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

@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 {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},
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 {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.},
}

Humans
China
*Rural Population
*Conservation of Natural Resources/methods
Geographic Information Systems
Spatial Analysis
Sustainable Development
Environment

@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.

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⁺ 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.

RESULTS: Among 28 immune subsets, CD4⁺ T-cell populations most strongly associated with overall survival (OS). A six-gene signature (KLF3, EZR, SMDT1, JPT1, ISG15, MT1X) derived from 111 CD4⁺ 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 < 0.05), indicating an immune-stromal ecosystem favoring tolerance. Single-cell RNA sequencing localized model genes to fibroblasts, ductal cells, and CD4⁺ T cells subsets. CellChat revealed globally intensified crosstalk in PC and strengthened CD4⁺ 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.

CONCLUSIONS: CD4⁺ T-cell subsets serve as central determinant of the immune landscape and clinical outcome in PC. The CD4⁺ 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.},
}

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

@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},
doi = {10.2196/81384},
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.

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.

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.

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.

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.},
}

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

@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 {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 = {},
number = {},
pages = {},
doi = {10.1186/s13002-025-00844-7},
pmid = {41699677},
issn = {1746-4269},
support = {grant agreement N° 714874//Horizon 2020 Framework Programme/ ; },
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.

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 = 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 ρ and Student's t-tests.

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' = 0.97 vs 0.52) and combined them more often (HD = 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.

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 {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.},
}

Animals
*Fishes/genetics
Biodiversity
*Ecosystem
*DNA, Environmental/analysis/genetics
Japan

@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},
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 {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.},
}

*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

@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},
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 {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 = {},
number = {},
pages = {127790},
doi = {10.1016/j.envpol.2026.127790},
pmid = {41687859},
issn = {1873-6424},
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 {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 {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.},
}

*Wood
Forests
*Databases, Factual
Biomass
Africa
Trees

@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.},
}

*Mining
*Nitrogen/analysis
*Metals, Rare Earth
*Ammonia/analysis
*Water Pollutants, Chemical
*Environmental Monitoring/methods
China
Rivers/chemistry
Models, Theoretical

@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 & 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.},
}

*Germination/genetics
Gene Expression Regulation, Plant
*Transcriptome
*Seeds/genetics/growth & development
Gene Expression Profiling
Plant Dormancy/genetics
Gene Ontology
Computational Biology/methods
Plant Proteins/genetics
Molecular Sequence Annotation

@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.},
}

*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

@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.},
}

*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

@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 = {},
doi = {10.3390/ijms27031163},
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.},
}

Animals
*Ultraviolet Rays/adverse effects
*Transcriptome/radiation effects
*Stress, Physiological/radiation effects/genetics
Gene Expression Profiling
*Wasps/genetics/radiation effects
Gene Ontology

@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 = {},
doi = {10.3390/molecules31030485},
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.},
}

*Aquatic Organisms/drug effects
Microalgae/drug effects
Bacteria/drug effects
*Toxicity Tests/methods
*Water Pollutants, Chemical/toxicity
Fungi/drug effects
Viruses/drug effects

@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 = {},
doi = {10.3390/foods15030599},
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 & 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 {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 = {},
doi = {10.3390/s26031070},
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 {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},
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.},
}

*Computational Biology/education
*Genomics/education
United States
Africa
Humans
*National Institutes of Health (U.S.)
*Education, Graduate
Biomedical Research

@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 & 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.},
}

Animals
*Mosquito Vectors/parasitology/microbiology
*Anopheles/parasitology/microbiology
*Symbiosis
*Bacteria/genetics/metabolism
*Malaria/prevention & control/transmission
Mosquito Control/methods
Plasmodium falciparum/drug effects
*Plasmodium

@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 ; *Water Pollutants, Chemical/toxicity/metabolism ; Japan ; Bacillus subtilis/metabolism ; Multiomics ; },
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.},
}

Biodegradation, Environmental
*Arsenicals/metabolism
*Water Pollutants, Chemical/toxicity/metabolism
Japan
Bacillus subtilis/metabolism
Multiomics

@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 ; *Nitrosamines/metabolism ; Bacteria/metabolism/genetics ; Multiomics ; 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.},
}

*Water Pollutants, Chemical/metabolism
*Microbiota
Biodegradation, Environmental
*Nitrosamines/metabolism
Bacteria/metabolism/genetics
Multiomics
Triazines

@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.},
}

*Microalgae/classification
*Harmful Algal Bloom
*Artificial Intelligence
*Environmental Monitoring/methods
Databases, Factual
Ecosystem

@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 {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 {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, Ø 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 & 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.},
}

*Klebsiella pneumoniae/genetics/classification/isolation & purification
*Computational Biology/methods
*Metagenome
Humans
Whole Genome Sequencing
Phylogeny
Klebsiella Infections/microbiology
Genome, Bacterial

@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.

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.

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.

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 {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.},
}

*Epitopes/immunology/chemistry
Humans
*Antibodies/immunology
*Fluorescent Antibody Technique/methods
*Computational Biology/methods
Animals

@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.},
}

*High-Throughput Nucleotide Sequencing/methods
*Software
*Sequence Analysis, DNA/methods
*DNA Barcoding, Taxonomic/methods
*Computational Biology/methods

@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.},
}

Animals
Bees
Europe
*Diptera
Pollination
Databases, Factual

@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.

RESULTS: We sequenced and assembled the complete mitochondrial genomes from multiple representatives of the P. guttatus 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 ‒ Pliocene (~ 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.

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.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12529-w.},
}

@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 = {Fermentation ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Temperature ; *Fungi/classification/genetics/metabolism/isolation & purification ; Metabolome ; Metabolomics/methods ; Machine Learning ; *Specimen Handling/methods ; Bread/microbiology ; Multiomics ; },
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.},
}

Fermentation
*Microbiota
*Bacteria/classification/genetics/isolation & purification/metabolism
Temperature
*Fungi/classification/genetics/metabolism/isolation & purification
Metabolome
Metabolomics/methods
Machine Learning
*Specimen Handling/methods
Bread/microbiology
Multiomics

@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.

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.

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 gut microbial composition was dominated by Proteobacteria, Bacteroidetes, and Firmicutes, showing a conserved structure; at the genus level, 11 dominant genera (including Wolbachia, Elizabethkingia, and Asaia) exhibited distinct species-specific distribution patterns. Diversity analysis revealed that the gut microbial richness of male individuals was significantly higher than that of females, and the β-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 olfactory genes in antennae through metabolites or signaling molecules, thereby influencing mosquito behaviors such as host localization, mating, and oviposition.

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.},
}

Animals
*Gastrointestinal Microbiome/genetics
Female
Male
*Culex/microbiology/genetics/physiology
Metagenomics
*Smell/genetics
Gene Expression Profiling
Arthropod Antennae/metabolism
Transcriptome
Computational Biology
Multiomics

@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},
doi = {10.1371/journal.pone.0342678},
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.

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.

RESULTS: Regression results showed significant associations between PFs and five community participation outcomes (R2 = 13% - 48%, p < 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 (ΔR² = 0.11, p < 0.05). Among individual EFs, after accounting for PFs, perceived financial resources was associated with ability to participate (B = 1.46, p = 0.018), and satisfaction with participation (B = 3.12, p < 0.001). Social support (B = -1.05, p = 0.022) and neighborhood safety (B = 1.3, p = 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.

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.},
}

Humans
*Multiple Sclerosis/psychology
Female
Male
Middle Aged
Adult
*Community Participation
Focus Groups
Geographic Information Systems
*Environment
Aged

@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 {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 = {},
number = {},
pages = {},
doi = {10.1186/s12888-026-07815-6},
pmid = {41664026},
issn = {1471-244X},
support = {RS-2023-KH135442//Ministry of Health and Welfare/ ; },
}

@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},
doi = {10.1371/journal.pmen.0000407},
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 {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.},
}

*Acoustics
Animals
*Ecosystem
*Sound
Time Factors
Sound Spectrography
*Vocalization, Animal
Signal Processing, Computer-Assisted
Biodiversity

@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.

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.

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.

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.},
}

Humans
Adolescent
*Mental Health
Male
Female
*Artificial Intelligence
*Health Promotion/methods
Rural Population
Mobile Applications
Longitudinal Studies
Digital Health

@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 = {},
number = {},
pages = {121352},
doi = {10.1016/j.jad.2026.121352},
pmid = {41655849},
issn = {1573-2517},
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 temporal 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 {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},
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 {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.},
}

*Honey/analysis
Philippines
*Forests
*Metabolomics/methods
Bees
Mass Spectrometry
Animals
Chromatography, Liquid
Multiomics

@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},
doi = {10.1371/journal.pcbi.1013918},
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.},
}

*Microbiota/physiology
*Biodiversity
*Models, Biological
Computational Biology
Cluster Analysis

@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},
doi = {10.1371/journal.pcbi.1013908},
pmid = {41592132},
issn = {1553-7358},
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.},
}

*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Polymerase Chain Reaction/methods
Computational Biology
Bias
Biodiversity

@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 Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; ZIA-MH002781//U.S. Department of Health & 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.},
}

Humans
*Attention Deficit Disorder with Hyperactivity/diagnosis/therapy
Models, Theoretical
*Psychiatry/methods
*Diagnosis, Computer-Assisted

@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},
doi = {10.1002/ecy.70317},
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.},
}

Animals
*Birds/physiology
*Vocalization, Animal/physiology
*Acoustics
*Environmental Monitoring/methods
*Databases, Factual

@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&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.},
}

*Machine Learning
*Mining
*Water Pollutants, Chemical/chemistry
Neural Networks, Computer
Computer Simulation
Models, Theoretical
Drainage

@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 = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovag020},
pmid = {41649413},
issn = {1472-765X},
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 {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},
doi = {10.1111/jre.70055},
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.

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 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.

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.

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.

TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.},
}

Humans
*Gastrointestinal Microbiome
Saliva/microbiology
*Periodontitis/microbiology/therapy/metabolism
Male
Feces/microbiology
Female
Metabolomics
Adult
Middle Aged
*Mouth/microbiology
Multiomics

@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.

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.

RESULTS: The results revealed distinct chemical signatures between poles: Arctic sediments were mainly contaminated by polycyclic aromatic hydrocarbons (∑PAHs, 18.5-685.7 ppb; phenanthrene was the most abundant), whereas Antarctic sediments showed relatively higher concentrations of chlorobenzenes (∑CBs, 1.9-3.6 ppb) and polychlorinated biphenyls (∑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.

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 {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 = {},
number = {},
pages = {},
pmid = {41644669},
issn = {1546-1718},
support = {1R21CA282380//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; 1R21CA282380//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; CO-J-24-170//Colorado University | UC Denver | Colorado Clinical and Translational Sciences Institute (CCTSI)/ ; NNF20OC0062294//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; R00HG011898//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; },
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 {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 = {},
number = {},
pages = {15578100261419486},
doi = {10.1177/15578100261419486},
pmid = {41642108},
issn = {1557-8100},
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 {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 ; *Hair Follicle/metabolism/cytology ; Cattle/genetics ; Wnt Signaling Pathway ; Gene Expression Regulation ; Multiomics ; },
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.},
}

Animals
*Hair Follicle/metabolism/cytology
Cattle/genetics
Wnt Signaling Pathway
Gene Expression Regulation
Multiomics

@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 {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},
doi = {10.1136/bmjopen-2025-107055},
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.

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.

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.

TRIAL REGISTRATION NUMBER: NCT04864275.},
}

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

@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},
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.

METHODS: This study enrolled 1007 adults with cLBP who met the National Institutes of Health defined criteria. Over 7 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 days of 10 or more hours each. Activity counts were categorized into sedentary, light, and moderate-to-very-vigorous based on Freedson Adult cutpoints.

RESULTS: Out of 1007 participants, 989 submitted EMA data (58.8 ± 16.5 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 = 3), while pain interference was 3 (IQR = 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 1 765 325 (IQR 796 995) activity counts/day and 9575 (IQR 4228) steps/day. Waist data showed 358 390 (IQR 223 758) 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 340 345 (IQR = 223 399) activity counts/day and a median of 3695 (IQR = 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.

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 {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.},
}

*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

@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 = {},
number = {},
pages = {},
doi = {10.1186/s13002-026-00852-1},
pmid = {41629941},
issn = {1746-4269},
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 {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 = {*Soil Microbiology ; *Snow/microbiology ; *Nitrogen/metabolism ; Nitrogen Cycle ; Nitrates/metabolism ; Seasons ; Metagenomics ; *Bacteria/genetics/metabolism/classification ; *Eutrophication ; Soil/chemistry ; Metabolomics ; Denitrification ; 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.},
}

*Soil Microbiology
*Snow/microbiology
*Nitrogen/metabolism
Nitrogen Cycle
Nitrates/metabolism
Seasons
Metagenomics
*Bacteria/genetics/metabolism/classification
*Eutrophication
Soil/chemistry
Metabolomics
Denitrification
Multiomics

@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.},
}

*Fossils
Animals
*Mammals
Paleontology
North America
Radiometric Dating
Databases, Factual

@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.},
}

Animals
Larva/microbiology/genetics
Gastrointestinal Microbiome
*Tribolium/microbiology/genetics
Genome, Mitochondrial
Bacteria/genetics/classification
Multiomics

@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},
doi = {10.1128/spectrum.01701-25},
pmid = {41405388},
issn = {2165-0497},
support = {//U.S. Department of Agriculture/ ; },
mesh = {Animals ; Genome, Viral ; Phylogeny ; *Picornaviridae/genetics/classification/isolation & 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.},
}

Animals
Genome, Viral
Phylogeny
*Picornaviridae/genetics/classification/isolation & purification
*Insecta/virology/genetics
Computational Biology/methods
RNA-Seq
RNA, Viral/genetics
Computer Simulation

@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.},
}

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

@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 {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 {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 {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.},
}

*Conservation of Natural Resources/methods
*Rivers
Climate Change
Fuzzy Logic
Decision Support Techniques

@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 & 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.},
}

*Biological Evolution
*Periodicals as Topic
*Publishing
*Ecology
*Databases, Factual
Academia

@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 = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69017-8},
pmid = {41617719},
issn = {2041-1723},
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 {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 = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68989-x},
pmid = {41611716},
issn = {2041-1723},
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 {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},
doi = {10.1002/eap.70174},
pmid = {41610871},
issn = {1051-0761},
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.},
}

*Grassland
*Conservation of Natural Resources/economics/methods
Animals
Pilot Projects
Cost-Benefit Analysis
*Environmental Restoration and Remediation/economics/methods
Kansas
Biodiversity

@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 = {},
doi = {10.1093/bioinformatics/btag005},
pmid = {41512299},
issn = {1367-4811},
support = {108290//Leverhulme Trust Research Fellowship/ ; },
mesh = {*Software ; *Genome, Bacterial ; Escherichia coli/genetics ; *Genomics/methods ; Algorithms ; *Computational Biology/methods ; Random Forest ; },
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.

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 12 741 accessory genes in 1000 Escherichia coli genomes was analysed in around 5 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.

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.},
}

*Software
*Genome, Bacterial
Escherichia coli/genetics
*Genomics/methods
Algorithms
*Computational Biology/methods
Random Forest

@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.},
}

Humans
Geographic Information Systems
*Social Behavior
Cognition
*Decision Making
*Feeding Behavior
Video Recording

@article {pmid41604932,
year = {2026},
author = {Xintong, M and Taiyu, Z and Bo, Z and Wei-Min, W and Naying, L and Yajing, W and Xin, L and Ruixi, L and Rehman, A and Shaoliang, Y and Yixin, H},
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 {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 {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 = {},
doi = {10.3390/nu18020330},
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.},
}

*Gastrointestinal Microbiome/drug effects
*Carotenoids/pharmacology/chemistry
*Computational Biology
Humans
Fermentation
Lycopene/pharmacology
Lutein/pharmacology
Bacteria/drug effects/genetics/classification
beta Carotene/pharmacology

@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 = {},
doi = {10.3390/microorganisms14010002},
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 {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 = {},
doi = {10.3390/medicina62010119},
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.},
}

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

@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 = {},
doi = {10.3390/cells15020157},
pmid = {41597231},
issn = {2073-4409},
support = {2024YFD2401102//National Key R&D ProgramNational Key R&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.},
}

Animals
*Carps/virology/microbiology
*Fish Diseases/virology/microbiology/genetics
*Intestinal Mucosa/virology/pathology/microbiology
Gastrointestinal Microbiome
Metagenomics
Transcriptome
Multiomics

@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 = {},
doi = {10.3390/ijms27021056},
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.},
}

Animals
*Palaemonidae/metabolism/genetics/drug effects
*Hepatopancreas/metabolism/drug effects/ultrastructure
*Sulfates/toxicity
Proteomics/methods
*Stress, Physiological
Transcriptome
Multiomics

@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 = {},
doi = {10.3390/bioengineering13010058},
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 {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 = {},
doi = {10.3390/healthcare14020261},
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 {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 & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07248-w},
pmid = {41593706},
issn = {1756-3305},
support = {Culifo3//BMLE/ ; TTU 01.708//Deutsches Zentrum für Infektionsforschung/ ; TTU 01.701 and TTU 01.708//Deutsches Zentrum für Infektionsforschung/ ; 500072465//Deutsche Forschungsgemeinschaft/ ; 497659464//Deutsche Forschungsgemeinschaft/ ; BB/P024270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 223743/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; GSO KT/24//Klaus Tschira Stiftung/ ; },
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.

METHODS: To address this gap, the current study aimed to characterize two recently established Culex pipiens cell lines: CPE/LULS50 (Culex pipiens pipiens & 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.

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.

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 {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 = {},
number = {},
pages = {},
doi = {10.1186/s12936-026-05797-0},
pmid = {41593685},
issn = {1475-2875},
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.

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.

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.

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 {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.},
}

*Biodegradation, Environmental
*Bacteria/genetics/metabolism/classification
*Databases, Genetic
Microbiota/genetics
Environmental Pollutants/metabolism
Metagenome
Metagenomics

@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 = {},
doi = {10.1093/nar/gkaf1507},
pmid = {41591842},
issn = {1362-4962},
support = {1R35GM150871-01/NH/NIH HHS/United States ; //Pew Charitable Trusts Foundation/ ; 2440082//National Science Foundation/ ; //Edward Mallinckrodt Jr. 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.},
}

*Plasmids/genetics
*Molecular Sequence Annotation/methods
*Databases, Genetic
Genome, Bacterial
Software
DNA Transposable Elements
Genes, Bacterial
Bacteria/genetics

@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},
doi = {10.1002/bies.70110},
pmid = {41588693},
issn = {1521-1878},
support = {23-7825575//Catalyst Science Fund, Revive & 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.},
}

Animals
*Anthozoa/genetics/physiology
Symbiosis
*Coral Bleaching
Genomics/methods
Coral Reefs
Conservation of Natural Resources
Climate Change
Oxidative Stress
Heat-Shock Response
Multiomics

@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 = {},
number = {},
pages = {},
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/ ; },
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 {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 = {},
number = {},
pages = {},
doi = {10.1186/s13002-026-00853-0},
pmid = {41588471},
issn = {1746-4269},
support = {Horizon ID 101159928//ETHCSTWIN/ ; },
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 {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 = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpag004},
pmid = {41578851},
issn = {1758-4469},
abstract = {Constrained carbon allocation towards 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 (NSC) and chemical defenses (terpenes, phenolics, resin flow) in mature Pinus edulis 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), 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 to 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 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 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 {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 = {},
number = {},
pages = {},
doi = {10.1186/s40337-026-01524-x},
pmid = {41578325},
issn = {2050-2974},
support = {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.

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.

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%.

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 {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 ; Homeostasis ; Eutrophication ; Metabolomics ; Transcriptome ; Nitrogen Isotopes ; Metabolic Reprogramming ; Multiomics ; },
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.},
}

*Diatoms/physiology/metabolism
*Carbon Dioxide/metabolism
*Nitrogen/metabolism
*Carbon/metabolism
Homeostasis
Eutrophication
Metabolomics
Transcriptome
Nitrogen Isotopes
Metabolic Reprogramming
Multiomics

@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).},
}

Egypt
*Rivers/chemistry
*Water Quality
*Geographic Information Systems
*Environmental Monitoring/methods
*Water Pollutants, Chemical/analysis
*Water Pollution/analysis
Ecosystem
*Industrial Waste/analysis

@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 = {},
number = {},
pages = {},
doi = {10.1186/s40345-025-00407-5},
pmid = {41575653},
issn = {2194-7511},
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.

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 months or longer. We aimed to evaluate their performance against established clinical measures and through inter-ambulatory assessment comparisons.

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.

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.

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 {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 = {},
number = {},
pages = {},
doi = {10.1002/ijc.70346},
pmid = {41575069},
issn = {1097-0215},
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.},
}