDE) situated in areas where pollution is aggravated, a differential game model of pollution control among the central government, water-supply area (WSA), PE and WDE is constructed based on the cost-sharing mechanism. The results show that: (1) The pressure coefficient has an apparent negative correlation with the effort level of the affected subject. (2) An increase in the amount of pollution elimination per unit of pollution control effort of WSA and PE will lead to their own investment in more efforts to improve the ecology of the basin, thus benefiting all participants in the system. (3) The cost-sharing rate of the central government on the WSA of the YHRWDP, the PE, and the WDE is influenced by several factors, which shows a stable monotonically increasing or decreasing relation. The results are an useful supplement to the research on natural river pollution control, and can also provide a reference for designing pollution control mechanisms of national water network.},
}
@article {pmid39957502,
year = {2025},
author = {Latini, L and Burini, G and Mazza, V and Grignani, G and De Donno, R and Bello, E and Tricarico, E and Malavasi, S and Nascetti, G and Canestrelli, D and Carere, C},
title = {Early-life environment shapes claw bilateral asymmetry in the European lobster (Homarus gammarus).},
journal = {Biology open},
volume = {14},
number = {3},
pages = {},
pmid = {39957502},
issn = {2046-6390},
support = {//Universite degli Studi della Tuscia/ ; //Universite degli Studi di Firenze/ ; //Universite Ca' Foscari Venezia/ ; //University of Florence/ ; },
mesh = {Animals ; *Nephropidae/growth &amp; development/anatomy &amp; histology/physiology ; *Environment ; *Hoof and Claw/anatomy &amp; histology/growth &amp; development ; },
abstract = {Developmental plasticity refers to an organism's ability to adjust its development in response to changing environmental conditions, leading to changes in behaviour, physiology, or morphology. This adaptability is crucial for survival and helps organisms to cope with environmental challenges throughout their lives. Understanding the mechanisms underlying developmental plasticity, particularly how environmental and ontogenetic factors shape functional traits, is fundamental for both evolutionary biology and conservation efforts. In this study we investigated the effects of early-life environmental conditions on the development of claw asymmetry in juvenile European lobsters (Homarus gammarus, N=244), a functional trait essential for survival and ecological success. Juveniles were randomly divided between four different rearing conditions characterized by the presence or absence of physical enrichments (e.g. substrate and shelters), which were introduced at different developmental stages in separated groups to assess the timing and nature of their effect. Results revealed that exposure to substrate alone, without additional stimuli, consistently promoted claw asymmetry, regardless of the timing of its introduction, while the 6th developmental stage emerged as the critical period for claw differentiation. By identifying the environmental factors that influence developmental outcomes in lobsters, and the timing of these effects, this study improves our understanding of developmental plasticity and offers valuable insights for optimizing conservation aquaculture and reintroduction strategies.},
}
@article {pmid39960184,
year = {2025},
author = {Ferdousee, S and Alam, MS and Hwangbo, M and Kim, J},
title = {Visualizing Methane-Cycling Microbial Dynamics in Coastal Wetlands.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {215},
pages = {},
doi = {10.3791/67715},
pmid = {39960184},
issn = {1940-087X},
mesh = {*Methane/metabolism ; *Wetlands ; Texas ; Geographic Information Systems ; Seashore ; },
abstract = {Coastal wetlands are the largest biotic source of methane, where methanogens convert organic matter into methane and methanotrophs oxidize methane, thus playing a critical role in regulating the methane cycle. The wetlands in South Texas, which are subject to frequent weather events, fluctuating salinity levels, and anthropogenic activities due to climate change, influence methane cycling. Despite the ecological importance of these processes, methane cycling in South Texas coastal wetlands remains insufficiently explored. To address this gap, we developed and optimized a method for detecting genes related to methanogens and methanotrophs, including mcrA as a biomarker for methanogens and pmoA1, pmoA2, and mmoX as biomarkers for methanotrophs. Additionally, this study aimed to visualize the spatial and temporal distribution patterns of methanogen and methanotroph abundance utilizing the geographic information system (GIS) software ArcGIS Pro. The integration of these molecular techniques with advanced geospatial visualization provided critical insights into the spatial and temporal distribution of methanogen and methanotroph communities across South Texas wetlands. Thus, the methodology established in this study offers a robust framework for mapping microbial dynamics in wetlands, enhancing our understanding of methane cycling under varying environmental conditions, and supporting broader ecological and environmental change studies.},
}
@article {pmid39963041,
year = {2025},
author = {Lima-Cordón, R and Mohabir, JT and Sooklall, M and Zurita, AM and Shieh, M and Knox, C and Gobran, S and Johnson, Z and Laws, M and Panchal, R and Niles-Robin, R and Cox, H and Grillet, ME and Moreno, JE and Herrera, S and Quinones, M and Early, AM and Tennessen, JA and Neafsey, DE},
title = {A Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14088},
pmid = {39963041},
issn = {1755-0998},
support = {U19 AI110818/AI/NIAID NIH HHS/United States ; U19AI110818//National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services/ ; INV-009416/GATES/Gates Foundation/United States ; INV-009416/GATES/Gates Foundation/United States ; },
mesh = {Animals ; *Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; *Sequence Analysis, DNA/methods ; *Diptera/genetics/classification ; *Insect Vectors/classification/genetics/parasitology ; Anopheles/genetics/parasitology/classification ; Humans ; *Disease Vectors ; },
abstract = {Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.},
}
@article {pmid39963945,
year = {2025},
author = {Giglio, VJ and Adelir-Alves, J and Balzaretti Merino, N and Bravo-Olivas, ML and Camp, EF and Casoli, E and Chávez-Dagostino, RM and Ferretti, E and Fraser, D and Grillo, AC and Jiménez-Guiérrez, S and Leite, KL and Lucrezi, S and Luiz, OJ and Luna-Pérez, B and McBride, J and Milanese, M and Moity, N and Pinheiro, JV and Renfro, B and Roche, R and Saliba, BM and Sara, A and Schiavetti, A and Toso, Y and Valle-Pérez, C and Ferreira, CEL},
title = {DiverReef: A global database of the behavior of recreational divers and their interactions with reefs over 20 years.},
journal = {Ecology},
volume = {106},
number = {2},
pages = {e4519},
doi = {10.1002/ecy.4519},
pmid = {39963945},
issn = {1939-9170},
support = {17/22273-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 111.210/2014//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {*Diving ; *Coral Reefs ; Animals ; *Databases, Factual ; *Recreation ; Humans ; Time Factors ; },
abstract = {Recreational diving is an important activity in reef environments worldwide, providing income and employment for coastal communities and connecting visiting divers to these ecosystems promoting conservation and stewardship. However, if poorly managed, diving has the potential to cause detrimental effects on benthic communities via mechanical damage caused by physical contact of divers with the reef, often in the form of unintentional fin kicks resulting from poor buoyancy. Understanding diver-reef interaction patterns is important to elucidate the potential impacts of diving tourism on the reef biota. The DiverReef database provides the first public dataset on the underwater behavior of recreational divers in shallow reef environments (<25 m depth) globally and their interactions with the reef seascape and/or reef benthic sessile organisms. The dataset comprises 20 years of data (2004-2023) by observing the behavior of 2311 recreational divers in nine countries at 19 diving destinations and 176 diving sites; 93% of the observations were in marine protected areas. The data were collected through on-site observations of divers' behavior during tourism activities and their physical interactions with the reef structure and/or benthic sessile reef organisms. Observers discreetly followed divers and recorded their behavior and interactions with the reef over set periods. Interactions were described as "contact" or "damage," the latter referring to when physical damage to a benthic organism or the reef structure was observed. Besides behavior, observers also recorded data on the type of diving activity (scuba or snorkeling), profiles of the divers (gender and experience), use of cameras by the divers, visibility, type of reef formation, and marine protection status of the dive site. The authors of this research expect that the data provided will be useful in advancing knowledge of how divers interact with reefs and in developing strategies to mitigate the potential detrimental effects of the diving industry on reef biota. Part of the data has already been used in reports and scientific articles. This dataset can be freely used for noncommercial purposes; we request that users of these data cite this data paper in all publications resulting from the use of this dataset.},
}
@article {pmid39968615,
year = {2025},
author = {Klarevas-Irby, JA and Nyaguthii, B and Farine, DR},
title = {Moving as a group imposes constraints on the energetic efficiency of movement.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2041},
pages = {20242760},
pmid = {39968615},
issn = {1471-2954},
support = {//Centre for the Advanced Study of Collective Behaviour/ ; //Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //Association for the Study of Animal Behaviour/ ; //H2020 European Research Council/ ; //Max Planck Society/ ; //Deutsche Forschungsgemeinschaft/ ; //Max Planck-Yale Center for Biodiversity Movement and Global Change/ ; },
mesh = {Animals ; *Energy Metabolism ; Movement ; *Galliformes/physiology ; Geographic Information Systems ; },
abstract = {Movement is a key part of life for many species. In solitary animals, the energetic costs of movement can be mitigated through energetically efficient strategies that produce faster, straighter movements. However, little is known about whether moving as part of a collective enhances or limits the ability of individual group members to express such strategies. Drawing on 6 years of population-level, high-resolution (1 Hz) GPS tracking of group-living vulturine guineafowl (Acryllium vulturinum), we detected 886 events from 94 tagged individuals where their groups made large, range-shifting displacements in response to changing environmental conditions. We contrasted these movements with data from 94 similarly large displacement events by 19 lone, dispersing individuals. Our results suggest that individuals in groups can significantly reduce their energetic cost of transport when making large displacements (15.3% more efficient relative to their normal daily ranging) by increasing the speed and straightness of their movements. However, even during their most efficient movements, individuals in groups could not achieve or maintain comparable increases in speed to lone individuals, resulting in significantly limited efficiency gains (35.7% less efficient than solitary individuals). Overall, this study provides evidence for a substantial energetic cost arising from collective movement.},
}
@article {pmid39969100,
year = {2025},
author = {Miller, L and Beaney, T and Hope, R and Cunningham, M and Robotham, JV and Pouwels, KB and Costelloe, CE},
title = {General practice antibiotic prescriptions attributable to respiratory syncytial virus by age and antibiotic class: an ecological analysis of the English population.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {80},
number = {4},
pages = {1116-1126},
pmid = {39969100},
issn = {1460-2091},
support = {//University of Oxford/ ; NIHR200915//UK Health Security Agency (UKHSA)/ ; //National Institute for Health and Care Research (NIHR) Royal Marsden/ ; //Institute of Cancer Research Biomedical Research Centre/ ; //Healthcare Associated Infections and Antimicrobial Resistance/ ; 2016-10-95//NIHR/ ; MRF-145-0004-TPG-AVISO//Medical Research Foundation National PhD Training Programme in Antimicrobial Resistance Research/ ; /WT_/Wellcome Trust/United Kingdom ; //National Institute for Health Research Health Protection Research Unit (NIHR HPRU)/ ; //National Institute for Health Research Health Protection Research Unit/ ; },
mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/classification ; *Respiratory Syncytial Virus Infections/drug therapy/epidemiology ; Infant ; Child, Preschool ; Aged ; England/epidemiology ; Adult ; Middle Aged ; *Respiratory Tract Infections/drug therapy/virology ; *General Practice/statistics &amp; numerical data ; Young Adult ; Child ; Male ; Female ; Adolescent ; *Drug Prescriptions/statistics &amp; numerical data ; Age Factors ; Infant, Newborn ; Respiratory Syncytial Virus, Human ; Practice Patterns, Physicians'/statistics &amp; numerical data ; Aged, 80 and over ; },
abstract = {BACKGROUND: Respiratory syncytial virus (RSV) may contribute to a substantial volume of antibiotic prescriptions in primary care. However, data on the type of antibiotics prescribed for such infections are only available for children <5 years in the UK. Understanding the contribution of RSV to antibiotic prescribing would facilitate predicting the impact of RSV preventative measures on antibiotic use and resistance. The objective of this study was to estimate the proportion of antibiotic prescriptions in English general practice attributable to RSV by age and antibiotic class.<br><br>METHODS: Generalized additive models examined associations between weekly counts of general practice antibiotic prescriptions and laboratory-confirmed respiratory infections from 2015 to 2018, adjusting for temperature, practice holidays and remaining seasonal confounders. We used general practice records from the Clinical Practice Research Datalink and microbiology tests for RSV, influenza, rhinovirus, adenovirus, parainfluenza, human metapneumovirus, Mycoplasma pneumoniae and Streptococcus pneumoniae from England's Second Generation Surveillance System.<br><br>RESULTS: An estimated 2.1% of antibiotics were attributable to RSV, equating to an average of 640 000 prescriptions annually. Of these, adults &#x2265;75&#x2005;years contributed to the greatest volume, with an annual average of 149&#x200a;078 (95% credible interval: 93&#x200a;733-206&#x200a;045). Infants 6-23&#x2005;months had the highest average annual rate at 6580 prescriptions per 100&#x200a;000 individuals (95% credible interval: 4522-8651). Most RSV-attributable antibiotic prescriptions were penicillins, macrolides or tetracyclines. Adults &#x2265;65&#x2005;years had a wider range of antibiotic classes associated with RSV compared with younger age groups.<br><br>CONCLUSIONS: Interventions to reduce the burden of RSV, particularly in older adults, could complement current strategies to reduce antibiotic use in England.},
}
@article {pmid39969985,
year = {2025},
author = {Zhang, J and Gao, X and Liang, C and Zhang, M and Zhang, S},
title = {Spatiotemporal pattern evolution analysis of ecological networks based on morphological spatial pattern analysis: a case study of Ningbo City, China.},
journal = {Integrated environmental assessment and management},
volume = {21},
number = {3},
pages = {540-554},
doi = {10.1093/inteam/vjaf027},
pmid = {39969985},
issn = {1551-3793},
support = {202148/WT_/Wellcome Trust/United Kingdom ; },
mesh = {China ; *Environmental Monitoring/methods ; Spatio-Temporal Analysis ; *Ecosystem ; Cities ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Biodiversity ; Urbanization ; },
abstract = {The exponential expansion of urban areas has precipitated a concomitant deterioration in the natural environment. Constructing ecological networks is vital in improving landscape connectivity, protecting biodiversity, and maintaining regional sustainable development. Ningbo, China, was set as the research area. Geographic information system and morphological spatial pattern analysis (MSPA) were used to determine the ecological source area. Subsequently, the corridor design model Linkage Mapper was used to ascertain and assess the linkages between the designated ecological source areas. The results showed that from 2000-2020, there was a large-scale change in land use type in Ningbo, with increasing complexity of patches and landscape fragmentation. The ecological sources of the three periods in Ningbo were primarily situated in the western, southern, and Hangzhou Bay coastal regions, exhibiting an uneven distribution in the eastern and western areas. The number of primary ecological corridors in Ningbo underwent a significant reduction, from 26 to 17, between the years 2000-2020. In terms of the distribution of ecological corridors, the primary corridors were concentrated in the central, southern, and western regions of the study area in 2000. By 2020, however, the primary ecological corridors within the study region were distributed mainly in a southerly direction. The interaction between north and south ecological sources was weakened, which adversely affected the species spread and ecosystem stability. After optimization, 12 ecological corridors and four ecological nodes were incorporated into Ningbo, 67 ecological breakpoints were identified, and four stepping stone patches were added. The study used spatiotemporal change trends, including land use type and landscape pattern, to examine the ecological network of Ningbo. In conclusion, the proposed optimization strategy is aligned with the current urban development context, offering a particularly pertinent reference point for Ningbo's ecological protection initiatives.},
}
@article {pmid39973045,
year = {2025},
author = {Panayi, P and Contreras, A and Peters, E and Bentall, R and Hardy, A and Berry, K and Sellwood, W and Dudley, R and Longden, E and Underwood, R and Steel, C and Jafari, H and Mason, L and Varese, F},
title = {A temporal network analysis of complex post-traumatic stress disorder and psychosis symptoms.},
journal = {Psychological medicine},
volume = {55},
number = {},
pages = {e43},
pmid = {39973045},
issn = {1469-8978},
support = {2488414//Economic and Social Research Council/ ; NIHR128623//Health Technology Assessment Programme/ ; //NIHR Maudsley Biomedical Research Centre/ ; },
mesh = {Humans ; *Stress Disorders, Post-Traumatic/epidemiology/psychology/physiopathology ; *Psychotic Disorders/epidemiology/psychology/physiopathology ; Male ; Adult ; Female ; Middle Aged ; Young Adult ; Comorbidity ; Ecological Momentary Assessment ; },
abstract = {BACKGROUND: Symptoms of complex post-traumatic stress disorder (cPTSD) may play a role in the maintenance of psychotic symptoms. Network analyses have shown interrelationships between post-traumatic sequelae and psychosis, but the temporal dynamics of these relationships in people with psychosis and a history of trauma remain unclear. We aimed to explore, using network analysis, the temporal order of relationships between symptoms of cPTSD (i.e. core PTSD and disturbances of self-organization [DSOs]) and psychosis in the flow of daily life.<br><br>METHODS: Participants with psychosis and comorbid PTSD (N&#xa0;=&#xa0;153) completed an experience-sampling study involving multiple daily assessments of psychosis (paranoia, voices, and visions), core PTSD (trauma-related intrusions, avoidance, hyperarousal), and DSOs (emotional dysregulation, interpersonal difficulties, negative self-concept) over six consecutive days. Multilevel vector autoregressive modeling was used to estimate three complementary networks representing different timescales.<br><br>RESULTS: Our between-subjects network suggested that, on average over the testing period, most cPTSD symptoms related to at least one positive psychotic symptom. Many average relationships persist in the contemporaneous network, indicating symptoms of cPTSD and psychosis co-occur, especially paranoia with hyperarousal and negative self-concept. The temporal network suggested that paranoia reciprocally predicted, and was predicted by, hyperarousal, negative self-concept, and emotional dysregulation from moment to moment. cPTSD did not directly relate to voices in the temporal network.<br><br>CONCLUSIONS: cPTSD and positive psychosis symptoms mutually maintain each other in trauma-exposed people with psychosis via the maintenance of current threat, consistent with cognitive models of PTSD. Current threat, therefore, represents a valuable treatment target in phased-based trauma-focused psychosis interventions.},
}
@article {pmid39973193,
year = {2025},
author = {Beltran, RS and Kilpatrick, AM and Adamczak, SK and Beumer, LT and Czapanskiy, MF and Davidson, SC and McLean, BS and Mueller, T and Payne, AR and Soria, CD and Weeks, BC and Williams, TM and Salguero-Gómez, R},
title = {Integrating animal tracking and trait data to facilitate global ecological discoveries.},
journal = {The Journal of experimental biology},
volume = {228},
number = {Suppl_1},
pages = {},
pmid = {39973193},
issn = {1477-9145},
support = {IOS 2052497//National Science Foundation/ ; //Office of Naval Research/ ; //David and Lucile Packard Foundation/ ; //Arnold and Mabel Beckman Foundation/ ; //Elysea Fund/ ; NE/X013766/1//Natural Environment Research Council/ ; 101044740//European Union/ ; //University of California/ ; 80NSSC21K1182/NASA/NASA/United States ; },
mesh = {Animals ; *Ecology/methods ; Locomotion ; *Animal Migration ; Databases, Factual ; },
abstract = {Understanding animal movement is at the core of ecology, evolution and conservation science. Big data approaches for animal tracking have facilitated impactful synthesis research on spatial biology and behavior in ecologically important and human-impacted regions. Similarly, databases of animal traits (e.g. body size, limb length, locomotion method, lifespan) have been used for a wide range of comparative questions, with emerging data being shared at the level of individuals and populations. Here, we argue that the proliferation of both types of publicly available data creates exciting opportunities to unlock new avenues of research, such as spatial planning and ecological forecasting. We assessed the feasibility of combining animal tracking and trait databases to develop and test hypotheses across geographic, temporal and biological allometric scales. We identified multiple research questions addressing performance and distribution constraints that could be answered by integrating trait and tracking data. For example, how do physiological (e.g. metabolic rates) and biomechanical traits (e.g. limb length, locomotion form) influence migration distances? We illustrate the potential of our framework with three case studies that effectively integrate trait and tracking data for comparative research. An important challenge ahead is the lack of taxonomic and spatial overlap in trait and tracking databases. We identify critical next steps for future integration of tracking and trait databases, with the most impactful being open and interlinked individual-level data. Coordinated efforts to combine trait and tracking databases will accelerate global ecological and evolutionary insights and inform conservation and management decisions in our changing world.},
}
@article {pmid39974046,
year = {2025},
author = {Slack, SD and Esquinca, E and Arehart, CH and Boorgula, MP and Szczesny, B and Romero, A and Campbell, M and Chavan, S and Rafaels, N and Watson, H and Landis, RC and Hansel, NN and Rotimi, CN and Olopade, CO and Figueiredo, CA and Ober, C and Liu, AH and Kenny, EE and Kammers, K and Ruczinski, I and Taub, MA and Daya, M and Gignoux, CR and Kechris, K and Barnes, KC and Mathias, RA and Johnson, RK},
title = {Prediction and Characterization of Genetically Regulated Expression of Target Tissues in Asthma.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {39974046},
support = {R01 AI132476/AI/NIAID NIH HHS/United States ; R01 HL104608/HL/NHLBI NIH HHS/United States ; },
abstract = {BACKGROUND: Genetic control of gene expression in asthma-related tissues is not well-characterized, particularly for African-ancestry populations, limiting advancement in our understanding of the increased prevalence and severity of asthma in those populations.<br><br>OBJECTIVE: To create novel transcriptome prediction models for asthma tissues (nasal epithelium and CD4+ T cells) and apply them in transcriptome-wide association study (TWAS) to discover candidate asthma genes.<br><br>METHODS: We developed and validated gene expression prediction databases for unstimulated CD4+ T cells (CD4+T) and nasal epithelium using an elastic net framework. Combining these with existing prediction databases (N=51), we performed TWAS of 9,284 individuals of African-ancestry to identify tissue-specific and cross-tissue candidate genes for asthma. For detailed Methods, please see the Supplemental Methods.<br><br>RESULTS: Novel databases for CD4+T and nasal epithelial gene expression prediction contain 8,351 and 10,296 genes, respectively, including four asthma loci (SCGB1A1, MUC5AC, ZNF366, LTC4S) not predictable with existing public databases. Prediction performance was comparable to existing databases and was most accurate for populations sharing ancestry with the training set (e.g. African ancestry). From TWAS, we identified 17 candidate causal asthma genes (adjusted P<0.1), including genes with tissue-specific (IL33 in nasal epithelium) and cross-tissue (CCNC and FBXW7) effects.<br><br>CONCLUSIONS: Expression of IL33, CCNC, and FBXW7 may affect asthma risk in African ancestry populations by mediating inflammatory responses. The addition of CD4+T and nasal epithelium prediction databases to the public sphere will improve ancestry representation and power to detect novel gene-trait associations from TWAS.},
}
@article {pmid39975655,
year = {2025},
author = {Gutiérrez, ME and Lahoz-Beltrá, R and Donayre-Torres, AJ},
title = {Editorial: Towards the embedding of artificial intelligence into synthetic organisms: engineering intelligence in microorganisms.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1562092},
doi = {10.3389/fgene.2025.1562092},
pmid = {39975655},
issn = {1664-8021},
}
@article {pmid39980161,
year = {2025},
author = {Smith, AR and Mueller, ER and Lewis, CE and Markland, A and Smerdon, C and Smith, AL and Sutcliffe, S and Wyman, JF and Low, LK and Miller, JM and , },
title = {Assessment of Environmental, Sociocultural, and Physiological Influences on Women's Toileting Decisions and Behaviors Using "Where I Go": Pilot Study of a Mobile App.},
journal = {JMIR mHealth and uHealth},
volume = {13},
number = {},
pages = {e56533},
pmid = {39980161},
issn = {2291-5222},
support = {P30 CA046592/CA/NCI NIH HHS/United States ; U24 DK106786/DK/NIDDK NIH HHS/United States ; U01 DK106858/DK/NIDDK NIH HHS/United States ; U01 DK106892/DK/NIDDK NIH HHS/United States ; U01 DK106893/DK/NIDDK NIH HHS/United States ; U01 DK106827/DK/NIDDK NIH HHS/United States ; U01 DK106908/DK/NIDDK NIH HHS/United States ; U01 DK106898/DK/NIDDK NIH HHS/United States ; U01 DK126045/DK/NIDDK NIH HHS/United States ; U01 DK106853/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; Female ; *Mobile Applications/standards/statistics &amp; numerical data ; Adult ; Pilot Projects ; Middle Aged ; Aged ; *Decision Making ; Aged, 80 and over ; Surveys and Questionnaires ; *Urination ; },
abstract = {BACKGROUND: Little is known about women's decisions around toileting for urination and how those decisions influence moment-to-moment behaviors to manage bladder needs. The new smartphone app "Where I Go" captures such nuanced and granular data in real-world environments.<br><br>OBJECTIVE: This study aims to describe participant engagement with "Where I Go", variation in novel parameters collected, and readiness for the data collection tool's use in population-based studies.<br><br>METHODS: "Where I Go" has three components: (1) real-time data, (2) short look-back periods (3-4 h), and (3) event location (GPS recorded at each interaction). The sample size was 44 women. Recording of real-time toileting events and responding to look-back questions was measured over 2 days of data collection. The participant's self-entered location descriptions and the automatic GPS recordings were compared.<br><br>RESULTS: A total of 44 women with an average age of 44 (range 21-85) years interacted with the app. Real-time reporting of at least 1 toileting event per day was high (38/44, 86%, on day 1 and 40/44, 91%, on day 2) with a median of 5 (IQR 3-7 on day 1 and IQR 3-8 on day 2) toileting events recorded each day. Toileting most commonly occurred at home (85/140, 61%, on day 1 and 129/171, 75%, on day 2) due to a need to go (114/140, 66%, on day 1 and 153/171, 74%, on day 2). The most common reasons for delaying toileting were "work duties" (33/140, 21%, on day 1 and 21/171, 11%, on day 2) and "errands or traveling" (19/140, 12%, on day 1 and 19/171, 10%, on day 2). Response to at least 1 look-back notification was similarly high (41/44, 93%, on day 1 and 42/44, 95%, on day 2), with number of responses higher on average on day 2 compared with day 1 (mean on day 1=3.2, 95% CI 3.0-3.5; mean on day 2=4.3, 95% CI 3.9-4.7; P<.001). Median additional toileting events reported on the look-back survey were 1 (IQR 1-2) and 2 (IQR 1-2) on days 1 and 2, respectively. Overall concordance between self-reported location recording and GPS was 76% (188/247). Participants reported lower urge ratings when at home versus away when reporting real-time toileting (median rating 61, IQR 41-84 vs 72, IQR 56-98), and daily fluid intake showed a small to medium positive correlation with toileting frequency (day 1 r=0.3, day 2 r=0.24). Toileting frequency reported in "Where I Go" showed a small positive correlation with the frequency item from the International Consultation on Incontinence Questionnaire (r=0.31 with day 1 toileting frequency and r=0.21 with day 2 toileting frequency).<br><br>CONCLUSIONS: "Where I Go" has potential to increase the understanding of factors that affect women's toileting decisions and long-term bladder health. We anticipate its use as a data collection tool in population-based studies.},
}
@article {pmid39980689,
year = {2025},
author = {Su, Z and Liu, L and Zhang, J and Guo, J and Wang, G and Zeng, X},
title = {A scientometric visualization analysis of the gut microbiota and gestational diabetes mellitus.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1485560},
pmid = {39980689},
issn = {1664-302X},
abstract = {BACKGROUND: The prevalence of gestational diabetes mellitus (GDM), a condition that is widespread globally, is increasing. The relationship between the gut microbiota and GDM has been a subject of research for nearly two decades, yet there has been no bibliometric analysis of this correlation. This study aimed to use bibliometrics to explore the relationship between the gut microbiota and GDM, highlighting emerging trends and current research hotspots in this field.<br><br>RESULTS: A total of 394 papers were included in the analysis. China emerged as the preeminent nation in terms of the number of publications on the subject, with 128 papers (32.49%), whereas the United States had the most significant impact, with 4,874 citations. The University of Queensland emerged as the most prolific institution, contributing 18 publications. Marloes Dekker Nitert was the most active author with 16 publications, and Omry Koren garnered the most citations, totaling 154. The journal Nutrients published the most studies (28 publications, 7.11%), whereas PLoS One was the most commonly co-cited journal, with a total of 805 citations. With respect to keywords, research focuses can be divided into 4 clusters, namely, "the interrelationship between the gut microbiota and pregnancy, childbirth," "the relationship between adverse metabolic outcomes and GDM," "the gut microbiota composition and metabolic mechanisms" and "microbiota and ecological imbalance." Key areas of focus include the interactions between the gut microbiota and individuals with GDM, as well as the formation and inheritance of the gut microbiota. Increasing attention has been given to the impact of probiotic supplementation on metabolism and pregnancy outcomes in GDM patients. Moreover, ongoing research is exploring the potential of the gut microbiota as a biomarker for GDM. These topics represent both current and future directions in this field.<br><br>CONCLUSION: This study provides a comprehensive knowledge map of the gut microbiota and GDM, highlights key research areas, and outlines potential future directions.},
}
@article {pmid39981105,
year = {2025},
author = {Plaitano, EG and McNeish, D and Bartels, SM and Bell, K and Dallery, J and Grabinski, M and Kiernan, M and Lavoie, HA and Lemley, SM and Lowe, MR and MacKinnon, DP and Metcalf, SA and Onken, L and Prochaska, JJ and Sand, CL and Scherer, EA and Stoeckel, LE and Xie, H and Marsch, LA},
title = {Adherence to a digital therapeutic mediates the relationship between momentary self-regulation and health risk behaviors.},
journal = {Frontiers in digital health},
volume = {7},
number = {},
pages = {1467772},
pmid = {39981105},
issn = {2673-253X},
support = {P30 CA023108/CA/NCI NIH HHS/United States ; UH3 DA041713/DA/NIDA NIH HHS/United States ; P30 DA029926/DA/NIDA NIH HHS/United States ; R37 DA009757/DA/NIDA NIH HHS/United States ; T32 DA037202/DA/NIDA NIH HHS/United States ; },
abstract = {INTRODUCTION: Smoking, obesity, and insufficient physical activity are modifiable health risk behaviors. Self-regulation is one fundamental behavior change mechanism often incorporated within digital therapeutics as it varies momentarily across time and contexts and may play a causal role in improving these health behaviors. However, the role of momentary self-regulation in achieving behavior change has been infrequently examined. Using a novel momentary self-regulation scale, this study examined how targeting self-regulation through a digital therapeutic impacts adherence to the therapeutic and two different health risk behavioral outcomes.<br><br>METHODS: This prospective interventional study included momentary data for 28 days from 50 participants with obesity and binge eating disorder and 50 participants who smoked regularly. An evidence-based digital therapeutic, called Laddr&#x2122;, provided self-regulation behavior change tools. Participants reported on their momentary self-regulation via ecological momentary assessments and health risk behaviors were measured as steps taken from a physical activity tracker and breathalyzed carbon monoxide. Medical regimen adherence was assessed as daily Laddr usage. Bayesian dynamic mediation models were used to examine moment-to-moment mediation effects between momentary self-regulation subscales, medical regimen adherence, and behavioral outcomes.<br><br>RESULTS: In the binge eating disorder sample, the perseverance [&#x3b2; 1&#x2009;=&#x2009;0.17, 95% CI&#x2009;=&#x2009;(0.06, 0.45)] and emotion regulation [&#x3b2; 1&#x2009;=&#x2009;0.12, 95% CI&#x2009;=&#x2009;(0.03, 0.27)] targets of momentary self-regulation positively predicted Laddr adherence on the following day, and higher Laddr adherence was subsequently a positive predictor of steps taken the same day for both perseverance [&#x3b2; 2&#x2009;=&#x2009;0.335, 95% CI&#x2009;=&#x2009;(0.030, 0.717)] and emotion regulation [&#x3b2; 2&#x2009;=&#x2009;0.389, 95% CI&#x2009;=&#x2009;(0.080, 0.738)]. In the smoking sample, the perseverance target of momentary self-regulation positively predicted Laddr adherence on the following day [&#x3b2;&#x2009;=&#x2009;0.91, 95% CI&#x2009;=&#x2009;(0.60, 1.24)]. However, higher Laddr adherence was not a predictor of CO values on the same day [&#x3b2; 2&#x2009;=&#x2009;-0.09, 95% CI&#x2009;=&#x2009;(-0.24, 0.09)].<br><br>CONCLUSIONS: This study provides evidence that a digital therapeutic targeting self-regulation can modify the relationships between momentary self-regulation, medical regimen adherence, and behavioral health outcomes. Together, this work demonstrated the ability to digitally assess the transdiagnostic mediating effect of momentary self-regulation on medical regimen adherence and pro-health behavioral outcomes.<br><br>CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier (NCT03774433).},
}
@article {pmid39982380,
year = {2025},
author = {Blumenstiel, JP and Kingan, SB and Garrigan, D and Hill, T and Vedanayagam, J},
title = {Nested likelihood-ratio testing of the nonsynonymous:synonymous ratio suggests greater adaptation in the piRNA machinery of Drosophila melanogaster compared with Drosophila ananassae and Drosophila willistoni, two species with higher repeat content.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {4},
pages = {},
pmid = {39982380},
issn = {2160-1836},
support = {//KU Medical Center Genome Sequencing Facility/ ; P20 GM103638/GM/NIGMS NIH HHS/United States ; UL1TR002366//Frontiers CTSA/ ; NIH U54 HD090216/GF/NIH HHS/United States ; //University of Kansas/ ; R00 GM137077/GM/NIGMS NIH HHS/United States ; S10 OD036343/OD/NIH HHS/United States ; UL1 TR002366/TR/NCATS NIH HHS/United States ; P30 GM145499/GM/NIGMS NIH HHS/United States ; P20GM103418//NIH-NIGMS/KINBRE/ ; DEB1209536//NSF-DDIG/ ; //University of Texas at San Antonio/ ; P20 GM103418/GM/NIGMS NIH HHS/United States ; 1413532//NSF MCB/ ; P20GM103638//NIH-NIGMS/COBRE/ ; R00GM137077//NIH-NIGMS/ ; },
mesh = {Animals ; *RNA, Small Interfering/genetics ; *Drosophila melanogaster/genetics ; DNA Transposable Elements ; Evolution, Molecular ; *Drosophila/genetics ; Likelihood Functions ; *Repetitive Sequences, Nucleic Acid ; *Adaptation, Physiological/genetics ; Piwi-Interacting RNA ; },
abstract = {Numerous studies have revealed a signature of strong adaptive evolution in the piwi-interacting RNA (piRNA) machinery of Drosophila melanogaster, but the cause of this pattern is not understood. Several hypotheses have been proposed. One hypothesis is that transposable element (TE) families and the piRNA machinery are co-evolving under an evolutionary arms race, perhaps due to antagonism by TEs against the piRNA machinery. A related, though not co-evolutionary, hypothesis is that recurrent TE invasion drives the piRNA machinery to adapt to novel TE strategies. A third hypothesis is that ongoing fluctuation in TE abundance leads to adaptation in the piRNA machinery that must constantly adjust between sensitivity for detecting new elements and specificity to avoid the cost of off-target gene silencing. Rapid evolution of the piRNA machinery may also be driven independently of TEs, and instead from other functions such as the role of piRNAs in suppressing sex-chromosome meiotic drive. We sought to evaluate the impact of TE abundance on adaptive evolution of the piRNA machinery in D. melanogaster and 2 species with higher repeat content-Drosophila ananassae and Drosophila willistoni. This comparison was achieved by employing a likelihood-based hypothesis testing framework based on the McDonald-Kreitman test. We show that we can reject a faster rate of adaptive evolution in the piRNA machinery of these 2 species. We propose that the high rate of adaptation in D. melanogaster is either driven by a recent influx of TEs that have occurred during range expansion or selection on other functions of the piRNA machinery.},
}
@article {pmid39982516,
year = {2025},
author = {Elkin-Frankston, S and McIntyre, J and Brunyé, TT and Gardony, AL and Hancock, CL and O'Donovan, MP and Bode, VG and Miller, EL},
title = {Beyond boundaries: a location-based toolkit for quantifying group dynamics in diverse contexts.},
journal = {Cognitive research: principles and implications},
volume = {10},
number = {1},
pages = {10},
pmid = {39982516},
issn = {2365-7464},
support = {W911QY1920003//U.S. Army Combat Capabilities Development Command Soldier Center/ ; 1934553//National Science Foundation/ ; 1931978//National Science Foundation/ ; },
mesh = {Humans ; *Group Processes ; Military Personnel ; Geographic Information Systems ; Movement/physiology ; Group Dynamics ; },
abstract = {Existing toolkits for analyzing movement dynamics in animal ecology primarily focus on individual or group behavior in habitats without predefined boundaries, while methods for studying human activity often cater to bounded environments, such as team sports played on defined fields. This leaves a gap in tools for modeling and analyzing human group dynamics in large-scale, unbounded, or semi-constrained environments. Examples of such contexts include tourist groups, cycling teams, search and rescue teams, and military units. To address this issue, we survey existing methods and metrics for characterizing individual and collective movement in humans and animals. Using a rich GPS dataset from groups of military personnel engaged in a foot march, we develop a comprehensive, general-purpose toolkit for quantifying group dynamics using location-based metrics during goal-directed movement in open environments. This toolkit includes a repository of Python functions for extracting and analyzing movement data, integrating cognitive factors such as decision-making, situational awareness, and group coordination. By extending location-based analytics to non-traditional domains, this toolkit enhances the understanding of collective movement, group behavior, and emergent properties shaped by cognitive processes. To demonstrate its practical utility, we present a use case utilizing metrics derived from the foot march data to predict group performance during a subsequent strategic and tactical exercise, highlighting the influence of cognitive and decision-making behaviors on team effectiveness.},
}
@article {pmid39982558,
year = {2025},
author = {Li, L and Gupta, A and Zhu, C and Xu, K and Watanabe, Y and Tanaka, M and Seki, M and Mochida, K and Kanno, Y and Seo, M and Nguyen, KH and Tran, CD and Chu, HD and Yin, H and Jia, KP and Tran, LP and Yin, X and Li, W},
title = {Strigolactone and karrikin receptors regulate phytohormone biosynthetic and catabolic processes.},
journal = {Plant cell reports},
volume = {44},
number = {3},
pages = {60},
pmid = {39982558},
issn = {1432-203X},
support = {XDA28110100//State Key Laboratory of Microbial Resources, Chinese Academy of Sciences/ ; 2022YFD1500505//National Key Research and Development Program of China/ ; 32370321//Natural Science Foundation of Jilin Province/ ; },
mesh = {*Furans/metabolism ; *Pyrans/metabolism ; *Lactones/metabolism ; *Heterocyclic Compounds, 3-Ring/metabolism ; *Plant Growth Regulators/genetics/metabolism ; Metabolism ; Gene Expression Regulation, Plant ; *Arabidopsis Proteins/genetics/metabolism ; Gene Expression Profiling ; Abscisic Acid/metabolism ; Indoleacetic Acids/metabolism ; Cyclopentanes/metabolism ; Genes, Plant ; *Arabidopsis/genetics/metabolism ; Genotype ; Cytokinins/genetics/metabolism ; Receptors, Cell Surface ; Hydrolases ; Oxylipins ; },
abstract = {Karrikin plays a more critical role in affecting the homeostasis of ABA and cytokinins, while strigolactones play a more critical role in influencing the homeostasis of jasmonic acid and gibberellins. Strigolactones (SLs) and karrikins (KARs) regulate plant growth and development through their crosstalk, and through the crosstalk between them and other phytohormones, such as abscisic acid (ABA) and auxin. However, how SL and KAR signaling pathways influence the levels of other phytohormones is still unknown. Here, we performed a comparative transcriptome analysis of the Arabidopsis thaliana double mutant dwarf14 karrikin-insensitive 2 (d14 kai2), deficient in SL and KAR perception, and the wild-type (WT) using their rosette leaves. Ten gene ontology terms related to phytohormones were enriched with differentially expressed genes derived from the 'd14 kai2 vs WT' comparison. Our data revealed that the levels of auxin, ABA and salicylic acid (SA) were higher in d14 and kai2 single and d14 kai2 mutant plants than in WT, which was consistent with the results of previous investigations. In contrast, the levels of cytokinins (CKs) were found to be lower in all single and double mutants than in WT. The levels of active gibberellins were lower in d14 and d14 kai2 mutants than in WT, while they were comparable in kai2 and WT plants. Similarly, the levels of jasmonic acid (JA) were lower in d14 and d14 kai2 plants, but higher in kai2 plants than in WT. Both transcriptome and qRT-PCR analyses indicated that SL and KAR signaling pathways affect the levels of auxin, SA, CKs, gibberellin 4 (GA4) and ABA by influencing the expression of their biosynthetic (in case of auxin, SA, GA4 and CKs) and catabolic (in case of ABA) genes. Collectively, our data demonstrated that KAI2 plays a more critical role in the homeostasis of ABA and CKs, while D14 plays a more critical role in the homeostasis of JA and gibberellins. Findings of this study indicate a complex and broad crosstalk among various phytohormones in plants, which can be considered for future exogenous applications and hormone engineering.},
}
@article {pmid39986902,
year = {2025},
author = {Lee, S and Kaufmann, CN and Lippi, CA and Ryan, SJ and Guo, Y},
title = {Untreated insomnia as a contributor to geographic disparities in risk for Alzheimer's disease and related dementias.},
journal = {Sleep health},
volume = {11},
number = {2},
pages = {131-132},
pmid = {39986902},
issn = {2352-7226},
support = {K01 AG061239/AG/NIA NIH HHS/United States ; R01 AG079391/AG/NIA NIH HHS/United States ; R01 HL163226/HL/NHLBI NIH HHS/United States ; R56 AG065251/AG/NIA NIH HHS/United States ; },
}
@article {pmid39987271,
year = {2025},
author = {Wuyun, D and Sun, L and Chen, Z and Li, Y and Han, M and Shi, Z and Ren, T and Zhao, H},
title = {A 10-meter resolution dataset of abandoned and reclaimed cropland from 2016 to 2023 in Inner Mongolia, China.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {317},
pmid = {39987271},
issn = {2052-4463},
abstract = {Amid growing global food security concerns and frequent armed conflicts, real-time monitoring of abandoned cropland is essential for strategic planning and crisis management. This study develops a method to map abandoned cropland accurately, crucial for maintaining the food supply chain and ecological balance. Utilizing Sentinel-1/2 satellite data, we employed multi-feature stacking and machine learning to create the ARCC10-IM (Abandoned and Reclaimed Cropland Classification at 10-meter resolution in Inner Mongolia) dataset, which tracks annual cropland activity. A novel temporal segmentation algorithm was developed to extract cropland abandonment and reclamation patterns annually, using sliding time windows over several years. This research differentiates cropland states-active cultivation, unstable fallowing, continuous abandonment, and reclamation-providing continuous, regional-scale maps with 10-meter resolution. ARCC10-IM is crucial for land planning, environmental monitoring, and agricultural management in arid areas like Inner Mongolia, enhancing decision-making and technology in land use tracking.},
}
@article {pmid39989610,
year = {2024},
author = {Liu, C and Downey, RJ and Salminen, JS and Rojas, SA and Richer, N and Pliner, EM and Hwang, J and Cruz-Almeida, Y and Manini, TM and Hass, CJ and Seidler, RD and Clark, DJ and Ferris, DP},
title = {Electrical brain activity during human walking with parametric variations in terrain unevenness and walking speed.},
journal = {Imaging neuroscience (Cambridge, Mass.)},
volume = {2},
number = {},
pages = {},
pmid = {39989610},
issn = {2837-6056},
support = {R01 NS104772/NS/NINDS NIH HHS/United States ; F32 AG072808/AG/NIA NIH HHS/United States ; S10 OD021726/OD/NIH HHS/United States ; U01 AG061389/AG/NIA NIH HHS/United States ; T32 AG062728/AG/NIA NIH HHS/United States ; },
abstract = {Mobile brain imaging with high-density electroencephalography (EEG) can provide insight into the cortical processes involved in complex human walking tasks. While uneven terrain is common in the natural environment and poses challenges to human balance control, there is limited understanding of the supraspinal processes involved with traversing uneven terrain. The primary objective of this study was to quantify electrocortical activity related to parametric variations in terrain unevenness for neurotypical young adults. We used high-density EEG to measure brain activity when 32 young adults walked on a novel custom-made uneven terrain treadmill surface with four levels of difficulty at a walking speed tailored to each participant. We identified multiple brain regions associated with uneven terrain walking. Alpha (8 - 13 Hz) and beta (13 - 30 Hz) spectral power decreased in the sensorimotor and posterior parietal areas with increasing terrain unevenness while theta (4 - 8 Hz) power increased in the mid/posterior cingulate area with terrain unevenness. We also found that within stride spectral power fluctuations increased with terrain unevenness. Our secondary goal was to investigate the effect of parametric changes in walking speed (0.25 m/s, 0.5 m/s, 0.75 m/s, 1.0 m/s) to differentiate the effects of walking speed from uneven terrain. Our results revealed that electrocortical activities only changed substantially with speed within the sensorimotor area but not in other brain areas. Together, these results indicate there are distinct cortical processes contributing to the control of walking over uneven terrain versus modulation of walking speed on smooth, flat terrain. Our findings increase our understanding of cortical involvement in an ecologically valid walking task and could serve as a benchmark for identifying deficits in cortical dynamics that occur in people with mobility deficits.},
}
@article {pmid39990132,
year = {2025},
author = {Keet, JH and Hui, C},
title = {One-hectare fine-scale dataset of a fynbos plant community in the Cape Floristic Region.},
journal = {Data in brief},
volume = {59},
number = {},
pages = {111334},
pmid = {39990132},
issn = {2352-3409},
abstract = {Cape fynbos, which forms part of the Cape Floristic Region (CFR) of South Africa, a global biodiversity hotspot, is renowned for its high levels of plant species endemism and diversity. This extraordinary ecosystem, characterised by nutrient-poor soils and fire-adapted vegetation, is a treasure trove of endemic flora. However, this fragile system faces increasing threats from habitat loss, climate change, and invasive species. Pristine fynbos, naturally high in plant diversity and which forms a large part of the CFR, presents an ideal opportunity to gather fine-scale data on community assembly patterns. Most fynbos vegetation surveys use a plot size of about 100 m[2], with no spatial structures within plots to demarcate individual subplots. Here, a groundbreaking dataset is presented that fully covers 1-hectare of pristine fynbos, systematically gridded into 50 × 50 subplots, each measuring 2 × 2 m, arranged evenly within a square-shaped survey site. Each plot was assigned a unique Y-X coordinate combination. For each plot, all plant species present were recorded, along with their total percentage covers and maximum height values. Total percentage covers were also recorded for bare soil, rock, and termite mounds. This dataset provides a valuable contribution to the field of fynbos ecology, as well as plant community ecology in general, and establishes a benchmark for future one-hectare surveys of similar fynbos vegetation types, delineating the fine-scale composition and structure of fynbos in the CFR. The dataset will be useful for a wide audience, including community and spatial ecologists, plant and environmental scientists, and biodiversity informaticians and statistical ecologists, offering ideal data for testing new metrics of diversity and compositional turnover.},
}
@article {pmid39990470,
year = {2025},
author = {Edwards, SV and Fang, B and Khost, D and Kolyfetis, GE and Cheek, RG and DeRaad, DA and Chen, N and Fitzpatrick, JW and McCormack, JE and Funk, WC and Ghalambor, CK and Garrison, E and Guarracino, A and Li, H and Sackton, TB},
title = {Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39990470},
issn = {2692-8205},
support = {R01 GM123489/GM/NIGMS NIH HHS/United States ; R01 HG011485/HG/NHGRI NIH HHS/United States ; R35 GM133412/GM/NIGMS NIH HHS/United States ; U01 DA047638/DA/NIDA NIH HHS/United States ; },
abstract = {Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including ~100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.},
}
@article {pmid39995103,
year = {2025},
author = {Campbell, IH and Needham, N and Grossi, H and Kamenska, I and Luz, S and Sheehan, S and Thompson, G and Thrippleton, MJ and Gibbs, MC and Leitao, J and Moses, T and Burgess, K and Rigby, BP and Simpson, SA and McIntosh, E and Brown, R and Meadowcroft, B and Creasy, F and Mitchell-Grigorjeva, M and Norrie, J and McLellan, A and Fisher, C and Zieliński, T and Gaggioni, G and Campbell, H and Smith, DJ},
title = {A pilot study of a ketogenic diet in bipolar disorder: clinical, metabolic and magnetic resonance spectroscopy findings.},
journal = {BJPsych open},
volume = {11},
number = {2},
pages = {e34},
pmid = {39995103},
issn = {2056-4724},
abstract = {BACKGROUND: Preliminary evidence suggests that a ketogenic diet may be effective for bipolar disorder.<br><br>AIMS: To assess the impact of a ketogenic diet in bipolar disorder on clinical, metabolic and magnetic resonance spectroscopy outcomes.<br><br>METHOD: Euthymic individuals with bipolar disorder (N = 27) were recruited to a 6- to 8-week single-arm open pilot study of a modified ketogenic diet. Clinical, metabolic and MRS measures were assessed before and after the intervention.<br><br>RESULTS: Of 27 recruited participants, 26 began and 20 completed the ketogenic diet. For participants completing the intervention, mean body weight fell by 4.2 kg (P < 0.001), mean body mass index fell by 1.5 kg/m[2] (P < 0.001) and mean systolic blood pressure fell by 7.4 mmHg (P < 0.041). The euthymic participants had average baseline and follow-up assessments consistent with them being in the euthymic range with no statistically significant changes in Affective Lability Scale-18, Beck Depression Inventory and Young Mania Rating Scale. In participants providing reliable daily ecological momentary assessment data (n = 14), there was a positive correlation between daily ketone levels and self-rated mood (r = 0.21, P < 0.001) and energy (r = 0.19 P < 0.001), and an inverse correlation between ketone levels and both impulsivity (r = -0.30, P < 0.001) and anxiety (r = -0.19, P < 0.001). From the MRS measurements, brain glutamate plus glutamine concentration decreased by 11.6% in the anterior cingulate cortex (P = 0.025) and fell by 13.6% in the posterior cingulate cortex (P = <0.001).<br><br>CONCLUSIONS: These findings suggest that a ketogenic diet may be clinically useful in bipolar disorder, for both mental health and metabolic outcomes. Replication and randomised controlled trials are now warranted.},
}
@article {pmid39995465,
year = {2025},
author = {Huang, J and Bibri, SE and Keel, P},
title = {Generative spatial artificial intelligence for sustainable smart cities: A pioneering large flow model for urban digital twin.},
journal = {Environmental science and ecotechnology},
volume = {24},
number = {},
pages = {100526},
pmid = {39995465},
issn = {2666-4984},
abstract = {Rapid urbanization, alongside escalating resource depletion and ecological degradation, underscores the critical need for innovative urban development solutions. In response, sustainable smart cities are increasingly turning to cutting-edge technologies-such as Generative Artificial Intelligence (GenAI), Foundation Models (FMs), and Urban Digital Twin (UDT) frameworks-to transform urban planning and design practices. These transformative tools provide advanced capabilities to analyze complex urban systems, optimize resource management, and enable evidence-based decision-making. Despite recent progress, research on integrating GenAI and FMs into UDT frameworks remains scant, leaving gaps in our ability to capture complex urban flows and multimodal dynamics essential to achieving environmental sustainability goals. Moreover, the lack of a robust theoretical foundation and real-world operationalization of these tools hampers comprehensive modeling and practical adoption. This study introduces a pioneering Large Flow Model (LFM), grounded in a robust foundational framework and designed with GenAI capabilities. It is specifically tailored for integration into UDT systems to enhance predictive analytics, adaptive learning, and complex data management functionalities. To validate its applicability and relevance, the Blue City Project in Lausanne City is examined as a case study, showcasing the ability of the LFM to effectively model and analyze urban flows-namely mobility, goods, energy, waste, materials, and biodiversity-critical to advancing environmental sustainability. This study highlights how the LFM addresses the spatial challenges inherent in current UDT frameworks. The LFM demonstrates its novelty in comprehensive urban modeling and analysis by completing impartial city data, estimating flow data in new locations, predicting the evolution of flow data, and offering a holistic understanding of urban dynamics and their interconnections. The model enhances decision-making processes, supports evidence-based planning and design, fosters integrated development strategies, and enables the development of more efficient, resilient, and sustainable urban environments. This research advances both the theoretical and practical dimensions of AI-driven, environmentally sustainable urban development by operationalizing GenAI and FMs within UDT frameworks. It provides sophisticated tools and valuable insights for urban planners, designers, policymakers, and researchers to address the complexities of modern cities and accelerate the transition towards sustainable urban futures.},
}
@article {pmid39996333,
year = {2025},
author = {Medeiros, W and Kralova, S and Oliveira, V and Ziemert, N and Sehnal, L},
title = {Antarctic bacterial natural products: from genomic insights to drug discovery.},
journal = {Natural product reports},
volume = {42},
number = {5},
pages = {774-787},
doi = {10.1039/d4np00045e},
pmid = {39996333},
issn = {1460-4752},
mesh = {*Biological Products/chemistry/pharmacology/metabolism ; Antarctic Regions ; *Drug Discovery ; *Bacteria/genetics/chemistry/metabolism ; Genomics ; Molecular Structure ; },
abstract = {Covering: up to the end of 2024Microbial life dominates the extreme continent Antarctica, playing a pivotal role in ecosystem functioning and serving as a reservoir of specialized metabolites known as natural products (NPs). NPs not only contribute to microbial adaptation to harsh conditions but also modulate microbial community structure. Long-term isolation and environmental pressures have shaped the genomes of Antarctic bacteria, suggesting that they also encode unique NPs. Since NPs are also an important source of drugs, we argue that investigating Antarctic bacterial NPs is essential not only for understanding their ecological role and evolution, but also for discovering new chemical structures, biosynthetic mechanisms, and potential new drugs. Yet, despite advances in omics technologies and increased scientific activities in Antarctica, relatively few new bacterial NPs have been discovered. The lack of systematic research activities focused on the exploration of Antarctic bacteria and their NPs constitutes a big problem considering the climate change issue, to which ecosystems in polar regions are the most sensitive areas on the Earth. Here, we highlight the currently available data on Antarctic bacteria, their biosynthetic potential, and the successful NP discoveries, while addressing the challenges in NP research and advocating for systematic, collaborative efforts aligned with the Antarctic Treaty System and the Antarctic Conservation Biogeographic Regions.},
}
@article {pmid40004070,
year = {2025},
author = {Brzhozovskiy, AG and Semenov, SD and Zherebker, AY and Bugrova, AE and Yurova, MN and Zhernov, YV and Kovaleva, OA and Semenov, AL and Abroskin, DP and Kruglov, SS and Fedoros, EI and Kononikhin, AS and Nikolaev, EN},
title = {Hepatoprotective Activity of Nature-Derived Polyphenols Studied by Mass Spectrometry Based Multi-OMICS Approach.},
journal = {International journal of molecular sciences},
volume = {26},
number = {4},
pages = {},
pmid = {40004070},
issn = {1422-0067},
support = {22-75-10140//Russian Science Foundation/ ; },
mesh = {Animals ; *Polyphenols/pharmacology/chemistry ; Mice ; Metabolomics/methods ; Proteomics/methods ; *Liver/drug effects/metabolism/pathology ; Mice, Inbred BALB C ; Mass Spectrometry/methods ; *Protective Agents/pharmacology/chemistry ; Pueraria/chemistry ; Carbon Tetrachloride/toxicity ; Metabolome/drug effects ; Male ; Plant Extracts/pharmacology/chemistry ; Disease Models, Animal ; Chemical and Drug Induced Liver Injury/metabolism/drug therapy ; Plant Roots/chemistry ; Multiomics ; },
abstract = {The aim of this study was to examine the hepatoprotective activity of multicomponent mixtures of natural origin in the BALB/C mouse model, with subacute liver failure (SALF) induced by the administration of toxin carbon tetrachloride (CCl4). The hepatoprotective activity of activated hydrolytic lignin (BP-Cx-1), humic acid peloids (HA), and isoflavones from kudzu Pueraria lobata roots (IFL) was evaluated using mass spectrometry (MS)-based omics technologies. Our MS-based approach revealed new insights into the molecular mechanisms of the hepatoprotective activity of multicomponent mixtures of natural origin. Significant differences were observed in the proteome and metabolome profiles of the urine and liver of BALB/c mice with SALF between a control group with CCl4 administration, intact controls, and groups receiving potential hepatoprotectors of natural origin (BP-Cx-1, HA, IFL). Proteomic and metabolomics analyses demonstrated that among the hepatoprotectors, IFL possessed the highest hepatoprotective potential, which correlated well with the relative effectiveness of the drugs recorded during in vitro studies. These results correlate with the relative effectiveness of the drugs recorded in previous in vitro and in vivo studies. The leading IFL activity may be attributed to a higher content of active polyphenolic components compared to heterogeneous HA and BP-Cx-1. Enrichment with active components by fractionation is a direction that can be explored for developing hepatoprotective agents based on natural complex polyphenols.},
}
@article {pmid40007687,
year = {2025},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , },
title = {The genome sequence of Red Underwing, Catocala nupta Linnaeus, 1767.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {36},
pmid = {40007687},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female specimen of Catocala nupta (Red Underwing; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence has a total length of 930.40 megabases. Most of the assembly (99.82%) is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.57 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,889 protein-coding genes.},
}
@article {pmid40007688,
year = {2025},
author = {Boyes, D and Lees, DC and Coates, BS and , and , and , and , and , and , and , and , },
title = {The genome sequence of the European Corn Borer, Ostrinia nubilalis Hübner, 1796.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {12},
pmid = {40007688},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female specimen of Ostrinia nubilalis (European Corn Borer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 495.50 megabases. Most of the assembly (99.87%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.24 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,780 protein-coding genes.},
}
@article {pmid40007820,
year = {2024},
author = {Grieco, F and Parisi, S and Simmenroth, A and Eichinger, M and Zirkel, J and König, S and Jünger, J and Geck, E and Schwienhorst-Stich, EM},
title = {Planetary health education in undergraduate medical education in Germany: results from structured interviews and an online survey within the national PlanetMedEd Project.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1507515},
pmid = {40007820},
issn = {2296-858X},
abstract = {BACKGROUND: In light of the accumulating evidence, awareness and urgency to act upon the three planetary crises - climate change, biodiversity loss, and pollution - the concept of Planetary Health underscores their profound implications for health and promotes actionable solutions to advance both wellbeing and ecological sustainability. Despite (inter)national calls to integrate Planetary Health into health workers' curricula, the current status of Planetary Health Education in undergraduate medical education in Germany is unclear. This study therefore aimed (a) to assess the current implementation of Planetary Health in undergraduate medical education in Germany and (b) to explore its characteristics as a foundation to develop evidence-informed recommendations for mainstreaming Planetary Health Education in medical schools in Germany.<br><br>METHODS: The study comprised structured interviews followed by an online survey, both targeting all 39 medical schools in Germany. In 2021, structured interviews were conducted with students, educators and deanery staff at medical schools. In 2023, educators and deanery staff participated in an online survey based on the findings from the interviews.<br><br>FINDINGS: In total, 80% of the 39 medical schools participated in the interviews, while 90% took part in the online survey. Based on integrated findings, 35 medical schools (90%) offered Planetary Health Education, with a median of two educational activities, including both stand-alone courses and lectures integrated into other courses. Despite an overall increase since winter semester 2021/2022, most educational activities were electives and not part of the mandatory curriculum. Innovative educational approaches and learning objectives differed significantly between mandatory and elective formats. In contrast to mandatory educational activities, student involvement was reported for the majority of electives and was significantly associated with transformative learning objectives.<br><br>INTERPRETATION: Despite a steady rise in teaching activities, mandatory Planetary Health Education remains insufficiently integrated into undergraduate medical education in Germany. Key criteria defining high-quality Planetary Health Education, such as innovative educational approaches, practical skills, and transformative learning, were primarily reflected in electives, that reach only a minority of students. To adequately equip the future healthcare workforce, the current barriers to successfully integrating Planetary Health into medical education must be systematically addressed and overcome.},
}
@article {pmid40011724,
year = {2025},
author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, Z and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS},
title = {Reply to: Causal claims, causal assumptions and protected area impact.},
journal = {Nature},
volume = {638},
number = {8052},
pages = {E42-E44},
pmid = {40011724},
issn = {1476-4687},
}
@article {pmid40012987,
year = {2024},
author = {McGregor, AP and Sumner-Rooney, L and Burkmar, R and Schoenauer, A and , and , and , and , and , and , and , },
title = {The genome sequence of the silver stretch spider, Tetragnatha montana (Simon, 1874) (Araneae: Tetragnathidae).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {288},
pmid = {40012987},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Tetragnatha montana (the silver stretch spider; Arthropoda; Arachnida; Araneae; Tetragnathidae). The genome sequence is 784.7 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.49 kilobases in length.},
}
@article {pmid40012989,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Olive Crescent, Trisateles emortualis (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {178},
pmid = {40012989},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Trisateles emortualis (the Olive Crescent; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 565.5 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 16.01 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,176 protein coding genes.},
}
@article {pmid40014700,
year = {2025},
author = {Chen, Z and Baeza, JA and Chen, C and Gonzalez, MT and González, VL and Greve, C and Kocot, KM and Arbizu, PM and Moles, J and Schell, T and Schwabe, E and Sun, J and Wong, NLWS and Yap-Chiongco, M and Sigwart, JD},
title = {A genome-based phylogeny for Mollusca is concordant with fossils and morphology.},
journal = {Science (New York, N.Y.)},
volume = {387},
number = {6737},
pages = {1001-1007},
doi = {10.1126/science.ads0215},
pmid = {40014700},
issn = {1095-9203},
mesh = {Animals ; Biological Evolution ; *Fossils ; *Genome ; *Mollusca/genetics/anatomy &amp; histology/classification ; Phylogeny ; },
abstract = {Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups-gastropods, bivalves, and cephalopods-each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success.},
}
@article {pmid40016792,
year = {2025},
author = {Mendoza, JN and Prūse, B and Ciriaco, A and Mendoza, A and Ciriaco, H and Buen, C and Pua, JJ and Primavera, F and Mattalia, G and Sõukand, R},
title = {Correction: Fishery and ecology-related knowledge about plants among fishing communities along Laguna Lake, Philippines.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {21},
number = {1},
pages = {11},
doi = {10.1186/s13002-025-00763-7},
pmid = {40016792},
issn = {1746-4269},
}
@article {pmid40017036,
year = {2025},
author = {Han, Y and Du, Q and Dai, Y and Gu, S and Lei, M and Liu, W and Zhang, W and Zhu, M and Feng, L and Si, H and Liu, J and Zan, Y},
title = {EasyOmics: A graphical interface for population-scale omics data association, integration, and visualization.},
journal = {Plant communications},
volume = {6},
number = {5},
pages = {101293},
pmid = {40017036},
issn = {2590-3462},
mesh = {*Software ; *Genomics/methods ; Genome-Wide Association Study ; *Computational Biology/methods ; User-Computer Interface ; Computer Graphics ; Quantitative Trait Loci ; Proteomics ; Metabolomics ; },
abstract = {The rapid growth of population-scale whole-genome resequencing, RNA sequencing, bisulfite sequencing, and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data. Association analyses of omics data, such as genome-, transcriptome-, proteome-, and methylome-wide association studies, along with integrative analyses of multiple omics datasets, require various bioinformatics tools, which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists. Here, we present EasyOmics, a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association, integration, and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, including data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration, and visualization. A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking. EasyOmics is a platform-independent software that can be run under all operating systems, with a docker container for quick installation. It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.},
}
@article {pmid40021550,
year = {2025},
author = {Post, AK and Richardson, AD},
title = {Predicting end-of-season timing across diverse North American grasslands.},
journal = {Oecologia},
volume = {207},
number = {3},
pages = {44},
pmid = {40021550},
issn = {1432-1939},
support = {EF-1065029//National Science Foundation/ ; EF-1702697//National Science Foundation/ ; DESC0016011//U.S. Department of Energy/ ; },
mesh = {*Grassland ; *Seasons ; *Climate Change ; North America ; Ecosystem ; },
abstract = {Climate change is altering the timing of seasonal vegetation cycles (phenology), with cascading consequences on larger ecosystem processes. Therefore, understanding the drivers of vegetation phenology is critical to predicting ecological impacts of climate change. While numerous phenology models exist to predict the timing of the start of the growing season (SOS), there are fewer end-of-season (EOS) models, and most perform poorly in grasslands, since they were made for forests. Our objective was to develop an improved EOS grassland phenology model. We used repeat digital imagery from the PhenoCam Network to extract EOS dates for 44 diverse North American grassland sites (212 site-years) that we fit to 20 new and 3 existing EOS models. All new EOS models (RMSE = 22-33 days between observed and predicted dates) performed substantially better than existing ones (RMSE = 43-46 days). The top model predicted EOS after surpassing a threshold of either accumulated cold temperatures or dryness, but only after a certain number of days following SOS. Including SOS date improved all model fits, indicating a strong correlation between start- and end-of-season timing. Model performance was further improved by independently optimizing parameters for six distinct climate regions (RMSE = 4-19 days). While the best model varied slightly by region, most included similar drivers as the top all-sites model. Thus, across diverse grassland sites, EOS is influenced by both weather (temperature, moisture) and SOS timing. Incorporating these new EOS models into Earth System Models should improve predictions of grassland dynamics and associated ecosystem processes.},
}
@article {pmid40022802,
year = {2025},
author = {Wang, H and Liu, C and Li, L and Kong, Y and Akbar, A and Zhou, X},
title = {High-precision inversion of urban river water quality via integration of riparian spatial structures and river spectral signatures.},
journal = {Water research},
volume = {278},
number = {},
pages = {123378},
doi = {10.1016/j.watres.2025.123378},
pmid = {40022802},
issn = {1879-2448},
mesh = {*Rivers/chemistry ; *Water Quality ; *Environmental Monitoring/methods ; Phosphorus/analysis ; Remote Sensing Technology ; Urbanization ; Cities ; China ; },
abstract = {With the ongoing process of urbanization, it poses challenges to the monitoring of water quality in urban rivers. The mainstream methods for remote sensing water quality monitoring rely on the optical characteristics of water to achieve water quality inversion, while overlooking the correlation between water quality and riparian zones. The spatial arrangement and scale fluctuation of the riparian zones exert a substantial influence on water quality as it serves as an intermediary region connecting riverine and terrestrial ecosystems. Therefore, this study firstly employed unmanned aerial vehicle (UAV)-borne multispectral remote sensing technology to capture the subtle variations in urban river water quality and obtain detailed spatial information of the riparian zone. The Liang-Kleeman information flow was subsequently employed to quantitatively assess the causal responses of the spatial composition of riparian zone to water quality parameters across various spatial scales. Finally, we developed a hierarchical ensemble learning model for water quality assessment by integrating the spatial characteristics of the riparian zone with the spectral properties of the water body. The result demonstrates that this model accurately delineated water quality grades for three key parameters: ammonia nitrogen (NH3N), chemical oxygen demand (COD), and total phosphorus (TP), achieving accuracies of 94.87 %, 92.31 %, and 89.74 %, respectively. Our study presents a water quality inversion method for urban rivers, which holds significant guidance for the monitoring and management of urban rivers and contributes to further promoting the sustainable development of cities.},
}
@article {pmid40023237,
year = {2025},
author = {Munteanu, A and Bortolini, M and Feltracco, M and Alterio, A and Cairns, WRL and Turetta, C and Barbaro, E and Barbante, C and Gambaro, A and Azzaro, M},
title = {Contamination by benzothiazoles in the Arctic: First evidence in the seawater of the Greenland Sea.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {371},
number = {},
pages = {125943},
doi = {10.1016/j.envpol.2025.125943},
pmid = {40023237},
issn = {1873-6424},
mesh = {*Benzothiazoles/analysis ; *Seawater/chemistry ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring ; Greenland ; Arctic Regions ; Water Pollution, Chemical/statistics &amp; numerical data ; },
abstract = {Benzothiazoles (BTHs), used in industrial chemistry, consumer products, and pharmaceuticals, are emerging contaminants due to their environmental presence and toxicological risks to aquatic life and human health. However, their environmental fate in seawater remains poorly investigated. This study reports for the first time the occurrence and distribution of six BTHs in the sub-Arctic seawater of the Greenland Sea. Using solid-phase extraction combined with ultrahigh performance liquid chromatography tandem mass spectrometry, total BTHs were detected at concentrations ranging from 0.2 to 1043 ng L[-1]. Benzothiazole, 2-hydroxy-benzothiazole, 2-methylthio-benzothiazole, and 2-methyl-benzothiazole exhibited higher mean concentrations (355 ± 335, 114 ± 80, 34 ± 7, 15 ± 8 ng L[-1], respectively) compared to 2-thiocyanomethylthio-benzothiazole (0.5 ± 0.9 ng L[-1]) and 2-amino-benzothiazole (0.3 ± 0.2 ng L[-1]). Local emissions and both short- and long-range transport may account for BTHs presence in the Greenland Sea. The spatial distribution of BTHs along the 75° N transect and in the water column appears influenced by the Greenland Sea Gyre circulation and deep convection processes. Total BTHs distribution showed no significant differences between superficial and water column concentrations or between the outermost and innermost transect zones, as determined by the Mann-Whitney test, although concentrations were generally higher in the zone influenced by the Norwegian Atlantic Current. The ecological risks of BTHs, assessed using the risk quotient methodology, indicate a low threat to aquatic life. This research underscores the need for monitoring BTHs in the Arctic to understand their sources, transport, and environmental fate, providing a foundation for future studies.},
}
@article {pmid40025088,
year = {2025},
author = {Kim, SY and Cheon, S and Park, C and Soh, HY},
title = {Integrating DNA metabarcoding and morphological analysis improves marine zooplankton biodiversity assessment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {7283},
pmid = {40025088},
issn = {2045-2322},
support = {RS-2018-KS181192//Korea Institute of Marine Science &amp; Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries, Korea/ ; No. RS-2024-00442775)//Global-Learning &amp; Academic research institution for Master's &#xb7; PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; Grant number: 2018-3416//Chonnam National University/ ; },
mesh = {Animals ; *Zooplankton/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Copepoda/genetics/classification ; Ecosystem ; China ; Oceans and Seas ; },
abstract = {Marine copepod communities play crucial roles in ocean ecosystems. However, their accurate assessment remains challenging due to taxonomic complexities. This study combines morphological and DNA metabarcoding approaches to evaluate copepod diversity and community structure in the northern East China Sea. Zooplankton samples were collected from 10 stations along a coastal-offshore gradient in August 2019. Morphological analysis identified 34 species from 25 genera, while DNA metabarcoding detected 31 species from 20 genera. Both methods revealed distinct coastal and offshore assemblages, with Paracalanus parvus s.l. as the dominant species across all stations. A significant positive correlation was found between morphology-based individual counts and metabarcoding sequence reads (Spearman's Rho = 0.58, p < 0.001), improving at the genus level (Rho = 0.70, p < 0.001). Redundancy analysis revealed that salinity, temperature, and phytoplankton density significantly influenced copepod distribution. Although both approaches captured similar broad-scale patterns, they provided complementary insights into community structure. Morphological identification was more effective for detecting Cyclopoida diversity, whereas DNA metabarcoding had greater sensitivity for specific Calanoid species. This study underscores the value of integrating traditional and molecular methods for marine biodiversity assessment, especially in the context of global environmental changes.},
}
@article {pmid40027489,
year = {2025},
author = {Bai, D and Chen, T and Xun, J and Ma, C and Luo, H and Yang, H and Cao, C and Cao, X and Cui, J and Deng, YP and Deng, Z and Dong, W and Dong, W and Du, J and Fang, Q and Fang, W and Fang, Y and Fu, F and Fu, M and Fu, YT and Gao, H and Ge, J and Gong, Q and Gu, L and Guo, P and Guo, Y and Hai, T and Liu, H and He, J and He, ZY and Hou, H and Huang, C and Ji, S and Jiang, C and Jiang, GL and Jiang, L and Jin, LN and Kan, Y and Kang, D and Kou, J and Lam, KL and Li, C and Li, C and Li, F and Li, L and Li, M and Li, X and Li, Y and Li, ZT and Liang, J and Lin, Y and Liu, C and Liu, D and Liu, F and Liu, J and Liu, T and Liu, T and Liu, X and Liu, Y and Liu, B and Liu, M and Lou, W and Luan, Y and Luo, Y and Lv, H and Ma, T and Mai, Z and Mo, J and Niu, D and Pan, Z and Qi, H and Shi, Z and Song, C and Sun, F and Sun, Y and Tian, S and Wan, X and Wang, G and Wang, H and Wang, H and Wang, H and Wang, J and Wang, J and Wang, K and Wang, L and Wang, SK and Wang, X and Wang, Y and Xiao, Z and Xing, H and Xu, Y and Yan, SY and Yang, L and Yang, S and Yang, Y and Yao, X and Yousuf, S and Yu, H and Lei, Y and Yuan, Z and Zeng, M and Zhang, C and Zhang, C and Zhang, H and Zhang, J and Zhang, N and Zhang, T and Zhang, YB and Zhang, Y and Zhang, Z and Zhou, M and Zhou, Y and Zhu, C and Zhu, L and Zhu, Y and Zhu, Z and Zou, H and Zuo, A and Dong, W and Wen, T and Chen, S and Li, G and Gao, Y and Liu, YX},
title = {EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.},
journal = {iMeta},
volume = {4},
number = {1},
pages = {e70001},
pmid = {40027489},
issn = {2770-596X},
abstract = {Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in-depth analysis of microbial communities at both the high-resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user-friendly pipeline that supports multiple analysis methods, including quality control and host removal, read-based, assembly-based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third-generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.},
}
@article {pmid40028774,
year = {2025},
author = {Fuzessy, L and Pizo, MA},
title = {NeoFrugivory: A comprehensive database for frugivory interactions and functional traits in the Neotropics.},
journal = {Ecology},
volume = {106},
number = {3},
pages = {e70049},
doi = {10.1002/ecy.70049},
pmid = {40028774},
issn = {1939-9170},
support = {2023/12469-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 21/02943-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 151167/2023-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304742/2019-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; *Fruit/physiology ; *Vertebrates/physiology ; *Databases, Factual ; Ecosystem ; *Herbivory ; *Feeding Behavior/physiology ; Plants/classification ; South America ; },
abstract = {Frugivory plays a crucial role in shaping Neotropical ecosystems, influencing plant dispersal, community dynamics, and ecosystem function. Despite its ecological significance, a systematic understanding of frugivore-fruit interactions spanning the entire Neotropical realm has been lacking. Therefore, we compiled the NeoFrugivory database, which addresses this gap by synthesizing data from a wide range of sources, including peer-reviewed literature, field studies, and existing databases. NeoFrugivory represents a comprehensive compilation of 10,175 unique frugivory interactions across the Neotropical region, the most diverse in terms of vertebrate frugivores, and consolidates information from 419 studies spanning from 1967 to 2023. It includes 2375 plant species and 758 terrestrial vertebrate species. In addition to documenting frugivory interactions, NeoFrugivory includes information on functional traits for both plants and vertebrates, such as body mass, diet, fruit morphology, and seed characteristics. The database encompasses diverse terrestrial vertebrate taxa, including species belonging to taxonomic groups such as Primates, Chiroptera, Birds, Artiodactyla/Perissodactyla, Reptilia, Carnivora, Marsupialia, and Rodentia. By providing a centralized repository of frugivory interactions, NeoFrugivory facilitates comprehensive analyses of ecological networks, evolutionary patterns, and ecosystem dynamics across the Neotropics, and NeoFrugivory provides a unique resource for researchers interested in exploring the intricate dynamics of plant-animal frugivory interactions in the Neotropics. This database enables researchers to explore the ecological roles of different frugivore taxa, identify keystone species, assess the resilience of mutualistic networks, and evaluate the impacts of environmental change on fruit-frugivore interactions. Furthermore, NeoFrugivory serves as a valuable resource for conservation practitioners, supporting the design and implementation of targeted conservation strategies aimed at preserving biodiversity and ecosystem function in the Neotropical region. Overall, NeoFrugivory represents a significant advancement in our understanding of frugivory dynamics in the Neotropics and provides a foundation for future research and conservation efforts in this ecologically diverse and critically important region. There are no copyright restrictions on the data; this paper should be cited when data are used in publications.},
}
@article {pmid40029426,
year = {2025},
author = {Zhang, J and Wang, Q and Gao, H and Qi, Q and He, W and Li, J and Yao, S and Li, W},
title = {Ecological suitability distribution of hop based on MaxEnt modeling.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {4},
pages = {346},
pmid = {40029426},
issn = {1573-2959},
mesh = {China ; *Humulus/growth &amp; development ; *Environmental Monitoring/methods ; Geographic Information Systems ; *Ecosystem ; Models, Theoretical ; Conservation of Natural Resources ; },
abstract = {Hop has been widely utilized in both food production and traditional medicine owing to their distinctive flavor and various pharmacological effects. In recent years, the increasing demand for hop has led to their cultivation in many regions across China. However, hops require specific ecological conditions, including climate, soil, precipitation, and temperature, which significantly affect their distribution and growth. To facilitate the standardization and scientific cultivation of hops, it is essential to clarify the distribution of their ecological suitability. In this study, we collected data from 95 hops distribution locations and 115 ecological factors to determine the areas suitable for hops cultivation using the Maximum Entropy (MaxEnt) model and Geographic Information System (GIS). The highly suitable areas are primarily located in the northwestern part of the Xinjiang Uygur Autonomous Region, the eastern part of Gansu Province, Shaanxi Province, the southwestern part of Shanxi Province, and parts of Ningxia Hui Autonomous Region and Yunnan Province. These findings provide valuable guidance for the scientific cultivation of hops, ensuring the efficient use of ecological resources and promoting sustainable cultivation practices.},
}
@article {pmid40030035,
year = {2025},
author = {Jin, J and Zhang, R and Li, J and Gao, F and Liao, Z and Yu, Y and Wang, Y and Bucci, D and Xiao, M and Ma, R and Ma, Q and Gao, S and Lio, J and Novais, F and Huang, SC and Zhu, J and Ghoneim, H and Wen, H and Li, Z and Sun, N and Xin, G},
title = {The NAE1-mediated neddylation operates as an essential post-translational modification checkpoint for effector CD8[+] T cells.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {10},
pages = {e2424061122},
pmid = {40030035},
issn = {1091-6490},
support = {1R01CA269984//HHS | NIH | National Cancer Institute (NCI)/ ; R01 AI162711/AI/NIAID NIH HHS/United States ; R01 CA269984/CA/NCI NIH HHS/United States ; P30 CA016058/CA/NCI NIH HHS/United States ; R01 HL162909/HL/NHLBI NIH HHS/United States ; RSG-23-1036499-01//American Cancer Society (ACS)/ ; CCR231013713//Susan G. Komen (SGK)/ ; },
mesh = {*CD8-Positive T-Lymphocytes/immunology/metabolism ; Animals ; *Protein Processing, Post-Translational ; Humans ; Mice ; *NEDD8 Protein/metabolism ; *Ubiquitin-Activating Enzymes/metabolism/genetics ; Receptors, Antigen, T-Cell/metabolism ; Lymphocyte Activation ; NFATC Transcription Factors/metabolism/genetics ; Colonic Neoplasms/immunology/pathology/metabolism ; Proteomics ; Mice, Inbred C57BL ; },
abstract = {Optimal activation of CD8+ T cells is crucial for immunity-mediated destruction of cancer, requiring a substantial amount of proteins involved in metabolism, proliferation, and effector function. Despite extensive studies emphasizing the role of transcriptional regulation in this process, paired transcriptomic and proteomic analyses reveal that the RNA profile is poorly correlated with protein levels. This discrepancy underscores the importance of post-translational modifications (PTMs) in controlling protein abundance during activation. However, the impact of PTMs on the CD8+ T cell protein dynamic remains underexplored. We identify that neddylation, a recently discovered PTM, is activated in response to T cell receptor (TCR) stimulation and enriched in effector CD8+ T cells from colon cancer patients. Mechanistically, we found the rate-limiting enzyme of neddylation, neural precursor cell expressed developmentally down-regulated protein 8 activating enzyme E1 (NAE1), is induced by the NFATc1, a critical transcription factor downstream of TCR signaling. Our observation revealed that genetic ablation of NAE1 significantly disturbed the proteomic landscape related to activation and mitochondrial function. As a result, CD8+ T cells lacking NAE1 exhibited severely compromised activation, proliferation, and survival, which was accompanied by impaired mitochondrial function. Consistently, deletion of NAE1 in CD8+ T cells abolished their antitumor function and promoted tumor progression. By contrast, the overexpression of NAE1 significantly improved the function of tumor-infiltrating CD8+ T cells. Overall, we uncovered neddylation, a previously underappreciated PTM, as a proteomic checkpoint for CD8+ T cell activation. Enforced expression of NAE1 offers promising therapeutic potential for boosting the antitumor CD8+ T cell responses.},
}
@article {pmid40033715,
year = {2025},
author = {Gorné, LD and Hendry, AP and Pelletier, F and Sanderson, S and Correa, C and Arias, C and Beausoleil, MO and Boisjoly, M and Crispo, E and Berner, D and De León, LF and DiBattista, JD and Haines, GE and Haller, BC and Kinnison, MT and Muttalib, S and McKellar, AE and O'Dea, RE and Reyes-Corral, WD and Ritchot, Y and Oke, KB and Wood, ZT and Farrugia, T and Gotanda, KM},
title = {PROCEED v6.1: Phenotypic rates of change evolutionary and ecological database.},
journal = {Ecology},
volume = {106},
number = {3},
pages = {e70009},
pmid = {40033715},
issn = {1939-9170},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Le Fonds Qu&#xe9;b&#xe9;cois de la Recherche sur la Nature et les Technologies/ ; //McGill University/ ; //National Science Foundation/ ; //Brock University/ ; },
mesh = {*Phenotype ; *Biological Evolution ; Animals ; *Databases, Factual ; *Ecosystem ; *Ecology ; },
abstract = {Populations must continuously respond to environmental change or risk extinction. These responses can be measured as phenotypic rates of change, which allow researchers to predict their contemporary evolutionary responses. In 1999, a database of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this database to examine the phenotypic responses as a function of the features of the study system (i.e., the population or set of populations, of a given species, that experienced a specific driver or disturbance), the measured traits, and methodological approaches. Therefore, PROCEED (Phenotypic Rates of Change Evolutionary and Ecological Database) is an ongoing compilation of rates of phenotypic change, typically calculated as Haldanes and Darwins, published in peer-reviewed literature (but also including data from theses and technical reports). Studies in this database measure the intraspecific change in quantitative (continuous or discrete) traits and report either the time elapsed from the onset of environmental novelty, or reference a historical or biological event reported in other sources (e.g., a mine opening or a well-documented biological invasion). Included studies either follow a single population through time (allochronic design) or compare two or more populations that diverged at a known time (synchronic design). Some included studies account for the total phenotypic variability in the field (i.e., phenotypic studies), while others employed common-garden or other quantitative genetic approaches to account for the heritable component of the phenotypic change (i.e., genetic studies). PROCEED includes systems in both natural and experimental conditions, provided that reproduction was not manipulated (i.e., artificial selection experiments were excluded). In the included experimental systems, the environment of the focal populations was manipulated (e.g., an herbivory exclusion experiment, where the type and load of herbivory are manipulated) but the studies did not deliberately select for trait values in the study population (e.g., the plant height). PROCEED does not include systems where the phenotypic change is presumably due to interspecific hybridization, polyploidy, or other chromosomal alterations. Here, we present the most recently updated PROCEED (Version 6.1). This new, curated version has 9263 records (n) collated from 326 studies, 1801 systems, and 428 species. The database includes records belonging to mammals (n = 686), birds (n = 1475), reptiles (n = 96), amphibians (n = 23), fishes (n = 3671), invertebrates (n = 1141, mostly arthropods), and plants (n = 2171). The maximum elapsed time between the environmental change and the sampling is 500 years but is typically less than 100 years (third quartile 89.5; median 45 years). The database also includes a set of variables describing biological and methodological aspects of the study system and measured traits, along with features of the sampling design in the primary source of information. This new version of PROCEED also includes a time series dataset comprising a subset of records included in the general dataset. These are allochronic studies with three or more sampling times throughout the entire study period. The time series dataset contains 655 time series (s)-belonging to 61 studies, from 156 systems, and 77 species-including mammals (s = 140), birds (s = 77), reptiles (s = 4), amphibians (s = 8), fishes (s = 404), and plants (s = 22). The data are released under a Creative Commons CC0 1.0 Universal Public Domain Dedication license.},
}
@article {pmid40034275,
year = {2025},
author = {Veneros, J and Hansen, AJ and Jantz, P and Roberts, D and Noguera-Urbano, E and García, L},
title = {Analysis of changes in temperature and precipitation in South American countries and ecoregions: Comparison between reference conditions and three representative concentration pathways for 2050.},
journal = {Heliyon},
volume = {11},
number = {4},
pages = {e42459},
pmid = {40034275},
issn = {2405-8440},
abstract = {Climate change is a global concern, and its impact on environmental variables such as temperature and annual precipitation is unknown spatially in the desert, andes, and rainforest ecoregions of Peru, Ecuador, and Colombia. In this study, we conducted a general review of climate drivers for South America (SA) and explored climate data using the GCM compareR package (General Circulation Models) and average ensembles for temperature and precipitation. Our results showed that all GCMs demonstrated increases in the annual mean temperature (BIO1) and in the mean temperature of the driest quarter (BIO9) for Peru, Ecuador, and Colombia for 2050 in three RCPs (2.6, 4.5, and 8.5). Also, most of the GCMs showed increases in the annual precipitation (BIO12) and the precipitation in the driest quarter (BIO17). We conducted non-parametric tests (Kruskal-Wallis Test) to assess if the medians of temperature and precipitation in the three ecoregions are equal for both the baseline and the climate change scenarios. We rejected the null hypothesis that the medians are equal for both temperatures and precipitation in the baseline vs. 2050 RCPs (2.6, 4.5, and 8.5). A spatial analysis was conducted to visualize the variations in temperature and precipitation between the RCPs versus the baseline, and the spatial variation at the country or ecoregion level can be observed. The annual mean temperature (°C) or annual precipitation (mm) divided by its standard deviation for each ecoregion (M metric) was analyzed to see how much the average temperature or the annual precipitation is relatively large compared to the variability or dispersion of temperatures or precipitation respectively; the average temperature and the annual precipitation for the baseline and the three RCPs are relatively large and associated with the variability or dispersion of their temperatures in the Napo moist forest compared to the other ecoregions. Our study provides important insights into the potential impacts of climate change on these ecosystems. Prospects in the Napo moist forest ecoregion, where significant changes in temperature and humidity have already occurred, and new species have invaded or evolved in the western Amazon rainforest, are particularly highlighted and reflected in terms of risk mitigation, ecosystem restoration, surveillance, and monitoring.},
}
@article {pmid40036964,
year = {2025},
author = {Jyoti, J and Hütt, MT},
title = {Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {4},
pages = {},
pmid = {40036964},
issn = {1367-4811},
mesh = {Algorithms ; *Microbial Interactions ; Humans ; *Microbiota ; *Computational Biology/methods ; },
abstract = {MOTIVATION: Inferring microbial interaction networks from microbiome data is a core task of computational ecology. An avenue of research to create reliable inference methods is based on a stylized view of microbiome data, starting from the assumption that the presences and absences of microbiomes, rather than the quantitative abundances, are informative about the underlying interaction network. With this starting point, inference algorithms can be based on the notion of attractors (asymptotic states) in Boolean networks. Boolean network framework offers a computationally efficient method to tackle this problem. However, often existing algorithms operating under a Boolean network assumption, fail to provide networks that can reproduce the complete set of initial attractors (abundance patterns). Therefore, there is a need for network inference algorithms capable of reproducing the initial stable states of the system.<br><br>RESULTS: We study the change of attractors in Boolean threshold dynamics on signed undirected graphs under small changes in network architecture and show, how to leverage these relationships to enhance network inference algorithms. As an illustration of this algorithmic approach, we analyse microbial abundance patterns from stool samples of humans with inflammatory bowel disease (IBD), with colorectal cancer and from healthy individuals to study differences between the interaction networks of the three conditions. The method reveals strong diversity in IBD interaction networks. The networks are first partially deduced by an earlier inference method called ESABO, then we apply the new algorithm developed here, EDAME, to this result to generate a network that comes nearest to satisfying the original attractors.<br><br>Implementation code is freely available at https://github.com/Jojo6297/edame.git.},
}
@article {pmid40038157,
year = {2025},
author = {Prescott, J and Keyser, AJ and Litwin, P and Dunbar, MD and McClelland, R and Ruple, A and Ernst, H and Butler, BL and Kauffman, M and Avery, A and Harrison, BR and Partida-Aguilar, M and McCoy, BM and Slikas, E and Greenier, AK and Muller, E and Algavi, YM and Bamberger, T and Creevy, KE and , and Borenstein, E and Snyder-Mackler, N and Promislow, DEL},
title = {Rationale and design of the Dog Aging Project precision cohort: a multi-omic resource for longitudinal research in geroscience.},
journal = {GeroScience},
volume = {47},
number = {4},
pages = {5725-5748},
pmid = {40038157},
issn = {2509-2723},
support = {U19 AG057377/AG/NIA NIH HHS/United States ; AG057377/AG/NIA NIH HHS/United States ; USDA/ARS 58-8050-9-004//U.S. Department of Agriculture/ ; AG057377/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; *Dogs/physiology ; Female ; Male ; *Aging/physiology ; Immunophenotyping ; Life Expectancy ; *Multiomics/methods/organization &amp; administration/standards ; Pets/physiology ; Research Design ; Longitudinal Studies ; *Geroscience/methods ; },
abstract = {A significant challenge in multi-omic geroscience research is the collection of high quality, fit-for-purpose biospecimens from a diverse and well-characterized study population with sufficient sample size to detect age-related changes in physiological biomarkers. The Dog Aging Project designed the precision cohort to study the mechanisms underlying age-related change in the metabolome, microbiome, and epigenome in companion dogs, an emerging model system for translational geroscience research. One thousand dog-owner pairs were recruited into cohort strata based on life stage, sex, size, and geography. We designed and built a novel implementation of the REDCap electronic data capture system to manage study participants, logistics, and biospecimen and survey data collection in a secure online platform. In collaboration with primary care veterinarians, we collected and processed blood, urine, fecal, and hair samples from 976 dogs. The resulting data include complete blood count, chemistry profile, immunophenotyping by flow cytometry, metabolite quantification, fecal microbiome characterization, epigenomic profile, urinalysis, and associated metadata characterizing sample conditions at collection and during lab processing. The project, which has already begun collecting second- and third-year samples from precision cohort dogs, demonstrates that scientifically useful biospecimens can be collected from a geographically dispersed population through collaboration with private veterinary clinics and downstream labs. The data collection infrastructure developed for the precision cohort can be leveraged for future studies. Most important, the Dog Aging Project is an open data project. We encourage researchers around the world to apply for data access and utilize this rich, constantly growing dataset in their own work.},
}
@article {pmid40038315,
year = {2025},
author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C},
title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {378},
pmid = {40038315},
issn = {2052-4463},
support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//&#xc9;cole Nationale d'Ing&#xe9;nieurs de Saint-Etienne (National Engineering School of Saint-&#xc9;tienne)/ ; },
mesh = {China ; *Microbiota ; *Bays/microbiology ; Archaea/genetics/classification ; Metagenome ; Bacteria/classification/genetics ; Oceans and Seas ; Metagenomics ; *Seawater/microbiology ; Multiomics ; },
abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.},
}
@article {pmid40041564,
year = {2025},
author = {Zhang, J and Qian, H and Wang, X},
title = {An online version and some updates of R package U.Taxonstand for standardizing scientific names in plant and animal species.},
journal = {Plant diversity},
volume = {47},
number = {1},
pages = {166-168},
pmid = {40041564},
issn = {2468-2659},
abstract = {•We present 'U.Taxonstand Online', a user-friendly web application for scientific name matching of both plants and animals.•U.Taxonstand Online provides a solution for the users with limited abilities of programming and data mining.•We add several new functions to clean and format the data for R package U.Taxonstand.},
}
@article {pmid40044867,
year = {2025},
author = {Aguirre-Gutiérrez, J and Rifai, SW and Deng, X and Ter Steege, H and Thomson, E and Corral-Rivas, JJ and Guimaraes, AF and Muller, S and Klipel, J and Fauset, S and Resende, AF and Wallin, G and Joly, CA and Abernethy, K and Adu-Bredu, S and Alexandre Silva, C and de Oliveira, EA and Almeida, DRA and Alvarez-Davila, E and Asner, GP and Baker, TR and Benchimol, M and Bentley, LP and Berenguer, E and Blanc, L and Bonal, D and Bordin, K and Borges de Lima, R and Both, S and Cabezas Duarte, J and Cardoso, D and de Lima, HC and Cavalheiro, L and Cernusak, LA and Dos Santos Prestes, NCC and da Silva Zanzini, AC and da Silva, RJ and Dos Santos Alves da Silva, R and de Andrade Iguatemy, M and De Sousa Oliveira, TC and Dechant, B and Derroire, G and Dexter, KG and Rodrigues, DJ and Espírito-Santo, M and Silva, LF and Domingues, TF and Ferreira, J and Simon, MF and Girardin, CAJ and Hérault, B and Jeffery, KJ and Kalpuzha Ashtamoorthy, S and Kavidapadinjattathil Sivadasan, A and Klitgaard, B and Laurance, WF and Dan, ML and Magnusson, WE and Campos-Filho, EM and Manoel Dos Santos, R and Manzatto, AG and Silveira, M and Marimon-Junior, BH and Martin, RE and Vieira, DLM and Metzker, T and Milliken, W and Moonlight, P and Moraes de Seixas, MM and Morandi, PS and Muscarella, R and Nava-Miranda, MG and Nyirambangutse, B and Silva, JO and Oliveras Menor, I and Francisco Pena Rodrigues, PJ and Pereira de Oliveira, C and Pereira Zanzini, L and Peres, CA and Punjayil, V and Quesada, CA and Réjou-Méchain, M and Riutta, T and Rivas-Torres, G and Rosa, C and Salinas, N and Bergamin, RS and Marimon, BS and Shenkin, A and Silva Rodrigues, PM and Figueiredo, AES and Garcia, QS and Spósito, T and Storck-Tonon, D and Sullivan, MJP and Svátek, M and Vieira Santiago, WT and Arn Teh, Y and Theruvil Parambil Sivan, P and Nascimento, MT and Veenendaal, E and Zo-Bi, IC and Dago, MR and Traoré, S and Patacca, M and Badouard, V and de Padua Chaves E Carvalho, S and White, LJT and Zhang-Zheng, H and Zibera, E and Zwerts, JA and Burslem, DFRP and Silman, M and Chave, J and Enquist, BJ and Barlow, J and Phillips, OL and Coomes, DA and Malhi, Y},
title = {Canopy functional trait variation across Earth's tropical forests.},
journal = {Nature},
volume = {641},
number = {8061},
pages = {129-136},
pmid = {40044867},
issn = {1476-4687},
support = {//Natural Environment Research Council/ ; //ERC Advanced Investigator Award/ ; //T-FORCES/ ; //NERC/ ; },
mesh = {Africa ; Asia ; Biodiversity ; *Earth, Planet ; *Forests ; Plant Leaves/physiology/chemistry/anatomy &amp; histology ; Soil/chemistry ; *Trees/physiology/anatomy &amp; histology/chemistry/classification ; Tropical Climate ; Uncertainty ; },
abstract = {Tropical forest canopies are the biosphere's most concentrated atmospheric interface for carbon, water and energy[1,2]. However, in most Earth System Models, the diverse and heterogeneous tropical forest biome is represented as a largely uniform ecosystem with either a singular or a small number of fixed canopy ecophysiological properties[3]. This situation arises, in part, from a lack of understanding about how and why the functional properties of tropical forest canopies vary geographically[4]. Here, by combining field-collected data from more than 1,800 vegetation plots and tree traits with satellite remote-sensing, terrain, climate and soil data, we predict variation across 13 morphological, structural and chemical functional traits of trees, and use this to compute and map the functional diversity of tropical forests. Our findings reveal that the tropical Americas, Africa and Asia tend to occupy different portions of the total functional trait space available across tropical forests. Tropical American forests are predicted to have 40% greater functional richness than tropical African and Asian forests. Meanwhile, African forests have the highest functional divergence-32% and 7% higher than that of tropical American and Asian forests, respectively. An uncertainty analysis highlights priority regions for further data collection, which would refine and improve these maps. Our predictions represent a ground-based and remotely enabled global analysis of how and why the functional traits of tropical forest canopies vary across space.},
}
@article {pmid40045055,
year = {2025},
author = {Shi, J and Gong, J and Zhang, Y and Kan, G},
title = {Spatiotemporal change in ecological quality of the Qinghai-Tibetan Plateau based on an improved remote sensing ecological index and Google Earth Engine platform.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {4},
pages = {355},
pmid = {40045055},
issn = {1573-2959},
mesh = {*Remote Sensing Technology ; *Environmental Monitoring/methods ; *Ecosystem ; China ; Tibet ; Spatio-Temporal Analysis ; Conservation of Natural Resources ; Geographic Information Systems ; },
abstract = {The Qinghai-Tibetan Plateau (QTP) serves as a vital ecological security barrier in China and globally. Evaluating changes in ecological quality on the QTP provides critical insights for regional conservation initiatives. This study, tailored to the unique characteristics of the region, develops an Improved Remote Sensing Ecological Index (IRSEI) framework by integrating Gross Primary Productivity (GPP) with the Normalized Difference Vegetation Index (NDVI), humidity (WET), Land Surface Temperature (LST), and the Negative Drought Index (NDBSI). This comprehensive index aims to provide a more precise assessment of the environmental quality of the alpine ecosystem. It investigates spatial and temporal variations in ecological quality across the QTP, as well as within individual geographic subregions from 2000 to 2020. The first principal component accounts for an average variance of 63.69%. Over the past 20 years, the spatial distribution pattern of IRSEI on the QTP has shown lower values in the northwest, higher values in the southeast, and predominantly poor grades throughout the region. The mean trend coefficient for IRSEI was 0.002, indicating a gradual improvement in ecological quality on the QTP over time. Among 11 influencing factors examined, NDVI and GPP exhibit significant positive correlation with ecological quality, with q statistics of 0.942 and 0.932, respectively, underscoring the substantial impact of vegetation cover on ecosystem quality. These findings provide a robust theoretical foundation for supporting ecological management, restoration efforts, and the evaluation of ecological restoration within the QTP, thereby promoting ecosystem balance.},
}
@article {pmid40045231,
year = {2025},
author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD},
title = {Cross-validation for training and testing co-occurrence network inference algorithms.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {74},
pmid = {40045231},
issn = {1471-2105},
support = {2125088//National Science Foundation/ ; },
mesh = {*Algorithms ; *Microbiota ; *Computational Biology/methods ; },
abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.<br><br>RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.<br><br>CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.},
}
@article {pmid40048849,
year = {2025},
author = {Bargheet, A and Noordzij, HT and Ponsero, AJ and Jian, C and Korpela, K and Valles-Colomer, M and Debelius, J and Kurilshikov, A and Pettersen, VK},
title = {Dynamics of gut resistome and mobilome in early life: a meta-analysis.},
journal = {EBioMedicine},
volume = {114},
number = {},
pages = {105630},
pmid = {40048849},
issn = {2352-3964},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Metagenomics/methods ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Metagenome ; Female ; Interspersed Repetitive Sequences ; *Drug Resistance, Bacterial/genetics ; Computational Biology/methods ; },
abstract = {BACKGROUND: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut.<br><br>METHODS: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers.<br><br>FINDINGS: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E.&#xa0;coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults.<br><br>INTERPRETATION: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow.<br><br>FUNDING: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Troms&#xf8; Research Foundation, Norway.},
}
@article {pmid40049043,
year = {2025},
author = {Huang, JN and Gao, CC and Ren, HY and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ},
title = {Multi-omics association pattern between gut microbiota and host metabolism of a filter-feeding fish in situ exposed to microplastics.},
journal = {Environment international},
volume = {197},
number = {},
pages = {109360},
doi = {10.1016/j.envint.2025.109360},
pmid = {40049043},
issn = {1873-6750},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Carps/microbiology/metabolism ; *Water Pollutants, Chemical/toxicity ; *Microplastics/toxicity ; Multiomics ; },
abstract = {Microplastics (MPs) are widespread in water environments and can affect gut microbiota and host metabolism of fish, but whether changes in host metabolism under MPs are mediated by gut microbiota remains unclear. Here, silver carp, a filter-feeding fish with important ecological functions, was in-situ exposure to environmentally relevant MPs. Multi-omics analysis and fecal microbiota transplantation were used to reveal the metabolic responses of carp along gut-liver-muscle axis. After three months of in situ exposure to MPs, community structure of gut microbiota of carp was reshaped, and five dominate phyla were significantly changed, including increased Cyanobacteria, Chloroflexi and Planctomycetota but decreased Firmicutes and Fusobacteriota. Weighted gene co-expression network analysis was further performed between these phyla and liver transcription spectrum, showing that the hub gene module contained up-regulated hppD, maiA and plg and activated ubiquinone and other terpenoid-quinone biosynthesis and phenylalanine metabolism. By fecal microbiota transplantation, the key gene module associated with core microbiota phyla of carp was verified in germ-free zebrafish. Interestingly, up-regulated hppD, maiA and plg and enriched phenylalanine metabolism were also observed in this module. Subsequently, metabolome performed in carp liver also shared activated phenylalanine metabolism, including increased trans-cinnamic acid and L-tyrosine. Furthermore, high-associated mapping showed that the differentially expressed metabolites (gamma-aminobutyric acid, ornithine and L-serine) related to amino acid metabolism in carp muscle were significantly accompanied with increased L-tyrosine in its liver. Overall, MPs exposure could change gut microbiome of silver carp and alter host metabolism especially amino acid metabolism along the gut-liver-muscle axis.},
}
@article {pmid40051336,
year = {2025},
author = {Birchard, K and Boccia, C and Lounder, H and Colston-Nepali, L and Friesen, VL},
title = {Popfinder: A Highly Effective Artificial Neural Network Package for Genetic Population Assignment.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14096},
pmid = {40051336},
issn = {1755-0998},
support = {//Environment and Climate Change Canada/ ; },
mesh = {*Neural Networks, Computer ; Animals ; *Genetics, Population/methods ; *Computational Biology/methods ; *Software ; *Birds/genetics/classification ; },
abstract = {The ability to assign biological samples to source populations with high accuracy and precision based on genetic variation is important for numerous applications from ecological studies through wildlife conservation to epidemiology. However, population assignment when genetic differentiation is low is challenging, and methods to address this problem are lacking. The application of artificial neural networks to population assignment using genomic data is highly promising. Here we present popfinder: a new, easy-to-use Python-based artificial neural network pipeline for genetic population assignment. We tested popfinder both with simulated genetic data from populations connected by varying levels of gene flow and with reduced-representation sequence data for three species of seabirds with weak to no population genetic structure. Popfinder was able to assign individuals to their source populations with high accuracy, precision and recall in most cases, including both simulated and empirical data sets, except in the empirical data set with the weakest population structure, where the comparator programs also performed poorly. Compared to other available software, popfinder was slower on the simulated data sets due to hyperparameter tuning and the fact that it does not reduce the dimensionality of the data set; however, all programs ran in seconds on empirical data sets. Additionally, popfinder provides a perturbation ranking method to help develop optimised SNP panels for genetic population assignment and is designed to be user-friendly. Finally, we caution users of all assignment programs to watch both for leakage of data during model training, which can lead to overfitting and inflation of performance metrics, and for unequal detection probabilities.},
}
@article {pmid40053042,
year = {2025},
author = {Duarte, T and Martin, GM and Anjos-Santos, D and Pessacq, P},
title = {Unraveling Plecoptera Diversity in Two Protected Areas of Argentine Patagonia.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {97},
number = {1},
pages = {e20240085},
doi = {10.1590/0001-3765202520240085},
pmid = {40053042},
issn = {1678-2690},
mesh = {Animals ; Argentina ; *Biodiversity ; *Neoptera/classification ; Forests ; Population Density ; Cluster Analysis ; *Animal Distribution ; *Insecta/classification ; Conservation of Natural Resources ; Parks, Recreational ; Geographic Information Systems ; },
abstract = {The Plecoptera taxonomy in Patagonia is well-documented, yet their distribution remains poorly understood, hindering comprehensive ecological and biogeographical studies. This study enhances knowledge of stonefly distribution in two Patagonian national parks: Nahuel Huapi and Los Alerces. Extensive fieldwork, georeferenced species records, and geographic information system data integration were conducted. Species richness was calculated using polygons (0.1° x 0.1° pixels) across ecoregions, with species indexed from rare to ubiquitous. Cluster analyses revealed faunal affinities across ecosystem complexes, and richness estimators (Jack1, Jack2, and Chao2) highlighted knowledge gaps. Results showed uneven species distribution, with the highest richness polygon (n = 19) in Los Alerces. The Northern Moist Forests hosted the most species, followed by the Transitional Cypress-Beech Forests. The rarest species were also found in these two complexes, as well as the Ecotone Steppe-Forest. Cluster analysis revealed strong affinities between the Northern Moist Forests of Nahuel Huapi and Ecotone Steppe-Forest. Richness estimators suggested up to 23 undocumented species. Though much remains to be learned about Plecoptera distribution in Patagonia, this study emphasizes the critical role of national parks in conserving biodiversity and provides a foundation for future conservation strategies, identifying new taxa records, including southernmost distributions.},
}
@article {pmid40053082,
year = {2025},
author = {Alibardi, L},
title = {Immunoreactivity of flexible and inflexible scales in different lizards indicates that the mature beta-layer contains different corneous proteins.},
journal = {Protoplasma},
volume = {262},
number = {5},
pages = {1129-1149},
pmid = {40053082},
issn = {1615-6102},
mesh = {Animals ; *Lizards/anatomy &amp; histology/genetics/immunology/metabolism ; Immunohistochemistry ; *Animal Scales/cytology/immunology/metabolism ; *Reptilian Proteins/chemistry/genetics/immunology/metabolism ; Computational Biology ; Amino Acid Sequence ; Epitopes/immunology ; Peptides/chemistry/metabolism ; Keratins/chemistry/metabolism ; },
abstract = {We have analyzed by immunohistochemical methods the Oberhautchen-beta layer, here abbreviated as beta-layer, of lizards with hard scales and lizards with softer scales. Different antibodies for detecting Corneous Beta Proteins (CBPs) have been utilized. The agamid beta-corneous layer is generally 3-4 times thicker than in geckos, and the surface microornamentation forms a honeycomb pattern. Geckos feature thinner beta-layers and a spinulated pattern and show immunolocalization for CBPs and isopeptide bonds, a product of transglutaminase catalysis, in their thin beta-layer. CBPs and isopeptide-bonds are detected in the superficial Oberhautchen and alpha-layer of agamids while the beta-layer is immuno-negative. Considering the limitations of immunolabeling methods, the unexpected result might derive from inaccessibility of antibodies to epitopes that are masked within the packed corneous material of the agamid beta-layer. However, bioinformatics analysis for CBPs sequenced in the few species of agamids so far known indicates that these proteins have low identity with those of other lizards. This suggests that agamids possess peculiar CBPs but low isopeptide bonds in their inflexible beta-layer. In contrast, the thinner and pliable beta-corneous layers of geckos may derive from the presence of isopeptide bonds mixed with lower amounts of CBPs. The differences in material properties of lizard scales, inflexibility versus pliability, are adaptive for the different ecological conditions of the species here analyzed.},
}
@article {pmid40054299,
year = {2025},
author = {Guarischi, M and Montagnani, E and Catalano, G and Saligari, E and Signorini, S and Gori, M},
title = {From motion to interaction: How multisensory information shapes motor behaviors in children with visual impairment.},
journal = {Research in developmental disabilities},
volume = {159},
number = {},
pages = {104956},
doi = {10.1016/j.ridd.2025.104956},
pmid = {40054299},
issn = {1873-3379},
mesh = {Humans ; Female ; Male ; Child ; *Social Interaction ; Cues ; *Vision Disorders/physiopathology/psychology ; Biomechanical Phenomena ; Child, Preschool ; Attention ; *Auditory Perception ; Visual Perception ; },
abstract = {BACKGROUND: The ability to move independently enables children to develop perceptual, cognitive, and social interaction skills. Concerning this, vision holds a key role. As a result, children with visual impairment (VI) might be more challenged in their ability to move within their surroundings and interact with their caregivers.<br><br>AIM: This study investigated whether the use of multisensory stimuli could influence the motor exploration of children with VI and shape their interaction with the caregivers. For this, the present work examined the variability of children's motor trajectory and the distance between children and caregivers in a setting with and without multisensory cues.<br><br>METHODS AND PROCEDURES: A Motion Capture System was used within an ecological playroom environment. The Strange Situation paradigm was simplified and adapted by placing three TechARMs in the corners of the playroom to deliver audio-visual stimuli, used instead of the stranger.<br><br>OUTCOMES AND RESULTS: Children with VI showed larger variability within their motor trajectory and kept a shorter distance from the caregivers when multisensory cues were introduced in the playroom.<br><br>CONCLUSIONS AND IMPLICATIONS: Multisensory signals were considered unusual and influenced the kinematic parameters. Motor control of the environment was achieved by managing attention flexibility. WHAT DOES THIS PAPER ADD?: This study enriches available evidence about the study of motor and social interaction in children with VI, highlighting how multisensory stimuli could either support or hinder social and motor behaviors. Moreover, enhancing ecological validity could drive progress in the development and application of technological devices to clinical and research setting.},
}
@article {pmid40055329,
year = {2025},
author = {Ferrer-Paris, JR and Sánchez-Mercado, A and Cornwell, WK and Ooi, M and Tozer, M and Mackenzie, BDE and Woodward, R and Denham, AJ and Auld, TD and Keith, DA},
title = {Fire ecology database for documenting plant responses to fire events in Australia.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {399},
pmid = {40055329},
issn = {2052-4463},
mesh = {*Fires ; *Plants ; *Databases, Factual ; Australia ; Biodiversity ; New South Wales ; *Plant Physiological Phenomena ; },
abstract = {An understanding of fire-response traits is essential for predicting how fire regimes structure plant communities and for informing fire management strategies for biodiversity conservation. Quantification of these traits is complex, encompassing several levels of data abstraction scaling up from field observations of individuals, to general categories of species responses. We developed the Fire Ecology Database to accommodate this complexity. Its conceptual framework is underpinned by a flexible data pipeline enabling links between fire-related trait data and event information at individual, population, and community levels. Key features include: (a) concise and documented trait and method vocabularies; (b) documented uncertainty in observations and aggregation; and (c) documented origin of data including field observations, laboratory experiments, and expert elicitation. We demonstrated application of our framework using data from new field surveys and existing data sets in New South Wales, Australia. The database includes 14 traits for 6,287 plant species derived from 8,936 field work records from 2007 to 2018, 7,054 field records from surveys after 2019, and 48,306 records from 301 existing sources.},
}
@article {pmid40055331,
year = {2025},
author = {Guerrero, PC and Contador, T and Díaz, A and Escobar, C and Orlando, J and Marín, C and Medina, P},
title = {Southern Islands Vascular Flora (SIVFLORA) dataset: A global plant database from Southern Ocean islands.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {397},
pmid = {40055331},
issn = {2052-4463},
mesh = {Islands ; *Biodiversity ; *Plants/classification ; Climate Change ; Ecosystem ; Oceans and Seas ; Databases, Factual ; },
abstract = {The Southern Islands Vascular Flora (SIVFLORA) dataset is a globally significant, open-access resource that compiles essential biodiversity data on vascular plants from islands across the Southern Ocean. The SIVFLORA dataset was generated through five steps: study area delimitation, compiling the dataset, validating and harmonizing taxonomy, structuring dataset attributes, and establishing file format and open access. Covering major taxonomic divisions, SIVFLORA offers a comprehensive overview of plant occurrences, comprising 14,589 records representing 886 species, 95 families, and 42 orders. This dataset documents that 58.62% of the taxa are native, 9.61% are endemic, and 31.77% are alien species. The Falkland/Malvinas Archipelago, the most species-rich, contrast sharply with less diverse islands like the South Orkney Archipelago. SIVFLORA serves as a taxonomically harmonized, interoperable resource for investigating plant diversity patterns, ecosystem responses to climate change in extreme environments, island biogeography, endemism, and the effects of anthropogenic pressures on Southern Ocean flora.},
}
@article {pmid40061226,
year = {2025},
author = {Ab Kadir, MA and Abdul Manaf, R and Mokhtar, SA and Ismail, LI},
title = {Identifying leptospirosis hotspots in Selangor: uncovering climatic connections using remote sensing and developing a predictive model.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18851},
pmid = {40061226},
issn = {2167-8359},
mesh = {*Leptospirosis/epidemiology ; Humans ; Malaysia/epidemiology ; Cross-Sectional Studies ; Geographic Information Systems ; *Remote Sensing Technology ; Incidence ; Climate Change ; Climate ; },
abstract = {BACKGROUND: Leptospirosis is an endemic disease in countries with tropical climates such as South America, Southern Asia, and Southeast Asia. There has been an increase in leptospirosis incidence in Malaysia from 1.45 to 25.94 cases per 100,000 population between 2005 and 2014. With increasing incidence in Selangor, Malaysia, and frequent climate change dynamics, a study on the disease hotspot areas and their association with the hydroclimatic factors could enhance disease surveillance and public health interventions.<br><br>METHODS: This ecological cross-sectional study utilised a geographic information system (GIS) and remote sensing techniques to analyse the spatiotemporal distribution of leptospirosis in Selangor from 2011 to 2019. Laboratory-confirmed leptospirosis cases (n&#xa0;= 1,045) were obtained from the Selangor State Health Department. Using ArcGIS Pro, spatial autocorrelation analysis (Moran's I) and Getis-Ord Gi* (hotspot analysis) was conducted to identify hotspots based on the monthly aggregated cases for each subdistrict. Satellite-derived rainfall and land surface temperature (LST) data were acquired from NASA's Giovanni EarthData website and processed into monthly averages. These data were integrated into ArcGIS Pro as thematic layers. Machine learning algorithms, including support vector machine (SVM), Random Forest (RF), and light gradient boosting machine (LGBM) were employed to develop predictive models for leptospirosis hotspot areas. Model performance was then evaluated using cross-validation and metrics such as accuracy, precision, sensitivity, and F1-score.<br><br>RESULTS: Moran's I analysis revealed a primarily random distribution of cases across Selangor, with only 20 out of 103 observed having a clustered distribution. Meanwhile, hotspot areas were mainly scattered in subdistricts throughout Selangor with clustering in the central region. Machine learning analysis revealed that the LGBM algorithm had the best performance scores compared to having a cross-validation score of 0.61, a precision score of 0.16, and an F1-score of 0.23. The feature importance score indicated river water level and rainfall contributes most to the model.<br><br>CONCLUSIONS: This GIS-based study identified a primarily sporadic occurrence of leptospirosis in Selangor with minimal spatial clustering. The LGBM algorithm effectively predicted leptospirosis hotspots based on the analysed hydroclimatic factors. The integration of GIS and machine learning offers a promising framework for disease surveillance, facilitating targeted public health interventions in areas at high risk for leptospirosis.},
}
@article {pmid40062319,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Alder Moth, Acronicta alni (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {68},
pmid = {40062319},
issn = {2398-502X},
abstract = {We present a genome assembly from a male Acronicta alni (Alder Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 470.37 megabases and 472.86 megabases. Most of haplotype 1 (98.95%) is scaffolded into 31 chromosomal pseudomolecules, including the Z chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 15.38 kilobases in length.},
}
@article {pmid40062320,
year = {2025},
author = {Boyes, D and Davis, J and , and , and , and , and , and , },
title = {The genome sequence of the Sandy Carpet moth, Perizoma flavofasciatum (Thunberg, 1792).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {40},
pmid = {40062320},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Perizoma flavofasciatum (Sandy Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 369.30 megabases. Most of the assembly (99.88%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,915 protein-coding genes.},
}
@article {pmid40063696,
year = {2025},
author = {Smith, LB and Ahlich, E and Lang, B and Bollepalli, S and Prioleau, T and Bartolome, A and Hughes Lansing, A and Rancourt, D},
title = {Glycemic variability and weight-focused eating behaviors among adolescents and young adults with type 1 diabetes†.},
journal = {Journal of pediatric psychology},
volume = {50},
number = {4},
pages = {326-334},
doi = {10.1093/jpepsy/jsaf009},
pmid = {40063696},
issn = {1465-735X},
support = {//Dexcom, Inc/ ; },
mesh = {Humans ; Female ; *Diabetes Mellitus, Type 1/blood/psychology/physiopathology ; Adolescent ; Young Adult ; Male ; *Feeding Behavior/physiology/psychology ; *Feeding and Eating Disorders ; *Hunger/physiology ; *Blood Glucose/metabolism/analysis ; Adult ; Weight Loss ; },
abstract = {OBJECTIVE: Type 1 diabetes (T1D) disease management and associated glycemic fluctuations can disrupt experiences of hunger and satiety, which may increase risk for disordered eating behaviors. Glycemic variability may be a useful trigger for just-in-time interventions for disordered eating behaviors. In this exploratory study, we hypothesized that two metrics of glycemic variability would be associated with greater hunger and predict eating behaviors for weight loss or maintenance in adolescents and young adults with T1D.<br><br>METHODS: Individuals with T1D were recruited from a university diabetes clinic (N&#x2009;=&#x2009;34; 50% female, Mage&#x2009;=&#x2009;19.53&#x2009;years, MHbA1c&#x2009;=&#x2009;7.98%; 29% Hispanic/Latinx; 79% White). Participants wore a blinded continuous glucose monitor for 5&#xa0;days, and completed ecological momentary assessments (four prompts per day) that included measures of hunger and eating behaviors for weight loss or maintenance purposes. Generalized and linear mixed models were used to test hypotheses.<br><br>RESULTS: Approximately 30% of participants were at risk for an eating disorder based on Diabetes Eating Problem Survey-Revised scores. Greater glycemic variability did not predict hunger, but was associated with increased odds of endorsing any eating behavior for weight loss or maintenance purposes within-person (ps<.05). Greater hunger was associated with increased odds of endorsing disordered eating behavior within-person (p<.05).<br><br>CONCLUSIONS: This exploratory study provides some preliminary evidence that times of greater hunger and glycemic variability may be when individuals with T1D may be at higher risk of engaging in behaviors to lose or maintain weight.},
}
@article {pmid40064777,
year = {2025},
author = {Crespo-Bellido, A and Martin, DP and Duffy, S},
title = {Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2912},
number = {},
pages = {125-143},
pmid = {40064777},
issn = {1940-6029},
mesh = {*Geminiviridae/genetics ; *Recombination, Genetic ; *Software ; Genome, Viral ; Algorithms ; Sequence Alignment ; *Computational Biology/methods ; Evolution, Molecular ; },
abstract = {Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.},
}
@article {pmid40064850,
year = {2025},
author = {Roman, J and Abraham, AJ and Kiszka, JJ and Costa, DP and Doughty, CE and Friedlaender, A and Hückstädt, LA and Marcondes, M and Wetsel, E and Pershing, AJ},
title = {Migrating baleen whales transport high-latitude nutrients to tropical and subtropical ecosystems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2125},
pmid = {40064850},
issn = {2041-1723},
mesh = {Animals ; *Ecosystem ; *Whales/physiology ; *Animal Migration/physiology ; Tropical Climate ; *Nutrients/metabolism ; Seasons ; Nitrogen/metabolism ; Biomass ; Oceans and Seas ; Female ; Urea/metabolism ; },
abstract = {Baleen whales migrate from productive high-latitude feeding grounds to usually oligotrophic tropical and subtropical reproductive winter grounds, translocating limiting nutrients across ecosystem boundaries in their bodies. Here, we estimate the latitudinal movement of nutrients through carcasses, placentas, and urea for four species of baleen whales that exhibit clear annual migration, relying on spatial data from publicly available databases, present and past populations, and measurements of protein catabolism and other sources of nitrogen from baleen whales and other marine mammals. Migrating gray, humpback, and North Atlantic and southern right whales convey an estimated 3784 tons N yr[-1] and 46,512 tons of biomass yr[-1] to winter grounds, a flux also known as the "great whale conveyor belt"; these numbers might have been three times higher before commercial whaling. We discuss how species recovery might help restore nutrient movement by whales in global oceans and increase the resilience and adaptative capacity of recipient ecosystems.},
}
@article {pmid40066908,
year = {2025},
author = {Weeks, F and Myerson, R and Gangnon, R and Dykema, J and Cornelius, C and Green, T},
title = {Intrapartum Care Experiences Associated With Postpartum Visit Attendance.},
journal = {Birth (Berkeley, Calif.)},
volume = {52},
number = {4},
pages = {652-658},
pmid = {40066908},
issn = {1523-536X},
support = {//Wisconsin Alumni Research Foundation/ ; },
mesh = {Humans ; Female ; Pregnancy ; Adult ; Wisconsin ; *Postnatal Care/statistics &amp; numerical data ; Young Adult ; *Patient Acceptance of Health Care/statistics &amp; numerical data ; *Quality of Health Care ; *Perinatal Care/statistics &amp; numerical data ; Postpartum Period ; Surveys and Questionnaires ; Patient Satisfaction ; },
abstract = {INTRODUCTION: The postpartum visit is an important opportunity to prevent pregnancy-related morbidity and mortality; however, about 1 in 10 birthing people do not attend this visit. Intrapartum care experiences are an understudied factor that may contribute to postpartum healthcare engagement.<br><br>MATERIALS AND METHODS: We analyze data from a novel survey supplement on intrapartum care experiences administered to a probability-based population sample of people who have recently given birth through the Wisconsin Pregnancy Risk Assessment Monitoring System.<br><br>RESULTS: In regression models adjusting for a robust set of individual characteristics and birth hospital clustering, we find that lower provider responsiveness during intrapartum care is associated with increased odds of forgoing the postpartum visit (aOR 1.4, 95% CI 1.0-2.0).<br><br>DISCUSSION: The quality of care received during the birth hospitalization may shape how birthing people feel about health care providers and their willingness to attend future visits. Experiences of care during the intrapartum period may contribute to future health care utilization. Improving these experiences is an opportunity to promote long-term health.},
}
@article {pmid40067093,
year = {2025},
author = {Zhang, G and Ristola, P and Su, H and Kumar, B and Zhang, B and Hu, Y and Elliot, MG and Drobot, V and Zhu, J and Staal, J and Larralde, M and Wang, S and Yi, Y and Yu, H},
title = {BioArchLinux: community-driven fresh reproducible software repository for life sciences.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {3},
pages = {},
pmid = {40067093},
issn = {1367-4811},
mesh = {*Software ; *Computational Biology/methods ; *Biological Science Disciplines ; Programming Languages ; Reproducibility of Results ; },
abstract = {MOTIVATION: The BioArchLinux project was initiated to address challenges in bioinformatics software reproducibility and freshness. Relying on Arch Linux's user-driven ecosystem, we aim to create a comprehensive and continuously updated repository for life sciences research.<br><br>RESULTS: BioArchLinux provides a PKGBUILD-based system for seamless software packaging and maintenance, enabling users to access the latest bioinformatics tools across multiple programming languages. The repository includes Docker images, Windows Subsystem for Linux (WSL) support, and Junest for nonroot environments, enhancing accessibility across platforms. Although being developed and maintained by a small core team, BioArchLinux is a fast-growing bioinformatics repository that offers a participatory and community-driven environment.<br><br>The repository, documentation, and tools are freely available at https://bioarchlinux.org and https://github.com/BioArchLinux. Users and developers are encouraged to contribute and expand this open-source initiative.},
}
@article {pmid40069723,
year = {2025},
author = {Pieroni, A and Zocchi, DM and Alrhmoun, M and Sulaiman, N and Bavorova, M and Sõukand, R},
title = {Not "just necessity"? Two-x-eco-cultural dilemmas and the ethnobiological importance of the informal grannies' markets in Moldova.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {21},
number = {1},
pages = {17},
pmid = {40069723},
issn = {1746-4269},
support = {714874/ERC_/European Research Council/International ; },
mesh = {Humans ; Moldova ; Female ; Middle Aged ; *Food Supply ; Aged ; Agriculture ; Biodiversity ; *Commerce ; Male ; Adult ; Conservation of Natural Resources ; Rural Population ; Culture ; },
abstract = {Informal food markets, particularly those managed by (elderly) women in post-communist Eastern Europe, represent a biocultural phenomenon of profound significance since globalisation and increasingly strict legal frameworks often threaten these reservoirs of biocultural food heritage. In the fall of 2022 and 2023, a preliminary field study was conducted by visiting the informal markets of six Moldovan centres: Chișinău, Orhei, Bălți, Călărași, Comrat, and Taraclia, and conversing with approximately 40 mid-aged and elderly sellers. We argue that these markets are crucial in sustaining small-scale farming, preserving biodiversity, and maintaining a connection between urban communities and rural communities and, ultimately, between these rural citizens and their nature, keeping small-scale family farming and domestic traditional gastronomic activities alive. By trading fresh, homegrown, and homemade food and goods (including handicrafts), these mid-aged and elderly vendors support local economies, promote environmental sustainability, and safeguard traditional ecological knowledge and cultural heritage. This paper explores how grannies' markets contribute to biocultural diversity and sustainable food practices, especially amid the country's recent turbulent political, socioeconomic, and demographic challenges. The analysis advocates for the survival rights of these ecological, economic, and cultural (2-x-eco-cultural) refugia and invites ethnobiologists, food studies and cultural heritage scholars, rural sociologists, and agricultural economists to defend the biocultural diversity of informal food markets, moving them from an "out of necessity" status to a solid pillar of a possible future, new, family farming and small-scale ecological and gastronomic (conscientious) tourism. Policymakers should protect and enhance these informal spaces, especially the socioecological farming systems behind them, as essential socioeconomic and environmental assets. They should emphasise their importance as hubs for biological diversity, cultural preservation, community cohesion, and ecological sustainability.},
}
@article {pmid40070804,
year = {2025},
author = {Vršanský, P and Sendi, H and Kotulová, J and Szwedo, J and Havelcová, M and Palková, H and Vršanská, L and Sakala, J and Puškelová, L and Golej, M and Biroň, A and Peyrot, D and Quicke, D and Néraudeau, D and Uher, P and Maksoud, S and Azar, D},
title = {Jurassic Park approached: a coccid from Kimmeridgian cheirolepidiacean Aintourine Lebanese amber.},
journal = {National science review},
volume = {12},
number = {3},
pages = {nwae200},
pmid = {40070804},
issn = {2053-714X},
abstract = {With the exception of a fly and a mite from the Triassic of Italy, all Mesozoic amber arthropods are from the Cretaceous. Late Jurassic Lebanese amber from Aintourine revealed a completely preserved adult coccid male (wing length 0.8 mm), Jankotejacoccus libanogloria gen. et sp. n., the earliest record of a plant sucking scale insect. Associated plant material included the cheirolepidiaceans Protopodocarpoxylon, Brachyphyllum and Classostrobus, plus Classopolis pollen, suggesting a forested temporary swamp habitat with ferns, tree ferns, water ferns, tall araucarian and ginkgoacean trees and shrubs. (Sub)tropic lateritic soil with vegetation debris underwent incomplete microbial decomposition in an anoxic water environment of peat swamp development. Strata-associated marine organisms support the Kimmeridgian age revealed by zircons. The discovery opens a new field of research in Jurassic amber fossils.},
}
@article {pmid40073274,
year = {2025},
author = {Aucello, R and Pernice, S and Tortarolo, D and Calogero, RA and Herrera-Rincon, C and Ronchi, G and Geuna, S and Cordero, F and Lió, P and Beccuti, M},
title = {UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {3},
pages = {},
pmid = {40073274},
issn = {1367-4811},
support = {//Ministero dell'Univerisita' e della Ricerca/ ; },
mesh = {*Models, Biological ; *Software ; *Systems Biology/methods ; Escherichia coli/metabolism/genetics ; Computer Simulation ; Clostridioides difficile ; *Computational Biology/methods ; },
abstract = {MOTIVATION: Computational models are crucial for addressing critical questions about systems evolution and deciphering system connections. The pivotal feature of making this concept recognizable from the biological and clinical community is the possibility of quickly inspecting the whole system, bearing in mind the different granularity levels of its components. This holistic view of system behaviour expands the evolution study by identifying the heterogeneous behaviours applicable, e.g. to the cancer evolution study.<br><br>RESULTS: To address this aspect, we propose a new modelling paradigm, UnifiedGreatMod, which allows modellers to integrate fine-grained and coarse-grained biological information into a unique model. It enables functional studies by combining the analysis of the system's multi-level stable states with its fluctuating conditions. This approach helps to investigate the functional relationships and dependencies among biological entities. This is achieved, thanks to the hybridization of two analysis approaches that capture a system's different granularity levels. The proposed paradigm was then implemented into the open-source, general modelling framework GreatMod, in which a graphical meta-formalism is exploited to simplify the model creation phase and R languages to define user-defined analysis workflows. The proposal's effectiveness was demonstrated by mechanistically simulating the metabolic output of Escherichia coli under environmental nutrient perturbations and integrating a gene expression dataset. Additionally, the UnifiedGreatMod was used to examine the responses of luminal epithelial cells to Clostridium difficile infection.<br><br>GreatMod https://qbioturin.github.io/epimod/, epimod_FBAfunctions https://github.com/qBioTurin/epimod_FBAfunctions, first case study E. coli &#xa0;https://github.com/qBioTurin/Ec_coli_modelling, second case study C. difficile &#xa0;https://github.com/qBioTurin/EpiCell_CDifficile.},
}
@article {pmid40074756,
year = {2025},
author = {Wei, P and Song, Y and Tian, R and Wang, Y and Chen, J and Yuan, Z and Zhou, W},
title = {CaecilianTraits, an individual level trait database of Caecilians worldwide.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {428},
pmid = {40074756},
issn = {2052-4463},
support = {32170445//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Amphibians/anatomy &amp; histology/classification ; *Databases, Factual ; Biological Evolution ; Biodiversity ; },
abstract = {Functional traits differ among species, which determine the ecological niche a species occupies and its ability to adapt to environment. However, differences in traits also exist at intraspecific level. Such variations shape differences in individual survival capabilities. Investigating intraspecific differences of functional traits is important for ecology, evolutionary biology and biodiversity conservation. Individual trait-based approaches have been applied in plant ecology. But for animals, most databases only provide data at the species level. In this study, we presented a global database of morphological traits for caecilians (Amphibia, Gymnophiona) at both species and individual level. Caecilians are a unique group of amphibians characterized by their secretive habits, which have limited our understanding of this taxon. We compiled the most comprehensive database covering 218 out of 222 known species, with 215 of them have individual level data. This database will facilitate research in the ecology, evolutionary biology, conservation biology, and taxonomy of caecilians. Furthermore, this dataset can be utilized to test ecological and evolutionary hypotheses at the individual level.},
}
@article {pmid40074806,
year = {2025},
author = {Tang, Y and Hu, H and Chen, S and Hao, B and Xu, X and Zhu, H and Zhan, W and Zhang, T and Hu, H and Chen, G},
title = {Multi-omics analysis revealed the novel role of NQO1 in microenvironment, prognosis and immunotherapy of hepatocellular carcinoma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8591},
pmid = {40074806},
issn = {2045-2322},
support = {24B0413//the Scientific Research Project of the Hunan Provincial Department of Education/ ; 2024JJ7455//Natural Science Foundation of Hunan Province/ ; 20224310NHYCG04//University of South China Clinical Research 4310 Program/ ; 20224310NHYCG01//University of South China Clinical Research 4310 Program/ ; 82473965//National Natural Science Foundation of China/ ; 2023JJ50156//the Natural Science Foundation of Hunan Province/ ; 202250045223//Science and technology innovation Program of Hengyang City/ ; ZYYD2024CG17//Central Government Guided Local Science and Technology Development Fund Project in Xinjiang Uygur Autonomous Region/ ; 2024WK4008//Hunan Province Innovation Ecological Construction Plan Science and Technology Assistance Project in Xinjiang Uygur Autonomous Region/ ; SYTG-Y202429//Health Technology Promotion Project in Xinjiang Uygur Autonomous Region/ ; },
mesh = {Humans ; *Carcinoma, Hepatocellular/therapy/genetics/pathology/mortality/immunology/metabolism ; *NAD(P)H Dehydrogenase (Quinone)/genetics/metabolism ; *Liver Neoplasms/therapy/genetics/pathology/mortality/immunology/metabolism ; *Tumor Microenvironment/genetics ; *Immunotherapy/methods ; Prognosis ; Male ; Gene Expression Regulation, Neoplastic ; Female ; Tumor-Associated Macrophages/immunology/metabolism ; Middle Aged ; Cell Line, Tumor ; Nomograms ; Multiomics ; },
abstract = {NAD(P)H dehydrogenase quinone 1 (NQO1) is overexpressed in various cancers and is strongly associated with an immunosuppressive microenvironment and poor prognosis. In this study, we explored the role of NQO1 in the microenvironment, prognosis and immunotherapy of Hepatocellular carcinoma (HCC) using multi-omics analysis and machine learning. The results revealed that NQO1 was significantly overexpressed in HCC cells. NQO1[+]HCC cells were correlated with poor prognosis and facilitated tumor-associated macrophages (TAMs) polarization to M2 macrophages. We identified core NQO1-related genes (NRGs) and developed the NRGs-related risk-scores in hepatocellular carcinoma (NRSHC). The comprehensive nomogram integrating NRSHC, age, and pathological tumor-node-metastasis (pTNM) Stage achieved an area under the curve (AUC) above 0.7, demonstrating its accuracy in predicting survival outcomes and immunotherapy responses of HCC patients. High-risk patients exhibited worse prognoses but greater sensitivity to immunotherapy. Additionally, a web-based prediction tool was designed to enhance clinical utility. In conclusion, NQO1 may play a critical role in M2 polarization and accelerates HCC progression. The NRSHC model and accompanying tools offer valuable insights for personalized HCC treatment.},
}
@article {pmid40079420,
year = {2025},
author = {Jurburg, SD},
title = {Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14102},
pmid = {40079420},
issn = {1755-0998},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Metagenomics/methods ; Microbiota ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.},
}
@article {pmid40086213,
year = {2025},
author = {Dong, L and Mu, L and Huang, X},
title = {Exploring lipid remodeling and antioxidant responses in Chlorella pyrenoidosa exposed to streptomycin sulfate stress.},
journal = {Food chemistry},
volume = {478},
number = {},
pages = {143565},
doi = {10.1016/j.foodchem.2025.143565},
pmid = {40086213},
issn = {1873-7072},
mesh = {*Chlorella/metabolism/drug effects/genetics ; *Streptomycin/pharmacology ; *Antioxidants/metabolism ; *Lipid Metabolism/drug effects ; Superoxide Dismutase/metabolism/genetics ; *Anti-Bacterial Agents/pharmacology ; Plant Proteins/metabolism/genetics ; Ascorbate Peroxidases/metabolism/genetics ; Stress, Physiological/drug effects ; Microalgae/drug effects/metabolism ; },
abstract = {Microalgae, particularly Chlorella pyrenoidosa, are valuable for bioactive compounds and biofuel production, but antibiotic use in large-scale cultivation can impact growth and biochemical productivity. This study examines the physiological and molecular responses of C. pyrenoidosa to streptomycin sulfate (STRS) stress. STRS exposure significantly reduced cell density (15.31 × 10[6] to 11.20 × 10[6] cells/mL, p < 0.001) and photosynthetic efficiency (Fv/fm from 0.45 to 0.15). Multi-omics analysis revealed a dual adaptive strategy: (1) activation of antioxidant defenses, including upregulated superoxide dismutase (SOD, 19-fold) and ascorbate peroxidase (APX, 32-fold); (2) lipid remodeling, with increased α-linolenic acid (ALA) content (17.43 % to 21.25 %, p < 0.001) due to β-oxidation downregulation. These findings enhance understanding of microalgal stress adaptation and highlight potential applications in biofuel and food/feed industries. Future studies should optimize genetic and cultivation strategies to enhance these adaptive traits while ensuring ecological sustainability.},
}
@article {pmid40086783,
year = {2025},
author = {Yang, JZ and Li, JH and Liu, JL and Zhou, AD and Wang, H and Xie, XL and Zhang, KK and Wang, Q},
title = {Multiomics analysis revealed the effects of polystyrene nanoplastics at different environmentally relevant concentrations on intestinal homeostasis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {372},
number = {},
pages = {126050},
doi = {10.1016/j.envpol.2025.126050},
pmid = {40086783},
issn = {1873-6424},
mesh = {Animals ; Mice ; *Polystyrenes/toxicity ; Homeostasis/drug effects ; *Microplastics/toxicity ; Gastrointestinal Microbiome/drug effects ; *Intestines/drug effects ; Male ; Metabolomics ; Multiomics ; },
abstract = {Nanoplastics pollution is a global issue, with the digestive tract being one of the first affected organs, requiring further research on its impact on intestinal health. This study involved orally exposing mice to polystyrene nanoplastics (PS-NPs) at doses of 0.1, 0.5, or 2.5 mg/d for 42 days. The effects on intestinal health were thoroughly assessed via microbiomics, metabolomics, transcriptomics, and molecular biology. Our study demonstrated that the administration of all three doses of PS-NPs resulted in increased colonic permeability, heightened colonic and peripheral inflammation, reduced levels of antimicrobial peptides, and shortened colonic length. These effects may be attributed to a reduction in the abundance of probiotic bacteria, such as Clostridia_UCG-014, Roseburia, and Akkermansia, alongside an increase in the abundance of the pathogenic bacterium Desulfovibrionaceae induced by PS-NPs. Furthermore, we underscored the crucial role of histidine metabolism in PS-NPs-induced colonic injury, characterized by a significant reduction of L-histidine, which is closely related to microbial ecological dysregulation. Corresponding to microbiota deterioration and metabolic dysregulation, transcriptome analysis revealed that PS-NPs may disrupt colonic immune homeostasis by activating the TLR4/MyD88/NF-κB/NLRP3 signaling pathway. In conclusion, this study provided novel insights into the mechanisms by which PS-NPs disrupt intestinal homeostasis through integrated multiomics analysis, revealing critical molecular pathway and providing a scientific basis for future risk assessment of nanoplastics exposure.},
}
@article {pmid40087683,
year = {2025},
author = {Mbuba, E and Mañas-Chavernas, N and Moore, SJ and Ruzige, PD and Kobe, D and Moore, J and Philipo, R and Kisoka, N and Pontiggia, G and Chacky, F and Mwalimu, CD and Cattin, PC and Wolleb, J and Sandkuehler, R and Ross, A},
title = {Estimating the hole surface area of insecticide-treated nets using image analysis, manual hole counting and exact hole measurements.},
journal = {Malaria journal},
volume = {24},
number = {1},
pages = {82},
pmid = {40087683},
issn = {1475-2875},
mesh = {*Insecticide-Treated Bednets/standards ; *Image Processing, Computer-Assisted/methods ; *Mosquito Control/methods ; Animals ; Humans ; },
abstract = {BACKGROUND: The physical integrity of insecticidal-treated nets (ITNs) is important for creating a barrier against host-seeking mosquitoes and, therefore, influences people's perception of the net's effectiveness and their willingness to use it. Monitoring the physical integrity of ITNs over time provides information for replenishment schedules and purchasing decisions. Currently, the assessment of physical integrity of ITNs is conducted by manually counting holes and estimating their size to class the net as functional or not. This approach is laborious to routinely conduct during field surveys of ITNs. Automated image analysis may provide a rapid assessment of the physical integrity of ITNs but it is not known if the images can capture sufficient information. As a first step, this study aimed to assess the agreement between estimated hole surface areas derived from (1) manually segmented images, (2) manual hole counting compared to (3) ground truth obtained by calibrated close-up shots of individual holes.<br><br>METHODS: The physical integrity of 75 ITNs purposely selected from an ongoing study was assessed by manual hole counting, image analysis and ground truth. For the image analysis, a graphical user interface was developed and used for the segmentation of holes visible in photographs taken from each side of the net. The hole surface area was then computed from this data. The agreement between the estimates from image analysis and manual hole counting was compared to the ground truth using the Bland-Altman method.<br><br>RESULTS: There was substantial agreement between the manually segmented image analysis estimates and the ground truth hole surface areas. The overall bias was small, with a mean ratio of the hole surface area from image analysis to the ground truth of 0.70, and the 95% limits of agreement ranging from 0.35 to 1.38. Manual hole counting underestimated the hole surface area compared to the ground truth, particularly among nets with holes above 10&#xa0;cm in diameter.<br><br>CONCLUSION: Images coupled with manual segmentation contain sufficient information to calculate hole surface area. This lays the groundwork for incorporating automatic hole detection, and then assessing whether this method will offer a fast and objective method for routine assessment of physical integrity of ITNs. While the WHO method underestimated the hole surface area, it remains useful in classifying nets as either serviceable or too torn because the cut-off is specific to this method.},
}
@article {pmid40087979,
year = {2025},
author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A},
title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14099},
pmid = {40087979},
issn = {1755-0998},
support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; },
mesh = {*Aquatic Organisms/parasitology ; *RNA, Ribosomal/genetics ; Microalgae/parasitology ; *Parasites/genetics/classification ; *Databases, Genetic ; },
abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.},
}
@article {pmid40088887,
year = {2025},
author = {Hartley, GA and Okhovat, M and Hoyt, SJ and Fuller, E and Pauloski, N and Alexandre, N and Alexandrov, I and Drennan, R and Dubocanin, D and Gilbert, DM and Mao, Y and McCann, C and Neph, S and Ryabov, F and Sasaki, T and Storer, JM and Svendsen, D and Troy, W and Wells, J and Core, L and Stergachis, A and Carbone, L and O'Neill, RJ},
title = {Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.},
journal = {Cell genomics},
volume = {5},
number = {4},
pages = {100808},
pmid = {40088887},
issn = {2666-979X},
support = {R01 HG007352/HG/NHGRI NIH HHS/United States ; },
mesh = {*Centromere/genetics ; Animals ; *DNA Transposable Elements/genetics ; *Epigenesis, Genetic ; DNA Methylation/genetics ; *Hylobates/genetics ; Karyotype ; CpG Islands/genetics ; Evolution, Molecular ; },
abstract = {Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here, we characterize fully assembled centromeres in the eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha-satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence that this epigenetic feature is conserved in the absence of satellite arrays. We uncovered a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, we identify duplications and deletions in HLE centromeres that distinguish them from other gibbons. Finally, we observed differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, and thus propose that a combination of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.},
}
@article {pmid40089216,
year = {2025},
author = {Torres-Roman, JS and Quispe-Vicuña, C and Benavente-Casas, A and Julca-Marin, D and Rios-Garcia, W and Challapa-Mamani, MR and Rio-Muñiz, LD and Ybaseta-Medina, J},
title = {Trends in stroke mortality in Latin America and the Caribbean from 1997 to 2020 and predictions to 2035: An analysis of gender, and geographical disparities.},
journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association},
volume = {34},
number = {6},
pages = {108286},
doi = {10.1016/j.jstrokecerebrovasdis.2025.108286},
pmid = {40089216},
issn = {1532-8511},
mesh = {Humans ; Latin America/epidemiology ; Female ; Male ; *Stroke/mortality/diagnosis ; Caribbean Region/epidemiology ; Risk Factors ; Sex Factors ; Middle Aged ; Sex Distribution ; Time Factors ; Databases, Factual ; Aged ; Adult ; *Health Status Disparities ; Age Distribution ; Forecasting ; Risk Assessment ; Age Factors ; Young Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Stroke is a leading cause of death and disability globally, with significant public health implications. In Latin America, while mortality rates have declined, the number of stroke cases has increased due to prevalent risk factors like high blood pressure and obesity. Unlike Europe, recent trends in stroke mortality in this region remain underreported.<br><br>OBJECTIVE: This study evaluates stroke mortality rates in Latin America Latin American and Caribbean (LAC) countries from 1997 to 2020 and predictions to 2035.<br><br>METHODS: This ecological observational study utilized mortality data from the World Health Organization database. Trends were analyzed using Joinpoint regression to evaluate the annual percent change (APC) by sex and country. Predicted mortality rates through 2035 were calculated using the Nordpred package in R. Changes in stroke mortality were assessed by disentangling the effects of population growth, aging, and risk factor modifications, based on age-specific rates and projections. Results were presented as absolute case numbers and relative percentages.<br><br>RESULTS: From 1997 to 2020, twelve countries presented significant reductions in stroke mortality rates for men in LAC, the main ones being Chile (-4.2 %), El Salvador (-4.2 %), and Puerto Rico (-4.0 %). Thirteen countries reported a reduction in their mortality for women, mainly in Puerto Rico (-4.3 %), Chile (-3.7 %), Argentina, El Salvador, and Uruguay (-3.5 %). By 2035, an increase in deaths among men and women is expected, mainly due to the increase in population structure and size. However, a decrease in the mortality rate will be reported, mainly due to the reduction of risk factors.<br><br>CONCLUSION: Our final findings show a reduction in stroke mortality trends in LAC countries between 1997 and 2020, due to creating public awareness about vascular risk factors by authorities and the implementation of effective health policies. By 2035, an overall increase in mortality is expected, mainly due to population change in each country.},
}
@article {pmid40091604,
year = {2025},
author = {Tu, M and Liu, N and He, ZS and Dong, XM and Gao, TY and Zhu, A and Yang, JB and Zhang, SB},
title = {Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum.},
journal = {Plant biotechnology journal},
volume = {23},
number = {6},
pages = {2162-2181},
pmid = {40091604},
issn = {1467-7652},
support = {202403AC100032//Key Research and Development Program of Yunnan Province/ ; YNWR-CYJS-2020-023//High-level Talent Support Plan of Yunnan Province/ ; XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 32170393//National Natural Science Foundation of China/ ; 2024YFF1306703//National Key Research and Development Program of China/ ; 202201AU070123//Yunnan Fundamental Research Project/ ; 202301AT070306//Yunnan Fundamental Research Project/ ; },
mesh = {*Flowers/metabolism/genetics ; *Orchidaceae/genetics/metabolism ; *Odorants/analysis ; Terpenes/metabolism ; Gene Expression Regulation, Plant ; Transcriptome ; Volatile Organic Compounds/metabolism ; Genomics ; Plant Proteins/metabolism/genetics ; Multiomics ; },
abstract = {Flower scent is a crucial determiner in pollinator attraction and a significant horticultural trait in ornamental plants. Orchids, which have long been of interest in evolutionary biology and horticulture, exhibit remarkable diversity in floral scent type and intensity. However, the mechanisms underlying floral scent biosynthesis and regulation in orchids remain largely unexplored. In this study, we focus on floral scent in Cymbidium tracyanum, a wild species known for its strong floral fragrance and as a primary breeding parent of commercial Cymbidium hybrids. We present a chromosome-level genome assembly of C. tracyanum, totaling 3.79 Gb in size. Comparative genomic analyses reveal significant expansion of gene families associated with terpenoid biosynthesis and related metabolic pathways in C. tracyanum. Integrative analysis of genomic, volatolomic and transcriptomic data identified terpenoids as the predominant volatile components in the flowers of C. tracyanum. We characterized the spatiotemporal patterns of these volatiles and identified CtTPS genes responsible for volatile terpenoid biosynthesis, validating their catalytic functions in vitro. Dual-luciferase reporter assays, yeast one-hybrid assays and EMSA experiments confirmed that CtTPS2, CtTPS3, and CtTPS8 could be activated by various transcription factors (i.e., CtAP2/ERF1, CtbZIP1, CtMYB2, CtMYB3 and CtAP2/ERF4), thereby regulating the production of corresponding monoterpenes and sesquiterpenes. Our study elucidates the biosynthetic and regulatory mechanisms of floral scent in C. tracyanum, which is of great significance for the breeding of fragrant Cymbidium varieties and understanding the ecological adaptability of orchids. This study also highlights the importance of integrating multi-omics data in deciphering key horticultural traits in orchids.},
}
@article {pmid40091737,
year = {2025},
author = {Slipetz, LR and Falk, A and Henry, TR},
title = {Missing Data in Discrete Time State-Space Modeling of Ecological Momentary Assessment Data: A Monte-Carlo Study of Imputation Methods.},
journal = {Multivariate behavioral research},
volume = {60},
number = {4},
pages = {695-710},
doi = {10.1080/00273171.2025.2469055},
pmid = {40091737},
issn = {1532-7906},
mesh = {*Ecological Momentary Assessment ; Humans ; *Monte Carlo Method ; *Models, Statistical ; Data Interpretation, Statistical ; Bias ; Computer Simulation ; Time Factors ; },
abstract = {When using ecological momentary assessment data (EMA), missing data is pervasive as participant attrition is a common issue. Thus, any EMA study must have a missing data plan. In this paper, we discuss missingness in time series analysis and the appropriate way to handle missing data when the data is modeled as an idiographic discrete time continuous measure state-space model. We found that Missing Completely at Random, Missing At Random, and Time-dependent Missing At Random data have less bias and variability than Autoregressive Time-dependent Missing At Random and Missing Not At Random. The Kalman filter excelled at handling missing data under most conditions. Contrary to the literature, we found that using a variety of methods, multiple imputations struggled to recover the parameters.},
}
@article {pmid40096239,
year = {2025},
author = {Dinnage, R and Kleineberg, M},
title = {Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills.},
journal = {PLoS computational biology},
volume = {21},
number = {3},
pages = {e1012887},
pmid = {40096239},
issn = {1553-7358},
mesh = {Animals ; *Birds/anatomy &amp; histology ; *Imaging, Three-Dimensional/methods ; Computational Biology ; *Beak/anatomy &amp; histology ; *Artificial Intelligence ; Deep Learning ; },
abstract = {Data on the three dimensional shape of organismal morphology is becoming increasingly available, and forms part of a new revolution in high-throughput phenomics that promises to help understand ecological and evolutionary processes that influence phenotypes at unprecedented scales. However, in order to meet the potential of this revolution we need new data analysis tools to deal with the complexity and heterogeneity of large-scale phenotypic data such as 3D shapes. In this study we explore the potential of generative Artificial Intelligence to help organize and extract meaning from complex 3D data. Specifically, we train a deep representational learning method known as DeepSDF on a dataset of 3D scans of the bills of 2,020 bird species. The model is designed to learn a continuous vector representation of 3D shapes, along with a 'decoder' function, that allows the transformation from this vector space to the original 3D morphological space. We find that approach successfully learns coherent representations: particular directions in latent space are associated with discernible morphological meaning (such as elongation, flattening, etc.). More importantly, learned latent vectors have ecological meaning as shown by their ability to predict the trophic niche of the bird each bill belongs to with a high degree of accuracy. Unlike existing 3D morphometric techniques, this method has very little requirements for human supervised tasks such as landmark placement, increasing it accessibility to labs with fewer labour resources. It has fewer strong assumptions than alternative dimension reduction techniques such as PCA. Once trained, 3D morphology predictions can be made from latent vectors very computationally cheaply. The trained model has been made publicly available and can be used by the community, including for finetuning on new data, representing an early step toward developing shared, reusable AI models for analyzing organismal morphology.},
}
@article {pmid40099017,
year = {2025},
author = {Sivell, O and Sivell, D and Mitchell, R and Webb, J and , and , and , and , and , and , and , },
title = {The genome sequence of the Small Red Damselfly, Ceriagrion tenellum (de Villers, 1789).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {79},
pmid = {40099017},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from a male specimen of Ceriagrion tenellum (Small Red Damselfly; Arthropoda; Insecta; Odonata; Coenagrionidae). The genome sequence has a total length of 2,077.00 megabases. Most of the assembly (99.28%) is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.21 kilobases in length.},
}
@article {pmid40102624,
year = {2025},
author = {Rank, M and Kather, A and Wilke, D and Steib-Bauert, M and Kern, WV and Röder, I and de With, K},
title = {Limitations of estimating antibiotic resistance using German hospital consumption data - a comprehensive computational analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9244},
pmid = {40102624},
issn = {2045-2322},
mesh = {Germany ; Humans ; *Anti-Bacterial Agents/therapeutic use ; *Hospitals/statistics &amp; numerical data ; Neural Networks, Computer ; *Drug Resistance, Microbial ; *Drug Resistance, Bacterial ; },
abstract = {For almost a century, antibiotics have played an important role in the treatment of infectious diseases. However, the efficacy of these very drugs is now threatened by the development of resistances, which pose major challenges to medical professionals and decision-makers. Thereby, the consumption of antibiotics in hospitals is an important driver that can be targeted directly. To illuminate the relation between consumption and resistance depicts a very important step in this procedure. With the help of comprehensive ecological and clinical data, we applied a variety of different computational approaches ranging from classical linear regression to artificial neural networks to analyze antibiotic resistance in Germany. These mathematical and statistical models demonstrate that the amount and particularly the structure of currently available data sets lead to contradictory results and do, therefore, not allow for profound conclusions. More effort and attention on both data collection and distribution is necessary to overcome this problem. In particular, our results suggest that at least monthly or quarterly antibiotic use and resistance data at the department and ward level for each hospital (including application route and type of specimen) are needed to reliably determine the extent to which antibiotic consumption influences resistance development.},
}
@article {pmid40102641,
year = {2026},
author = {Kalvapalle, PB and Staubus, A and Dysart, MJ and Gambill, L and Reyes Gamas, K and Lu, LC and Silberg, JJ and Stadler, LB and Chappell, J},
title = {Information storage across a microbial community using universal RNA barcoding.},
journal = {Nature biotechnology},
volume = {44},
number = {2},
pages = {269-276},
pmid = {40102641},
issn = {1546-1696},
support = {2021-33522-35356//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; 1805901//National Science Foundation (NSF)/ ; 1828869//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2237512//National Science Foundation (NSF)/ ; FWP 78814//U.S. Department of Energy (DOE)/ ; A23-0202-004//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation/ ; },
mesh = {*Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *DNA Barcoding, Taxonomic/methods ; Escherichia coli/genetics ; Plasmids/genetics ; *Information Storage and Retrieval/methods ; RNA, Bacterial/genetics ; RNA, Catalytic/genetics ; Wastewater/microbiology ; },
abstract = {Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.},
}
@article {pmid40102961,
year = {2025},
author = {Hinojosa-Alvarez, S and Mendoza-Portillo, V and Chavez-Santoscoy, RA and Hernández-Pérez, J and Felix-Ceniceros, A and Magallón-Gayón, E and Mar-Silva, AF and Ochoa-Zavala, M and Díaz-Jaimes, P},
title = {The draft genome assembly of the cosmopolitan pelagic fish dolphinfish Coryphaena hippurus.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {5},
pages = {},
pmid = {40102961},
issn = {2160-1836},
support = {CF-2023-G-493//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; },
mesh = {Animals ; *Genome ; Molecular Sequence Annotation ; *Genomics/methods ; *Perciformes/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; *Fishes/genetics ; Whole Genome Sequencing ; Computational Biology/methods ; },
abstract = {For the first time, the complete genome assembly of the dolphinfish (Coryphaena hippurus), a tropical cosmopolitan species with commercial fishing importance was sequenced. Using a combination of Illumina and Nanopore sequencing technologies, a draft genome of 497.8 Mb was assembled into 6,044 contigs, with an N50 of 200.9 kb and a BUSCO genome completeness score of 89%. This high-quality genome assembly provides a valuable resource to study adaptive evolutionary processes and supports conservation and management strategies for this ecologically and economically significant species.},
}
@article {pmid40108248,
year = {2025},
author = {Mammides, C and Ieronymidou, C and Papadopoulos, H},
title = {An ecoacoustic dataset collected on the island of Cyprus in the Mediterranean Basin biodiversity hotspot.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {461},
pmid = {40108248},
issn = {2052-4463},
support = {101090273//European Commission (EC)/ ; },
mesh = {Cyprus ; *Biodiversity ; *Acoustics ; Animals ; *Vocalization, Animal ; Islands ; },
abstract = {There is growing interest in using novel technologies for large-scale biodiversity monitoring. Passive acoustic monitoring (PAM) represents a promising approach for surveying vocalizing animals. However, further development of PAM methods is needed to improve their accuracy. The availability of extensive ecoacoustic datasets from biodiverse areas can facilitate this development. In this study, we present a large ecoacoustic dataset (1.58 TB) collected at sixty-one study sites on the island of Cyprus between March and May 2023. The dataset comprises >313,000 audio files, representing over 5,200 hours of recordings. It can be used for a range of applications, such as developing and refining species identification algorithms, acoustic indices, and protocols for processing acoustic data to exclude non-focal sounds, e.g., those produced by human activities. It can also be used to explore fundamental ecological questions. To facilitate its use, the complete dataset has been made available on the Hugging Face repository and the ARBIMON platform, operated by Rainforest Connection[TM], which offers a range of free tools for ecoacoustic analyses.},
}
@article {pmid40108281,
year = {2025},
author = {Dong, J and Dai, W and Xu, J and Zhang, H and Li, Y and Xie, F},
title = {Impact and elastic modulus of coal mining on terrestrial ecosystems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9454},
pmid = {40108281},
issn = {2045-2322},
support = {CSC202306420029//China Scholarship Council/ ; Lumeidike (2022) No.14//Key Research Projects of Shandong Bureau of Coal Geology/ ; },
abstract = {The energy consumption structure is gradually evolving into a "diversified energy structure" against the backdrop of the global implementation of energy-saving and low-carbon policies. Coal, as the main energy source in China, is difficult to change in the short term, given the characteristics of China's energy and resource endowments, as well as the actual social and economic development at the present stage. Nevertheless, coal mining inevitably leads to a range of ecological issues. Identifying the impact of coal mining on terrestrial ecosystems and adopting resilient recovery measures are crucial prerequisites for advancing green coal mining efforts and attaining carbon peaking and carbon neutrality goals. Using China's open-pit coal mining as a case study: (1) the research examines the fundamental attributes and evolving patterns of spatial distribution among these mines within the country. Furthermore, it delineates the life cycle stages and distinctive features of the five principal open-pit coal mines. The life cycle of a coal mining area is divided into four distinct development phases: the initial phase, the accelerated phase, the stable phase, and the declining phase. The spatial relationship between the life cycle stages of coal mining and ecosystem succession is elucidated by examining the evolutionary types of ecosystems within coal mine area. In the accelerated and stable development phase, the adverse effects of coal mining on the ecosystem are in a long-term increasing trend, causing the key elements of the ecosystem to gradually surpass their threshold values. The ecosystem is out of balance, severely damaged, and gradually undergoing degradation or extreme degradation. The types of ecological succession in coal mining areas can be categorized as follows: terrestrial succession leading to a new terrestrial ecosystem, terrestrial to aquatic ecosystem transitions, or the development of an amphibious symbiotic ecosystem. (2) The research quantitatively assessed the impact of surface coal mining on terrestrial ecosystems by utilizing remote sensing data in conjunction with coal production information. In 2022, the affected areas of the five major open-pit coal mines due to coal mining activities amounted to approximately 0.02% of China's total land area. Meanwhile, the nationwide affected areas of all open-pit coal mines combined reached to approximately 0.13% of China's land area. Open-pit coal mining activities have a significant impact on the surface. (3) By incorporating the ecological resilience theory, we establish a model for the ecosystem's elastic modulus in coal mining areas, taking into account landscape diversity, vegetation coverage, land type, and climate factors, which are based on the concepts of elastic strength and elastic limit. A conceptual model for recognizing ecological thresholds in coal mining areas is developed by incorporating the comprehensive integrity index of the ecosystem. The comprehensive integrity of the ecosystem within a coal mining area undergoes significant alterations as it crosses three distinct ecological thresholds: the elastic point, the yield point, and the mutational point. There should be a corresponding constant (or constant interval) at the three ecological thresholds of ecosystem resilience, the elastic point, the yield point, and the mutational point, which is closely related to the scale of mining operations, mining technology, and the service life in coal mining areas. The established models for identifying ecological thresholds and the resilience modulus degree serve as both theoretical references and practical bases for managing the progress and trends of ecosystem changes during coal resource extraction, making ecological restoration in coal mine areas more target-oriented and specific.},
}
@article {pmid40111995,
year = {2025},
author = {Eales, O and Shearer, FM and McCaw, JM},
title = {How immunity shapes the long-term dynamics of influenza H3N2.},
journal = {PLoS computational biology},
volume = {21},
number = {3},
pages = {e1012893},
pmid = {40111995},
issn = {1553-7358},
mesh = {Humans ; *Influenza, Human/immunology/epidemiology/transmission/virology ; *Influenza A Virus, H3N2 Subtype/immunology/genetics ; Computational Biology ; *Models, Immunological ; Adult ; Aged ; Middle Aged ; Adolescent ; },
abstract = {Since its emergence in 1968, influenza A H3N2 has caused yearly epidemics in temperate regions. While infection confers immunity against antigenically similar strains, new antigenically distinct strains that evade existing immunity regularly emerge ('antigenic drift'). Immunity at the individual level is complex, depending on an individual's lifetime infection history. An individual's first infection with influenza typically elicits the greatest response with subsequent infections eliciting progressively reduced responses ('antigenic seniority'). The combined effect of individual-level immune responses and antigenic drift on the epidemiological dynamics of influenza are not well understood. Here we develop an integrated modelling framework of influenza transmission, immunity, and antigenic drift to show how individual-level exposure, and the build-up of population level immunity, shape the long-term epidemiological dynamics of H3N2. Including antigenic seniority in the model, we observe that following an initial decline after the pandemic year, the average annual attack rate increases over the next 80 years, before reaching an equilibrium, with greater increases in older age-groups. Our analyses suggest that the average attack rate of H3N2 is still in a growth phase. Further increases, particularly in the elderly, may be expected in coming decades, driving an increase in healthcare demand due to H3N2 infections.},
}
@article {pmid40112992,
year = {2025},
author = {Wei, L and Luo, Z and Wu, X and Liu, C and Shi, Y and Zhang, Q and Chen, M and Qin, W},
title = {Multi-omics analysis provided insights into the fruit softening of postharvest okra under carboxymethyl chitosan treatment.},
journal = {International journal of biological macromolecules},
volume = {307},
number = {Pt 3},
pages = {142149},
doi = {10.1016/j.ijbiomac.2025.142149},
pmid = {40112992},
issn = {1879-0003},
mesh = {*Chitosan/analogs &amp; derivatives/pharmacology ; *Fruit/drug effects/metabolism/genetics ; *Abelmoschus/genetics/metabolism/drug effects ; Gene Expression Regulation, Plant/drug effects ; Transcriptome/drug effects ; *Metabolomics/methods ; Metabolome/drug effects ; Gene Expression Profiling ; Pectins/metabolism ; Multiomics ; },
abstract = {To understand the potential regulatory mechanism of carboxymethyl chitosan (CMCS) treatment on postharvest softening of okra, a joint analysis of physiologic index, transcriptome and metabolome was used. The results showed that CMCS could delay the deterioration of the apparent quality of okra and reduce the degradation of chlorophyll. CMCS can reduce the accumulation of WSP and CSP and the decrease of NSP, and inhibit the enzyme activities of pectin degradation (PE, PG, PL). The results of metabolic pathways related to quality and texture showed that CMCS could increase the metabolic level of pentose phosphate pathway (PPP), inhibit the expression of membrane lipid degradation-related genes, and balance the expression of antioxidant-related genes. Ethylene and abscisic acid (ABA) are two important phytohormones. CMCS down-regulates the biosynthesis of ethylene and increases the expression of ABA. The combined analysis of transcriptome and metabolome showed that CMCS could significantly up-regulate flavonoid biosynthesis metabolites and transcriptional expression levels. Cellulose and pectin are important polymers to maintain the rigidity of okra cell wall. CMCS treatment can slow down the accumulation of cellulose by regulating the expression of DEGs related to cellulose synthesis (CesA) and degradation (EGase). CMCS slowed down the degradation of pectin by down-regulating the expression of pectin degradation-related genes. These results indicate that the quality of okra is deteriorated and the fruit is softened during cold storage. CMCS treatment can improve the nutritional quality of okra and slow down its texture decline. In this study, the regulatory effect of CMCS on softening and quality deterioration of okra during cold storage was discussed at the molecular level, which provided a reference for improving the quality of postharvest okra.},
}
@article {pmid40115327,
year = {2025},
author = {Hesson, JC and Haba, Y and McBride, CS and Sheerin, E and Mathers, TC and Paulini, M and Pointon, DB and Torrance, JW and Sadasivan Baby, C and Wood, JMD and , and , and McCarthy, SA and Lawniczak, MKN and Makunin, A},
title = {A chromosomal reference genome sequence for the northern house mosquito, Culex pipiens form pipiens, Linnaeus, 1758.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {107},
pmid = {40115327},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Culex pipiens sensu stricto (the northern house mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Sweden. The genome sequence is 533 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.},
}
@article {pmid40117176,
year = {2025},
author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP},
title = {Healthy microbiome-moving towards functional interpretation.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40117176},
issn = {2047-217X},
support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Dysbiosis/microbiology ; Phylogeny ; *Microbiota ; Principal Component Analysis ; Computational Biology/methods ; },
abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.<br><br>FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.<br><br>CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).},
}
@article {pmid40120189,
year = {2025},
author = {Sun, Q and Li, D and He, Y and Ping, Q and Wang, L and Li, Y},
title = {Improved anaerobic digestion of waste activated sludge under ammonia stress by nanoscale zero-valent iron/peracetic acid pretreatment and hydrochar regulation: Insights from multi-omics analyses.},
journal = {Water research},
volume = {279},
number = {},
pages = {123497},
doi = {10.1016/j.watres.2025.123497},
pmid = {40120189},
issn = {1879-2448},
mesh = {*Sewage ; *Ammonia ; Anaerobiosis ; Iron/chemistry ; Methane ; *Peracetic Acid/chemistry ; Multiomics ; },
abstract = {This study developed a novel strategy combining a nanoscale zero-valent iron (nZVI)/peracetic acid (PAA) pretreatment and hydrochar regulation to enhance anaerobic digestion of waste activated sludge (WAS) under ammonia-stressed conditions. The strategy significantly enhanced methane production at ammonia concentrations below 3000 mg/L, with the regulation groups (AN3000/REG) achieving a 50.1 % increase in cumulative methane yield. Metagenomic analysis demonstrated a 14.2 % enrichment of key functional microorganisms, including syntrophic fatty acid-oxidizing bacteria and hydrogenotrophic methanogens, in the AN3000/REG groups. Some of them promote the conversion of butyrate and valerate to acetate through the upregulation of key genes in the fatty acid β-oxidation pathway, thereby supplying sufficient substrates for acetoclastic methanogenesis. Beyond enhancing acetoclastic methanogenesis, the AN3000/REG groups exhibited significant upregulation of other metabolic pathways, with a 34.2 % increase in syntrophic acetate oxidation-hydrogenotrophic methanogenesis genes and a 17.1 % increase in methanol/methylotrophic methanogenesis-related genes. These findings were further validated by the metatranscriptomic and metaproteomic combination analyses. Furthermore, the AN3000/REG groups exhibited a significant enhancement in direct interspecies electron transfer, with functional microbes (e.g., Geobacter, Methanosarcina, and Methanobacterium), pili, and cytochrome c showing significant increases of 1.38-fold, 12.7-fold, and 5.6-fold, respectively. This might be due to the synergistic effects of nZVI and hydrochar in the regulation groups. Additionally, metabolomic analyses revealed that the regulation strategy improved the microbial adaptability to ammonia stress by modulating metabolic products, such as alkaloids. Our study not only provides a promising strategy for alleviating ammonia inhibition during the anaerobic digestion of WAS but also provides a strong basis for understanding the underlying mechanism under ammonia-stressed conditions.},
}
@article {pmid40120582,
year = {2025},
author = {Pinkert, S and Reuber, V and Krug, LM and Heidrich, L and Rehling, F and Brandl, R and Farwig, N},
title = {Burrowing facilitated the survival of mammals in harsh and fluctuating climates.},
journal = {Current biology : CB},
volume = {35},
number = {8},
pages = {1779-1790.e3},
doi = {10.1016/j.cub.2025.02.064},
pmid = {40120582},
issn = {1879-0445},
mesh = {Animals ; *Mammals/physiology ; *Climate Change ; Biological Evolution ; Biodiversity ; Phylogeny ; *Climate ; Ecosystem ; *Behavior, Animal ; },
abstract = {Species' ability to cope with climatic instability varies greatly, influenced by factors such as dispersal, physiological adaptations, and phylogenetic conservatism. Here, we investigate how burrowing behavior, a key component of species' endurance strategies and ecosystem functioning, shaped the contemporary patterns of species richness and range size as well as the diversification of mammalian lineages. Analyzing 4,407 terrestrial mammal species, excluding bats, combined with novel trait data on 3,096 species, we reveal contrasting responses to climatic factors between burrowing and non-burrowing species. Burrowing lineages are disproportionately species-rich at lower temperatures and productivity. Both range size and species richness steeply increase with climate seasonality in burrowing species as opposed to non-burrowing species. The proportion of burrowing species increases with latitude, with regions above 20°, especially those exhibiting greater Pleistocene temperature changes, being almost exclusively composed of burrowing species. Trait conservatism, higher net diversification rates, and Eocene peak diversification provide the evolutionary context for these contemporary patterns, underscoring the role of burrowing for mammalian radiations into temperate climates. Moreover, the lower extinction rate of burrowing species and peak diversification at the Cretaceous-Paleogene (K-Pg) boundary support the longstanding hypothesis that burrowing behavior promoted survival during the "impact winter" that marks the replacement of non-avian dinosaurs by mammals. Our study highlights the potential of readily available trait information for understanding the ecological and evolutionary processes that shape species distributions through space and time. The careful integration of divergent environmental constraints bears vast improvements for forecasts of species' responses to climatic changes and global models of biodiversity patterns.},
}
@article {pmid40121109,
year = {2025},
author = {Hanly, J and Anon, and Perret, J and Khan, A},
title = {Disability in ecology and evolution.},
journal = {Trends in ecology &amp; evolution},
volume = {40},
number = {4},
pages = {309-314},
doi = {10.1016/j.tree.2025.02.005},
pmid = {40121109},
issn = {1872-8383},
}
@article {pmid40121181,
year = {2025},
author = {Eaton, WD and McGee, KM and Glahn, A and Lemenze, A and Soteropoulos, P},
title = {Use of a logging road in a Costa Rican forest changes the composition and stability of soil microbial decomposer communities, and the conversion of organic carbon into biomass.},
journal = {Journal of applied microbiology},
volume = {136},
number = {4},
pages = {},
doi = {10.1093/jambio/lxaf075},
pmid = {40121181},
issn = {1365-2672},
support = {//Pace University Dyson College Office of the Dean/ ; },
mesh = {*Soil Microbiology ; Costa Rica ; *Forests ; Biomass ; *Carbon/metabolism/analysis ; *Fungi/metabolism/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Actinobacteria/metabolism/genetics/isolation &amp; purification ; Nitrogen/analysis/metabolism ; Acidobacteria/metabolism/genetics/isolation &amp; purification ; *Forestry ; Trees ; },
abstract = {AIMS: The effects of a tropical forest logging road on soil C and N, and the compositions of Actinobacteria, Acidobacteria, and wood rot/lignin-degrading fungal (WRT/LD) decomposer communities were evaluated.<br><br>METHODS AND RESULTS: Soils from a healthy Costa Rican old growth forest before Hurricane Otto and from an adjacent, recently formed logging road built after Hurricane Otto were collected over 4 years and assessed for C and N metrics, and characteristics of the three decomposer communities determined by Illumina amplicon sequencing methods. The Logging Road negatively impacted the soil total organic C, respiration, biomass C, qCO2, and total N, while the Actinobacterial and Acidobacterial communities changed from stable compositions of copiotrophic taxa in the rich forest soil to stable compositions of oligotrophic taxa in the poor logging road soil, and the WRT/LD community changed from stable compositions of copiotrophic taxa in the forest soils to an unstable community of oligotrophic taxa with almost no overlap in genera between logging road soils.<br><br>CONCLUSIONS: The logging road negatively influenced 3 decomposer communities and associated C and N metrics, with the two bacterial communities taxonomically stabilizing, but the fungal community taxonomically diverging into an unstable composition over time. Monitoring efforts are on-going to provide local forest land managers with potential indicators of soil ecosystem damage and recovery.},
}
@article {pmid40121238,
year = {2025},
author = {Kelliher, JM and Rodriguez, FE and Johnson, LYD and Roux, S and Smith, M and Clum, A and Lynch, W and Bias, CH and Finks, SS and Keenum, I and Kiledal, EA and Lin, HA and Longley, R and McDonald, R and Pitot, TM and Rodríguez-Ramos, J and Shen, J and Sprockett, DD and Swift, J and Yadav, A and Eloe-Fadrosh, EA},
title = {Quantifying the impact of workshops promoting microbiome data standards and data stewardship.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9887},
pmid = {40121238},
issn = {2045-2322},
support = {The work conducted by the National Microbiome Data Collaborative (https://ror.org/05cwx3318) is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL).//U.S. Department of Energy/ ; },
mesh = {*Microbiota ; Humans ; Surveys and Questionnaires ; Education ; Research Personnel/education ; },
abstract = {The field of microbiome research continues to grow at a rapid pace, with multi-omics approaches becoming widely used to interrogate diverse microbiome samples. However, due to lagging awareness and implementation of standards and data stewardship, many datasets are produced that are not comparable, reproducible, or reusable. In 2021, the National Microbiome Data Collaborative launched its Ambassador Program, which utilizes a community-learning model to annually train a cohort of early-career researchers in microbiome data stewardship best practices. These Ambassadors then host workshops and other events to communicate these themes to their respective microbiome research communities. To quantify the impact of this learning model for promoting awareness of and experience with microbiome data, we conducted a survey of workshop participants from events hosted by the 2023 Ambassador cohort. The 2023 cohort of 13 National Microbiome Data Collaborative Ambassadors collectively hosted 21 events, reaching over 550 researchers. The Ambassadors distributed an anonymous post-workshop survey to their event participants to quantify the effectiveness of the training materials, the workshop format, and the thematic content. From the 21 events, survey results were successfully collected for 15 of those events from a total of 122 researchers. Overall, 122 participants working with a range of microbiome types and from a variety of institutions responded to the survey and reported overwhelmingly positive experiences with the workshop content and materials, with 98% of respondents reporting that they gained knowledge from the event. Participants across the events also reported an increase in their post-workshop understanding of metadata standards, principles for microbiome data management and reporting, and the importance of standardization in microbiome data processing. Participants also expressed a willingness to apply what they learned about microbiome data stewardship to their own research. The results of this study demonstrate the effectiveness of hands-on workshops and community-learning for communicating data stewardship best practices to microbiome researchers. The lessons learned and details about the implementation of this cohort-based learning model contained herein are intended to assist other groups in their efforts to create or improve similar learning strategies.},
}
@article {pmid40123484,
year = {2025},
author = {Poulin, R},
title = {To bin or not to bin: why parasite abundance data should not be lumped into categories for statistical analysis.},
journal = {Parasitology},
volume = {152},
number = {3},
pages = {338-345},
pmid = {40123484},
issn = {1469-8161},
mesh = {Animals ; *Host-Parasite Interactions ; *Parasites/physiology ; *Parasitology/methods ; Data Interpretation, Statistical ; *Parasitic Diseases/parasitology ; },
abstract = {The impact of macroparasites on their hosts is proportional to the number of parasites per host, or parasite abundance. Abundance values are count data, i.e. integers ranging from 0 to some maximum number, depending on the host-parasite system. When using parasite abundance as a predictor in statistical analysis, a common approach is to bin values, i.e. group hosts into infection categories based on abundance, and test for differences in some response variable (e.g. a host trait) among these categories. There are well-documented pitfalls associated with this approach. Here, I use a literature review to show that binning abundance values for analysis has been used in one-third of studies published in parasitological journals over the past 15 years, and half of the studies in ecological and behavioural journals, often without any justification. Binning abundance data into arbitrary categories has been much more common among studies using experimental infections than among those using naturally infected hosts. I then use simulated data to demonstrate that true and significant relationships between parasite abundance and host traits can be missed when abundance values are binned for analysis, and vice versa that when there is no underlying relationship between abundance and host traits, analysis of binned data can create a spurious one. This holds regardless of the prevalence of infection or the level of parasite aggregation in a host sample. These findings argue strongly for the practice of binning abundance data as a predictor variable to be abandoned in favour of more appropriate analytical approaches.},
}
@article {pmid40125538,
year = {2025},
author = {Broad, GR and Holt, S and Sivess, L and Boyes, D and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Scorched Wing moth, Plagodis dolabraria (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {111},
pmid = {40125538},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Plagodis dolabraria (Scorched Wing; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 939.07 megabases. Most of the assembly (99.59%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.97 kilobases in length.},
}
@article {pmid40125978,
year = {2025},
author = {Bailey, N and Stevison, L and Samuk, K},
title = {Correcting for Bias in Estimates of θ w and Tajima's D From Missing Data in Next-Generation Sequencing.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14104},
pmid = {40125978},
issn = {1755-0998},
support = {R35 GM147501/GM/NIGMS NIH HHS/United States ; R35GM147501/GM/NIGMS NIH HHS/United States ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Genetics, Population/methods ; *Genetic Variation ; Software ; *Computational Biology/methods ; Bias ; },
abstract = {Population genetic analyses use information from the site frequency spectrum to infer evolutionary processes. Two summary statistics, Watterson's estimator (θ w) of genetic diversity, and Tajima's D , used for detecting non-neutral evolution, are among the most frequently computed statistics utilising this information. However, missing information in genomic data, particularly as encoded in the Variant Call Format (VCF), can bias these estimates, leading to incorrect evolutionary inferences. We assessed the impact of missing data on the estimation of these statistics using various population genetic software packages (VCFtools, PopGenome, pegas and scikit-allel). By simulating neutral genomic data with varying levels of missing genotypes and sites, we found consistent underestimation of θ w across programs. We found a consequent bias in estimates of Tajima's D , though the direction varied by software. We developed and implemented correction methods as functions in an update of the popular pixy software, significantly reducing these biases. Our findings highlight the need for accurate data handling in population genomics to avoid misinterpretations of evolutionary phenomena.},
}
@article {pmid40132265,
year = {2025},
author = {Gu, J and Shen, Y and Guo, L and Chen, Z and Zhou, D and Ji, G and Gu, A},
title = {Investigation of the mechanisms of liver injury induced by emamectin benzoate exposure at environmental concentrations in zebrafish: A multi-omics approach to explore the role of the gut-liver axis.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {138008},
doi = {10.1016/j.jhazmat.2025.138008},
pmid = {40132265},
issn = {1873-3336},
mesh = {Animals ; Zebrafish ; *Ivermectin/analogs &amp; derivatives/toxicity ; *Liver/drug effects/metabolism/pathology ; Gastrointestinal Microbiome/drug effects ; *Chemical and Drug Induced Liver Injury/metabolism/pathology/etiology ; *Water Pollutants, Chemical/toxicity ; Metabolomics ; Lipid Metabolism/drug effects ; *Insecticides/toxicity ; RNA, Ribosomal, 16S/genetics ; Multiomics ; },
abstract = {Emamectin benzoate (EMB) is a lipophilic pesticide that enters aquatic systems and adversely affects non-target organisms. This study investigated the long-term effects of EMB on zebrafish, exposing them to concentrations of 0, 0.1, 1, and 10 μg/L from the 4-hour post-fertilization (hpf) embryo stage to the 120-day post-fertilisation (dpf) adult stage. We found that exposure to 1 μg/L EMB induced liver damage, manifested as impaired liver function (elevated aspartate aminotransferase (AST) and alanine aminotransferase (ALT)), histopathological damage (lipid accumulation), as well as inflammatory and oxidative damage, with a dose - dependent effect. Non-targeted metabolomic analysis revealed an increase in lipid molecules in the liver, affecting the pathways related to glycerophospholipid metabolism. In addition, EMB exposure resulted in damage to the intestinal barrier and inflammatory responses in zebrafish. 16S rRNA sequencing demonstrated that EMB exposure resulted in notable alterations in the gut microbiota composition. Notably, the abundance of Plesiomonas and Cetobacterium increased in the EMB exposure group and exhibited a positive correlation with the majority of liver lipid metabolites. In contrast, reductions in Muribaculaceae and Alloprevotella were negatively correlated. The results of this study indicate that long-term exposure to EMB disrupts the gut microbiota, leading to the dysregulation of hepatic phospholipid metabolism. These findings provide new insights into the health risks associated with EMB and highlight its potential threats to higher organisms, including mammals.},
}
@article {pmid40132633,
year = {2025},
author = {Liu, X and Milesi, E and Fontsere, C and Owens, HL and Heinsohn, R and Gilbert, MTP and Crates, R and Nogués-Bravo, D and Morales, HE},
title = {Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2043},
pages = {20242480},
pmid = {40132633},
issn = {1471-2954},
support = {//The European Molecular Biology Organization/ ; //Mohamed bin Zayed Species Conservation Fund/ ; //Danish National Research Foundation/ ; /ERC_/European Research Council/International ; 25925//Villum Fonden/ ; },
mesh = {Animals ; *Extinction, Biological ; Endangered Species ; *Genome ; *Genetic Variation ; Conservation of Natural Resources ; Ecosystem ; Australia ; Genomics ; Biodiversity ; Population Dynamics ; *Passeriformes/genetics ; },
abstract = {Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.},
}
@article {pmid40133528,
year = {2025},
author = {Pekar, JE and Wang, Y and Wang, JC and Shao, Y and Taki, F and Forgione, LA and Amin, H and Clabby, T and Johnson, K and Torian, LV and Braunstein, SL and Pathela, P and Omoregie, E and Hughes, S and Suchard, MA and Vasylyeva, TI and Lemey, P and Wertheim, JO},
title = {Transmission dynamics of the 2022 mpox epidemic in New York City.},
journal = {Nature medicine},
volume = {31},
number = {5},
pages = {1464-1473},
pmid = {40133528},
issn = {1546-170X},
support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; AI135995//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153044//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135992//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P30 AI036214/AI/NIAID NIH HHS/United States ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; R01 AI135992/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; New York City/epidemiology ; Male ; Female ; *Epidemics ; *HIV Infections/epidemiology/transmission/virology ; Phylogeny ; HIV-1/genetics ; Phylogeography ; Homosexuality, Male ; Disease Outbreaks ; Sexual Behavior ; Mpox, Monkeypox ; },
abstract = {The 2022 global mpox epidemic was caused by transmission of MPXV clade IIb, lineage B.1 through sexual contact networks, with New York City (NYC) experiencing the first and largest outbreak in the United States. By performing phylogeographic analysis of MPXV genomes sampled from 757 individuals in NYC between April 2022 and April 2023, and 3,287 MPXV genomes sampled around the world, we identify over 200 introductions of MPXV into NYC with at least 84 leading to onward transmission. These infections primarily occurred among men who have sex with men, transgender women and nonbinary individuals. Through a comparative analysis with HIV in NYC, we find that both MPXV and HIV genomic cluster sizes are best fit by scale-free distributions, and that people in MPXV clusters are more likely to have previously received an HIV diagnosis and be a member of a recently growing HIV transmission cluster. We model MPXV transmission through sexual contact networks and show that highly connected individuals would be disproportionately infected at the start of an epidemic, which would likely result in the exhaustion of the most densely connected parts of the network, and, therefore, explain the rapid expansion and decline of the NYC outbreak. By coupling the genomic epidemiology of MPXV and HIV with epidemic modeling, we demonstrate that the transmission dynamics of MPXV in NYC can be understood by general principles of sexually transmitted pathogens.},
}
@article {pmid40136165,
year = {2025},
author = {Aquino, &#xc9;C and Borowicc, SL and Alves-Souza, SN and Teixeira, RA and Ishitani, LH and Malta, DC and Morais Neto, OL},
title = {Distribution of garbage codes in the Mortality Information System, Brazil, 2000 to 2020.},
journal = {Ciencia &amp; saude coletiva},
volume = {30},
number = {3},
pages = {e09442023},
doi = {10.1590/1413-81232025303.09442023},
pmid = {40136165},
issn = {1678-4561},
mesh = {Brazil/epidemiology ; Humans ; *Information Systems/statistics &amp; numerical data ; Cause of Death/trends ; Time Factors ; Linear Models ; *Mortality/trends ; },
abstract = {The analysis of the causes of death is essential to understand the main problems that affect the health level of the population of a region or country. The garbage codes (GC) provide little useful information about causes of death. This study aims to identify the proportion of GC among the deaths registered and to analyze their temporal distribution in Brazil from 2000 to 2020. It's an ecological time-series study of the evolution of the proportion of GC in Brazil. Time series analysis was performed using segmented linear regression models (joinpoint). Between 2000 and 2020, 39.9% of deaths that occurred in Brazil were coded with GC. Between 2000 and 2007, there was a continuous and persistent reduction in the proportion of GC (APC -2.1; P < 0.001). Between 2007 and 2015, there continued to be a reduction, albeit to a lesser extent (APC = -0.7; P = 0.013). Between 2015 and 2018, there was no significant trend of the proportion of GC (APC = -2.3; P = 0.172), which persisted from 2018 (APC 3.2; P < 0.079). Although a reduction in the proportion of GC in Brazil was observed until 2018, this trend did not persist after that year. Reducing the proportion of GC allows managers to plan health policies more adequately for the population.},
}
@article {pmid40136166,
year = {2025},
author = {Ferrari, YAC and Jesus, CVF and Batista, JFC and Silva, BEBD and Cavalcante, AB and Lima, CA},
title = {Secular trend of cervical cancer mortality in Brazil and regions.},
journal = {Ciencia &amp; saude coletiva},
volume = {30},
number = {3},
pages = {e09962023},
doi = {10.1590/1413-81232025303.09962023},
pmid = {40136166},
issn = {1678-4561},
mesh = {Humans ; Brazil/epidemiology ; Female ; *Uterine Cervical Neoplasms/mortality/epidemiology ; Middle Aged ; Adult ; Aged ; Young Adult ; Age Distribution ; Adolescent ; Mortality/trends ; Age Factors ; },
abstract = {The scope of this study was to describe the secular trend of cervical cancer mortality in Brazil and its various regions from 1980 to 2021. It involved a populational and ecological study, based on data available at the Department of Informatics of the Unified Health System, using codes 180 and C53. Crude rates, age-specific rates, and age-standardized rates were calculated for the Brazilian and world population. The Average Annual Percent Change (AAPC) was obtained by trend analysis using the Joinpoint Regression Program, with a significance level of 0.05 and 95% confidence intervals (95%CI). There were 171,793 deaths from cervical cancer. In Brazil (AAPC -0.3; CI95%-1.0; 0.4), North (AAPC 0.6; 95%CI -0.1; 1.3) and South (AAPC 0.0; 95%CI -0.5; 0.5) the trends were stationary, increasing in the Northeast (AAPC 0.6; 95%CI 0.3; 0.8) and in the Midwest (AAPC -1.3; 95%CI -1.5; -1.1), and decreasing in the Southeast (AAPC -0.9; 95%CI -1.4; -0.5). Regional differences indicate that public policies need to be improved regarding women's access to a health system that offers adequate prevention, screening and treatment through management strategies that include the most vulnerable population.},
}
@article {pmid40139065,
year = {2025},
author = {Sfriso, AA and Juhmani, AS and Tomio, Y and Wedyan, M and Cunsolo, F and Forlani, G and Sfriso, A and Ferretti, G and Coltorti, M and Munari, C and Mistri, M},
title = {Microbial dynamics in seagrass restoration: Unveiling hidden indicators of ecological success.},
journal = {Marine environmental research},
volume = {208},
number = {},
pages = {107089},
doi = {10.1016/j.marenvres.2025.107089},
pmid = {40139065},
issn = {1879-0291},
mesh = {*Geologic Sediments/microbiology ; *Zosteraceae/physiology ; *Microbiota ; *Environmental Restoration and Remediation ; Ecosystem ; },
abstract = {Seagrass transplantation significantly alters sediment microbial communities, shaping their composition and metabolic functions. One year after Zostera marina transplantation, the microbial community structure and functions at the recipient site began shifting toward those of the donor site. Key microbial taxa associated with seagrass meadow sediment, such as Firmicutes (Hungateiclostridiaceae, Defluviitaleaceae) and Campylobacterota (Sulfurovum), increased in abundance, correlating with sediment organic matter content and carbon availability. Four functional groups were identified, each with distinct metabolic roles: (1) Opportunistic Anaerobic Degraders, (2) Seagrass-Driven Carbon Recyclers, (3) Anaerobic Fermenters and Hydrocarbon Recyclers and (4) Oxygen-Linked Carbon and Sulfur Cyclers. The sediments of transplanted Z. marina meadows exhibited increased cellulolysis and aerobic chemoheterotrophy, along with a reduction in nitrogen metabolism one year post transplant. Despite these microbial shifts, sediment isotopic signatures remained indicative of algal biomass, suggesting an incomplete transition toward a mature seagrass environment. Multivariate analysis further confirmed that the microbial community at the recipient site had not yet fully converged with that of the donor meadow, indicating that complete sediment maturation may require longer timescales. These findings demonstrate that microbial community composition and functional annotations serve as early indicators of seagrass restoration success. Long-term monitoring is essential to track ecosystem recovery and assess the stabilization of sediment conditions.},
}
@article {pmid40139213,
year = {2025},
author = {Tam, CC and Young, SD and Harrison, S and Li, X and Litwin, AH},
title = {Theory-Based Social Media Intervention for Nonmedical Use of Prescription Opioids in Young Adults: Protocol for a Randomized Controlled Trial.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e65847},
pmid = {40139213},
issn = {1929-0748},
support = {K01 DA058768/DA/NIDA NIH HHS/United States ; },
mesh = {Humans ; *Social Media ; Young Adult ; Male ; Female ; *Analgesics, Opioid/adverse effects ; *Opioid-Related Disorders/prevention &amp; control/psychology/therapy ; Randomized Controlled Trials as Topic ; Peer Group ; Adult ; Adolescent ; *Prescription Drug Misuse/prevention &amp; control ; Pragmatic Clinical Trials as Topic ; },
abstract = {BACKGROUND: The nonmedical use of prescription opioids (NMUPO) in young adults in the United States is concerning and is robustly influenced by many psychosocial factors. Given the advantages of flexibility, wide coverage, and real-time responses and assessment, using social media appears to be a promising and innovative approach to delivering psychosocial intervention to young adults. However, few theory-based social media interventions are available for NMUPO targeting this at-risk population.<br><br>OBJECTIVE: Guided by the information-motivation-behavioral skills model, the proposed research aims to address critical gaps by theoretically exploring psychosocial content associated with NMUPO among young adults via formative assessment. These findings will then be used to develop and evaluate the feasibility and preliminary efficacy of a peer-led social media intervention to reduce NMUPO among young adults.<br><br>METHODS: The proposed study will comprise serial research activities. First, formative research will be conducted through semistructured interviews among 30 young adults engaged in NMUPO. Qualitative data will be synthesized using a pragmatic approach for identifying psychosocial content associated with NMUPO. Second, qualitative findings will be used for developing a peer-led social media intervention to reduce NMUPO among young adults by integrating promising psychotherapy principles and incorporating them with well-trained recovery coaches. Third, the social media intervention will be evaluated through a 12-week randomized controlled trial among 70 young adults (n=35, 50% in the intervention group and control group) engaged in NMUPO via mixed methods, including pre- and postintervention surveys, social media paradata (eg, time-series reactions to posts) collection, and ecological momentary assessment during the intervention. The control group will not receive an intervention but will complete the pre- and postintervention surveys. The primary outcomes will be feasibility, usability, and acceptability, while the secondary outcomes will be psychosocial and behavioral measures, such as past-3-month NMUPO, intention, psychological distress, self-efficacy, resilience, and coping strategies.<br><br>RESULTS: The proposed study was funded in May 2024. Social media campaigns have received responses from a total of 379 individuals, with 24 (6.3%) identified as eligible. As of February 10, 2025, we have completed formative interviews with 8 eligible participants.<br><br>CONCLUSIONS: The proposed study will be one of the first efforts to develop and deliver a theory-based peer-led intervention on social media, incorporating empirical findings on the psychosocial mechanism of NMUPO. The findings of the proposed study will provide valuable insights into opioid risk reduction for young adults through an innovative approach. If the tested trial is found to be feasible, the proposed study will contribute to future scaled-up and fully powered psychosocial interventions among young adults and other key populations at risk for NMUPO.<br><br>TRIAL REGISTRATION: ClincialTrials.gov NCT06469749; https://clinicaltrials.gov/study/NCT06469749.<br><br>DERR1-10.2196/65847.},
}
@article {pmid40140737,
year = {2025},
author = {Tahir Ul Qamar, M and Fatima, K and Rao, MJ and Tang, Q and Sadaqat, M and Ding, B and Chen, LL and Zhu, XT},
title = {Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {388},
pmid = {40140737},
issn = {1471-2229},
mesh = {*Citrus/genetics/microbiology ; Genomics ; *Genome, Plant ; *Plant Diseases/microbiology/genetics ; Genetic Variation ; *Multigene Family ; Phylogeny ; *Plant Proteins/genetics/metabolism ; Genes, Plant ; },
abstract = {Citrus is an important nutritional fruit globally; however, its yield is affected by various stresses. This study presents the draft pangenome of Citrus, developed using 11 species to examine their genetic diversity and identify members of the germin-like proteins (GLPs) gene family involved in disease responsiveness. The developed sequence-based pangenome contains 954 Mb sequence and 74,755 genes. The comparative genomics analysis revealed the presence-absence variations (PAVs) among the Citrus genomes and species-specific protein-coding genes. Gene-based pangenome analysis revealed 4,936 new genes missing in the reference genome and highlighted the core and shell genes with putative functions in stress regulation. The pangenome-wide identification of GLP gene family members indicated the intraspecies diversity among the members across 11 genomes by analyzing their gene structure, motifs, and chromosomal distribution patterns. The synteny and evolutionary constraints analyses of Citrus GLPs provide detailed evidence of their evolutionary conservation and divergence. Further, the interaction, functional enrichment, and promoter analysis revealed their involvement in abiotic-, biotic-stress, signaling, and development-related pathways. The expression patterns of C. sinensis GLPs were studied in Huanglongbing (HLB) and Citrus canker disease. Several genes including CsGLPs1-2 and CsGLPs8-4 showed changes in expression patterns under both disease conditions. The qRT-PCR analysis revealed that these two genes were highly expressed in leaves infected with HLB disease across seven HLB-tolerant and susceptible citrus species. This Citrus pangenome and pangenes family study offers a comprehensive resource and new insights into the structural and functional diversity, identifying candidate genes that are important for future research to understand the stress-responsive mechanisms in Citrus.},
}
@article {pmid40143245,
year = {2025},
author = {Culot, A and Abriat, G and Furlong, KP},
title = {High-Performance Genome Annotation for a Safer and Faster-Developing Phage Therapy.},
journal = {Viruses},
volume = {17},
number = {3},
pages = {},
pmid = {40143245},
issn = {1999-4915},
mesh = {*Genome, Viral ; *Bacteriophages/genetics ; *Molecular Sequence Annotation/methods ; *Computational Biology/methods ; *Phage Therapy/methods ; Humans ; },
abstract = {Phage therapy, which uses phages to decrease bacterial load in an ecosystem, introduces a multitude of gene copies (bacterial and phage) into said ecosystem. While it is widely accepted that phages have a significant impact on ecology, the mechanisms underlying their impact are not well understood. It is therefore paramount to understand what is released in the said ecosystem, to avoid alterations with difficult-to-predict-but potentially huge-consequences. An in-depth annotation of therapeutic phage genomes is therefore essential. Currently, the average published phage genome has only 20-30% functionally annotated genes, which represents a hurdle to overcome to deliver safe phage therapy, for both patients and the environment. This study aims to compare the effectiveness of manual versus automated phage genome annotation methods. Twenty-seven phage genomes were annotated using SEA-PHAGE and Rime Bioinformatics protocols. The structural (gene calling) and functional annotation results were compared. The results suggest that during the structural annotation step, the SEA-PHAGE method was able to identify an average of 1.5 more genes per phage (typically a frameshift gene) and 5.3 gene start sites per phage. Despite this difference, the impact on functional annotation appeared to be limited: on average, 1.2 genes per phage had erroneous functions, caused by the structural annotation. Rime Bioinformatics' tool (rTOOLS, v2) performed better at assigning functions, especially where the SEA-PHAGE methods assigned hypothetical proteins: 7.0 genes per phage had a better functional annotation on average, compared to SEA PHAGE's 1.7. The method comparison detailed in this article indicate that (1) manual structural annotation is marginally superior to rTOOLS automated structural annotation; (2) rTOOLS automated functional annotation is superior to manual functional annotation. Previously, the only way to obtain a high-quality annotation was by using manual protocols, such as SEA-PHAGES. In the relatively new field of phage therapy, which requires support to advance, manual work can be problematic due to its high cost. Rime Bioinformatics' rTOOLS software allows for time and money to be saved by providing high-quality genome annotations that are comparable to manual results, enabling a safer and faster-developing phage therapy.},
}
@article {pmid40144399,
year = {2021},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the poplar hawk-moth, Laothoe populi (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {6},
number = {},
pages = {237},
pmid = {40144399},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Laothoe populi (the poplar hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 576 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.},
}
@article {pmid40147302,
year = {2025},
author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD},
title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.},
journal = {Water research},
volume = {280},
number = {},
pages = {123511},
doi = {10.1016/j.watres.2025.123511},
pmid = {40147302},
issn = {1879-2448},
mesh = {*Floods ; Salinity ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Metabolomics ; Microbiota ; Multiomics ; },
abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.},
}
@article {pmid40155652,
year = {2025},
author = {Rehbein, M and Escobari, B and Fischer, S and Güntsch, A and Haas, B and Matheisen, G and Perschl, T and Wieshuber, A and Engel, T},
title = {Quantitative and qualitative Data on historical Vertebrate Distributions in Bavaria 1845.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {525},
pmid = {40155652},
issn = {2052-4463},
support = {442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Vertebrates ; Animals ; *Biodiversity ; Germany ; History, 19th Century ; Ecosystem ; *Animal Distribution ; },
abstract = {Archival collections contain an underutilized wealth of biodiversity data, encapsulated in government files and other historical documents. In 1845, the Bavarian government conducted a comprehensive national survey on the occurrence of 44 selected vertebrate species across the country. The detailed expert responses from 119 forestry offices, totalling 520 handwritten pages, have been preserved in the Bavarian State Archives. In this study, we digitized, annotated, geographically referenced, and published these historical records, making them widely available as data for research and conservation planning. Our dataset, openly accessible through the Global Biodiversity Information Facility (GBIF) and Zenodo, contains 5,467 species occurrence records from 1845. Besides the binary presence/absence data, we have also published the original textual survey responses, which contain rich qualitative information, such as species abundances, population trends, habitats, forest management practices, and human-nature relationships. This information can be further processed and interpreted to address a range of questions in historical and contemporary ecology.},
}
@article {pmid40155956,
year = {2025},
author = {van Kessel, SAM and Wielders, CCH and Schoffelen, AF and Verbon, A},
title = {Enhancing antimicrobial resistance surveillance and research: a systematic scoping review on the possibilities, yield and methods of data linkage studies.},
journal = {Antimicrobial resistance and infection control},
volume = {14},
number = {1},
pages = {25},
pmid = {40155956},
issn = {2047-2994},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial ; Antimicrobial Stewardship ; *Information Storage and Retrieval/methods ; *Epidemiological Monitoring ; },
abstract = {BACKGROUND: Surveillance data on antimicrobial resistance (AMR) determinants such as antibiotic use, prevalence of AMR, antimicrobial stewardship, and infection prevention and control are mostly analysed and reported separately, although they are inextricably linked to each other. The impact of surveillance and research can be enhanced by linking these data. This systematic scoping review aims to summarize the studies that link AMR data and evaluate whether they yield new results, implications, or recommendations for practice.<br><br>METHODS: For this review, data linkage is defined as the process of linking records, from at least two independent data sources on either (I) at least two AMR determinants or (II) one AMR determinant and one or more general population characteristics. Data linkage should be performed on the level of a certain entity which, in the context of this review, can encompass persons, healthcare institutes, geographical regions or countries. A systematic literature search was performed on February 7th 2025 in Embase.com, PubMed and Scopus to identify AMR data linkage studies.<br><br>RESULTS: Forty-eight articles were included in our review. Most data linkage studies used two data sources, and most studies were published in the last 5 years (n&#x2009;=&#x2009;23 in 2020-2024). A predominance of studies linked data on geographical location, and thirteen studies linked data on individual patient level. Findings demonstrate that the majority of studies (43/48) had added value and provided recommendations for clinical practice and future policies or had suggestions for further research and surveillance. Additionally, data linkage studies appeared to be suitable for hypothesis generating. Several limitations were identified. Most studies had ecological designs, which are prone to ecological fallacy and unobserved confounding, making it hard to establish causality.<br><br>CONCLUSION: This systematic scoping review showed that AMR data linkage studies are increasingly performed. They have potential to gain a more comprehensive understanding of AMR dynamics by generating hypotheses, assisting in optimisation of surveillance, and interpretation of data in the context of guideline/policy development. To increase the added value of data linkage, more studies should be performed to improve knowledge on methodological approaches, data access, data management, and governance issues.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid40156461,
year = {2025},
author = {Sharma, G and Deuis, JR and Jia, X and Crawford, T and Rahnama, S and Undheim, EAB and Vetter, I and Chin, YK and Mobli, M},
title = {Refining the NaV1.7 pharmacophore of a class of venom-derived peptide inhibitors via a combination of in silico screening and rational engineering.},
journal = {FEBS letters},
volume = {599},
number = {12},
pages = {1717-1732},
pmid = {40156461},
issn = {1873-3468},
support = {FTl10100925//Australian Research Council/ ; DE160101142//Australian Research Council/ ; APP1102267//National Health and Medical Research Council/ ; APP1080405//National Health and Medical Research Council/ ; 2017086//National Health and Medical Research Council/ ; APP1034958//National Health and Medical Research Council/ ; //University of Queensland/ ; 101039862/ERC_/European Research Council/International ; },
mesh = {*NAV1.7 Voltage-Gated Sodium Channel/chemistry/metabolism/genetics ; Humans ; *Peptides/chemistry/pharmacology ; Animals ; *Voltage-Gated Sodium Channel Blockers/chemistry/pharmacology ; Structure-Activity Relationship ; Amino Acid Sequence ; Computer Simulation ; Protein Engineering ; *Scorpion Venoms/chemistry/pharmacology ; Computational Biology ; Pharmacophore ; },
abstract = {Ion channels are among the main targets of venom peptides. Extensive functional screening has identified a number of these peptides as modulators of the voltage-gated sodium channel subtype NaV1.7, a potential target for the treatment of chronic pain. In this study, we used a bioinformatic approach that can automatically identify NaV1.7 gating modifier toxins from sequence information alone. The method further enables the incorporation of evolutionarily accessible sequence space in structure-activity relationship studies. The in silico method identified a putative NaV1.7 inhibitor, μ-theraphotoxin Cg4a, which we produced recombinantly and confirmed as a NaV1.7 inhibitor. Using structural and mutagenesis studies, we propose an improved definition of the pharmacophore of this class of NaV1.7 inhibitors, aiding future in silico screening and classification of NaV1.7 inhibitors.},
}
@article {pmid40163742,
year = {2025},
author = {Ghassemi Nedjad, C and Bolteau, M and Bourneuf, L and Paulevé, L and Frioux, C},
title = {Seed2LP: seed inference in metabolic networks for reverse ecology applications.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {4},
pages = {},
pmid = {40163742},
issn = {1367-4811},
support = {//French National Research Agency/ ; },
mesh = {*Metabolic Networks and Pathways ; *Software ; *Computational Biology/methods ; Models, Biological ; Algorithms ; },
abstract = {MOTIVATION: A challenging problem in microbiology is to determine nutritional requirements of microorganisms and culture them, especially for the microbial dark matter detected solely with culture-independent methods. The latter foster an increasing amount of genomic sequences that can be explored with reverse ecology approaches to raise hypotheses on the corresponding populations. Building upon genome-scale metabolic networks (GSMNs) obtained from genome annotations, metabolic models predict contextualized phenotypes using nutrient information.<br><br>RESULTS: We developed the tool Seed2LP, addressing the inverse problem of predicting source nutrients, or seeds, from a GSMN and a metabolic objective. The originality of Seed2LP is its hybrid model, combining a scalable and discrete Boolean approximation of metabolic activity, with the numerically accurate flux balance analysis (FBA). Seed inference is highly customizable, with multiple search and solving modes, exploring the search space of external and internal metabolites combinations. Application to a benchmark of 107 curated GSMNs highlights the usefulness of a logic modelling method over a graph-based approach to predict seeds, and the relevance of hybrid solving to satisfy FBA constraints. Focusing on the dependency between metabolism and environment, Seed2LP is a computational support contributing to address the multifactorial challenge of culturing possibly uncultured microorganisms.<br><br>Seed2LP is available on https://github.com/bioasp/seed2lp.},
}
@article {pmid40165685,
year = {2025},
author = {Gu, Y and Meng, L and Wang, Y and Wu, Z and Pan, Y and Zhao, Y and Detto, M and Wu, J},
title = {Uncovering the role of solar radiation and water stress factors in constraining decadal intra-site spring phenology variability in diverse ecosystems across the Northern Hemisphere.},
journal = {The New phytologist},
volume = {246},
number = {5},
pages = {1986-2003},
pmid = {40165685},
issn = {1469-8137},
support = {#2017804//Carbon Mitigation Initiative of Princeton University and NSF grant/ ; //HKU Seed Funding for Strategic Interdisciplinary Research Scheme/ ; #17305321//Hong Kong Research Grant Council General Research Fund/ ; #C5062-21GF//Hong Kong Research Grant Council Collaborative Research Fund/ ; #31922090//National Natural Science Foundation of China/ ; //Innovation and Technology Fund (funding support to State Key Laboratories of Agrobiotechnology)/ ; //HKU Science Faculty RAE Improvement Fund 2023-24/ ; },
mesh = {*Ecosystem ; *Seasons ; *Sunlight ; *Water ; *Stress, Physiological ; Soil/chemistry ; Rain ; },
abstract = {The spring phenology has advanced significantly over recent decades with climate change, impacting large-scale biogeochemical cycles, climate feedback, and other essential ecosystem processes. Although numerous prognostic models have been developed for spring phenology, regional analyses of the optimality (OPT) strategy model that incorporate environmental variables beyond temperature and photoperiod remain lacking. We investigated the roles of solar radiation (SR) and three water stress factors (precipitation (P), soil moisture, and vapor pressure deficit (VPD)) on spring phenology from 1982 to 2015 using the OPT model with Global Inventory Modeling and Mapping Studies NDVI3g dataset and environmental data from TerraClimate, CRU_TS, and Global Land Data Assimilation System across the Northern Hemisphere (> 30°N). Our results show that SR and water stress factors significantly impacted intrasite decadal spring phenology variability, with water stress factors dominant in grassland ecosystems while SR dominated in the rest of the ecosystem types. Enhanced models incorporating SR (OPT-S) and VPD (OPT-VPD) outperformed the original OPT model, likely due to improved representation of the adaptive strategy of spring phenology to optimize photosynthetic carbon gain while minimizing frost risk. Our research enhances the understanding of the key environmental drivers influencing decadal spring phenology variation in the Northern Hemisphere and contributes to more accurate forecasts of ecological responses to global environmental change.},
}
@article {pmid40167332,
year = {2025},
author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF},
title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14105},
pmid = {40167332},
issn = {1755-0998},
support = {CEEC/0482/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0069/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/BIA/00329/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/50027/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0048/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; },
mesh = {*Metagenomics/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Metagenome ; },
abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.},
}
@article {pmid40168108,
year = {2025},
author = {Wang, TY and Wu, YW and Lu, HJ and Liao, TY and Tai, JH and Huang, SP and Wang, FY and Yu, TH and Ting, CT and Chaw, SM and Wang, HY},
title = {Chromosome-Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e14110},
pmid = {40168108},
issn = {1755-0998},
support = {23-23//Biodiversity Research Center, Academia Sinica/ ; MOST 102-2311-B-001-019//National Science and Technology Council/ ; MOST 108-2621-B-001-002//National Science and Technology Council/ ; MOST 109-2311-B-002-023-MY3//National Science and Technology Council/ ; 113L7223//National Taiwan University/ ; },
mesh = {Animals ; DNA Transposable Elements ; *Perciformes/genetics/classification ; *Genome ; *Evolution, Molecular ; *Chromosomes/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The percomorph fish clade Gobioidei is a suborder that comprises over 2200 species distributed in nearly all aquatic habitats. To understand the genetics underlying their species diversification, we sequenced and annotated the genome of the loach goby, Rhyacichthys aspro, an early-diverging group, and compared it with nine additional Gobioidei species. Within Gobioidei, the loach goby possesses the smallest genome at 594 Mb, and a rise in species diversity from early-diverging to more recently diverged lineages is mirrored by enlarged genomes and a higher presence of transposable elements (TEs), particularly DNA transposons. These DNA transposons are enriched in genic and regulatory regions and their copy number increase is strongly correlated with substitution rate, suggesting that DNA repair after transposon excision/insertion leads to nearby mutations. Consequently, the proliferation of DNA transposons might be the crucial driver of Gobioidei diversification and adaptability. The loach goby genome also points to mechanisms of ecological adaptation. It contains relatively few genes for lateral line development but an overrepresentation of synaptic function genes, with genes putatively under selection linked to synapse organisation and calcium signalling, implicating a sensory system distinct from other Gobioidei species. We also see an overabundance of genes involved in neurocranium development and renal function, adaptations likely connected to its flat morphology suited for strong currents and an amphidromous life cycle. Comparative analyses with hill-stream loaches and the European eel reveal convergent adaptations in body shape and saltwater balance. These findings shed new light on the loach goby's survival mechanisms and the broader evolutionary trends within Gobioidei.},
}
@article {pmid40169791,
year = {2025},
author = {Ding, DY and Tang, Z and Zhu, B and Ren, H and Shalek, AK and Tibshirani, R and Nolan, GP},
title = {Quantitative characterization of tissue states using multiomics and ecological spatial analysis.},
journal = {Nature genetics},
volume = {57},
number = {4},
pages = {910-921},
pmid = {40169791},
issn = {1546-1718},
support = {P01 AI177687/AI/NIAID NIH HHS/United States ; U54 HG010426/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; *Spatial Analysis ; *Genomics/methods ; Single-Cell Analysis/methods ; Multiomics ; },
abstract = {The spatial organization of cells in tissues underlies biological function, and recent advances in spatial profiling technologies have enhanced our ability to analyze such arrangements to study biological processes and disease progression. We propose MESA (multiomics and ecological spatial analysis), a framework drawing inspiration from ecological concepts to delineate functional and spatial shifts across tissue states. MESA introduces metrics to systematically quantify spatial diversity and identify hot spots, linking spatial patterns to phenotypic outcomes, including disease progression. Furthermore, MESA integrates spatial and single-cell multiomics data to facilitate an in-depth, molecular understanding of cellular neighborhoods and their spatial interactions within tissue microenvironments. Applying MESA to diverse datasets demonstrates additional insights it brings over prior methods, including newly identified spatial structures and key cell populations linked to disease states. Available as a Python package, MESA offers a versatile framework for quantitative decoding of tissue architectures in spatial omics across health and disease.},
}
@article {pmid40170100,
year = {2025},
author = {Sato, K and Watanabe, S and Noda, T and Koizumi, T and Yoda, K and Watanabe, YY and Sakamoto, KQ and Isokawa, T and Yoshida, MA and Aoki, K and Takahashi, A and Iwata, T and Nishizawa, H and Maekawa, T and Kawabe, R and Watanuki, Y},
title = {Biologging intelligent Platform (BiP): an integrated and standardized platform for sharing, visualizing, and analyzing biologging data.},
journal = {Movement ecology},
volume = {13},
number = {1},
pages = {23},
pmid = {40170100},
issn = {2051-3933},
abstract = {Sharing biologging data can facilitate collaborative research and biological conservation by providing maps showing animals' distribution and movements. It is a critical social mission to preserve not only horizontal position data, but also behavioral data such as diving depth, flight altitude, speed, and acceleration, as well as physiological data such as body temperature, along with related metadata, ensuring their preservation for future generation. Moreover, although biologging was initially developed in the field of biology, it now contributes to diverse fields such as meteorology and oceanography, leading to expanded opportunities for secondary data utilization. In light of social and academic requirements, we developed "Biologging intelligent Platform (BiP)", which adheres to internationally recognized standards for sensor data and metadata storage. As a result, BiP not only stores sensor data along with metadata but also standardizes this information to facilitate secondary data analysis, facilitating broader applications of biologging data across various disciplines. By visiting the website (https://www.bip-earth.com) and completing the user registration, data owners can interactively upload sensor data, input metadata associated with individual animals, devices, and deployments, standardize data formats, and choose between open and private settings for sharing data. Anyone interested in utilizing the data can access metadata and visualized route maps, irrespective of the data's open or private status. Users can freely download open datasets that are available under the CC BY 4.0 license, which permits copying, redistribution, and modification while adhering to the metadata's credit requirements. To use private datasets, users can contact the data owner to request permission. A unique feature of BiP is the Online Analytical Processing (OLAP) tools that calculate environmental parameters, such as surface currents, ocean winds, and waves from data collected by animals. Algorithms published in some previous studies are integrated into the OLAP which can estimate the environmental and behavioral parameters. To enhance data accessibility, BiP allows users to search for datasets using the DOI of the paper in which the data was used. We believe that linking with other databases for data exchange and multi-repository storage could enhance the sustainability of the data itself.},
}
@article {pmid40171521,
year = {2025},
author = {Boyes, D and Hutchinson, F and Crowley, LM and , and , and , and , and , and , and , },
title = {The genome sequence of the Large Birch Bell moth, Large Birch Roller, Epinotia brunnichana (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {101},
pmid = {40171521},
issn = {2398-502X},
abstract = {We present a genome assembly from a female Epinotia brunnichana (Large Birch Bell, Large Birch Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 943.10 megabases. Most of the assembly (99.68%) is scaffolded into 29 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,003 protein-coding genes.},
}
@article {pmid40171777,
year = {2025},
author = {Zhao, W and Han, Q and Yang, F and Zhao, Y},
title = {Enhancing Enzyme Commission Number Prediction With Contrastive Learning and Agent Attention.},
journal = {Proteins},
volume = {93},
number = {9},
pages = {1507-1517},
doi = {10.1002/prot.26822},
pmid = {40171777},
issn = {1097-0134},
support = {32101590//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; 32071838//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; },
mesh = {*Enzymes/chemistry/metabolism/classification ; Databases, Protein ; *Machine Learning ; *Computational Biology/methods ; Algorithms ; Software ; Data Mining ; Proteins/chemistry ; },
abstract = {The accurate prediction of enzyme function is crucial for elucidating disease mechanisms and identifying drug targets. Nevertheless, existing enzyme commission (EC) number prediction methods are limited by database coverage and the depth of sequence information mining, hindering the efficiency and precision of enzyme function annotation. Therefore, this study introduces ProteEC-CLA (Protein EC number prediction model with Contrastive Learning and Agent Attention). ProteEC-CLA utilizes contrastive learning to construct positive and negative sample pairs, which not only enhances sequence feature extraction but also improves the utilization of unlabeled data. This process helps the model learn the differences in sequence features, thereby enhancing its ability to predict enzyme function. Integrating the pre-trained protein language model ESM2, the model generates informative sequence embeddings for deep functional correlation analysis, significantly enhancing prediction accuracy. With the incorporation of the Agent Attention mechanism, ProteEC-CLA's ability to comprehensively capture local details and global features is enhanced, ensuring high-accuracy predictions on complex sequences. The results demonstrate that ProteEC-CLA performs exceptionally well on two independent and representative datasets. In the standard dataset, it achieves 98.92% accuracy at the EC4 level. In the more challenging clustered split dataset, ProteEC-CLA achieves 93.34% accuracy and an F1-score of 94.72%. With only enzyme sequences as input, ProteEC-CLA can accurately predict EC numbers up to the fourth level, significantly enhancing annotation efficiency and accuracy, which makes it a highly efficient and precise functional annotation tool for enzymology research and applications.},
}
@article {pmid40173380,
year = {2025},
author = {Zagorščak, M and Abdelhakim, L and Rodriguez-Granados, NY and Široká, J and Ghatak, A and Bleker, C and Blejec, A and Zrimec, J and Novák, O and Pěnčík, A and Baebler, &#x160; and Perez Borroto, L and Schuy, C and Županič, A and Afjehi-Sadat, L and Wurzinger, B and Weckwerth, W and Pompe Novak, M and Knight, MR and Strnad, M and Bachem, C and Chaturvedi, P and Sonnewald, S and Sasidharan, R and Panzarová, K and Gruden, K and Teige, M},
title = {Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato.},
journal = {Plant physiology},
volume = {197},
number = {4},
pages = {},
pmid = {40173380},
issn = {1532-2548},
support = {//H2020-SFS-2019-2/ ; P4-0165//Slovenian Research Agency/ ; //Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.1.01/0.0/0.0/16_026/0008446//European Regional Development Fund-Project/ ; },
mesh = {*Solanum tuberosum/physiology/genetics/metabolism ; *Stress, Physiological/genetics ; Phenotype ; Droughts ; Proteomics ; Metabolomics ; Gene Expression Regulation, Plant ; Transcriptome ; Plant Leaves/physiology ; Plant Tubers ; Multiomics ; },
abstract = {Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.},
}
@article {pmid40173850,
year = {2025},
author = {Vivien, R and Martin, P},
title = {Maintaining taxonomic accuracy in genetic databases: A duty for taxonomists-Reanalysis of the DNA sequences from Mercan et al. (2024) on the genus Potamothrix (Annelida, Clitellata) in Turkish lakes.},
journal = {Zootaxa},
volume = {5575},
number = {4},
pages = {555-562},
doi = {10.11646/zootaxa.5575.4.5},
pmid = {40173850},
issn = {1175-5334},
mesh = {Turkey ; Animals ; Lakes ; Phylogeny ; *Databases, Genetic/standards ; *Databases, Nucleic Acid/standards ; Sequence Analysis, DNA ; *Polychaeta/classification/genetics ; },
abstract = {Public DNA sequence databases such as GenBank are widely used for identification of organisms in ecological and taxonomic studies. It is important that these public databases contain as few mistakes as possible and that any errors detected in these databases are reported. Here, we reanalyzed the COI sequences of Mercan et al. (2024) and showed that they were mistakenly considered by these authors as belonging to different populations (haplotypes) within the species Potamothrix hammoniensis (Tubificinae). We found that they corresponded to four distinct Tubificinae lineages (species), Pothamothrix alatus paravanicus, Potamothrix bavaricus, Tubifex sp. and Potamothrix sp. Despite these identification errors, the data from Mercan et al. (2024) remain interesting as they provide new information on the diversity of the genus Potamothrix in Turkey. Prompt measures must be taken to correct these errors and prevent them from being detrimental to future studies.},
}
@article {pmid40175491,
year = {2025},
author = {Zhang, H and Guo, G and Li, H and Wang, T and Ni, J and Meng, H},
title = {A new numerical method for calculating residual deformation in mined-out areas considering water-rock interaction and its application.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11207},
pmid = {40175491},
issn = {2045-2322},
support = {2023YFC3804201//National Key R&amp;D Program of China/ ; },
abstract = {Globally, extensive land regions have fallen victim to coal mining subsidence, rendering the reuse of goaf sites a crucial concern. The residual deformation amount of these sites is the linchpin for determining their reusability. Presently, numerical computations of residual deformation in goafs, which overlook water-rock coupling, breed significant errors, posing severe threats to the safety of on-site structures. To remedy the situation, this research hinges on the mechanical experiment results of fractured rock masses under water-rock interaction within the goaf. By leveraging an embedded programming language, it pinpoints the irregular damage range of overlying strata due to water-rock effects. Then, corresponding mechanical parameters are allocated to the surrounding rocks at diverse spatial positions, with the erosive impact of water-soaked coal pillars also factored in. This gives rise to a novel numerical method that more precisely gauges groundwater's influence on strata movement and surface subsidence. Using the 01 working face of a Shandong mine as a practical backdrop, the new method verifies its reliability and accuracy. When contrasted with traditional approaches, be it neglecting water filling or assuming full saturation in the goaf, it slashes the calculation error by 20%, furnishing new approaches for residual deformation calculation and novel perspectives for evaluating site stability under complex geological conditions.},
}
@article {pmid40175550,
year = {2025},
author = {Pärtel, M and Tamme, R and Carmona, CP and Riibak, K and Moora, M and Bennett, JA and Chiarucci, A and Chytrý, M and de Bello, F and Eriksson, O and Harrison, S and Lewis, RJ and Moles, AT and Öpik, M and Price, JN and Amputu, V and Askarizadeh, D and Atashgahi, Z and Aubin, I and Azcárate, FM and Barrett, MD and Bashirzadeh, M and Bátori, Z and Beenaerts, N and Bergholz, K and Birkeli, K and Biurrun, I and Blanco-Moreno, JM and Bloodworth, KJ and Boisvert-Marsh, L and Boldgiv, B and Brancalion, PHS and Brearley, FQ and Brown, C and Bueno, CG and Buffa, G and Cahill, JF and Campos, JA and Cangelmi, G and Carbognani, M and Carcaillet, C and Cerabolini, BEL and Chevalier, R and Clavel, JS and Costa, JM and Cousins, SAO and Čuda, J and Dairel, M and Dalle Fratte, M and Danilova, A and Davison, J and Deák, B and Del Vecchio, S and Dembicz, I and Dengler, J and Dolezal, J and Domene, X and Dvorsky, M and Ejtehadi, H and Enrico, L and Epikhin, D and Eskelinen, A and Essl, F and Fan, G and Fantinato, E and Fazlioglu, F and Fernández-Pascual, E and Ferrara, A and Fidelis, A and Fischer, M and Flagmeier, M and Forte, TGW and Fraser, LH and Fujinuma, J and Furquim, FF and Garris, B and Garris, HW and Giorgis, MA and Giusso Del Galdo, G and González-Robles, A and Good, MK and Guardiola, M and Guarino, R and Guerrero, I and Guillemot, J and Güler, B and Guo, Y and Haesen, S and Hejda, M and Heleno, RH and Høye, TT and Hrivnák, R and Huang, Y and Hunter, JT and Iakushenko, D and Ibáñez, R and Ingerpuu, N and Irl, SDH and Janíková, E and Jansen, F and Jeltsch, F and Jentsch, A and Jiménez-Alfaro, B and Jõks, M and Jouri, MH and Karami, S and Katal, N and Kelemen, A and Khairullin, BI and Khuroo, AA and Komatsu, KJ and Konečná, M and Kook, E and Korell, L and Koroleva, N and Korznikov, KA and Kozhevnikova, MV and Kozub, &#x141; and Laanisto, L and Lager, H and Lanta, V and Lasagno, RG and Lembrechts, JJ and Li, L and Lisner, A and Liu, H and Liu, K and Liu, X and Lucas-Borja, ME and Ludewig, K and Lukács, K and Luther-Mosebach, J and Macek, P and Marignani, M and Michalet, R and Miglécz, T and Moeslund, JE and Moeys, K and Montesinos, D and Moreno-Jiménez, E and Moysiyenko, I and Mucina, L and Muñoz-Rojas, M and Murillo, RA and Nambahu, SM and Neuenkamp, L and Normand, S and Nowak, A and Nuche, P and Oja, T and Onipchenko, VG and Pachedjieva, KL and Paganeli, B and Peco, B and Peralta, AML and Pérez-Haase, A and Peri, PL and Petraglia, A and Peyre, G and Plaza-Álvarez, PA and Plue, J and Prentice, HC and Prokhorov, VE and Radujković, D and Rahmanian, S and Reitalu, T and Ristow, M and Robin, AA and Robles, AB and Rodríguez Ginart, DA and Román, R and Roos, RE and Rosati, L and Sádlo, J and Salimbayeva, K and Sánchez de Dios, R and Sanchir, K and Sattler, C and Scasta, JD and Schmiedel, U and Schrader, J and Schultz, NL and Sellan, G and Serra-Diaz, JM and Silan, G and Skálová, H and Skobel, N and Sonkoly, J and Štajerová, K and Svitková, I and Świerszcz, S and Tanentzap, AJ and Tanentzap, FM and Tarifa, R and Tejero, P and Tekeev, DK and Tholin, M and Thormodsæter, RS and Tian, Y and Tokaryuk, A and Tölgyesi, C and Tomaselli, M and Tordoni, E and Török, P and Tóthmérész, B and Toussaint, A and Touzard, B and Trindade, DPF and Tsakalos, JL and Türkiş, S and Valencia, E and Valerio, M and Valkó, O and Van Meerbeek, K and Vandvik, V and Villellas, J and Virtanen, R and Vítková, M and Vojík, M and von Hessberg, A and von Oppen, J and Wagner, V and Wan, JZ and Wang, CJ and Wani, SA and Weiss, L and Wevill, T and Xiao, S and Zárate Martínez, O and Zobel, M},
title = {Global impoverishment of natural vegetation revealed by dark diversity.},
journal = {Nature},
volume = {641},
number = {8064},
pages = {917-924},
pmid = {40175550},
issn = {1476-4687},
mesh = {*Biodiversity ; *Plants/classification ; *Conservation of Natural Resources ; *Anthropogenic Effects ; Humans ; Human Activities ; Ecosystem ; },
abstract = {Anthropogenic biodiversity decline threatens the functioning of ecosystems and the many benefits they provide to humanity[1]. As well as causing species losses in directly affected locations, human influence might also reduce biodiversity in relatively unmodified vegetation if far-reaching anthropogenic effects trigger local extinctions and hinder recolonization. Here we show that local plant diversity is globally negatively related to the level of anthropogenic activity in the surrounding region. Impoverishment of natural vegetation was evident only when we considered community completeness: the proportion of all suitable species in the region that are present at a site. To estimate community completeness, we compared the number of recorded species with the dark diversity-ecologically suitable species that are absent from a site but present in the surrounding region[2]. In the sampled regions with a minimal human footprint index, an average of 35% of suitable plant species were present locally, compared with less than 20% in highly affected regions. Besides having the potential to uncover overlooked threats to biodiversity, dark diversity also provides guidance for nature conservation. Species in the dark diversity remain regionally present, and their local populations might be restored through measures that improve connectivity between natural vegetation fragments and reduce threats to population persistence.},
}
@article {pmid40178345,
year = {2025},
author = {Riobueno-Naylor, A and Gomez, I and Quan, S and Hutt Vater, C and Montes, M and Hoskova, B and Lai, BS},
title = {Methods for integrating public datasets: insights from youth disaster mental health research.},
journal = {European journal of psychotraumatology},
volume = {16},
number = {1},
pages = {2481699},
pmid = {40178345},
issn = {2000-8066},
mesh = {Humans ; Adolescent ; *Disasters ; United States/epidemiology ; *Mental Health/statistics &amp; numerical data ; Male ; Female ; *Depression/epidemiology ; *Datasets as Topic ; Databases, Factual ; },
abstract = {Introduction: Weather-related disasters pose significant risks to youth mental health. Exposure to multiple disasters is becoming more common; however, the effects of such exposure remain understudied. This study demonstrates the application of integrative data approaches and FAIR (Findable, Accessible, Interoperable, Reusable) data principles to evaluate the relationship between cumulative disaster exposure and youth depression and suicidality in the United States, taking into account contextual factors across levels of social ecology.Methods: We combined data from five public sources, including the Youth Risk Behavior Surveillance System (YRBS), Federal Emergency Management Agency (FEMA), United States Census Bureau, Center for Homeland Defense and Security School Shooting Safety Compendium, and Global Terrorism Database. The integrative dataset included 415,701 youth from 37 districts across the United States who completed the YRBS between 1999 and 2021. The YRBS served as the core dataset.Results: This data note highlights strategies for harmonizing diverse data formats, addressing geographic and temporal inconsistencies, and validating integrated datasets. Automated data cleaning and visualization techniques enhance accuracy and efficiency. Planning for sensitivity analyses before data cleaning is recommended to improve the data integration process and enhance the robustness of findings.Discussion: This integrative approach demonstrates how leveraging FAIR principles can advance trauma research by facilitating large-scale analyses of complex public health questions. The methods provide a replicable framework for examining population-level impacts of phenomena and highlight opportunities for expanding trauma research.},
}
@article {pmid40179162,
year = {2025},
author = {Davín, AA and Woodcroft, BJ and Soo, RM and Morel, B and Murali, R and Schrempf, D and Clark, JW and Álvarez-Carretero, S and Boussau, B and Moody, ERR and Szánthó, LL and Richy, E and Pisani, D and Hemp, J and Fischer, WW and Donoghue, PCJ and Spang, A and Hugenholtz, P and Williams, TA and Szöllősi, GJ},
title = {A geological timescale for bacterial evolution and oxygen adaptation.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6742},
pages = {eadp1853},
doi = {10.1126/science.adp1853},
pmid = {40179162},
issn = {1095-9203},
support = {/ERC_/European Research Council/International ; },
mesh = {*Oxygen/metabolism ; Phylogeny ; *Biological Evolution ; Oxidation-Reduction ; *Bacteria/metabolism/classification/genetics ; Machine Learning ; Photosynthesis ; Adaptation, Physiological ; Cyanobacteria/genetics/metabolism ; },
abstract = {Microbial life has dominated Earth's history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE). We combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial time tree. Extant bacterial phyla trace their diversity to the Archaean and Proterozoic, and bacterial families prior to the Phanerozoic. We infer that most bacterial phyla were ancestrally anaerobic and adopted aerobic lifestyles after the GOE. However, in the cyanobacterial ancestor, aerobic metabolism likely predated the GOE, which may have facilitated the evolution of oxygenic photosynthesis.},
}
@article {pmid40179423,
year = {2025},
author = {Dejeante, R and Valeix, M and Chamaillé-Jammes, S},
title = {Do Mixed-Species Groups Travel as One? An Investigation on Large African Herbivores Monitored Using Animal-Borne Video Collars.},
journal = {The American naturalist},
volume = {205},
number = {4},
pages = {451-458},
doi = {10.1086/734410},
pmid = {40179423},
issn = {1537-5323},
mesh = {Animals ; Video Recording ; *Herbivory ; *Giraffes/physiology ; *Equidae/physiology ; *Antelopes/physiology ; Social Behavior ; Geographic Information Systems ; Ecosystem ; },
abstract = {AbstractAlthough prey foraging in mixed-species groups benefit from a reduced risk of predation, whether heterospecific groupmates move together in the landscape, and more generally to what extent mixed-species groups remain cohesive over time and space, remains unknown. Here, we used GPS collars with video cameras to investigate the movements of plains zebras (Equus quagga) in mixed-species groups. Blue wildebeest (Connochaetes taurinus), impalas (Aepyceros melampus), and giraffes (Giraffa camelopardalis) commonly form mixed-species groups with zebras in savanna ecosystems. We found that zebras adjust their movement decisions solely on the basis of the presence of giraffes, being more likely to move in zebra-giraffe herds, and this was correlated with a higher cohesion of such groups. Additionally, zebras moving with giraffes spent more time grazing, suggesting that zebras benefit from foraging in the proximity of giraffes. Our results provide new insights into animal movements in mixed-species groups, contributing to a better consideration of mutualism in movement ecology.},
}
@article {pmid40179878,
year = {2025},
author = {Li, Y and Liu, X and Guo, L and Han, K and Fang, S and Wan, X and Wang, D and Xu, X and Jiang, L and Fan, G and Xu, M},
title = {SpaGRN: Investigating spatially informed regulatory paths for spatially resolved transcriptomics data.},
journal = {Cell systems},
volume = {16},
number = {4},
pages = {101243},
doi = {10.1016/j.cels.2025.101243},
pmid = {40179878},
issn = {2405-4720},
mesh = {Animals ; *Transcriptome/genetics ; *Gene Expression Profiling/methods ; Humans ; *Gene Regulatory Networks/genetics ; Drosophila/genetics ; Computational Biology/methods ; },
abstract = {Cells spatially organize into distinct cell types or functional domains through localized gene regulatory networks. However, current spatially resolved transcriptomics analyses fail to integrate spatial constraints and proximal cell influences, limiting the mechanistic understanding of tissue organization. Here, we introduce SpaGRN, a statistical framework that reconstructs cell-type- or functional-domain-specific, dynamic, and spatial regulons by coupling intracellular spatial regulatory causality with extracellular signaling path information. Benchmarking across synthetic and real datasets demonstrates SpaGRN's superior precision over state-of-the-art tools in identifying context-dependent regulons. Applied to diverse spatially resolved transcriptomics platforms (Stereo-seq, STARmap, MERFISH, CosMx, Slide-seq, and 10x Visium), complex cancerous samples, and 3D datasets of developing Drosophila embryos and larvae, SpaGRN not only provides a versatile toolkit for decoding receptor-mediated spatial regulons but also reveals spatiotemporal regulatory mechanisms underlying organogenesis and inflammation.},
}
@article {pmid40180917,
year = {2025},
author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA},
title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3204},
pmid = {40180917},
issn = {2041-1723},
support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; },
abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.},
}
@article {pmid40180992,
year = {2025},
author = {González, AL and Merder, J and Andraczek, K and Brose, U and Filipiak, M and Harpole, WS and Hillebrand, H and Jackson, MC and Jochum, M and Leroux, SJ and Nessel, MP and Onstein, RE and Paseka, R and Perry, GLW and Rugenski, A and Sitters, J and Sperfeld, E and Striebel, M and Zandona, E and Aymes, JC and Blanckaert, A and Bluhm, SL and Doi, H and Eisenhauer, N and Farjalla, VF and Hood, J and Kratina, P and Labonne, J and Lovelock, CE and Moody, EK and Mozsár, A and Nash, L and Pollierer, MM and Potapov, A and Romero, GQ and Roussel, JM and Scheu, S and Scheunemann, N and Seeber, J and Steinwandter, M and Susanti, WI and Tiunov, A and Dézerald, O},
title = {StoichLife: A Global Dataset of Plant and Animal Elemental Content.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {569},
pmid = {40180992},
issn = {2052-4463},
support = {DFG HI848/26-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR 5000//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG 493345801//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RGPIN-2020-04132//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 310119/2018-9//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (National Council for Scientific and Technological Development)/ ; NAF\R2\180791//Royal Society/ ; DP0986179//Department of Education and Training | Australian Research Council (ARC)/ ; DP160103669//Department of Education and Training | Australian Research Council (ARC)/ ; 22-14-00363)//Russian Science Foundation (RSF)/ ; },
mesh = {*Plants/chemistry ; Animals ; Ecosystem ; Phosphorus/analysis ; Nitrogen/analysis ; Carbon/analysis ; },
abstract = {The elemental content of life is a key trait shaping ecology and evolution, yet organismal stoichiometry has largely been studied on a case-by-case basis. This limitation has hindered our ability to identify broad patterns and mechanisms across taxa and ecosystems. To address this, we present StoichLife, a global dataset of 28,049 records from 5,876 species spanning terrestrial, freshwater, and marine realms. Compiled from published and unpublished sources, StoichLife documents elemental content and stoichiometric ratios (%C, %N, %P, C:N, C:P, and N:P) for individual plants and animals. The dataset is standardized and, where available, includes information on taxonomy, habitat, body mass (for animals), geography, and environmental conditions such as temperature, solar radiation, and nutrient availability. By providing an unprecedented breadth of organismal stoichiometry, StoichLife enables the exploration of global patterns, ecological and evolutionary drivers, and context-dependent variations. This resource advances our understanding of the chemical makeup of life and its responses to environmental change, supporting progress in ecological stoichiometry and related fields.},
}
@article {pmid40181527,
year = {2025},
author = {Mills, MB and Shenkin, A and Wilkes, P and Disney, M and Page, S and Berrio, JC and Kaduk, J and Malhi, Y and Robert, R and Nilus, R and Riutta, T},
title = {Investigating the accuracy of tropical woody stem CO2 efflux estimates: scaling methods, and vertical and diel variation.},
journal = {The New phytologist},
volume = {246},
number = {5},
pages = {2004-2014},
pmid = {40181527},
issn = {1469-8137},
support = {CA20118//European Cooperation in Science and Technology/ ; PRA 11.23//Royal Geographical Society/ ; NE/P011780/1//Natural Environment Research Council/ ; NE/Y006216/1//National Centre for Earth Observation/ ; NE/S007350/1//Central England NERC Training Alliance/ ; },
mesh = {*Plant Stems/metabolism/anatomy &amp; histology ; *Carbon Dioxide/metabolism ; *Tropical Climate ; *Wood/metabolism ; Trees/metabolism ; Borneo ; Malaysia ; },
abstract = {Stem CO2 efflux (EA) significantly contributes to autotrophic and ecosystem respiration in tropical forests, but field methodologies often introduce biases and uncertainty. This study evaluates these biases and their impact on scaling EA at the stand-level. Diel and vertical patterns of EA were investigated, along with the accuracy of estimating stem surface area from allometric equations vs terrestrial light dection and ranging (LiDAR) scanning (TLS) in Maliau Basin Conservation Area, Sabah, Malaysian Borneo. Diel EA exhibited no uniform pattern due to inter-tree variability, but results suggest measuring EA before 15:00 h. EA was significantly higher on buttresses and above the first major branching point, but vertical variations in EA did not impact stand-level EA when stem surface area was accurately estimated. Allometric equations underestimated total stem surface area by c. 40% compared with TLS, but applying a site-specific correction factor yielded a similar stand-level EA and total stem surface area to TLS. This study provides guidance for measuring EA in the field and suggests that measuring at one time point and one height along the stem can produce accurate results if conducted using the correct time frame and if stem surface area is accurately estimated.},
}
@article {pmid40185844,
year = {2025},
author = {Amin, NU and Islam, F and Umar, M and Muhammad, W and Rahman, SU and Gaafar, AZ and Shah, TA and Dauelbait, M and Bourhia, M},
title = {Evaluation of crop phenology using remote sensing and decision support system for agrotechnology transfer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11582},
pmid = {40185844},
issn = {2045-2322},
mesh = {*Remote Sensing Technology/methods ; *Crops, Agricultural/growth &amp; development ; Biomass ; *Agriculture/methods ; *Decision Support Techniques ; Plant Leaves/growth &amp; development ; Seasons ; },
abstract = {The decision support system for agro-technology transfer (DSSAT) is a worldwide crop modeling platform used for crops growth, yield, leaf area index (LAI), and biomass estimation under varying climatic, soil and management conditions. This study integrates DSSAT with satellite remote sensing (RS) data to estimates canopy state variables like LAI and biomass. For LAI estimation, Moderate Resolution Imaging Spectroradiometer (MODIS) product (MCD15A3H for LAI and MOD17A2 / MOD17A3 products for biomass) are used. Field data for Sheikhupura district is provided by National Agriculture Research Council (NARC) and used for the calibration and validation of the model. The results indicate strong agreement between the DSSAT and RS derived estimates. Correlation coefficients (R[2]) for LAI varied from 0.82 to 0.90, while for biomass ranged from 0.92 to 0.99 over two farms and two growing seasons (2012-2014). The index of agreement (D-index) ranged from 0.79 to 0.96 across the two farms and two growing seasons (2012-2014) affirming the model's durability. However, the biomass estimated from RS data is underestimated due to saturation phenomenon in the optical RS. The performance metrics, comprising the coefficient of residual mass (CRM) and normalized root mean square error (nRMSE), further substantiate the approach utilized. This study will help decision and policymakers and researchers to apply geospatial techniques for the sustainable agriculture practices.},
}
@article {pmid40186616,
year = {2025},
author = {Chen, L and Guo, Y and López-Güell, K and Ma, J and Dong, Y and Xie, J and Alhambra, DP},
title = {Immunity Debt for Seasonal Influenza After the COVID-19 Pandemic and as a Result of Nonpharmaceutical Interventions: An Ecological Analysis and Cohort Study.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {20},
pages = {e2410513},
pmid = {40186616},
issn = {2198-3844},
support = {82373593//National Natural Science Foundation of China/ ; 82103865//National Natural Science Foundation of China/ ; 2022YFC2705300//National Key Research and Development Program of China/ ; 2024YFC3308300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *COVID-19/epidemiology/prevention &amp; control/immunology ; *Influenza, Human/epidemiology/immunology/prevention &amp; control/transmission ; Seasons ; Pandemics/prevention &amp; control ; SARS-CoV-2 ; Cohort Studies ; Europe/epidemiology ; },
abstract = {Non-pharmaceutical interventions (NPIs) during the COVID-19 pandemic significantly reduced influenza transmission. This study explores the hypothesis of "immunity debt" which suggests increased vulnerability to influenza following reduced exposure during the pandemic. World Health Organization aggregated data on influenza from 116 countries and its association with NPI intensity as measured by the COVID-19 Stringency Index is analyzed. Where individual-level data available (France, the United Kingdom, Spain, Italy, Belgium, and Romania), the analyses of influenza monthly rates in six European countries (France, the United Kingdom, Spain, Italy, Belgium, and Romania) are replicated. The results indicate globally a 46.3% (95% CI: 15.79-70.78%) reduction in influenza cases during COVID-19 restrictions in the winter season, followed by a 131.7% (95% CI: 34.95-255.78%) increase in the first postrelaxation winter and a 161.2% (95% CI: 31.88-382.16%) increase in the summer as compared to the predicted level based on historical influenza epidemic trends. In addition, a positive association between the Stringency Index and post-relaxation influenza surge is observed globally (R[2] = 0.14-0.17) and replicated regionally. The findings support the population immunity debt hypothesis for influenza and call for proactive preparations against its consequences in future pandemics.},
}
@article {pmid40188731,
year = {2025},
author = {Li, Y and Huang, S and Jiang, S and Yang, L and Huang, J and Yang, Q and Jiang, Z and Shi, J and Ma, Z and Li, E and Zhou, F},
title = {Multi-omics insights into antioxidant and immune responses in Penaeus monodon under ammonia-N, low salinity, and combined stress.},
journal = {Ecotoxicology and environmental safety},
volume = {295},
number = {},
pages = {118156},
doi = {10.1016/j.ecoenv.2025.118156},
pmid = {40188731},
issn = {1090-2414},
mesh = {Animals ; *Penaeidae/immunology/physiology/drug effects ; *Ammonia/toxicity ; Salinity ; *Antioxidants/metabolism ; *Water Pollutants, Chemical/toxicity ; Oxidative Stress ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Stress, Physiological ; Transcriptome ; Nitrogen/toxicity ; Multiomics ; },
abstract = {Ammonia nitrogen and salinity are critical environmental factors that significantly impact marine organisms and present substantial threats to Penaeus monodon species within aquaculture systems. This study utilized a comprehensive multi-omics approach, encompassing transcriptomics, metabolomics, and gut microbiome analysis, to systematically examine the biological responses of shrimp subjected to low salinity, ammonia nitrogen stress, and their combined conditions. Metabolomic analysis demonstrated that exposure to ammonia nitrogen stress markedly influenced the concentrations of antioxidant-related metabolites, such as glutathione, suggesting that shrimp mitigate oxidative stress by augmenting their antioxidant capacity. The transcriptomic analysis revealed an upregulation of genes linked to energy metabolism and immune responses and antioxidant enzymes. Concurrently, gut microbiome analysis demonstrated that ammonia nitrogen stress resulted in a marked increase in Vibrio populations and a significant decrease in Photobacterium, indicating that alterations in microbial community structure are intricately associated with the shrimp stress response. A comprehensive analysis further indicated that the combined stressors of ammonia nitrogen and salinity exert a synergistic effect on the immune function and physiological homeostasis of shrimp by modulating antioxidant metabolic pathways and gut microbial communities. These findings provide critical systematic data for elucidating the mechanisms through which ammonia nitrogen and salinity influence marine ecosystems, offering substantial implications for environmental protection and ecological management.},
}
@article {pmid40194740,
year = {2025},
author = {Nieman, DC and Sakaguchi, CA and Williams, JC and Lawson, J and Lambirth, KC and Omar, AM and Mulani, FA and Zhang, Q},
title = {Gut Prevotella copri abundance linked to elevated post-exercise inflammation.},
journal = {Journal of sport and health science},
volume = {14},
number = {},
pages = {101039},
pmid = {40194740},
issn = {2213-2961},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Prevotella/isolation &amp; purification ; *Inflammation/microbiology ; Feces/microbiology ; Male ; Adult ; *Exercise/physiology ; Oxylipins/blood ; *Bicycling/physiology ; Arachidonic Acid/blood ; Young Adult ; },
abstract = {PURPOSE: This study aimed to examine the linkage between gut microbiome taxa and exercise-induced inflammation.<br><br>METHODS: Twenty-five cyclists provided 4 stool samples during a 10-week period and cycled vigorously for 2.25 h at 67% maximal oxygen uptake (VO2max) in a laboratory setting. Blood samples were collected pre- and post-exercise, with additional samples collected at 1.5-h, 3-h, and 24-h post exercise. Primary outcomes included stool microbiome composition and alpha diversity via whole genome shotgun (WGS) sequencing (averaged from 4 stool samples) and a targeted panel of 75 plasma oxylipins. A total of 5719 taxa were identified, and the 339 that were present in more than 20% of stool samples were used in the analysis. Alpha diversity was calculated by evenness, and the Analysis of Composition of Microbiomes (ANCOM) differential abundance analysis was performed using Quantitative Insights Into Microbial Ecology-2 (QIIME2). A composite variable was calculated from 8 pro-inflammatory oxylipins generated from arachidonic acid (ARA) and cytochrome P-450 (CYP).<br><br>RESULTS: ARA-CYP oxylipins were significantly elevated for at least 3-h post-exercise (p < 0.001); they were strongly and positively related to Prevotella copri (P. copri) abundance (R[2]&#x202f;=&#x202f;0.676, p < 0.001) and negatively related to gut microbiome alpha diversity (R[2]&#x202f;=&#x202f;0.771, p < 0.001).<br><br>CONCLUSION: This analysis revealed for the first time a novel, positive relationship between gut microbiome P. copri abundance in cyclists and post-exercise pro-inflammatory oxylipins. These data demonstrate that about two-thirds of the wide variance in inflammation following prolonged and intensive exercise is largely explained by the abundance of a single gut bacterial species: P. copri.},
}
@article {pmid40196448,
year = {2025},
author = {Rotstein, NM and Cohen, ZD and Welborn, A and Zbozinek, TD and Akre, S and Jones, KG and Null, KE and Pontanares, J and Sanchez, KL and Flanagan, DC and Halavi, SE and Kittle, E and McClay, MG and Bui, AAT and Narr, KL and Welsh, RC and Craske, MG and Kuhn, TP},
title = {Investigating low intensity focused ultrasound pulsation in anhedonic depression-A randomized controlled trial.},
journal = {Frontiers in human neuroscience},
volume = {19},
number = {},
pages = {1478534},
pmid = {40196448},
issn = {1662-5161},
abstract = {INTRODUCTION: Anhedonic depression is a subtype of depression characterized by deficits in reward processing. This subtype of depression is associated with higher suicide risk and longer depressive episodes, underscoring the importance of effective treatments. Anhedonia has also been found to correlate with alterations in activity in several subcortical regions, including the caudate head and nucleus accumbens. Low intensity focused ultrasound pulsation (LIFUP) is an emerging technology that enables non-invasive stimulation of these subcortical regions, which were previously only accessible with surgically-implanted electrodes.<br><br>METHODS: This double-blinded, sham-controlled study aims to investigate the effects of LIFUP to the left caudate head and right nucleus accumbens in participants with anhedonic depression. Participants in this protocol will undergo three sessions of LIFUP over the span of 5-9 days. To investigate LIFUP-related changes, this 7-week protocol collects continuous digital phenotyping data, an array of self-report measures of depression, anhedonia, and other psychopathology, and magnetic resonance imaging (MRI) before and after the LIFUP intervention. Primary self-report outcome measures include Ecological Momentary Assessment, the Positive Valence Systems Scale, and the Patient Health Questionnaire. Primary imaging measures include magnetic resonance spectroscopy and functional MRI during reward-based tasks and at rest. Digital phenotyping data is collected with an Apple Watch and participants' personal iPhones throughout the study, and includes information about sleep, heart rate, and physical activity.<br><br>DISCUSSION: This study is the first to investigate the effects of LIFUP to the caudate head or nucleus accumbens in depressed subjects. Furthermore, the data collected for this protocol covers a wide array of potentially affected modalities. As a result, this protocol will help to elucidate potential impacts of LIFUP in individuals with anhedonic depression.},
}
@article {pmid40197051,
year = {2025},
author = {Shamash, M and Sinha, A and Maurice, CF},
title = {Improving gut virome comparisons using predicted phage host information.},
journal = {mSystems},
volume = {10},
number = {5},
pages = {e0136424},
pmid = {40197051},
issn = {2379-5077},
mesh = {*Bacteriophages/genetics/classification/physiology ; *Virome/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; Feces/virology/microbiology ; Metagenomics/methods ; Computational Biology/methods ; Bacteria/virology ; },
abstract = {UNLABELLED: The human gut virome is predominantly made up of bacteriophages (phages), viruses that infect bacteria. Metagenomic studies have revealed that phages in the gut are highly individual specific and dynamic. These features make it challenging to perform meaningful cross-study comparisons. While several taxonomy frameworks exist to group phages and improve these comparisons, these strategies provide little insight into the potential effects phages have on their bacterial hosts. Here, we propose the use of predicted phage host families (PHFs) as a functionally relevant, qualitative unit of phage classification to improve these cross-study analyses. We first show that bioinformatic predictions of phage hosts are accurate at the host family level by measuring their concordance to Hi-C sequencing-based predictions in human and mouse fecal samples. Next, using phage host family predictions, we determined that PHFs reduce intra- and interindividual ecological distances compared to viral contigs in a previously published cohort of 10 healthy individuals, while simultaneously improving longitudinal virome stability. Lastly, by reanalyzing a previously published metagenomics data set with >1,000 samples, we determined that PHFs are prevalent across individuals and can aid in the detection of inflammatory bowel disease-specific virome signatures. Overall, our analyses support the use of predicted phage hosts in reducing between-sample distances and providing a biologically relevant framework for making between-sample virome comparisons.<br><br>IMPORTANCE: The human gut virome consists mainly of bacteriophages (phages), which infect bacteria and show high individual specificity and variability, complicating cross-study comparisons. Furthermore, existing taxonomic frameworks offer limited insight into their interactions with bacterial hosts. In this study, we propose using predicted phage host families (PHFs) as a higher-level classification unit to enhance functional cross-study comparisons. We demonstrate that bioinformatic predictions of phage hosts align with Hi-C sequencing results at the host family level in human and mouse fecal samples. We further show that PHFs reduce ecological distances and improve virome stability over time. Additionally, reanalysis of a large metagenomics data set revealed that PHFs are widespread and can help identify disease-specific virome patterns, such as those linked to inflammatory bowel disease.},
}
@article {pmid40198416,
year = {2025},
author = {Huan, F and Gao, S and Gu, Y and Ni, L and Wu, M and Li, Y and Liu, M and Yang, Y and Xiao, A and Liu, G},
title = {Molecular Allergology: Epitope Discovery and Its Application for Allergen-Specific Immunotherapy of Food Allergy.},
journal = {Clinical reviews in allergy &amp; immunology},
volume = {68},
number = {1},
pages = {37},
pmid = {40198416},
issn = {1559-0267},
support = {32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; },
mesh = {Humans ; *Food Hypersensitivity/therapy/immunology ; *Allergens/immunology/chemistry/genetics ; *Desensitization, Immunologic/methods ; Animals ; *Epitopes, T-Lymphocyte/immunology ; *Epitopes, B-Lymphocyte/immunology ; *Epitopes/immunology ; Computational Biology ; Epitope Mapping ; },
abstract = {The prevalence of food allergy continues to rise, posing a significant burden on health and quality of life. Research on antigenic epitope identification and hypoallergenic agent design is advancing allergen-specific immunotherapy (AIT). This review focuses on food allergens from the perspective of molecular allergology, provides an overview of integration of bioinformatics and experimental validation for epitope identification, highlights hypoallergenic agents designed based on epitope information, and offers a valuable guidance to the application of hypoallergenic agents in AIT. With the development of molecular allergology, the characterization of the amino acid sequence and structure of the allergen at the molecular level facilitates T-/B-cell epitope identification. Alignment of the identified epitopes in food allergens revealed that the amino acid sequence of T-/B-cell epitopes barely overlapped, providing crucial data to design allergen molecules as a promising form for treating (FA) food allergy. Manipulating antigenic epitopes can reduce the allergenicity of allergens to obtain hypoallergenic agents, thereby minimizing the severe side effects associated with AIT. Currently, hypoallergenic agents are mainly developed through synthetic epitope peptides, genetic engineering, or food processing methods based on the identified epitope. New strategies such as DNA vaccines, signaling molecules coupling, and nanoparticles are emerging to improve efficiency. Although significant progress has been made in designing hypoallergenic agents for AIT, the challenge in clinical translation is to determine the appropriate dose and duration of treatment to induce long-term immune tolerance.},
}
@article {pmid40198742,
year = {2025},
author = {Choi, H and Lee, CH},
title = {The impact of climate change on ecology of tick associated with tick-borne diseases.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012903},
pmid = {40198742},
issn = {1553-7358},
mesh = {*Climate Change ; *Tick-Borne Diseases/transmission/epidemiology/prevention &amp; control ; Animals ; *Ticks/physiology ; Humans ; *Models, Biological ; Population Dynamics ; Computational Biology ; },
abstract = {Infectious diseases have caused significant economic and human losses worldwide. Growing concerns exist regarding climate change potentially exacerbating the spread of these diseases, particularly those transmitted by vectors such as ticks and mosquitoes. Tick-borne diseases, such as Severe Fever with Thrombocytopenia Syndrome (SFTS), can be particularly detrimental to elderly and immunocompromised individuals. This study utilizes a mathematical modeling approach to predict changes in tick populations under climate change scenarios, incorporating tick ecology and climate-sensitive parameters. Sensitivity analysis is performed to investigate the factors influencing tick population dynamics. The study further explores effective tick control strategies and their cost-effectiveness in the context of climate change. The findings indicate that the efficacy of tick population reduction varies greatly depending on the timing of control measure implementation and the effectiveness of the control strategies exhibits a strong dependence on the duration of implementation. Furthermore, as climate change intensifies, tick populations are projected to increase, leading to a rise in control costs and SFTS cases. In light of these findings, identifying and implementing appropriate control measures to manage tick populations under climate change will be increasingly crucial.},
}
@article {pmid40198914,
year = {2025},
author = {Holmqvist, S and Kaplan, M and Chaturvedi, R and Shou, H and Giovannetti, T},
title = {Longitudinal and Combined Smartwatch and Ecological Momentary Assessment in Racially Diverse Older Adults: Feasibility, Adherence, and Acceptability Study.},
journal = {JMIR human factors},
volume = {12},
number = {},
pages = {e69952},
pmid = {40198914},
issn = {2292-9495},
support = {F31 AG089944/AG/NIA NIH HHS/United States ; R01 AG062503/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Ecological Momentary Assessment/statistics &amp; numerical data ; Male ; Aged ; Female ; Feasibility Studies ; Middle Aged ; *Patient Compliance/statistics &amp; numerical data ; Aged, 80 and over ; Longitudinal Studies ; *Smartphone ; *Mobile Applications ; *Cognitive Dysfunction/diagnosis ; *Wearable Electronic Devices/statistics &amp; numerical data ; },
abstract = {BACKGROUND: Due to the rising prevalence of Alzheimer disease and related dementias, easily deployable tools to quantify risk are needed. Smartphones and smartwatches enable unobtrusive and continuous monitoring, but there is limited information regarding the feasibility, adherence, and acceptability of digital data collection among racially diverse older adults.<br><br>OBJECTIVE: This paper examined the feasibility, adherence, and acceptability of a 4-week combined smartwatch monitoring and ecological momentary assessment (EMA) study in a racially diverse sample of older adults.<br><br>METHODS: A total of 44 older adults (aged &#x2265;55 y) with either mild cognitive impairment or healthy cognition completed an informed consent comprehension quiz, baseline cognitive testing, training regarding digital data collection, and questionnaires. Participants were instructed to wear a Garmin Vivosmart 4 smartwatch for 23 h/d for 4 weeks, sync 2 smartphone apps (Garmin and Labfront) daily, and complete a daily EMA survey with automated prompts for surveys and charging. Training time, smartwatch adherence (eg, wear time), daily EMA survey response rate, and performance on the consent quiz were quantified. Associations between feasibility and adherence metrics and participant factors were evaluated. Self-reported usability of the apps and smartwatch was collected at study end.<br><br>RESULTS: Consent comprehension quiz scores were high (mean 97.33%, SD 6.86% correct), and training sessions lasted on average 17.93 (SD 6.89) minutes. During the 4-week study, participants wore the smartwatch for an average of 21 h/d (SD 1.53) and showed an average response rate of 94% (SD 9.58%) to daily EMA surveys. In unadjusted bivariate analyses, age, race, and cognition were associated with feasibility and adherence measures, but only age and race remained significant in multivariate models. After accounting for all participant factors, older age was a significant predictor of longer training time, and Black race was a significant predictor of lower daily wear time. On the usability survey, all participants (45/45, 100%) indicated willingness to participate in future smartwatch studies, >80% (37/45) had a positive experience, and >90% (41/45) were satisfied with smartphone app syncing.<br><br>CONCLUSIONS: Smartwatch monitoring, requiring daily wear, smartphone syncing, and daily EMA survey completion, is highly feasible in older adults because adherence to daily wear and EMA surveys was high, as was general satisfaction on usability surveys. Although older participants may require more training on smartwatch and smartphone procedures and automated prompting during the study period, longitudinal monitoring with the Garmin Vivosmart 4 smartwatch and Labfront app is acceptable and feasible for collecting nearly continuous data in Black and White older adults, including those with mild cognitive impairment and those without.},
}
@article {pmid40199921,
year = {2025},
author = {Chaudhary, VB and Nokes, LF and González, JB and Cooper, PO and Katula, AM and Mares, EC and Pehim Limbu, S and Robinson, JN and Aguilar-Trigueros, CA},
title = {TraitAM, a global spore trait database for arbuscular mycorrhizal fungi.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {588},
pmid = {40199921},
issn = {2052-4463},
support = {DEB-2205650//National Science Foundation (NSF)/ ; Feodor Lynen Fellowship//Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation)/ ; },
mesh = {Databases, Factual ; *Mycorrhizae/genetics ; Phylogeny ; *Spores, Fungal/genetics ; Symbiosis ; },
abstract = {Knowledge regarding organismal traits supports a better understanding of the relationship between form and function and can be used to predict the consequences of environmental stressors on ecological and evolutionary processes. Most plants on Earth form symbioses with mycorrhizal fungi, but our ability to make trait-based inferences for these fungi is limited due to a lack of publicly available trait data. Here, we present TraitAM, a comprehensive database of multiple spore traits for all described species of the most common group of mycorrhizal fungi, the arbuscular mycorrhizal (AM) fungi (subphylum Glomeromycotina). Trait data for 344 species were mined from original species descriptions and used to calculate newly developed fungal trait metrics that can be employed to explore both intra- and inter-specific variation in traits. TraitAM also includes an updated phylogenetic tree that can be used to conduct phylogenetically-informed multivariate analyses of AM fungal traits. TraitAM will aid our further understanding of the biology, ecology, and evolution of these globally widespread, symbiotic fungi.},
}
@article {pmid40200134,
year = {2025},
author = {Hu, X and Pan, L and Fu, C and Zhu, Q and Hao, J and Wang, X and Nawaz, M and Qu, J and Zhang, J and Chen, Y and Zong, J and Liao, L and Tang, M and Wang, Z},
title = {A multi-omics analysis reveals candidate genes for Cd tolerance in Paspalum vaginatum.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {441},
pmid = {40200134},
issn = {1471-2229},
support = {No.321RC475//Hainan Natural Science Foundation high-level Talents Project/ ; No.321RC475//Hainan Natural Science Foundation high-level Talents Project/ ; ZDYF2023XDNY078//the Hainan Province Science and Technology Special Fund/ ; XTCX2022STC10//Collaborative Innovation Center Project of Ecological Civilization in Hainan University/ ; KJRC2023C21//Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; No.32060409//the National Natural Science Foundation of China/ ; XTCX2022NYB08//Collaborative Innovation Center Project of Nanfan and High-Efficiency Tropical Agriculture in Hainan University/ ; },
mesh = {*Cadmium/toxicity ; *Paspalum/genetics/drug effects/metabolism/physiology ; Genome-Wide Association Study ; *Genes, Plant ; Gene Expression Regulation, Plant ; Multiomics ; },
abstract = {Cadmium (Cd) pollution in the farmland has become a serious global issue threatening both human health and plant biomass production. Seashore paspalum (Paspalum vaginatum Sw.), a halophytic turfgrass, has been recognized as a Cd-tolerant species. However, the underlying genetic basis of natural variations in Cd tolerance still remains unknown. This study is possibly the first to apply genome-wide association studies (GWAS) and selective sweep analysis to identify potential Cd stress-responsive genes in P. vaginatum. We identified a total of 89 candidate genes and 656 putative selective sweeps regions. Based on the correlation analysis of differentially expressed metabolites (DEMs) and differentially expressed genes (DEGs), we identified the 55 key genes associated with metabolic changes induced by Cd treatment as the Cd tolerance-related genes. These genes showed significantly higher expression in Cd-tolerant accessions as compared to Cd-susceptive accessions. Therefore, our multi-omics study revealed the molecular and genetic basis of Cd tolerance, which may help develop Cd tolerant crop varieties.},
}
@article {pmid40200140,
year = {2025},
author = {Antala, M and Kovar, M and Sporinová, L and Filacek, A and Juszczak, R and Zivcak, M and Shomali, A and Prasad, R and Brestic, M and Rastogi, A},
title = {High-throughput phenotyping of buckwheat (Fagopyrum esculentum Moench.) genotypes under water stress: exploring drought resistance for sustainable agriculture.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {444},
pmid = {40200140},
issn = {1471-2229},
support = {23-04221 L//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 731013//Horizon 2020 Framework Programme/ ; 2021/43/I/NZ9/01356//Narodowym Centrum Nauki/ ; BWS/BIL/2022/1/00120//Narodowa Agencja Wymiany Akademickiej/ ; },
mesh = {*Fagopyrum/genetics/physiology/growth &amp; development ; Genotype ; *Droughts ; Phenotype ; Dehydration ; Crops, Agricultural/genetics/physiology ; Agriculture ; Stress, Physiological ; Plant Breeding ; Drought Resistance ; },
abstract = {BACKGROUND: As global agriculture faces the challenge of climate change, characterized by longer and more severe drought episodes, there is an increasing need for crop diversification and improved plant breeding. Buckwheat is one of the climate-resilient candidates for future important crops with remarkable adaptability to various biotic and abiotic stresses. As an underbred crop, a large number of genotypes should be assessed for the breeding of superior plants. Therefore, this study investigates the response of various buckwheat genotypes to water stress by high-throughput phenotyping and auxiliary plant physiology measurements.<br><br>RESULTS: We assessed six buckwheat genotypes from different regions under mild and severe water stress, focusing on morphological and physiological changes to understand drought tolerance mechanisms. Our findings revealed that reallocation of assimilated carbon from growth to secondary metabolite production is a common response to drought stress. Among the genotypes tested, Panda emerged as the most drought-resistant, with its morphology remaining the most stable under mild water stress and its ability to rapidly accumulate protective pigments in response to drought. Silver Hull also demonstrated resilience, maintaining its aboveground biomass under mild water stress at levels comparable to the control group. Additionally, the response magnitude to drought stress was linked to the biomass production potential of the genotypes, which was higher for those from warmer regions (Bhutan, Zimbabwe) and lower for those from colder regions (Poland, Canada).<br><br>CONCLUSION: The diversity in genotypic responses highlights the significant role of genetic variability in shaping drought resistance strategies in buckwheat. This research not only enhances our understanding of buckwheat's physiological responses to water stress but also holds promise for developing drought-resistant buckwheat varieties. These advancements are crucial for promoting sustainable agriculture in the face of climate change.},
}
@article {pmid40200522,
year = {2025},
author = {Dsouza, N and Cohen, E and Ossebaard, H and van Meurs, H and Sijm-Eeken, M},
title = {The Ecological Footprint of Gynecology: Lessons from Dutch Hospitals and Implications for Future Healthcare Management.},
journal = {Studies in health technology and informatics},
volume = {323},
number = {},
pages = {424-428},
doi = {10.3233/SHTI250125},
pmid = {40200522},
issn = {1879-8365},
mesh = {Netherlands ; *Gynecology/organization &amp; administration ; Humans ; Quality Improvement/organization &amp; administration ; Female ; Models, Organizational ; },
abstract = {In 2023, global temperatures reached record-breaking highs, highlighting the urgent need for climate action. Healthcare is responsible for 4-8% of global carbon emissions, contributing to global warming and impacting the health of billions of people. Within healthcare, gynecology has a significant ecological footprint due to its high volume and broad range of care services. However, little is known on how gynecology departments' management structures, information systems and processes can be optimized to reduce the ecological footprint of this specialty. Therefore, a sustainability maturity model based on Donabedian's structure-process-outcome model for quality improvement was used to assess sustainability performance in two gynecology practices with different organizational structures (centralized vs. decentralized). Maturity model scores and interview findings were analyzed to extract lessons and recommendations for optimizing sustainability within gynecology. As the first assessment of its kind, this study provides a foundation for healthcare management seeking to improve environmental performance in gynecological care.},
}
@article {pmid40205052,
year = {2025},
author = {Yoo, D and Rhie, A and Hebbar, P and Antonacci, F and Logsdon, GA and Solar, SJ and Antipov, D and Pickett, BD and Safonova, Y and Montinaro, F and Luo, Y and Malukiewicz, J and Storer, JM and Lin, J and Sequeira, AN and Mangan, RJ and Hickey, G and Monfort Anez, G and Balachandran, P and Bankevich, A and Beck, CR and Biddanda, A and Borchers, M and Bouffard, GG and Brannan, E and Brooks, SY and Carbone, L and Carrel, L and Chan, AP and Crawford, J and Diekhans, M and Engelbrecht, E and Feschotte, C and Formenti, G and Garcia, GH and de Gennaro, L and Gilbert, D and Green, RE and Guarracino, A and Gupta, I and Haddad, D and Han, J and Harris, RS and Hartley, GA and Harvey, WT and Hiller, M and Hoekzema, K and Houck, ML and Jeong, H and Kamali, K and Kellis, M and Kille, B and Lee, C and Lee, Y and Lees, W and Lewis, AP and Li, Q and Loftus, M and Loh, YHE and Loucks, H and Ma, J and Mao, Y and Martinez, JFI and Masterson, P and McCoy, RC and McGrath, B and McKinney, S and Meyer, BS and Miga, KH and Mohanty, SK and Munson, KM and Pal, K and Pennell, M and Pevzner, PA and Porubsky, D and Potapova, T and Ringeling, FR and Rocha, JL and Ryder, OA and Sacco, S and Saha, S and Sasaki, T and Schatz, MC and Schork, NJ and Shanks, C and Smeds, L and Son, DR and Steiner, C and Sweeten, AP and Tassia, MG and Thibaud-Nissen, F and Torres-González, E and Trivedi, M and Wei, W and Wertz, J and Yang, M and Zhang, P and Zhang, S and Zhang, Y and Zhang, Z and Zhao, SA and Zhu, Y and Jarvis, ED and Gerton, JL and Rivas-González, I and Paten, B and Szpiech, ZA and Huber, CD and Lenz, TL and Konkel, MK and Yi, SV and Canzar, S and Watson, CT and Sudmant, PH and Molloy, E and Garrison, E and Lowe, CB and Ventura, M and O'Neill, RJ and Koren, S and Makova, KD and Phillippy, AM and Eichler, EE},
title = {Complete sequencing of ape genomes.},
journal = {Nature},
volume = {641},
number = {8062},
pages = {401-418},
pmid = {40205052},
issn = {1476-4687},
support = {R01 MH120295/MH/NIMH NIH HHS/United States ; UH3 AG064706/AG/NIA NIH HHS/United States ; R01 HG010329/HG/NHGRI NIH HHS/United States ; R01 AG056169/AG/NIA NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; T32 GM007748/GM/NIGMS NIH HHS/United States ; P20 GM139769/GM/NIGMS NIH HHS/United States ; U24 HG010263/HG/NHGRI NIH HHS/United States ; R35 GM133747/GM/NIGMS NIH HHS/United States ; P51 OD011092/OD/NIH HHS/United States ; R56 AG056169/AG/NIA NIH HHS/United States ; P01 AI152999/AI/NIAID NIH HHS/United States ; R35 HG011332/HG/NHGRI NIH HHS/United States ; T32 HG012344/HG/NHGRI NIH HHS/United States ; R35 GM122550/GM/NIGMS NIH HHS/United States ; R35 GM133600/GM/NIGMS NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R35 GM142916/GM/NIGMS NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; R35 GM146886/GM/NIGMS NIH HHS/United States ; UH2 AG064706/AG/NIA NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; R01 HG014490/HG/NHGRI NIH HHS/United States ; R35 GM146926/GM/NIGMS NIH HHS/United States ; R35 GM151348/GM/NIGMS NIH HHS/United States ; R35 GM151945/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; Centromere/genetics ; Chromosomes, Mammalian/genetics ; Evolution, Molecular ; Genome ; Gorilla gorilla/genetics ; Haplotypes/genetics ; Heterochromatin/genetics ; *Hominidae/genetics/classification ; Pan paniscus/genetics ; Pan troglodytes/genetics ; Phylogeny ; Segmental Duplications, Genomic/genetics ; Telomere/genetics ; *Whole Genome Sequencing ; },
abstract = {The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies[1-3]. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.},
}
@article {pmid40208899,
year = {2025},
author = {Minier, L and Rouch, J and Sabbagh, B and Bertucci, F and Parmentier, E and Lecchini, D and Sèbe, F and Mathevon, N and Emonet, R},
title = {Visualization and quantification of coral reef soundscapes using CoralSoundExplorer software.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012050},
pmid = {40208899},
issn = {1553-7358},
mesh = {*Coral Reefs ; *Software ; Animals ; Acoustics ; Anthozoa/physiology ; Sound ; Machine Learning ; Computational Biology ; Polynesia ; Ecosystem ; *Environmental Monitoring/methods ; },
abstract = {Despite hosting some of the highest concentrations of biodiversity and providing invaluable goods and services in the oceans, coral reefs are under threat from global change and other local human impacts. Changes in living ecosystems often induce changes in their acoustic characteristics, but despite recent efforts in passive acoustic monitoring of coral reefs, rapid measurement and identification of changes in their soundscapes remains a challenge. Here we present the new open-source software CoralSoundExplorer, which is designed to study and monitor coral reef soundscapes. CoralSoundExplorer uses machine learning approaches and is designed to eliminate the need to extract conventional acoustic indices. To demonstrate CoralSoundExplorer's functionalities, we use and analyze a set of recordings from three coral reef sites, each with different purposes (undisturbed site, tourist site and boat site), located on the island of Bora-Bora in French Polynesia. We explain the CoralSoundExplorer analysis workflow, from raw sounds to ecological results, detailing and justifying each processing step. We detail the software settings, the graphical representations used for visual exploration of soundscapes and their temporal dynamics, along with the analysis methods and metrics proposed. We demonstrate that CoralSoundExplorer is a powerful tool for identifying disturbances affecting coral reef soundscapes, combining visualizations of the spatio-temporal distribution of sound recordings with new quantification methods to characterize soundscapes at different temporal scales.},
}
@article {pmid40211980,
year = {2025},
author = {Elena Schmitz, J and Rahmann, S},
title = {A comprehensive review and evaluation of species richness estimation.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
pmid = {40211980},
issn = {1477-4054},
mesh = {*Biodiversity ; Computer Simulation ; Animals ; Computational Biology/methods ; Algorithms ; },
abstract = {MOTIVATION: The statistical problem of estimating the total number of distinct species in a population (or distinct elements in a multiset), given only a small sample, occurs in various areas, ranging from the unseen species problem in ecology to estimating the diversity of immune repertoires. Accurately estimating the true richness from very small samples is challenging, in particular for highly diverse populations with many rare species. Depending on the application, different estimation strategies have been proposed that incorporate explicit or implicit assumptions about either the species distribution or about the sampling process. These methods are scattered across the literature, and an extensive overview of their assumptions, methodology, and performance is currently lacking.<br><br>RESULTS: We comprehensively review and evaluate a variety of existing methods on real and simulated data with different compositions of rare and abundant species. Our evaluation shows that, depending on species composition, different methods provide the most accurate richness estimates. Simple methods based on the observed number of singletons yield accurate asymptotic lower bounds for several of the tested simulated species compositions, but tend to underestimate the true richness for heterogeneous populations and small samples containing 1% to 5% of the population. When the population size is known, upsampling (extrapolating) estimators such as PreSeq and RichnEst yield accurate estimates of the total species richness in a sample that is up to 10 times larger than the observed sample.<br><br>AVAILABILITY: Source code for data simulation and richness estimation is available at https://gitlab.com/rahmannlab/speciesrichness.},
}
@article {pmid40213351,
year = {2025},
author = {Fehér, &#xc1;M and Bajory, Z and Czimbalmos, N and Burián, K and Lázár, A and Rárosi, F and Köves, B},
title = {Single-dose vs prolonged antibiotic prophylaxis of fosfomycin for transrectal prostate biopsy: a single-center prospective, randomized, controlled trial.},
journal = {Prostate international},
volume = {13},
number = {1},
pages = {28-33},
pmid = {40213351},
issn = {2287-8882},
abstract = {BACKGROUND: Transrectal prostate biopsy is a commonly performed urological procedure in which antibiotic prophylaxis is recommended. Fluoroquinolone-type antibiotics are no longer acceptable in the EU. Fosfomycin-trometamol may be used, but there is no evidence regarding its ideal dose and administration time.<br><br>METHODS: Patients who underwent prostate biopsy between 2021 and 2023 were evaluated prospectively. 204 patients were randomized into two arms: 102 patients (Arm A) received a single-dose of fosfomycin-trometamol one hour before surgery, and 102 patients (Arm B) received one additional dose of fosfomycin-trometamol 48&#xa0;hours after the first dose. Urine tests and questionnaires were administered during the postoperative period and the subsequent four weeks to identify any symptoms, infectious, or other complications.<br><br>RESULTS: There was no statistical difference in the rate of asymptomatic bacteriuria (4.90% (5) vs. 8.82% (9), P&#xa0;=&#xa0;0.27) symptomatic urinary tract infection (0% (0) vs. 1.96% (2), P&#xa0;=&#xa0;0.50), or febrile urinary tract infection (0% (0) vs. 0.98% (1), P&#xa0;=&#xa0;1) between the groups. Only hematuria was significantly more common in Arm B (6.86% (7) vs. 16.67% (17), P&#xa0;=&#xa0;0.03), whereas other complications did not differ significantly. There was no statistical difference in hospitalization (0.98% (1) vs. 2.94 (3), P&#xa0;=&#xa0;0.62) or mortality rate (0 % (0) vs. 0.98% (1), P&#xa0;=&#xa0;1). Sub-group analysis of previous antibiotic users showed no difference in terms of complications.<br><br>CONCLUSION: There is no significant difference in infectious complications between single-dose and prolonged prophylaxis of fosfomycin-trometamol for transrectal prostate biopsy. A single-dose of fosfomycin one hour before biopsy is an ideal choice with a better ecological impact compared with prolonged antibiotic prophylaxis for transrectal prostate biopsy.},
}
@article {pmid40213769,
year = {2025},
author = {Yi, S and Liu, Y and Wu, Q and Zhao, D and Li, Z and Peng, X and Liao, G and Wang, S},
title = {Glycosylation of oral bacteria in modulating adhesion and biofilm formation.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2486650},
pmid = {40213769},
issn = {2000-2297},
abstract = {BACKGROUND: Glycosylation is a ubiquitous biochemical process that covalently attaches glycans to proteins or lipids, which plays a pivotal role in modulating the structure and function of these biomolecules. This post-translational modification is prevalent in living organisms and intricately regulates various biological processes, including signaling transduction, recognition, and immune responses. In the oral environment, bacteria ingeniously use glycosylation to enhance their adhesion to oral surfaces, which is a key step in biofilm formation and subsequent development. This adhesion process is intimately associated with the onset and progression of oral diseases, including dental caries and periodontal disease.<br><br>OBJECTIVE: This review aims to describe the types and mechanisms of glycosylation in oral bacteria, and to understand the role of glycosylation in the adhesion, biofilm formation and virulence of oral bacteria.<br><br>METHODS: We reviewed articles on glycosylation in a variety of oral bacteria.<br><br>CONCLUSION: In cariogenic bacteria and periodontopathic pathogens, glycosylation facilitates adhesion and subsequent biofilm maturation on tooth surface. &#xa0;&#xa0;Distinct glycosylation patterns in oral bacteria shape biofilm structure and function, influencing microbial interactions and community stability. &#xa0;&#xa0;Pathogen-specific glycosylation signatures enhance virulence and ecological competitiveness, contributing to disease progression. Glycosylation plays a critical role in bacterial virulence and community &#xa0;interactions, with significant implications for oral health and disease development.},
}
@article {pmid40218748,
year = {2025},
author = {Meng, J and Wang, Y and Liu, W and Yang, X and He, P},
title = {Research on the Development of an Inland Lake Bathymetry Estimation Model Based on Multispectral Data.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {7},
pages = {},
pmid = {40218748},
issn = {1424-8220},
support = {41901285//the National Natural Science Foundation of China/ ; },
abstract = {Lakes play a crucial role in regional economic development and ecological construction. The variation in lake water depth has a direct impact on local economic activities, such as agriculture, livestock farming, and fisheries, as well as the stability of hydrological conditions and water ecology. In response to the lack of unified evaluation in the application of remote sensing water-depth estimation models for inland lakes, this study systematically compares the performance of numerical models and machine learning models for water-depth estimation in inland lakes. A machine learning-based water-depth estimation model construction methodology suitable for inland lakes is proposed. This study introduces an innovative approach by integrating machine learning techniques with multispectral remote sensing data, improving the accuracy and applicability of water-depth estimation models for inland lakes. The results show the following: (1) The machine learning models based on random forest (RF), BP neural networks (BP), and AdaBoost demonstrate better performance (R[2] = 0.88, 0.72, and 0.61; MAE = 0.12 m, 0.24 m, and 0.31 m; RMSE = 0.32 m, 0.48 m, and 0.57 m) compared to the multi-band logarithmic ratio (MLR) model (R[2] = 0.59; MAE = 0.32 m; RMSE = 0.58 m); (2) the machine learning water-depth estimation model constructed based on this methodology exhibits improved precision (R[2] = 0.92, 0.89, and 0.80; MAE = 0.11 m, 0.17 m, and 0.25 m; RMSE = 0.25 m, 0.30 m, and 0.41 m). This suggests that the methodology is more suitable for the estimation of water depth in medium- and small-sized lakes; (3) The machine learning model developed in this study, combined with multispectral remote sensing imagery, achieves the accuracy required for the evaluation of water depths for practical water resources. This model enables the rapid acquisition of high-precision underwater three-dimensional topographic maps, providing more accurate and timely hydrological data support for lake water resource management.},
}
@article {pmid40222989,
year = {2025},
author = {Mu, K and Wang, Z and Tang, J and Zhang, J and Han, W},
title = {The satisfaction of ecological environment in sports public services by artificial intelligence and big data.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12748},
pmid = {40222989},
issn = {2045-2322},
mesh = {Humans ; *Artificial Intelligence ; *Big Data ; *Sports ; Surveys and Questionnaires ; Neural Networks, Computer ; *Personal Satisfaction ; },
abstract = {In order to gain a more accurate understanding and enhance the relationship between the fitness ecological environment and artificial intelligence (AI)-driven sports public services, this study combines a Convolutional Neural Network (CNN) approach based on residual modules and attention mechanisms with the SERVQUAL evaluation model. The method employed involves the analysis of big data collected from questionnaire surveys, literature reviews, and interviews. This study critically examines the impact of advanced AI technologies on residents' satisfaction with the fitness ecological environment in sports public services and conducts theoretical analysis of the obtained data. The results show that the quality of sports public services empowered by AI significantly influences residents' satisfaction with the fitness ecological environment, such as running, swimming, ball games and other sports with high requirements for sports service quality and ecological environment. Only the good public sports service quality matching with them can meet the needs of the ecological environment for fitness, and stimulate the enthusiasm of the people for fitness. The study also shows that swimming, running and all kinds of ball games account for the largest proportion of all sports. To sum up, the satisfaction of residents' fitness ecological environment is greatly affected by the quality of public sports services, which is mainly reflected in the good and perfect sports environment and facilities that can provide residents with a wealth of fitness options, greatly improving the sports ecological environment. This study is helpful to realize the relationship between sports public service and sports ecological environment. It contributes to understanding the role of AI and deep learning in enhancing the correlation between sports public service and the ecological environment of sports.},
}
@article {pmid40223273,
year = {2025},
author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW},
title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412001},
pmid = {40223273},
issn = {1738-8872},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Metagenomics/trends ; Multiomics/trends ; *Host Microbial Interactions/physiology ; *Translational Research, Biomedical/methods/trends ; Precision Medicine/methods/trends ; },
abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.},
}
@article {pmid40226649,
year = {2024},
author = {Tamm, J and Takano, K and Just, L and Ehring, T and Rosenkranz, T and Kopf-Beck, J},
title = {Ecological Momentary Assessment versus Weekly Questionnaire Assessment of Change in Depression.},
journal = {Depression and anxiety},
volume = {2024},
number = {},
pages = {9191823},
pmid = {40226649},
issn = {1520-6394},
mesh = {Humans ; *Ecological Momentary Assessment ; Male ; Female ; Adult ; Middle Aged ; Surveys and Questionnaires/standards ; *Depression/diagnosis/therapy ; *Outcome Assessment, Health Care/methods ; Reproducibility of Results ; Pessimism/psychology ; Psychiatric Status Rating Scales ; Rumination, Cognitive ; },
abstract = {OBJECTIVE: Ecological momentary assessment (EMA) is increasingly used to monitor depressive symptoms in clinical trials, but little is known about the comparability of its outcomes to those of clinical interviews and questionnaires. In our study, we administered EMA and questionnaires to measure change in depressive symptoms and repetitive negative thinking (RNT) in a clinical trial and investigated (a) the size of intervention effects associated with both techniques and (b) their validity in predicting clinical interview outcomes (i.e., global functioning).<br><br>MATERIALS AND METHODS: Seventy-one depressed patients were randomly assigned to one of three psychological interventions. The EMA comprised a concise item set (four items per scale) and was administered three times per day during a 7-week intervention period. Conversely, questionnaires were assessed weekly (WQA), encompassing their full sets of items of depressive symptoms and RNT.<br><br>RESULTS: While EMA excelled in detecting significant intervention effects, WQA demonstrated greater strength in predicting clinician ratings of global functioning. Additionally, we observed significant differences in time effects (slopes) between the two techniques. WQA scores decreased steeper over time and were more extreme, e.g., higher at baseline and lower postintervention, than EMA scores.<br><br>CONCLUSIONS: Although clinical interviews, questionnaires, and EMA outcomes are related, they assess changes in depression differently. EMA may be more sensitive to intervention effects, but all three methods harbor potential bias, raising validity and reliability questions. Therefore, to enhance the validity and reliability of clinical trial assessments, we emphasize the importance of EMA approaches that combine subjective self-reports with objectively measured behavioral markers. This trial is registered with osf.io/9fuhn.},
}
@article {pmid40227267,
year = {2025},
author = {Cassaro, A and Pacelli, C and Fanelli, G and Baqué, M and Maturilli, A and Leo, P and Lelli, V and de Vera, JP and Onofri, S and Timperio, A},
title = {Biomarker Preservation in Antarctic Sandstones after Prolonged Space Exposure Outside the International Space Station During the ESA EXPOSE-E Lichens and Fungi Experiment.},
journal = {Astrobiology},
volume = {25},
number = {5},
pages = {331-345},
doi = {10.1089/ast.2024.0068},
pmid = {40227267},
issn = {1557-8070},
mesh = {*Lichens ; Antarctic Regions ; *Biomarkers/analysis ; *Extraterrestrial Environment/chemistry ; *Space Flight ; Mars ; Exobiology ; *Fungi ; Spacecraft ; Spectrum Analysis, Raman ; },
abstract = {A primary aim of current and future space exploration missions is the detection and identification of chemical and biological indicators of life, namely biomarkers, on Mars. The Mars Sample Return NASA-ESA program will bring to Earth samples of martian soil, acquired from up to 7 cm depth. The ESA Rosalind Franklin rover will search for signs of life in the subsurface (down to a depth of 2 meters), given the highly radioactive conditions on Mars' surface, which are not ideal for life as we know it and for the preservation of its traces. In the frame of the Lichens and Fungi Experiment, small fragments of Antarctic sandstones colonized by cryptoendolithic microbial communities were exposed to space and simulated martian conditions in low Earth orbit for 18 months, aboard the EXPOSE-E payload. Through the use of Raman and infrared spectroscopies, as well as a metabolomic approach, we aimed to detect organic compounds in a quartz mineral matrix. The results show that pigments, such as melanin, carotenoids, and chlorophyll, lipids, and amino acids, maintained their stability within minerals under simulated martian conditions in space, which makes them ideal biomarkers for the exploration of putative life on Mars.},
}
@article {pmid40229216,
year = {2025},
author = {Zhang, X and Lu, B and Jin, LN and Yang, S and Wang, C and Tai, J and Li, D and Chen, J},
title = {Emission Dynamics and Public Health Implications of Airborne Pathogens and Antimicrobial Resistance from Urban Waste Collection Facilities.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {16},
pages = {8060-8072},
doi = {10.1021/acs.est.4c12108},
pmid = {40229216},
issn = {1520-5851},
mesh = {Humans ; *Air Microbiology ; Bacteria ; Cities ; Drug Resistance, Microbial ; Public Health ; *Waste Disposal Facilities ; },
abstract = {Airborne pathogens and antimicrobial resistance (AMR) present significant global health threats. Household waste collection facilities (WCFs), crucial initial nodes in urban waste management systems, have been understudied in regards to their role in emitting these hazards. This study investigated the abundance, composition, sources, driving mechanisms, and health risks associated with pathogens and AMR originating from WCFs in a major city, using culture-based analysis, high-throughput sequencing, and health risk modeling, respectively. The atmospheric escape rates of culturable bacteria (43.4%), fungi (71.7%), and antibiotic-resistant bacteria (ARB) (43.7%) were estimated based on the concentration differences between the interior and exterior of the WCFs by using SourceTracker2 analysis. Health risk assessments showed that annual infection risks for waste-handling workers ranged from 0.194 to 0.489, far exceeding the World Health Organization's acceptable limit of 10[-4]. Community exposure risks were notable up to 220 m downwind from WCFs, marking the maximum extent of pathogen dispersion. Our analysis suggests that approximately 6.3% of the megacity's area (equivalent to 400 km[2]) is within potential risk zones influenced by WCF emissions. These results underscore the critical need to evaluate and mitigate the public health risks posed by airborne pathogens and AMR emitted from WCFs in megacities globally.},
}
@article {pmid40229317,
year = {2025},
author = {Sabadel, AJM and Riekenberg, P and Ayala-Diaz, M and Belk, MC and Bennett, J and Bode, A and Bury, SJ and Dabouineau, L and Delgado, J and Finucci, B and García-Seoane, R and Giari, L and Henkens, J and IJsseldijk, LL and Joling, T and Kerr-Hislop, O and MacLeod, CD and Meyer, L and McGill, RAR and Negro, E and Quillfeldt, P and Reed, C and Roberts, C and Sayyaf Dezfuli, B and Schmidt, O and Sturbois, A and Suchomel, AD and Thieltges, DW and van der Lingen, CD and van der Meer, MTJ and Viana, IG and Weston, M and Willis, TJ and Filion, A},
title = {Establishing a comprehensive host-parasite stable isotope database to unravel trophic relationships.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {623},
pmid = {40229317},
issn = {2052-4463},
support = {CAWX2207//Ministry of Business, Innovation and Employment (MBIE)/ ; },
mesh = {*Host-Parasite Interactions ; Animals ; Nitrogen Isotopes/analysis ; Carbon Isotopes ; *Databases, Factual ; Sulfur Isotopes/analysis ; *Parasites ; },
abstract = {Over the past decades, stable isotopes have been infrequently used to characterise host-parasite trophic relationships. This is because we have not yet identified consistent patterns in stable isotope values between parasites and their host tissues across species, which are crucial for understanding host-parasite dynamics. To address this, we initiated a worldwide collaboration to establish a unique database of stable isotope values of novel host-parasite pairs, effectively doubling the existing data in published literature. This database includes nitrogen, carbon, and sulphur stable isotope values. We present 3213 stable isotope data entries, representing 586 previously unpublished host-parasite pairs. Additionally, while existing literature was particularly limited in sulphur isotope values, we tripled information on this crucial element. By publishing unreported host-parasite pairs from previously unsampled areas of the world and using appropriate host tissues, our dataset stands unparalleled. We anticipate that end-users will utilise our database to uncover generalisable patterns, deepening our understanding of the complexities of parasite-host relationships and driving future research efforts in stable isotope parasitology.},
}
@article {pmid40232549,
year = {2025},
author = {Xu, F and Jiang, C and Liu, Q and Yang, R and Li, W and Wei, Y and Bao, L and Tong, H},
title = {Source identification of polycyclic aromatic hydrocarbons (PAHs) in river sediments within a hilly agricultural watershed of Southwestern China: an integrated study based on Pb isotopes and PMF method.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {5},
pages = {174},
pmid = {40232549},
issn = {1573-2983},
support = {NO. 2023YFC3705904//National Key Research and Development Plan of China/ ; NO. 2023YFC3705904//National Key Research and Development Plan of China/ ; NO. 2021-043//Stationing Point Tracking Research of Ecological Barrier Construction in the upper Yangtze River of Sichuan Province/ ; NO. 2021-043//Stationing Point Tracking Research of Ecological Barrier Construction in the upper Yangtze River of Sichuan Province/ ; NO. 41977169//National Natural Science Foundation of China/ ; NO. 41977169//National Natural Science Foundation of China/ ; SKLGP2022Z009//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; SKLGP2022Z009//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; },
mesh = {China ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Geologic Sediments/chemistry/analysis ; *Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring/methods ; *Lead/analysis ; Agriculture ; Isotopes/analysis ; Geographic Information Systems ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs) in sediments represent a pervasive environmental issue that poses significant ecological risks. This study employed a combination of geographic information systems, diagnostic ratios, correlation analysis, Pb isotope ratios, and positive matrix factorization (PMF) to elucidate the potential sources of 16 priority PAHs in river sediments from a hilly agricultural watershed in Southwestern China. The results indicated that PAHs concentrations ranged from 55.9 to 6083.5 ng/g, with a mean value of 1582.1 ± 1528.9 ng/g, reflecting high levels of contamination throughout the watershed. The predominant class of PAHs identified was high molecular weight (HMW) PAHs. Diagnostic ratios and correlation analysis suggested that the presence of PHAs is likely attributed primarily to emissions from industrial dust and combustion of coal and petroleum. Furthermore, correlation analysis revealed a significant association between Pb and PAHs, indicating potential shared sources for both pollutants. Additionally, Pb isotopic analysis demonstrated that aerosols may be the primary contributor to Pb accumulation within this environment. Given the similarity in origins between Pb and PAHs, it can be inferred that PAHs predominantly originate from aerosols associated with coal combustion, industrial dust emissions, and vehicle exhaust. This inference is further supported by PMF results which yielded consistent findings with those derived from Pb isotopes analysis. Moreover, PMF estimated three major sources contributing 57.63%, 23.57%, and 18.80%, respectively. These findings provide novel insights into identifying the sources of PAHs in river sediments within hilly agricultural watersheds in Southwest China, thereby establishing a scientific foundation for enhancing environmental quality in agricultural regions.},
}
@article {pmid40233751,
year = {2025},
author = {McKenzie, PF and Berardi, AE and Hopkins, R},
title = {Delayed flowering phenology of red-flowering plants in response to hummingbird migration.},
journal = {Current biology : CB},
volume = {35},
number = {9},
pages = {2175-2182.e3},
pmid = {40233751},
issn = {1879-0445},
support = {R35 GM142742/GM/NIGMS NIH HHS/United States ; },
mesh = {*Birds ; Animals ; *Flowers/growth &amp; development/physiology ; Animal Migration ; Pollination ; North America ; Datasets as Topic ; Seasons ; Pigmentation ; Time Factors ; *Magnoliopsida/physiology ; Crowdsourcing ; },
abstract = {The radiation of angiosperms is marked by a phenomenal diversity of floral size, shape, color, scent, and reward.[1][,][2][,][3][,][4] The multi-dimensional response to selection to optimize pollination has generated correlated suites of these floral traits across distantly related species, known as "pollination syndromes."[5][,][6][,][7][,][8][,][9] The ability to test the broad utility of pollination syndromes and expand upon the generalities of these syndromes is constrained by limited trait data, creating a need for new approaches that can integrate vast, unstructured records from community-science platforms. Here, we compile the largest North American flower color dataset to date, using GPT-4 with Vision to classify color in over 11,000 species across more than 1.6 million iNaturalist observations. We discover that red- and orange-flowering species (classic "hummingbird pollination" colors) bloom later in eastern North America compared with other colors, corresponding to the arrival of migratory hummingbirds. Our findings reveal how seasonal flowering phenology, in addition to floral color and morphology, can contribute to the hummingbird pollination syndrome in regions where these pollinators are migratory. Our results highlight phenology as an underappreciated dimension of pollination syndromes and underscore the utility of integrating artificial intelligence with community-science data. The potential breadth of analysis offered by community-science datasets, combined with emerging data extraction techniques, could accelerate discoveries about the evolutionary and ecological drivers of biological diversity.},
}
@article {pmid40235568,
year = {2025},
author = {Davies, H and Noble, PJ and Fins, IS and Pinchbeck, G and Singleton, D and Pirmohamed, M and Killick, D},
title = {Developing electronic health records as a source of real-world data for veterinary pharmacoepidemiology.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1550468},
pmid = {40235568},
issn = {2297-1769},
abstract = {Spontaneous reporting of adverse events (AEs) by veterinary professionals and the public is the cornerstone of post-marketing safety surveillance for veterinary medicinal products (VMPs). However, studies suggest that most veterinary AEs remain unreported. Veterinary medicine regulators, including the United Kingdom Veterinary Medicines Directorate and the European Medicines Agency, have included the exploration of big data utilization to support pharmacovigilance efforts in their regulatory strategies. In this study, we describe the application of veterinary electronic healthcare records (EHRs) from the SAVSNET veterinary first opinion informatics system to conduct pharmacoepidemiological analyses. Five VMP-AE pairs were selected for investigation in a proof-of-concept study, where drug exposure was identified from semi-structured treatment data and AEs from the unstructured free-text clinical narrative. Dictionaries were developed to identify AEs based on standard terminology. The precision of these dictionaries improved when they were expanded using word vectorization and expert opinion. A key strength of first-opinion EHR datasets is their ability to enable cohort studies and facilitate calculations of absolute incidence and relative risk. Thus, we demonstrate that unstructured free-text clinical narratives can be used to identify outcomes for veterinary pharmacoepidemiological studies and, consequently, support and expand pharmacovigilance efforts based on spontaneous AE reports.},
}
@article {pmid40238239,
year = {2025},
author = {Sutori, S and Eliasson, ET and Mura, F and Ortiz, V and Catrambonephd, V and Hadlaczky, G and Todorov, I and Alfeo, AL and Cardi, V and Cimino, MGCA and Mioni, G and Raya, MA and Valenza, G and Carli, V and Gentili, C},
title = {Acceptability, Usability, and Insights Into Cybersickness Levels of a Novel Virtual Reality Environment for the Evaluation of Depressive Symptoms: Exploratory Observational Study.},
journal = {JMIR formative research},
volume = {9},
number = {},
pages = {e68132},
pmid = {40238239},
issn = {2561-326X},
mesh = {Humans ; *Virtual Reality ; Male ; Female ; Adult ; *Depression/diagnosis/psychology ; Young Adult ; Italy ; Surveys and Questionnaires ; User-Computer Interface ; Pilot Projects ; Self Report ; },
abstract = {BACKGROUND: There is a clear need for enhanced mental health assessment, depressive symptom (DS) evaluation being no exception. A promising approach to this aim is using virtual reality (VR), which entails the potential of adding a wider set of assessment domains with enhanced ecological validity. However, whilst several studies have used VR for both diagnostic and treatment purposes, its acceptance, in particular how exposure to virtual environments affects populations with psychiatric conditions remains unknown.<br><br>OBJECTIVE: This study aims to report on the acceptability, usability, and cybersickness levels of a pilot VR environment designed for the purpose of differentiating between individuals with DSs.<br><br>METHODS: The exploratory study, conducted in Italy, included 50 healthy controls and 50 young adults with mild-to-moderate DSs (without the need for a formal diagnosis). The study used an observational design with approximately 30 minutes of VR exposure followed by a self-report questionnaire battery. The battery included a questionnaire based on the Theoretical Framework of Acceptability, the System Usability Scale as well as the Simulator Sickness Questionnaire.<br><br>RESULTS: Results indicate that the majority found VR acceptable for the purposes of mental health screening and treatment. However, for diagnostics, there was a clear preference for VR to be used by mental health professionals as a supplementary tool, as opposed to a stand-alone solution. In practice, following exposure to the pilot VR environment, generally, good levels of acceptability and usability were reported, but areas in need of improvement were identified (such as self-efficacy). Self-reported cybersickness levels were comparable to literature averages but were considerably higher among those with DSs.<br><br>CONCLUSIONS: These findings raise questions about the potential interplay between underlying somatic symptoms of depression and VR-induced cybersickness and call for more attention from the scientific community both in terms of methodology as well as potential clinical and theoretical implications. Conclusively, user support indicates a potential for VR to aid mental health assessment, but further research is needed to understand how exposure to virtual environments might affect populations with varying severity and other forms of psychiatric symptoms.<br><br>RR2-10.1186/ISRCTN16396369.},
}
@article {pmid40238767,
year = {2025},
author = {Rodrigues, RDS and Cionek, VM and Barreto, AS and Branco, JO},
title = {Seabird strandings on the Brazilian coast: What influences spatial and temporal patterns?.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0317335},
pmid = {40238767},
issn = {1932-6203},
mesh = {Animals ; Brazil ; *Animal Migration/physiology ; *Birds/physiology ; Seasons ; Spatio-Temporal Analysis ; Ecosystem ; Biodiversity ; },
abstract = {Seabirds exhibit physiological adaptations that allow them to forage in the marine environment and undertake long-distance migrations during non-reproductive periods. As a result, they face various natural and anthropogenic pressures, which can lead to extreme fatigue and even death. Stranded bodies that float in the sea can wash ashore, providing valuable ecological information. This study aimed to analyze seabird strandings along the south and southeast coasts of Brazil between 2016 and 2019, focusing on spatiotemporal and potential environmental and anthropogenic influences. Using data from the Santos Basin Beach Monitoring Project, we calculated ecological indices of abundance, richness, and diversity for the entire seabird community and separately by migratory behavior (resident, southern migratory, northern migratory). Statistical modeling revealed a strong decreasing trend in strandings from south to north, with higher events on the southern coast (Santa Catarina and Paraná) and lower on the southeast coast (São Paulo). Resident species and northern migratory species showed peak strandings in spring, while southern migratory peaked in winter. These spatial and temporal patterns reflected birds' home ranges, reproductive cycles, and migratory behaviors. Environmental variables influenced strandings differently depending on species migration behavior and ecological indices, highlighting the role of oceanographic processes in carcass drift and the impact of climatic events on species mortality. This study is the first to demonstrate a spatiotemporal pattern of seabird strandings on the Brazilian coast, providing valuable insights into seabird dynamics in the Santos Basin and offering important data for conservation efforts.},
}
@article {pmid40240877,
year = {2025},
author = {Li, W and Chu, C and Zhang, T and Sun, H and Wang, S and Liu, Z and Wang, Z and Li, H and Li, Y and Zhang, X and Geng, Z and Wang, Y and Li, Y and Zhang, H and Fan, W and Wang, Y and Xu, X and Cheng, L and Zhang, D and Xiong, Y and Li, H and Zhou, B and Guan, Q and Deng, CH and Han, Y and Ma, H and Han, Z},
title = {Pan-genome analysis reveals the evolution and diversity of Malus.},
journal = {Nature genetics},
volume = {57},
number = {5},
pages = {1274-1286},
pmid = {40240877},
issn = {1546-1718},
support = {CARS-27//Earmarked Fund for China Agriculture Research System/ ; 32172522//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32422077//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2019M661344//China Postdoctoral Science Foundation/ ; },
mesh = {*Malus/genetics/classification ; *Genome, Plant/genetics ; Phylogeny ; *Genetic Variation ; *Evolution, Molecular ; Polyploidy ; Genomics/methods ; Disease Resistance/genetics ; },
abstract = {Malus Mill., a genus of temperate perennial trees with great agricultural and ecological value, has diversified through hybridization, polyploidy and environmental adaptation. Limited genomic resources for wild Malus species have hindered the understanding of their evolutionary history and genetic diversity. We sequenced and assembled 30 high-quality Malus genomes, representing 20 diploids and 10 polyploids across major evolutionary lineages and geographical regions. Phylogenomic analyses revealed ancient gene duplications and conversions, while six newly defined genome types, including an ancestral type shared by polyploid species, facilitated the detection of strong signals for extensive introgressions. The graph-based pan-genome captured shared and species-specific structural variations, facilitating the development of a molecular marker for apple scab resistance. Our pipeline for analyzing selective sweep identified a mutation in MdMYB5 having reduced cold and disease resistance during domestication. This study advances Malus genomics, uncovering genetic diversity and evolutionary insights while enhancing breeding for desirable traits.},
}
@article {pmid40245036,
year = {2025},
author = {Hu, J and Weber, JN and Fuess, LE and Steinel, NC and Bolnick, DI and Wang, M},
title = {A spectral framework to map QTLs affecting joint differential networks of gene co-expression.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012953},
pmid = {40245036},
issn = {1553-7358},
support = {R01 AI123659/AI/NIAID NIH HHS/United States ; R35 GM142891/GM/NIGMS NIH HHS/United States ; },
mesh = {*Quantitative Trait Loci/genetics ; *Gene Regulatory Networks/genetics ; Animals ; Computational Biology/methods ; *Chromosome Mapping/methods ; Phenotype ; Genotype ; Models, Genetic ; Gene Expression Profiling/methods ; },
abstract = {Studying the mechanisms underlying the genotype-phenotype association is crucial in genetics. Gene expression studies have deepened our understanding of the genotype → expression → phenotype mechanisms. However, traditional expression quantitative trait loci (eQTL) methods often overlook the critical role of gene co-expression networks in translating genotype into phenotype. This gap highlights the need for more powerful statistical methods to analyze genotype → network → phenotype mechanism. Here, we develop a network-based method, called spectral network quantitative trait loci analysis (snQTL), to map quantitative trait loci affecting gene co-expression networks. Our approach tests the association between genotypes and joint differential networks of gene co-expression via a tensor-based spectral statistics, thereby overcoming the ubiquitous multiple testing challenges in existing methods. We demonstrate the effectiveness of snQTL in the analysis of three-spined stickleback (Gasterosteus aculeatus) data. Compared to conventional methods, our method snQTL uncovers chromosomal regions affecting gene co-expression networks, including one strong candidate gene that would have been missed by traditional eQTL analyses. Our framework suggests the limitation of current approaches and offers a powerful network-based tool for functional loci discoveries.},
}
@article {pmid40245396,
year = {2025},
author = {Melia, R and Musacchio Schafer, K and Rogers, ML and Wilson-Lemoine, E and Joiner, TE},
title = {The Application of AI to Ecological Momentary Assessment Data in Suicide Research: Systematic Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e63192},
pmid = {40245396},
issn = {1438-8871},
mesh = {Humans ; *Ecological Momentary Assessment ; *Artificial Intelligence ; *Suicide ; *Suicidal Ideation ; },
abstract = {BACKGROUND: Ecological momentary assessment (EMA) captures dynamic processes suitable to the study of suicidal ideation and behaviors. Artificial intelligence (AI) has increasingly been applied to EMA data in the study of suicidal processes.<br><br>OBJECTIVE: This review aims to (1) synthesize empirical research applying AI strategies to EMA data in the study of suicidal ideation and behaviors; (2) identify methodologies and data collection procedures used, suicide outcomes studied, AI applied, and results reported; and (3) develop a standardized reporting framework for researchers applying AI to EMA data in the future.<br><br>METHODS: PsycINFO, PubMed, Scopus, and Embase were searched for published articles applying AI to EMA data in the investigation of suicide outcomes. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines were used to identify studies while minimizing bias. Quality appraisal was performed using CREMAS (adapted STROBE [Strengthening the Reporting of Observational Studies in Epidemiology] Checklist for Reporting Ecological Momentary Assessment Studies).<br><br>RESULTS: In total, 1201 records were identified across databases. After a full-text review, 12 (1%) articles, comprising 4398 participants, were included. In the application of AI to EMA data to predict suicidal ideation, studies reported mean area under the curve (0.74-0.86), sensitivity (0.64-0.81), specificity (0.73-0.86), and positive predictive values (0.72-0.77). Studies met between 4 and 13 of the 16 recommended CREMAS reporting standards, with an average of 7 items met across studies. Studies performed poorly in reporting EMA training procedures and treatment of missing data.<br><br>CONCLUSIONS: Findings indicate the promise of AI applied to self-report EMA in the prediction of near-term suicidal ideation. The application of AI to EMA data within suicide research is a burgeoning area hampered by variations in data collection and reporting procedures. The development of an adapted reporting framework by the research team aims to address this.<br><br>TRIAL REGISTRATION: Open Science Framework (OSF); https://doi.org/10.17605/OSF.IO/NZWUJ and PROSPERO CRD42023440218; https://www.crd.york.ac.uk/PROSPERO/view/CRD42023440218.},
}
@article {pmid40246854,
year = {2025},
author = {He, B and Zhang, H and Qin, T and Shi, B and Wang, Q and Dong, W},
title = {A simultaneous EEG and eye-tracking dataset for remote sensing object detection.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {651},
pmid = {40246854},
issn = {2052-4463},
support = {42230103//National Science Foundation of China | Key Programme/ ; },
mesh = {*Electroencephalography ; Humans ; *Eye-Tracking Technology ; *Remote Sensing Technology ; Artificial Intelligence ; },
abstract = {We introduce the EEGET-RSOD, a simultaneous electroencephalography (EEG) and eye-tracking dataset for remote sensing object detection. This dataset contains EEG and eye-tracking data when 38 remote sensing experts located specific objects in 1,000 remote sensing images within a limited time frame. This task reflects the typical cognitive processes associated with human visual search and object identification in remote sensing imagery. To our knowledge, EEGET-RSOD is the first publicly available dataset to offer synchronized eye-tracking and EEG data for remote sensing images. This dataset will not only advance the study of human visual cognition in real-world environment, but also bridge the gap between human cognition and artificial intelligence, enhancing the interpretability and reliability of AI models in geospatial applications.},
}
@article {pmid40247093,
year = {2025},
author = {Yang, J and Chen, YN and Fang, CY and Li, Y and Ke, HQ and Guo, RQ and Xiang, P and Xiao, YL and Zhang, LW and Liu, H},
title = {Investigating immune cell infiltration and gene expression features in pterygium pathogenesis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13352},
pmid = {40247093},
issn = {2045-2322},
support = {ZKF2024042//National clinical key specialty ophthalmology open foundation/ ; ZKF2024041//National clinical key specialty ophthalmology open foundation/ ; 202208535051//China Scholarship Council/ ; 81860171//National Natural Science Foundation of China/ ; 82460201//National Natural Science Foundation of China/ ; 202205AC160016//Yunnan Young and middle-aged Academic and technical leader Project/ ; L2019029//Yunnan Provincial Health Committee Training program for leading medical talents/ ; YDYXJJ2024-0003//Yunnan University Medical Research Foundation/ ; },
mesh = {Humans ; *Pterygium/genetics/immunology/pathology ; Gene Expression Profiling ; Computational Biology/methods ; Conjunctiva/pathology/metabolism/immunology ; Transcriptome ; *Gene Expression Regulation ; Biomarkers/metabolism ; },
abstract = {Pterygium is a prevalent ocular disease characterized by abnormal conjunctival tissue proliferation, significantly impacting patients' quality of life. However, the underlying molecular mechanisms driving pterygium pathogenesis remain inadequately understood. This study aimed to investigate gene expression changes following pterygium excision and their association with immune cell infiltration. Clinical samples of pterygium and adjacent relaxed conjunctival tissue were collected for transcriptomic analysis using RNA sequencing combined with bioinformatics approaches. Machine learning algorithms, including LASSO, SVM-RFE, and Random Forest, were employed to identify potential diagnostic biomarkers. GO, KEGG, GSEA, and GSVA were utilized for enrichment analysis. Single-sample GSEA was employed to analyze immune infiltration. The GSE2513 and GSE51995 datasets from the GEO database, along with clinical samples, were selected for validation analysis. Differentially expressed genes (DEGs) were identified from the PRJNA1147595 and GSE2513 datasets, revealing 2437 DEGs and 172 differentially regulated genes (DRGs), respectively. There were 52 co-DEGs shared by both datasets, and four candidate biomarkers (FN1, SPRR1B, SERPINB13, EGR2) with potential diagnostic value were identified through machine learning algorithms. Single-sample GSEA demonstrated increased Th2 cell infiltration and decreased CD8 + T cell presence in pterygium tissues, suggesting a crucial role of the immune microenvironment in pterygium pathogenesis. Analysis of the GSE51995 dataset and qPCR results revealed significantly higher expression levels of FN1 and SPRR1B in pterygium tissues compared to conjunctival tissues, but SERPINB13 and EGR2 expression levels were not statistically significant. Furthermore, we identified four candidate drugs targeting the two feature genes FN1 and SPRR1B. This study provides valuable insights into the molecular characteristics and immune microenvironment of pterygium. The identification of potential biomarkers FN1 and SPRR1B highlights their significance in pterygium pathogenesis and lays a foundation for further exploration aimed at integrating these findings into clinical practice.},
}
@article {pmid40247661,
year = {2025},
author = {Abraham, AJ and Duvall, ES and Doughty, CE and Riond, B and Ortmann, S and Terranova, M and le Roux, E and Clauss, M},
title = {Sodium Retention in Large Herbivores: Physiological Insights and Zoogeochemical Consequences.},
journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology},
volume = {343},
number = {6},
pages = {664-676},
pmid = {40247661},
issn = {2471-5646},
support = {//A.J.A. acknowledges Horizon Europe Marie Sk&#x142;odowska-Curie Actions Grant Agreement No. 101062339./ ; },
mesh = {Animals ; Cattle/physiology ; Feces/chemistry ; *Herbivory/physiology ; *Sodium/urine/metabolism ; Horses/physiology/metabolism ; Female ; },
abstract = {The assimilation, retention, and release of nutrients by animals fundamentally shapes their physiology and contributions to ecological processes (e.g., zoogeochemistry). Yet, information on the transit of nutrients through the bodies of large mammals remains scarce. Here, we examined how sodium (Na), a key element for animal health and ecosystem functioning, travels differently through fecal and urinary systems of cows (Bos taurus) and horses (Equus ferus caballus). We provided a large dose of Na and compared its timing of release in feces and urine to that of nonabsorbable markers. Na excretion by urine occurred approximately twice as fast as excretion by feces, yet both were shorter than indigestible particle markers. These differences correspond to rapid absorption of Na in the upper gastrointestinal tract and transport by blood to the kidneys (urine Na excretion) or resecretion of Na into the lower intestinal tract (fecal Na excretion). Interestingly, for cows, we found a second peak of Na excretion in urine and feces > 96 h after dosage. This result may indicate that surplus Na can be rapidly absorbed and stored in specific body cells (e.g., skin), from which it is later released. Using a propagule dispersal model, we found that the distance of cattle- and horse-driven nutrient dispersal by urine was 31% and 36% less than the fecal pathway and 60% and 41% less than the particle marker pathway, which is commonly used to estimate nutrient dispersal. Future physiological and zoogeochemical studies should resolve different pathways of nutrient retention and release from large mammals.},
}
@article {pmid40248649,
year = {2025},
author = {Boyes, D and Januszczak, I and , and , and , and , and , and , and , and , and Mitchell, R},
title = {The genome sequence of the Warted Knot-Horn moth, Acrobasis repandana Fabricius, 1798.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {50},
pmid = {40248649},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female specimen of Acrobasis repandana (Warted Knot-Horn moth; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence has a total length of 620.40 megabases. Most of the assembly (99.78%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.21 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,522 protein-coding genes.},
}
@article {pmid40249276,
year = {2025},
author = {May, SA and Rosenbaum, SW and Pearse, DE and Kardos, M and Primmer, CR and Baetscher, DS and Waples, RS},
title = {The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids.},
journal = {Molecular ecology},
volume = {34},
number = {23},
pages = {e17758},
pmid = {40249276},
issn = {1365-294X},
support = {//USDA-ARS/ ; },
mesh = {*Genomics/methods/trends ; Animals ; *Salmonidae/genetics ; Genome ; Computational Biology ; },
abstract = {The increasing feasibility of whole-genome sequencing has been highly anticipated, promising to transform our understanding of the biology of nonmodel species. Notably, dramatic cost reductions beginning around 2007 with the advent of high-throughput sequencing inspired publications heralding the 'genomics revolution', with predictions about its future impacts. Although such predictions served as useful guideposts, value is added when statements are evaluated with the benefit of hindsight. Here, we review 10 key predictions made early in the genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on predictions concerning applied aspects of genomics and examples involving salmonid species which, due to their socioeconomic and ecological significance, have been frontrunners in applications of genomics in nonmodel species. Predicted outcomes included enhanced analytical power, deeper insights into the genetic basis of phenotype and fitness variation, disease management and breeding program advancements. Although many predictions have materialised, several expectations remain unmet due to technological, analytical and knowledge barriers. Additionally, largely unforeseen advancements, including the identification and management applicability of large-effect loci, close-kin mark-recapture, environmental DNA and gene editing have added under-anticipated value. Finally, emerging innovations in artificial intelligence and bioinformatics offer promising new directions. This retrospective evaluation of the impacts of the genomic revolution offers insights into the future of genomics for nonmodel species.},
}
@article {pmid40249863,
year = {2025},
author = {Wu, Q and Cheng, S and Zhang, W and Zhao, J and Zhang, L and Lv, M and Ma, J and Ding, J and Wang, S and Zheng, X and Gao, J and Liu, R and Yin, Y and Shi, J and Qu, G and Jiang, G},
title = {Heterogeneous Single-Cell Distribution of Trace-Level Metal Mixtures in Tetrahymena thermophila Using Mass Cytometry.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {16},
pages = {7855-7866},
doi = {10.1021/acs.est.4c12818},
pmid = {40249863},
issn = {1520-5851},
mesh = {*Tetrahymena thermophila/metabolism ; *Metals, Heavy ; Water Pollutants, Chemical ; },
abstract = {The uptake of heavy metals by unicellular organisms can lead to the bioaccumulation of these metals in higher organisms, detrimentally affecting organismal health and ultimately impacts the ecosystems. By studying the uptake and accumulation of heavy metals in unicellular organisms, we gain insights into potential risks associated with low-dose heavy metal exposure in aquatic environments. Thus, to investigate the accumulation characteristics of Mo, Ag, Cd, Sn, Sb, Hg, Tl, and Pb mixtures in single Tetrahymena thermophila cells, we developed a label-free approach for the simultaneous absolute quantification of multiple metals in a single cell using mass cytometry. Our results demonstrated the dynamic changes in metal concentrations in T. thermophila, and the competition between metals in uptake and excretory pathways resulted in heterogeneous accumulation and bioconcentration of these metals. Additionally, our findings revealed the limited capacity of T. thermophila to excrete Cd and Hg, suggesting a higher risk for T. thermophila cells when exposed to Cd and Hg over an extended period. Therefore, the current study provides valuable data for a more comprehensive understanding of the impact of low-dose heavy metals on aquatic ecosystems.},
}
@article {pmid40253432,
year = {2025},
author = {Kelliher, JM and Aljumaah, M and Bordenstein, SR and Brister, JR and Chain, PSG and Dundore-Arias, JP and Emerson, JB and Fernandes, VMC and Flores, R and Gonzalez, A and Hansen, ZA and Hatcher, EL and Jackson, SA and Kellogg, CA and Madupu, R and Miller, CML and Mirzayi, C and Moustafa, AM and Mungall, C and Oliver, A and Pariente, N and Pett-Ridge, J and Record, S and Reji, L and Reysenbach, AL and Rich, VI and Richardson, L and Schriml, LM and Shabman, RS and Sierra, MA and Sullivan, MB and Sundaramurthy, P and Thibault, KM and Thompson, LR and Tighe, S and Vereen, E and Eloe-Fadrosh, EA},
title = {Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {40},
pmid = {40253432},
issn = {2524-6372},
support = {2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; },
abstract = {Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard. No equivalent effort has occurred for environmental, synthetic, and non-human host-associated microbiomes. To address this growing need within the microbiome research community, we convened the Microbiome Data Management in Action Workshop (June 12-13, 2024, in Atlanta, GA, USA), to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. The 50 attendees, representing the diverse and interdisciplinary nature of microbiome research, discussed recent progress and challenges, and brainstormed actionable recommendations and paths forward for coordinated environmental microbiome data management and the modifications necessary for the STORMS guidelines to be applied to environmental, non-human host, and synthetic microbiomes. The outcomes of this workshop will form the basis of a formalized data management roadmap to be implemented across the field. These best practices will drive scientific innovation now and in years to come as these data continue to be used not only in targeted reanalyses but in large-scale models and machine learning efforts.},
}
@article {pmid40253884,
year = {2025},
author = {Wang, X and Zhao, C and Huang, G and Liu, H and Zhu, X and Huang, J},
title = {Quantifying leachate discharge and assessing environmental risks of gully-type coal-based solid waste dumps in small watersheds: A refined hydrological modeling approach for mitigation strategies.},
journal = {Water research},
volume = {282},
number = {},
pages = {123655},
doi = {10.1016/j.watres.2025.123655},
pmid = {40253884},
issn = {1879-2448},
mesh = {*Water Pollutants, Chemical/analysis ; *Coal ; Environmental Monitoring/methods ; Models, Theoretical ; Hydrology ; Risk Assessment ; *Solid Waste/analysis ; *Refuse Disposal ; },
abstract = {Rainfall-induced leaching from extensive coal-based solid waste storage results in a long-term risk to watershed's water quality and safety. The leachate carries heavy metals and other contaminants, which migrate and accumulate through the watershed, leading to a persistent deterioration of downstream water environment. However, the lack of systematic research on the release, accumulation, and spatial-scale migration dynamics of leachate limits effective management of diffused leachate pollutions. This study presents a novel cross-scale coupling framework which integrates multi-source remote sensing data with Soil and Water Assessment Tool (SWAT) model, employing a strategy that transfers parameters from large basins to accurately quantify the hydrological processes in coal waste sub-basins. Additionally, a comprehensive analysis is performed on the hydrological characteristics, leachate generation, and watershed migration dynamics in gangue dump sub-watersheds, providing a new methodological framework for managing mining-related leachate pollution. The large basin model demonstrated strong performance (R[2] = 0.79, NSE = 0.66 for calibration; R[2] = 0.74, NSE = 0.59 for verification), while the sub-basin model exhibited excellent accuracy (R[2] = 0.94, NSE = 0.92 for calibration; R[2] = 0.81, NSE = 0.77 for verification). High-resolution drone data estimated the annual leachate production to be 3366.87 m[3]. Simulations revealed that leachate migration peaks in the summer months (July to September), significantly increasing downstream pollution risks. Risk assessments indicate that vegetation in land restoration areas reduces leachate production and migration via evapotranspiration and other processes. This study provides an adaptable methodological framework for managing mining-related leachate pollution and highlights the critical importance of optimal reclamation strategies for mitigating pollution and restoring degraded landscapes.},
}
@article {pmid40258091,
year = {2025},
author = {Hashem, I and Wang, J and Van Impe, JFM},
title = {A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012974},
pmid = {40258091},
issn = {1553-7358},
mesh = {*Algorithms ; *Models, Biological ; Computational Biology/methods ; Computer Simulation ; Biofilms/growth &amp; development ; },
abstract = {Individual-based modeling (IbM) is an instrumental tool for simulating spatial microbial growth, with applications in both microbial ecology and biochemical engineering. Unlike Cellular Automata (CA), which use a fixed grid of cells with predefined rules for interactions, IbMs model the individual behaviors of cells, allowing complex population dynamics to emerge. IbMs require more detailed modeling of individual interactions, which introduces significant computational challenges, particularly in resolving spatial overlaps between cells. Traditionally, this is managed using arrays or kd-trees, which require numerous pairwise comparisons and become inefficient as population size increases. To address this bottleneck, we introduce the Discretized Overlap Resolution Algorithm (DORA), which employs a grid-based framework to efficiently manage overlaps. By discretizing the simulation space further and assigning circular cells to specific grid units, DORA transforms the computationally intensive pairwise comparison process into a more efficient grid-based operation. This approach significantly reduces the computational load, particularly in simulations with large cell populations. Our evaluation of DORA, through simulations of microbial colonies and biofilms under varied nutrient conditions, demonstrates its superior computational efficiency and ability to accurately capture microbial growth dynamics compared to conventional methods. DORA's grid-based strategy enables the modeling of densely populated microbial communities within practical computational timeframes, thereby expanding the scope and applicability of individual-based modeling.},
}
@article {pmid40259303,
year = {2025},
author = {Yano, KM and Zucchi, P and Novais, MAP},
title = {Psychiatric hospitalizations in the Unified Health System: an observational study on hospitalization rates from 2012 to 2023.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {1463},
pmid = {40259303},
issn = {1471-2458},
support = {2022/10716-2//S&#xe3;o Paulo State Research Foundation (FAPESP)/ ; },
mesh = {Humans ; *Hospitalization/trends/statistics &amp; numerical data ; Brazil/epidemiology ; Female ; Male ; Adult ; Middle Aged ; Adolescent ; *Mental Disorders/therapy/epidemiology ; Aged ; Young Adult ; Aged, 80 and over ; Child ; Infant ; Child, Preschool ; *National Health Programs/statistics &amp; numerical data ; Infant, Newborn ; },
abstract = {BACKGROUND: Psychiatric care in Brazil is based on the National Mental Health Policy and is aligned with the guidelines of the Brazilian Unified Health System. It is based on the preeminence of care in the extra-hospital context over the hospital context. Hospital admissions should occur solely when extra-hospital resources prove insufficient for the proper management of the mental health condition.<br><br>METHOD: It refers to a time series investigation of a descriptive, ecological, and observational nature. We used publicly available hospital admissions data from the Brazilian Unified Health System's Department of Informatics. The study looked at information on diseases in ICD-10 group V that affected both men and women aged 0 to 80 or older, from 2012 to 2023. The information was analyzed using the statistical software SPSS 20.0, as well as Jointpoint, through permutation tests, with the aim of evaluating the temporal trend of hospitalization and mortality rates. The joinpoint regression model used a log-linear method to set up a series of connected lines on a logarithmic scale and the Monte Carlo permutation method to figure out the direction or statistical significance. A significance level of 5% was established for the execution of all statistical tests.<br><br>RESULTS: Overall, a trend of reduction in psychiatric hospitalization rates was observed. However, these trends exhibited fluctuations when analyzed in isolation with respect to the type of disorder, gender, and age group. In contrast to the general trend, the number of hospitalizations for affective disorders and disorders linked to stress and somatization went up. This was especially true between 2021 and 2023, when the number of hospitalizations for other disorders went down more significantly. The predominance of hospitalizations in the male gender was significant. However, the trends of decrease were less pronounced in the male group, especially regarding hospitalizations associated with alcohol and other substance use, which draws attention to the hospitalization rates of the female sex. As it relates to dementias, the national picture shows that hospitalizations are going down, and most of the patients are women and older adults or people who are very old. However, an analysis of the state scenario showed that hospitalizations went up for adults, more than for the elderly combined, with more men than women.<br><br>CONCLUSION: the results achieved in this research confirm the findings, both nationally and internationally. Studies have shown that investments made through the National Mental Health Policy and the effects of Covid-19 led to a drop in the number of people admitted to psychiatric hospitals. This was because of the restructuring of the care model, which meant that hospitalizations had to be prioritized to meet the needs of Covid-19, which hurt people with mental disorders.},
}
@article {pmid40266389,
year = {2025},
author = {Xinyi, B and Qingbiao, G and Songbo, W and Jin, L and Jiren, X},
title = {Identifying the spatio-temporal evolution and driving mechanisms of ecosystem service value in high groundwater table coal mining areas.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {5},
pages = {581},
pmid = {40266389},
issn = {1573-2959},
support = {No. 2024cx2152//the Graduate Innovation Fund Project of Anhui University of Science and Technology/ ; 2024cxcysj094//the Provincial graduate student innovation and entrepreneurship practice project/ ; NO. KSXTJC202401//Engineering Research Center of Mining Area Environmental And Disaster Cooperative Monitoring (Anhui University of Science and Technology)/ ; No. 52274164//the Natural Science Foundation of China/ ; No. 2308085Y31//the Anhui Provincial Natural Science Foundation/ ; No. 2022QNRC001//the Young Elite Scientists Sponsorship Program by CAST/ ; No. GJNY-21-41-15//the Open Fund of State Key Laboratory of Water Resource Protection and Utilization in Coal Mining/ ; },
mesh = {*Coal Mining ; *Environmental Monitoring ; *Ecosystem ; *Groundwater/chemistry ; *Conservation of Natural Resources/methods ; Spatio-Temporal Analysis ; China ; },
abstract = {In coal mining areas with high groundwater tables, surface subsidence has emerged as a non-negligible phenomenon, stemming from long-term coal mining activities. Employing the Huainan mining area as an exemplar, this research meticulously examines the temporal and spatial attributes of ecosystem service value (ESV) across distinct timeframes of 2005, 2010, 2015, and 2020, utilizing the refined equivalent factor approach in conjunction with spatial analysis methodologies. To delve into the primary forces driving the observed changes, the optimal parameter-based geographical detector (OPGD) model is subsequently utilized as a tool for analysis. Lastly, the study delves into the trade-offs and synergies existing between four exemplary services at the grid level, utilizing Spearman correlation coefficient and bivariate spatial autocorrelation. The findings suggest that: (1) From 2005 to 2020, the total ESV in the Huainan mining area demonstrated a general increasing tendency, primarily attributed to the increase in waters. (2) Throughout the research period, the ecosystem service functions in the coal mining area all exhibited relatively significant hydrological regulation and waste treatment capabilities. (3) Vegetation factors significantly influenced the ESV in the Huainan mining area. (4) The Huainan mining area predominantly exhibited synergistic effects among ecosystem services, with the most pronounced synergy occurring between cultural services (CS) and regulating services (RS). All services were transitioning towards an enhanced trend of synergistic effects. (5) Significant spatial variations are present in the observed trade-offs and synergies among diverse ecosystem services. The aforementioned research findings will provide scientific theoretical guidance for rational mining activities and ecological environmental governance in coal mining areas.},
}
@article {pmid40270457,
year = {2025},
author = {Selim, S and San, BT and Koc-San, D and Selim, C},
title = {A two-level approach to geospatial identification of optimal pitaya cultivation sites using multi-criteria decision analysis.},
journal = {Journal of the science of food and agriculture},
volume = {105},
number = {11},
pages = {5851-5862},
doi = {10.1002/jsfa.14297},
pmid = {40270457},
issn = {1097-0010},
mesh = {*Fruit/growth &amp; development/chemistry ; Geographic Information Systems ; Decision Support Techniques ; *Cactaceae/growth &amp; development/chemistry ; Soil/chemistry ; Temperature ; },
abstract = {BACKGROUND: Pitaya, also known as dragon fruit, is one of the most popular and expensive fruits in the world. It has been commercially produced since the early 20th century. This plant requires a specific growing environment and ecological conditions, so it is typically cultivated under greenhouse conditions in Türkiye. However, there is a clear need for a comprehensive assessment of outdoor adaptation and/or outdoor growing areas for sustainable yield at the regional scale.<br><br>RESULTS: This study presents a multi-criteria decision-making analysis-based geographical information system (GIS) study to identify and evaluate the suitability of outdoor growing areas for pitaya. In this study, eight crucial factors were identified for outdoor pitaya cultivation: temperature, rainfall, soil pH, soil depth, land use capability, altitude, slope and aspect. An analytical hierarchy process was conducted to determine the weights for each parameter, followed by a weighted overlay analysis using GIS tools. The range of weight values was obtained between 0.2748 and 0.0319. The area of the best places for pitaya cultivation was calculated to be 9245.7&#x2009;ha (11.7%). It was determined that 32.63%, 37.57% and 18.1% of the locations were moderately suitable, less appropriate and unsuitable, respectively.<br><br>CONCLUSION: The selection of comparable production sites will be guided by the study. Such suitable site selection studies are extremely significant since the cultivation of the pitaya plant, which has a high commercial value for economically developing countries, will be crucial to the growth of agricultural employment in these nations. Future research will be guided by this study's methodology and analysis strategies. &#xa9; 2025 Society of Chemical Industry.},
}
@article {pmid40273037,
year = {2025},
author = {Wu, KC and Belza, B and L Berry, D and M Lewis, F and L Hartzler, A and Zaslavsky, O},
title = {UTI risk factors in older people living with dementia: A conceptual framework and a scoping review.},
journal = {Dementia (London, England)},
volume = {24},
number = {7},
pages = {1417-1446},
doi = {10.1177/14713012251326129},
pmid = {40273037},
issn = {1741-2684},
mesh = {Humans ; *Dementia/complications ; Risk Factors ; *Urinary Tract Infections/prevention &amp; control/epidemiology ; Aged ; },
abstract = {Background and Aims: UTIs greatly impact hospitalization rates for people living with dementia. This study aims to craft a framework through a scoping review, assessing UTI symptoms, risk factors, and non-pharmacological prevention strategies in older people living with dementia. Research Design and Methods: Our scoping review followed PRISMA-ScR guidelines, exploring databases (PubMed, CINAHL, Embase, Web of Science) for topics like geriatric care, urinary tract issues published from January 1977 to April 2023. Two reviewers assessed data, organizing it using the Social-Ecological Model to construct the UTI Prevention (UTIP) framework. Results: The literature review scrutinized 1394 articles, selecting 14 through rigorous evaluation. It detailed demographic characteristics, synthesized UTI symptoms, 14 risk factors, and seven outcomes for older people living with dementia. Moreover, it outlined ten preventive domains and proposed a comprehensive UTI Prevention (UTIP) framework spanning individual, relational, community, and societal levels. This framework aims to prevent UTIs among older people living with dementia, integrating risk factors and outcomes to bolster effective prevention strategies for this population. Discussion and Implications: The review introduced a UTIP framework, and non-pharmacological preventive measures tailored for elderly people living with dementia. However, some factors in the framework require further validation to strengthen their associations with outcomes. Preventive measures from studies had limitations like small sample sizes, bias risks, and inconsistent findings. Future research should prioritize robust randomized trials with strong statistical power, strict criteria, and consistent individual-level interventions to boost outcome reliability and validity. Such efforts will enhance the credibility of findings and contribute significantly to refining preventive strategies for this vulnerable population.},
}
@article {pmid40273274,
year = {2025},
author = {Chen, N},
title = {The impact of the rural digital economy on China's new-type urbanization.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321663},
pmid = {40273274},
issn = {1932-6203},
mesh = {China ; *Urbanization/trends ; *Rural Population ; Humans ; *Economic Development/trends ; Agriculture ; },
abstract = {The Chinese government is vigorously implementing the rural revitalization strategy and accelerating the process of new-type urbanization. The rapid development of the rural digital economy has emerged as a new driving force for new-type urbanization. This study aims to explore how the rural digital economy impacts China's new-type urbanization from direct, heterogeneous, and indirect perspectives. Using the provincial-level panel data in China from 2014 to 2022, a mixed-methods approach is employed for the empirical research. The CRITIC and Entropy TOPSIS are used to assess the comprehensive development level and temporal characteristics of the rural digital economy and new-type urbanization. Moreover, a global-local auto-correlation analysis is carried out to depict the spatial distribution of the two variables. Subsequently, a two-way fixed effects model is constructed to verify the direct impact of the rural digital economy on new-type urbanization, as well as its structural and spatial heterogeneity characteristics. Finally, an mediating effect model is established to explore the impact paths through which the rural digital economy impacts new-type urbanization. The results show that the rural digital economy has significantly promoted new-type urbanization. Specifically, rural digital infrastructure, digital transformation of agriculture, agricultural production service informatization have a significant positive effect, while the role of rural life digitization is not significant. The rural digital economy has more significant positive impact on population agglomeration and economic growth, followed by social public service, but has no significant impact on ecological environmental protection and urban-rural coordination. Additionally, the qualitative analysis identifies geographical region, poverty, demographic structure and social equality as notable influencing factors in this impact. Further mechanism analysis result indicates that the rural digital economy impacts new-type urbanization through rural human capital improvement, agricultural economic growth and rural industrial structure upgrading. This research contributes to the existing body of knowledge by providing the practical path of rural development to promote new-type urbanization in the context of the digital economy, also clarifies the weak points and key links in this process. It also highlights the need for further research into the institutional factors that influence this relationship to enhances the policy applicability.},
}
@article {pmid40273607,
year = {2025},
author = {Nkoh, JN and Ye, T and Shang, C and Li, C and Tu, J and Li, S and Wu, Z and Chen, P and Hussain, Q and Esemu, SN},
title = {Deciphering the mechanisms for preferential tolerance of Escherichia coli BL21 to Cd(II) over Cu(II) and Ni(II): A combined physiological, biochemical, and multiomics perspective.},
journal = {Ecotoxicology and environmental safety},
volume = {297},
number = {},
pages = {118195},
doi = {10.1016/j.ecoenv.2025.118195},
pmid = {40273607},
issn = {1090-2414},
mesh = {*Escherichia coli/drug effects/physiology/metabolism ; *Cadmium/toxicity ; *Nickel/toxicity ; *Copper/toxicity ; Oxidative Stress/drug effects ; Escherichia coli Proteins/metabolism/genetics ; Hydrogen Peroxide/metabolism ; Multiomics ; },
abstract = {Environmental pollution severely affects ecological functions/health, and nondegradable pollutants such as heavy metals (HMs) cause significant damage to living organisms. Escherichia coli is one of the most studied life forms, and its response to oxidative stress is driven by a complex ensemble of mechanisms driven by transcriptomic-level adjustments. However, the magnitude of the physiological, metabolic, and biochemical alterations and their relationships with transcriptomic changes remain unclear. Studying the growth of E. coli in Cd-, Cu-, and Ni-polluted media at pH 5.0, we observed that (i) downregulation of the alkyl hydroperoxide complex, glutathione reductase, and glutathione S-transferase by Cd inhibited H2O2 degradation, and the accumulated H2O2 was respectively 2.7, 1.7, and 2.4 times greater than that in the control, Cu, and Ni treatments; (ii) Zn-associated resistance protein (ZraP) was the major scavenger of Cd, with a 140.7-fold increase in its expression; (iii) the P-type Cu[+] transporter (CopA), multicopper oxidase (CueO), and heteromultimeric transport system (CusCBAF) controlled the excretion and detoxification of Cu; (iv) the Cd[2+]/Zn[2+]/Pb[2+]-exporting P-type ATPase (ZntA) and transcriptional activator ZntR were the major transporters of Ni; (v) Cd upregulated biofilm formation and synthesis of secondary metabolites more than Cu and Ni, which resulted in increased adsorption and improved tolerance; and (vi) the activity of superoxide dismutase in Cu-spiked cells was 153.2 %, 141.7 %, and 172.7 % higher and corresponded to 85.7 %, 524.5 %, and 491.5 % lower O2[●][-] in the control, Cd-, and Ni-spiked cells, respectively. This study reveals E. coli's preferential tolerance mechanisms to Cd rather than Cu and Ni and demonstrates mechanisms for its survival in highly polluted environments.},
}
@article {pmid40275133,
year = {2025},
author = {Antala, M and Kovar, M and Sporinová, L and Filacek, A and Juszczak, R and Zivcak, M and Shomali, A and Prasad, R and Brestic, M and Rastogi, A},
title = {Correction: High-throughput phenotyping of buckwheat (Fagopyrum esculentum Moench.) genotypes under water stress: exploring drought resistance for sustainable agriculture.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {517},
pmid = {40275133},
issn = {1471-2229},
}
@article {pmid40275196,
year = {2025},
author = {Li, Q},
title = {Assessing and adjusting for bias in ecological analysis using multiple sample datasets.},
journal = {BMC medical research methodology},
volume = {25},
number = {1},
pages = {112},
pmid = {40275196},
issn = {1471-2288},
support = {P2C HD042854/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; Bias ; Kenya ; *Ecology/methods ; *Datasets as Topic ; Health Surveys ; Models, Statistical ; Data Interpretation, Statistical ; Computer Simulation ; },
abstract = {BACKGROUND: Ecological analysis utilizes group-level aggregate measures to investigate the complex relationships between individuals or groups and their environment. Despite its extensive applications across various disciplines, this approach remains susceptible to several biases, including ecological fallacy.<br><br>METHODS: Our study identified another significant source of bias in ecological analysis when using multiple sample datasets, a common practice in fields such as public health and medical research. We show this bias is proportional to the sampling fraction used during data collection. We propose two adjustment methods to address this bias: one that directly accounts for the sampling fraction and another based on measurement error models. The effectiveness of these adjustments is evaluated through formal mathematical derivations, simulations, and empirical analysis using data from the 2014 Kenya Demographic and Health Survey.<br><br>RESULTS: Our findings reveal that the sampling fraction bias can lead to significant underestimation of true relationships when using aggregate measures from multiple sample datasets. Both adjustment methods effectively mitigate this bias, with the measurement-error-adjusted estimator showing particular robustness in real-world applications. The results highlight the importance of accounting for sampling fraction bias in ecological analyses to ensure accurate inference.<br><br>CONCLUSION: Beyond the ecological fallacy uncovered by Robinson's seminar work, our research identified another critical bias in ecological analysis that is likely just as prevalent and consequential. The proposed adjustment methods provide potential tools for researchers to adjust for this bias, thereby improving the validity of ecological inferences. This study underscores the need for caution when pooling aggregate measures from multiple sample datasets and offers potential solutions to enhance the reliability of ecological analyses in various research domains.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid40276974,
year = {2025},
author = {Blin, K and Shaw, S and Vader, L and Szenei, J and Reitz, ZL and Augustijn, HE and Cediel-Becerra, JDD and de Crécy-Lagard, V and Koetsier, RA and Williams, SE and Cruz-Morales, P and Wongwas, S and Segurado Luchsinger, AE and Biermann, F and Korenskaia, A and Zdouc, MM and Meijer, D and Terlouw, BR and van der Hooft, JJJ and Ziemert, N and Helfrich, EJN and Masschelein, J and Corre, C and Chevrette, MG and van Wezel, GP and Medema, MH and Weber, T},
title = {antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation.},
journal = {Nucleic acids research},
volume = {53},
number = {W1},
pages = {W32-W38},
pmid = {40276974},
issn = {1362-4962},
support = {//Hessian Ministry for Science and the Arts/ ; MSC 101072485//Horizon Europe Programme/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; 948770//Horizon 2020/ ; DNRF137//Danish National Research Foundation/ ; 101000392//Horizon 2020/ ; //Translational Biodiversity Genomics/ ; //Microbial Secondary Metabolites/ ; RM1GM145426/NH/NIH HHS/United States ; KICH1.LWV04.21.013//NWO/ ; 101055020//ERC/ ; G061821N//FWO/ ; R01 GM070641/GM/NIGMS NIH HHS/United States ; I008520N//FWO/ ; NNF22OC0079021//Novo Nordisk Foundation/ ; 504947087//German Research Foundation/ ; //The Royal Thai Government/ ; RM1 GM145426/GM/NIGMS NIH HHS/United States ; TTU09.716//German Center for Infection Research/ ; OCENW.XL21.XL21.088//ERC/ ; },
mesh = {*Multigene Family ; *Genetic Techniques ; *Software ; *Polyketide Synthases/metabolism ; *Peptide Synthases/metabolism ; Terpenes/chemistry ; },
abstract = {Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in microbial interactions and soil health, but are also crucial for the development of pharmaceuticals or agrochemicals. Over the past decades, advancements in genome sequencing have enabled the identification of large numbers of biosynthetic gene clusters directly from microbial genomes. Since its inception in 2011, antiSMASH (https://antismash.secondarymetabolites.org/), has become the leading tool for detecting and characterizing these gene clusters in bacteria and fungi. This paper introduces version 8 of antiSMASH, which has increased the number of detectable cluster types from 81 to 101, and has improved analysis support for terpenoids and tailoring enzymes, as well as improvements in the analysis of modular enzymes like polyketide synthases and nonribosomal peptide synthetases. These modifications keep antiSMASH up-to-date with developments in the field and extend its overall predictive capabilities for natural product genome mining.},
}
@article {pmid40277515,
year = {2025},
author = {Kargarandehkordi, A and Li, S and Lin, K and Phillips, KT and Benzo, RM and Washington, P},
title = {Fusing Wearable Biosensors with Artificial Intelligence for Mental Health Monitoring: A Systematic Review.},
journal = {Biosensors},
volume = {15},
number = {4},
pages = {},
pmid = {40277515},
issn = {2079-6374},
support = {MedRes_2023_00002689//Hawai'i Community Foundation/ ; 2406251//U.S. National Science Foundation/ ; 1U54GM138062-02A1/NH/NIH HHS/United States ; U54 GM138062/GM/NIGMS NIH HHS/United States ; U54GM138062/GM/NIGMS NIH HHS/United States ; },
mesh = {*Wearable Electronic Devices ; *Biosensing Techniques ; Humans ; *Artificial Intelligence ; *Mental Health ; Monitoring, Physiologic ; Heart Rate ; },
abstract = {The development of digital instruments for mental health monitoring using biosensor data from wearable devices can enable remote, longitudinal, and objective quantitative benchmarks. To survey developments and trends in this field, we conducted a systematic review of artificial intelligence (AI) models using data from wearable biosensors to predict mental health conditions and symptoms. Following PRISMA guidelines, we identified 48 studies using a variety of wearable and smartphone biosensors including heart rate, heart rate variability (HRV), electrodermal activity/galvanic skin response (EDA/GSR), and digital proxies for biosignals such as accelerometry, location, audio, and usage metadata. We observed several technical and methodological challenges across studies in this field, including lack of ecological validity, data heterogeneity, small sample sizes, and battery drainage issues. We outline several corresponding opportunities for advancement in the field of AI-driven biosensing for mental health.},
}
@article {pmid40278529,
year = {2025},
author = {Fabio, RA and Semino, M and Perina, M and Martini, M and Riccio, E and Pili, G and Pani, D and Chessa, M},
title = {Virtual Reality as a Tool for Upper Limb Rehabilitation in Rett Syndrome: Reducing Stereotypies and Improving Motor Skills.},
journal = {Pediatric reports},
volume = {17},
number = {2},
pages = {},
pmid = {40278529},
issn = {2036-749X},
abstract = {BACKGROUND/OBJECTIVES: Rett Syndrome (RTT) is a rare neurodevelopmental disorder that causes the loss of motor, communicative, and cognitive skills. While no cure exists, rehabilitation plays a crucial role in improving quality of life. Virtual Reality (VR) has shown promise in enhancing motor function and reducing stereotypic behaviors in RTT. This study aims to assess the impact of VR training on upper limb motor skills in RTT patients, focusing on reaching and hand-opening tasks, as well as examining its role in motivation and engagement during rehabilitation.<br><br>METHODS: Twenty RTT patients (aged 5-33) were randomly assigned to an experimental group (VR training) and a control group (standard rehabilitation). Pre- and post-tests evaluated motor skills and motivation in both VR and real-world contexts. The VR training involved 40 sessions over 8 weeks, focusing on fine motor tasks. Non-parametric statistical methods were used to analyze the data.<br><br>RESULTS: Results indicated significant improvements in the experimental group for motor parameters, including reduced stereotypy intensity and frequency, faster response times, and increased correct performance. These improvements were consistent across VR and ecological conditions. Moreover, attention time increased, while the number of aids required decreased, highlighting enhanced engagement and independence. However, motivation levels remained stable throughout the sessions.<br><br>CONCLUSIONS: This study demonstrates the potential of VR as a tool for RTT rehabilitation, addressing both motor and engagement challenges. Future research should explore the customization of VR environments to maximize the generalization of skills and sustain motivation over extended training periods.},
}
@article {pmid40284070,
year = {2025},
author = {Lu, F and Yi, B and Qin, K and Bu, ZJ},
title = {Long-Term Nitrogen Addition Eliminates the Cooling Effect on Climate in a Temperate Peatland.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
pmid = {40284070},
issn = {2223-7747},
support = {U23A2003//National Natural Science Foundation of China/ ; 42407354//National Natural Science Foundation of China/ ; 42371050//National Natural Science Foundation of China/ ; 20210402032GH//Jilin Provincial Science and Technology Development Pro-ject/ ; 20230203002SF//Jilin Provincial Science and Technology Development Pro-ject/ ; JP230021//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Peatlands play a crucial role in global carbon (C) sequestration, but their response to long-term nitrogen (N) deposition remains uncertain. This study investigates the effects of 12 years of simulated N addition on CO2 and CH4 fluxes in a temperate peatland through in situ monitoring. The results demonstrate that long-term N addition significantly reduces net ecosystem exchange (NEE), shifting the peatland from a C sink to a C source. This transition is primarily driven by a decline in aboveground plant productivity, as Sphagnum mosses were suppressed and even experienced mortality, while graminoid plants thrived under elevated N conditions. Although graminoid cover increased, it did not compensate for the GPP loss caused by Sphagnum decline. Instead, it further increased CH4 emissions. These findings suggest that sustained N input may diminish the C sequestration function of peatlands, significantly weakening their global cooling effect.},
}
@article {pmid40286830,
year = {2025},
author = {Yu, X and Yao, R and Yao, R and Jin, X and Huang, J and Liang, Q and Jin, LN and Sun, J},
title = {Mechanistic understanding of the toxic effects of tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP) to Escherichia coli: Evidence from alterations in biomarker expression and perturbations of the metabolic network.},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {295},
number = {},
pages = {110211},
doi = {10.1016/j.cbpc.2025.110211},
pmid = {40286830},
issn = {1532-0456},
mesh = {*Escherichia coli/drug effects/metabolism ; Oxidative Stress/drug effects ; Biomarkers/metabolism ; *Organophosphates/toxicity ; *Metabolic Networks and Pathways/drug effects ; *Flame Retardants/toxicity ; Reactive Oxygen Species/metabolism ; Metabolomics ; Escherichia coli Proteins/metabolism ; *Plasticizers/toxicity ; },
abstract = {Tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP), emerging flame retardants and plasticizers, have garnered increasing attention due to their potential risks to ecosystem. A few researches regarding the toxicological mechanisms of TnBP and TCP had been performed, while molecular-level toxic effects of them and metabolic response using microbial models are the lack of relevant investigation. Thus, we investigated the cytotoxicity, oxidative stress response, and metabolic response in E. coli exposed to TnBP and TCP. Exposure to them significantly increased the activities of antioxidant enzymes, indicating activation of the antioxidant defense system. Excessive accumulation of reactive oxygen species (ROS) triggered various biological events, including a reduction in membrane potential (MP), decrease of adenosine triphosphatase (ATPase) activity, and increased malondialdehyde (MDA) content. These findings suggested that oxidative damage compromised membrane proteins function, membrane stability, and intracellular homeostasis. GC-MS and LC-MS-based metabolomics analyses revealed that TnBP and TCP strongly disrupted multiple metabolic pathways, including carbohydrate metabolism, nucleotide metabolism, lipid metabolism, beta-alanine metabolism, pyruvate metabolism and oxidative phosphorylation. These disruptions highlighted the inhibitory effects on molecular functions and metabolic processes. Notably, lipids biomarkers e.g., PC(11:0/16:0), PA(17:1(9Z)/18:2(9Z,12Z)), PE(17:0/14:1(9Z)), and LysoPE(0:0/18:1(11Z)) were significantly altered, verifying that the regulation of lipid-associated metabolite synthesis plays a protective role in maintaining cellular membrane function. In summary, this study enhances our understanding of TnBP and TCP toxicity in E. coli, providing novel insights into their toxicological mechanisms at molecular and network levels. These findings underscore the ecological risks posed by organophosphate flame retardants in aquatic ecosystem.},
}
@article {pmid40286849,
year = {2025},
author = {Bartas, M and Petrovič, M and Brázda, V and Trenz, O and Ďurčanský, A and Šťastný, J},
title = {CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome.},
journal = {The Journal of biological chemistry},
volume = {301},
number = {6},
pages = {108537},
pmid = {40286849},
issn = {1083-351X},
mesh = {Animals ; *CpG Islands ; *Drosophila melanogaster/genetics ; DNA Methylation ; Internet ; *Software ; *Genome, Insect ; },
abstract = {With continuous advances in DNA sequencing methods, accessibility to high-quality genomic information for all living organisms is ever-increasing. However, to interpret this information effectively and formulate hypotheses, users often require higher level programming skills. Therefore, the generation of web-based tools is becoming increasingly popular. CpG island regions in genomes are often found in gene promoters and are prone to DNA methylation, with their methylation status determining if a gene is expressed. Notably, understanding the biological impact of CpX modifications on genomic regulation is becoming increasingly important as these modifications have been associated with diseases such as cancer and neurodegeneration. However, there is currently no easy-to-use, scalable tool to detect and quantify CpX islands in full genomes. We have developed a Java-based web server for CpX island analyses that benefits from the DNA Analyzer Web server environment and overcomes several limitations. For a pilot demonstration study, we selected a well-described model organism Drosophila melanogaster. Subsequent analysis of the obtained CpX islands revealed several interesting and previously undescribed phenomena. One of them is the fact, that nearly half of long CpG islands were located on chromosome X, and that long CpA and CpT islands were significantly overrepresented at the subcentromeric regions of autosomes (chr2 and chr3) and also on chromosome Y. Wide genome overlays of predicted CpX islands revealed their co-occurrence with various (epi)genomics features comprising cytosine methylations, accessible chromatin, transposable elements, or binding of transcription factors and other proteins. CpX Hunter is freely available as a web tool at: https://bioinformatics.ibp.cz/#/analyse/cpg.},
}
@article {pmid40287646,
year = {2025},
author = {He, L and Zou, Q and Wang, Y},
title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {111},
pmid = {40287646},
issn = {1471-2105},
support = {62102269//National Natural Science Foundation of China/ ; },
mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Software ; *Gene Expression Profiling/methods ; *Microbiota ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation ; },
abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.<br><br>RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.<br><br>CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .},
}
@article {pmid40287826,
year = {2025},
author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT},
title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.},
journal = {Nucleic acids research},
volume = {53},
number = {8},
pages = {},
pmid = {40287826},
issn = {1362-4962},
support = {DBI1356288NSF//NSF/ ; },
mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; },
abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.},
}
@article {pmid40287834,
year = {2025},
author = {Mohanty, A and Srinivasan, A and Udupaa, P and Catchpoole, D},
title = {Multiomics and tumor banking: comprehensive plaforms- integrating cancer diversity, biomarker discovery and personalised cancer care in India.},
journal = {Human molecular genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/hmg/ddaf033},
pmid = {40287834},
issn = {1460-2083},
abstract = {Biobanks are innovative biomedical research infrastructures that play a crucial role in advancing cancer research by supporting investigations into the etiology, progression, and therapeutic interventions of the disease. Biobanks have significantly contributed to personalized medicine by providing high-quality bio specimen resources and expertise in tissue handling, essential for understanding the interplay of genetic, ecological, and lifestyle factors on cancer biology, human health, and mortality. By linking bio specimens with clinical, pathological, and epidemiological data, biobanks are central in the discovery and development of cancer therapeutics through biomarkers. In this review, the importance of managing biobanks as integral parts of data generation and analytics continuum driving precision medicine is pointed out. The advent of multi-OMICS analytics, combined with artificial intelligence, systems biology, and deep machine learning, has elevated the importance of bio banking human bio specimens as not only a biological resource but also an informatics asset. Here, we examine the impact of bio banking in facilitating translational, bench-to-bedside cancer research, with a focus on multi-OMICS data-driven biomarker discovery and precision oncology. In addition, we discuss one of the major innovations in biobank management: the hub-and-spoke model. This centralized system leverages core expertise and resources while collecting bio specimens from diverse geographic regions, thereby capturing the heterogeneity of cancer biology. The hub-and-spoke approach is particularly advantageous for countries like India, characterized by vast geographic and demographic diversity. It ensures complete coverage of the different types of cancers, disease stages, and population groups in addressing the complexity and diversity of cancer biology.},
}
@article {pmid40288322,
year = {2025},
author = {Zhou, H and Wu, Z and Wang, X and Jiang, L and Sun, H and Li, H and Yan, Z and Wang, Y and Yao, X and Zhang, C and Tang, J},
title = {6PPD-quinone exposure induces oxidative damage and physiological disruption in Eisenia fetida: An integrated analysis of phenotypes, multi-omics, and intestinal microbiota.},
journal = {Journal of hazardous materials},
volume = {493},
number = {},
pages = {138334},
doi = {10.1016/j.jhazmat.2025.138334},
pmid = {40288322},
issn = {1873-3336},
mesh = {*Oligochaeta/drug effects/physiology/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Soil Pollutants/toxicity ; *Oxidative Stress/drug effects ; *Phenylenediamines/toxicity ; Phenotype ; Reactive Oxygen Species/metabolism ; Metabolomics ; Transcriptome/drug effects ; Multiomics ; Benzoquinones ; },
abstract = {The environmental prevalence of the tire wear-derived emerging pollutant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q) has increasingly raised public concern. However, knowledge of the adverse effects of 6PPD-Q on soil fauna is scarce. In this study, we elucidated its impact on soil fauna, specifically on the earthworm Eisenia fetida. Our investigation encompassed phenotypic, multi-omics, and microbiota analyses to assess earthworm responses to a gradient of 6PPD-Q contamination (10, 100, 1000, and 5000 μg/kg dw soil). Post-28-day exposure, 6PPD-Q was found to bioaccumulate in earthworms, triggering reactive oxygen species production and consequent oxidative damage to coelomic and intestinal tissues. Transcriptomic and metabolomic profiling revealed several physiological perturbations, including inflammation, immune dysfunction, metabolic imbalances, and genetic toxicity. Moreover, 6PPD-Q perturbed the intestinal microbiota, with high dosages significantly suppressing microbial functions linked to metabolism and information processing (P < 0.05). These alterations were accompanied by increased mortality and weight loss in the earthworms. Specifically, at an environmental concentration of 6PPD-Q (1000 μg/kg), we observed a substantial reduction in survival rate and physiological disruptions. This study provides important insights into the environmental hazards of 6PPD-Q to soil biota and reveals the underlying toxicological mechanisms, underscoring the need for further research to mitigate its ecological footprint.},
}
@article {pmid40292044,
year = {2025},
author = {Edelson, JB and Huang, J and Wang, Z and Tam, V and Lefktowitz, D and O'Connor, MJ and White, R and Ha, L and Wittlieb-Weber, CA and Rossano, JW and Lin, K and Cousino, MK and Lane-Fall, M and O'Byrne, ML},
title = {Identifying the determinants of health-related quality of life in children after heart transplant.},
journal = {JHLT open},
volume = {8},
number = {},
pages = {100250},
pmid = {40292044},
issn = {2950-1334},
support = {K23 HL169833/HL/NHLBI NIH HHS/United States ; },
abstract = {BACKGROUND: Pediatric heart transplant (PHT) recipients have impaired health-related quality of life (HRQOL) that is not fully explained by cardiac limitations. Environment is known to influence HRQOL in other chronic disease populations but is less understood in PHT. Understanding the determinants of HRQOL is a necessary step in identifying high-risk groups and designing actionable interventions.<br><br>METHODS: This cross-sectional study includes 8- to 18-year heart transplant (HT) recipients and their families. Generalized estimating equations were used to evaluate the associations of individual characteristics (diagnosis, pulmonary capillary wedge pressure [PCWP], cardiac index [CI]), microenvironment (parent education level, financial security, parental stress [PSI], assessment of child anxiety) and macroenvironment [Child Opportunity Index (COI)] with HRQOL.<br><br>RESULTS: Of 31 participants, 32% self-identified as Black, and 40% had congenital heart disease. On cardiac catheterization, 61% had a CI &#x2265;3&#xa0;liter/min/m[2] and PCWP &#x2264;10&#xa0;mm&#xa0;Hg. Most households had &#x2265;1 parent who had completed college (58%); 28% of households expressed difficulty paying bills. The PSI showed elevated parental stress [64.5 (interquartile range [IQR] 52.0, 77.8)], while the COI was low [73.0 (IQR 44.5, 89.0)] as was HRQOL [Pediatric Quality of Life 4.0 Core Scales 71.7 (IQR 64.2-82.5), Pediatric Cardiac Quality of Life Index 61.8 (IQR 55.7-74.8)]. Higher parental stress (p = 0.036), higher parental perception of child anxiety (p = 0.058), lower Max VO2 (p = 0.059), and higher PCWP (p = 0.006) were independently associated with worse quality of life.<br><br>CONCLUSIONS: HRQOL in children after heart transplant is reduced and determined not only by traditional measures of cardiovascular function, but also by patient psychology and their household environment, highlighting the utility of using an adapted ecological systems framework to understand HRQOL.},
}
@article {pmid40292360,
year = {2025},
author = {Andersen, ZJ and Badyda, A and Tzivian, L and Dzhambov, AM and Paunovic, K and Savic, S and Jacquemin, B and Dragic, N},
title = {Air pollution inequalities in Europe: A deeper understating of challenges in Eastern Europe and pathways forward towards closing the gap between East and West.},
journal = {Environmental epidemiology (Philadelphia, Pa.)},
volume = {9},
number = {3},
pages = {e383},
pmid = {40292360},
issn = {2474-7882},
}
@article {pmid40293859,
year = {2025},
author = {Wastler, HM and Cowan, HR and Breitborde, NJK and Tabares, JV and Yu, M and Pan, X and Boettner, B and Browning, C and Bryan, CJ},
title = {Ecological Momentary Assessment of Emotion Regulation and Suicidal Ideation in First-Episode Psychosis.},
journal = {Schizophrenia bulletin},
volume = {51},
number = {6},
pages = {1718-1729},
pmid = {40293859},
issn = {1745-1701},
support = {YIG-0-184-20//American Foundation for Suicide Prevention/ ; },
mesh = {Humans ; *Ecological Momentary Assessment ; *Suicidal Ideation ; *Psychotic Disorders/physiopathology ; Male ; Female ; *Emotional Regulation/physiology ; Adult ; Young Adult ; Adolescent ; *Affect/physiology ; },
abstract = {Individuals with first-episode psychosis (FEP) are at increased risk for suicide, though few studies have examined the extent to which emotion regulation abnormalities contribute to this risk. The current study sought to address this gap by examining which stages of emotion regulation (ie, identification, selection, implementation) are related to suicidal ideation among individuals with FEP. Forty-one participants completed 28 days of ecological momentary assessment to assess suicidal ideation, negative affect, and emotion regulation in real-time. Results indicated that all 3 stages of emotion regulation were related to suicidal ideation in FEP. Specifically, within-person emotion regulation interacted with between-person negative affect to predict concurrent suicidal ideation (identification stage). Additionally, decreased use of adaptive strategies and increased use of maladaptive strategies were associated with more severe suicidal ideation (selection stage). Finally, decreased emotion regulation effectiveness was associated with more severe suicidal ideation (implementation stage). These findings suggest that emotion regulation difficulties might contribute to the high rates of suicide risk among individuals with FEP. Additional research is needed to determine whether these emotion regulation difficulties are unique to FEP or if they also appear in other high-risk groups.},
}
@article {pmid40294093,
year = {2025},
author = {Williams, B and Balvanera, SM and Sethi, SS and Lamont, TAC and Jompa, J and Prasetya, M and Richardson, L and Chapuis, L and Weschke, E and Hoey, A and Beldade, R and Mills, SC and Haguenauer, A and Zuberer, F and Simpson, SD and Curnick, D and Jones, KE},
title = {Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1013029},
pmid = {40294093},
issn = {1553-7358},
mesh = {*Coral Reefs ; Animals ; Acoustics ; *Unsupervised Machine Learning ; *Artificial Intelligence ; Ecosystem ; Algorithms ; Neural Networks, Computer ; Computational Biology ; Fishes/physiology ; Machine Learning ; Environmental Monitoring/methods ; },
abstract = {Passive acoustic monitoring can offer insights into the state of coral reef ecosystems at low-costs and over extended temporal periods. Comparison of whole soundscape properties can rapidly deliver broad insights from acoustic data, in contrast to detailed but time-consuming analysis of individual bioacoustic events. However, a lack of effective automated analysis for whole soundscape data has impeded progress in this field. Here, we show that machine learning (ML) can be used to unlock greater insights from reef soundscapes. We showcase this on a diverse set of tasks using three biogeographically independent datasets, each containing fish community (high or low), coral cover (high or low) or depth zone (shallow or mesophotic) classes. We show supervised learning can be used to train models that can identify ecological classes and individual sites from whole soundscapes. However, we report unsupervised clustering achieves this whilst providing a more detailed understanding of ecological and site groupings within soundscape data. We also compare three different approaches for extracting feature embeddings from soundscape recordings for input into ML algorithms: acoustic indices commonly used by soundscape ecologists, a pretrained convolutional neural network (P-CNN) trained on 5.2 million hrs of YouTube audio, and CNN's which were trained on each individual task (T-CNN). Although the T-CNN performs marginally better across tasks, we reveal that the P-CNN offers a powerful tool for generating insights from marine soundscape data as it requires orders of magnitude less computational resources whilst achieving near comparable performance to the T-CNN, with significant performance improvements over the acoustic indices. Our findings have implications for soundscape ecology in any habitat.},
}
@article {pmid40295704,
year = {2024},
author = {Grunnill, M and Eshaghi, A and Damodaran, L and Nagra, S and Gharouni, A and Braukmann, T and Clark, S and Peci, A and Isabel, S and Banh, P and Plessis, LD and Murall, CL and Colijn, C and Mubareka, S and Hasso, M and Bahl, J and Mostafa, HH and Gubbay, JB and Patel, SN and Wu, J and Duvvuri, VR},
title = {Inferring enterovirus D68 transmission dynamics from the genomic data of two 2022 North American outbreaks.},
journal = {Npj viruses},
volume = {2},
number = {1},
pages = {34},
pmid = {40295704},
issn = {2948-1767},
abstract = {Enterovirus D68 (EV-D68) has emerged as a significant cause of acute respiratory illness in children globally, notably following its extensive outbreak in North America in 2014. A recent outbreak of EV-D68 was observed in Ontario, Canada, from August to October 2022. Our phylogenetic analysis revealed a notable genetic similarity between the Ontario outbreak and a concurrent outbreak in Maryland, USA. Utilizing Bayesian phylodynamic modeling on whole genome sequences (WGS) from both outbreaks, we determined the median peak time-varying reproduction number (Rt) to be 2.70, 95% HPD (1.76, 4.08) in Ontario and 2.10, 95% HPD (1.41, 3.17) in Maryland. The Rt trends in Ontario closely matched those derived via EpiEstim using reported case numbers. Our study also provides new insights into the median infection duration of EV-D68, estimated at 7.94 days, 95% HPD (4.55, 12.8) in Ontario and 10.8 days, 95% HPD (5.85, 18.6) in Maryland, addressing the gap in the existing literature surrounding EV-D68's infection period. We observed that the estimated Time since the Most Recent Common Ancestor (TMRCA) and the epidemic's origin coincided with the easing of COVID-19 related social contact restrictions in both areas. This suggests that the relaxation of non-pharmaceutical interventions, initially implemented to control COVID-19, may have inadvertently facilitated the spread of EV-D68. These findings underscore the effectiveness of phylodynamic methods in public health, demonstrating their broad application from local to global scales and underscoring the critical role of pathogen genomic data in enhancing public health surveillance and outbreak characterization.},
}
@article {pmid40295976,
year = {2025},
author = {Liberati, F and Pose Marino, TM and Bottoni, P and Canestrelli, D and Castrignanò, T},
title = {HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {113},
pmid = {40295976},
issn = {1471-2105},
mesh = {*Software ; *Transcriptome ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Computational Biology/methods ; Databases, Genetic ; RNA-Seq/methods ; },
abstract = {BACKGROUND: Recent years have seen a substantial increase in RNA-seq data production, with this technique becoming the primary approach for gene expression studies across a wide range of non-model organisms. The majority of these organisms lack a well-annotated reference genome to serve as a basis for studying differentially expressed genes (DEGs). As an alternative cost-effective protocol to using a reference genome, the assembly of RNA-seq raw reads is performed to produce what is referred to as a 'de novo transcriptome,' serving as a reference for subsequent DEGs' analysis. This assembly step for conventional DEGs analysis pipelines for non-model organisms is a computationally expensive task. Furthermore, the complexity of the de novo transcriptome assembly workflows poses a challenge for researchers in implementing best-practice techniques and the most recent software versions, particularly when applied to various organisms of interest.<br><br>RESULTS: To address computational challenges in transcriptomic analyses of non-model organisms, we present HPC-T-Assembly, a tool for de novo transcriptome assembly from RNA-seq data on high-performance computing (HPC) infrastructures. It is designed for straightforward setup via a Web-oriented interface, allowing analysis configuration for several species. Once configuration data is provided, the entire parallel computing software for assembly is automatically generated and can be launched on a supercomputer with a simple command line. Intermediate and final outputs of the assembly pipeline include additional post-processing steps, such as assembly quality control, ORF prediction, and transcript count matrix construction.<br><br>CONCLUSION: HPC-T-Assembly allows users, through a user-friendly Web-oriented interface, to configure a run for simultaneous assemblies of RNA-seq data from multiple species. The parallel pipeline, launched on HPC infrastructures, significantly reduces computational load and execution times, enabling large-scale transcriptomic and meta-transcriptomics analysis projects.},
}
@article {pmid40296452,
year = {2025},
author = {Wang, S and Kaur, S and Kunath, BJ and May, P and Richardson, L and Rogers, AB and Wilmes, P and Finn, RD and Vizcaíno, JA},
title = {An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.},
journal = {Proteomics},
volume = {25},
number = {17-18},
pages = {33-42},
pmid = {40296452},
issn = {1615-9861},
support = {/WT_/Wellcome Trust/United Kingdom ; 223745/Z/21/Z//Wellcome/ ; //EMBL Core Funding/ ; C19/BM/13684739//National Research Fund Luxembourg (FNR)/ ; },
mesh = {*Metagenomics/methods ; *Proteomics/methods ; Humans ; Databases, Protein ; Metagenome ; *Transcriptome ; Animals ; Pilot Projects ; },
abstract = {The availability of public metaproteomics, metagenomics and metatranscriptomics data in public resources such as MGnify (for metagenomics/metatranscriptomics) and the PRIDE database (for metaproteomics), continues to increase. When these omics techniques are applied to the same samples, their integration offers new opportunities to understand the structure (metagenome) and functional expression (metatranscriptome and metaproteome) of the microbiome. Here, we describe a pilot study aimed at integrating public multi-meta-omics datasets from studies based on human gut and marine hatchery samples. Reference search databases (search DBs) were built using assembled metagenomic (and metatranscriptomic, where available) sequence data followed by de novo gene calling, using both data from the same sampling event and from independent samples. The resulting protein sets were evaluated for their utility in metaproteomics analysis. In agreement with previous studies, the highest number of peptide identifications was generally obtained when using search DBs created from the same samples. Data integration of the multi-omics results was performed in MGnify. For that purpose, the MGnify website was extended to enable the visualisation of the resulting peptide/protein information from three reanalysed metaproteomics datasets. A workflow (https://github.com/PRIDE-reanalysis/MetaPUF) has been developed allowing researchers to perform equivalent data integration, using paired multi-omics datasets. This is the first time that a data integration approach for multi-omics datasets has been implemented from public data available in the world-leading MGnify and PRIDE resources.},
}
@article {pmid40297776,
year = {2025},
author = {Schwarzerova, J and Olesova, D and Jureckova, K and Kvasnicka, A and Kostoval, A and Friedecky, D and Sekora, J and Pomenkova, J and Provaznik, V and Popelinsky, L and Weckwerth, W},
title = {Enhanced metabolomic predictions using concept drift analysis: identification and correction of confounding factors.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf073},
pmid = {40297776},
issn = {2635-0041},
abstract = {MOTIVATION: The increasing use of big data and optimized prediction methods in metabolomics requires techniques aligned with biological assumptions to improve early symptom diagnosis. One major challenge in predictive data analysis is handling confounding factors-variables influencing predictions but not directly included in the analysis.<br><br>RESULTS: Detecting and correcting confounding factors enhances prediction accuracy, reducing false negatives that contribute to diagnostic errors. This study reviews concept drift detection methods in metabolomic predictions and selects the most appropriate ones. We introduce a new implementation of concept drift analysis in predictive classifiers using metabolomics data. Known confounding factors were confirmed, validating our approach and aligning it with conventional methods. Additionally, we identified potential confounding factors that may influence biomarker analysis, which could introduce bias and impact model performance.<br><br>Based on biological assumptions supported by detected concept drift, these confounding factors were incorporated into correction of prediction algorithms to enhance their accuracy. The proposed methodology has been implemented in Semi-Automated Pipeline using Concept Drift Analysis for improving Metabolomic Predictions (SAPCDAMP), an open-source workflow available at https://github.com/JanaSchwarzerova/SAPCDAMP.},
}
@article {pmid40298711,
year = {2025},
author = {Prado, SI and Novais, MAP},
title = {Acute viral bronchiolitis in Brazil: characteristics of length of stay and hospital costs.},
journal = {Ciencia &amp; saude coletiva},
volume = {30},
number = {4},
pages = {e07402023},
doi = {10.1590/1413-81232025304.07402023},
pmid = {40298711},
issn = {1678-4561},
mesh = {Humans ; Brazil ; Infant ; Retrospective Studies ; *Length of Stay/statistics &amp; numerical data/economics ; Acute Disease ; Child, Preschool ; *Hospitalization/economics/statistics &amp; numerical data ; *Bronchiolitis, Viral/economics/therapy/epidemiology ; *Hospital Costs/statistics &amp; numerical data ; Longitudinal Studies ; Male ; Female ; National Health Programs/economics ; },
abstract = {The objective of the study was to evaluate the length of stay in pediatric hospitalizations for acute viral bronchiolitis in the Brazilian Health System (SUS) and the costs of hospitalizations. This was a quantitative, observational, and ecological study, based on a retrospective and longitudinal analysis of data from the Department of Informatics of the Unified Health System (DATASUS; 2012-2021) using descriptive statistics and Tukey's paired test. Regarding the mean value of AIH/HAA Hospital Admission Authorization, among the regions, the high costs of hospitalizations are located more frequent in the Southeast region and the lowest proportion is directed to the corresponds to the North region. In the length of hospital stay among the regions, the shortest mean stay was identified in the Central West region (2.5 days) and the greatest stay in the Northeast region (3.1 days). Considering the age group of one year of life, its representativeness was 57% when compared to the age group of 1-4 years (43%). The fragility of the implementation of primary public policies in the prevention of bronchiolitis contributes to high hospital costs and significant economic impacts on the national healthcare system.},
}
@article {pmid40299786,
year = {2025},
author = {Xiao, Y and Elmasry, M and Bai, JDK and Chen, A and Chen, Y and Jackson, B and Johnson, JO and Prasanna, P and Chen, C and Damaghi, M},
title = {Eco-Evolutionary Guided Pathomic Analysis Detects Biomarkers to Predict Ductal Carcinoma In Situ Upstaging.},
journal = {Cancer research},
volume = {85},
number = {13},
pages = {2537-2547},
doi = {10.1158/0008-5472.CAN-24-2070},
pmid = {40299786},
issn = {1538-7445},
support = {R21CA258493-02S1//National Institutes of Health (NIH)/ ; R01GM148970//National Institute of General Medical Sciences (NIGMS)/ ; U01 CA261841/CA/NCI NIH HHS/United States ; R01 CA297843/CA/NCI NIH HHS/United States ; R01CA272601//National Institutes of Health (NIH)/ ; R01 CA272601/CA/NCI NIH HHS/United States ; U01CA261841//National Institutes of Health (NIH)/ ; R01CA249016//National Institutes of Health (NIH)/ ; R01CA297843//National Institutes of Health (NIH)/ ; },
mesh = {Humans ; Female ; *Breast Neoplasms/pathology/metabolism/diagnosis/genetics ; *Biomarkers, Tumor/metabolism/analysis ; *Carcinoma, Intraductal, Noninfiltrating/pathology/metabolism/diagnosis/genetics ; Tumor Microenvironment ; Retrospective Studies ; Neoplasm Staging ; Disease Progression ; Middle Aged ; Prognosis ; },
abstract = {UNLABELLED: Cancers evolve in a dynamic ecosystem. Thus, characterizing the ecological dynamics of cancer is crucial to understanding cancer evolution, which can lead to the discovery of biomarkers to predict disease progression. Ductal carcinoma in situ (DCIS) is an early-stage breast cancer characterized by abnormal epithelial cell growth confined within the milk ducts, and biomarkers are needed to predict which cases will progress to aggressive disease. In this study, we showed that ecological analysis of hypoxia and acidosis biomarkers can significantly improve prediction of DCIS upstaging. Quantitative analyses were performed on immunohistologic images from a retrospective cohort of DCIS specimens collected from biopsy samples. First, an eco-evolutionary designed approach was developed to define habitats in the tumor intraductal microenvironment based on oxygen diffusion distance. Then, cancer cells with metabolic phenotypes attributed to their habitats were identified, including a hypoxia-responding CA9+ phenotype and an acid-adapted LAMP2b+ phenotype. Whereas these markers have traditionally shown limited, if any, predictive capabilities for DCIS progression when analyzed from an ecological perspective, their power to differentiate between non-upstaged and upstaged DCIS increased significantly. Additionally, the distribution of distinct niches with specific spatial patterns of these biomarkers predicted patient upstaging. The niches were characterized by pattern analysis of both cellular and spatial features. A random forest classifier that was trained and underwent a five-fold validation on the biopsy cohort achieved an AUC of 0.74 for predicting clinical outcome. These results affirm the importance of tumor ecological features in eco-evolutionary-designed approaches for biomarker discovery.<br><br>SIGNIFICANCE: Evolutionary dynamics of the various niches composing the tumor ecosystem can be harnessed for predicting cancer progression, demonstrating how eco-evolutionary-designed approaches can guide biomarkers discovery studies in the era of digital pathology. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI.},
}
@article {pmid40303041,
year = {2024},
author = {McDuie, F and T Overton, C and A Lorenz, A and L Matchett, E and L Mott, A and A Mackell, D and T Ackerman, J and De La Cruz, SEW and Patil, VP and Prosser, DJ and Takekawa, JY and Orthmeyer, DL and Pitesky, ME and Díaz-Muñoz, SL and Riggs, BM and Gendreau, J and Reed, ET and Petrie, MJ and Williams, CK and Buler, JJ and Hardy, MJ and Ladman, BS and Legagneux, P and Bêty, J and Thomas, PJ and Rodrigue, J and Lefebvre, J and Casazza, ML},
title = {Mitigating Risk: Predicting H5N1 Avian Influenza Spread with an Empirical Model of Bird Movement.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {5525298},
pmid = {40303041},
issn = {1865-1682},
mesh = {Animals ; *Influenza in Birds/epidemiology/virology/transmission/prevention &amp; control ; *Influenza A Virus, H5N1 Subtype/physiology ; *Animal Migration ; Birds ; Geographic Information Systems ; Disease Outbreaks/veterinary ; Animals, Wild ; },
abstract = {Understanding timing and distribution of virus spread is critical to global commercial and wildlife biosecurity management. A highly pathogenic avian influenza virus (HPAIv) global panzootic, affecting ~600 bird and mammal species globally and over 83 million birds across North America (December 2023), poses a serious global threat to animals and public health. We combined a large, long-term waterfowl GPS tracking dataset (16 species) with on-ground disease surveillance data (county-level HPAIv detections) to create a novel empirical model that evaluated spatiotemporal exposure and predicted future spread and potential arrival of HPAIv via GPS tracked migratory waterfowl through 2022. Our model was effective for wild waterfowl, but predictions lagged HPAIv detections in poultry facilities and among some highly impacted nonmigratory species. Our results offer critical advance warning for applied biosecurity management and planning and demonstrate the importance and utility of extensive multispecies tracking to highlight potential high-risk disease spread locations and more effectively manage outbreaks.},
}
@article {pmid40303815,
year = {2023},
author = {Wielgus, E and Klamm, A and Conraths, FJ and Dormann, CF and Henrich, M and Kronthaler, F and Heurich, M},
title = {First-Passage Time Analysis Based on GPS Data Offers a New Approach to Estimate Restricted Zones for the Management of Infectious Diseases in Wildlife: A Case Study Using the Example of African Swine Fever.},
journal = {Transboundary and emerging diseases},
volume = {2023},
number = {},
pages = {4024083},
pmid = {40303815},
issn = {1865-1682},
mesh = {Animals ; *African Swine Fever/prevention &amp; control/epidemiology/transmission ; *Geographic Information Systems ; Swine ; Animals, Wild ; *Sus scrofa ; Germany/epidemiology ; Female ; Disease Outbreaks/veterinary/prevention &amp; control ; Male ; African Swine Fever Virus ; },
abstract = {An essential part of any disease containment and eradication policy is the implementation of restricted zones, but determining the appropriate size of these zones can be challenging for managers. We designed a new method, based on animal movement, to help assess how large restricted zones should be after a spontaneous outbreak to successfully control infectious diseases in wildlife. Our approach uses first-passage time (FPT) analysis and Cox proportional hazard (CPH) models to calculate and compare the risk of an animal leaving different-sized areas. We illustrate our approach using the example of the African swine fever (ASF) virus and its wild pig reservoir host species, the wild boar (Sus scrofa), and we investigate the feasibility of applying this method to other systems. Using GPS data from 57 wild boar living in the Hainich National Park, Germany, we calculate the time spent by each individual in areas of different sizes using FPT analysis. We apply CPH models on the derived data to compare the risk of leaving areas of different sizes and to assess the effects of season and the sex of the wild boar on the risk of leaving. We conduct survival analyses to estimate the risk of leaving an area over time. Our results indicate that the risk of leaving an area decreases exponentially by 10% for each 100 m increase in radius size so that the differences were more pronounced for small sizes. Furthermore, the probability of leaving increases exponentially with time. Wild boar had a similar risk of leaving an area of a given size throughout the year, except in spring and winter, when females had a much lower risk of leaving. Our findings are in agreement with the literature on wild boar movement, further validating our method, and repeated analyses with location data resampled at different rates gave similar results. Our results may be applicable only to our study area, but they demonstrate the applicability of the proposed method to any ecosystem where wild boar populations are likely to be infected with ASF and where restricted zones should be established accordingly. The outlined approach relies solely on the analysis of movement data and provides a useful tool to determine the optimal size of restricted zones. It can also be applied to future outbreaks of other diseases.},
}
@article {pmid40304278,
year = {2025},
author = {Lentendu, G and Singer, D and Agatha, S and Bahram, M and Hannula, SE and Helder, J and Tedersoo, L and Traunspurger, W and Geisen, S and Lara, E},
title = {EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e14118},
doi = {10.1111/1755-0998.14118},
pmid = {40304278},
issn = {1755-0998},
support = {PID2021-128499NB-I00 10.13039/501100011033//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 182531//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Soil/parasitology ; *Eukaryota/classification/genetics/physiology ; Animals ; Nematoda/classification/genetics ; *Computational Biology/methods ; Fungi/classification/genetics ; *Soil Microbiology ; },
abstract = {The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss a standardised approach to functionally classify the soil eukaryome in a holistic way. Here we compiled EukFunc, the first functional reference database that characterises the most abundant and functionally important soil eukaryotic groups: fungi, nematodes and protists. We classified the 14,060 species in the database based on their mode of nutrient acquisition into the main functional classes of symbiotroph (40%), saprotroph (26%), phototroph (17%), predator (16%) and unknown (2%). EukFunc provides further detailed information about nutrition mode, including a secondary functional class (i.e., for organisms with multiple nutrition modes), and preyed or associated organisms for predatory or symbiotic taxa, respectively. EukFunc is available in multiple formats for user-friendly functional analyses of specific taxa or annotations of metabarcoding datasets, both embedded in the R package EukFunc. Using a soil dataset from alpine and subalpine meadows, we highlighted the extended ecological insights obtained from combining functional information across the entire soil eukaryome as compared to focusing on fungi, protists or nematodes individually. EukFunc streamlines the annotation process, enhances efficiency and accuracy, and facilitates the investigation of the functional roles of soil eukaryotes-a prerequisite to better understanding soil systems.},
}
@article {pmid40305182,
year = {2025},
author = {Uemura, NA and Nakane, D},
title = {Type IV Pili in Thermophilic Bacteria: Mechanisms and Ecological Implications.},
journal = {Biomolecules},
volume = {15},
number = {4},
pages = {},
pmid = {40305182},
issn = {2218-273X},
support = {24KJ1131//Japan Society for the Promotion of Science/ ; 21K07020//Japan Society for the Promotion of Science/ ; 22H05066//Japan Society for the Promotion of Science/ ; },
mesh = {*Fimbriae, Bacterial/metabolism/physiology ; *Thermus thermophilus/metabolism/physiology/genetics ; },
abstract = {Type IV pili (T4P) machinery is critical for bacterial surface motility, protein secretion, and DNA uptake. This review highlights the ecological significance of T4P-dependent motility in Thermus thermophilus, a thermophilic bacterium isolated from hot springs. Unlike swimming motility, the T4P machinery enables bacteria to move over two-dimensional surfaces through repeated cycles of extension and retraction of pilus filaments. Notably, T. thermophilus exhibits upstream-directed migration under shear stress, known as rheotaxis, which appears to represent an adaptive strategy unique to thermophilic bacteria thriving in rapid water flows. Furthermore, T4P contributes to the capture of DNA and phages, indicating their multifunctionality in natural environments. Understanding the T4P dynamics provides insights into bacterial survival and evolution in extreme habitats.},
}
@article {pmid40306212,
year = {2025},
author = {Nica, I and Georgescu, I},
title = {The ecological impact of agricultural production on CO2 emissions in India: Pathways to sustainable agriculture.},
journal = {Journal of environmental management},
volume = {384},
number = {},
pages = {125548},
doi = {10.1016/j.jenvman.2025.125548},
pmid = {40306212},
issn = {1095-8630},
mesh = {India ; *Agriculture ; *Carbon Dioxide/analysis ; Animals ; },
abstract = {This study examines the relationship between CO2 emissions and agricultural production in India from 1990 to 2023, using an Autoregressive Distributed Lag (ARDL) model. Key agricultural indicators analyzed include the Food Production Index (FPI), Cereal Production (CP), Livestock Production Index (LPI), and the value added by Agriculture, Forestry, and Fishing (AFF). The results show that on the long run, a 1 % increase in FPI leads to a 7.86 unit increase in CO2 emissions per capita, while a 1 % increase in livestock production results in a 3.28 unit decrease in CO2 emissions per capita. In the short run, a similar increase in food production and livestock production also influences CO2 emissions, with notable but varying impacts over time. These findings underline the environmental trade-offs between food security and CO2 emissions, emphasizing the need for sustainable agricultural practices. This research contributes to existing literature by utilizing a broad set of agricultural indicators and robust ARDL analysis to examine both short- and long-term effects, providing a more comprehensive understanding of agricultural sustainability. The study was prompted by India's rapid agricultural growth, driven by its growing population and economic expansion, which has raised significant environmental concerns. Unlike prior research that often takes a generalized or global approach, this study offers an India-specific analysis that captures the country's distinct socio-economic and ecological conditions. By focusing on nationally relevant agricultural indicators and sustainability challenges, the research provides context-sensitive insights that can support effective and targeted policy design. The findings highlight the importance of policies that align agricultural productivity with sustainability, supporting the UN Sustainable Development Goals on climate action and food security.},
}
@article {pmid40307287,
year = {2025},
author = {Wu, J and He, D and Wang, Y and Liu, S and Du, Y and Wang, H and Tan, S and Zhang, D and Xie, J},
title = {An integrated transcriptome, metabolome, and microbiome dataset of Populus under nutrient-poor conditions.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {717},
pmid = {40307287},
issn = {2052-4463},
mesh = {*Metabolome ; *Microbiota ; Nutrients ; Plant Roots/microbiology/metabolism ; *Populus/microbiology/genetics/metabolism ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; *Transcriptome ; Datasets as Topic ; },
abstract = {The rhizosphere microbiota recruited by plants contributes significantly to maintaining host productivity and resisting stress. However, the genetic mechanisms by which plants regulate this recruitment process remain largely unclear. Here, we generated a comprehensive dataset, including 27 root transcriptomes, 27 root metabolomes, and 54 bulk or rhizosphere soil 16S rRNA amplicons across nine poplar species from four sections grown in nutrient-poor natural soil, along with eleven growth phenotype data. We provided a thorough description of this dataset, followed by a comprehensive co-expression network analysis example that broke down the wall of the four-way relationship between plant gene-metabolite-microbe-phenotype, thus identifying the links between plant gene expression, metabolite accumulation, growth behavior, and rhizosphere microbiome variation under nutrient-poor conditions. Overall, this dataset enhances our understanding of plant and microbe interactions, offering valuable strategies and novel insights for resolving how plants regulate rhizosphere microbial compositions and functions, thereby improving host fitness, which will benefit future research.},
}
@article {pmid40307720,
year = {2025},
author = {Moreau, SJM and Marchal, L and Boulain, H and Musset, K and Labas, V and Tomas, D and Gauthier, J and Drezen, JM},
title = {Multi-omic approach to characterize the venom of the parasitic wasp Cotesia congregata (Hymenoptera: Braconidae).},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {431},
pmid = {40307720},
issn = {1471-2164},
support = {ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; SMHART project 35069//European Regional Development Fund/ ; SMHART project 35069//European Regional Development Fund/ ; },
mesh = {Animals ; *Wasps/genetics/virology/metabolism ; *Wasp Venoms/genetics/metabolism/chemistry ; Female ; *Proteomics/methods ; Insect Proteins/genetics/metabolism/chemistry ; Multiomics ; },
abstract = {BACKGROUND: Cotesia congregata is a parasitoid Hymenoptera belonging to the Braconidae family and carrying CCBV (Cotesia congregata Bracovirus), an endosymbiotic polydnavirus. CCBV virus is considered as the main virulence factor of this species, which has raised questions, over the past thirty years, about the potential roles of venom in the parasitic interaction between C. congregata and its host, Manduca sexta (Lepidoptera: Sphingidae). To investigate C. congregata venom composition, we identified genes overexpressed in the venom glands (VGs) compared to ovaries, analyzed the protein composition of this fluid and performed a detailed analysis of conserved domains of these proteins.<br><br>RESULTS: Of the 14 140 known genes of the C. congregata genome, 659 genes were significantly over-expressed (with 10-fold or higher changes in expression) in the VGs of female C. congregata, compared with the ovaries. We identified 30 proteins whose presence was confirmed in venom extracts by proteomic analyses. Twenty-four of these were produced as precursor molecules containing a predicted signal peptide. Six of the proteins lacked a predicted signal peptide, suggesting that venom production in C. congregata also involves non-canonical secretion mechanisms. We have also analysed 18 additional proteins and peptides of interest whose presence in venom remains uncertain, but which could play a role in VG function.<br><br>CONCLUSIONS: Our results show that the venom of C. congregata not only contains proteins (including several enzymes) homologous to well-known venomous compounds, but also original proteins that appear to be specific to this species. This exhaustive study sheds a new light on this venom composition, the molecular diversity of which was unexpected. These data pave the way for targeted functional analyses and to better understand the evolutionary mechanisms that have led to the formation of the venomous arsenals we observe today in parasitoid insects.},
}
@article {pmid40312707,
year = {2025},
author = {Ketchaji, A and Fokam, J and Assah, F and Ateba, F and Wandji, ML and Pamen, JNB and Djoko, GRP and Seugnou, CDN and Kah, E and Atangana, AF and Ateudjieu, J},
title = {The impact of short message service reminders or peer home visits on adherence to antiretroviral therapy and viral load suppression among HIV-Infected adolescents in Cameroon: a randomized controlled trial.},
journal = {AIDS research and therapy},
volume = {22},
number = {1},
pages = {49},
pmid = {40312707},
issn = {1742-6405},
mesh = {Humans ; *HIV Infections/drug therapy/virology ; Adolescent ; Female ; Cameroon/epidemiology ; Male ; *Viral Load/drug effects ; *Text Messaging ; *House Calls ; Young Adult ; *Medication Adherence ; *Anti-HIV Agents/therapeutic use ; *Reminder Systems ; Peer Group ; },
abstract = {BACKGROUND: Adherence to antiretroviral therapy (ART) and viral load suppression (VLS) constitute one of the key challenges to control human immunodeficiency virus (HIV), especially during adolescence. This trial aimed at assessing the impact of short message services (SMS) or peer home visits (PHV) on adherence to ART and VL suppression among adolescents living with HIV (ALWHIV) in Cameroon.<br><br>METHODS: A randomized controlled trial (RCT) was conducted from July 2018 to February 2019 at the Mother and Child Center of the Chantal Biya Foundation in Yaounde. Eligible ALWHIV (15-19 years), with a fully disclosed HIV status, with availability of phone and guardian's consent, were randomly assigned to receive either daily SMS or bi-weekly PHV for a six-months period. The control-group received standard of care according to the national guidelines. Study investigators and participants were not blinded to the interventions group allocation, and no adverse events or side effects were observed. Adjusted logistic regression was used to assess the impact of interventions on outcomes. The study was approved by The Pan-African Clinical Trials Registry with PACTR201904582515723 at (www.pactr.org).<br><br>RESULTS: Adherence to ART increased in the PHV (aRR: 4.3; 95% CI: 2.2-8.3; p&#x2009;<&#x2009;0.001) and SMS (aRR: 3.1, 95% CI: 2.1-5.3; p&#x2009;<&#x2009;0.001) groups compared to the control-group. Likewise, VL suppression was higher in PHV (aRR: 2.1; 95% CI: 1.9-7.5 p&#x2009;<&#x2009;0.001) and SMS (aRR: 3.2; 95% CI: 1.8-5.4; p&#x2009;<&#x2009;0.001) groups compared to the control-group. Based on CI, both interventions showed similar benefits on improving adherence and VLS.<br><br>CONCLUSIONS: Among ALHIV, SMS or PHV contribute substantially to improving adherence and VL suppression among ALWHIV. Implementing such strategies would support efforts in eliminating pediatric AIDS in low- and middle-income countries.},
}
@article {pmid40314555,
year = {2025},
author = {Yu, Z and Li, S and Yang, W and Chen, J and Rahman, MA and Wang, C and Ma, W and Yao, X and Xiong, J and Xu, C and Zhou, Y and Chen, J and Huang, K and Gao, X and Fensholt, R and Weng, Q and Zhou, W},
title = {Enhancing Climate-Driven Urban Tree Cooling with Targeted Nonclimatic Interventions.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {18},
pages = {9082-9092},
doi = {10.1021/acs.est.4c14275},
pmid = {40314555},
issn = {1520-5851},
mesh = {*Trees ; Cities ; *Climate ; },
abstract = {Urban trees play a pivotal role in mitigating heat, yet the global determinants and patterns of their cooling efficiency (CE) remain elusive. Here, we quantify the diel CE of 229 cities across four climatic zones and employ a machine-learning model to assess the influence of variables on CE. We found that for every 10% increase in tree cover, surface temperatures are reduced by 0.25 °C during the day and 0.04 °C at night. Trees in humid regions exhibit the highest daytime CE, while those in arid zones demonstrate the greatest cooling effect at night. This can be explained by the difference in canopy density between the humid and arid zones. During the day, the high canopy density in the humid zone converts more solar radiation into latent heat flux. At night, the low canopy density in the arid zone intercepts less longwave radiation, which favors surface cooling. While climatic factors contribute nearly twice as much to CE as nonclimatic ones, our findings suggest that optimizing CE is possible by managing variables within specific thresholds due to their nonlinear effects. For instance, we revealed that in arid regions, an impervious surface coverage of approximately 60% is optimal, whereas in humid areas, reducing it to around 40% maximizes cooling benefits. These insights underscore the need for targeted management of nonclimatic factors to sustain tree cooling benefits and offer practical guidance for designing climate-resilient, nature-based urban strategies.},
}
@article {pmid40316929,
year = {2025},
author = {Demsash, AW and Abebe, R and Gezimu, W and Kitil, GW and Tizazu, MA and Lambebo, A and Bekele, F and Alemu, SS and Jarso, MH and Dube, GN and Wedajo, LF and Purohit, S and Kalayou, MH},
title = {Data-driven machine learning algorithm model for pneumonia prediction and determinant factor stratification among children aged 6-23 months in Ethiopia.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {647},
pmid = {40316929},
issn = {1471-2334},
mesh = {Humans ; Ethiopia/epidemiology ; Infant ; *Pneumonia/epidemiology/diagnosis ; *Machine Learning ; Female ; Male ; Algorithms ; Risk Factors ; },
abstract = {INTRODUCTION: Pneumonia is the leading cause of child morbidity and mortality and accounts for 5.6 million under-five child deaths. Pneumonia has a significant impact on the quality of life, the country's economy, and the survival of children. Therefore, this study aimed to develop data-driven predictive model using machine learning algorithms to predict pneumonia and stratify the determinant factors among children aged 6-23 months in Ethiopia.<br><br>METHODS: A total of 2035 samples of children were used from the 2016 Ethiopian Demographic and Health Survey dataset. Jupyter Notebook from Anaconda Navigators was used for data management and analysis. Important libraries such as Pandas, Seaborn, and Numpy were imported from Python. The data was pre-processed into a training and testing dataset with a 4:1 ratio, and tenfold cross-validation was used to reduce bias and enhance the models' performance. Six machine learning algorithms were used for model building and comparison, and confusion matrix elements were used to evaluate the performance of each algorithm. Principal component analysis and heatmap function were used for correlation detection between features. Feature importance score was used to identify and stratify the most important predictors of pneumonia.<br><br>RESULTS: From 2035 total samples, 16.6%, 20.1%, and 24.2% of children had short rapid breath, fever, and cough respectively. The overall magnitude of pneumonia among children aged 6-23&#xa0;months was 31.3% based on the 2016 EDHS report. A random forest algorithm is the relatively best performance model to predict pneumonia and stratify its determinates with 91.3% accuracy. The health facility visits, child sex, initiation of breastfeeding, birth interval, birth weight, husbands' education, women's age, and region, are the top eight important predictors of pneumonia among children with important scores of more than 5% to 20% respectively.<br><br>CONCLUSIONS: Random forest is the best model to predict pneumonia and stratify its determinant factors. The implications of this study are profound for advanced research methodology, tailored to promote effective health interventions such as lifestyle modification and behavioral intervention, based on individuals' unique features, specifically for stakeholders to take proactive childcare interventions. The study would serve as pioneering evidence for future research, and researchers are recommended to use deep learning algorithms to enhance prediction accuracy.},
}
@article {pmid40317095,
year = {2025},
author = {Seizer, L and Pascher, A and Branz, S and Schmitt, N and Löchner, J and Schuller, BW and Rohleder, N and Renner, TJ},
title = {Bridging acute and chronic stress effects on inflammation: protocol for a mixed-methods intensive longitudinal study.},
journal = {BMC psychology},
volume = {13},
number = {1},
pages = {464},
pmid = {40317095},
issn = {2050-7283},
mesh = {Humans ; Longitudinal Studies ; *Stress, Psychological/metabolism/immunology/complications ; *Inflammation/metabolism/psychology/immunology ; Saliva/chemistry ; Male ; Female ; Young Adult ; Chronic Disease ; Adult ; Ecological Momentary Assessment ; Biomarkers/metabolism ; Cytokines/metabolism ; Research Design ; },
abstract = {Acute stress triggers adaptive physiological responses-including transient increases in inflammatory cytokines-while chronic stress is associated with sustained inflammatory activity that may underlie the development of various disorders. Despite extensive research on each stress type individually, the transition and interaction between them remain underexplored. This study aims to address this gap by employing an intensive longitudinal measurement burst design. Healthy university students will be recruited and monitored over three one-week assessment bursts, spaced by three-month breaks. Participants will complete ecological momentary assessments four times daily, recording their emotional states, stress experiences, and daily incidents. Simultaneously, saliva samples will be collected at matching time points to measure biomarkers of immune and stress system activity. In addition, daily audio diaries will provide qualitative context through advanced speech analysis techniques. Data will be analyzed using a multi-level modeling approach to differentiate within-person dynamics from between-person variability, accounting for potential moderators. The findings are expected to shed light on how repeated acute stressors transition into chronic stress and how chronic stress burden may influence acute stress responses.},
}
@article {pmid40318544,
year = {2025},
author = {Gomes, MLS and Cestari, VRF and Florêncio, RS and Yamamura, M and Santos, JO and Sales, LBF and Silva, RR and Oriá, MOB},
title = {Spatial-temporal analysis of cervical cancer screening and social and health indicators in Brazil.},
journal = {Public health},
volume = {243},
number = {},
pages = {105747},
doi = {10.1016/j.puhe.2025.105747},
pmid = {40318544},
issn = {1476-5616},
mesh = {Humans ; Female ; Brazil/epidemiology ; *Uterine Cervical Neoplasms/diagnosis/epidemiology ; Adult ; Middle Aged ; *Early Detection of Cancer/statistics &amp; numerical data ; Spatio-Temporal Analysis ; Socioeconomic Factors ; *Health Status Indicators ; },
abstract = {OBJECTIVE: To identify the spatial-temporal patterns of cervical cancer (CC) screening in Brazil from 2013 to 2022 and its relationship with social and health indicators.<br><br>STUDY DESIGN: This ecological study uses data from the Cancer Information System (SISCAN) of the Brazilian Unified Health System's Department of Informatics.<br><br>METHODS: The study analyzed women aged 25 to 64 who underwent CC screening in 5570 municipalities across Brazil. Global Moran's I and the Local Index of Spatial Autocorrelation (LISA) were employed to investigate clustering. The purely spatial scan statistic technique was used for spatial cluster detection. Temporal trends were assessed using joinpoint regression. GeoDa, SaTScan, GWR, and QGIS software were used for the analysis.<br><br>RESULTS: The global clustering analysis of CC screening proportions revealed significant spatial autocorrelation (Moran's I&#xa0;=&#xa0;0.530). Clusters of municipalities with low screening rates were significantly observed in the Northern (Amap&#xe1;, Amazonas, Rond&#xf4;nia, Roraima) and Northeastern (Piau&#xed;, Pernambuco) regions. The Gini Index (&#x3b2;&#xa0;=&#xa0;-2.60), the Municipal Human Development Index (MHDI) (&#x3b2;&#xa0;=&#xa0;-10.5), and the Social Vulnerability Index (SVI) (&#x3b2;&#xa0;=&#xa0;-9.14) showed negative associations. Conversely, Family Health Strategy (FHS) coverage (&#x3b2;&#xa0;=&#xa0;2.18) demonstrated a positive impact on screening rates. In terms of temporal trends, the screening proportion gradually increased from 5.4&#xa0;% in 2014 to 10.5&#xa0;% in 2022.<br><br>CONCLUSION: Areas with a high risk of low CC screening rates were identified in the Northern and Northeastern regions of Brazil, which are characterized by socioeconomic and demographic disparities, vulnerabilities, and inequalities.},
}
@article {pmid40318638,
year = {2025},
author = {Aguilar-Gómez, D and Bejder, J and Graae, J and Ko, Y and Vaughn, A and Clement, K and Tristani-Firouzi, M and Lee, JY and Nordsborg, NB and Nielsen, R and Ilardo, M},
title = {Genetic and training adaptations in the Haenyeo divers of Jeju, Korea.},
journal = {Cell reports},
volume = {44},
number = {5},
pages = {115577},
pmid = {40318638},
issn = {2211-1247},
support = {R00 HG011658/HG/NHGRI NIH HHS/United States ; R01 GM138634/GM/NIGMS NIH HHS/United States ; R35 GM153400/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Diving/physiology ; Female ; *Adaptation, Physiological/genetics ; Republic of Korea ; Adult ; Selection, Genetic ; Pregnancy ; Blood Pressure/genetics ; },
abstract = {Natural selection and relative isolation have shaped the genetics and physiology of unique human populations from Greenland to Tibet. Another such population is the Haenyeo, the all-female Korean divers renowned for their remarkable diving abilities in frigid waters. Apnea diving induces considerable physiological strain, particularly in females diving throughout pregnancy. In this study, we explore the hypothesis that breath-hold diving has shaped physiological and genetic traits in the Haenyeo. We identified pronounced bradycardia during diving, a likely training effect. We paired natural selection and genetic association analyses to investigate adaptive genetic variation that may mitigate the effects of diving on pregnancy through an associated reduction of diastolic blood pressure. Finally, we identified positively selected variation in a gene previously associated with cold water tolerance, which may contribute to reduced hypothermia susceptibility. These findings highlight the importance of traditional diving populations for understanding genetic and physiological adaptation.},
}
@article {pmid40318965,
year = {2025},
author = {Lucca, E and Kofinas, D and Avellán, T and Kleemann, J and Mooren, CE and Blicharska, M and Teutschbein, C and Sperotto, A and Sušnik, J and Milliken, S and Fader, M and Đorđević, D and Dašić, T and Vasilić, V and Taiwo, B and Baubekova, A and Pineda-Martos, R and Spyropoulou, A and Baganz, GFM and El Jeitany, J and Oral, HV and Merheb, M and Castelli, G and Pagano, A and Sambo, B and Suškevičs, M and Arnold, M and Rađenović, T and Psomas, A and Masia, S and La Jeunesse, I and Amorocho-Daza, H and Das, SS and Bresci, E and Munaretto, S and Brouwer, F and Laspidou, C},
title = {Corrigendum to "Integrating 'nature' in the water-energy-food nexus: Current perspectives and future directions" [Science of The Total Environment, Volume 966, 2025, 178600].},
journal = {The Science of the total environment},
volume = {980},
number = {},
pages = {179482},
doi = {10.1016/j.scitotenv.2025.179482},
pmid = {40318965},
issn = {1879-1026},
}
@article {pmid40319413,
year = {2025},
author = {Wang, Y and Mao, Z and Yu, J and Feng, B and Zhang, Z and Zhong, L and Tang, Y},
title = {Construction of risk management system for polluted sites in coal industry clusters.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {6},
pages = {195},
pmid = {40319413},
issn = {1573-2983},
mesh = {*Coal Industry ; *Risk Management/methods ; China ; *Coal ; *Environmental Pollution/prevention &amp; control/statistics &amp; numerical data ; Soil/chemistry ; Groundwater/chemistry ; Environmental Restoration and Remediation ; Environmental Monitoring ; Risk Assessment ; Decision Making, Organizational ; *Coal Mining ; Decision Making, Computer-Assisted ; Algorithms ; *Environmental Pollutants/analysis ; },
abstract = {Coal has always been the main source of energy in China, accounting for more than 60% of primary energy production and consumption. As a result of coal mining, coal industry agglomerations such as mining, coal chemical industry, and so on have been gradually formed, and there are many types of industries in the agglomerations, complex sources of pollutants, and sensitive soil and water environments, and all kinds of industrial sites and solid waste dumps of coal-related industries may pollute the soil and groundwater, and have a certain impact on the ecological environment. However, at present, there is a lack of a targeted region-wide pollution risk management technology system for the polluted sites in the agglomeration area, therefore, it is particularly important to construct a scientific and complete soil-groundwater risk management system and propose more targeted and effective control strategies for the polluted sites in the coal industry agglomeration area. Based on the domestic and international experience and historical data, this paper takes the coal industry cluster area as the research object classifies the land in the area according to the land use type into construction land, agricultural land, and another ecological land, and carries out the risk zoning and grading based on the dosage-effect model and the potential ecological hazard index method respectively, assesses the appropriateness, feasibility, and necessity of the implementation of risk control for the polluted plots, and then designs and develops a risk control decision-making framework by using the hierarchical analysis method. Hierarchical analysis was used to design and develop a decision-making framework for risk management, and finally, the optimal risk management and remediation strategy was proposed based on the AHP + TOPSIS algorithm, which combined with the contaminated land conditions to propose a suitable solution.},
}
@article {pmid40319682,
year = {2025},
author = {Hwang, H and Kim, D and Kim, S and Kim, JY and Kim, ES and Yang, T and Lee, N and Piao, Y and Park, BJ and Lee, DK},
title = {Optimizing urban green spaces using a decision-support model for carbon sequestration and ecological connectivity.},
journal = {Journal of environmental management},
volume = {384},
number = {},
pages = {125058},
doi = {10.1016/j.jenvman.2025.125058},
pmid = {40319682},
issn = {1095-8630},
mesh = {*Carbon Sequestration ; *Decision Support Techniques ; Cities ; *Conservation of Natural Resources/methods ; Ecosystem ; },
abstract = {Urban green spaces (UGSs) are vital for enhancing urban ecological health and resident well-being. However, their diverse functions need to be balanced based on spatial limitations and varying stakeholder preferences. Integrated planning approaches are needed to exploit the multiple benefits of UGSs. This study introduces a multi-objective decision-support model designed to optimize UGS planning by simultaneously addressing carbon sequestration, ecological connectivity, and cost constraints. The model incorporates the non-dominated sorting genetic algorithm II to identify Pareto-optimal solutions for tailored decision-making strategies that balance different priorities. The model indicated that ecological connectivity can be improved by 7.57 % while meeting carbon-reduction and budgetary targets. The model effectively balanced trade-offs, underscoring the importance of both the quantity and strategic placement of green space. This decision-support framework empowers decision-makers to rapidly simulate and validate optimal scenarios, effectively balance competing objectives, and provide a scientific basis through verifiable feedback, ultimately promoting the development of sustainable urban environments.},
}
@article {pmid40321106,
year = {2025},
author = {Brazier, T and Stetsenko, R and Roze, D and Glémin, S},
title = {Mating system and the evolution of recombination rates in seed plants.},
journal = {Journal of evolutionary biology},
volume = {38},
number = {7},
pages = {920-929},
doi = {10.1093/jeb/voaf008},
pmid = {40321106},
issn = {1420-9101},
support = {ANR-19-CE12472//Agence Nationale de la Recherche/ ; },
mesh = {*Magnoliopsida/genetics ; Genome, Plant ; Chromosomes, Plant ; Genome Size ; *Recombination, Genetic ; *Biological Evolution ; *Self-Fertilization/genetics ; Pollination ; Life History Traits ; Datasets as Topic ; Longevity ; Selection, Genetic ; },
abstract = {Meiotic recombination is a central mechanism underlying sexual reproduction among eukaryotes. In many species, the recombination rate is strongly constrained by chromosome size, as the number of crossovers per chromosome generally ranges between one and no more than a few (around three to five). Yet, recombination rates are variable and can evolve between species, in particular when they differ in their reproductive system. According to theory, indirect selection towards higher recombination rates is expected to be stronger in inbred populations, such as selfing species compared with randomly mating species. To test for the impact of the mating system on the evolution of recombination rates, we leveraged a dataset with genetic maps, genome sizes, chromosome numbers, and life history traits in 200 seed plant species. After controlling for the chromosome size effect, the phylogeny, and map quality, we found a joint positive effect of the mating system and longevity on recombination rates, with higher recombination rates in mixed-mating and selfing species. We also found that mixed-mating and selfing species had a significantly higher number of crossovers in larger chromosomes than outcrossing species, suggesting selection for relaxed crossover interference in these former species. Our results point to the mating system as an important factor potentially shaping the evolution of recombination despite mechanical constraints acting on the number of crossovers per chromosome.},
}
@article {pmid40323496,
year = {2025},
author = {Oyelayo, EA and Taiwo, TJ and Oyelude, SO and Alao, JO},
title = {The global impact of industrialisation and climate change on antimicrobial resistance: assessing the role of Eco-AMR Zones.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {6},
pages = {625},
pmid = {40323496},
issn = {1573-2959},
mesh = {*Industrial Development ; *Drug Resistance, Microbial/genetics ; *Climate Change ; Temperature ; Environmental Monitoring ; Genes, Microbial ; Computational Biology ; Anti-Bacterial Agents ; },
abstract = {This study examines the relationship between industrialisation, climate change, and antimicrobial resistance (AMR) gene prevalence. Data analysis from the top 20 highly industrialised and the top 20 least industrialised nations revealed that industrial activities significantly contribute to global warming, with temperature increases of up to 2 °C observed in highly industrialised regions. These environmental changes influence the distribution and evolution of AMR genes, as rising temperatures can affect bacterial resistance in a manner similar to antibiotics. Through a bioinformatics approach, a marked disparity in AMR gene frequencies was observed between highly industrialised and less industrialised nations, with developed countries reporting higher frequencies due to extensive antibiotic use and advanced monitoring systems. 'Eco-AMR Zones' is proposed as a solution to specialised areas by promoting sustainable industrial practices, enforcing pollution controls, and regulating antibiotic use to mitigate AMR's environmental and public health impacts. These zones, supported by collaboration across various sectors, offer a promising approach to preserving antibiotic effectiveness and reducing environmental degradation. The study emphasises the importance of integrated global strategies that address both the ecological and public health challenges posed by AMR, advocating for sustainable practices, international collaboration, and ongoing research to combat the evolving threats of climate change and antimicrobial resistance.},
}
@article {pmid40324092,
year = {2025},
author = {Compton, ZT and Vincze, O and Mellon, W and Tollis, M and Abegglen, L and Schiffman, JD and Giraudeau, M and Boddy, AM and Maley, CC},
title = {Paradoxical indeed.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {19},
pages = {e2504512122},
pmid = {40324092},
issn = {1091-6490},
support = {R01 CA140657/CA/NCI NIH HHS/United States ; U54 CA217376/CA/NCI NIH HHS/United States ; T32 CA272303/CA/NCI NIH HHS/United States ; },
}
@article {pmid40324147,
year = {2025},
author = {Gilpin, W},
title = {Optimization hardness constrains ecological transients.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1013051},
pmid = {40324147},
issn = {1553-7358},
mesh = {*Ecosystem ; *Models, Biological ; Computer Simulation ; Computational Biology ; Biological Evolution ; },
abstract = {Living systems operate far from equilibrium, yet few general frameworks provide global bounds on biological transients. In high-dimensional biological networks like ecosystems, long transients arise from the separate timescales of interactions within versus among subcommunities. Here, we use tools from computational complexity theory to frame equilibration in complex ecosystems as the process of solving an analogue optimization problem. We show that functional redundancies among species in an ecosystem produce difficult, ill-conditioned problems, which physically manifest as transient chaos. We find that the recent success of dimensionality reduction methods in describing ecological dynamics arises due to preconditioning, in which fast relaxation decouples from slow solving timescales. In evolutionary simulations, we show that selection for steady-state species diversity produces ill-conditioning, an effect quantifiable using scaling relations originally derived for numerical analysis of complex optimization problems. Our results demonstrate the physical toll of computational constraints on biological dynamics.},
}
@article {pmid40325107,
year = {2025},
author = {Pitogo, KME and Meneses, CG and Flores, ABA and Saavedra, AJL and Amarga, AKS and Angeles, MD and Lucañas, CC and Decena, SCP and Venturina, REL and Fidelino, JS and Pantinople, D and Cabañas, AJC and Herr, MW and Bernstein, JM and Chan, KO and Sanguila, MB and Mallari, NA and Brown, RM and Supsup, CE},
title = {Caught in statistical noise: pitfalls of a unidimensional approach to understanding biodiversity-conflict relationships.},
journal = {npj biodiversity},
volume = {4},
number = {1},
pages = {17},
pmid = {40325107},
issn = {2731-4243},
}
@article {pmid40326463,
year = {2025},
author = {Vogelsmeier, LVDE and Jongerling, J and Ulitzsch, E},
title = {Accounting for Measurement Invariance Violations in Careless Responding Detection in Intensive Longitudinal Data: Exploratory vs. Partially Constrained Latent Markov Factor Analysis.},
journal = {Multivariate behavioral research},
volume = {60},
number = {5},
pages = {878-897},
doi = {10.1080/00273171.2025.2492016},
pmid = {40326463},
issn = {1532-7906},
mesh = {Humans ; Longitudinal Studies ; Factor Analysis, Statistical ; *Markov Chains ; *Models, Statistical ; Computer Simulation ; Data Interpretation, Statistical ; },
abstract = {Intensive longitudinal data (ILD) collection methods like experience sampling methodology can place significant burdens on participants, potentially resulting in careless responding, such as random responding. Such behavior can undermine the validity of any inferences drawn from the data if not properly identified and addressed. Recently, a confirmatory mixture model (here referred to as fully constrained latent Markov factor analysis, LMFA) has been introduced as a promising solution to detect careless responding in ILD. However, this method relies on the key assumption of measurement invariance of the attentive responses, which is easily violated due to shifts in how participants interpret items. If the assumption is violated, the ability of the fully constrained LMFA to accurately identify careless responding is compromised. In this study, we evaluated two more flexible variants of LMFA-fully exploratory LMFA and partially constrained LMFA-to distinguish between careless and attentive responding in the presence of non-invariant attentive responses. Simulation results indicated that the fully exploratory LMFA model is an effective tool for reliably detecting and interpreting different types of careless responding while accounting for violations of measurement invariance. Conversely, the partially constrained model struggled to accurately detect careless responses. We end by discussing potential reasons for this.},
}
@article {pmid40327938,
year = {2025},
author = {Wang, H and Xie, G and Zhang, Z and Han, J and Zhang, Y and Xu, T and Yin, D},
title = {PFHxA and PFHxS promote breast cancer progression in 3D culture: MEX3C-associated immune infiltration revealed by bioinformatics and machine learning.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138458},
doi = {10.1016/j.jhazmat.2025.138458},
pmid = {40327938},
issn = {1873-3336},
mesh = {Humans ; Machine Learning ; Cell Line, Tumor ; Female ; *Fluorocarbons/toxicity ; Computational Biology ; Cell Movement/drug effects ; Cell Proliferation/drug effects ; *RNA-Binding Proteins/genetics/metabolism ; Tumor Microenvironment/drug effects ; *Triple Negative Breast Neoplasms/immunology/pathology/genetics ; *Sulfonic Acids/toxicity ; Disease Progression ; },
abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants with widespread use and bioaccumulative potential. Short-chain PFAS such as perfluorohexanoic acid (PFHxA) and perfluorohexane sulfonate (PFHxS) have been introduced as safer alternatives to long-chain PFAS, yet their toxicological impacts remain poorly defined. In this study, we employed a 3D Gelatin methacryloyl (GelMA) hydrogel model to mimic the tumor microenvironment and investigated the effects of PFHxA and PFHxS on triple-negative breast cancer (TNBC) progression. At environmentally relevant concentrations (0.1-10 μM), both compounds significantly enhanced proliferation, migration, and invasion of MDA-MB-231 cells. Transcriptomic and machine learning analyses identified MEX3C as a key gene upregulated by PFAS exposure. Gene set enrichment analysis (GSEA) revealed activation of the PI3K-AKT-mTOR signaling pathway, which was further supported by siRNA-mediated knockdown of MEX3C, leading to a marked reduction in the expression levels of phosphorylated PI3K, AKT, and mTOR proteins. Furthermore, immune cell co-culture experiments showed that MDA-MB-231 cells with high MEX3C expression promoted M2 macrophage polarization, suppressed M1 polarization, and enhanced macrophage chemotactic activity, the immunomodulatory effects were significantly attenuated upon MEX3C knockdown. These findings establish MEX3C as a central mediator of PFAS-induced tumor progression and immune remodeling. This study provides mechanistic insight into the carcinogenic potential of emerging short-chain PFAS and underscores the need for stricter regulation to safeguard public health.},
}
@article {pmid40328721,
year = {2025},
author = {Zhang, H and Wen, T and Wang, Z and Zhao, X and Wu, H and Xiang, P and Ma, Y},
title = {[Multi-omics analysis of hormesis effect of lanthanum chloride on carotenoid synthesis in Rhodotorula mucilaginosa].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {4},
pages = {1631-1648},
doi = {10.13345/j.cjb.240537},
pmid = {40328721},
issn = {1872-2075},
mesh = {*Lanthanum/pharmacology ; *Rhodotorula/metabolism/drug effects/genetics ; *Carotenoids/metabolism ; *Hormesis/drug effects ; Fermentation ; Multiomics ; },
abstract = {Hormesis effect has been observed in the secondary metabolite synthesis of microorganisms induced by rare earth elements. However, the underlying molecular mechanism remains unclear. To analyze the molecular mechanism of the regulatory effect of Rhodotorula mucilaginosa in the presence of lanthanum chloride, different concentrations of lanthanum chloride were added to the fermentation medium of Rhodotorula mucilaginosa, and the carotenoid content was subsequently measured. It was found that the concentrations of La[3+] exerting the promotional and inhibitory effects were 0-100 mg/L and 100-400 mg/L, respectively. Furthermore, the expression of 33 genes and the synthesis of 55 metabolites were observed to be up-regulated, while the expression of 85 genes and the synthesis of 123 metabolites were found to be down-regulated at the concentration range of the promotional effect. Notably, the expression of carotenoid synthesis-related genes except AL1 was up-regulated. Additionally, the content of β-carotene, lycopene, and astaxanthin demonstrated increases of 10.74%, 5.02%, and 3.22%, respectively. The expression of 5 genes and the synthesis of 91 metabolites were up-regulated, while the expression of 35 genes and the synthesis of 138 metabolites were down-regulated at the concentration range of the inhibitory effect. Meanwhile, the content of β-carotene, lycopene, and astaxanthin decreased by 21.73%, 34.81%, and 35.51%, respectively. In summary, appropriate concentrations of rare earth ions can regulate the synthesis of secondary metabolites by modulating the activities of various enzymes involved in metabolic pathways, thereby exerting the hormesis effect. The findings of this study not only contribute to our comprehension for the mechanism of rare earth elements in organisms but also offer a promising avenue for the utilization of rare earth elements in diverse fields, including agriculture, pharmaceuticals, and healthcare.},
}
@article {pmid40329386,
year = {2025},
author = {Hou, L and Zhao, Z and Steger-Mähnert, B and Jiao, N and Herndl, GJ and Zhang, Y},
title = {Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {114},
pmid = {40329386},
issn = {2049-2618},
support = {42206098//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 42125603//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; MELRS2327//State Key Laboratory of Marine Environmental Science/ ; I4978-B//Austrian Science Fund/ ; },
mesh = {*Snow/microbiology ; Gammaproteobacteria/metabolism/genetics/classification ; Metagenomics/methods ; Metagenome ; *Seawater/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Phytoplankton/microbiology/metabolism ; Multiomics ; },
abstract = {BACKGROUND: Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.<br><br>RESULTS: Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).<br><br>CONCLUSIONS: Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.},
}
@article {pmid40329811,
year = {2025},
author = {Yang, Y and Liu, X and Wu, J and Svenning, JC and Liu, J and Shrestha, N},
title = {A comprehensive county-level distribution database of alien and invasive plants in China.},
journal = {Ecology},
volume = {106},
number = {5},
pages = {e70084},
pmid = {40329811},
issn = {1939-9170},
support = {2022YFC2601100//National Key Research and Development Program of China/ ; DNRF173//Danmarks Grundforskningsfond/ ; },
mesh = {*Introduced Species ; China ; *Plants/classification ; *Databases, Factual ; Biodiversity ; },
abstract = {Over the past half century, international trade and exchange have continued to increase in China, resulting in the widespread introduction of alien plant species. The accumulation of these alien species has accelerated invasion events, posing serious threats to local ecological security and economic development. Comprehensive and accurate species distribution records are extremely important for early detection, understanding dispersal dynamics, and supporting various management strategies and research initiatives. However, biodiversity databases, both global and local, often lack comprehensive and high-resolution distribution data for alien invasive plant species (AIPs). This limitation is particularly evident in China, where local databases typically provide coarse spatial data, often restricted to the provincial level, leading to a substantial underestimation of the actual distribution of AIPs. Here, we fill this gap by creating the most comprehensive distribution database for AIPs in China at a much finer spatial resolution. By integrating 73,469 distribution records from China's online herbarium, biodiversity databases, flora, published literature, and 173,396 georeferenced records from GBIF, we built the county-level distribution database for 400 AIPs and report for the first time their presence in 2684 administrative counties in China (92.5% of the total counties). Notably, our database provides 2.58 times more distribution records than global biodiversity data repositories such as GBIF and also includes the earliest introduction dates for each AIP. The temporal range of the records spans from 1607 to 2023, capturing over 400 years of AIP presence in China. These rigorously quality-controlled georeferenced data can be used to examine the dynamics and influencing factors of plant invasions in China. They can also serve as the most updated data reference for policy makers in designing effective AIP management policies in China. We encourage users to cite this data paper when utilizing the data, and there are no restrictions on its use for non-commercial purposes.},
}
@article {pmid40331936,
year = {2025},
author = {Li, H and Wang, R and Pan, J and Chen, J and Hao, X},
title = {Bioinformatics Analysis of the Glutamate-Gated Chloride Channel Family in Bursaphelenchus xylophilus.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
pmid = {40331936},
issn = {1422-0067},
support = {202403//Key Laboratory of National Forestry and Grassland Administration on Prevention and Control Technology of Pine Wilt Disease/ ; 202401BD070001-115//Yunnan Fundamental Research Projects/ ; LXXK-2023M06, LXXK-2024Z04//Southwest Forestry University Forestry major in Yunnan Province First-Class Construction Discipline/ ; },
mesh = {*Chloride Channels/genetics/metabolism/chemistry ; Animals ; *Computational Biology/methods ; Phylogeny ; *Tylenchida/genetics/metabolism ; Multigene Family ; Amino Acid Sequence ; },
abstract = {Glutamate-gated chloride channels (GluCls), a class of ion channels found in the nerve and muscle cells of invertebrates, are involved in vital life processes. Bursaphelenchus xylophilus, the pathogen of pine wilt disease, has induced major economic and ecological losses in invaded areas of Asia and Europe. We identified 33 GluCls family members by sequence alignment analysis. A subsequent bioinformatic analysis revealed the physicochemical properties, protein structure, and gene expression patterns in different developmental stages. The results showed that GluCls genes are distributed across all six chromosomes of B. xylophilus. These proteins indicated a relatively conserved structure by NCBI-conserved domains and InterPro analysis. A gene structure analysis revealed that GluCls genes consist of 5 to 14 exons. Expression pattern analysis revealed BxGluCls were extensively involved in the development of second instar larvae of B. xylophilus. Furthermore, BxGluCls15, BxGluCls25, and BxGluCls28 were mainly associated with the development of eggs of B. xylophilus. BxGluCls12, BxGluCls18, and BxGluCls32 were predominantly linked to nematode resistance and adaptation. Investigation the structure and expression patterns of BxGluCls is crucial to understand the developmental trends of B. xylophilus. It also helps identify molecular targets for the development of biopesticides or drugs designed to control this nematode.},
}
@article {pmid40332368,
year = {2025},
author = {Zheng, K and Feng, Y and Liu, R and Zhang, Y and Fan, D and Zhong, K and Tang, X and Zhang, Q and Cao, S},
title = {Bioinformatics Analysis Reveals the Evolutionary Characteristics of the Phoebe bournei ARF Gene Family and Its Expression Patterns in Stress Adaptation.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
pmid = {40332368},
issn = {1422-0067},
mesh = {*Gene Expression Regulation, Plant ; *Stress, Physiological/genetics ; Phylogeny ; *Evolution, Molecular ; *Computational Biology/methods ; *Plant Proteins/genetics/metabolism ; *Transcription Factors/genetics/metabolism ; *Multigene Family ; *Adaptation, Physiological/genetics ; *Poaceae/genetics ; Indoleacetic Acids/metabolism ; Promoter Regions, Genetic ; },
abstract = {Auxin response factors (ARFs) are pivotal transcription factors that regulate plant growth, development, and stress responses. Yet, the genomic characteristics and functions of ARFs in Phoebe bournei remain undefined. In this study, 25 PbARF genes were identified for the first time across the entire genome of P. bournei. Phylogenetic analysis categorized these genes into five subfamilies, with members of each subfamily displaying similar conserved motifs and gene structures. Notably, Classes III and V contained the largest number of members. Collinearity analysis suggested that segmental duplication events were the primary drivers of PbARF gene family expansion. Structural analysis revealed that all PbARF genes possess a conserved B3 binding domain and an auxin response element, while additional motifs varied among different classes. Promoter cis-acting element analysis revealed that PbARF genes are extensively involved in hormonal responses-particularly to abscisic acid and jasmonic acid and abiotic stresses-as well as abiotic stresses, including heat, drought, light, and dark. Tissue-specific expression analysis showed that PbARF25, PbARF23, PbARF19, PbARF22, and PbARF20 genes (class III), and PbARF18 and PbARF11 genes (class V) consistently exhibited high expression levels in the five tissues. In addition, five representative PbARF genes were analyzed using qRT-PCR. The results demonstrated significant differences in the expression of PbARF genes under various abiotic stress conditions (drought, salt stress, light, and dark), indicating their important roles in stress response. This study laid a foundation for elucidating the molecular evolution mechanism of ARF genes in P. bournei and for determining the candidate genes for stress-resistance breeding.},
}
@article {pmid40333133,
year = {2025},
author = {Niculescu, AG and Mitache, MM and Grumezescu, AM and Chifiriuc, MC and Mihai, MM and Tantu, MM and Tantu, AC and Popa, LG and Grigore, GA and Cristian, RE and Popa, MI and Vrancianu, CO},
title = {From Microbial Ecology to Clinical Challenges: The Respiratory Microbiome's Role in Antibiotic Resistance.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40333133},
issn = {2076-0817},
support = {CNFIS-FDI-2024-F-0484 INOVEX//University of Bucharest/ ; Pillar III, Component C9/Investment no. 8 (I8) - contract CF 68//; Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; project no. 23020101, Contract no. 7N from 3 January 2023//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID)/ ; },
mesh = {Humans ; *Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Respiratory Tract Infections/microbiology/drug therapy ; *Drug Resistance, Microbial ; Probiotics ; *Drug Resistance, Bacterial ; *Respiratory System/microbiology ; },
abstract = {Antibiotic resistance represents a growing public health threat, with airborne drug-resistant strains being especially alarming due to their ease of transmission and association with severe respiratory infections. The respiratory microbiome plays a pivotal role in maintaining respiratory health, influencing the dynamics of antibiotic resistance among airborne pathogenic microorganisms. In this context, this review proposes the exploration of the complex interplay between the respiratory microbiota and antimicrobial resistance, highlighting the implications of microbiome diversity in health and disease. Moreover, strategies to mitigate antibiotic resistance, including stewardship programs, alternatives to traditional antibiotics, probiotics, microbiota restoration techniques, and nanotechnology-based therapeutic interventions, are critically presented, setting an updated framework of current management options. Therefore, through a better understanding of respiratory microbiome roles in antibiotic resistance, alongside emerging therapeutic strategies, this paper aims to shed light on how the global health challenges posed by multi-drug-resistant pathogens can be addressed.},
}
@article {pmid40334559,
year = {2025},
author = {Semcesen, PO and Wells, MG and Sherlock, C and Gutierrez, RF and Rochman, CM},
title = {Wind driven transport of macroplastic debris in a large urban harbour measured by GPS-tracked drifters.},
journal = {Marine pollution bulletin},
volume = {217},
number = {},
pages = {118034},
doi = {10.1016/j.marpolbul.2025.118034},
pmid = {40334559},
issn = {1879-3363},
mesh = {*Wind ; *Plastics/analysis ; *Environmental Monitoring/methods ; Ontario ; Geographic Information Systems ; },
abstract = {The transport pathways of floating plastic debris in Toronto Harbour, Ontario, Canada, were assessed using a series of GPS-tracked drifter bottles. The drifter trajectories were largely controlled by winds, and they could traverse the 2 km wide harbour within a day. The average ratio of drifter speed to wind speed (the wind factor) is consistent with values of 2-5 % used in modelling dispersion of marine debris. However, significant variability in wind factors meant some drifters travelled 2-5 times faster than expected in small waterbodies (Toronto Harbour), and as much as 7 times faster in large waterbodies (Lake Ontario). Importantly, based on our calculated wind factor equations and the coincident accumulation of our drifters with real plastic debris, we can justify the use of wind factors when studying plastic debris transport. Most (75 %) of the drifters that were released in the harbour, stayed within the harbour, accumulating downwind. However, 14 of all 66 drifters escaped Toronto Harbour, where ∼70 % escaped through the West Gap while ∼30 % escaped via the Outer Harbour. One drifter made a 290 km journey across Lake Ontario in a period of 14 days, demonstrating that Toronto is a potential source of plastic debris throughout Lake Ontario.},
}
@article {pmid40335533,
year = {2025},
author = {Pakulnicka, J and Kruk, M},
title = {Water beetle networks differences and migration between natural lakes and post-exploitation water bodies.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15898},
pmid = {40335533},
issn = {2045-2322},
mesh = {Animals ; *Coleoptera/physiology ; *Lakes ; Ecosystem ; *Animal Migration ; Biodiversity ; },
abstract = {Water deficits are a serious problem around the world, which also affects young landscapes, where lakes are most abundant. This poses a threat to many habitats and biological diversity found here. The relationships between species in the ecological networks of lakes at different stages of development and in nearby post-exploitation water bodies remain poorly understood. To better understand the functioning of beetle communities in different ecosystems, we created five network models that we subjected to graph analysis. By analysing the general attributes of the network (number of neighbours, shortest path, characteristic path length, clustering coefficient, network centralisation, network density and network heterogeneity) and those related to the nodes (NCC-Node Closeness Centrality, NBC-Node Betweenness Centrality, NDC-Node Degree Centrality) and to the edges (EBC-Edge Betweenness Centrality and correlations between the biomass of species as nodes), we were able to determine the role of each species in the networks and the relationships between the species. We then used the machine learning ensemble modelling XGBoost-SHAP to identify species that are particularly important in migrations between water bodies and to assess the direction and strength of migrations using Shapley values. Our analyses are based on faunal material from 25 lakes (mesotrophic, eutrophic, dystrophic) and 31-post-exploitation water bodies (clay pits and gravel pits) in northern Poland, in the Masurian Lake District. We found a total of 169 species representing different ecological and functional components. We have shown that the structures of the network between the biomass of species in the analysed five water types differ significantly. The highest value for network density was recorded in eutrophic lakes and clay ponds, the lowest in dystrophic lakes. In eutrophic lakes these are mainly eurybionts, in clay pits-rheophiles and in gravel pits-argilophiles and tyrphophiles. The relationship between the species with the highest NBC and EBC values is particularly important in order to maintain the stability of the network. The periphery of the network usually consists of larger predators that do not compete with each other. By analysing the migration directions of beetles between different ecosystems, we were able to demonstrate a greater affinity of the beetle fauna, especially the argilophiles (e.g. Scarodytes halensis and Laccobius minutus) inhabiting gravel pits, to dystrophic lakes. The beetles in clay pits originate mainly from mesotrophic lakes. These are mainly rheophiles, mostly weakly flying species, such as: Haliplus fluviatilis, Haliplus fulvus, Ilybius fenestratus, Hygrotus vericolor and Haliplus flavicollis. These species are important for the stability of ecological networks in the studied lake types. Their movements between the ecosystems studied in turn contribute to the functional connectivity between the individual lakes, which ensures the stabilisation of biotic relationships at the landscape level. At the same time, they generally also indicate the optimisation of environmental conditions in post-exploitation water bodies, which makes them potential substitute habitats for natural lakes.},
}
@article {pmid40338955,
year = {2025},
author = {Benjamin, JR and Neibauer, J and Anthony, H and Vazquez, J and Rawhouser, A and Dunham, JB},
title = {A partner-driven decision support model to inform the reintroduction of bull trout.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323427},
pmid = {40338955},
issn = {1932-6203},
mesh = {Animals ; *Trout/physiology ; *Conservation of Natural Resources/methods ; Ecosystem ; *Decision Support Techniques ; Decision Making ; },
abstract = {Assessments of species reintroductions involve a series of complex decisions that include human perspectives and ecological contexts. Here, we present a reintroduction assessment involving bull trout (Salvelinus confluentus) using a structured decision-making process. We approached this assessment by engaging partners representing public utilities, government agencies, and Tribes with shared interests in a potential reintroduction. These individuals identified objectives, decision alternatives, and ecological scenarios that were incorporated into a co-produced simulation-based model of potential reintroduction outcomes. The model included mathematical representations of habitat availability, life history expression, and assumptions regarding constraints on potential bull trout populations. Within each recipient stream, partners chose to explore a wide range of decision alternatives and simulated scenarios affecting reintroduction success. Results suggested that 1) reintroductions using eggs or adults were most optimal, 2) adding more individuals resulted in diminishing returns, 3) access to migratory habitat could improve success, and 4) the diversity of opportunities for life history expression led to improved reintroduction opportunities. In addition, modeled scenarios indicated some recipient streams consistently produced lower abundance of reintroduced bull trout. This work contributes a novel example to a growing portfolio of reintroduction assessments that may inform future conservation for bull trout and many other species facing similar challenges.},
}
@article {pmid40339581,
year = {2025},
author = {Pekar, JE and Lytras, S and Ghafari, M and Magee, AF and Parker, E and Wang, Y and Ji, X and Havens, JL and Katzourakis, A and Vasylyeva, TI and Suchard, MA and Hughes, AC and Hughes, J and Rambaut, A and Robertson, DL and Dellicour, S and Worobey, M and Wertheim, JO and Lemey, P},
title = {The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.},
journal = {Cell},
volume = {188},
number = {12},
pages = {3167-3183.e18},
pmid = {40339581},
issn = {1097-4172},
support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 AI135992/AI/NIAID NIH HHS/United States ; },
mesh = {*Chiroptera/virology ; Animals ; SARS-CoV-2/genetics ; Phylogeny ; Phylogeography ; *Severe acute respiratory syndrome-related coronavirus/genetics/classification ; Humans ; COVID-19/virology ; Genome, Viral ; Disease Reservoirs/virology ; *Betacoronavirus/genetics/classification ; Evolution, Molecular ; },
abstract = {The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. We find that the direct ancestors of SARS-CoV and SARS-CoV-2 are unlikely to have reached their respective sites of emergence via dispersal in the bat reservoir alone, supporting interactions with intermediate hosts through wildlife trade playing a role in zoonotic spillover. These results can guide future sampling efforts and demonstrate that viral genomic regions extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.},
}
@article {pmid40341906,
year = {2025},
author = {Shoemaker, WR and Sánchez, &#xc1; and Grilli, J},
title = {Macroecological patterns in experimental microbial communities.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1013044},
pmid = {40341906},
issn = {1553-7358},
mesh = {*Models, Biological ; *Ecology/methods ; Biodiversity ; Ecosystem ; *Microbiota/physiology ; Computational Biology ; },
abstract = {Ecology has historically benefited from the characterization of statistical patterns of biodiversity within and across communities, an approach known as macroecology. Within microbial ecology, macroecological approaches have identified universal patterns of diversity and abundance that can be captured by effective models. Experimentation has simultaneously played a crucial role, as the advent of high-replication community time-series has allowed researchers to investigate underlying ecological forces. However, there remains a gap between experiments performed in the laboratory and macroecological patterns documented in natural systems, as we do not know whether these patterns can be recapitulated in the lab and whether experimental manipulations produce macroecological effects. This work aims at bridging the gap between experimental ecology and macroecology. Using high-replication time-series, we demonstrate that microbial macroecological patterns observed in nature exist in a laboratory setting, despite controlled conditions, and can be unified under the Stochastic Logistic Model of growth (SLM). We found that demographic manipulations (e.g., migration) impact observed macroecological patterns. By modifying the SLM to incorporate said manipulations alongside experimental details (e.g., sampling), we obtain predictions that are consistent with macroecological outcomes. By combining high-replication experiments with ecological models, microbial macroecology can be viewed as a predictive discipline.},
}
@article {pmid40343039,
year = {2025},
author = {Cuenca, PR and Souza, FN and do Nascimento, RC and da Silva, AG and Eyre, MT and Santana, JO and de Oliveira, DS and de Souza, EVR and Palma, FAG and de Carvalho Santiago, DC and Dos Santos Ribeiro, P and Dos Santos, PEF and Khalil, H and Read, JM and Cremonese, C and Costa, F and Giorgi, E},
title = {Using step selection functions to analyse human mobility using telemetry data in infectious disease epidemiology: a case study of leptospirosis.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40343039},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI160780/AI/NIAID NIH HHS/United States ; },
abstract = {Human movement plays a critical role in the transmission of infectious diseases, especially those with environmental drivers like leptospirosis-a zoonotic bacterial infection linked to mud and water contact. Using GPS loggers, we collected detailed telemetry data to understand how fine-scale movements can be analysed in the context of an infectious disease. We recruited individuals living in urban slums in Salvador, Brazil to analyse how they interact with environmental risk factors such as domestic rubbish piles, open sewers, and a local stream. We aimed to identify differences in movement patterns inside the study areas by gender, age, and leptospirosis serological status. Step-selection functions, a spatio-temporal model used in animal movement ecology, estimated selection coefficients to represent the likelihood of movement toward specific environmental factors. With 128 participants wearing GPS devices for 24 to 48 hours, recording locations every 35 seconds during active daytime hours, we segmented movements into morning, midday, afternoon, and evening. Our results suggested women moved closer to the central stream and farther from open sewers compared to men, while serologically positive individuals avoided open sewers. This study introduces a novel method for analysing human telemetry data in infectious disease research.},
}
@article {pmid40343940,
year = {2025},
author = {Longo, L and Veronese, M and Cagnato, C and Sorrentino, G and Tetruashvili, A and Belfer-Cohen, A and Jakeli, N and Meshveliani, T and Meneghetti, M and Zoleo, A and Marcomini, A and Artioli, G and Badetti, E and Hardy, K},
title = {Direct evidence for processing Isatis tinctoria L., a non-nutritional plant, 32-34,000 years ago.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0321262},
pmid = {40343940},
issn = {1932-6203},
mesh = {*Plant Leaves/chemistry/ultrastructure ; Humans ; *Isatis/chemistry/anatomy &amp; histology ; Spectrum Analysis, Raman ; Spectroscopy, Fourier Transform Infrared ; Archaeology ; History, Ancient ; },
abstract = {Recovering evidence for the intentional use of plants in the Palaeolithic is challenging due to their perishable nature as, unlike chipped stone or bone artefacts, plant remains are rarely preserved. This has created a paradigm for the Palaeolithic in which plants seldom feature, resulting in a partial and skewed perspective; in fact, plants were as essential to human life then as they are today. Here, we combine morphological and spectroscopic analyses (µ-Raman, µ-FTIR) to provide robust multiscale physical and biomolecular evidence for the deliberate pounding and grinding of Isatis tinctoria L. leaves 34-32,000 years ago. The leaf epidermis fragments were found entrapped in the topography of the used surface of unmodified pebbles, in association with use-wear traces. Although their bitter taste renders them essentially inedible, the leaves have well-recognised medicinal properties and contain indigotin precursors, the chromophore responsible for the blue colour of woad, a plant-based dye that is insoluble in water. We used a stringent approach to contamination control and biomolecular analysis to provide evidence for a new perspective on human behaviour, and the applied technical and ecological knowledge that is likely to have prevailed in the Upper Palaeolithic. Whether this plant was used as a colourant, as medicine, or indeed for both remains unknown, but offers a new perspective on the fascinating possibilities of non-edible plant use.},
}
@article {pmid40344046,
year = {2025},
author = {Ramihangihajason, TA and Weber, JL and Rakotondraompiana, S and Roger, E and Faramalala, MH and Rakotoniaina, S},
title = {Natural capital accounting as a decision support tool for environmental management of a protected area in Madagascar.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0321948},
pmid = {40344046},
issn = {1932-6203},
mesh = {Madagascar ; *Conservation of Natural Resources/methods ; Ecosystem ; Biodiversity ; Forests ; Animals ; *Decision Support Techniques ; Humans ; Birds ; },
abstract = {Ecosystem change affects the availability of resources and services provided by nature. Ecosystem Natural capital accounting helps track these changes and supports better decision-making for managing the environment. This approach aims to assess changes in the stocks and flows of natural resources and the possibility to integrate them into economic and political decisions. The protected area of Mahavavy-Kinkony Complex, in North-Western of Madagascar, was chosen to implement this approach due to its many types of ecosystems as well as important reserves of threatened birds. In five years (2013-2018), we have observed a reduction in woodland cover (forest and mangrove) due to both regulated and illegal logging, linked to urban expansion and increasing of human pressure. This loss of woodland compromises not only biodiversity but also the capacity of ecosystems to provide ecosystem services. At the same time, the silting up of surface waters is compromising water quality and the health of aquatic ecosystems. In addition, the increase in agricultural land at the expense of forested areas raises concerns about the continuing degradation of natural ecosystems. All of these changes can be observed inside local socio-ecological landscape type. Each socio-ecological landscape type shows the potential variation in the production of ecosystem services.},
}
@article {pmid40344154,
year = {2025},
author = {Babič, J and Kunavar, T and Oztop, E and Kawato, M},
title = {Success-efficient/failure-safe strategy for hierarchical reinforcement motor learning.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1013089},
pmid = {40344154},
issn = {1553-7358},
mesh = {Humans ; *Reinforcement, Psychology ; *Learning/physiology ; Male ; Female ; Computational Biology ; Movement/physiology ; Adult ; Young Adult ; Psychomotor Performance/physiology ; Motor Skills/physiology ; },
abstract = {Our study explores how ecological aspects of motor learning enhance survival by improving movement efficiency and mitigating injury risks during task failures. Traditional motor control theories mainly address isolated body movements and often overlook these ecological factors. We introduce a novel computational motor control approach, incorporating ecological fitness and a strategy that alternates between success-driven movement efficiency and failure-driven safety, akin to win-stay/lose-shift tactics. In our experiments, participants performed squat-to-stand movements under novel force perturbations. They adapted effectively through various adaptive motor control mechanisms to avoid falls, reducing failure rates rapidly. The results indicate a high-level ecological controller in human motor learning that switches objectives between safety and movement efficiency, depending on failure or success. This approach is supported by policy learning, internal model adaptation, and adaptive feedback control. Our findings offer a comprehensive perspective on human motor control, integrating risk management in a hierarchical reinforcement learning framework for real-world environments.},
}
@article {pmid40344217,
year = {2025},
author = {Schindler, Z and Larysch, E and Fornoff, F and Kröner, K and Obladen, N and Klein, AM and Seifert, T and Vonderach, C and Morhart, C},
title = {Flower power: Modeling floral resources of wild cherry (Prunus avium L.) for bee pollinators based on 3D data.},
journal = {Ecology},
volume = {106},
number = {5},
pages = {e70103},
pmid = {40344217},
issn = {1939-9170},
support = {2819NA071//Bundesministerium f&#xfc;r Ern&#xe4;hrung und Landwirtschaft/ ; },
mesh = {*Pollination/physiology ; *Flowers/physiology ; Animals ; Bees/physiology ; *Models, Biological ; *Prunus avium/physiology ; },
abstract = {Pollinator declines pose a threat to ecosystems and food production. Agriculture contributes to, but also suffers from, the erosion of pollination services. Our study explores the potential of trees in agricultural landscapes to support pollinators by providing floral resources. Our overarching objective is the quantification of floral resources produced by wild cherry (Prunus avium L.) that can be used by flower-visiting and pollinating insects such as bees. Using an innovative approach, we combine pollen measurements with manual counts of flowers on branches and 3D data derived from terrestrial laser scanning. This approach allows us to scale up flower numbers from branches to entire trees. The derived models for estimating the probability of flower occurrence (R[2] c = 0.52, R[2] m = 0.50) and the number of flowers per branch (R[2] c = 0.88, R[2] m = 0.84), as well as the number of flowers per tree (R[2] = 0.83), show good model fits with only a small set of predictors. The model fits indicate that, at the branch level, predicting flowering probability is more challenging than predicting flower abundance. We found differences in the number of flowers per branch in different crown sections, suggesting that floral resources are heterogeneously distributed. Furthermore, we demonstrate that the number of flowers per tree increases exponentially with tree dimension (stem diameter, crown volume). Therefore, large trees provide disproportionately more floral resources than small trees and are particularly worthy of conservation efforts. For example, our models estimate that a single tree with a stem diameter of 25 cm carries 195,535 flowers (95% CI: 159,991-237,318), thus providing about 57 cm[3] (95% CI: 32-88 cm[3]) of pollen and producing 170 g (95% CI: 48-345 g) nectar sugar per 24 h. This amount of pollen is sufficient to rear, for example, 5202 larvae (95% CI: 2886-8022) of Lasioglossum laticeps, a common and generalist sweat bee of cherry trees. In contrast, a smaller tree with a stem diameter of 10 cm provides only 8% of these resources. In conclusion, we demonstrate how our results contribute to the broader single-large-or-several-small debate in nature conservation by highlighting the value of large trees. Additionally, we show how information gathered at the branch level may be nondestructively upscaled to entire trees.},
}
@article {pmid40344895,
year = {2025},
author = {Kičić, M and Scheuer, S and Korpilo, S and Vuletić, D and Seletković, A and Haase, D and Krajter Ostoić, S},
title = {Relationships between urban green space types, cultural ecosystem services and disservices - a Public Participation Geographic Information System study in Zagreb, Croatia.},
journal = {The Science of the total environment},
volume = {981},
number = {},
pages = {179549},
doi = {10.1016/j.scitotenv.2025.179549},
pmid = {40344895},
issn = {1879-1026},
mesh = {Croatia ; *Geographic Information Systems ; Cities ; *Ecosystem ; *Conservation of Natural Resources/methods ; *Community Participation ; Humans ; *Parks, Recreational ; },
abstract = {Urban green spaces are important providers of ecosystem services in cities, however cultural ecosystem services remain difficult to quantify. Different types of urban green spaces provide various cultural ecosystem services and differ in how they are perceived and utilized by citizens. In this study, we used a Public Participation GIS (PPGIS) survey to collect data on citizens' perceptions and use of cultural ecosystem services and disservices provided by different types of urban green spaces in Zagreb, Croatia. We collected spatial data from 384 respondents on the perceived provision of 19 different attributes of cultural ecosystem services and disservices in 20 defined types of urban green spaces. We used descriptive statistics, spatial metrics, multivariate analysis and visualization techniques to explore and explain 5757 spatial points collected with the PPGIS questionnaire. Results confirm the importance of parks and forests but also that the water elements and greenery around residential buildings serve as important urban green space for providing benefits for citizens of Zagreb. Based on results presented, cultural ecosystem services are perceived as more important than disservices but in some places both co-exist. Our study builds on current literature by providing a systematic, city-wide assessment of cultural ecosystem services related to different types of urban green spaces, while advancing the availability of methods for their quantification.},
}
@article {pmid40345178,
year = {2025},
author = {O'Callaghan, ME and Casey, M and Pearl, D and Hickey, O and Fosse, A and Sigurðsson, SE and Savage, DW and Vehviläinen-Julkunen, K and Bykachev, K and Parviainen, A and Parker, H and Condell, J and Leavey, G and Hart, N and Weihe, P and Petersen, MS and Glynn, L},
title = {COVID-19 open data: An ecological study and international collaboration examining pandemic trends in Northern Periphery arctic countries.},
journal = {Health informatics journal},
volume = {31},
number = {2},
pages = {14604582251315588},
doi = {10.1177/14604582251315588},
pmid = {40345178},
issn = {1741-2811},
mesh = {*International Cooperation ; Humans ; *COVID-19/epidemiology ; Arctic Regions/epidemiology ; *Pandemics/statistics &amp; numerical data ; SARS-CoV-2 ; *Public Health/trends ; },
abstract = {Objectives: In the early stages of the COVID-19 pandemic, evidence generation lagged behind public health responses. This study describes an international collaboration of frontline clinicians who used open data describing COVID-19 trends to generate "practice-based evidence". Methods: Open data resources from nine Northern Periphery and Arctic (NPA) countries were harnessed using the open-source programming language 'R' and our collaborations analyses and insights were published on a public-facing website. The website's visualisations guided teleconference discussions from September 2020 to March 2021, focusing on contextualizing national responses, especially in rural regions. Results: This project facilitated shared learning from COVID-19 trends and highlighted key aspects of national responses. Notably, rural NPA regions experienced less COVID-19 cases and mortality in the first year of the pandemic. Conclusion: This international collaborative effort, driven by open data analysis, provided a platform to share real-world insights. The study offers a potential template for future pandemics and emphasises the importance of sustaining open data resources, including granular data like excess mortality, for effective pandemic learning.},
}
@article {pmid40346072,
year = {2025},
author = {Bosso, L and Saviano, S and Abagnale, M and Bellardini, D and Bolinesi, F and Botte, V and Buondonno, A and Carotenuto, Y and Casotti, R and Chiusano, ML and Cipolletta, F and Conversano, F and De Domenico, F and Del Gaizo, G and Donnarumma, V and Furia, M and Iudicone, D and Kokoszka, F and Laface, F and Licandro, P and Mangoni, O and Margiotta, F and Mazzocchi, MG and Miralto, M and Montresor, M and Pansera, M and Pedà, C and Percopo, I and Raffini, F and Russo, L and Romeo, T and Saggiomo, M and Sarno, D and Trano, AC and Vannini, J and Vargiu, M and Zampicinini, G and Zingone, A and Cianelli, D and D'Alelio, D},
title = {GIS-based integration of marine data for assessment and management of a highly anthropized coastal area.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16200},
pmid = {40346072},
issn = {2045-2322},
mesh = {Italy ; *Geographic Information Systems ; *Environmental Monitoring/methods ; Ecosystem ; Humans ; *Conservation of Natural Resources ; Oceans and Seas ; Animals ; Food Chain ; },
abstract = {Monitoring coastal marine environments by evaluating and comparing their chemical, physical, biological, and anthropogenic components is essential for ecological assessment and socio-economic development. In this study, we conducted an integrated multivariate analysis to assess the descriptors of the Marine Strategy Framework Directive at a regional scale in the Tyrrhenian Sea (Italy), with a specific focus on the densely populated coastal zone of the Campania region. Physical, chemical, and biological data were collected and analyzed in 22 sampling sites during three oceanographic surveys in the Gulf of Gaeta (GoG), Naples (GoN), and Salerno (GoS) in autumn 2020. Our results indicated that these three gulfs were distinct overall, with GoN being more divergent and heterogeneous than GoG and GoS. The marine area studied in the GoN had more favorable hydrographic and trophic conditions and food web characteristics, except for the mesozooplankton biomass, and was closer to socio-economic factors compared to the GoS and GoG. Our analysis helped us find the key ecological features that define different sub-regions and connect them to social and economic factors, including human activities. We highlighted the relevance of primary and secondary variables in terms of the comprehensive ecological assessment of a marine area and its impact on specific socio-economic activities. These findings support the need to describe and integrate multiple descriptors at the spatial scale.},
}
@article {pmid40346497,
year = {2025},
author = {Sigwart, JD and Wong, NLWS and González, VL and Machado, FM and Greve, C and Schell, T and Chen, Z},
title = {Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {460},
pmid = {40346497},
issn = {1471-2164},
mesh = {Animals ; *Bivalvia/genetics/anatomy &amp; histology/classification ; Phylogeny ; *Genome ; *Animal Shells/anatomy &amp; histology ; *Geologic Sediments ; *Adaptation, Physiological/genetics ; *Genomics/methods ; },
abstract = {BACKGROUND: In this study, we present the first chromosome-scale genome of Verpa penis (Linnaeus, 1758), and the first for the bivalve clade Anomalodesmata. The present study has two separate foci. Primarily, we provide the genetic resource to bridge further studies from genome to phenome and propose hypotheses to guide future empirical investigations. Secondarily, based on morphology, we outline a conceptual exploration to address their adaptation. Watering-pot shells have been called "the weirdest bivalves" for their fused tubular shell resembling the spout of a watering can. This adventitious tube arose twice convergently in clavagelloidean bivalves. However, previous literature has never provided a convincing adaptive pathway.<br><br>RESULTS: The genome assembly of V. penis was about 507&#xa0;Mb, with contig N50 of 5.33&#xa0;Mb, and has 96.5% of sequences anchored onto 19 pseudochromosomes. Phylogenomic analyses of this new genome in context of other bivalves confirms the placement for Anomalodesmata as sister to the clade Imparidentia. Contrary to expectations from its highly modified body plan, there is no evidence of chromosome reduction compared to the ancestral karyotype of heterodont bivalves (1&#xa0;N&#x2009;=&#x2009;19). Drawing on established principles from engineering as well as morphology, the thought experiment about the adventitious tube seeks to extend current understanding by exploring parallels with other built structures. A new hypothesis explains one possible interpretation of the adaptive significance of this body form: it is potentially structurally optimised for vertical stability in relatively soft sediments, with parallels to the engineering principles of a suction anchor.<br><br>CONCLUSIONS: While the conclusions presented here on morphological interpretations are theoretical, this serves as a foundation for further empirical validation and refinement. Our study offers new insights to a long-standing mystery in molluscan body forms and provides genomic resources that are relevant to understanding molluscan evolution, biomineralisation, and biomimetic design.},
}
@article {pmid40348945,
year = {2025},
author = {Chen, J and Liu, J and Liu, S and Li, Z and Gao, C and Wang, Z and Huang, S and Jiang, Z and Yang, H},
title = {Multiomics reveals the synergistic response of gut microbiota and spider A. ventricosus to lead and cadmium toxicity.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {114},
number = {5},
pages = {77},
pmid = {40348945},
issn = {1432-0800},
support = {32001205//National Natural Science Foundation of China/ ; 2023JJ30299//Natural Science Foundation of Hunan Province/ ; 2019JJ50236//Natural Science Foundation of Hunan Province/ ; },
mesh = {Animals ; *Cadmium/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Lead/toxicity ; *Spiders/physiology/drug effects ; Metagenomics ; Multiomics ; },
abstract = {The potential crosstalk between the host and gut microbiota (GM) under heavy metal compound pollution remains unexplored. Herein, using comprehensive analysis of metagenomics, metabolomics, behavioral analysis, and cell morphology to investigate the causal relationship between GM and host responses to cadmium (Cd) and lead (Pb) toxicities. Results indicate that Pb and Cd pollution, alone or together, hinder spider predatory behavior and change the composition and function of GM. Combined exposure reduces protein and exogenous compound metabolism, while single exposure affects energy and lipid metabolism. Gut microbiota helps spider antioxidant activity by increasing glutathione, lipoic acid, and L-cysteine. Oxidative damage, increased Enterobacteriaceae (Salmonella), and lipopolysaccharide (LPS) may harm the midgut barrier. Upregulation of choline and acetylcholine, and downregulation of spermidine, may initiate neurotoxicity. Inhibiting actinomycetes might boost sodium gallate for detoxifying single contaminants. Combined pollution detoxification may involve downregulation of indole synthesis metabolic bacteria, tryptophan, indole metabolites, cytochrome P450 (CYP450), and an increase in Desulfobulbia could remove heavy metals and reduce oxidative stress. Combined pollution has a synergistic effect, making the toxicity of multiple pollutants greater than their individual effects, impacting metal resistance genes (MRGs), and antibiotic resistance ontology (AROs) which used for classifying and describing antibiotic resistance, midgut barrier integrity, oxidative stress, and detoxification. The results help to elucidate the interplay of GM and host's reactions, and aid in monitoring and bioremediation of heavy metal pollution.},
}
@article {pmid40351335,
year = {2024},
author = {Li, S and Fan, C and Kargarandehkordi, A and Sun, Y and Slade, C and Jaiswal, A and Benzo, RM and Phillips, KT and Washington, P},
title = {Monitoring Substance Use with Fitbit Biosignals: A Case Study on Training Deep Learning Models Using Ecological Momentary Assessments and Passive Sensing.},
journal = {AI (Basel, Switzerland)},
volume = {5},
number = {4},
pages = {2725-2738},
pmid = {40351335},
issn = {2673-2688},
support = {U54 GM138062/GM/NIGMS NIH HHS/United States ; },
abstract = {Substance use disorders affect 17.3% of Americans. Digital health solutions that use machine learning to detect substance use from wearable biosignal data can eventually pave the way for real-time digital interventions. However, difficulties in addressing severe between-subject data heterogeneity have hampered the adaptation of machine learning approaches for substance use detection, necessitating more robust technological solutions. We tested the utility of personalized machine learning using participant-specific convolutional neural networks (CNNs) enhanced with self-supervised learning (SSL) to detect drug use. In a pilot feasibility study, we collected data from 9 participants using Fitbit Charge 5 devices, supplemented by ecological momentary assessments to collect real-time labels of substance use. We implemented a baseline 1D-CNN model with traditional supervised learning and an experimental SSL-enhanced model to improve individualized feature extraction under limited label conditions. Results: Among the 9 participants, we achieved an average area under the receiver operating characteristic curve score across participants of 0.695 for the supervised CNNs and 0.729 for the SSL models. Strategic selection of an optimal threshold enabled us to optimize either sensitivity or specificity while maintaining reasonable performance for the other metric. Conclusion: These findings suggest that Fitbit data have the potential to enhance substance use monitoring systems. However, the small sample size in this study limits its generalizability to diverse populations, so we call for future research that explores SSL-powered personalization at a larger scale.},
}
@article {pmid40352255,
year = {2025},
author = {Seminar, KB and Damayanthi, E and Priandana, K and Imantho, H and Ligar, BW and Seminar, AU and Krishnajaya, AD and Aditya, MR and Suherman, MIH and Fillah, IF},
title = {AI-based system for food and beverage selection towards precision nutrition in Indonesian restaurants.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1590523},
pmid = {40352255},
issn = {2296-861X},
abstract = {The complexity surrounding food selection is attributable to the variability in foods, restaurants, and diners. The diversity of foods, where each dish may have a unique recipe across different restaurants, needs to be accounted for in personalized nutrition. However, personalized food selection poses a combinatorial challenge in selecting the most suitable food at a specific restaurant. The key question is how a diner visiting a particular restaurant can be assisted in selecting optimal foods and beverages based on factors such as sex, age, height, weight, and history of non-communicable diseases (NCDs). In this study, a genetic algorithm (GA) is used to develop a system that can address this issue in the context of Indonesian restaurants. In this system, a database with data on registered diners and foods is maintained. Foods comprise staple foods, side dishes, vegetables, and beverages, each containing its energy and nutrient content for a given restaurant. The nutritional adequacy of a single meal is determined by comparing the energy and nutrient content of the menu with the diner's nutritional needs. The novelty of the proposed system lies in combining scientific nutritional data with individual diner profiles for the selection of the best meal for a diner. This system differs from the existing food recommender applications in Indonesia, which typically do not consider specific diners, personalized nutrition, and NCD history. The proposed system is the first developed application prototype for Indonesian restaurants to overcome the inefficiency of the existing applications. In this study, the structure and chromosome content of the food, its corresponding energy and nutrient contents, and GA operators such as crossover, mutation, and tournament selection for determining the best meal using the defined fitness functions are discussed. The proposed system has been tested at Karimata Restaurant and proved to be highly suitable for the ultimate goal of meal selection for individual diners with different needs, and it can be replicated at other restaurants. Furthermore, user-centered evaluation has revealed that the system (a) increases nutritional understanding and health awareness; (b) is easy to use with comprehensive functions; and (c) promotes user satisfaction with personalized recommendations.},
}
@article {pmid40357641,
year = {2025},
author = {Pourmohsenin, B and Wiese, A and Ziemert, N},
title = {AutoMLST2: a web server for phylogeny and microbial taxonomy.},
journal = {Nucleic acids research},
volume = {53},
number = {W1},
pages = {W45-W50},
pmid = {40357641},
issn = {1362-4962},
support = {101000794//H2020-FNR-11-2020: SECRETED/ ; TTU09.717//German Center for Infection Research/ ; 390838134//Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection/ ; },
mesh = {*Phylogeny ; *Software ; Internet ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Genome, Bacterial ; Genome, Archaeal ; Databases, Genetic ; },
abstract = {Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology, ecology, and drug discovery, yet it remains a challenging task. AutoMLST2 (https://automlst2.ziemertlab.com) is a web server designed to facilitate automated phylogenetic reconstruction and microbial taxonomy analysis for bacterial and archaeal genomes. It builds on the foundation of AutoMLST, which remains widely used due to its user-friendly interface compared to similar tools. Given its continued popularity and utility, we have enhanced AutoMLST to leverage newer reference databases and computational tools. AutoMLST2 integrates the Genome Taxonomy Database, extends support to archaeal genomes, and improves analytical flexibility. Key improvements include more customizable processing modes, containerization to prevent queue accumulations, and parallel computing for large-scale studies. By incorporating up-to-date databases and workflows, AutoMLST2 continues to provide an accessible and efficient platform for researchers in microbiology, evolutionary ecology, and natural product discovery.},
}
@article {pmid40359589,
year = {2025},
author = {Silva, MKP and Nicoleti, VYU and Rodrigues, BDPP and Araujo, ASF and Ellwanger, JH and de Almeida, JM and Lemos, LN},
title = {Exploring deep learning in phage discovery and characterization.},
journal = {Virology},
volume = {609},
number = {},
pages = {110559},
doi = {10.1016/j.virol.2025.110559},
pmid = {40359589},
issn = {1096-0341},
mesh = {*Deep Learning ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Metagenomics/methods ; Computational Biology/methods ; Genome, Viral ; Neural Networks, Computer ; Metagenome ; Algorithms ; },
abstract = {Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The discovery of novel bacteriophages using large-scale metagenomic data has been accelerated by the accessibility of deep learning (Artificial Intelligence), the increased computing power of graphical processing units (GPUs), and new bioinformatics tools. This review addresses the recent revolution in bacteriophage research, ranging from the adoption of neural network algorithms applied to metagenomic data to the use of pre-trained language models, such as BERT, which have improved the reconstruction of viral metagenome-assembled genomes (vMAGs). This article also discusses the main aspects of bacteriophage biology using deep learning, highlighting the advances and limitations of this approach. Finally, prospects of deep-learning-based metagenomic algorithms and recommendations for future investigations are described.},
}
@article {pmid40361012,
year = {2025},
author = {Barkan, R and Cooke, I and Watson, SA and Strugnell, JM},
title = {Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis).},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {474},
pmid = {40361012},
issn = {1471-2164},
mesh = {Animals ; *Gastropoda/genetics/physiology ; *Heat-Shock Response/genetics ; *Gene Expression Profiling ; *Transcriptome ; Computational Biology/methods ; },
abstract = {BACKGROUND: As climate change causes marine heat waves to become more intense and frequent, marine species increasingly suffer from heat stress. This stress can result in reduced growth, disrupted breeding cycles, vulnerability to diseases and pathogens, and increased mortality rates. Abalone (genus Haliotis) are an ecologically significant group of marine gastropods and are among the most highly valued seafood products. However, heat stress events have had devastating impacts on both farmed and wild populations. Members of this genus are among the most susceptible marine species to climate change impacts, with over 40% of all abalone species listed as threatened with extinction. This has motivated researchers to explore the genetics linked to heat stress in abalone. A substantial portion of publicly available studies has employed transcriptomic approaches to investigate abalone genetic response to heat stress. However, to date, no meta-analysis has been conducted to determine the common response to heat stress (i.e. the core response) across the genus. This study uses a standardized bioinformatic pipeline to reanalyze and compare publicly available RNA-seq datasets from different heat stress studies on abalone.<br><br>RESULTS: Nine publicly available RNA-seq datasets from nine different heat-stress studies on abalone from seven different abalone species and three hybrids were included in the meta-analysis. We identified a core set of 74 differentially expressed genes (DEGs) in response to heat stress in at least seven out of nine studies. This core set of DEGs mainly included genes associated with alternative splicing, heat shock proteins (HSPs), Ubiquitin-Proteasome System (UPS), and other protein folding and protein processing pathways.<br><br>CONCLUSIONS: The detection of a consistent set of genes that respond to heat stress across various studies, despite differences in experimental design (e.g. stress intensity, species studied-geographical distribution, preferred temperature range, etc.), strengthens our proposal that these genes are key elements of the heat stress response in abalone. The identification of the core response to heat stress in abalone lays an important foundation for future research. Ultimately, this study will aid conservation efforts and aquaculture through the identification of resilient populations, genetic-based breeding programs, possible manipulations such as early exposure to stress, gene editing and the use of immunostimulants to enhance thermal tolerance.},
}
@article {pmid40361718,
year = {2025},
author = {Nițescu, M and Nedelescu, MM and Moroşan, E and Simionescu, AA and Furtunescu, FL and Ştefănescu, BE and Tusaliu, M and Panaitescu, E and Stanciu, AM and Stoian, IM},
title = {Assessment of Food Safety Knowledge and Practices Among Medical Students.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
pmid = {40361718},
issn = {2304-8158},
abstract = {Food safety is an important requirement for protecting human health worldwide. In particular, medical students' education on food safety is essential for them as future physicians, and university education is the first step in acquiring this knowledge. We performed an online survey with 1277 respondents among medical students to assess knowledge, attitudes, and practices (KAPs) related to food safety regarding microbiological contamination. Our findings showed that more than half of the respondents presented a low level of food safety knowledge, with a score between 11-60 points, and only 6% managed to score between 81 and 100 points, which was considered a high level of knowledge. On the contrary, we found that most participants had a high level of good practice: 58% scored more than 25 points, 39% had an average level of good practice (scoring between 21 and 25 points), and 3% of respondents had a low level of good practice (scoring below 21 points). We also noticed a statistically significant difference between total scores of preclinical and clinical years of study among medical students (p = 0.005) regarding food safety knowledge. The frequency of cooking was positively correlated with the level of food safety knowledge, but not with food safety practices. Our study shows that better knowledge on food safety is needed among medical students. Improving knowledge and awareness of food safety in relation to microbiological contamination is a good way to protect themselves and to promote the correct food safety knowledge and measures among their patients.},
}
@article {pmid40365044,
year = {2025},
author = {Ogba, P and Baumann, A and Alabi, T and Archer, N and Eniojukan, J and Ibhawoh, B and DiLiberto, DD},
title = {Enhancing IPTp-SP uptake: Community and stakeholder recommendations for improving access and utilisation - insights from a study in Bayelsa-Nigeria.},
journal = {MalariaWorld journal},
volume = {16},
number = {},
pages = {9},
pmid = {40365044},
issn = {2214-4374},
abstract = {BACKGROUND: Malaria remains a major global health challenge, disproportionately affecting pregnant women and children. In Nigeria, malaria in pregnancy contributes to 70.5% of maternal morbidity and 41.1% of maternal mortality. Recognising these risks, the World Health Organization recommends intermittent preventive treatment with sulfadoxine-pyrimethamine (IPTp-SP) as a key strategy for malaria in pregnancy prevention. However, despite its proven effectiveness, pregnant women's uptake of IPTp-SP remains unacceptably low. This study presents participant-driven recommendations to enhance IPTp-SP uptake, structured within the socio-ecological framework.<br><br>MATERIALS AND METHODS: This study employed an exploratory descriptive qualitative approach to examine the community-level contextual factors influencing IPTp-SP uptake. Data were collected from 53 participants in two communities in Bayelsa, Nigeria. Individual interviews were conducted with 17 key stakeholders (spouses, mothers-in-law, religious leaders, community leaders, and traditional birth attendants) and 6 focus group discussions with 36 pregnant women. Data management and coding were conducted using NVivo 14 QSR International software, following an inductive-deductive thematic analysis approach.<br><br>RESULTS: Participants proposed multi-level interventions to address barriers to IPTp-SP uptake at the individual, interpersonal, community, and healthcare system levels. Key recommendations include: Community-wide education campaigns to raise awareness of IPTp-SP's benefits; comprehensive training for healthcare providers to enhance their knowledge and prescription of IPTp-SP; integration of traditional birth attendants into the formal healthcare system; community-level distribution of IPTp-SP to improve access for pregnant women who do not attend antenatal care; government intervention to ensure the functionality of health centers; addressing workforce shortages, and guaranteeing a consistent supply of IPTp-SP.<br><br>CONCLUSION: These evidence-based, participant-driven recommendations offer a holistic and scalable strategy to improve pregnant women's uptake of IPTp-SP in Nigeria and other malaria-endemic regions. Implementing these recommendations can strengthen malaria prevention efforts, improve maternal and child health outcomes, and support broader public health initiatives.},
}
@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 &amp; numerical data ; Male ; Adult ; Middle Aged ; Female ; Motorcycles/statistics &amp; numerical data ; *Wounds and Injuries/mortality ; Adolescent ; Young Adult ; Pedestrians/statistics &amp; numerical data ; Databases, Factual ; Bicycling/injuries/statistics &amp; numerical data ; Aged ; Child ; },
abstract = {OBJECTIVES: To identify and address potential misclassification of traffic fatalities in Colombia from 2010 to 2021.<br><br>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.<br><br>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%.<br><br>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.},
}
@article {pmid40367572,
year = {2025},
author = {Wang, H and Li, L and Wu, J and Yuan, X and Hong, L and Pu, L and Qin, S and Li, L and Yang, H and Zhang, J},
title = {Multi-omics analyses reveal differences in intestinal flora composition and serum metabolites in Cherry Valley broiler ducks of different body weights.},
journal = {Poultry science},
volume = {104},
number = {8},
pages = {105275},
pmid = {40367572},
issn = {1525-3171},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Ducks/microbiology/blood/physiology/growth &amp; development ; *Body Weight ; RNA, Ribosomal, 16S/analysis ; Metabolomics ; *Metabolome ; Male ; Bacteria/classification/isolation &amp; purification ; Multiomics ; },
abstract = {Fledgling broiler ducks vary in body weight and growth rate. The aim of this study was to investigate the relationship between serum metabolites and the intestinal microbiota in Cherry Valley broiler ducks with different finishing weights and to reveal differences in their metabolic regulation and microbial composition. Serum and cecum content samples were collected from Cherry Valley broiler ducks of different finishing weights. Metabolites were identified and compared using untargeted metabolomics, 16S rRNA gene sequencing, multivariate statistics and bioinformatics. Six key findings emerged. First, serum biochemical parameters showed that AST and ALT levels were significantly lower in the high weight group (Group H) than in the low weight group (Group L), and serum immunoglobulin IgG levels were significantly higher in group H. Second, the chorionic height to crypt depth ratio of the duodenum was significantly higher in group H than in group L. Third, the gut microbial community diversity or abundance was lower in broiler ducks in group L. Fourth, LEfSe analysis showed that the biomarker for group L was Streptococcus, whereas for group H it was Faecalibacterium. Fifth, a total of 127 differential metabolites were identified (49 up-regulated and 78 down-regulated). Finally, Spearman's correlation analysis showed that Spearman's correlation analyses showed that the Lipid-related serum metabolites were higher in low-body recombinant broiler ducks, mainly Lathosterol, Cholesterol, Cynaratriol and Leukotriene B4. In addition to lipid-associated serum metabolites in high-body recombination, The water-soluble vitamin-like metabolite Pantothenate and the antibiotic-like metabolite Tylosin were high. The cecum microbiota is strongly associated with metabolites, especially Faecalibacterium, unclassified Tannerellaceae, Subdoligranulum, Alistipes, and [Ruminococcus] torques_group, with which it exhibits strong Correlation. Broiler ducks with higher body weights have a better intestinal villous structure, enhanced digestion and absorption, higher levels of immunoglobulin secretion and superior growth performance. Broiler ducks with different body weights differed in plasma metabolites and cecum flora. Spearman's correlation analyses showed that the Correlation between differential metabolites and differential gut microbial genera.},
}
@article {pmid40368894,
year = {2025},
author = {Yi, S and Li, X and Liu, Y and Dong, X and Tu, W},
title = {A sub-meter resolution urban surface albedo dataset for 34 U.S. cities based on deep learning.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {789},
pmid = {40368894},
issn = {2052-4463},
support = {2314709//National Science Foundation (NSF)/ ; },
abstract = {Surface albedo is a key determinant of urban heat islands, which modulates the amount of solar energy absorbed or reflected by urban surfaces, influencing microclimate and thermal comfort. However, high-resolution albedo is usually not available, which makes the understanding of the urban thermal environment at hyperlocal difficult. This study presents the first high-resolution urban albedo maps for 34 major U.S. cities using advanced deep learning models and multisource remote sensing data. By differentiating between impervious and pervious surfaces using a combination of NAIP imagery, roof albedo data, building footprints, land cover classifications, and Sentinel-2 imagery, this work achieves sub-meter resolution in albedo mapping. Employing U-Net for impervious surface classification along with impervious (ISA) and pervious surface albedo (PSA) prediction, these models were validated in selected cities, with ISA showing an R[2] of 0.9028 and MAE of 0.0057, and PSA demonstrating an R[2] of 0.9538 and MAE of 0.0027, highlighting the precision and reliability. The datasets, made publicly available, offer essential insights for urban planning and environmental monitoring.},
}
@article {pmid40369175,
year = {2025},
author = {Barroux, M and Househam, J and Lakatos, E and Ronel, T and Baker, AM and Salié, H and Mossner, M and Smith, K and Kimberley, C and Nowinski, S and Berner, A and Gunasri, V and Borgmann, M and Liffers, S and Jansen, M and Caravagna, G and Steiger, K and Slotta-Huspenina, J and Weichert, W and Zapata, L and Giota, E and Lorenzen, S and Alberstmeier, M and Chain, B and Friess, H and Bengsch, B and Schmid, RM and Siveke, JT and Quante, M and Graham, TA},
title = {Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of esophageal adenocarcinoma.},
journal = {Nature cancer},
volume = {6},
number = {5},
pages = {820-837},
pmid = {40369175},
issn = {2662-1347},
support = {U54 CA217376/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Esophageal Neoplasms/immunology/genetics/therapy/pathology/drug therapy ; *Tumor Microenvironment/immunology/genetics/drug effects ; *Adenocarcinoma/immunology/genetics/therapy/pathology/drug therapy ; Neoadjuvant Therapy ; Male ; Female ; Middle Aged ; Aged ; Transcriptome ; },
abstract = {Locally advanced esophageal adenocarcinoma remains difficult to treat and the ecological and evolutionary dynamics responsible for resistance and recurrence are incompletely understood. Here, we performed longitudinal multiomic analysis of patients with esophageal adenocarcinoma in the MEMORI trial. Multi-region multi-timepoint whole-exome and paired transcriptome sequencing was performed on 27 patients before, during and after neoadjuvant treatment. We found major transcriptomic changes during treatment with upregulation of immune, stromal and oncogenic pathways. Genetic data revealed that clonal sweeps through treatment were rare. Imaging mass cytometry and T cell receptor sequencing revealed remodeling of the tumor microenvironment during treatment. The presence of genetic immune escape, a less-cytotoxic T cell phenotype and a lack of clonal T cell expansions were linked to poor treatment response. In summary, there were widespread transcriptional and environmental changes through treatment, with limited clonal replacement, suggestive of phenotypic plasticity.},
}
@article {pmid40369670,
year = {2025},
author = {Wu, B and Luo, D and Yue, Y and Yan, H and He, M and Ma, X and Zhao, B and Xu, B and Zhu, J and Wang, J and Jia, J and Sun, M and Xie, Z and Wang, X and Huang, L},
title = {New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {128},
pmid = {40369670},
issn = {1474-760X},
support = {2021YFYZ0013//Sichuan Province Research Grant/ ; SCCXTD-2020-16//Modern Agricultural Industry System Sichuan Forage Innovation Team/ ; 32071867//National Natural Science Foundation of China/ ; },
mesh = {*Panicum/genetics/physiology ; *Haplotypes ; *Genome, Plant ; *Cold-Shock Response/genetics ; Ecotype ; Gene Expression Regulation, Plant ; Genome-Wide Association Study ; Cold Temperature ; Gene Expression Profiling ; Plant Proteins/genetics/metabolism ; Transcriptome ; Multiomics ; },
abstract = {BACKGROUND: Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance compared to the lowland ecotype, but the underlying molecular mechanisms remain unclear.<br><br>RESULTS: Here, we present a high-quality haplotype-resolved genome of the upland ecotype "Jingji31." We then conduct multi-omics analysis to explore the mechanism underlying its cold tolerance. By comparative transcriptome analysis of the upland and lowland ecotypes, we identify many genes with ecotype-specific differential expression, particularly members of the cold-responsive (COR) gene family, under cold stress. Notably, AFB1, ATL80, HOS10, and STRS2 gene families show opposite expression changes between the two ecotypes. Based on the haplotype-resolved genome of "Jingji31," we detect more cold-induced allele-specific expression genes in the upland ecotype than in the lowland ecotype, and these genes are significantly enriched in the COR gene family. By genome-wide association study, we detect an association signal related to the overwintering rate, which overlaps with a selective sweep region containing a cytochrome P450 gene highly expressed under cold stress. Heterologous overexpression of this gene in rice alleviates leaf chlorosis and wilting under cold stress. We also verify that expression of this gene is suppressed by a structural variation in the promoter region.<br><br>CONCLUSIONS: Based on the high-quality haplotype-resolved genome and multi-omics analysis of upland switchgrass, we characterize candidate genes responsible for cold tolerance. This study advances our understanding of plant cold tolerance, which provides crop breeding for improved cold tolerance.},
}
@article {pmid40371522,
year = {2025},
author = {Dong, WZ and Su, WC and Gou, R and Zhou, HY and Liu, DY},
title = {[Spatial and temporal evolution of ecological risk in Guizhou Province, China from the perspective of ecosystem services and ecosystem health].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {4},
pages = {1211-1221},
doi = {10.13287/j.1001-9332.202504.021},
pmid = {40371522},
issn = {1001-9332},
mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; Risk Assessment ; Rivers ; Spatio-Temporal Analysis ; Geographic Information Systems ; *Environmental Monitoring/methods ; Ecology ; Models, Theoretical ; },
abstract = {Guizhou Province is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River. Karst landform in Guizhou is developed, with fragile ecological background. The ecological risk assessment and control of Karst landform are of great significance to ecological security and sustainable development of southwest China and the upper reaches of those two rivers. Based on the InVEST model and vigor-organization-resi-lience model, we quantitatively evaluated the ecosystem services and ecosystem health and constructed the ecological risk assessment model of Guizhou Province. With the help of GIS technology, spatial autocorrelation analysis method and gravity center migration model, we analyzed the spatial and temporal variations of ecological risk in Guizhou Province from 2000 to 2020. The results showed that ecosystem services in Guizhou Province increased from 2000 to 2020, with an annual average growth rate of 0.3%. The ecosystem health status was generally well and showed a good trend, and the annual average growth rate of ecosystem health was 12.6%. The ecological risk was dominated by medium ecological risk. The proportion of extremely low ecological risk area and low ecological risk area increased, the proportion of medium and above ecological risk area decreased, and the overall ecological risk showed a downward trend. The low ecological risk areas were mainly located in the south and southeast of Guizhou Province, while the high ecological risk areas were distributed in the central, western and northern parts of Guizhou Province. The global Moran's I of ecological risk in 2000, 2005, 2010, 2015, and 2020 were 0.856, 0.836, 0.844, 0.804, and 0.768, respectively, indicating that the positive correlation of ecological risk in spatial distribution, but the spatial correlation and spatial agglomeration characteristics were weakened. During the study period, the centroid and trajectory of ecological risk in Guizhou Province were consistent with the distribution area of its corresponding ecological risk. From 2000 to 2020, the spatial distribution pattern of ecological risk in Guizhou Pro-vince was relatively stable. With the evolution of time, the dispersion of spatial distribution of extremely high ecological risk and low ecological risk increased. Ecological risk assessment based on ecosystem services and ecosystem health would provide scientific basis for regional ecological risk management and control.},
}
@article {pmid40371524,
year = {2025},
author = {Li, YH and Zhang, Y},
title = {[Wilderness network construction in Lincang City of Yunnan Province, Southwest China based on landscape connectivity].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {4},
pages = {1233-1243},
doi = {10.13287/j.1001-9332.202504.026},
pmid = {40371524},
issn = {1001-9332},
mesh = {China ; *Conservation of Natural Resources/methods ; *Ecosystem ; Geographic Information Systems ; *Wilderness ; Cities ; *Environment Design ; Models, Theoretical ; *City Planning ; },
abstract = {Constructing wilderness networks based on landscape connectivity is crucial for wilderness conservation. We calculated the continuous spectrum of the wilderness with GIS, identified wilderness sources with morphological spatial pattern analysis (MSPA), constructed wilderness corridors and networks and extracted wilderness strategic points with minimum cumulative resistance model (MCR) and circuit theory. We further analyzed the characte-ristics of the wilderness network, and proposed wilderness protection strategies and ecological planning suggestions for Lincang City. Results showed that wilderness was mainly distributed at 1000-2500 m elevation, with a spatial pattern of more in the south and east, less in the north and west in Lincang City. Grade 3 wilderness covered 55% of the total area, indicating high quality of the study area. Based on the MSPA analysis, we found 27 wilderness sources, most of which were distributed in the eastern and southern areas such as Linxiang and Cangyuan. The western and northern such as Fengqing and Yongde had fewer wilderness sources. There were 63 wilderness corridors in the wilderness network, including 16 important corridors and 47 general corridors. There were 186 strategic points in the wilderness network, including 53 wilderness nodes and 133 barrier points. We constructed the wilderness network of Lincang based in the identified wilderness source areas and extracted wilderness corridors, which had the advantages of high stability, strong resistance to interference, efficient connectivity. Finally, we proposed the "three-zone as a whole" protection strategy and ecological planning suggestions, which had referential value for establishing an ecological security pattern in Lincang City and the practicalization of wilderness protection in China.},
}
@article {pmid40371923,
year = {2025},
author = {Cirino, T and Pinto, L and Iwan, M and Dougha, A and Lučić, B and Kraljević, A and Navoyan, Z and Tevosyan, A and Yeghiazaryan, H and Khondkaryan, L and Abelyan, N and Atoyan, V and Babayan, N and Iwashita, Y and Kimura, K and Komasaka, T and Shishido, K and Nakamura, T and Asada, M and Jain, S and Zakharov, AV and Wang, H and Liu, W and Chupakhin, V and Uesawa, Y},
title = {Consensus Modeling Strategies for Predicting Transthyretin Binding Affinity from Tox24 Challenge Data.},
journal = {Chemical research in toxicology},
volume = {38},
number = {6},
pages = {1061-1071},
pmid = {40371923},
issn = {1520-5010},
mesh = {*Prealbumin/metabolism/chemistry ; Humans ; Protein Binding ; Binding Sites ; },
abstract = {Transthyretin (TTR) is a key transporter of the thyroid hormone thyroxine, and chemicals that bind to TTR, displacing the hormone, can disrupt the endocrine system, even at low concentrations. This study evaluates computational modeling strategies developed during the Tox24 Challenge, using a data set of 1512 compounds tested for TTR binding affinity. Individual models from nine top-performing teams were analyzed for performance and uncertainty using regression metrics and applicability domains (AD). Consensus models were developed by averaging predictions across these models, with and without consideration of their ADs. While applying AD constraints in individual models generally improved external prediction accuracy (at the expense of reduced chemical space coverage), it had limited additional benefit for consensus models. Results showed that consensus models outperformed individual models, achieving a root-mean-square error (RMSE) of 19.8% on the test set, compared to an average RMSE of 20.9% for the nine individual models. Outliers consistently identified in several of these models indicate potential experimental artifacts and/or activity cliffs, requiring further investigation. Substructure importance analysis revealed that models prioritized different chemical features, and consensus averaging harmonized these divergent perspectives. These findings highlight the value of consensus modeling in improving predictive performance and addressing model limitations. Future work should focus on expanding chemical space coverage and refining experimental data sets to support public health protection.},
}
@article {pmid40376739,
year = {2025},
author = {Arnold, LE and Hendrix, K and Pan, X and Vollebregt, MA and Yu, M and Kerson, C and Arns, M and Hatsu, IE and DeBeus, R and Hollway, J and Roley-Roberts, ME},
title = {Lifestyle Effects in a Randomized Controlled Trial of Neurofeedback for Attention-Deficit/Hyperactivity Disorder.},
journal = {Journal of child and adolescent psychopharmacology},
volume = {35},
number = {9},
pages = {491-499},
doi = {10.1089/cap.2025.0019},
pmid = {40376739},
issn = {1557-8992},
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/therapy ; Male ; Child ; *Neurofeedback/methods ; Female ; *Life Style ; Exercise ; Surveys and Questionnaires ; Sleep Hygiene ; Treatment Outcome ; },
abstract = {Objectives/Background: Multiple factors influence symptom severity in Attention Deficit/Hyperactivity Disorder (ADHD). We examined four of these: diet, sleep hygiene, exercise, and lighting, in the International Collaborative ADHD Neurofeedback (ICAN) randomized clinical trial, which found large significant improvement with both active neurofeedback and control condition without treatment difference. Methods: A total of 142 participants aged 7-10 had breakfast and lunch intake and exercise recorded at each neurofeedback session. Parents completed the Children's Sleep Habits Questionnaire (CSHQ). Parents and teachers rated inattention on Conners3. Lifestyle changes were correlated with inattention changes. Results: At baseline, CSHQ correlated with parent-rated inattention (r = 0.17, p = 0.04), and length of sleep correlated with teacher-rated inattention (r = 0.20, p = 0.03). From baseline to treatment end food group variety (p = 0.029, d = 0.22) and sleep problems (p < 0.0001, d = -0.49) improved significantly, exercise time and protein intake marginally (p = 0.06 - 0.08). Parent-rated inattention improvement correlated with CSHQ improvement (Rho = 0.26, p = 0.002) and marginally with protein intake increase (Rho = 0.18, p = 0.06). The three components of the light-emitting-diode (LED)-induced circadian pathway hypothesis were significant. Conclusions: Most measures improved, but few significantly. How much they impact classroom attention remains unclear. Although parent ratings of inattention improvement correlated with sleep problems improvement, composited parent/teacher ratings (primary outcome) did not. The circadian pathway hypothesis associated with LED lighting was supported. These findings warrant further studies examining the role sleep hygiene can play in improving ADHD symptoms. Meanwhile, attention to sleep hygiene seems appropriate in any treatment plan for ADHD.},
}
@article {pmid40378227,
year = {2025},
author = {Ha, MK and Postovskaya, A and Kuznetsova, M and Meysman, P and Van Deuren, V and Van Ierssel, S and De Reu, H and Schippers, J and Peeters, K and Besbassi, H and Heyndrickx, L and Willems, B and Mariën, J and Bartholomeus, E and Vercauteren, K and Beutels, P and Van Damme, P and Lion, E and Vlieghe, E and Laukens, K and Coenen, S and Naesens, R and Ariën, KK and Ogunjimi, B},
title = {Celluloepidemiology-A paradigm for quantifying infectious disease dynamics on a population level.},
journal = {Science advances},
volume = {11},
number = {20},
pages = {eadt2926},
pmid = {40378227},
issn = {2375-2548},
mesh = {Humans ; *COVID-19/epidemiology/immunology/virology ; *SARS-CoV-2/immunology ; T-Lymphocytes/immunology ; Machine Learning ; Receptors, Antigen, T-Cell/immunology/metabolism ; Flow Cytometry ; *Communicable Diseases/epidemiology/immunology ; },
abstract = {To complement serology as a tool in public health interventions, we introduced the "celluloepidemiology" paradigm where we leveraged pathogen-specific T cell responses at a population level to advance our epidemiological understanding of infectious diseases, using SARS-CoV-2 as a model. Applying flow cytometry and machine learning on data from more than 500 individuals, we showed that the number of T cells with positive expression of functional markers not only could distinguish patients who recovered from COVID-19 from controls and pre-COVID donors but also identify previously unrecognized asymptomatic patients from mild, moderate, and severe recovered patients. The celluloepidemiology approach was uniquely capable to differentiate health care worker groups with different SARS-CoV-2 exposures from each other. T cell receptor (TCR) profiling strengthened our analysis by revealing that SARS-CoV-2-specific TCRs were more abundant in patients than in controls. We believe that adding data on T cell reactivity will complement serology and augment the value of infection morbidity modeling for populations.},
}
@article {pmid40378285,
year = {2025},
author = {Campbell, KR and Goeva, A},
title = {Cells Keep Diverse Company in Diseased Tissues.},
journal = {Cancer research},
volume = {85},
number = {13},
pages = {2351-2352},
doi = {10.1158/0008-5472.CAN-25-2070},
pmid = {40378285},
issn = {1538-7445},
mesh = {Disease Progression ; *Multiomics/methods ; *Spatial Analysis ; Palatine Tonsil/cytology/pathology ; Germinal Center/cytology/pathology ; Spleen/cytology/pathology ; Lupus Erythematosus, Systemic/pathology ; Disease Models, Animal ; *Neoplasms/mortality/pathology ; Humans ; Animals ; Mice ; },
abstract = {Emerging spatial profiling technologies have revolutionized our understanding of how tissue architecture shapes disease progression, yet the contribution of cellular diversity remains underexplored. In this issue, Ding and colleagues introduce multiomics and ecological spatial analysis (MESA), an ecology-inspired framework that integrates spatial and single-cell expression data to quantify tissue diversity across multiple scales. MESA both identifies distinct cellular neighborhoods and computes a variety of diversity metrics alongside the identification of diversity "hotspots." Applied to human tonsil tissue, MESA revealed previously undetected germinal center organization, whereas in spleen tissue of a murine lupus model, MESA highlights increasing cellular diversity with disease progression. Importantly, diversity hotspots do not correspond to conventional compartments identified by existing methods, presenting an orthogonal metric of spatial organization. In colorectal cancer, MESA's diversity metrics outperformed established subtypes at predicting patient survival, whereas in hepatocellular carcinoma, multiomic integration identified significantly more ligand-receptor interactions between immune cells compared with single-modality analysis. This work establishes cellular diversity within tissues as a critical correlate of disease progression and underscores the value of multiomic integration in spatial biology. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI.},
}
@article {pmid40378593,
year = {2025},
author = {Broel, N and Daumüller, F and Ali, A and Lemanschick, J and Maibach, K and Mewe, C and Bunk, B and Spröer, C and Baschien, C and Zorn, H and Schlüter, H and Rühl, M and Janssen, S and Gand, M},
title = {Unravelling the enzymatic wood decay repertoire of Cerrena zonata: A multi-omics approach.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128214},
doi = {10.1016/j.micres.2025.128214},
pmid = {40378593},
issn = {1618-0623},
mesh = {Lignin/metabolism ; *Wood/metabolism/microbiology ; Fungal Proteins/genetics/metabolism ; Glycoside Hydrolases/metabolism/genetics ; Peroxidases/metabolism/genetics ; Laccase/metabolism/genetics ; Biomass ; *Basidiomycota/enzymology/genetics/metabolism ; Genomics ; Gene Expression Profiling ; Genome, Fungal ; Proteomics ; Hydrolysis ; Multiomics ; },
abstract = {Lignocellulosic biomass (LCB), such as wheat straw, bagasse, or wood, is a cost-effective, sustainable carbon source but remains challenging to utilize due to the recalcitrance of lignin, which hinders efficient carbohydrate hydrolysis. Effective LCB degradation demands a wide range of enzymes, and commercial enzyme cocktails often require physical or chemical pretreatments. A fully enzymatic degradation could drastically improve the efficiency of these processes. Basidiomycota fungi naturally possess diverse enzymes suited for LCB breakdown. The white-rot fungus Cerrena zonata, a member of the phylum Basidiomycota, was analyzed for its Carbohydrate-Active Enzymes (CAZymes) using a multi-omics approach. Genomic and transcriptomic analyses of C. zonata identified 20,816 protein-encoding genes, including 487 CAZymes (2.3 %). Cultivating C. zonata with and without LCB addition revealed a total of 147 proteins, of which 36 were CAZymes (13 auxiliary activities (AA), 3 carbohydrate esterases, and 20 glycoside hydrolases). In accordance, laccase, manganese peroxidase (MnP) as well as versatile peroxidase (VP) activities were detected in the fungal culture supernatants. Furthermore, relevant enzymes were visualized via zymography. Consistent with these results, five putative peroxidases (AA2) and three putative laccases (AA1_1) were identified in all -omics dimensions. Further structure and sequence analysis of AA2 proteins supports that two proteins were classified as VPs and three as MnPs, based on their active and Mn[2 +] binding sites. In summary, C. zonata possesses a broad enzyme spectrum expressed under varied conditions, highlighting its potential for identifying efficient lignin-degrading enzymes for enzymatic pretreatment of food industry side streams and other LCBs.},
}
@article {pmid40379663,
year = {2025},
author = {Iminjili, V and Crowther, A and Fisher, MT and Kay, A and Roberts, P and Goldstein, S and Boivin, N and Fernandes, R},
title = {A dataset of scientific dates from archaeological sites in eastern Africa spanning 5000 BCE to 1800 CE.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {801},
pmid = {40379663},
issn = {2052-4463},
mesh = {*Archaeology ; Africa, Eastern ; History, Ancient ; History, 18th Century ; Humans ; },
abstract = {Large collections of archaeological spatiotemporal data can reveal past cultural and demographic trends, land use strategies, and processes of environmental adaptation. Within Africa, archaeological Big Data can contribute to the study of the spread of agriculture, domesticated species, and specific artefacts and technologies, as well as their ecological impacts. Although reviews addressing these topics are available for different parts of the continent, existing mid-late Holocene archaeology datasets have yet to be compiled into a central, open-access, standardized informatic-oriented dataset. Here we present Wanyika, a dataset of scientific dates from archaeological sites in eastern Africa spanning almost 7 millennia, from ~5000 BCE to 1800 CE. This dataset compiles published scientific dates and associated botanical, faunal, iron, and ceramic finds from sites in Kenya, Tanzania, the Comoros Islands, and Madagascar. The records also include data for megafauna extinctions in Madagascar. We describe the spatiotemporal coverage of the dataset, how the data were collected, the structure of the dataset, and the applied quality control measures.},
}
@article {pmid40381407,
year = {2025},
author = {Lei, L and Sha, W and Liu, Q and Liu, S and Zhou, Y and Li, R and Duan, Y and Fu, S and Li, H and Liao, R and Li, L and Zhou, R and Zhou, C and Liu, H},
title = {Hepatotoxic effects of exposure to different concentrations of Dibutyl phthalate (DBP) in Schizothorax prenanti: Insights from a multi-omics analysis.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {285},
number = {},
pages = {107390},
doi = {10.1016/j.aquatox.2025.107390},
pmid = {40381407},
issn = {1879-1514},
mesh = {*Dibutyl Phthalate/toxicity ; Animals ; *Liver/drug effects/pathology/metabolism ; *Water Pollutants, Chemical/toxicity ; *Cyprinidae/physiology ; Oxidative Stress/drug effects ; Multiomics ; },
abstract = {Dibutyl phthalate (DBP) is one of the most widely used phthalate esters (PAEs) that raise increasing ecotoxicological concerns due to their harmful effects on living organisms and ecosystems. Recently, while PAEs pollution in the Yangtze River has attracted significant attention, little research has been conducted on the impact of PAEs stress on S. prenanti, an endemic and valuable species in the Yangtze River. In this study, one control group (C-L) and three experimental groups: T1-L (3 µg/L), T2-L (30 µg/L), and T3-L (300 µg/L) were established with reference to the DBP concentration in the environment. For the first time, we investigated the effects of DBP stress on the liver of S. prenanti using histomorphological, physiological, and biochemical indexes, as well as a joint multi-omics analysis. The results revealed that compared to the C-L group, liver structural damage and stress were not significant in the environmental concentration group (T1-L) and the number of differential genes and differential metabolites were lower. However, as DBP stress concentration increased, the liver damage became severe, with significant vacuolation and hemolysis observed in the T2-L and T3-L groups. The TUNEL assay revealed a significant increase in the number of apoptotic cells along with a notable rise in differential genes and metabolites in the T2-L and T3-L groups. Oxidative stress markers (T-AOC, SOD, CAT, and GSH-PX) were also significantly higher in the T2-L and T3-L groups. RNA-Seq analysis showed that the protein processing in the endoplasmic reticulum pathway was most significantly -enriched differential gene pathway shared by both C-L vs T2-L and C-L vs T3-L, with most of the genes in this pathway showing significant up-regulation. This suggests that the protein processing in the endoplasmic reticulum pathway may play a key role in protecting the liver from injuries caused by high DBP stress. Interestingly, C XI, C XII, C XIII, C XIV and C XV in the chemical carcinogenesis - reactive oxygen species pathway were significantly down-regulated in the T2-L and T3-L groups based on combined transcriptomic and metabolomic analyses, suggesting that DBP causes liver injury by disrupting mitochondria. This comprehensive histomorphometric and multi-omics study demonstrated that the current DBP concentration in the habitat of S. prenanti in the upper reaches of the Yangtze River temporarily causes less liver damage. However, with increasing of DBP concentration, DBP could still cause serious liver damage to S. prenanti. This study provides a new mechanistic understanding of the liver response mechanism of S. prenanti under different concentrations of DBP stress and offers basic data for the ecological protection of the Yangtze River.},
}
@article {pmid40386543,
year = {2025},
author = {Ramos, E and Schweizer, M and Wu, MY and Sahli, C and Latt, C and Lunak, M and Crochet, PA and Salzburger, W and Meier, J and Marques, DA and , and , and , and , and , },
title = {The genome sequence of the Yellow-legged Gull, Larus michahellis Naumann, 1840.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {129},
pmid = {40386543},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Larus michahellis (Yellow-legged Gull; Chordata; Aves; Charadriiformes; Laridae). The genome sequence has a total length of 1,405.56 megabases. Most of the assembly (90.55%) is scaffolded into 35 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.79 kilobases in length.},
}
@article {pmid40386950,
year = {2025},
author = {Cordeiro, AL and Cusack, DF and Guerrero-Ramírez, N and Norby, RJ and Toro, L and Wong, MY and Wright, SJ and Cabugao, KGM and Andersen, KM and Fuchslueger, L and Iversen, CM and Soper, F and Ghimire, OP and Lugli, LF and Miron, AC and Valverde-Barrantes, O and Arnaud, M and Batterman, SA and Dietterich, LH and Lee, MY and Weemstra, M and Yaffar, D and Addo-Danso, SD and Pierick, K and Bridges, R and Easton, C and Felsing, I and Gonçalves, NB and Krudop, R and McKinzie, MR and Perbohner, J and Pozzoli-Oropeza, AN and Samaniego, M and Smilor, AW and Vargas, IS and Webb, L and Powers, JS and McCormack, ML},
title = {TropiRoot 1.0: Database of tropical root characteristics across environments.},
journal = {Ecology},
volume = {106},
number = {5},
pages = {e70074},
doi = {10.1002/ecy.70074},
pmid = {40386950},
issn = {1939-9170},
mesh = {*Plant Roots/physiology/anatomy &amp; histology ; *Tropical Climate ; *Databases, Factual ; Ecosystem ; Biodiversity ; },
abstract = {Tropical ecosystems contain the world's largest biodiversity of vascular plants. Yet, our understanding of tropical functional diversity and its contribution to global diversity patterns is constrained by data availability. This discrepancy underscores an urgent need to bridge data gaps by incorporating comprehensive tropical root data into global datasets. Here, we provide a database of tropical root characteristics. This new database, TropiRoot 1.0, will be instrumental in evaluating an array of hypotheses pertaining to root functional ecology and plant biogeography, both within the tropics and relative to other global biomes. The data compilation was conducted by the TropiRoot Initiative, in partnership with the Fine-Root Ecology Database (FRED) and the Global Root Trait (GRooT) database, Colorado State University (CSU) and the Smithsonian Tropical Research Institute (STRI). Literature search and data extraction were conducted between 2020 and 2024. Literature was identified using Web of Science, Scopus, and complemented using the expert knowledge of members of TropiRoot. To provide broad environmental and geographical distributions, literature searches included root characteristics (traits) across global change drivers, natural gradients, and from different continents. We adopted FRED standardized data columns and streamlined the format to enhance accessibility for data extraction across various user groups. This optimized framework resulted in a smaller, yet comprehensive datasheet. To make the database compatible with other global root trait initiatives, column identification was standardized following the codes provided by FRED. These efforts culminated in data extracted from 104 new sources, resulting in more than 8000 rows of data (either species or community data). Most of the data in TropiRoot 1.0 include root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology, and root chemistry. This initiative represents a 30% increase in the currently available data for tropical roots in FRED. TropiRoot 1.0 contains root characteristics from 25 different countries, where seven are located in Asia, six in South America, five in Central America and the Caribbean, four in Africa, two in North America, and 1 in Oceania. Due to the volume of data, when ancillary data were available, including soil data, these data were either extracted and included in the database or its availability was recorded in an additional column. Multiple contributors checked the entries for outliers during the collation process to ensure data quality. For text-based observations, we examined all cells to ensure that their content relates to their specific categories. For numerical observations, we ordered each numerical value from least to greatest and plotted the values, checking apparent outliers against the data in their respective sources and correcting or removing incorrect or impossible values. Some data (soil and aboveground) have different columns for the same variable presented in different units, including originally published units, but root characteristics data had units converted to match those reported in FRED. By filling a gap from global databases, TropiRoot 1.0 expands our knowledge of otherwise so far underrepresented regions and our ability to assess global trends. This advancement can be used to improve tropical forest representation in vegetation models. The data are freely available and should be cited when used.},
}
@article {pmid40389091,
year = {2025},
author = {Narita, M and Matsugaki, R and Muramatsu, K and Fushimi, K and Matsuda, S},
title = {Obesity and risk of post-operative pneumonia among older adult patients with hip fracture: An obesity paradox.},
journal = {Clinical nutrition ESPEN},
volume = {68},
number = {},
pages = {342-347},
doi = {10.1016/j.clnesp.2025.05.020},
pmid = {40389091},
issn = {2405-4577},
mesh = {Humans ; *Hip Fractures/surgery/complications ; Aged ; Male ; *Obesity/complications ; Female ; *Pneumonia/etiology/epidemiology ; Body Mass Index ; *Postoperative Complications/epidemiology/etiology ; Risk Factors ; Aged, 80 and over ; Incidence ; Obesity Paradox ; },
abstract = {BACKGROUND &amp; AIM: Hip fracture is a condition with a high incidence among older adults and is associated with a high post-operative mortality rate. Post-operative pneumonia is one of the most important risk factors for mortality, making its prevention essential. In recent years, reports on obesity paradoxes have increasingly been documented. Therefore, this study aimed to investigate the relationship between body mass index (BMI) and the risk of developing post-operative pneumonia using a large database.<br><br>METHOD: We included 407,203 patients aged 75 years or older who underwent surgery for hip fracture between 2014 and 2018 using Diagnosis Procedure Combination data, a healthcare reimbursement system. Patients were classified into six BMI categories: <16.0, 16.0-16.9, 17.0-18.4, 18.5-24.9, 25.0-29.9, and &#x2265;30 kg/m[2]. Multilevel logistic regression analysis was performed based on BMI 18.5-24.9 kg/m[2] to determine odds ratios for post-operative pneumonia.<br><br>RESULTS: The data of 332,768 patients were included in the final analysis. Those with BMI <18.5 kg/m[2] demonstrated significantly higher odds of developing post-operative pneumonia compared to those with BMI between 18.5 and 24.9 kg/m[2], BMI <16.0 kg/m[2] (adjusted odds ratio [AOR: 2.14, 95 % confidence interval [CI: 2.01-2.27 p < 0.001); BMI 16.0-16.9 kg/m[2] (AOR: 1.57, 95 % CI: 1.46-1.69, p < 0.001); and BMI 17.0-18.4 kg/m[2] (AOR: 1.31, 95 % CI: 1.24-1.39, p < 0.001). Conversely, patients with BMI 25.0-29.9 kg/m[2] showed a reduced risk of post-operative pneumonia compared to the other groups (AOR: 0.83, 95 % CI: 0.76-0.91, p < 0.001). Notably, a J-curve relationship was observed between BMI and the incidence of post-operative pneumonia.<br><br>CONCLUSION: Patients with higher BMI had a lower risk of developing post-operative pneumonia, revealing the presence of an obesity paradox between hip fracture and post-operative pneumonia. Patients with low BMI are at a higher risk and may benefit from enhanced preventive measures to mitigate the risk of pneumonia.},
}
@article {pmid40393068,
year = {2025},
author = {Williams, CM and Scelza, BA and Slack, SD and Font-Porterias, N and Al-Hindi, DR and Mathias, RA and Watson, H and Barnes, KC and Lange, E and Johnson, RK and Gignoux, CR and Ramachandran, S and Henn, BM},
title = {A rapid accurate approach to inferring pedigrees in endogamous populations.},
journal = {Genetics},
volume = {230},
number = {4},
pages = {},
pmid = {40393068},
issn = {1943-2631},
support = {R35 GM133531/GM/NIGMS NIH HHS/United States ; BCS-1534682//NSF/ ; T32 GM128596/GF/NIH HHS/United States ; R35GM139628/GF/NIH HHS/United States ; R35 GM139628/GM/NIGMS NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; R35GM133531/GF/NIH HHS/United States ; },
mesh = {*Pedigree ; Humans ; Haplotypes ; Algorithms ; Male ; *Genetics, Population/methods ; Female ; Machine Learning ; },
abstract = {Accurate reconstruction of pedigrees from genetic data remains a challenging problem. Many relationship categories (e.g. half-sibships vs avuncular) can be difficult to distinguish without external information. Pedigree inference algorithms are often trained on European-descent families in urban locations. Thus, existing methods tend to perform poorly in endogamous populations for which there may be reticulations within the pedigrees and elevated haplotype sharing. We present a simple, rapid algorithm which initially uses only high-confidence first-degree relationships to seed a machine learning step based on summary statistics of identity-by-descent sharing. One of these statistics, our "haplotype score," is novel and can be used to: (1) distinguish half-sibling pairs from avuncular or grandparent-grandchildren pairs; and (2) assign individuals to ancestor vs descendant generation. We test our approach in a sample of 700 individuals from northern Namibia, sampled from an endogamous population called the Himba. Due to a culture of concurrent relationships in the Himba, there is a high proportion of half-sibships. We accurately identify first through fourth-degree relationships and distinguish between various second-degree relationships: half-sibships, avuncular pairs, and grandparent-grandchildren. We further validate our approach in a second African-descent dataset, the Barbados Asthma Genetics Study, and a European-descent founder population from Quebec. Accurate reconstruction of relatives facilitates estimation of allele frequencies, tracing allele trajectories, improved phasing, heritability and other population genomic questions.},
}
@article {pmid40393297,
year = {2025},
author = {Yang, H and Zhou, J and Zhou, J},
title = {Integrated multi-omics and DNA stable-isotope probing approaches to reveal soil-ryegrass response to ionic rare earth mineral ammonium-lead contamination.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138658},
doi = {10.1016/j.jhazmat.2025.138658},
pmid = {40393297},
issn = {1873-3336},
mesh = {*Lolium/drug effects/metabolism/growth &amp; development/genetics ; *Soil Pollutants/toxicity ; *Lead/toxicity ; Plant Roots/drug effects/metabolism/growth &amp; development ; Soil/chemistry ; *Ammonium Compounds/toxicity ; Oxidative Stress/drug effects ; Nitrogen/metabolism ; Nitrogen Isotopes ; Multiomics ; },
abstract = {The extensive use of ammonium (NH4[+]) sulfate in ionic rare earth mining has resulted in soil contamination with NH4[+] and lead (Pb), posing significant challenges for ecological restoration. Here, multi-omics and DNA stable-isotope probing (DNA-SIP) approaches were utilized to investigate soil nitrogen cycling and the molecular response of ryegrass (Lolium perenne L.) to NH4[+] (180-720 mg kg[-1])-Pb[2+] (207-828 mg kg[-1]) co-contamination. A synergistic interaction between NH4[+] and Pb[2+] was observed, significantly inhibited ryegrass growth, and induced oxidative stress and mitochondrial swelling. The EC50 toxicity thresholds were 383 mg kg[-1] for NH4[+] and 512 mg kg[-1] for Pb. The Integrated Biomarker Response (IBRv2) model elucidated the synergistic toxic effects. Transcriptomic and metabolomic analyses indicated that ryegrass roots enhanced carbon metabolism and antioxidant response pathways related to stress tolerance. Galactose metabolism and lysine degradation were identified as key pathways associated with stress response. Co-contamination with NH4[+] and Pb[2+] reduced ryegrass root [15]N-total nitrogen (TN) by 30 % while increasing soil [15]N-NH4[+] residue by 95 % and decreasing [15]N-microbial biomass nitrogen (MBN) by 59 %, compared to NH4[+] single contamination. DNA-SIP analysis revealed that ryegrass cultivation under NH4[+]- Pb[2+] co-contamination increased the abundance of plant growth-promoting rhizobacteria (Dyella), acid-tolerant nitrogen (Acidibacter), and sulfur-cycling taxa (Desulfosporosinus). The presence of raffinose and chlorogenic acid in ryegrass root metabolites was associated with shifts in the structure and composition of using NH4[+] active microbial taxa. These findings provide valuable insights into plant-soil-microbe interactions under multi-pollutant stress and offer practical strategies for phytoremediation and ecological restoration in areas affected by mining.},
}
@article {pmid40393855,
year = {2025},
author = {Zhivkoplias, E and da Silva, JM and Blasiak, R},
title = {How transdisciplinarity can help biotech-driven biodiversity research.},
journal = {Trends in biotechnology},
volume = {43},
number = {9},
pages = {2105-2116},
doi = {10.1016/j.tibtech.2025.04.008},
pmid = {40393855},
issn = {1879-3096},
mesh = {*Biodiversity ; *Biotechnology ; Conservation of Natural Resources ; Humans ; },
abstract = {The Kunming-Montreal Global Biodiversity Framework marks a significant step toward conserving genetic diversity on a global scale. Sequencing advancements have broadened biodiversity studies by enabling the mapping of species distributions, increasing understanding of ecological interactions, and monitoring genetic diversity. However, these tools are hindered by inequalities and biases, particularly in biodiversity-rich developing countries. To navigate these challenges, we propose strategies using the existing biotechnological toolbox to make biodiversity data more accessible and useful for research and development. This includes increasing funding for database curation, improving metadata standards, addressing inequalities in technological capacity, and supporting holistic capacity-building programmes. Implementing these strategies can unlock new opportunities for biodiversity research aligned with sustainable development principles and can contribute to improved conservation outcomes.},
}
@article {pmid40397662,
year = {2025},
author = {Li, S and Zou, J and Wu, J and Sun, B and Zhao, M and Liu, D and Cheng, Q and Tan, H and Ma, J},
title = {New Insights into Natural Polyphenol-Enhanced Fe(III)/Peracetic Acid System under Acidic pH Conditions: The Overlooked Role of Coexisting Hydrogen Peroxide.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {21},
pages = {10608-10619},
doi = {10.1021/acs.est.5c01622},
pmid = {40397662},
issn = {1520-5851},
mesh = {Hydrogen Peroxide/chemistry ; *Polyphenols/chemistry ; Hydrogen-Ion Concentration ; *Peracetic Acid/chemistry ; Hydroxybenzoates ; Iron ; Ferric Compounds/chemistry ; },
abstract = {Natural polyphenols have been extensively utilized as reducing agents to enhance contaminant degradation in the Fe(III)/peracetic acid (PAA) system. However, the roles of coexisting hydrogen peroxide (H2O2) remain insufficiently explored. This study, using protocatechuic acid (PCA) as a representative natural polyphenol, demonstrated that contaminant removal within the PCA/Fe(III)/PAA system under acidic pH conditions exhibited two kinetic stages: an initial rapid stage driven by PAA, followed by a slower stage driven by H2O2. The presence of H2O2 facilitated the complete degradation (100%) of contaminants even at low concentrations (<1.0 μM). Interestingly, these two stages contributed differently to various contaminants' degradation. Mechanistic investigations revealed that Fe(IV) was the major reactive species (RSs) for contaminant degradation during the PAA stage, while [•]OH dominated during the H2O2 stage. In brief, H2O2 enriched the generation pathways and types of RSs. Notably, besides PCA itself, the reaction intermediates (i.e., phenoxy radicals) formed during the reaction between PCA and RSs also played a key role in reducing Fe(III), which explained why the PCA/Fe(III)/PAA system was able to maintain sufficient Fe(II) to further interact with H2O2. Overall, this study highlighted the synergistic role of coexisting H2O2 and provided valuable insights for optimizing various contaminants' degradation in actual waters using PAA-based Fenton-like systems.},
}
@article {pmid40398052,
year = {2025},
author = {Guo, Z and Li, J and Hu, J and An, G and Wang, C},
title = {Deciphering the joint intracellular and extracellular regulatory strategies of toxigenic Microcystis to achieve intraspecific competitive advantage: An integrated multi-omics analysis with novel allelochemicals identified.},
journal = {Water research},
volume = {283},
number = {},
pages = {123774},
doi = {10.1016/j.watres.2025.123774},
pmid = {40398052},
issn = {1879-2448},
mesh = {*Microcystis/metabolism ; *Pheromones ; Microcystins ; Proteomics ; Metabolomics ; Multiomics ; },
abstract = {Global increase in Microcystis-dominated cyanobacterial blooms (MCBs) severely threatens ecological and human health. Intraspecific interaction between microcystin (MC)-producing (MC[+]) Microcystis and co-existing MC-free (MC[-]) Microcystis influences the relative abundance of MC[+]Microcystis, ultimately determining the toxicity and hazard of MCBs. However, specific allelochemicals driving this interaction and underlying molecular mechanisms remain unclear. This study confirmed that intraspecific interaction promoted the competitive advantage of MC[+]Microcystis over MC[-]Microcystis and unveiled the joint intracellular and extracellular regulatory strategies of MC[+]Microcystis based on proteomics-metabolomics analyses and biochemical validation. Intracellularly, MC[+]Microcystis enhanced pentose phosphate pathway and lipid and fatty acid biosynthesis to maintain cellular functions and membrane stability, but inhibited glycolysis, tricarboxylic acid cycle, and protein biosynthesis to optimize energy utilization for growth and proliferation. Extracellularly, MC[+]Microcystis released allelochemicals, including cytidine diphosphate-diacylglycerol and N-acyl-homoserine lactones, to inhibit MC[-]Microcystis growth by 13.53% and 16.39%, respectively, thereby achieving its competitive advantage. In contrast, MC[-]Microcystis exhibited the suppressed photosynthesis and oxidative phosphorylation, imbalanced anti-inflammatory responses, nucleic acid degradation, and membrane damage, resulting in its competitive disadvantage in co-culture. These findings provide new insights into the competitive dynamics between MC[+] and MC[-]Microcystis, and their involved implications for aquatic ecosystem health.},
}
@article {pmid40399277,
year = {2025},
author = {Petit, MJ and Flory, C and Gu, Q and Fares, M and Lamont, D and Score, A and Davies, K and Bell-Sakyi, L and Scaturro, P and Brennan, B and Kohl, A},
title = {Multi-omics analysis of SFTS virus infection in Rhipicephalus microplus cells reveals antiviral tick factors.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4732},
pmid = {40399277},
issn = {2041-1723},
support = {MC_UU_00034/5//RCUK | Medical Research Council (MRC)/ ; SC 314/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 210462/Z/18/Z//Wellcome Trust (Wellcome)/ ; TICKITS 890970//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; MC_UU_12014/8//RCUK | Medical Research Council (MRC)/ ; /WT_/Wellcome Trust/United Kingdom ; MC_UU_00034/4//RCUK | Medical Research Council (MRC)/ ; },
mesh = {Animals ; *Rhipicephalus/virology/genetics/immunology ; Cell Line ; Proteomics/methods ; Virus Replication ; *Phlebovirus/physiology/genetics ; Transcriptome ; Host-Pathogen Interactions/genetics ; RNA Helicases/metabolism/genetics ; Proteome ; *Severe Fever with Thrombocytopenia Syndrome/virology ; Gene Expression Profiling ; Multiomics ; },
abstract = {The increasing prevalence of tick-borne arboviral infections worldwide necessitates advanced control strategies, particularly those targeting vectors, to mitigate the disease burden. However, the cellular interactions between arboviruses and ticks, especially for negative-strand RNA viruses, remain largely unexplored. Here, we employ a proteomics informed by transcriptomics approach to elucidate the cellular response of the Rhipicephalus microplus-derived BME/CTVM6 cell line to severe fever with thrombocytopenia syndrome virus (SFTSV) infection. We generate the de novo transcriptomes and proteomes of SFTSV- and mock-infected tick cells, identifying key host responses and regulatory pathways. Additionally, interactome analysis of the viral nucleoprotein (N) integrated host responses with viral replication and dsRNA-mediated gene silencing screen reveals two anti-SFTSV effectors: the N interacting RNA helicases DHX9 and UPF1. Collectively, our results provide insights into the antiviral responses of R. microplus vector cells and highlight critical SFTSV restriction factors, while enriching transcriptomic and proteomic resources for future research.},
}
@article {pmid40401771,
year = {2025},
author = {Callens, M and Le Berre, G and Van den Bulcke, L and Lolivier, M and Derycke, S},
title = {An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e14126},
doi = {10.1111/1755-0998.14126},
pmid = {40401771},
issn = {1755-0998},
support = {RT/24/DNASense_ILVO//Belgian Federal Science Policy Office/ ; //Biodiversa+/ ; //Belgian Federal Public Service Economy/ ; BAR0159//Directorate-General for Regional Policy of the European Union/ ; },
mesh = {*Metagenomics/methods ; Animals ; *Invertebrates/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Computational Biology/methods ; Sequence Analysis, DNA ; },
abstract = {DNA-based techniques are a popular approach for assessing biodiversity in ecological research, especially for organisms which are difficult to detect or identify morphologically. Metabarcoding, the most established method for determining species composition and relative abundance in bulk samples, can be more sensitive and time- and cost-effective than traditional morphological approaches. However, one drawback of this method is PCR bias caused by between-species variation in the amplification efficiency of a marker gene. Metagenomics, bypassing PCR amplification, has been proposed as an alternative to overcome this bias. Several studies have already shown the promising potential of metagenomics, but they all indicate the unavailability of reference genomes for most species in any ecosystem as one of the primary bottlenecks preventing its wider implementation. In this study, we present a strategy that combines unassembled reads of low-coverage whole genome sequencing and publicly available reference genomes to construct a genomic reference database, thus circumventing high sequencing costs and intensive bioinformatic processing. We show that this approach is superior to metabarcoding for approximating relative biomass of macrobenthos species from bulk samples. Furthermore, these results can be obtained with a sequencing effort comparable to metabarcoding. The strategy presented here can thus accelerate the implementation of metagenomics in biodiversity assessments, as it should be relatively easy to adopt by laboratories familiar with metabarcoding and can be used as an accessible alternative.},
}
@article {pmid40402004,
year = {2025},
author = {Brunk, KM and Kramer, HA and Peery, MZ and Kahl, S and Wood, CM},
title = {Assessing spatial variability and efficacy of surrogate species at an ecosystem scale.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {39},
number = {5},
pages = {e70058},
pmid = {40402004},
issn = {1523-1739},
support = {//Arthur Vining Davis Foundations/ ; FKZ 01|S22072//German Federal Ministry of Education and Research/ ; //Josh Holshuh/ ; //University of Wisconsin's Office of the Vice Chancellor for Research/ ; 20-ECOF20-0017//NASA Biodiversity and Ecological Forecasting Program/ ; //National Park Service/ ; 19-RP-NEU-043//California Climate Investment Forest Health Research Program/ ; FKZ 67KI31040E//German Federal Ministry of Environment, Nature Conservation, and Nuclear Safety/ ; //USDA Forest Service Region 5/ ; },
mesh = {*Conservation of Natural Resources/methods ; Animals ; California ; *Biodiversity ; *Birds/physiology ; *Ecosystem ; Forests ; },
abstract = {Preserving biodiversity is a central goal of conservation, but, in practice, monitoring biodiversity often involves assessing population trends for one or a handful of species that are presumed proxies for biodiversity. Despite the popularity of surrogate species strategies, the links between biodiversity and surrogate species are rarely tested, especially across the broad spatial scales at which they are applied. We quantitatively evaluated a prominent surrogate species strategy across 25,000 km[2] of California's Sierra Nevada, an ecosystem undergoing substantial forest loss due to changing fire regimes and climate. We used passive acoustic monitoring and multispecies occupancy models to quantify pairwise co-occurrence among 6 indicator species and much of the avian community (63 species). We found that 95% of the sampled avian community had a positive association with at least one indicator species and that latitude played an important role in shaping co-occurrence for many species. Our work provides an important test of a long-standing conservation tool, suggests that a well-chosen suite of surrogate species can represent the occurrence patterns of a large portion of the rest of the community, and demonstrates the importance of explicitly considering the spatial scale over which surrogate species are effective.},
}
@article {pmid40403917,
year = {2025},
author = {Wang, H and Lei, W and Wu, M and Guo, J and He, S and Shen, N and Li, C and Wang, L},
title = {Spatial distribution and ecological risks of neonicotinoids in surface waters of Eastern China.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {378},
number = {},
pages = {126507},
doi = {10.1016/j.envpol.2025.126507},
pmid = {40403917},
issn = {1873-6424},
mesh = {China ; *Water Pollutants, Chemical/analysis ; *Neonicotinoids/analysis ; *Insecticides/analysis ; *Environmental Monitoring ; Risk Assessment ; Rivers/chemistry ; Nitro Compounds/analysis ; Thiamethoxam/analysis ; Guanidines/analysis ; Animals ; },
abstract = {Over the past two decades, neonicotinoid insecticides (NNIs) have been extensively used in agricultural activities. Due to its high-water solubility, NNIs are primarily found in surface waters, contaminating them and posing significant ecological risks. However complex watershed environments pose challenges in elucidating the pollution characteristics and ecological risks of NNIs in large-scale waters. This study focused on typical surface waters in Eastern China, exploring the spatial characteristics, driving factors, and ecological risks of NNIs. The total concentration of NNIs (Σ8NNIs) ranges from 2.3 ng/L to 1377.8 ng/L. This concentration range exceeded the European water environment toxicity thresholds, with 86 of the sites surpassing the chronic toxicity threshold (8.3 ng/L) and 14 of the sites exceeding the acute toxicity threshold (200 ng/L). Thiamethoxam (THIA), imidacloprid (IMI), and dinotefuran (DIN) were detected with high rates and concentrations. Spatially, the Σ8NNIs in the Yangtze River (YZ, 140.0 ng/L) are significantly higher than in the north of Beijing-Hangzhou Grand Canal (BHN, 62.8 ng/L), Taihu Lake (TH, 36.6 ng/L), and Taihu Basin (THB, 21.9 ng/L). Moreover, Σ8NNIs in the south of Beijing-Hangzhou Grand Canal (BHS, 326.5 ng/L) are significantly higher than in BHN (62.8 ng/L). The spatial distribution of NNI components indicated that DIN and THIA dominated in YZ (37 %), THIA (34 %) and DIN (20 %) in BHN, IMI (53 %) in BHS, DIN (53 %) in TH, and THIA (49 %) and DIN (31 %) in THB. Correlation analysis and linear mixed modeling identified land use, pH, and dissolved oxygen (DO) as significant factors influencing the occurrence of NNIs, with DO emerging as a crucial element. The species sensitivity distribution (SSD) results showed the acute and chronic toxicity thresholds of NNIs for 5 % of aquatic species were 716 ng/L and 166 ng/L respectively with 19 sites exceeding the chronic toxicity threshold and 1 sites surpassing the acute toxicity threshold.},
}
@article {pmid40404082,
year = {2025},
author = {Zhang, S and Qiang, J and Liu, H and Zhou, J and Li, J and Chen, J and Ding, Q and Qian, K},
title = {An efficient and precise (micro)plastic identification method: feature infrared spectra extraction based on EIS-VIP-CARS and ANN modeling.},
journal = {Environmental research},
volume = {279},
number = {Pt 2},
pages = {121916},
doi = {10.1016/j.envres.2025.121916},
pmid = {40404082},
issn = {1096-0953},
mesh = {*Neural Networks, Computer ; *Environmental Monitoring/methods ; *Microplastics/analysis ; Algorithms ; Spectrophotometry, Infrared/methods ; },
abstract = {Understanding microplastics' (MPs) ecological impact necessitates their precise identification. To address the issue of the competitive adaptive reweighted sampling (CARS) algorithm extracting numerous feature wavenumber points (FWPs) that often miss transmittance peaks (TPs), resulting in high computational load and low accuracy in artificial neural network (ANN) models, this study introduces a novel approach. Initially, the equal interval sampling (EIS) method is employed to capture the main information of the full spectra. Subsequently, the variable importance in projection (VIP) is innovatively integrated into the CARS to formulate the EIS-VIP-CARS method for extracting feature spectra (FS). Using 20 typical MPs as the subjects, this study compares the identification performance of ANN models using full-spectra, EIS, CARS, EIS-CARS, VIP-CARS, and EIS-VIP-CARS. The results show that VIP-CARS extracts 128 FWPs, a reduction of 49.41 % compared to CARS. Moreover, the distribution of these FWPs is more concentrated around the TPs and their vicinity. The accuracy of MPs by the ANN model based on VIP-CARS is generally higher than that of CARS. EIS-VIP-CARS extracts 55 FWPs, representing a reduction of 58.65 % and 57.03 % compared to EIS and VIP-CARS, respectively. The overall distribution of these points closely aligns with the distribution of functional groups. The ANN model based on EIS-VIP-CARS can achieve a similar accuracy for MPs as the model based on EIS, both greater than 99 %, demonstrating good generalization ability. The accuracies of the MNN and convolutional neural network (CNN) models are higher than those of the SNN model, but the modeling time is longer. The ANN model established using the EIS-VIP-CARS is an efficient and precise approach for the identification of MPs in infrared spectroscopy. This study provides technical references for the research on the environmental behavior of MPs and is also of significant importance for the classification and management of plastic waste.},
}
@article {pmid40404775,
year = {2025},
author = {Wang, J and Xu, Y and Zhu, H and Chen, C and Zhao, Y and Wang, Y},
title = {CheloniansTraits: a comprehensive trait database of global turtles and tortoises.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {840},
pmid = {40404775},
issn = {2052-4463},
support = {32271734//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Turtles/anatomy &amp; histology ; Animals ; Databases, Factual ; Biological Evolution ; Life History Traits ; Conservation of Natural Resources ; },
abstract = {Turtles and tortoises (chelonians) possess a variety of ecological characteristics, including long lifespans and protective shells, which have enabled them to survive and adapt to environmental challenges since the Triassic period. However, many characteristics of chelonians have turned into disadvantages for their populations in the Anthropocene. Currently, there remains a lack of comprehensive data on the morphological, life-history, and ecological characteristics of all chelonians on a global scale. Consequently, our study aims to collect a complete trait database of global chelonians (CheloniansTraits), which may help bridge the knowledge gap regarding the identity and ecology of global chelonians and thereby aiding future conservation endeavors. We compiled 69 trait data for all 358 recognized chelonian species, utilizing ~2,000 literature sources, covering 33 morphological, 21 life-history, 7 ecological traits, and 8 conservation information. This database serves as a uniquely valuable resource for exploring evolutionary, biogeographical, and ecological inquiries related to chelonians, as well as elucidating key aspects of ecological strategy variation among species.},
}
@article {pmid40404926,
year = {2025},
author = {Pringle, S and Dallimer, M and Goddard, MA and Le Goff, LK and Hart, E and Langdale, SJ and Fisher, JC and Abad, SA and Ancrenaz, M and Angeoletto, F and Auat Cheein, F and Austen, GE and Bailey, JJ and Baldock, KCR and Banin, LF and Banks-Leite, C and Barau, AS and Bashyal, R and Bates, AJ and Bicknell, JE and Bielby, J and Bosilj, P and Bush, ER and Butler, SJ and Carpenter, D and Clements, CF and Cully, A and Davies, KF and Deere, NJ and Dodd, M and Drinkwater, R and Driscoll, DA and Dutilleux, G and Dyrmann, M and Edwards, DP and Farhadinia, MS and Faruk, A and Field, R and Fletcher, RJ and Foster, CW and Fox, R and Francksen, RM and Franco, AMA and Gainsbury, AM and Gardner, CJ and Giorgi, I and Griffiths, RA and Hamaza, S and Hanheide, M and Hayward, MW and Hedblom, M and Helgason, T and Heon, SP and Hughes, KA and Hunt, ER and Ingram, DJ and Jackson-Mills, G and Jowett, K and Keitt, TH and Kloepper, LN and Kramer-Schadt, S and Labisko, J and Labrosse, F and Lawson, J and Lecomte, N and de Lima, RF and Littlewood, NA and Marshall, HH and Masala, GL and Maskell, LC and Matechou, E and Mazzolai, B and McConnell, A and Melbourne, BA and Miriyev, A and Nana, ED and Ossola, A and Papworth, S and Parr, CL and Payo-Payo, A and Perry, G and Pettorelli, N and Pillay, R and Potts, SG and Prendergast-Miller, MT and Qie, L and Rolley-Parnell, P and Rossiter, SJ and Rowcliffe, M and Rumble, H and Sadler, JP and Sandom, CJ and Sanyal, A and Schrodt, F and Sethi, SS and Shabrani, A and Siddall, R and Smith, SC and Snep, RPH and Soulsbury, CD and Stanley, MC and Stephens, PA and Stephenson, PJ and Struebig, MJ and Studley, M and Svátek, M and Tang, G and Taylor, NK and Umbers, KDL and Ward, RJ and White, PJC and Whittingham, MJ and Wich, S and Williams, CD and Yakubu, IB and Yoh, N and Zaidi, SAR and Zmarz, A and Zwerts, JA and Davies, ZG},
title = {Opportunities and challenges for monitoring terrestrial biodiversity in the robotics age.},
journal = {Nature ecology &amp; evolution},
volume = {9},
number = {6},
pages = {1031-1042},
pmid = {40404926},
issn = {2397-334X},
mesh = {*Biodiversity ; *Robotics/methods ; *Conservation of Natural Resources/methods ; *Environmental Monitoring/methods/instrumentation ; Delphi Technique ; },
abstract = {With biodiversity loss escalating globally, a step change is needed in our capacity to accurately monitor species populations across ecosystems. Robotic and autonomous systems (RAS) offer technological solutions that may substantially advance terrestrial biodiversity monitoring, but this potential is yet to be considered systematically. We used a modified Delphi technique to synthesize knowledge from 98 biodiversity experts and 31 RAS experts, who identified the major methodological barriers that currently hinder monitoring, and explored the opportunities and challenges that RAS offer in overcoming these barriers. Biodiversity experts identified four barrier categories: site access, species and individual identification, data handling and storage, and power and network availability. Robotics experts highlighted technologies that could overcome these barriers and identified the developments needed to facilitate RAS-based autonomous biodiversity monitoring. Some existing RAS could be optimized relatively easily to survey species but would require development to be suitable for monitoring of more 'difficult' taxa and robust enough to work under uncontrolled conditions within ecosystems. Other nascent technologies (for instance, new sensors and biodegradable robots) need accelerated research. Overall, it was felt that RAS could lead to major progress in monitoring of terrestrial biodiversity by supplementing rather than supplanting existing methods. Transdisciplinarity needs to be fostered between biodiversity and RAS experts so that future ideas and technologies can be codeveloped effectively.},
}
@article {pmid40406849,
year = {2025},
author = {Han, Y and Cai, J and Chen, Y and Zhang, Y and Jin, LN and Chen, T and Li, J and Zhang, G and Chen, J},
title = {Concurrent Formation of Low-Maturity EC and BrC in Biomass and Coal Burning: O-PAH as a Precursor.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {24},
pages = {12083-12095},
doi = {10.1021/acs.est.4c13299},
pmid = {40406849},
issn = {1520-5851},
mesh = {*Coal ; *Biomass ; *Carbon ; *Polycyclic Aromatic Hydrocarbons ; Soot ; },
abstract = {Black carbon (BC) significantly influences climate change through light absorption. Traditional emission inventories equate BC with elemental carbon (EC) and overlook the variability in its properties across sources, leading to uncertainties in climate predictions. This study shows that EC from solid fuel combustion contains substantial low-maturity EC (char), whose emissions increase alongside the light absorption of soluble organic carbon (OC) as the fuel aromaticity rises. Concurrently, the abundance of oxygenated polycyclic aromatic hydrocarbons (O-PAHs) in soluble OC also increases. This suggests that char and brown carbon (BrC) share similar formation pathways with O-PAHs as key precursors. Time-resolved analysis during combustion cycles revealed a significant positive correlation between O-PAHs, the light absorption of soluble OC, and char emissions, further supporting this shared pathway. The nonbonding orbitals in BrC and char facilitate n → π* transitions in the visible region, which are more wavelength-dependent than the π → π* transition in high-maturity EC (soot). This study highlights char as a light-absorbing intermediate, influencing light absorption of EC emitted from solid fuel combustion. These insights into the formation pathways and optical properties of carbonaceous aerosols enhance our understanding of their climate impacts and underscore the need to differentiate between char and soot in climate models to improve accuracy.},
}
@article {pmid40407023,
year = {2025},
author = {Pang, D and Zhu, R and Zhao, H and Wang, T},
title = {Probabilistic exponential family inverse regression and its applications.},
journal = {Biometrics},
volume = {81},
number = {2},
pages = {},
doi = {10.1093/biomtc/ujaf065},
pmid = {40407023},
issn = {1541-0420},
support = {12222111//National Natural Science Foundation of China/ ; 12331009//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Algorithms ; Computer Simulation ; *Models, Statistical ; Regression Analysis ; Likelihood Functions ; *Biometry/methods ; Data Interpretation, Statistical ; },
abstract = {Rapid advances in high-throughput sequencing technologies have led to the fast accumulation of high-dimensional data, which is harnessed for understanding the implications of various factors on human disease and health. While dimension reduction plays an essential role in high-dimensional regression and classification, existing methods often require the predictors to be continuous, making them unsuitable for discrete data, such as presence-absence records of species in community ecology and sequencing reads in single-cell studies. To identify and estimate sufficient reductions in regressions with discrete predictors, we introduce probabilistic exponential family inverse regression (PrEFIR), assuming that, given the response and a set of latent factors, the predictors follow one-parameter exponential families. We show that the low-dimensional reductions result not only from the response variable but also from the latent factors. We further extend the latent factor modeling framework to the double exponential family by including an additional parameter to account for the dispersion. This versatile framework encompasses regressions with all categorical or a mixture of categorical and continuous predictors. We propose the method of maximum hierarchical likelihood for estimation, and develop a highly parallelizable algorithm for its computation. The effectiveness of PrEFIR is demonstrated through simulation studies and real data examples.},
}
@article {pmid40407387,
year = {2025},
author = {Wang, M and Chen, X and Liu, M and Luo, H and Zhang, S and Guo, J and Wang, J and Zhou, L and Zhang, N and Li, H and Wang, C and Li, L and Wang, Z and Wang, H and Guo, Z and Li, Y and Wang, Y},
title = {Decoding herbal combination models through systematic strategies: insights from target information and traditional Chinese medicine clinical theory.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
pmid = {40407387},
issn = {1477-4054},
support = {2021CXGC010509//2021 Shandong Provincial Key RD Program (Major Technological Innovation Project)/ ; 2022ZDYF0410//Key RD Projects of Ningxia Hui Nationality Autonomous Region in 2022/ ; },
mesh = {*Medicine, Chinese Traditional/methods ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Humans ; Arthritis, Rheumatoid/drug therapy ; Databases, Factual ; Animals ; },
abstract = {Traditional Chinese medicine (TCM) utilizes intricate herbal formulations that exemplify the principles of compatibility and synergy. However, the rapid proliferation of herbal data has resulted in redundant information, complicating the understanding of their potential mechanisms. To address this issue, we first established a comprehensive database that encompasses 992 herbs, 18 681 molecules, and 2168 targets. Consequently, we implemented a multi-network strategy based on a core information screening method to elucidate the highly intertwined relationships among the targets of various herbs and to refine herbal target information. Within a non-redundant network framework, separation and overlap analysis demonstrated that the networking of herbs preserves essential clinical information, including their properties, meridians, and therapeutic classifications. Furthermore, two notable trends emerged from the statistical analyses of classical TCM formulas: the separation of herbs and the overlap between herbs and diseases. This phenomenon is termed the herbal combination model (HCM), validated through statistical analyses of two representative case studies: the common cold and rheumatoid arthritis. Additionally, in vivo and in vitro experiments with the new formula YanChuanQin (YanHuSuo-Corydalis Rhizoma, ChuanWu-Aconiti Radix, and QinJiao-Gentianae Macrophyllae Radix) for acute gouty arthritis further support the HCM. Overall, this computational method provides a systematic network strategy for exploring herbal combinations in complex and poorly understood diseases from a non-redundant perspective.},
}
@article {pmid40407563,
year = {2025},
author = {Araujo, ACB and Souza, OF and Kersanach, BB and Mozzer, JSC and Feitosa, VL and Brandão, VA and Alencar, FEC and Oliveira, NS and Silva, AVBD and Abreu, LC},
title = {Trends in Congenital Syphilis Incidence and Mortality in Brazil's Southeast Region: A Time-Series Analysis (2008-2022).},
journal = {Epidemiologia (Basel, Switzerland)},
volume = {6},
number = {2},
pages = {},
pmid = {40407563},
issn = {2673-3986},
support = {182023//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Esp&#xed;rito Santo/ ; },
abstract = {Congenital syphilis (CS) is an important infectious cause of miscarriage, stillbirth, and neonatal morbidity and mortality. Despite the advances in diagnosis and treatment, CS continues to challenge health systems with increasing incidence and mortality rates in recent years worldwide. Given this, the present study aims to comparatively analyze the temporal trends in CS incidence and mortality in Brazil's Southeast Region from 2008 to 2022. This is an ecological time-series study using secondary data on congenital syphilis from the states of Espírito Santo, Minas Gerais, Rio de Janeiro, and São Paulo. The data was extracted from the Brazilian Health System Informatics Department. Incidence and mortality rates were calculated per 100,000 live births. Joinpoint regression models were employed to identify trends in annual percentage change and average annual percentage change with 95% confidence intervals. The temporal trend of CS incidence in Brazil's Southeast Region increased 12.8% between 2008 and 2022. Minas Gerais, São Paulo, Espírito Santo, and Rio de Janeiro showed increasing temporal trends of 21.4%, 14.1%, 14.0%, and 10.9%, respectively. The temporal trend of CS mortality in Brazil's Southeast Region rose 11.9% between 2008 and 2022. Minas Gerais, São Paulo, and Rio de Janeiro exhibited increasing mortality temporal trends of 21.9%, 20.8%, and 10.1%, respectively. In contrast, Espírito Santo showed reduced mortality, with no deaths in 2021 and 2022. The temporal trend of CS incidence increased in all states of Brazil's Southeast Region between 2008 and 2022, highlighting the need to reassess control measures. The temporal trend of CS mortality also increased during the same period, except in Espírito Santo. Considering that CS is preventable with adequate prenatal care and low-cost measures, these findings can serve as instruments to support strengthening public health policies.},
}
@article {pmid40407930,
year = {2025},
author = {Bate, JB and Dagamac, NHA},
title = {Wallow land suitability assessment using GIS-based multicriteria decision-making framework.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {6},
pages = {668},
pmid = {40407930},
issn = {1573-2959},
mesh = {*Geographic Information Systems ; *Conservation of Natural Resources/methods ; Animals ; *Environmental Monitoring/methods ; Ecosystem ; Philippines ; Decision Making ; Biodiversity ; },
abstract = {Protected areas are the frontlines of biodiversity conservation, featuring critical landscapes and microhabitats that are fitted for the survival of the organisms that have restricted populations. The determination of land suitability and habitat connectivity in these protected areas are important for species with specialized adaptive behavior that requires favorable conditions to survive. The Bubalus mindorensis is a critically endangered bovine of the Philippines which utilizes mud or water puddles to address heat stress through body submersion, known as wallowing. With Mts. Iglit-Baco National Park (MIBNP) harboring the largest remaining subpopulation of the tamaraw, the preservation of its natural landscapes is critical for tamaraw survival. Here, the potential wallows in MIBNP were determined using the weighted overlay analysis (WOA) assisted by the analytical hierarchy process (AHP). Using environmental variables that were influential to the creation of wallows, an equal-weighed scenario and an AHP-assisted scenario wallow suitability map was generated. Moderate and highly suitable areas were found at the north-central portion of the mountain, coinciding with the current and future conservation zones of the tamaraw, whereas low suitable areas dominate the other half, aggregating at the corners due to build areas and agriculture. The result of the study provides supplementary information in constructing future conservation strategies for an endemic species with global importance, particularly in its possible range expansion within the park. Furthermore, this study provides a framework for future conservation efforts, which helps in the management of critical landscapes for species with specialized adaptive behaviors through GIS-based multicriteria decision-making.},
}
@article {pmid40408146,
year = {2025},
author = {Fontanarrosa, P and Clare, C and Fedorec, AJH and Barnes, CP},
title = {MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {5},
pages = {},
pmid = {40408146},
issn = {1367-4811},
support = {BB/W013770/1//Bioengineered Cells &amp; Systems/ ; BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Software ; *Microbiota ; Bayes Theorem ; *Computational Biology/methods ; *Microbial Interactions ; Machine Learning ; Computer Simulation ; },
abstract = {SUMMARY: The study of microbial communities is vital for understanding their impact on environmental, health, and technological domains. The Modelling and Inference of MICrobiomes Project (MIMIC) introduces a Python package designed to advance the simulation, inference, and prediction of microbial community interactions and dynamics. Addressing the complex nature of microbial ecosystems, MIMIC integrates a suite of mathematical models, including previously used approaches such as Generalized Lotka-Volterra (gLV), Gaussian Processes (GP), and Vector Autoregression (VAR) plus newly developed models for integrating multi-omic data, to offer a versatile framework for analyzing microbial dynamics. By leveraging Bayesian inference and machine learning techniques, MIMIC provides the ability to infer the dynamics of microbial communities from empirical data, facilitating a deeper understanding of their complex biological processes, unveiling possible unknown ecological interactions, and enabling the design of microbial communities. Such insights could help to advance microbial ecology research, optimizing biotechnological applications, and contribute to environmental sustainability and public health strategies. MIMIC is designed for flexibility and ease of use, aiming to support researchers and practitioners in microbial ecology and microbiome research.<br><br>MIMIC is freely available under the MIT License at https://github.com/ucl-cssb/MIMIC. It is implemented in Python (version 3.7 or higher) and is compatible with Windows, macOS, and Linux operating systems. MIMIC depends on standard Python libraries including NumPy, SciPy, and PyMC. Comprehensive examples and tutorials (including the main text demonstrations) are provided as Jupyter notebooks in the examples/directory and at the MIMIC Docs website, along with detailed installation instructions and real-world data use cases. The software will remain freely available for at least two years following publication. A code snapshot for this publication is also available at Zenodo: https://doi.org/10.5281/zenodo.15149003.},
}
@article {pmid40408306,
year = {2025},
author = {Bukat, A and Bukowicki, M and Bykowski, M and Kuczkowska, K and Nowakowski, S and Śliwińska, A and Kowalewska, &#x141;},
title = {GRANA: An AI-based tool for accelerating chloroplast grana nanomorphology analysis using hybrid intelligence.},
journal = {Plant physiology},
volume = {198},
number = {2},
pages = {},
pmid = {40408306},
issn = {1532-2548},
support = {2019/35/D/NZ3/03904//National Science Centre, Poland/ ; BOB-IDUB-622-523/2024//University of Warsaw/ ; },
mesh = {*Artificial Intelligence ; *Software ; *Chloroplasts/ultrastructure ; *Thylakoids/ultrastructure ; Neural Networks, Computer ; Photosynthesis ; },
abstract = {Grana are fundamental structural units of the intricate chloroplast membrane network. Investigating their nanomorphology is essential for understanding photosynthetic efficiency regulation. Here, we present GRANA (Graphical Recognition and Analysis of Nanostructural Assemblies), an artificial intelligence-enhanced, user-friendly software tool that recognizes grana on thylakoid network electron micrographs and generates a complex set of their structural parameters. GRANA employs 3 artificial neural networks of different architectures and binds them in a 1-click workflow. Its output is designed to facilitate hybrid intelligence analysis, securing fast and reliable results from large datasets. The GRANA tool is over 100 times faster compared with currently used manual approaches. As a proof of concept, we have successfully applied GRANA software to diverse grana structures across different land plant species grown under various conditions, demonstrating the wide range of potential applications for our software. GRANA tool supports large-scale analysis of grana nanomorphological features, facilitating advancements in photosynthesis-oriented studies.},
}
@article {pmid40409688,
year = {2025},
author = {Zaabaar, E and Zhang, Y and Kam, KW and Li, Y and Zhang, XJ and Ho, M and Liu, D and Ng, MP and Ip, P and Young, A and Pang, CP and Tham, CC and Kwan, MP and Chen, LJ and Yam, JC},
title = {Association of residential air pollution with visual impairment in adults: The UK Biobank study.},
journal = {Asia-Pacific journal of ophthalmology (Philadelphia, Pa.)},
volume = {14},
number = {6},
pages = {100209},
doi = {10.1016/j.apjo.2025.100209},
pmid = {40409688},
issn = {2162-0989},
mesh = {UK Biobank/statistics &amp; numerical data ; Visual Acuity ; *Vision Disorders/diagnosis/epidemiology/etiology ; Nitrogen Oxides/analysis/toxicity ; *Air Pollutants/analysis/toxicity ; Particulate Matter/analysis/toxicity ; Principal Component Analysis ; Ecological Parameter Monitoring/statistics &amp; numerical data ; *Air Pollution/adverse effects/statistics &amp; numerical data ; Blindness/diagnosis/epidemiology/etiology ; *Environmental Exposure/adverse effects/statistics &amp; numerical data ; United Kingdom/epidemiology ; Persons with Visual Disabilities/statistics &amp; numerical data ; Humans ; Male ; Female ; Middle Aged ; Prospective Studies ; Adult ; Aged ; },
abstract = {PURPOSE: To investigate the association of joint exposure to residential air pollutants with different severities of visual impairment (VI) in adults.<br><br>METHODS: Exposure to particulate matter and oxides of nitrogen were evaluated in 95,246 adults aged 40-70 years. Joint exposure to the pollutants was calculated using principal component analysis to create an air pollution score. Subjects were categorized by distance visual acuity into bilateral normal vision, near normal vision, unilateral VI, socially significant VI, and blindness and low vision.<br><br>RESULTS: A unit rise in air pollution score was associated with 9.2&#x202f;%, 4.1&#x202f;%, and 1.8&#x202f;% increased risks of blindness and low vision, adjusted OR (AOR) =&#x202f;1.092 (95&#x202f;% CI, 1.057-1.129); socially significant VI, AOR =&#x202f;1.041 (95&#x202f;% CI, 1.016-1.066); and unilateral VI, AOR =&#x202f;1.018 (95&#x202f;% CI, 1.007-1.029), respectively. Compared to subjects in the lowest quartile of air pollution score, those in the highest quartile had 69.2&#x202f;%, 30.5&#x202f;%, and 9.9&#x202f;% greater risks of blindness and low vision, AOR =&#x202f;1.692 (95&#x202f;% CI, 1.355-2.114), socially significant VI, AOR =&#x202f;1.305 (95&#x202f;% CI, 1.127-1.513), and unilateral VI, AOR =&#x202f;1.099 (95&#x202f;% CI, 1.035-1.167), respectively while those in the third quartile had 40.5&#x202f;% and 25.6&#x202f;% higher risks of blindness and low vision, AOR =&#x202f;1.405 (95&#x202f;% CI, 1.121-1.760) and socially significant VI, AOR =&#x202f;1.256 (95&#x202f;% CI, 1.086-1.453), respectively. There was a significant trend of increasing risk of blindness and low vision, as well as socially significant VI, as pollution levels rose.<br><br>CONCLUSION: Joint exposure to air pollutants increased the risks of poor vision and blindness, suggesting that reducing such exposure could alleviate the disease burden of VI.},
}
@article {pmid40410961,
year = {2025},
author = {Zhang, L and Zhang, L and Gao, S and Huang, C and Dai, Q},
title = {Structural balance and evolution of cooperation in a population with hybrid interactions.},
journal = {Physical review. E},
volume = {111},
number = {4-1},
pages = {044309},
doi = {10.1103/PhysRevE.111.044309},
pmid = {40410961},
issn = {2470-0053},
abstract = {This study explores the evolution of cooperation in populations with mixed pairwise and three-body interactions, investigating the impact of higher-order interaction density ρ and individual interaction preference α. Our results reveal that sparse higher-order interactions markedly boost cooperation, exhibiting two critical phase transitions as ρ changes. These transitions underscore the delicate equilibrium needed for optimal cooperation, as excessive higher-order interactions can diminish returns. The preference parameter α significantly influences cooperation sustainability, with intermediate values maximizing cooperative outcomes, particularly when the temptation to defect r is not strong. Crucially, our findings demonstrate that hybrid social dilemmas structurally encode emergent cooperation pathways that are unattainable within homogeneous interaction frameworks, emphasizing the importance of modeling mixed interactions to capture real-world complexity. These insights offer valuable guidance for designing systems aimed at promoting cooperative behavior across social, ecological, and artificial domains.},
}
@article {pmid40412934,
year = {2025},
author = {Zhu, Q and Cai, Y and Hu, Z},
title = {Effects of bactericides and sulphate reducing bacteria addition on acidification and microbial community structure of newly produced coal gangue.},
journal = {Journal of environmental sciences (China)},
volume = {156},
number = {},
pages = {311-320},
doi = {10.1016/j.jes.2024.06.024},
pmid = {40412934},
issn = {1001-0742},
mesh = {*Coal ; Sulfates/metabolism ; *Bacteria/metabolism ; Hydrogen-Ion Concentration ; *Microbiota ; *Soil Microbiology ; },
abstract = {Microbiologically driven acidic pollution of coal gangue has become a major environmental problem in coal gangue dumps in coal mining areas. Addition of bactericides and sulphate reducing bacteria (SRB) is an effective means to control the acidic pollution of coal gangue, but their mechanism of action has not been fully investigated. By adding bactericide, SRB and bactericide-SRB to the newly produced coal gangue, respectively, the effects of these treatments on the microbial community structure were observed. Changes in pH and electrical conductivity (EC) of the gangue leaching solution, as well as the microbial community composition and functional abundance on the gangue surface were analysed by leaching simulation experiments and 16S rRNA sequencing. The results showed that (1) the addition of bactericide-SRB was the most effective treatment to elevate pH before 8 d, while the addition of SRB performed best after 22 d (2) The addition of bactericide and SRB drastically changed the microbial community structure on the gangue surface. Simultaneous addition of both had the best inhibitory effect on pathogenic bacteria and Thiobacillus. (3) All three treatments promote higher abundance of genes related to nitrogen cycling, but reflected in different gene functions. Microorganisms with sulfate respiration function in the experimental group all showed different increases. The abundance of other sulfur cycle genes decreased substantially. However, Human Pathogens All had higher abundance than control check (CK) in each treatment, which may indicate that the addition of either bactericides or SRB increases the risk of microbial pathogenicity to humans.},
}
@article {pmid40413228,
year = {2025},
author = {Fan, J and Zhang, Y and Nie, X and Liu, Y and Wei, S and Peng, H and Li, H and Zhang, M and Ning, L and Wang, S and Qin, L and Zheng, Y and Xing, Y},
title = {Comprehensive curation and validation of genomic datasets for chestnut.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {860},
pmid = {40413228},
issn = {2052-4463},
mesh = {*Fagaceae/genetics ; *Genome, Plant ; Genomics ; Databases, Genetic ; Molecular Sequence Annotation ; Data Curation ; },
abstract = {The Chinese chestnut (Castanea mollissima) stands out as a plant with significant ecological and economic value, excellent nutritional quality and natural resistance to pests and diseases. Recent strides in high-throughput techniques have enabled the continuous accumulation of genomic data on chestnuts, presenting a promising future for genetic research and advancing traits in this species. To facilitate the accessibility and utility of this data, we have curated and analyzed a collection of genomic datasets for eight Castanea species, including functional annotations, 213 RNA-Seq samples, and 330 resequencing samples. These datasets are publicly available on Figshare and are also available through other platforms such as GEO and EVA, providing a valuable resource for researchers studying Castanea genetics, functional genomics, and evolutionary biology. Furthermore, the datasets are integrated into the Castanea Genome Database (CGD, http://castaneadb.net), which serves as a complementary platform, offering advanced data mining and analysis tools, including BLAST, Batch Query, GO/KEGG Enrichment Analysis, and Synteny Viewer, to enhance the usability of the curated datasets.},
}
@article {pmid40413976,
year = {2025},
author = {Bai, Z and Zhang, D and Zhang, S and Li, T and Wang, G and Xu, X and Pan, X and Zhong, Q and Zhou, W and Pu, Y and Jia, Y},
title = {Integrating multi-omics and biomarkers to reveal the stress mechanisms of high fluoride on earthworms.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138706},
doi = {10.1016/j.jhazmat.2025.138706},
pmid = {40413976},
issn = {1873-3336},
mesh = {Animals ; *Oligochaeta/drug effects/metabolism/genetics ; Reactive Oxygen Species/metabolism ; Biomarkers/metabolism ; Oxidative Stress/drug effects ; *Soil Pollutants/toxicity ; *Fluorides/toxicity ; Apoptosis/drug effects ; Multiomics ; },
abstract = {Excessive fluorine accumulation poses a significant threat to soil ecology and even human health, yet its impact on soil fauna, especially earthworms, remains poorly understood. This study employed multi-omics and biomarkers to investigate high fluorine-induced biochemical changes that cause tissue damages in Eisenia fetida. The results demonstrated that earthworms exhibited obvious damage with fluorine addition exceeding 200 mg kg[-1], with stress levels escalating as fluorine contents increased. Further analysis of the underlying mechanisms revealed that fluorine could upregulate genes encoding mitochondrial respiratory chain complexes I-III and downregulate those for IV-V, leading to reactive oxygen species (ROS) accumulation despite antioxidant system activation. The resulting ROS interfered with deoxyribonucleoside triphosphate synthesis, prompting homologous recombination as the main DNA repair mechanism. Additionally, fluorine-induced ROS also attacked and disrupted protein and lipid related metabolisms ultimately causing oxidative damages. These cumulative oxidative damages from high fluorine contents subsequently triggered autophagy or apoptosis, resulting in tissue ulceration and epithelial exfoliation. Therefore, high fluorine could threaten earthworms by inducing ROS accumulation and subsequent biomolecule damages.},
}
@article {pmid40414334,
year = {2025},
author = {Dou, X and Liu, Q and Fan, Q and Guo, J and Qi, W},
title = {Comprehensive analysis of common heavy metals in the Yellow River over 20 Years: Spatiotemporal distribution, migration characteristics, traceability, and potential risk evaluation.},
journal = {Environmental research},
volume = {281},
number = {},
pages = {121931},
doi = {10.1016/j.envres.2025.121931},
pmid = {40414334},
issn = {1096-0953},
mesh = {*Metals, Heavy/analysis ; *Water Pollutants, Chemical/analysis ; *Rivers/chemistry ; China ; *Environmental Monitoring ; Risk Assessment ; Geologic Sediments/chemistry ; Spatio-Temporal Analysis ; },
abstract = {Heavy metal pollution posed a great threat to the global aquatic ecological environment, especially in the Yellow River where the utilization rate of water resources was as high as 80 %. This study addressed the spatiotemporal distribution, sources, and ecological risks of seven heavy metals (As, Cd, Cr, Cu, Ni, Pb, Zn) in the Yellow River by analyzing historical data collected from 2000 to 2020. The annual heavy metal fluxes increased from Qinghai to Henan section, then decreased from Henan to Shandong section. Similarly, concentrations of Cu, Ni, Pb, and Zn peaked in the sediments of the Henan section. These trends might be attributed to the interception effects of the Xiaolangdi and Sanmenxia Dams. The annual fluxes from 2016 to 2020 increased by an average of 162.6 % compared to that from 2011 to 2015, likely reflecting the impact of ongoing economic growth (33.36 %) and SS increase (69.68 %). The annual fluxes of SS demonstrated a significant correlation with all heavy metal fluxes, underscoring their role as a critical transport medium in aquatic ecosystem. The fluxes of Cd and Pb were most strongly influenced by human factors. While most metals in surface water present negligible risks to aquatic life, Cd in sediments presents a considerable ecological threat. Furthermore, the highest potential ecological risk index (RI) was observed in the river sections in Gansu and Inner Mongolia, mainly due to Cd, which contributed up to 85.87 %. The findings establish a fundamental framework for safeguarding the aquatic ecosystem of the Yellow River and managing its heavy metal contamination.},
}
@article {pmid40414987,
year = {2025},
author = {Jia, L and Liu, Z and Li, Y},
title = {Spatiotemporal dynamics of rural settlement evolution in Guangdong Province, China.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18244},
pmid = {40414987},
issn = {2045-2322},
support = {23BDJ019//National Planning Office of Philosophy and Social Science/ ; 23BDJ019//National Planning Office of Philosophy and Social Science/ ; },
mesh = {China ; *Rural Population/statistics &amp; numerical data ; Humans ; *Urbanization/trends ; Spatio-Temporal Analysis ; *Population Dynamics ; Socioeconomic Factors ; Industrial Development ; Geographic Information Systems ; },
abstract = {This study analyzes the spatiotemporal dynamics of rural settlement evolution in Guangdong Province, China, examining their transformation amid rapid urbanization and industrialization over the past 20 years. Rural settlements serve as primary spatial carriers for production and living activities, embodying multiple functions including production, living, ecological, and cultural aspects. Using GIS-based analytical tools, including landscape pattern indices, average nearest neighbor index, kernel density estimation, and geographical detector methods, we examined settlement evolution patterns and their driving factors. Results show a continuous decline in settlement numbers, while patch areas exhibited a U-shaped trend of decreasing then increasing. Settlement patterns shifted from "reduction" to "integration", with intensifying spatial agglomeration over time. The Pearl River Delta and Eastern Guangdong regions followed similar trajectories, reflecting the impact of urbanization and industrialization on rural development. Multiple factors, including natural conditions, socioeconomic variables, and locational accessibility, drove these changes. The spatial distribution of rural settlements demonstrates an overall trend of agglomeration, which has gradually intensified over time, leading to significant variations in settlement density across different regions. The findings reveal significant regional disparities and temporal changes in settlement patterns, highlighting the complex interplay between rural transformation and urban development. This research contributes to understanding rural transformation processes in developing countries and emphasizes the need for differentiated approaches in spatial planning and rural revitalization strategies to address the challenges of disordered land expansion and population hollowing while promoting sustainable rural development.},
}
@article {pmid40415801,
year = {2025},
author = {Yang, P and Wang, X and Yang, J and Yan, B and Sheng, H and Li, Y and Yang, Y and Wang, J},
title = {AI-Driven Multiscale Study on the Mechanism of Polygonati Rhizoma in Regulating Immune Function in STAD.},
journal = {ACS omega},
volume = {10},
number = {19},
pages = {19770-19796},
pmid = {40415801},
issn = {2470-1343},
abstract = {Polygonati Rhizoma, a traditional Chinese medicine, has demonstrated immunomodulatory and anticancer properties, yet its precise mechanisms in stomach adenocarcinoma (STAD) remain underexplored. This study aims to uncover the multitarget mechanisms of Polygonati Rhizoma in regulating the tumor immune microenvironment in STAD using artificial intelligence (AI)-driven network pharmacology, bioinformatics, and single-cell RNA sequencing, offering new insights into its immunotherapeutic potential. This study harnessed the power of AI to unravel the molecular mechanisms underlying Polygonati Rhizoma's effects. AI-driven methodologies screened 38 putative constituents, retaining 8 based on ADME criteria. Machine Learning algorithms predicted potential targets, which were cross-referenced with 5,569 immune-related genes from GeneCards, revealing 52 immune-associated targets. Differential expression analysis of the STAD data set identified 18 overlapping DEGs with prognostic significance and immune cell infiltration correlations. Key targets (AKT1, TP53, PTGS2 and VEGFA) emerged as central nodes in the network, with AI-assisted molecular docking confirming strong binding affinities, particularly between diosgenin and these core proteins. Molecular dynamics simulations further validated these interactions. Single-cell RNA sequencing revealed distinct target-gene expression patterns across malignant, stromal, and immune cell subsets in digestive-system tumors. In vitro, Polygonati Rhizoma extract significantly inhibited HGC-27 cell viability and increased intracellular ROS levels. These findings underscore the critical role of AI in integrating multiscale analyses, unveiling a multitarget immunomodulatory and antitumor mechanism for Polygonati Rhizoma in STAD, and providing a foundation for future preclinical and clinical studies.},
}
@article {pmid40416669,
year = {2025},
author = {Gaievskyi, S and Delfrate, N and Ragazzoni, L and Bahattab, A},
title = {Use of multi-criteria decision analysis (MCDA) to support decision-making during health emergencies: a scoping review.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1584026},
pmid = {40416669},
issn = {2296-2565},
mesh = {Humans ; *Decision Support Techniques ; *Decision Making ; *Emergencies ; },
abstract = {BACKGROUND: The mismatch between the health needs of populations affected by emergencies and resources devoted to response is projected to further increase. Making the response more effective is one of the solutions to meet the growing needs. Multi-criteria decision analysis (MCDA) has been successfully used to increase effectiveness in various fields by supporting decision-making. However, no review of its application to all-hazard health emergencies has been done to date.<br><br>METHODS: A review of peer-reviewed English-language articles published since 2004 was conducted in May 2024 using Scopus, PubMed and Web of Science databases. The review focused on the empirical application of MCDA to support decision-making during health emergencies. The review was guided by the Joanna Briggs Institute methodology for scoping reviews and adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews. Quantitative data were analyzed using summary statistics and qualitative data were analyzed using content analysis.<br><br>RESULTS: Seventy-one articles were included after screening. The articles described the MCDA application to support a variety of decision problems related to health emergency management. However, the technique was mostly applied to infectious hazards management and only seldom to other hazards. The review also found a lack of standardized methodology for identifying alternatives and criteria, weighting, computation of model output, methods of dealing with uncertainty, and stakeholder engagement.<br><br>CONCLUSION: The review provides an overview of the current use of the MCDA approach to support decision-making in health emergency management and informs areas of future development. The review emphasizes that while MCDA is already used for infectious hazards, it is underutilized for other types of health emergencies. Developing tailored MCDA approaches for health emergencies, including defining evaluation criteria and stakeholder engagement, may improve uptake of the technique and benefit the efforts to meet the growing health needs of the population affected by emergencies, https://osf.io/6kd5s/.},
}
@article {pmid40417563,
year = {2024},
author = {Foreman, MA and Ross, A and Burgess, APH and Myneni, S and Franklin, A},
title = {Barriers and Facilitators of Digital Health Use for Self-Management of Hypertensive Disorders by Black Pregnant Women.},
journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium},
volume = {2024},
number = {},
pages = {433-442},
pmid = {40417563},
issn = {1942-597X},
mesh = {Humans ; Female ; Pregnancy ; *Self-Management ; *Black or African American ; *Hypertension, Pregnancy-Induced/therapy/ethnology ; Adult ; Interviews as Topic ; Telemedicine ; Digital Health ; },
abstract = {Although digital health tools are increasingly common for managing health conditions, these applications are often developed without consideration of differences across user populations. A reproducible framework is needed to support tailoring applications to include cultural considerations, potentially leading to better adoption and more effective use. As a first step, this study captures a snapshot of Black women's barriers and facilitators in using digital health products for self-management of hypertensive disorders of pregnancy (HDP). One-on-one semi-structured interviews were conducted with 17 Black pregnant women with HDP. We established a unique model for cultural tailoring with these experiences using Black feminist theory and the CDC's Social-Ecological Model (SEM). 38 themes across the four levels of SEM were found through grounded theory. These themes can inform the feature development of a digital health intervention. Future work will instantiate and validate a framework that provides theoretical constructs for developing culturally tailored digital health interventions.},
}
@article {pmid40419494,
year = {2025},
author = {Jucker, T and Fischer, FJ and Chave, J and Coomes, DA and Caspersen, J and Ali, A and Loubota Panzou, GJ and Feldpausch, TR and Falster, D and Usoltsev, VA and Jackson, TD and Adu-Bredu, S and Alves, LF and Aminpour, M and Angoboy Ilondea, B and Anten, NPR and Antin, C and Askari, Y and Ayyappan, N and Banin, LF and Barbier, N and Battles, JJ and Beeckman, H and Bocko, YE and Bond-Lamberty, B and Bongers, F and Bowers, S and van Breugel, M and Chantrain, A and Chaudhary, R and Dai, J and Dalponte, M and Dimobe, K and Domec, JC and Doucet, JL and Dupuy Rada, JM and Duursma, RA and Enríquez, M and van Ewijk, KY and Farfán-Rios, W and Fayolle, A and Ferretti, M and Forni, E and Forrester, DI and Gilani, H and Godlee, JL and Haeni, M and Hall, JS and He, JK and Hemp, A and Hernández-Stefanoni, JL and Higgins, SI and Holdaway, RJ and Hussain, K and Hutley, LB and Ichie, T and Iida, Y and Jiang, HS and Joshi, PR and Kaboli, H and Kazempour Larsary, M and Kenzo, T and Kloeppel, BD and Kohyama, TS and Kunwar, S and Kuyah, S and Kvasnica, J and Lin, S and Lines, ER and Liu, H and Lorimer, C and Loumeto, JJ and Malhi, Y and Marshall, PL and Mattsson, E and Matula, R and Meave, JA and Mensah, S and Mi, X and Momo, ST and Moncrieff, GR and Mora, F and Muñoz, R and Nissanka, SP and Nur Hajar, ZS and O'Hara, KL and Pearce, S and Pelissier, R and Peri, PL and Ploton, P and Poorter, L and Pour, MJ and Pourbabaei, H and Ribeiro, SC and Ryan, C and Sanaei, A and Sanger, J and Schlund, M and Sellan, G and Shenkin, A and Sonké, B and Sterck, FJ and Svátek, M and Takagi, K and Trugman, AT and Vadeboncoeur, MA and Valipour, A and Vanderwel, MC and Vovides, AG and Waldner, P and Wang, W and Wang, LQ and Wirth, C and Woods, M and Xiang, W and de Aquino Ximenes, F and Xu, Y and Yamada, T and Zavala, MA and Zimmermann, NE},
title = {The global spectrum of tree crown architecture.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4876},
pmid = {40419494},
issn = {2041-1723},
support = {NE/S01537X/1//RCUK | Natural Environment Research Council (NERC)/ ; },
mesh = {*Trees/anatomy &amp; histology/physiology/classification ; Ecosystem ; *Plant Stems/anatomy &amp; histology ; Photosynthesis ; Climate ; Biological Evolution ; Phylogeny ; },
abstract = {Trees can differ enormously in their crown architectural traits, such as the scaling relationships between tree height, crown width and stem diameter. Yet despite the importance of crown architecture in shaping the structure and function of terrestrial ecosystems, we lack a complete picture of what drives this incredible diversity in crown shapes. Using data from 374,888 globally distributed trees, we explore how climate, disturbance, competition, functional traits, and evolutionary history constrain the height and crown width scaling relationships of 1914 tree species. We find that variation in height-diameter scaling relationships is primarily controlled by water availability and light competition. Conversely, crown width is predominantly shaped by exposure to wind and fire, while also covarying with functional traits related to mechanical stability and photosynthesis. Additionally, we identify several plant lineages with highly distinctive stem and crown forms, such as the exceedingly slender dipterocarps of Southeast Asia, or the extremely wide crowns of legume trees in African savannas. Our study charts the global spectrum of tree crown architecture and pinpoints the processes that shape the 3D structure of woody ecosystems.},
}
@article {pmid40425079,
year = {2025},
author = {Mambully, S and Ramesh, V and Rani, S and Khatoon, M and A, J and Patil, AV and Palavesam, A and Sengupta, PP and Patil, SS and Kp, S},
title = {Genotype patterns and evolutionary rates: uncovering Japanese encephalitis virus spread across Asia's climate regions.},
journal = {Acta tropica},
volume = {267},
number = {},
pages = {107676},
doi = {10.1016/j.actatropica.2025.107676},
pmid = {40425079},
issn = {1873-6254},
mesh = {*Encephalitis Virus, Japanese/genetics/classification/isolation &amp; purification ; *Encephalitis, Japanese/epidemiology/virology/transmission ; *Evolution, Molecular ; *Genotype ; Humans ; Asia/epidemiology ; Phylogeny ; Viral Envelope Proteins/genetics ; Climate ; Animals ; Phylogeography ; },
abstract = {Japanese Encephalitis Virus (JEV) is a highly endemic zoonotic virus, consistently found in Asia and parts of the Western Pacific, and it's a major cause of human encephalitis. JEV belongs to a family of antigenically related viruses such as West Nile Virus (WNV), Murray Valley encephalitis virus (MVEV), and Aichi Lake Fever Virus (ALFV) and is transmitted by mosquitoes. Persistent outbreaks of the disease necessitate detailed studies to understand their transmission dynamics and develop effective prevention strategies. This study explores the evolutionary dynamics and spatial transmission of JEV, concentrating on the envelope protein (E) structural gene sequences obtained from across Asia's diverse climatic regions. Evolutionary modeling of the JEV E gene revealed a higher evolutionary rate in tropical regions compared to temperate regions, with nucleotide substitution rates estimated at 1.12 × 10[-3] per site per year for tropical regions and 5.284 × 10[-4] for temperate regions. The time to the most recent common ancestor (tMRCA) was traced to 1796 from Korea for temperate regions, and 1865 from Indonesia for tropical regions. Among the five genotypes of JEV, Genotype I (GI) and III (GIII) were established all over Southeast Asia; moreover, GI revealed a higher evolutionary rate, reflecting its adaptability to diverse ecological niches. The phylogeographic analysis highlighted significant contributions to virus diffusion by China, Korea, and Japan in temperate zones and by Vietnam in tropical zones. By analyzing genetic sequences from various regions and time periods, this study delivered valuable intuitions into transmission pathways. The findings highlighted the necessity of ongoing surveillance and evolutionary monitoring to track the spread and emergence of novel variations of JEV, which are crucial not just for managing JEV outbreaks but also for guiding immunization programs and public health initiatives.},
}
@article {pmid40425424,
year = {2025},
author = {Cardoso, P and Branco, V and Correia, L and Emerson, BC and Laine, VN and Lopes, M},
title = {Automated biodiversity research critically requires multidisciplinary expertise.},
journal = {Trends in ecology &amp; evolution},
volume = {40},
number = {7},
pages = {626-628},
doi = {10.1016/j.tree.2025.05.003},
pmid = {40425424},
issn = {1872-8383},
mesh = {*Biodiversity ; *Conservation of Natural Resources/methods ; *Automation ; *Ecology/methods ; *Computational Biology/methods ; },
abstract = {Data-driven computational methods in taxonomy, ecology, and conservation biology are revolutionising these disciplines, from data collection to analysis and interpretation. However, effective automation requires both critical thinking about the limitations of the data and methods, and thorough training and validation by experts, supported by strong interdisciplinary collaboration.},
}
@article {pmid40425680,
year = {2025},
author = {Péter, SA and Gallo, T and Mullinax, J and Roess, A and Palomo-Munoz, G and Anderson, T},
title = {Integrating human mobility and animal movement data reveals complex space-use between humans and white-tailed deer in urban environments.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18588},
pmid = {40425680},
issn = {2045-2322},
support = {AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; },
mesh = {Animals ; *Deer/physiology ; Humans ; Zoonoses/transmission ; Animals, Wild ; Ecosystem ; Maryland ; Cities ; Wasting Disease, Chronic/transmission ; COVID-19/transmission/epidemiology/virology ; SARS-CoV-2 ; Geographic Information Systems ; },
abstract = {Human expansion into wildlife habitats has increased the need to understand human-wildlife interactions, necessitating interdisciplinary approaches to assess zoonotic disease transmission risks and public health impacts. This study integrated fine-grained human foot traffic data with hourly GPS data from 38 white-tailed deer (Odocoileus virginianus), a species linked to SARS-CoV-2, brucella, and chronic wasting disease, in Howard County, Maryland. We explored spatial and temporal overlap between human and deer activity over 24 months (2018-2019) across a hexagonal tessellation with metrics like hourly popularity and visit counts. Negative binomial models were fitted to the visit counts of each deer and humans per tessellation area, using landscape features as predictors. A separate deer-only model included commercial human activity as another predictor. Spatial analysis showed deer and humans sharing spaces in the study area, with results indicating deer using more populated residential areas and areas with commercial activity. Temporal analysis showed deer avoiding commercial spaces during daytime but using them in late evening and early morning. These findings highlight the complex space use between species and the importance of integrating detailed human mobility and animal movement data when managing wildlife-human conflict and zoonotic disease transmission, particularly in urban areas with a high probability of deer-human interactions.},
}
@article {pmid40426056,
year = {2025},
author = {Charest, J and Loebenstein, P and Mach, RL and Mach-Aigner, AR},
title = {FunFEA: an R package for fungal functional enrichment analysis.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {138},
pmid = {40426056},
issn = {1471-2105},
mesh = {*Genome, Fungal ; *Software ; Molecular Sequence Annotation/methods ; *Fungi/genetics ; Gene Ontology ; Databases, Genetic ; Genomics/methods ; Computational Biology/methods ; },
abstract = {BACKGROUND: The functional annotation of fungal genomes is critical for understanding their biological processes and ecological roles. While existing tools support functional enrichment analysis from publicly available annotations of well-established model organisms, few are tailored to the specific needs of the fungal research community. Furthermore, many tools struggle with processing functional annotations of novel species, for which no publicly available functional annotations are yet available.<br><br>RESULTS: FunFEA is an R package designed for functional enrichment analysis of fungal genomes. It supports COG/KOG (Clusters of Orthologous Genes), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations, and generates background frequency models from publicly available annotations for overrepresentation analysis, within a set of experimentally defined genes or proteins. Additionally, FunFEA can process eggNOG-mapper annotations, thus enabling functional enrichment analysis of novel genomes. The package offers a suite of tools for generation of background frequency models, functional enrichment analysis, as well as visualization of enriched functional categories. On release, the package includes precomputed models for 65 commonly used fungal strains in academic research and strains listed on the WHO fungal priority pathogens list.<br><br>CONCLUSIONS: FunFEA fills a critical need for a specialized tool in fungal genomics, providing valuable insights into fungal biology. Additionally, its ability to process eggNOG-mapper annotations makes it an essential resource for researchers, helping to drive further exploration of fungal functional diversity and pathways and derive biological insights from novel genomes.},
}
@article {pmid40427823,
year = {2025},
author = {Santos, AFB and Nunes, M and Filipa-Silva, A and Pimentel, V and Pingarilho, M and Abrantes, P and Miranda, MNS and Crespo, MTB and Abecasis, AB and Parreira, R and Seabra, SG},
title = {Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {5},
pages = {},
pmid = {40427823},
issn = {1660-4601},
support = {PTDC/CTA AMB/29586/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia, Portugal 568 through projects AgriWWAter/ ; 706, Internalproject IBETXplore 2017//VirusFreeWater/ ; GHTM- UID/04413/2020//Internal exploratory Project WasteWaterVir/ ; LA/P/0117/2020//LA-REAL/ ; },
mesh = {*Wastewater/virology ; *Computational Biology/methods ; *Virome ; Portugal ; *Metagenomics/methods ; *Viruses/classification/isolation &amp; purification/genetics ; },
abstract = {This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools-Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2-on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample-tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.},
}
@article {pmid40431635,
year = {2025},
author = {Rodrigues, GVP and Santos, JPN and Ferreira, LYM and Conceição, LBA and Porto, JAM and Aguiar, ERGR},
title = {Theobroma cacao Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance.},
journal = {Viruses},
volume = {17},
number = {5},
pages = {},
pmid = {40431635},
issn = {1999-4915},
support = {Financial Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; //Conselho Nacional de Pesquisa Cient&#xed;fica (CNPq)/ ; },
mesh = {*Cacao/virology ; *Virome/genetics ; Plant Diseases/virology ; RNA-Seq ; Computational Biology/methods ; Phylogeny ; *Plant Viruses/genetics/classification/isolation &amp; purification ; Genome, Viral ; Badnavirus/genetics/isolation &amp; purification/classification ; Microbiota ; },
abstract = {Cocoa (Theobroma cacao L.) is a major agricultural commodity, essential for the global chocolate industry and the livelihoods of millions of farmers. However, viral diseases pose a significant threat to cocoa production, with Badnavirus species causing severe losses in Africa. Despite its economic importance, the overall virome of T. cacao remains poorly characterized, limiting our understanding of viral diversity and potential disease interactions. This study aims to assess the cocoa-associated virome by analyzing 109 publicly available RNA-seq libraries from nine BioProjects, covering diverse conditions and geographic regions. We implemented a comprehensive bioinformatics pipeline integrating multiple viral sequence enrichment steps, a hybrid assembly strategy using different assemblers, and sequence similarity searches against NCBI non-redundant databases. Our approach identified ten putative novel viruses associated with the cocoa microbiome and a novel Badnavirus species. These findings provide new insights into the viral landscape of T. cacao, characterizing the diversity of cacao-associated viruses and their potential ecological roles. Expanding the catalog of viruses associated with cocoa plants not only enhances our understanding of plant-virus-microbiome interactions but also contributes to the development of more effective disease surveillance and management strategies, ultimately supporting sustainable cocoa production.},
}
@article {pmid40432231,
year = {2025},
author = {Tian, XC and Nie, S and Domingues, D and Rossi Paschoal, A and Jiang, LB and Mao, JF},
title = {PlantLncBoost: key features for plant lncRNA identification and significant improvement in accuracy and generalization.},
journal = {The New phytologist},
volume = {247},
number = {3},
pages = {1538-1549},
pmid = {40432231},
issn = {1469-8137},
support = {2022YFD2200103//National Key R&amp;D Program of China/ ; 32171816//National Natural Science Foundation of China/ ; ZR2022YQ23//Natural Science Fund for Excellent Young Scholars of Shandong Province/ ; 2025A1515012969//Guangdong Basic and Applied Basic Research Foundation/ ; #440412/2022-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico - CNPq/ ; Project: NAPI Bioinformatica #66.2021//Funda&#xe7;&#xe3;o Arauc&#xe1;ria/ ; },
mesh = {*RNA, Long Noncoding/genetics ; *RNA, Plant/genetics ; *Computational Biology/methods ; Algorithms ; *Plants/genetics ; RNA, Messenger/genetics ; *Software ; Open Reading Frames/genetics ; },
abstract = {Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification models. Here, we present PlantLncBoost, a novel computational tool designed to improve the generalization in plant lncRNA identification. By integrating advanced gradient boosting algorithms with comprehensive feature selection, our approach achieves both high accuracy and generalizability. We conducted an extensive analysis of 1662 features and identified three key features - ORF coverage, complex Fourier average, and atomic Fourier amplitude - that effectively distinguish lncRNAs from mRNAs. We assessed the performance of PlantLncBoost using comprehensive datasets from 20 plant species. The model exhibited exceptional performance, with an accuracy of 96.63%, a sensitivity of 98.42%, and a specificity of 94.93%, significantly outperforming existing tools. Further analysis revealed that the features we selected effectively capture the differences between lncRNAs and mRNAs across a variety of plant species. PlantLncBoost represents a significant advancement in plant lncRNA identification. It is freely accessible on GitHub (https://github.com/xuechantian/PlantLncBoost) and has been integrated into a comprehensive analysis pipeline, Plant-LncRNA-pipeline v.2 (https://github.com/xuechantian/Plant-LncRNA-pipeline-v2).},
}
@article {pmid40432488,
year = {2025},
author = {Min, J and Kim, B and Park, Y and Son, Y and Park, W},
title = {Bacterial cell wall synthesis and recycling: new antimicrobial targets and vaccine development.},
journal = {Critical reviews in microbiology},
volume = {51},
number = {6},
pages = {1364-1383},
doi = {10.1080/1040841X.2025.2510250},
pmid = {40432488},
issn = {1549-7828},
mesh = {*Cell Wall/metabolism/drug effects ; *Bacterial Vaccines/immunology ; Humans ; *Vaccine Development ; *Peptidoglycan/biosynthesis/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/metabolism ; Bacterial Proteins/metabolism ; },
abstract = {Almost all bacteria have peptidoglycan (PG) components that are essential for virulence and are absent in humans, making them a top-priority target for antibiotics and vaccines. The rise of multidrug-resistant bacteria (MRB) necessitates urgent expansion of our arsenal of inhibitors targeting the PG cell wall. This review addresses our understanding of PG biosynthesis and recycling processes, emphasizing the need to identify novel target proteins and redesign existing PG-targeted antimicrobial peptides. Building on our understanding of cell wall biochemistry and biogenesis derived from Escherichia coli, we also aim to compare and elucidate the cell wall processes in other pathogens, such as Acinetobacter baumannii and Salmonella Typhimurium, where knowledge remains incomplete. We cover in detail the distinct roles of PG-related proteins in Gram-negative bacteria, strategies to block PG biosynthesis/recycling pathways, and their potential as novel antibiotic targets to address the growing challenge of antibiotic resistance. Finally, we review the application of rigorous immuno-informatics analysis and several immune filters to construct epitope-specific vaccines displaying PG-related proteins on the surface of outer membrane vesicles (OMVs), aiming to combat MRB proliferation.},
}
@article {pmid40433986,
year = {2024},
author = {He, Y and Mulqueeney, JM and Watt, EC and Salili-James, A and Barber, NS and Camaiti, M and Hunt, ESE and Kippax-Chui, O and Knapp, A and Lanzetti, A and Rangel-de Lázaro, G and McMinn, JK and Minus, J and Mohan, AV and Roberts, LE and Adhami, D and Grisan, E and Gu, Q and Herridge, V and Poon, STS and West, T and Goswami, A},
title = {Opportunities and Challenges in Applying AI to Evolutionary Morphology.},
journal = {Integrative organismal biology (Oxford, England)},
volume = {6},
number = {1},
pages = {obae036},
pmid = {40433986},
issn = {2517-4843},
abstract = {Artificial intelligence (AI) is poised to revolutionize many aspects of science, including the study of evolutionary morphology. While classical AI methods such as principal component analysis and cluster analysis have been commonplace in the study of evolutionary morphology for decades, recent years have seen increasing application of deep learning to ecology and evolutionary biology. As digitized specimen databases become increasingly prevalent and openly available, AI is offering vast new potential to circumvent long-standing barriers to rapid, big data analysis of phenotypes. Here, we review the current state of AI methods available for the study of evolutionary morphology, which are most developed in the area of data acquisition and processing. We introduce the main available AI techniques, categorizing them into 3 stages based on their order of appearance: (1) machine learning, (2) deep learning, and (3) the most recent advancements in large-scale models and multimodal learning. Next, we present case studies of existing approaches using AI for evolutionary morphology, including image capture and segmentation, feature recognition, morphometrics, and phylogenetics. We then discuss the prospectus for near-term advances in specific areas of inquiry within this field, including the potential of new AI methods that have not yet been applied to the study of morphological evolution. In particular, we note key areas where AI remains underutilized and could be used to enhance studies of evolutionary morphology. This combination of current methods and potential developments has the capacity to transform the evolutionary analysis of the organismal phenotype into evolutionary phenomics, leading to an era of "big data" that aligns the study of phenotypes with genomics and other areas of bioinformatics.},
}
@article {pmid40435494,
year = {2025},
author = {Berger, M and Ehlers, JP and Nitsche, J},
title = {Aligning With the Goals of the Planetary Health Concept Regarding Ecological Sustainability and Digital Health: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e71795},
pmid = {40435494},
issn = {1438-8871},
mesh = {*Telemedicine ; Climate Change ; Humans ; Global Health ; Delivery of Health Care ; Artificial Intelligence ; Digital Health ; },
abstract = {BACKGROUND: Climate change, driven by greenhouse gas emissions, threatens human health and biodiversity. While the digitalization of health care, including telemedicine and artificial intelligence, offers sustainability benefits, it also raises concerns about energy use and electronic waste. Balancing these factors is key to a sustainable health care future.<br><br>OBJECTIVE: The objective of this review was to examine the extent to which digitalization in the health care sector influences environmental sustainability. Specifically, it aimed to assess how digitalization can contribute to reducing the health care sector's impact on global climate change. From these findings, conclusions were drawn regarding the extent to which digitalization aligns with the objectives of the Planetary Health movement and how these 2 movements may mutually reinforce each other.<br><br>METHODS: A scoping review guided by the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) 2020 guidelines using databases such as PubMed and Scopus was conducted, and 58 quantitative studies from 2009 to 2024 were analyzed for environmental, social, and economic outcomes aligned with Planetary Health goals.<br><br>RESULTS: This review analyzed 58 studies on the environmental impact of digitalization in health care primarily focusing on telemedicine, which was examined in 91% (53/58) of the studies. Most studies (56/58, 97%) quantified transport-related emissions avoided through digitalization, with some also assessing emissions from health care facilities, medical equipment, and energy consumption. Findings indicated that telemedicine significantly reduces carbon dioxide emissions, with total avoided emissions amounting to approximately 830 million kg. A substantial proportion of the studies (36/58, 62%) focused on social aspects, highlighting factors such as patient satisfaction, time efficiency, and overall convenience. In addition, economic considerations were analyzed in 48% (28/58) of the studies, emphasizing cost reductions and resource optimization. However, only 12% (7/58) of the studies evaluated the full life cycle impact of digital technologies, highlighting the need for further research on their long-term environmental sustainability.<br><br>CONCLUSIONS: This review calls for further research beyond telemedicine, advocating for life cycle analyses and actionable strategies for a sustainable digitalization in health care systems. The Planetary Health framework is highlighted as a guide for ensuring sustainable digital transformation in health care.},
}
@article {pmid40435606,
year = {2025},
author = {Guo, J and Xie, Y and Dou, X and Qi, W and Liao, Y and Cao, X and Peng, J and Liu, H},
title = {Combining source identification and risk assessment to uncover spatial risk patterns in an agricultural lake.},
journal = {Journal of environmental management},
volume = {387},
number = {},
pages = {125966},
doi = {10.1016/j.jenvman.2025.125966},
pmid = {40435606},
issn = {1095-8630},
mesh = {*Lakes ; Agriculture ; *Environmental Monitoring/methods ; Risk Assessment ; Geologic Sediments ; Water Pollutants, Chemical/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; Metals, Heavy/analysis ; Bayes Theorem ; Water Quality ; Rivers ; },
abstract = {Pollutant source identification and risk assessment underpin environmental management, necessitating innovative methods for both pollution source identification and comprehensive evaluation to enhance management efficiency. In this study, we developed a novel integrated framework that combines Bayesian isotope mixing, positive matrix factorization (PMF), random forest, and spatial autocorrelation for multi-pollutant source identification and risk assessment. The Bayesian isotope mixing model revealed that fertilizers accounted for 61 % of the nitrate in the lake and 46 % of the nitrate in the river. Furthermore, PMF analysis indicated that polycyclic aromatic hydrocarbons (PAHs) in sediments and soil were primarily sourced from vehicular emissions (32 %), while heavy metals (40 %) were mainly from vehicular emissions and agricultural activities. Using a comprehensive pollution assessment framework for water and sediment quality, we found that water quality ranged from "medium" to "excellent", and sediment quality ranged from "good" to "excellent". Among various evaluation indices, CODMn, As, F[-], TP, Pb, and Zn were pivotal in determining comprehensive water quality. Key indices for sediment quality evaluation included Flua, BaP, BaA, Pyr, Ant, Pb, and As, primarily sourced from automobile emissions and agricultural activities. Spatial autocorrelation analysis demonstrated a spatial relationship between water quality and sediment quality, covering 43 % of the area. High-pollution areas (13 %) were concentrated around natural river inlets, while low-pollution zones (17 %) were located near ecological water replenishment river inlets. This underscores the significant influence of inflowing water quality on sediment conditions. This study highlights the development of a comprehensive pollution assessment framework to evaluate sediment and soil pollution, as well as to identify high-risk zones of compound pollution in water and sediment. Furthermore, the framework's universal applicability for agricultural lake systems enables the identification of high-risk zones through water-sediment interaction analysis.},
}
@article {pmid40435619,
year = {2025},
author = {Matuszewska, D and Kiedrzyńska, E and Jóźwik, A and Kiedrzyński, M},
title = {An analysis of catchment factors associated with heavy metal export into the Baltic Sea and nature-based solutions aimed at its limitation.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138727},
doi = {10.1016/j.jhazmat.2025.138727},
pmid = {40435619},
issn = {1873-3336},
mesh = {*Metals, Heavy/analysis ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Baltic States ; Oceans and Seas ; Animals ; Aquaculture ; Rivers ; },
abstract = {The aim of the article was to determine the shares of individual Baltic countries participating in the inflow of metal loads to the Baltic Sea and identify patterns of similarity between these countries regarding the causes of heavy metal load generation. The analyses used HELCOM and EUROSTAT data. The findings indicate that Finland and Sweden generate the highest total loads of heavy metals flowing in through rivers. However, Lithuania and Finland are distinguished by high metal loads calculated per km[2] of catchment area. Clustering countries in terms of their similarity in the heavy metal loads provided to the Baltic resulted in three groups. Finland and Lithuania generates the highest mean loads of cadmium, chromium, nickel and zinc per unit area [kg/km[2]/year]. Estonia and Latvia generates the highest mean annual loads of lead, mercury and copper. Poland, Germany and Sweden generates the lowest heavy metal loads. Multidimensional data analysis showed a strong correlation between aquaculture production in the Baltic Sea catchment area, the number of cattle, beef, mutton, pigs, poultry, and meat produced from them, the amount of waste, trucks, cereal production, the use of nitrogen fertilizers, and the loads of heavy metals reaching the Baltic Sea with river waters. Therefore, there is a need for continuous monitoring of the loads and transfer of heavy metals to the Baltic Sea, and for activities aimed at eliminating them from the environment. For this purpose, Nature-Based Solutions can be used, as they represent inexpensive, nature-friendly methods for removing pollutants from surface waters.},
}
@article {pmid40440249,
year = {2025},
author = {Guevara Rodríguez, DM and Pichihua Grandez, JD and Dianderas, FV and Del Carmen Sara, J},
title = {Incidence of cerebrovascular disease in Peru from 2015 to 2023.},
journal = {PLOS global public health},
volume = {5},
number = {5},
pages = {e0004559},
pmid = {40440249},
issn = {2767-3375},
abstract = {Cerebrovascular disease (stroke) is one of the leading causes of mortality and disability worldwide, particularly in low- and middle-income countries. This study aims to estimate the incidence of stroke in Peru between 2015 and 2023 using national hospital discharge data provided by the National Health Superintendency. We conducted a mixed ecological study using records of stroke cases reported across various healthcare systems, including the Ministry of Health, Social Security, and private entities. Hospitalizations were categorized according to ICD-10 codes (I60-I64) and stratified by age, sex, and region. Incidence rates were calculated using population projections from the National Institute of Statistics and Informatics. A total of 89,776 hospital discharges for stroke were analyzed, yielding an incidence rate of 3.11 per 10,000 persons over the study period, with a predominance in men and individuals over 60 years of age. Cerebral infarction was the most common diagnosis, particularly among those over 40 years old. Incidence varied significantly across regions, with Lima and Callao consistently exceeding the national average. The results highlight disparities in healthcare access and the need for targeted public health interventions. Our findings provide a 9-year overview of stroke in Peru, offering evidence to estimate hospital bed demand and prioritize preventive and management strategies-particularly in regions with higher vulnerability.},
}
@article {pmid40441315,
year = {2025},
author = {Zhang, B and Yang, M and Liu, W},
title = {Integrating multi-omics analysis unveils the key mechanisms of PQS-enhanced Algicidal activity in Enterobacter hormaechei F2.},
journal = {Genomics},
volume = {117},
number = {4},
pages = {111060},
doi = {10.1016/j.ygeno.2025.111060},
pmid = {40441315},
issn = {1089-8646},
mesh = {Quorum Sensing/drug effects ; *Enterobacter/genetics/drug effects/metabolism ; *Quinolones/pharmacology/metabolism ; Proteomics ; Metabolomics ; Bacterial Proteins/metabolism/genetics ; Transcriptome ; Multiomics ; },
abstract = {Quorum sensing, as a pivotal bacterial signaling pathway, exhibits substantial potential for regulating algicidal activity. This study pioneers the integration of multi-omics analyses (transcriptomics, proteomics, metabolomics) with phenotypic profiling to systematically unravel the molecular mechanisms underlying Pseudomonas Quinolone Signal (2-heptyl-3-hydroxy-4(1H)-quinolinone, PQS)-enhanced algicidal activity in Enterobacter hormaechei F2. Co-cultivation with PQS triggered marked reductions in algal biomass and chlorophyll-a levels, outperforming traditional approaches. Fourier-transform infrared spectroscopy (FTIR) revealed PQS-induced metabolic disruption and membrane degradation in algal cells. Transcriptomic profiling identified novel regulatory hubs, including upregulated glycolysis (tktA, transketolase), fatty acid degradation (fadE, acyl-CoA dehydrogenase), and chemotaxis (malE, maltose-binding protein) pathways. Proteomics confirmed PQS-driven enrichment of terpenoid precursors, notably DXS synthase (1-deoxy-D-xylulose-5-phosphate synthase), and quorum sensing effectors. Metabolomics highlighted amino acid derivatives (e.g., L-glutamate) and heterocyclic antibiotics as dominant algicidal metabolites. Crucially, multi-omics integration delineated a core network of 46 key nodes (e.g., ribose transporter rbsB, L-glutamate) coordinating energy metabolism, motility, and algicide synthesis. Fatty acid degradation enzymes (e.g., FadE) and flagellar assembly regulators (e.g., FlgK) emerged as previously unrecognized targets, with PQS significantly enhancing bacterial swarming motility (p < 0.01) and biofilm formation. These findings establish the first mechanistic framework linking PQS signaling to algicidal process, demonstrating its role in synchronizing metabolic flux toward terpenoid synthesis while optimizing bacterial-algal interactions. Key pathways-including chemotaxis (malE) and terpenoid biosynthesis (DXS synthase)-provide actionable targets for engineering bioaugmented consortia or precision algicidal formulations. This work advances quorum sensing-driven strategies for sustainable harmful algal bloom (HAB) mitigation, offering scalable solutions for aquaculture and eutrophic water remediation with minimal ecological disruption. By bridging molecular mechanisms to field applications, the study underscores the translational potential of this approach in global water security initiatives.},
}
@article {pmid40441709,
year = {20