@article {pmid40185844,
year = {2025},
author = {Amin, NU and Islam, F and Umar, M and Muhammad, W and Rahman, SU and Gaafar, AZ and Shah, TA and Dauelbait, M and Bourhia, M},
title = {Evaluation of crop phenology using remote sensing and decision support system for agrotechnology transfer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11582},
pmid = {40185844},
issn = {2045-2322},
mesh = {*Remote Sensing Technology/methods ; *Crops, Agricultural/growth & development ; Biomass ; *Agriculture/methods ; *Decision Support Techniques ; Plant Leaves/growth & development ; Seasons ; },
abstract = {The decision support system for agro-technology transfer (DSSAT) is a worldwide crop modeling platform used for crops growth, yield, leaf area index (LAI), and biomass estimation under varying climatic, soil and management conditions. This study integrates DSSAT with satellite remote sensing (RS) data to estimates canopy state variables like LAI and biomass. For LAI estimation, Moderate Resolution Imaging Spectroradiometer (MODIS) product (MCD15A3H for LAI and MOD17A2 / MOD17A3 products for biomass) are used. Field data for Sheikhupura district is provided by National Agriculture Research Council (NARC) and used for the calibration and validation of the model. The results indicate strong agreement between the DSSAT and RS derived estimates. Correlation coefficients (R[2]) for LAI varied from 0.82 to 0.90, while for biomass ranged from 0.92 to 0.99 over two farms and two growing seasons (2012-2014). The index of agreement (D-index) ranged from 0.79 to 0.96 across the two farms and two growing seasons (2012-2014) affirming the model's durability. However, the biomass estimated from RS data is underestimated due to saturation phenomenon in the optical RS. The performance metrics, comprising the coefficient of residual mass (CRM) and normalized root mean square error (nRMSE), further substantiate the approach utilized. This study will help decision and policymakers and researchers to apply geospatial techniques for the sustainable agriculture practices.},
}

*Remote Sensing Technology/methods
*Crops, Agricultural/growth & development
Biomass
*Agriculture/methods
*Decision Support Techniques
Plant Leaves/growth & development
Seasons

@article {pmid40181527,
year = {2025},
author = {Mills, MB and Shenkin, A and Wilkes, P and Disney, M and Page, S and Berrio, JC and Kaduk, J and Malhi, Y and Robert, R and Nilus, R and Riutta, T},
title = {Investigating the accuracy of tropical woody stem CO2 efflux estimates: scaling methods, and vertical and diel variation.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70122},
pmid = {40181527},
issn = {1469-8137},
support = {CA20118//European Cooperation in Science and Technology/ ; PRA 11.23//Royal Geographical Society/ ; NE/P011780/1//Natural Environment Research Council/ ; NE/Y006216/1//National Centre for Earth Observation/ ; NE/S007350/1//Central England NERC Training Alliance/ ; },
abstract = {Stem CO2 efflux (EA) significantly contributes to autotrophic and ecosystem respiration in tropical forests, but field methodologies often introduce biases and uncertainty. This study evaluates these biases and their impact on scaling EA at the stand-level. Diel and vertical patterns of EA were investigated, along with the accuracy of estimating stem surface area from allometric equations vs terrestrial light dection and ranging (LiDAR) scanning (TLS) in Maliau Basin Conservation Area, Sabah, Malaysian Borneo. Diel EA exhibited no uniform pattern due to inter-tree variability, but results suggest measuring EA before 15:00 h. EA was significantly higher on buttresses and above the first major branching point, but vertical variations in EA did not impact stand-level EA when stem surface area was accurately estimated. Allometric equations underestimated total stem surface area by c. 40% compared with TLS, but applying a site-specific correction factor yielded a similar stand-level EA and total stem surface area to TLS. This study provides guidance for measuring EA in the field and suggests that measuring at one time point and one height along the stem can produce accurate results if conducted using the correct time frame and if stem surface area is accurately estimated.},
}

@article {pmid40180992,
year = {2025},
author = {González, AL and Merder, J and Andraczek, K and Brose, U and Filipiak, M and Harpole, WS and Hillebrand, H and Jackson, MC and Jochum, M and Leroux, SJ and Nessel, MP and Onstein, RE and Paseka, R and Perry, GLW and Rugenski, A and Sitters, J and Sperfeld, E and Striebel, M and Zandona, E and Aymes, JC and Blanckaert, A and Bluhm, SL and Doi, H and Eisenhauer, N and Farjalla, VF and Hood, J and Kratina, P and Labonne, J and Lovelock, CE and Moody, EK and Mozsár, A and Nash, L and Pollierer, MM and Potapov, A and Romero, GQ and Roussel, JM and Scheu, S and Scheunemann, N and Seeber, J and Steinwandter, M and Susanti, WI and Tiunov, A and Dézerald, O},
title = {StoichLife: A Global Dataset of Plant and Animal Elemental Content.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {569},
pmid = {40180992},
issn = {2052-4463},
support = {DFG HI848/26-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR 5000//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG 493345801//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RGPIN-2020-04132//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 310119/2018-9//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; 310119/2018-9//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; NAF\R2\180791//Royal Society/ ; DP0986179//Department of Education and Training | Australian Research Council (ARC)/ ; DP160103669//Department of Education and Training | Australian Research Council (ARC)/ ; 22-14-00363)//Russian Science Foundation (RSF)/ ; },
mesh = {*Plants/chemistry ; Animals ; Ecosystem ; Phosphorus/analysis ; Nitrogen/analysis ; Carbon/analysis ; },
abstract = {The elemental content of life is a key trait shaping ecology and evolution, yet organismal stoichiometry has largely been studied on a case-by-case basis. This limitation has hindered our ability to identify broad patterns and mechanisms across taxa and ecosystems. To address this, we present StoichLife, a global dataset of 28,049 records from 5,876 species spanning terrestrial, freshwater, and marine realms. Compiled from published and unpublished sources, StoichLife documents elemental content and stoichiometric ratios (%C, %N, %P, C:N, C:P, and N:P) for individual plants and animals. The dataset is standardized and, where available, includes information on taxonomy, habitat, body mass (for animals), geography, and environmental conditions such as temperature, solar radiation, and nutrient availability. By providing an unprecedented breadth of organismal stoichiometry, StoichLife enables the exploration of global patterns, ecological and evolutionary drivers, and context-dependent variations. This resource advances our understanding of the chemical makeup of life and its responses to environmental change, supporting progress in ecological stoichiometry and related fields.},
}

*Plants/chemistry
Animals
Ecosystem
Phosphorus/analysis
Nitrogen/analysis
Carbon/analysis

@article {pmid39936183,
year = {2025},
author = {Brait, N and Hackl, T and Lequime, S},
title = {detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14083},
doi = {10.1111/1755-0998.14083},
pmid = {39936183},
issn = {1755-0998},
mesh = {*Computational Biology/methods ; *Genomics/methods ; *Software ; Genome, Viral ; *Viruses/genetics ; Sensitivity and Specificity ; },
abstract = {Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.},
}

*Computational Biology/methods
*Genomics/methods
*Software
Genome, Viral
*Viruses/genetics
Sensitivity and Specificity

@article {pmid39925235,
year = {2025},
author = {Shi, T and Gao, Z and Zhang, Y and Rausher, MD and Chen, J},
title = {A Strategy of Assessing Gene Copy Number Differentiation Between Populations Using Ultra-Fast De Novo Assembly of Next-Generation Sequencing Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14080},
doi = {10.1111/1755-0998.14080},
pmid = {39925235},
issn = {1755-0998},
support = {31570220//National Natural Science Foundation of China/ ; 31870208//National Natural Science Foundation of China/ ; 32170240//National Natural Science Foundation of China/ ; KFJ-BRP-007-009//Biological Resources Program, CAS/ ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *DNA Copy Number Variations ; *Computational Biology/methods ; *Genetics, Population/methods ; *Gene Dosage ; Sequence Analysis, DNA/methods ; },
abstract = {Gene duplication and loss play pivotal roles in the evolutionary dynamics of genomes, contributing to species phenotypic diversity and adaptation. However, detecting copy number variations (CNVs) in homoploid populations and newly-diverged species using short reads from next-generation sequencing (NGS) with traditional methods can often be challenging due to uneven read coverage caused by variations in GC content and the presence of repetitive sequences. To address these challenges, we developed a novel pipeline, ST4gCNV, which leverages ultra-fast de novo assemblies of NGS data to detect gene-specific CNVs between populations. The pipeline effectively reduces the variance of read coverage due to technical factors such as GC bias, providing a reliable CNV detection with a minimum sequencing depth of 10. We successfully apply ST4gCNV to the resequencing analysis of homoploid species Nelumbo nucifera and Nelumbo lutea (lotus). We reveal significant CNV-driven differentiation between these species, particularly in genes related to petal colour diversity such as those involved in the anthocyanin pathway. By highlighting the extensive gene duplication and loss events in Nelumbo, our study demonstrates the utility of ST4gCNV in population genomics and underscores its potential of integrating genomic CNV analysis with traditional SNP-based resequencing analysis.},
}

*High-Throughput Nucleotide Sequencing/methods
*DNA Copy Number Variations
*Computational Biology/methods
*Genetics, Population/methods
*Gene Dosage
Sequence Analysis, DNA/methods

@article {pmid39801085,
year = {2025},
author = {Anderson, EC and Giglio, RM and DeSaix, MG and Smyser, TJ},
title = {gscramble: Simulation of Admixed Individuals Without Reuse of Genetic Material.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14069},
doi = {10.1111/1755-0998.14069},
pmid = {39801085},
issn = {1755-0998},
support = {//National Wildlife Research Center/ ; //Southwest Fisheries Science Center/ ; },
mesh = {*Computer Simulation ; *Computational Biology/methods ; *Genetics, Population/methods ; Genotype ; *Software ; },
abstract = {While a best practice for evaluating the behaviour of genetic clustering algorithms on empirical data is to conduct parallel analyses on simulated data, these types of simulation techniques often involve sampling genetic data with replacement. In this paper we demonstrate that sampling with replacement, especially with large marker sets, inflates the perceived statistical power to correctly assign individuals (or the alleles that they carry) back to source populations-a phenomenon we refer to as resampling-induced, spurious power inflation (RISPI). To address this issue, we present gscramble, a simulation approach in R for creating biologically informed individual genotypes from empirical data that: (1) samples alleles from populations without replacement and (2) segregates alleles based on species-specific recombination rates. This framework makes it possible to simulate admixed individuals in a way that respects the physical linkage between markers on the same chromosome and which does not suffer from RISPI. This is achieved in gscramble by allowing users to specify pedigrees of varying complexity in order to simulate admixed genotypes, segregating and tracking haplotype blocks from different source populations through those pedigrees, and then sampling-using a variety of permutation schemes-alleles from empirical data into those haplotype blocks. We demonstrate the functionality of gscramble with both simulated and empirical data sets and highlight additional uses of the package that users may find valuable.},
}

*Computer Simulation
*Computational Biology/methods
*Genetics, Population/methods
Genotype
*Software

@article {pmid40180917,
year = {2025},
author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA},
title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3204},
pmid = {40180917},
issn = {2041-1723},
support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; },
abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.},
}

Humans
*Gastrointestinal Microbiome/genetics
Metagenome/genetics
*Metagenomics/methods
*Bacterial Proteins/genetics/metabolism
*Bacteria/genetics/classification/metabolism
Phylogeny
Computational Biology/methods

@article {pmid40179423,
year = {2025},
author = {Dejeante, R and Valeix, M and Chamaillé-Jammes, S},
title = {Do Mixed-Species Groups Travel as One? An Investigation on Large African Herbivores Monitored Using Animal-Borne Video Collars.},
journal = {The American naturalist},
volume = {205},
number = {4},
pages = {451-458},
doi = {10.1086/734410},
pmid = {40179423},
issn = {1537-5323},
mesh = {Animals ; Video Recording ; *Herbivory ; *Giraffes/physiology ; *Equidae/physiology ; *Antelopes/physiology ; Social Behavior ; Geographic Information Systems ; Ecosystem ; },
abstract = {AbstractAlthough prey foraging in mixed-species groups benefit from a reduced risk of predation, whether heterospecific groupmates move together in the landscape, and more generally to what extent mixed-species groups remain cohesive over time and space, remains unknown. Here, we used GPS collars with video cameras to investigate the movements of plains zebras (Equus quagga) in mixed-species groups. Blue wildebeest (Connochaetes taurinus), impalas (Aepyceros melampus), and giraffes (Giraffa camelopardalis) commonly form mixed-species groups with zebras in savanna ecosystems. We found that zebras adjust their movement decisions solely on the basis of the presence of giraffes, being more likely to move in zebra-giraffe herds, and this was correlated with a higher cohesion of such groups. Additionally, zebras moving with giraffes spent more time grazing, suggesting that zebras benefit from foraging in the proximity of giraffes. Our results provide new insights into animal movements in mixed-species groups, contributing to a better consideration of mutualism in movement ecology.},
}

Animals
Video Recording
*Herbivory
*Giraffes/physiology
*Equidae/physiology
*Antelopes/physiology
Social Behavior
Geographic Information Systems
Ecosystem

@article {pmid40179162,
year = {2025},
author = {Davín, AA and Woodcroft, BJ and Soo, RM and Morel, B and Murali, R and Schrempf, D and Clark, JW and Álvarez-Carretero, S and Boussau, B and Moody, ERR and Szánthó, LL and Richy, E and Pisani, D and Hemp, J and Fischer, WW and Donoghue, PCJ and Spang, A and Hugenholtz, P and Williams, TA and Szöllősi, GJ},
title = {A geological timescale for bacterial evolution and oxygen adaptation.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6742},
pages = {eadp1853},
doi = {10.1126/science.adp1853},
pmid = {40179162},
issn = {1095-9203},
mesh = {*Oxygen/metabolism ; Phylogeny ; *Biological Evolution ; Oxidation-Reduction ; *Bacteria/metabolism/classification/genetics ; Machine Learning ; Photosynthesis ; Adaptation, Physiological ; Cyanobacteria/genetics/metabolism ; },
abstract = {Microbial life has dominated Earth's history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE). We combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial time tree. Extant bacterial phyla trace their diversity to the Archaean and Proterozoic, and bacterial families prior to the Phanerozoic. We infer that most bacterial phyla were ancestrally anaerobic and adopted aerobic lifestyles after the GOE. However, in the cyanobacterial ancestor, aerobic metabolism likely predated the GOE, which may have facilitated the evolution of oxygenic photosynthesis.},
}

*Oxygen/metabolism
Phylogeny
*Biological Evolution
Oxidation-Reduction
*Bacteria/metabolism/classification/genetics
Machine Learning
Photosynthesis
Adaptation, Physiological
Cyanobacteria/genetics/metabolism

@article {pmid40178345,
year = {2025},
author = {Riobueno-Naylor, A and Gomez, I and Quan, S and Hutt Vater, C and Montes, M and Hoskova, B and Lai, BS},
title = {Methods for integrating public datasets: insights from youth disaster mental health research.},
journal = {European journal of psychotraumatology},
volume = {16},
number = {1},
pages = {2481699},
doi = {10.1080/20008066.2025.2481699},
pmid = {40178345},
issn = {2000-8066},
mesh = {Humans ; Adolescent ; *Disasters ; United States/epidemiology ; *Mental Health/statistics & numerical data ; Male ; Female ; *Depression/epidemiology ; *Datasets as Topic ; Databases, Factual ; },
abstract = {Introduction: Weather-related disasters pose significant risks to youth mental health. Exposure to multiple disasters is becoming more common; however, the effects of such exposure remain understudied. This study demonstrates the application of integrative data approaches and FAIR (Findable, Accessible, Interoperable, Reusable) data principles to evaluate the relationship between cumulative disaster exposure and youth depression and suicidality in the United States, taking into account contextual factors across levels of social ecology.Methods: We combined data from five public sources, including the Youth Risk Behavior Surveillance System (YRBS), Federal Emergency Management Agency (FEMA), United States Census Bureau, Center for Homeland Defense and Security School Shooting Safety Compendium, and Global Terrorism Database. The integrative dataset included 415,701 youth from 37 districts across the United States who completed the YRBS between 1999 and 2021. The YRBS served as the core dataset.Results: This data note highlights strategies for harmonizing diverse data formats, addressing geographic and temporal inconsistencies, and validating integrated datasets. Automated data cleaning and visualization techniques enhance accuracy and efficiency. Planning for sensitivity analyses before data cleaning is recommended to improve the data integration process and enhance the robustness of findings.Discussion: This integrative approach demonstrates how leveraging FAIR principles can advance trauma research by facilitating large-scale analyses of complex public health questions. The methods provide a replicable framework for examining population-level impacts of phenomena and highlight opportunities for expanding trauma research.},
}

Humans
Adolescent
*Disasters
United States/epidemiology
*Mental Health/statistics & numerical data
Male
Female
*Depression/epidemiology
*Datasets as Topic
Databases, Factual

@article {pmid40175550,
year = {2025},
author = {Pärtel, M and Tamme, R and Carmona, CP and Riibak, K and Moora, M and Bennett, JA and Chiarucci, A and Chytrý, M and de Bello, F and Eriksson, O and Harrison, S and Lewis, RJ and Moles, AT and Öpik, M and Price, JN and Amputu, V and Askarizadeh, D and Atashgahi, Z and Aubin, I and Azcárate, FM and Barrett, MD and Bashirzadeh, M and Bátori, Z and Beenaerts, N and Bergholz, K and Birkeli, K and Biurrun, I and Blanco-Moreno, JM and Bloodworth, KJ and Boisvert-Marsh, L and Boldgiv, B and Brancalion, PHS and Brearley, FQ and Brown, C and Bueno, CG and Buffa, G and Cahill, JF and Campos, JA and Cangelmi, G and Carbognani, M and Carcaillet, C and Cerabolini, BEL and Chevalier, R and Clavel, JS and Costa, JM and Cousins, SAO and Čuda, J and Dairel, M and Dalle Fratte, M and Danilova, A and Davison, J and Deák, B and Del Vecchio, S and Dembicz, I and Dengler, J and Dolezal, J and Domene, X and Dvorsky, M and Ejtehadi, H and Enrico, L and Epikhin, D and Eskelinen, A and Essl, F and Fan, G and Fantinato, E and Fazlioglu, F and Fernández-Pascual, E and Ferrara, A and Fidelis, A and Fischer, M and Flagmeier, M and Forte, TGW and Fraser, LH and Fujinuma, J and Furquim, FF and Garris, B and Garris, HW and Giorgis, MA and Giusso Del Galdo, G and González-Robles, A and Good, MK and Guardiola, M and Guarino, R and Guerrero, I and Guillemot, J and Güler, B and Guo, Y and Haesen, S and Hejda, M and Heleno, RH and Høye, TT and Hrivnák, R and Huang, Y and Hunter, JT and Iakushenko, D and Ibáñez, R and Ingerpuu, N and Irl, SDH and Janíková, E and Jansen, F and Jeltsch, F and Jentsch, A and Jiménez-Alfaro, B and Jõks, M and Jouri, MH and Karami, S and Katal, N and Kelemen, A and Khairullin, BI and Khuroo, AA and Komatsu, KJ and Konečná, M and Kook, E and Korell, L and Koroleva, N and Korznikov, KA and Kozhevnikova, MV and Kozub, Ł and Laanisto, L and Lager, H and Lanta, V and Lasagno, RG and Lembrechts, JJ and Li, L and Lisner, A and Liu, H and Liu, K and Liu, X and Lucas-Borja, ME and Ludewig, K and Lukács, K and Luther-Mosebach, J and Macek, P and Marignani, M and Michalet, R and Miglécz, T and Moeslund, JE and Moeys, K and Montesinos, D and Moreno-Jiménez, E and Moysiyenko, I and Mucina, L and Muñoz-Rojas, M and Murillo, RA and Nambahu, SM and Neuenkamp, L and Normand, S and Nowak, A and Nuche, P and Oja, T and Onipchenko, VG and Pachedjieva, KL and Paganeli, B and Peco, B and Peralta, AML and Pérez-Haase, A and Peri, PL and Petraglia, A and Peyre, G and Plaza-Álvarez, PA and Plue, J and Prentice, HC and Prokhorov, VE and Radujković, D and Rahmanian, S and Reitalu, T and Ristow, M and Robin, AA and Robles, AB and Rodríguez Ginart, DA and Román, R and Roos, RE and Rosati, L and Sádlo, J and Salimbayeva, K and Sánchez de Dios, R and Sanchir, K and Sattler, C and Scasta, JD and Schmiedel, U and Schrader, J and Schultz, NL and Sellan, G and Serra-Diaz, JM and Silan, G and Skálová, H and Skobel, N and Sonkoly, J and Štajerová, K and Svitková, I and Świerszcz, S and Tanentzap, AJ and Tanentzap, FM and Tarifa, R and Tejero, P and Tekeev, DK and Tholin, M and Thormodsæter, RS and Tian, Y and Tokaryuk, A and Tölgyesi, C and Tomaselli, M and Tordoni, E and Török, P and Tóthmérész, B and Toussaint, A and Touzard, B and Trindade, DPF and Tsakalos, JL and Türkiş, S and Valencia, E and Valerio, M and Valkó, O and Van Meerbeek, K and Vandvik, V and Villellas, J and Virtanen, R and Vítková, M and Vojík, M and von Hessberg, A and von Oppen, J and Wagner, V and Wan, JZ and Wang, CJ and Wani, SA and Weiss, L and Wevill, T and Xiao, S and Zárate Martínez, O and Zobel, M},
title = {Global impoverishment of natural vegetation revealed by dark diversity.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40175550},
issn = {1476-4687},
abstract = {Anthropogenic biodiversity decline threatens the functioning of ecosystems and the many benefits they provide to humanity[1]. As well as causing species losses in directly affected locations, human influence might also reduce biodiversity in relatively unmodified vegetation if far-reaching anthropogenic effects trigger local extinctions and hinder recolonization. Here we show that local plant diversity is globally negatively related to the level of anthropogenic activity in the surrounding region. Impoverishment of natural vegetation was evident only when we considered community completeness: the proportion of all suitable species in the region that are present at a site. To estimate community completeness, we compared the number of recorded species with the dark diversity-ecologically suitable species that are absent from a site but present in the surrounding region[2]. In the sampled regions with a minimal human footprint index, an average of 35% of suitable plant species were present locally, compared with less than 20% in highly affected regions. Besides having the potential to uncover overlooked threats to biodiversity, dark diversity also provides guidance for nature conservation. Species in the dark diversity remain regionally present, and their local populations might be restored through measures that improve connectivity between natural vegetation fragments and reduce threats to population persistence.},
}

@article {pmid40173850,
year = {2025},
author = {Vivien, R and Martin, P},
title = {Maintaining taxonomic accuracy in genetic databases: A duty for taxonomists-Reanalysis of the DNA sequences from Mercan et al. (2024) on the genus Potamothrix (Annelida, Clitellata) in Turkish lakes.},
journal = {Zootaxa},
volume = {5575},
number = {4},
pages = {555-562},
doi = {10.11646/zootaxa.5575.4.5},
pmid = {40173850},
issn = {1175-5334},
mesh = {Turkey ; Animals ; Lakes ; Phylogeny ; *Databases, Genetic/standards ; *Databases, Nucleic Acid/standards ; Sequence Analysis, DNA ; *Polychaeta/classification/genetics ; },
abstract = {Public DNA sequence databases such as GenBank are widely used for identification of organisms in ecological and taxonomic studies. It is important that these public databases contain as few mistakes as possible and that any errors detected in these databases are reported. Here, we reanalyzed the COI sequences of Mercan et al. (2024) and showed that they were mistakenly considered by these authors as belonging to different populations (haplotypes) within the species Potamothrix hammoniensis (Tubificinae). We found that they corresponded to four distinct Tubificinae lineages (species), Pothamothrix alatus paravanicus, Potamothrix bavaricus, Tubifex sp. and Potamothrix sp. Despite these identification errors, the data from Mercan et al. (2024) remain interesting as they provide new information on the diversity of the genus Potamothrix in Turkey. Prompt measures must be taken to correct these errors and prevent them from being detrimental to future studies.},
}

Turkey
Animals
Lakes
Phylogeny
*Databases, Genetic/standards
*Databases, Nucleic Acid/standards
Sequence Analysis, DNA
*Polychaeta/classification/genetics

@article {pmid40111995,
year = {2025},
author = {Eales, O and Shearer, FM and McCaw, JM},
title = {How immunity shapes the long-term dynamics of influenza H3N2.},
journal = {PLoS computational biology},
volume = {21},
number = {3},
pages = {e1012893},
pmid = {40111995},
issn = {1553-7358},
mesh = {Humans ; *Influenza, Human/immunology/epidemiology/transmission/virology ; *Influenza A Virus, H3N2 Subtype/immunology/genetics ; Computational Biology ; *Models, Immunological ; Adult ; Aged ; Middle Aged ; Adolescent ; },
abstract = {Since its emergence in 1968, influenza A H3N2 has caused yearly epidemics in temperate regions. While infection confers immunity against antigenically similar strains, new antigenically distinct strains that evade existing immunity regularly emerge ('antigenic drift'). Immunity at the individual level is complex, depending on an individual's lifetime infection history. An individual's first infection with influenza typically elicits the greatest response with subsequent infections eliciting progressively reduced responses ('antigenic seniority'). The combined effect of individual-level immune responses and antigenic drift on the epidemiological dynamics of influenza are not well understood. Here we develop an integrated modelling framework of influenza transmission, immunity, and antigenic drift to show how individual-level exposure, and the build-up of population level immunity, shape the long-term epidemiological dynamics of H3N2. Including antigenic seniority in the model, we observe that following an initial decline after the pandemic year, the average annual attack rate increases over the next 80 years, before reaching an equilibrium, with greater increases in older age-groups. Our analyses suggest that the average attack rate of H3N2 is still in a growth phase. Further increases, particularly in the elderly, may be expected in coming decades, driving an increase in healthcare demand due to H3N2 infections.},
}

Humans
*Influenza, Human/immunology/epidemiology/transmission/virology
*Influenza A Virus, H3N2 Subtype/immunology/genetics
Computational Biology
*Models, Immunological
Adult
Aged
Middle Aged
Adolescent

@article {pmid39880083,
year = {2025},
author = {Vande Moortele, T and Verschaffelt, P and Huang, Q and Doncheva, NT and Holstein, T and Jachmann, C and Dawyndt, P and Martens, L and Mesuere, B and Van Den Bossche, T},
title = {PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.},
journal = {Molecular & cellular proteomics : MCP},
volume = {24},
number = {3},
pages = {100918},
pmid = {39880083},
issn = {1535-9484},
mesh = {*Software ; *Metabolic Networks and Pathways ; Humans ; *Proteomics/methods ; Gastrointestinal Microbiome ; User-Computer Interface ; Proteome/metabolism ; *Computational Biology/methods ; Caloric Restriction ; },
abstract = {Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with the potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.},
}

*Software
*Metabolic Networks and Pathways
Humans
*Proteomics/methods
Gastrointestinal Microbiome
User-Computer Interface
Proteome/metabolism
*Computational Biology/methods
Caloric Restriction

@article {pmid39609363,
year = {2025},
author = {Xu, S and Akhatayeva, Z and Liu, J and Feng, X and Yu, Y and Badaoui, B and Esmailizadeh, A and Kantanen, J and Amills, M and Lenstra, JA and Johansson, AM and Coltman, DW and Liu, GE and Curik, I and Orozco-terWengel, P and Paiva, SR and Zinovieva, NA and Zhang, L and Yang, J and Liu, Z and Wang, Y and Yu, Y and Li, M},
title = {Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations.},
journal = {Science China. Life sciences},
volume = {68},
number = {4},
pages = {934-960},
pmid = {39609363},
issn = {1869-1889},
mesh = {Animals ; *Livestock/genetics ; *Genomics/methods ; *Breeding/methods ; *Ruminants/genetics ; *Genome ; Phenotype ; Multiomics ; },
abstract = {Ruminant livestock provide a rich source of products, such as meat, milk, and wool, and play a critical role in global food security and nutrition. Over the past few decades, genomic studies of ruminant livestock have provided valuable insights into their domestication and the genetic basis of economically important traits, facilitating the breeding of elite varieties. In this review, we summarize the main advancements for domestic ruminants in reference genome assemblies, population genomics, and the identification of functional genes or variants for phenotypic traits. These traits include meat and carcass quality, reproduction, milk production, feed efficiency, wool and cashmere yield, horn development, tail type, coat color, environmental adaptation, and disease resistance. Functional genomic research is entering a new era with the advancements of graphical pangenomics and telomere-to-telomere (T2T) gap-free genome assembly. These advancements promise to improve our understanding of domestication and the molecular mechanisms underlying economically important traits in ruminant livestock. Finally, we provide new perspectives and future directions for genomic research on ruminant genomes. We suggest how ever-increasing multiomics datasets will facilitate future studies and molecular breeding in livestock, including the potential to uncover novel genetic mechanisms underlying phenotypic traits, to enable more accurate genomic prediction models, and to accelerate genetic improvement programs.},
}

Animals
*Livestock/genetics
*Genomics/methods
*Breeding/methods
*Ruminants/genetics
*Genome
Phenotype
Multiomics

@article {pmid40175491,
year = {2025},
author = {Zhang, H and Guo, G and Li, H and Wang, T and Ni, J and Meng, H},
title = {A new numerical method for calculating residual deformation in mined-out areas considering water-rock interaction and its application.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11207},
pmid = {40175491},
issn = {2045-2322},
support = {2023YFC3804201//National Key R&D Program of China/ ; },
abstract = {Globally, extensive land regions have fallen victim to coal mining subsidence, rendering the reuse of goaf sites a crucial concern. The residual deformation amount of these sites is the linchpin for determining their reusability. Presently, numerical computations of residual deformation in goafs, which overlook water-rock coupling, breed significant errors, posing severe threats to the safety of on-site structures. To remedy the situation, this research hinges on the mechanical experiment results of fractured rock masses under water-rock interaction within the goaf. By leveraging an embedded programming language, it pinpoints the irregular damage range of overlying strata due to water-rock effects. Then, corresponding mechanical parameters are allocated to the surrounding rocks at diverse spatial positions, with the erosive impact of water-soaked coal pillars also factored in. This gives rise to a novel numerical method that more precisely gauges groundwater's influence on strata movement and surface subsidence. Using the 01 working face of a Shandong mine as a practical backdrop, the new method verifies its reliability and accuracy. When contrasted with traditional approaches, be it neglecting water filling or assuming full saturation in the goaf, it slashes the calculation error by 20%, furnishing new approaches for residual deformation calculation and novel perspectives for evaluating site stability under complex geological conditions.},
}

@article {pmid40171521,
year = {2025},
author = {Boyes, D and Hutchinson, F and Crowley, LM and , and , and , and , and , and , and , },
title = {The genome sequence of the Large Birch Bell moth, Large Birch Roller, Epinotia brunnichana (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {101},
pmid = {40171521},
issn = {2398-502X},
abstract = {We present a genome assembly from a female Epinotia brunnichana (Large Birch Bell, Large Birch Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 943.10 megabases. Most of the assembly (99.68%) is scaffolded into 29 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,003 protein-coding genes.},
}

@article {pmid40170100,
year = {2025},
author = {Sato, K and Watanabe, S and Noda, T and Koizumi, T and Yoda, K and Watanabe, YY and Sakamoto, KQ and Isokawa, T and Yoshida, MA and Aoki, K and Takahashi, A and Iwata, T and Nishizawa, H and Maekawa, T and Kawabe, R and Watanuki, Y},
title = {Biologging intelligent Platform (BiP): an integrated and standardized platform for sharing, visualizing, and analyzing biologging data.},
journal = {Movement ecology},
volume = {13},
number = {1},
pages = {23},
pmid = {40170100},
issn = {2051-3933},
abstract = {Sharing biologging data can facilitate collaborative research and biological conservation by providing maps showing animals' distribution and movements. It is a critical social mission to preserve not only horizontal position data, but also behavioral data such as diving depth, flight altitude, speed, and acceleration, as well as physiological data such as body temperature, along with related metadata, ensuring their preservation for future generation. Moreover, although biologging was initially developed in the field of biology, it now contributes to diverse fields such as meteorology and oceanography, leading to expanded opportunities for secondary data utilization. In light of social and academic requirements, we developed "Biologging intelligent Platform (BiP)", which adheres to internationally recognized standards for sensor data and metadata storage. As a result, BiP not only stores sensor data along with metadata but also standardizes this information to facilitate secondary data analysis, facilitating broader applications of biologging data across various disciplines. By visiting the website (https://www.bip-earth.com) and completing the user registration, data owners can interactively upload sensor data, input metadata associated with individual animals, devices, and deployments, standardize data formats, and choose between open and private settings for sharing data. Anyone interested in utilizing the data can access metadata and visualized route maps, irrespective of the data's open or private status. Users can freely download open datasets that are available under the CC BY 4.0 license, which permits copying, redistribution, and modification while adhering to the metadata's credit requirements. To use private datasets, users can contact the data owner to request permission. A unique feature of BiP is the Online Analytical Processing (OLAP) tools that calculate environmental parameters, such as surface currents, ocean winds, and waves from data collected by animals. Algorithms published in some previous studies are integrated into the OLAP which can estimate the environmental and behavioral parameters. To enhance data accessibility, BiP allows users to search for datasets using the DOI of the paper in which the data was used. We believe that linking with other databases for data exchange and multi-repository storage could enhance the sustainability of the data itself.},
}

@article {pmid39934999,
year = {2025},
author = {De Moor, D and Skelton, M and , and Amici, F and Arlet, ME and Balasubramaniam, KN and Ballesta, S and Berghänel, A and Berman, CM and Bernstein, SK and Bhattacharjee, D and Bliss-Moreau, E and Brotcorne, F and Butovskaya, M and Campbell, LAD and Carosi, M and Chatterjee, M and Cooper, MA and Cowl, VB and De la O, C and De Marco, A and Dettmer, AM and Dhawale, AK and Erinjery, JJ and Evans, CL and Fischer, J and García-Nisa, I and Giraud, G and Hammer, R and Hansen, MF and Holzner, A and Kaburu, S and Konečná, M and Kumara, HN and Larrivaz, M and Leca, JB and Legrand, M and Lehmann, J and Li, JH and Lezé, AS and MacIntosh, A and Majolo, B and Maréchal, L and Marty, PR and Massen, JJM and Maulany, RI and McCowan, B and McFarland, R and Merieau, P and Meunier, H and Micheletta, J and Mishra, PS and Sah, SAM and Molesti, S and Morrow, KS and Müller-Klein, N and Ngakan, PO and Palagi, E and Petit, O and Pflüger, LS and di Sorrentino, EP and Raghaven, R and Raimbault, G and Ram, S and Reichard, UH and Riley, EP and Rincon, AV and Ruppert, N and Sadoughi, B and Santhosh, K and Schino, G and Sheeran, LK and Silk, JB and Singh, M and Sinha, A and Sosa, S and Stribos, MS and Sueur, C and Tiddi, B and Tkaczynski, PJ and Trebouet, F and Widdig, A and Whitehouse, J and Wooddell, LJ and Xia, DP and von Fersen, L and Young, C and Schülke, O and Ostner, J and Neumann, C and Duboscq, J and Brent, LJN},
title = {MacaqueNet: Advancing comparative behavioural research through large-scale collaboration.},
journal = {The Journal of animal ecology},
volume = {94},
number = {4},
pages = {519-534},
doi = {10.1111/1365-2656.14223},
pmid = {39934999},
issn = {1365-2656},
support = {864461//H2020 European Research Council/ ; LSC-AF2023_03//Leibniz ScienceCampus EEGA/ ; },
mesh = {Animals ; *Behavioral Research/methods ; Macaca/physiology ; Behavior, Animal ; Databases, Factual ; Social Behavior ; },
abstract = {There is a vast and ever-accumulating amount of behavioural data on individually recognised animals, an incredible resource to shed light on the ecological and evolutionary drivers of variation in animal behaviour. Yet, the full potential of such data lies in comparative research across taxa with distinct life histories and ecologies. Substantial challenges impede systematic comparisons, one of which is the lack of persistent, accessible and standardised databases. Big-team approaches to building standardised databases offer a solution to facilitating reliable cross-species comparisons. By sharing both data and expertise among researchers, these approaches ensure that valuable data, which might otherwise go unused, become easier to discover, repurpose and synthesise. Additionally, such large-scale collaborations promote a culture of sharing within the research community, incentivising researchers to contribute their data by ensuring their interests are considered through clear sharing guidelines. Active communication with the data contributors during the standardisation process also helps avoid misinterpretation of the data, ultimately improving the reliability of comparative databases. Here, we introduce MacaqueNet, a global collaboration of over 100 researchers (https://macaquenet.github.io/) aimed at unlocking the wealth of cross-species data for research on macaque social behaviour. The MacaqueNet database encompasses data from 1981 to the present on 61 populations across 14 species and is the first publicly searchable and standardised database on affiliative and agonistic animal social behaviour. We describe the establishment of MacaqueNet, from the steps we took to start a large-scale collective, to the creation of a cross-species collaborative database and the implementation of data entry and retrieval protocols. We share MacaqueNet's component resources: an R package for data standardisation, website code, the relational database structure, a glossary and data sharing terms of use. With all these components openly accessible, MacaqueNet can act as a fully replicable template for future endeavours establishing large-scale collaborative comparative databases.},
}

Animals
*Behavioral Research/methods
Macaca/physiology
Behavior, Animal
Databases, Factual
Social Behavior

@article {pmid39760247,
year = {2025},
author = {Lee, CE and Messer, LF and Wattiez, R and Matallana-Surget, S},
title = {Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms.},
journal = {Proteomics},
volume = {25},
number = {7},
pages = {e202400208},
doi = {10.1002/pmic.202400208},
pmid = {39760247},
issn = {1615-9861},
support = {//Joint UKRI Natural Environment Research Council (NERC) and National Research Foundation (NRF) Singapore/ ; NE/V009621/1//UKRI NERC/NRF/ ; NRF-SEAP-2020-0001//UKRI NERC/NRF/ ; NE/S007342/1//NERC Scottish Universities Partnership for Environmental Research (SUPER) Doctoral Training Partnership (DTP)/ ; },
mesh = {*Biofilms/growth & development ; *Bacterial Proteins/metabolism/genetics ; Proteomics/methods ; Plastics/metabolism ; Proteome/metabolism/analysis ; Bacteria/genetics/metabolism/classification ; Microbiota/genetics/physiology ; Metagenome/genetics ; Polyethylene/metabolism ; Metagenomics/methods ; Multiomics ; },
abstract = {Marine plastispheres represent dynamic microhabitats where microorganisms colonise plastic debris and interact. Metaproteomics has provided novel insights into the metabolic processes within these communities; however, the early metabolic interactions driving the plastisphere formation remain unclear. This study utilised metaproteomic and metagenomic approaches to explore early plastisphere formation on low-density polyethylene (LDPE) over 3 (D3) and 7 (D7) days, focusing on microbial diversity, activity and biofilm development. In total, 2948 proteins were analysed, revealing dominant proteomes from Pseudomonas and Marinomonas, with near-complete metagenome-assembled genomes (MAGs). Pseudomonas dominated at D3, whilst at D7, Marinomonas, along with Acinetobacter, Vibrio and other genera became more prevalent. Pseudomonas and Marinomonas showed high expression of reactive oxygen species (ROS) suppression proteins, associated with oxidative stress regulation, whilst granule formation, and alternative carbon utilisation enzymes, also indicated nutrient limitations. Interestingly, 13 alkanes and other xenobiotic degradation enzymes were expressed by five genera. The expression of toxins, several type VI secretion system (TVISS) proteins, and biofilm formation proteins by Pseudomonas indicated their competitive advantage against other taxa. Upregulated metabolic pathways relating to substrate transport also suggested enhanced nutrient cross-feeding within the more diverse biofilm community. These insights enhance our understanding of plastisphere ecology and its potential for biotechnological applications.},
}

*Biofilms/growth & development
*Bacterial Proteins/metabolism/genetics
Proteomics/methods
Plastics/metabolism
Proteome/metabolism/analysis
Bacteria/genetics/metabolism/classification
Microbiota/genetics/physiology
Metagenome/genetics
Polyethylene/metabolism
Metagenomics/methods
Multiomics

@article {pmid39660842,
year = {2025},
author = {Xu, C and Song, LY and Li, J and Zhang, LD and Guo, ZJ and Ma, DN and Dai, MJ and Li, QH and Liu, JY and Zheng, HL},
title = {MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data.},
journal = {Plant, cell & environment},
volume = {48},
number = {5},
pages = {2950-2962},
doi = {10.1111/pce.15318},
pmid = {39660842},
issn = {1365-3040},
support = {//This work was supported by the Natural Science Foundation of China (NSFC) (32171740, 31870581); the National Key Research and Development Program of China (2017YFC0506102)/ ; },
mesh = {*Databases, Genetic ; Transcriptome ; Avicennia/genetics ; Gene Expression Profiling ; Computational Biology/methods ; Multiomics ; },
abstract = {Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets.},
}

*Databases, Genetic
Transcriptome
Avicennia/genetics
Gene Expression Profiling
Computational Biology/methods
Multiomics

@article {pmid40168108,
year = {2025},
author = {Wang, TY and Wu, YW and Lu, HJ and Liao, TY and Tai, JH and Huang, SP and Wang, FY and Yu, TH and Ting, CT and Chaw, SM and Wang, HY},
title = {Chromosome-Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14110},
doi = {10.1111/1755-0998.14110},
pmid = {40168108},
issn = {1755-0998},
support = {23-23//Biodiversity Research Center, Academia Sinica/ ; MOST 102-2311-B-001-019//National Science and Technology Council/ ; MOST 108-2621-B-001-002//National Science and Technology Council/ ; MOST 109-2311-B-002-023-MY3//National Science and Technology Council/ ; 113L7223//National Taiwan University/ ; },
abstract = {The percomorph fish clade Gobioidei is a suborder that comprises over 2200 species distributed in nearly all aquatic habitats. To understand the genetics underlying their species diversification, we sequenced and annotated the genome of the loach goby, Rhyacichthys aspro, an early-diverging group, and compared it with nine additional Gobioidei species. Within Gobioidei, the loach goby possesses the smallest genome at 594 Mb, and a rise in species diversity from early-diverging to more recently diverged lineages is mirrored by enlarged genomes and a higher presence of transposable elements (TEs), particularly DNA transposons. These DNA transposons are enriched in genic and regulatory regions and their copy number increase is strongly correlated with substitution rate, suggesting that DNA repair after transposon excision/insertion leads to nearby mutations. Consequently, the proliferation of DNA transposons might be the crucial driver of Gobioidei diversification and adaptability. The loach goby genome also points to mechanisms of ecological adaptation. It contains relatively few genes for lateral line development but an overrepresentation of synaptic function genes, with genes putatively under selection linked to synapse organisation and calcium signalling, implicating a sensory system distinct from other Gobioidei species. We also see an overabundance of genes involved in neurocranium development and renal function, adaptations likely connected to its flat morphology suited for strong currents and an amphidromous life cycle. Comparative analyses with hill-stream loaches and the European eel reveal convergent adaptations in body shape and saltwater balance. These findings shed new light on the loach goby's survival mechanisms and the broader evolutionary trends within Gobioidei.},
}

@article {pmid40165685,
year = {2025},
author = {Gu, Y and Meng, L and Wang, Y and Wu, Z and Pan, Y and Zhao, Y and Detto, M and Wu, J},
title = {Uncovering the role of solar radiation and water stress factors in constraining decadal intra-site spring phenology variability in diverse ecosystems across the Northern Hemisphere.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70104},
pmid = {40165685},
issn = {1469-8137},
support = {#2017804//Carbon Mitigation Initiative of Princeton University and NSF grant/ ; //HKU Seed Funding for Strategic Interdisciplinary Research Scheme/ ; #17305321//Hong Kong Research Grant Council General Research Fund/ ; #C5062-21GF//Hong Kong Research Grant Council Collaborative Research Fund/ ; #31922090//National Natural Science Foundation of China/ ; //Innovation and Technology Fund (funding support to State Key Laboratories of Agrobiotechnology)/ ; //HKU Science Faculty RAE Improvement Fund 2023-24/ ; },
abstract = {The spring phenology has advanced significantly over recent decades with climate change, impacting large-scale biogeochemical cycles, climate feedback, and other essential ecosystem processes. Although numerous prognostic models have been developed for spring phenology, regional analyses of the optimality (OPT) strategy model that incorporate environmental variables beyond temperature and photoperiod remain lacking. We investigated the roles of solar radiation (SR) and three water stress factors (precipitation (P), soil moisture, and vapor pressure deficit (VPD)) on spring phenology from 1982 to 2015 using the OPT model with Global Inventory Modeling and Mapping Studies NDVI3g dataset and environmental data from TerraClimate, CRU_TS, and Global Land Data Assimilation System across the Northern Hemisphere (> 30°N). Our results show that SR and water stress factors significantly impacted intrasite decadal spring phenology variability, with water stress factors dominant in grassland ecosystems while SR dominated in the rest of the ecosystem types. Enhanced models incorporating SR (OPT-S) and VPD (OPT-VPD) outperformed the original OPT model, likely due to improved representation of the adaptive strategy of spring phenology to optimize photosynthetic carbon gain while minimizing frost risk. Our research enhances the understanding of the key environmental drivers influencing decadal spring phenology variation in the Northern Hemisphere and contributes to more accurate forecasts of ecological responses to global environmental change.},
}

@article {pmid40155956,
year = {2025},
author = {van Kessel, SAM and Wielders, CCH and Schoffelen, AF and Verbon, A},
title = {Enhancing antimicrobial resistance surveillance and research: a systematic scoping review on the possibilities, yield and methods of data linkage studies.},
journal = {Antimicrobial resistance and infection control},
volume = {14},
number = {1},
pages = {25},
pmid = {40155956},
issn = {2047-2994},
mesh = {Humans ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Antimicrobial Stewardship ; Information Storage and Retrieval ; },
abstract = {BACKGROUND: Surveillance data on antimicrobial resistance (AMR) determinants such as antibiotic use, prevalence of AMR, antimicrobial stewardship, and infection prevention and control are mostly analysed and reported separately, although they are inextricably linked to each other. The impact of surveillance and research can be enhanced by linking these data. This systematic scoping review aims to summarize the studies that link AMR data and evaluate whether they yield new results, implications, or recommendations for practice.

METHODS: For this review, data linkage is defined as the process of linking records, from at least two independent data sources on either (I) at least two AMR determinants or (II) one AMR determinant and one or more general population characteristics. Data linkage should be performed on the level of a certain entity which, in the context of this review, can encompass persons, healthcare institutes, geographical regions or countries. A systematic literature search was performed on February 7th 2025 in Embase.com, PubMed and Scopus to identify AMR data linkage studies.

RESULTS: Forty-eight articles were included in our review. Most data linkage studies used two data sources, and most studies were published in the last 5 years (n = 23 in 2020-2024). A predominance of studies linked data on geographical location, and thirteen studies linked data on individual patient level. Findings demonstrate that the majority of studies (43/48) had added value and provided recommendations for clinical practice and future policies or had suggestions for further research and surveillance. Additionally, data linkage studies appeared to be suitable for hypothesis generating. Several limitations were identified. Most studies had ecological designs, which are prone to ecological fallacy and unobserved confounding, making it hard to establish causality.

CONCLUSION: This systematic scoping review showed that AMR data linkage studies are increasingly performed. They have potential to gain a more comprehensive understanding of AMR dynamics by generating hypotheses, assisting in optimisation of surveillance, and interpretation of data in the context of guideline/policy development. To increase the added value of data linkage, more studies should be performed to improve knowledge on methodological approaches, data access, data management, and governance issues.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology/therapeutic use
Antimicrobial Stewardship
Information Storage and Retrieval

@article {pmid40036964,
year = {2025},
author = {Jyoti, J and Hütt, MT},
title = {Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {4},
pages = {},
doi = {10.1093/bioinformatics/btaf095},
pmid = {40036964},
issn = {1367-4811},
mesh = {*Algorithms ; Humans ; *Microbial Interactions ; Microbiota ; Computational Biology/methods ; },
abstract = {MOTIVATION: Inferring microbial interaction networks from microbiome data is a core task of computational ecology. An avenue of research to create reliable inference methods is based on a stylized view of microbiome data, starting from the assumption that the presences and absences of microbiomes, rather than the quantitative abundances, are informative about the underlying interaction network. With this starting point, inference algorithms can be based on the notion of attractors (asymptotic states) in Boolean networks. Boolean network framework offers a computationally efficient method to tackle this problem. However, often existing algorithms operating under a Boolean network assumption, fail to provide networks that can reproduce the complete set of initial attractors (abundance patterns). Therefore, there is a need for network inference algorithms capable of reproducing the initial stable states of the system.

RESULTS: We study the change of attractors in Boolean threshold dynamics on signed undirected graphs under small changes in network architecture and show, how to leverage these relationships to enhance network inference algorithms. As an illustration of this algorithmic approach, we analyse microbial abundance patterns from stool samples of humans with inflammatory bowel disease (IBD), with colorectal cancer and from healthy individuals to study differences between the interaction networks of the three conditions. The method reveals strong diversity in IBD interaction networks. The networks are first partially deduced by an earlier inference method called ESABO, then we apply the new algorithm developed here, EDAME, to this result to generate a network that comes nearest to satisfying the original attractors.

Implementation code is freely available at https://github.com/Jojo6297/edame.git.},
}

*Algorithms
Humans
*Microbial Interactions
Microbiota
Computational Biology/methods

@article {pmid40086783,
year = {2025},
author = {Yang, JZ and Li, JH and Liu, JL and Zhou, AD and Wang, H and Xie, XL and Zhang, KK and Wang, Q},
title = {Multiomics analysis revealed the effects of polystyrene nanoplastics at different environmentally relevant concentrations on intestinal homeostasis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {372},
number = {},
pages = {126050},
doi = {10.1016/j.envpol.2025.126050},
pmid = {40086783},
issn = {1873-6424},
mesh = {Animals ; Mice ; *Polystyrenes/toxicity ; *Homeostasis/drug effects ; *Gastrointestinal Microbiome/drug effects ; Microplastics/toxicity ; Nanoparticles/toxicity ; Male ; Mice, Inbred C57BL ; Colon/drug effects ; Intestines/drug effects ; Multiomics ; },
abstract = {Nanoplastics pollution is a global issue, with the digestive tract being one of the first affected organs, requiring further research on its impact on intestinal health. This study involved orally exposing mice to polystyrene nanoplastics (PS-NPs) at doses of 0.1, 0.5, or 2.5 mg/d for 42 days. The effects on intestinal health were thoroughly assessed via microbiomics, metabolomics, transcriptomics, and molecular biology. Our study demonstrated that the administration of all three doses of PS-NPs resulted in increased colonic permeability, heightened colonic and peripheral inflammation, reduced levels of antimicrobial peptides, and shortened colonic length. These effects may be attributed to a reduction in the abundance of probiotic bacteria, such as Clostridia_UCG-014, Roseburia, and Akkermansia, alongside an increase in the abundance of the pathogenic bacterium Desulfovibrionaceae induced by PS-NPs. Furthermore, we underscored the crucial role of histidine metabolism in PS-NPs-induced colonic injury, characterized by a significant reduction of L-histidine, which is closely related to microbial ecological dysregulation. Corresponding to microbiota deterioration and metabolic dysregulation, transcriptome analysis revealed that PS-NPs may disrupt colonic immune homeostasis by activating the TLR4/MyD88/NF-κB/NLRP3 signaling pathway. In conclusion, this study provided novel insights into the mechanisms by which PS-NPs disrupt intestinal homeostasis through integrated multiomics analysis, revealing critical molecular pathway and providing a scientific basis for future risk assessment of nanoplastics exposure.},
}

Animals
Mice
*Polystyrenes/toxicity
*Homeostasis/drug effects
*Gastrointestinal Microbiome/drug effects
Microplastics/toxicity
Nanoparticles/toxicity
Male
Mice, Inbred C57BL
Colon/drug effects
Intestines/drug effects
Multiomics

@article {pmid40155652,
year = {2025},
author = {Rehbein, M and Escobari, B and Fischer, S and Güntsch, A and Haas, B and Matheisen, G and Perschl, T and Wieshuber, A and Engel, T},
title = {Quantitative and qualitative Data on historical Vertebrate Distributions in Bavaria 1845.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {525},
pmid = {40155652},
issn = {2052-4463},
support = {442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Vertebrates ; Germany ; Animals ; *Biodiversity ; History, 19th Century ; Ecosystem ; Conservation of Natural Resources ; Forests ; },
abstract = {Archival collections contain an underutilized wealth of biodiversity data, encapsulated in government files and other historical documents. In 1845, the Bavarian government conducted a comprehensive national survey on the occurrence of 44 selected vertebrate species across the country. The detailed expert responses from 119 forestry offices, totalling 520 handwritten pages, have been preserved in the Bavarian State Archives. In this study, we digitized, annotated, geographically referenced, and published these historical records, making them widely available as data for research and conservation planning. Our dataset, openly accessible through the Global Biodiversity Information Facility (GBIF) and Zenodo, contains 5,467 species occurrence records from 1845. Besides the binary presence/absence data, we have also published the original textual survey responses, which contain rich qualitative information, such as species abundances, population trends, habitats, forest management practices, and human-nature relationships. This information can be further processed and interpreted to address a range of questions in historical and contemporary ecology.},
}

*Vertebrates
Germany
Animals
*Biodiversity
History, 19th Century
Ecosystem
Conservation of Natural Resources
Forests

@article {pmid40144399,
year = {2021},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the poplar hawk-moth, Laothoe populi (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {6},
number = {},
pages = {237},
pmid = {40144399},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Laothoe populi (the poplar hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 576 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.},
}

@article {pmid40143245,
year = {2025},
author = {Culot, A and Abriat, G and Furlong, KP},
title = {High-Performance Genome Annotation for a Safer and Faster-Developing Phage Therapy.},
journal = {Viruses},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/v17030314},
pmid = {40143245},
issn = {1999-4915},
mesh = {*Genome, Viral ; *Bacteriophages/genetics/classification ; *Molecular Sequence Annotation ; *Computational Biology/methods ; *Phage Therapy/methods ; Humans ; },
abstract = {Phage therapy, which uses phages to decrease bacterial load in an ecosystem, introduces a multitude of gene copies (bacterial and phage) into said ecosystem. While it is widely accepted that phages have a significant impact on ecology, the mechanisms underlying their impact are not well understood. It is therefore paramount to understand what is released in the said ecosystem, to avoid alterations with difficult-to-predict-but potentially huge-consequences. An in-depth annotation of therapeutic phage genomes is therefore essential. Currently, the average published phage genome has only 20-30% functionally annotated genes, which represents a hurdle to overcome to deliver safe phage therapy, for both patients and the environment. This study aims to compare the effectiveness of manual versus automated phage genome annotation methods. Twenty-seven phage genomes were annotated using SEA-PHAGE and Rime Bioinformatics protocols. The structural (gene calling) and functional annotation results were compared. The results suggest that during the structural annotation step, the SEA-PHAGE method was able to identify an average of 1.5 more genes per phage (typically a frameshift gene) and 5.3 gene start sites per phage. Despite this difference, the impact on functional annotation appeared to be limited: on average, 1.2 genes per phage had erroneous functions, caused by the structural annotation. Rime Bioinformatics' tool (rTOOLS, v2) performed better at assigning functions, especially where the SEA-PHAGE methods assigned hypothetical proteins: 7.0 genes per phage had a better functional annotation on average, compared to SEA PHAGE's 1.7. The method comparison detailed in this article indicate that (1) manual structural annotation is marginally superior to rTOOLS automated structural annotation; (2) rTOOLS automated functional annotation is superior to manual functional annotation. Previously, the only way to obtain a high-quality annotation was by using manual protocols, such as SEA-PHAGES. In the relatively new field of phage therapy, which requires support to advance, manual work can be problematic due to its high cost. Rime Bioinformatics' rTOOLS software allows for time and money to be saved by providing high-quality genome annotations that are comparable to manual results, enabling a safer and faster-developing phage therapy.},
}

*Genome, Viral
*Bacteriophages/genetics/classification
*Molecular Sequence Annotation
*Computational Biology/methods
*Phage Therapy/methods
Humans

@article {pmid40140737,
year = {2025},
author = {Tahir Ul Qamar, M and Fatima, K and Rao, MJ and Tang, Q and Sadaqat, M and Ding, B and Chen, LL and Zhu, XT},
title = {Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {388},
pmid = {40140737},
issn = {1471-2229},
mesh = {*Citrus/genetics ; *Multigene Family ; *Genome, Plant ; Genomics ; Plant Diseases/genetics/microbiology ; Plant Proteins/genetics/metabolism ; Genetic Variation ; Phylogeny ; Genes, Plant ; Gene Expression Regulation, Plant ; Disease Resistance/genetics ; },
abstract = {Citrus is an important nutritional fruit globally; however, its yield is affected by various stresses. This study presents the draft pangenome of Citrus, developed using 11 species to examine their genetic diversity and identify members of the germin-like proteins (GLPs) gene family involved in disease responsiveness. The developed sequence-based pangenome contains 954 Mb sequence and 74,755 genes. The comparative genomics analysis revealed the presence-absence variations (PAVs) among the Citrus genomes and species-specific protein-coding genes. Gene-based pangenome analysis revealed 4,936 new genes missing in the reference genome and highlighted the core and shell genes with putative functions in stress regulation. The pangenome-wide identification of GLP gene family members indicated the intraspecies diversity among the members across 11 genomes by analyzing their gene structure, motifs, and chromosomal distribution patterns. The synteny and evolutionary constraints analyses of Citrus GLPs provide detailed evidence of their evolutionary conservation and divergence. Further, the interaction, functional enrichment, and promoter analysis revealed their involvement in abiotic-, biotic-stress, signaling, and development-related pathways. The expression patterns of C. sinensis GLPs were studied in Huanglongbing (HLB) and Citrus canker disease. Several genes including CsGLPs1-2 and CsGLPs8-4 showed changes in expression patterns under both disease conditions. The qRT-PCR analysis revealed that these two genes were highly expressed in leaves infected with HLB disease across seven HLB-tolerant and susceptible citrus species. This Citrus pangenome and pangenes family study offers a comprehensive resource and new insights into the structural and functional diversity, identifying candidate genes that are important for future research to understand the stress-responsive mechanisms in Citrus.},
}

*Citrus/genetics
*Multigene Family
*Genome, Plant
Genomics
Plant Diseases/genetics/microbiology
Plant Proteins/genetics/metabolism
Genetic Variation
Phylogeny
Genes, Plant
Gene Expression Regulation, Plant
Disease Resistance/genetics

@article {pmid40139213,
year = {2025},
author = {Tam, CC and Young, SD and Harrison, S and Li, X and Litwin, AH},
title = {Theory-Based Social Media Intervention for Nonmedical Use of Prescription Opioids in Young Adults: Protocol for a Randomized Controlled Trial.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e65847},
doi = {10.2196/65847},
pmid = {40139213},
issn = {1929-0748},
mesh = {Humans ; *Social Media ; Young Adult ; Male ; Female ; Analgesics, Opioid ; Adult ; Adolescent ; Opioid-Related Disorders/psychology ; },
abstract = {BACKGROUND: The nonmedical use of prescription opioids (NMUPO) in young adults in the United States is concerning and is robustly influenced by many psychosocial factors. Given the advantages of flexibility, wide coverage, and real-time responses and assessment, using social media appears to be a promising and innovative approach to delivering psychosocial intervention to young adults. However, few theory-based social media interventions are available for NMUPO targeting this at-risk population.

OBJECTIVE: Guided by the information-motivation-behavioral skills model, the proposed research aims to address critical gaps by theoretically exploring psychosocial content associated with NMUPO among young adults via formative assessment. These findings will then be used to develop and evaluate the feasibility and preliminary efficacy of a peer-led social media intervention to reduce NMUPO among young adults.

METHODS: The proposed study will comprise serial research activities. First, formative research will be conducted through semistructured interviews among 30 young adults engaged in NMUPO. Qualitative data will be synthesized using a pragmatic approach for identifying psychosocial content associated with NMUPO. Second, qualitative findings will be used for developing a peer-led social media intervention to reduce NMUPO among young adults by integrating promising psychotherapy principles and incorporating them with well-trained recovery coaches. Third, the social media intervention will be evaluated through a 12-week randomized controlled trial among 70 young adults (n=35, 50% in the intervention group and control group) engaged in NMUPO via mixed methods, including pre- and postintervention surveys, social media paradata (eg, time-series reactions to posts) collection, and ecological momentary assessment during the intervention. The control group will not receive an intervention but will complete the pre- and postintervention surveys. The primary outcomes will be feasibility, usability, and acceptability, while the secondary outcomes will be psychosocial and behavioral measures, such as past-3-month NMUPO, intention, psychological distress, self-efficacy, resilience, and coping strategies.

RESULTS: The proposed study was funded in May 2024. Social media campaigns have received responses from a total of 379 individuals, with 24 (6.3%) identified as eligible. As of February 10, 2025, we have completed formative interviews with 8 eligible participants.

CONCLUSIONS: The proposed study will be one of the first efforts to develop and deliver a theory-based peer-led intervention on social media, incorporating empirical findings on the psychosocial mechanism of NMUPO. The findings of the proposed study will provide valuable insights into opioid risk reduction for young adults through an innovative approach. If the tested trial is found to be feasible, the proposed study will contribute to future scaled-up and fully powered psychosocial interventions among young adults and other key populations at risk for NMUPO.

TRIAL REGISTRATION: ClincialTrials.gov NCT06469749; https://clinicaltrials.gov/study/NCT06469749.

DERR1-10.2196/65847.},
}

Humans
*Social Media
Young Adult
Male
Female
Analgesics, Opioid
Adult
Adolescent
Opioid-Related Disorders/psychology

@article {pmid40139065,
year = {2025},
author = {Sfriso, AA and Juhmani, AS and Tomio, Y and Wedyan, M and Cunsolo, F and Forlani, G and Sfriso, A and Ferretti, G and Coltorti, M and Munari, C and Mistri, M},
title = {Microbial dynamics in seagrass restoration: Unveiling hidden indicators of ecological success.},
journal = {Marine environmental research},
volume = {208},
number = {},
pages = {107089},
doi = {10.1016/j.marenvres.2025.107089},
pmid = {40139065},
issn = {1879-0291},
abstract = {Seagrass transplantation significantly alters sediment microbial communities, shaping their composition and metabolic functions. One year after Zostera marina transplantation, the microbial community structure and functions at the recipient site began shifting toward those of the donor site. Key microbial taxa associated with seagrass meadow sediment, such as Firmicutes (Hungateiclostridiaceae, Defluviitaleaceae) and Campylobacterota (Sulfurovum), increased in abundance, correlating with sediment organic matter content and carbon availability. Four functional groups were identified, each with distinct metabolic roles: (1) Opportunistic Anaerobic Degraders, (2) Seagrass-Driven Carbon Recyclers, (3) Anaerobic Fermenters and Hydrocarbon Recyclers and (4) Oxygen-Linked Carbon and Sulfur Cyclers. The sediments of transplanted Z. marina meadows exhibited increased cellulolysis and aerobic chemoheterotrophy, along with a reduction in nitrogen metabolism one year post transplant. Despite these microbial shifts, sediment isotopic signatures remained indicative of algal biomass, suggesting an incomplete transition toward a mature seagrass environment. Multivariate analysis further confirmed that the microbial community at the recipient site had not yet fully converged with that of the donor meadow, indicating that complete sediment maturation may require longer timescales. These findings demonstrate that microbial community composition and functional annotations serve as early indicators of seagrass restoration success. Long-term monitoring is essential to track ecosystem recovery and assess the stabilization of sediment conditions.},
}

@article {pmid40136166,
year = {2025},
author = {Ferrari, YAC and Jesus, CVF and Batista, JFC and Silva, BEBD and Cavalcante, AB and Lima, CA},
title = {Secular trend of cervical cancer mortality in Brazil and regions.},
journal = {Ciencia & saude coletiva},
volume = {30},
number = {3},
pages = {e09962023},
doi = {10.1590/1413-81232025303.09962023},
pmid = {40136166},
issn = {1678-4561},
mesh = {Brazil/epidemiology ; Humans ; Female ; *Uterine Cervical Neoplasms/mortality ; Adult ; Middle Aged ; Mortality/trends ; Young Adult ; Aged ; Adolescent ; National Health Programs/organization & administration/trends ; },
abstract = {The scope of this study was to describe the secular trend of cervical cancer mortality in Brazil and its various regions from 1980 to 2021. It involved a populational and ecological study, based on data available at the Department of Informatics of the Unified Health System, using codes 180 and C53. Crude rates, age-specific rates, and age-standardized rates were calculated for the Brazilian and world population. The Average Annual Percent Change (AAPC) was obtained by trend analysis using the Joinpoint Regression Program, with a significance level of 0.05 and 95% confidence intervals (95%CI). There were 171,793 deaths from cervical cancer. In Brazil (AAPC -0.3; CI95%-1.0; 0.4), North (AAPC 0.6; 95%CI -0.1; 1.3) and South (AAPC 0.0; 95%CI -0.5; 0.5) the trends were stationary, increasing in the Northeast (AAPC 0.6; 95%CI 0.3; 0.8) and in the Midwest (AAPC -1.3; 95%CI -1.5; -1.1), and decreasing in the Southeast (AAPC -0.9; 95%CI -1.4; -0.5). Regional differences indicate that public policies need to be improved regarding women's access to a health system that offers adequate prevention, screening and treatment through management strategies that include the most vulnerable population.},
}

Brazil/epidemiology
Humans
Female
*Uterine Cervical Neoplasms/mortality
Adult
Middle Aged
Mortality/trends
Young Adult
Aged
Adolescent
National Health Programs/organization & administration/trends

@article {pmid40133528,
year = {2025},
author = {Pekar, JE and Wang, Y and Wang, JC and Shao, Y and Taki, F and Forgione, LA and Amin, H and Clabby, T and Johnson, K and Torian, LV and Braunstein, SL and Pathela, P and Omoregie, E and Hughes, S and Suchard, MA and Vasylyeva, TI and Lemey, P and Wertheim, JO},
title = {Transmission dynamics of the 2022 mpox epidemic in New York City.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40133528},
issn = {1546-170X},
support = {AI135992//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153044//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135995//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153044//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135995//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153044//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135995//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135992//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; },
abstract = {The 2022 global mpox epidemic was caused by transmission of MPXV clade IIb, lineage B.1 through sexual contact networks, with New York City (NYC) experiencing the first and largest outbreak in the United States. By performing phylogeographic analysis of MPXV genomes sampled from 757 individuals in NYC between April 2022 and April 2023, and 3,287 MPXV genomes sampled around the world, we identify over 200 introductions of MPXV into NYC with at least 84 leading to onward transmission. These infections primarily occurred among men who have sex with men, transgender women and nonbinary individuals. Through a comparative analysis with HIV in NYC, we find that both MPXV and HIV genomic cluster sizes are best fit by scale-free distributions, and that people in MPXV clusters are more likely to have previously received an HIV diagnosis and be a member of a recently growing HIV transmission cluster. We model MPXV transmission through sexual contact networks and show that highly connected individuals would be disproportionately infected at the start of an epidemic, which would likely result in the exhaustion of the most densely connected parts of the network, and, therefore, explain the rapid expansion and decline of the NYC outbreak. By coupling the genomic epidemiology of MPXV and HIV with epidemic modeling, we demonstrate that the transmission dynamics of MPXV in NYC can be understood by general principles of sexually transmitted pathogens.},
}

@article {pmid40132633,
year = {2025},
author = {Liu, X and Milesi, E and Fontsere, C and Owens, HL and Heinsohn, R and Gilbert, MTP and Crates, R and Nogués-Bravo, D and Morales, HE},
title = {Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2043},
pages = {20242480},
doi = {10.1098/rspb.2024.2480},
pmid = {40132633},
issn = {1471-2954},
support = {//The European Molecular Biology Organization/ ; //Mohamed bin Zayed Species Conservation Fund/ ; //Danish National Research Foundation/ ; /ERC_/European Research Council/International ; 25925//Villum Fonden/ ; },
mesh = {Animals ; *Endangered Species ; *Extinction, Biological ; Conservation of Natural Resources ; Ecosystem ; Genomics ; Biodiversity ; Genetic Variation ; Australia ; Birds/genetics ; Passeriformes/genetics/physiology ; },
abstract = {Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.},
}

Animals
*Endangered Species
*Extinction, Biological
Conservation of Natural Resources
Ecosystem
Genomics
Biodiversity
Genetic Variation
Australia
Birds/genetics
Passeriformes/genetics/physiology

@article {pmid40096239,
year = {2025},
author = {Dinnage, R and Kleineberg, M},
title = {Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills.},
journal = {PLoS computational biology},
volume = {21},
number = {3},
pages = {e1012887},
pmid = {40096239},
issn = {1553-7358},
mesh = {Animals ; *Birds/anatomy & histology ; *Imaging, Three-Dimensional/methods ; *Artificial Intelligence ; Beak/anatomy & histology ; Computational Biology ; Deep Learning ; },
abstract = {Data on the three dimensional shape of organismal morphology is becoming increasingly available, and forms part of a new revolution in high-throughput phenomics that promises to help understand ecological and evolutionary processes that influence phenotypes at unprecedented scales. However, in order to meet the potential of this revolution we need new data analysis tools to deal with the complexity and heterogeneity of large-scale phenotypic data such as 3D shapes. In this study we explore the potential of generative Artificial Intelligence to help organize and extract meaning from complex 3D data. Specifically, we train a deep representational learning method known as DeepSDF on a dataset of 3D scans of the bills of 2,020 bird species. The model is designed to learn a continuous vector representation of 3D shapes, along with a 'decoder' function, that allows the transformation from this vector space to the original 3D morphological space. We find that approach successfully learns coherent representations: particular directions in latent space are associated with discernible morphological meaning (such as elongation, flattening, etc.). More importantly, learned latent vectors have ecological meaning as shown by their ability to predict the trophic niche of the bird each bill belongs to with a high degree of accuracy. Unlike existing 3D morphometric techniques, this method has very little requirements for human supervised tasks such as landmark placement, increasing it accessibility to labs with fewer labour resources. It has fewer strong assumptions than alternative dimension reduction techniques such as PCA. Once trained, 3D morphology predictions can be made from latent vectors very computationally cheaply. The trained model has been made publicly available and can be used by the community, including for finetuning on new data, representing an early step toward developing shared, reusable AI models for analyzing organismal morphology.},
}

Animals
*Birds/anatomy & histology
*Imaging, Three-Dimensional/methods
*Artificial Intelligence
Beak/anatomy & histology
Computational Biology
Deep Learning

@article {pmid40136165,
year = {2025},
author = {Aquino, ÉC and Borowicc, SL and Alves-Souza, SN and Teixeira, RA and Ishitani, LH and Malta, DC and Morais Neto, OL},
title = {Distribution of garbage codes in the Mortality Information System, Brazil, 2000 to 2020.},
journal = {Ciencia & saude coletiva},
volume = {30},
number = {3},
pages = {e09442023},
doi = {10.1590/1413-81232025303.09442023},
pmid = {40136165},
issn = {1678-4561},
mesh = {Brazil/epidemiology ; Humans ; *Information Systems/statistics & numerical data/standards ; *Cause of Death/trends ; Linear Models ; Mortality/trends ; Time Factors ; },
abstract = {The analysis of the causes of death is essential to understand the main problems that affect the health level of the population of a region or country. The garbage codes (GC) provide little useful information about causes of death. This study aims to identify the proportion of GC among the deaths registered and to analyze their temporal distribution in Brazil from 2000 to 2020. It's an ecological time-series study of the evolution of the proportion of GC in Brazil. Time series analysis was performed using segmented linear regression models (joinpoint). Between 2000 and 2020, 39.9% of deaths that occurred in Brazil were coded with GC. Between 2000 and 2007, there was a continuous and persistent reduction in the proportion of GC (APC -2.1; P < 0.001). Between 2007 and 2015, there continued to be a reduction, albeit to a lesser extent (APC = -0.7; P = 0.013). Between 2015 and 2018, there was no significant trend of the proportion of GC (APC = -2.3; P = 0.172), which persisted from 2018 (APC 3.2; P < 0.079). Although a reduction in the proportion of GC in Brazil was observed until 2018, this trend did not persist after that year. Reducing the proportion of GC allows managers to plan health policies more adequately for the population.},
}

Brazil/epidemiology
Humans
*Information Systems/statistics & numerical data/standards
*Cause of Death/trends
Linear Models
Mortality/trends
Time Factors

@article {pmid40073274,
year = {2025},
author = {Aucello, R and Pernice, S and Tortarolo, D and Calogero, RA and Herrera-Rincon, C and Ronchi, G and Geuna, S and Cordero, F and Lió, P and Beccuti, M},
title = {UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {3},
pages = {},
pmid = {40073274},
issn = {1367-4811},
support = {//Ministero dell'Univerisita' e della Ricerca/ ; },
mesh = {*Models, Biological ; Humans ; Software ; Escherichia coli/metabolism ; Systems Biology/methods ; Computational Biology/methods ; Computer Simulation ; },
abstract = {MOTIVATION: Computational models are crucial for addressing critical questions about systems evolution and deciphering system connections. The pivotal feature of making this concept recognizable from the biological and clinical community is the possibility of quickly inspecting the whole system, bearing in mind the different granularity levels of its components. This holistic view of system behaviour expands the evolution study by identifying the heterogeneous behaviours applicable, e.g. to the cancer evolution study.

RESULTS: To address this aspect, we propose a new modelling paradigm, UnifiedGreatMod, which allows modellers to integrate fine-grained and coarse-grained biological information into a unique model. It enables functional studies by combining the analysis of the system's multi-level stable states with its fluctuating conditions. This approach helps to investigate the functional relationships and dependencies among biological entities. This is achieved, thanks to the hybridization of two analysis approaches that capture a system's different granularity levels. The proposed paradigm was then implemented into the open-source, general modelling framework GreatMod, in which a graphical meta-formalism is exploited to simplify the model creation phase and R languages to define user-defined analysis workflows. The proposal's effectiveness was demonstrated by mechanistically simulating the metabolic output of Escherichia coli under environmental nutrient perturbations and integrating a gene expression dataset. Additionally, the UnifiedGreatMod was used to examine the responses of luminal epithelial cells to Clostridium difficile infection.

GreatMod https://qbioturin.github.io/epimod/, epimod_FBAfunctions https://github.com/qBioTurin/epimod_FBAfunctions, first case study E. coli  https://github.com/qBioTurin/Ec_coli_modelling, second case study C. difficile  https://github.com/qBioTurin/EpiCell_CDifficile.},
}

*Models, Biological
Humans
Software
Escherichia coli/metabolism
Systems Biology/methods
Computational Biology/methods
Computer Simulation

@article {pmid40125538,
year = {2025},
author = {Broad, GR and Holt, S and Sivess, L and Boyes, D and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Scorched Wing moth, Plagodis dolabraria (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {111},
doi = {10.12688/wellcomeopenres.23761.1},
pmid = {40125538},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Plagodis dolabraria (Scorched Wing; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 939.07 megabases. Most of the assembly (99.59%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.97 kilobases in length.},
}

@article {pmid40121238,
year = {2025},
author = {Kelliher, JM and Rodriguez, FE and Johnson, LYD and Roux, S and Smith, M and Clum, A and Lynch, W and Bias, CH and Finks, SS and Keenum, I and Kiledal, EA and Lin, HA and Longley, R and McDonald, R and Pitot, TM and Rodríguez-Ramos, J and Shen, J and Sprockett, DD and Swift, J and Yadav, A and Eloe-Fadrosh, EA},
title = {Quantifying the impact of workshops promoting microbiome data standards and data stewardship.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9887},
pmid = {40121238},
issn = {2045-2322},
support = {The work conducted by the National Microbiome Data Collaborative (https://ror.org/05cwx3318) is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL).//U.S. Department of Energy/ ; },
mesh = {*Microbiota ; Humans ; Surveys and Questionnaires ; Research Personnel ; },
abstract = {The field of microbiome research continues to grow at a rapid pace, with multi-omics approaches becoming widely used to interrogate diverse microbiome samples. However, due to lagging awareness and implementation of standards and data stewardship, many datasets are produced that are not comparable, reproducible, or reusable. In 2021, the National Microbiome Data Collaborative launched its Ambassador Program, which utilizes a community-learning model to annually train a cohort of early-career researchers in microbiome data stewardship best practices. These Ambassadors then host workshops and other events to communicate these themes to their respective microbiome research communities. To quantify the impact of this learning model for promoting awareness of and experience with microbiome data, we conducted a survey of workshop participants from events hosted by the 2023 Ambassador cohort. The 2023 cohort of 13 National Microbiome Data Collaborative Ambassadors collectively hosted 21 events, reaching over 550 researchers. The Ambassadors distributed an anonymous post-workshop survey to their event participants to quantify the effectiveness of the training materials, the workshop format, and the thematic content. From the 21 events, survey results were successfully collected for 15 of those events from a total of 122 researchers. Overall, 122 participants working with a range of microbiome types and from a variety of institutions responded to the survey and reported overwhelmingly positive experiences with the workshop content and materials, with 98% of respondents reporting that they gained knowledge from the event. Participants across the events also reported an increase in their post-workshop understanding of metadata standards, principles for microbiome data management and reporting, and the importance of standardization in microbiome data processing. Participants also expressed a willingness to apply what they learned about microbiome data stewardship to their own research. The results of this study demonstrate the effectiveness of hands-on workshops and community-learning for communicating data stewardship best practices to microbiome researchers. The lessons learned and details about the implementation of this cohort-based learning model contained herein are intended to assist other groups in their efforts to create or improve similar learning strategies.},
}

*Microbiota
Humans
Surveys and Questionnaires
Research Personnel

@article {pmid40121181,
year = {2025},
author = {Eaton, WD and McGee, KM and Glahn, A and Lemenze, A and Soteropoulos, P},
title = {Use of a logging road in a Costa Rican forest changes the composition and stability of soil microbial decomposer communities, and the conversion of organic carbon into biomass.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf075},
pmid = {40121181},
issn = {1365-2672},
abstract = {AIMS: The effects of a tropical forest logging road on soil C and N, and the compositions of Actinobacteria, Acidobacteria, and wood rot/lignin-degrading fungal (WRT/LD) decomposer communities were evaluated.

METHODS AND RESULTS: Soils from a healthy Costa Rican old growth forest before Hurricane Otto and from an adjacent, recently formed logging road built after Hurricane Otto were collected over 4 years and assessed for C and N metrics, and characteristics of the 3 decomposer communities determined by Illumina amplicon sequencing methods. The Logging Road negatively impacted the soil total organic C, respiration, biomass C, qCO2, and total N, while the Actinobacterial and Acidobacterial communities changed from stable compositions of copiotrophic taxa in the rich forest soil to stable compositions of oligotrophic taxa in the poor logging road soil, and the wood rot/lignin degrading (WRT/LD) community changed from stable compositions of copiotrophic taxa in the forest soils to an unstable community of oligotrophic taxa with almost no overlap in genera between Logging Road soils.

CONCLUSIONS: The logging road negatively influenced 3 decomposer communities and associated C and N metrics, with the two bacterial communities taxonomically stabilizing, but the fungal community taxonomically diverging into an unstable composition over time. Monitoring efforts are on-going to provide local forest land managers with potential indicators of soil ecosystem damage and recovery.},
}

@article {pmid40121109,
year = {2025},
author = {Hanly, J and Anon, and Perret, J and Khan, A},
title = {Disability in ecology and evolution.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2025.02.005},
pmid = {40121109},
issn = {1872-8383},
}

@article {pmid40120582,
year = {2025},
author = {Pinkert, S and Reuber, V and Krug, LM and Heidrich, L and Rehling, F and Brandl, R and Farwig, N},
title = {Burrowing facilitated the survival of mammals in harsh and fluctuating climates.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.02.064},
pmid = {40120582},
issn = {1879-0445},
abstract = {Species' ability to cope with climatic instability varies greatly, influenced by factors such as dispersal, physiological adaptations, and phylogenetic conservatism. Here, we investigate how burrowing behavior, a key component of species' endurance strategies and ecosystem functioning, shaped the contemporary patterns of species richness and range size as well as the diversification of mammalian lineages. Analyzing 4,407 terrestrial mammal species, excluding bats, combined with novel trait data on 3,096 species, we reveal contrasting responses to climatic factors between burrowing and non-burrowing species. Burrowing lineages are disproportionately species-rich at lower temperatures and productivity. Both range size and species richness steeply increase with climate seasonality in burrowing species as opposed to non-burrowing species. The proportion of burrowing species increases with latitude, with regions above 20°, especially those exhibiting greater Pleistocene temperature changes, being almost exclusively composed of burrowing species. Trait conservatism, higher net diversification rates, and Eocene peak diversification provide the evolutionary context for these contemporary patterns, underscoring the role of burrowing for mammalian radiations into temperate climates. Moreover, the lower extinction rate of burrowing species and peak diversification at the Cretaceous-Paleogene (K-Pg) boundary support the longstanding hypothesis that burrowing behavior promoted survival during the "impact winter" that marks the replacement of non-avian dinosaurs by mammals. Our study highlights the potential of readily available trait information for understanding the ecological and evolutionary processes that shape species distributions through space and time. The careful integration of divergent environmental constraints bears vast improvements for forecasts of species' responses to climatic changes and global models of biodiversity patterns.},
}

@article {pmid40049043,
year = {2025},
author = {Huang, JN and Gao, CC and Ren, HY and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ},
title = {Multi-omics association pattern between gut microbiota and host metabolism of a filter-feeding fish in situ exposed to microplastics.},
journal = {Environment international},
volume = {197},
number = {},
pages = {109360},
doi = {10.1016/j.envint.2025.109360},
pmid = {40049043},
issn = {1873-6750},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Microplastics ; *Water Pollutants, Chemical/metabolism/toxicity ; *Carps/microbiology ; Liver/metabolism ; Zebrafish ; Multiomics ; },
abstract = {Microplastics (MPs) are widespread in water environments and can affect gut microbiota and host metabolism of fish, but whether changes in host metabolism under MPs are mediated by gut microbiota remains unclear. Here, silver carp, a filter-feeding fish with important ecological functions, was in-situ exposure to environmentally relevant MPs. Multi-omics analysis and fecal microbiota transplantation were used to reveal the metabolic responses of carp along gut-liver-muscle axis. After three months of in situ exposure to MPs, community structure of gut microbiota of carp was reshaped, and five dominate phyla were significantly changed, including increased Cyanobacteria, Chloroflexi and Planctomycetota but decreased Firmicutes and Fusobacteriota. Weighted gene co-expression network analysis was further performed between these phyla and liver transcription spectrum, showing that the hub gene module contained up-regulated hppD, maiA and plg and activated ubiquinone and other terpenoid-quinone biosynthesis and phenylalanine metabolism. By fecal microbiota transplantation, the key gene module associated with core microbiota phyla of carp was verified in germ-free zebrafish. Interestingly, up-regulated hppD, maiA and plg and enriched phenylalanine metabolism were also observed in this module. Subsequently, metabolome performed in carp liver also shared activated phenylalanine metabolism, including increased trans-cinnamic acid and L-tyrosine. Furthermore, high-associated mapping showed that the differentially expressed metabolites (gamma-aminobutyric acid, ornithine and L-serine) related to amino acid metabolism in carp muscle were significantly accompanied with increased L-tyrosine in its liver. Overall, MPs exposure could change gut microbiome of silver carp and alter host metabolism especially amino acid metabolism along the gut-liver-muscle axis.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Microplastics
*Water Pollutants, Chemical/metabolism/toxicity
*Carps/microbiology
Liver/metabolism
Zebrafish
Multiomics

@article {pmid39833389,
year = {2025},
author = {Schroeder, MW and Frumkin, MR and Mace, RA},
title = {Proof-of-concept for integrating multimodal digital health assessments into lifestyle interventions for older adults with dementia risk factors.},
journal = {Journal of behavioral medicine},
volume = {48},
number = {2},
pages = {373-384},
pmid = {39833389},
issn = {1573-3521},
support = {1 K23 AG075257-01/AG/NIA NIH HHS/United States ; 1 K23 AG075257-01/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; Aged ; Female ; Male ; *Actigraphy/instrumentation ; *Dementia/psychology/therapy ; *Ecological Momentary Assessment ; *Mindfulness ; Pilot Projects ; Life Style ; Middle Aged ; Risk Factors ; Proof of Concept Study ; Aged, 80 and over ; Sleep ; Digital Health ; },
abstract = {Multimodal digital health assessments overcome the limitations of patient-reported outcomes by allowing for continuous and passive monitoring but remain underutilized in older adult lifestyle interventions for brain health. Therefore, we aim to (1) report ecological momentary assessment (EMA) and ActiGraph adherence among older adults during a lifestyle intervention; and (2) use dynamic data collected via EMA and ActiGraph to examine person-specific patterns of mindfulness, steps, and sleep throughout the intervention. We analyzed EMA and ActiGraph data from a pilot study of the 8-week My Healthy Brain program (N = 10) lifestyle group for older adults (60+) with subjective cognitive decline. EMA adherence metrics included proportion of EMA completed and the proportion of days with at least 10 mindfulness minutes. ActiGraph GT9X adherence metrics included the number of valid wear days (≥ 7 h) and the number of days participants achieved their step goal. We used linear mixed-effects models to examine person-specific patterns of step count, sleep efficiency, and mindfulness practice. On average, participants completed 39 of the 49 possible EMAs (80%) during the program. ActiGraph adherence was slightly higher than EMA (M = 61.40 days, 87.71%). Participants achieved the daily mindfulness goal (10 min/day) and step goal on 46.32% and 55.10% of days, respectively. Dynamic data revealed that on average, participant step counts increased by approximately 16.5 steps per day (b = 16.495, p = 0.002). However, some participants exhibited no changes while improvements made by other participants returned to baseline levels of activity. There was substantial heterogeneity in trajectories of mindfulness practice and sleep efficiency. EMA and ActiGraph are feasible for older adults enrolled in dementia risk reduction lifestyle interventions. Future studies are needed to better understand how mechanisms of lifestyle behaviors captured by EMA and ActiGraph are related to cognitive outcomes in older adults.},
}

Humans
Aged
Female
Male
*Actigraphy/instrumentation
*Dementia/psychology/therapy
*Ecological Momentary Assessment
*Mindfulness
Pilot Projects
Life Style
Middle Aged
Risk Factors
Proof of Concept Study
Aged, 80 and over
Sleep
Digital Health

@article {pmid38582819,
year = {2025},
author = {Li, M and Wu, L and Shi, Y and Wu, L and Afzal, F and Jia, Y and Huang, Y and Hu, B and Chen, J and Huang, J},
title = {Bioinformatics and Functional Analysis of OsASMT1 Gene in Response to Abiotic Stress.},
journal = {Biochemical genetics},
volume = {63},
number = {2},
pages = {1527-1540},
pmid = {38582819},
issn = {1573-4927},
support = {2023NSFSC1270//The Sichuan Natural Science Foundation Project/ ; SKL-KF202316//The Open Project Program of State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/ ; },
mesh = {*Stress, Physiological ; *Computational Biology/methods ; *Oryza/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Gene Expression Regulation, Plant ; Sodium Chloride/pharmacology ; Salt Stress ; },
abstract = {The study aimed to elucidate the functional characteristics of OsASMT1 gene under copper (Cu) or sodium chloride (NaCl) stress. Bioinformatics scrutiny unveiled that OsASMT1 is situated on chromosome 9. Its protein architecture, comprising dimerization and methyltransferase domains, showed significant similarities to OsASMT2 and OsASMT3. High expression in roots and panicles, along with abiotic stress putative cis-regulatory elements in the promoter, indicated potential stress responsiveness. Real-time quantitative PCR confirmed OsASMT1 induction under Cu and NaCl stress in rice. Surprisingly, yeast expressing OsASMT1 did not exhibit enhanced resistance to abiotic stresses. The results of subcellular localization analysis indicated that OsASMT1 plays a role in the cytoplasm. While OsASMT1 responded to Cu and NaCl stress in rice, its heterologous expression in yeast failed to confer abiotic stress resistance, highlighting the need for further investigation of its functional implications.},
}

*Stress, Physiological
*Computational Biology/methods
*Oryza/genetics/metabolism
*Plant Proteins/genetics/metabolism
*Gene Expression Regulation, Plant
Sodium Chloride/pharmacology
Salt Stress

@article {pmid40115327,
year = {2025},
author = {Hesson, JC and Haba, Y and McBride, CS and Sheerin, E and Mathers, TC and Paulini, M and Pointon, DB and Torrance, JW and Sadasivan Baby, C and Wood, JMD and , and , and McCarthy, SA and Lawniczak, MKN and Makunin, A},
title = {A chromosomal reference genome sequence for the northern house mosquito, Culex pipiens form pipiens, Linnaeus, 1758.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {107},
pmid = {40115327},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Culex pipiens sensu stricto (the northern house mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Sweden. The genome sequence is 533 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.},
}

@article {pmid40108281,
year = {2025},
author = {Dong, J and Dai, W and Xu, J and Zhang, H and Li, Y and Xie, F},
title = {Impact and elastic modulus of coal mining on terrestrial ecosystems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9454},
pmid = {40108281},
issn = {2045-2322},
support = {CSC202306420029//China Scholarship Council/ ; Lumeidike (2022) No.14//Key Research Projects of Shandong Bureau of Coal Geology/ ; },
abstract = {The energy consumption structure is gradually evolving into a "diversified energy structure" against the backdrop of the global implementation of energy-saving and low-carbon policies. Coal, as the main energy source in China, is difficult to change in the short term, given the characteristics of China's energy and resource endowments, as well as the actual social and economic development at the present stage. Nevertheless, coal mining inevitably leads to a range of ecological issues. Identifying the impact of coal mining on terrestrial ecosystems and adopting resilient recovery measures are crucial prerequisites for advancing green coal mining efforts and attaining carbon peaking and carbon neutrality goals. Using China's open-pit coal mining as a case study: (1) the research examines the fundamental attributes and evolving patterns of spatial distribution among these mines within the country. Furthermore, it delineates the life cycle stages and distinctive features of the five principal open-pit coal mines. The life cycle of a coal mining area is divided into four distinct development phases: the initial phase, the accelerated phase, the stable phase, and the declining phase. The spatial relationship between the life cycle stages of coal mining and ecosystem succession is elucidated by examining the evolutionary types of ecosystems within coal mine area. In the accelerated and stable development phase, the adverse effects of coal mining on the ecosystem are in a long-term increasing trend, causing the key elements of the ecosystem to gradually surpass their threshold values. The ecosystem is out of balance, severely damaged, and gradually undergoing degradation or extreme degradation. The types of ecological succession in coal mining areas can be categorized as follows: terrestrial succession leading to a new terrestrial ecosystem, terrestrial to aquatic ecosystem transitions, or the development of an amphibious symbiotic ecosystem. (2) The research quantitatively assessed the impact of surface coal mining on terrestrial ecosystems by utilizing remote sensing data in conjunction with coal production information. In 2022, the affected areas of the five major open-pit coal mines due to coal mining activities amounted to approximately 0.02% of China's total land area. Meanwhile, the nationwide affected areas of all open-pit coal mines combined reached to approximately 0.13% of China's land area. Open-pit coal mining activities have a significant impact on the surface. (3) By incorporating the ecological resilience theory, we establish a model for the ecosystem's elastic modulus in coal mining areas, taking into account landscape diversity, vegetation coverage, land type, and climate factors, which are based on the concepts of elastic strength and elastic limit. A conceptual model for recognizing ecological thresholds in coal mining areas is developed by incorporating the comprehensive integrity index of the ecosystem. The comprehensive integrity of the ecosystem within a coal mining area undergoes significant alterations as it crosses three distinct ecological thresholds: the elastic point, the yield point, and the mutational point. There should be a corresponding constant (or constant interval) at the three ecological thresholds of ecosystem resilience, the elastic point, the yield point, and the mutational point, which is closely related to the scale of mining operations, mining technology, and the service life in coal mining areas. The established models for identifying ecological thresholds and the resilience modulus degree serve as both theoretical references and practical bases for managing the progress and trends of ecosystem changes during coal resource extraction, making ecological restoration in coal mine areas more target-oriented and specific.},
}

@article {pmid40108248,
year = {2025},
author = {Mammides, C and Ieronymidou, C and Papadopoulos, H},
title = {An ecoacoustic dataset collected on the island of Cyprus in the Mediterranean Basin biodiversity hotspot.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {461},
pmid = {40108248},
issn = {2052-4463},
support = {101090273//European Commission (EC)/ ; },
mesh = {Cyprus ; *Biodiversity ; Animals ; *Acoustics ; Vocalization, Animal ; Mediterranean Region ; Islands ; },
abstract = {There is growing interest in using novel technologies for large-scale biodiversity monitoring. Passive acoustic monitoring (PAM) represents a promising approach for surveying vocalizing animals. However, further development of PAM methods is needed to improve their accuracy. The availability of extensive ecoacoustic datasets from biodiverse areas can facilitate this development. In this study, we present a large ecoacoustic dataset (1.58 TB) collected at sixty-one study sites on the island of Cyprus between March and May 2023. The dataset comprises >313,000 audio files, representing over 5,200 hours of recordings. It can be used for a range of applications, such as developing and refining species identification algorithms, acoustic indices, and protocols for processing acoustic data to exclude non-focal sounds, e.g., those produced by human activities. It can also be used to explore fundamental ecological questions. To facilitate its use, the complete dataset has been made available on the Hugging Face repository and the ARBIMON platform, operated by Rainforest Connection[TM], which offers a range of free tools for ecoacoustic analyses.},
}

Cyprus
*Biodiversity
Animals
*Acoustics
Vocalization, Animal
Mediterranean Region
Islands

@article {pmid40067093,
year = {2025},
author = {Zhang, G and Ristola, P and Su, H and Kumar, B and Zhang, B and Hu, Y and Elliot, MG and Drobot, V and Zhu, J and Staal, J and Larralde, M and Wang, S and Yi, Y and Yu, H},
title = {BioArchLinux: community-driven fresh reproducible software repository for life sciences.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {3},
pages = {},
doi = {10.1093/bioinformatics/btaf106},
pmid = {40067093},
issn = {1367-4811},
mesh = {*Software ; *Computational Biology/methods ; *Biological Science Disciplines/methods ; Programming Languages ; Reproducibility of Results ; },
abstract = {MOTIVATION: The BioArchLinux project was initiated to address challenges in bioinformatics software reproducibility and freshness. Relying on Arch Linux's user-driven ecosystem, we aim to create a comprehensive and continuously updated repository for life sciences research.

RESULTS: BioArchLinux provides a PKGBUILD-based system for seamless software packaging and maintenance, enabling users to access the latest bioinformatics tools across multiple programming languages. The repository includes Docker images, Windows Subsystem for Linux (WSL) support, and Junest for nonroot environments, enhancing accessibility across platforms. Although being developed and maintained by a small core team, BioArchLinux is a fast-growing bioinformatics repository that offers a participatory and community-driven environment.

The repository, documentation, and tools are freely available at https://bioarchlinux.org and https://github.com/BioArchLinux. Users and developers are encouraged to contribute and expand this open-source initiative.},
}

*Software
*Computational Biology/methods
*Biological Science Disciplines/methods
Programming Languages
Reproducibility of Results

@article {pmid40102624,
year = {2025},
author = {Rank, M and Kather, A and Wilke, D and Steib-Bauert, M and Kern, WV and Röder, I and de With, K},
title = {Limitations of estimating antibiotic resistance using German hospital consumption data - a comprehensive computational analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9244},
pmid = {40102624},
issn = {2045-2322},
mesh = {Germany/epidemiology ; Humans ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Hospitals ; Drug Resistance, Microbial ; Drug Resistance, Bacterial ; Neural Networks, Computer ; },
abstract = {For almost a century, antibiotics have played an important role in the treatment of infectious diseases. However, the efficacy of these very drugs is now threatened by the development of resistances, which pose major challenges to medical professionals and decision-makers. Thereby, the consumption of antibiotics in hospitals is an important driver that can be targeted directly. To illuminate the relation between consumption and resistance depicts a very important step in this procedure. With the help of comprehensive ecological and clinical data, we applied a variety of different computational approaches ranging from classical linear regression to artificial neural networks to analyze antibiotic resistance in Germany. These mathematical and statistical models demonstrate that the amount and particularly the structure of currently available data sets lead to contradictory results and do, therefore, not allow for profound conclusions. More effort and attention on both data collection and distribution is necessary to overcome this problem. In particular, our results suggest that at least monthly or quarterly antibiotic use and resistance data at the department and ward level for each hospital (including application route and type of specimen) are needed to reliably determine the extent to which antibiotic consumption influences resistance development.},
}

Germany/epidemiology
Humans
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Hospitals
Drug Resistance, Microbial
Drug Resistance, Bacterial
Neural Networks, Computer

@article {pmid39066964,
year = {2025},
author = {Árvay, J and Hauptvogl, M and Demková, L and Jančo, I and Jakabová, S and Mleczek, M},
title = {GIS-based Visualization of Elemental Distribution in Neoboletus Luridiformis Fruiting Body.},
journal = {Biological trace element research},
volume = {203},
number = {4},
pages = {2271-2283},
pmid = {39066964},
issn = {1559-0720},
support = {1/0602/22//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; },
mesh = {*Fruiting Bodies, Fungal/chemistry/metabolism ; Trace Elements/analysis ; Geographic Information Systems ; Agaricales/chemistry/metabolism ; },
abstract = {The fruiting body of Neoboletus luridiformis (Scarletina bolete) mushroom was used to determine the level of bioconcentration and subsequent distribution of seventeen elements (Ag, Al, Ba, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, Pb, Se, Sr, and Zn). A two-centimeter-thick vertical section of the entire fruit body was divided into 101 partial sub-samples where the contents of the studied elements were determined using ICP OES. The actual distribution of the elements in the fruiting body profile was visualized using a GIS interpolation method resulting in distribution maps. The study provides valuable insights into the distribution patterns of 17 elements within the fruiting body of N. luridiformis. Based on the visualization of the elemental content, the determined elements can be divided into three categories. Elements accumulated primarily (i) in the cap (Al, Ag, Ca, Cd, Cu, Fe, K, Mg, Ni, and Zn), (ii) in the stipe (Ba, Mn, Na, Pb, and Se), and (iii) elements with non-specific distribution (Cr and Sr). Since such detailed information supported by graphical visualization has not been published to date, the information in this study will help to better understand the accumulation and distribution of elements within the fruiting bodies of wild as well as cultivated mushroom species.},
}

*Fruiting Bodies, Fungal/chemistry/metabolism
Trace Elements/analysis
Geographic Information Systems
Agaricales/chemistry/metabolism

@article {pmid40099017,
year = {2025},
author = {Sivell, O and Sivell, D and Mitchell, R and Webb, J and , and , and , and , and , and , and , },
title = {The genome sequence of the Small Red Damselfly, Ceriagrion tenellum (de Villers, 1789).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {79},
pmid = {40099017},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Ceriagrion tenellum (Small Red Damselfly; Arthropoda; Insecta; Odonata; Coenagrionidae). The genome sequence has a total length of 2,077.00 megabases. Most of the assembly (99.28%) is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.21 kilobases in length.},
}

@article {pmid39938845,
year = {2025},
author = {Rakkannan, G and Mohanty, AK and Das, II and Nayak, S and Sahoo, L and Kumar, R and Rasal, A and Rather, MA and Ahmad, I and Sundaray, JK},
title = {Triflumezopyrim induced oxidative stress, DNA damage and apoptosis on Labeo rohita: Insights from Bioinformatics, Histopathological and Molecular approaches.},
journal = {International journal of biological macromolecules},
volume = {304},
number = {Pt 2},
pages = {140911},
doi = {10.1016/j.ijbiomac.2025.140911},
pmid = {39938845},
issn = {1879-0003},
mesh = {Animals ; *Oxidative Stress/drug effects ; *DNA Damage/drug effects ; *Apoptosis/drug effects ; Computational Biology/methods ; Carps/metabolism/genetics ; Water Pollutants, Chemical/toxicity ; Molecular Docking Simulation ; Cyprinidae ; 8-Hydroxy-2'-Deoxyguanosine/metabolism ; Liver/drug effects/pathology/metabolism ; },
abstract = {Triflumezopyrim is a novel mesoionic pesticide used in Asian rice fields to control brown plant hopper, which can reach aquatic environments through drift during application or surface runoff. Thus, this study aimed to investigate the effect of chronic exposure of sub-lethal concentrations of triflumezopyrim (2.468 ppm, 1.480 ppm, and 0.740 ppm) on freshwater carp, Labeo rohita.This study encompassed a multi-pronged approach, including molecular docking studies to elucidate the interactions between triflumezopyrim and selected proteins, an assessment of 8-OHdG (8-hydroxy-2-deoxyguanosine) activity to gauge DNA damage, histopathological examinations to identify cellular alterations, and expression of genes involved in oxidative stress, DNA repair, and apoptosis in L. rohita. We observed dose-dependent responses in 8-OHdG activity and the expression of select genes, with higher concentrations of triflumezopyrim yielding more pronounced transcriptional alterations. Notably, histopathological examinations of liver and brain tissues vividly portrayed the impact of triflumezopyrim on L. rohita. These findings contribute to the assessment of biological toxicity and the environmental footprint left by chemical pollutants such as triflumezopyrim. The study emphasizes the crucial role of monitoring histopathological alterations, 8-OHdG activity and gene expression changes as potential biomarkers for assessing exposures to triflumezopyrim. This research provides valuable insights into the ecological implications of triflumezopyrim in aquatic ecosystems.},
}

Animals
*Oxidative Stress/drug effects
*DNA Damage/drug effects
*Apoptosis/drug effects
Computational Biology/methods
Carps/metabolism/genetics
Water Pollutants, Chemical/toxicity
Molecular Docking Simulation
Cyprinidae
8-Hydroxy-2'-Deoxyguanosine/metabolism
Liver/drug effects/pathology/metabolism

@article {pmid24192328,
year = {2013},
author = {Weston, ED and Whitfield, DP and Travis, JM and Lambin, X},
title = {When do young birds disperse? Tests from studies of golden eagles in Scotland.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {42},
pmid = {24192328},
issn = {1472-6785},
mesh = {*Animal Distribution ; Animals ; Geographic Information Systems ; Raptors/*physiology ; Scotland ; },
abstract = {BACKGROUND: Dispersal comprises three broad stages - departure from the natal or breeding locations, subsequent travel, and settlement. These stages are difficult to measure, and vary considerably between sexes, age classes, individuals and geographically. We used tracking data from 24 golden eagles, fitted with long-lived GPS satellite transmitters as nestlings, which we followed during their first year. We estimated the timing of emigration from natal sites using ten previously published methods. We propose and evaluate two new methods. The first of these uses published ranging distances of parents as a measure of the natal home range, with the requirement that juveniles must exceed it for a minimum of 10 days (a literature-based measure of the maximum time that a juvenile can survive without food from its parents). The second method uses the biggest difference in the proportion of locations inside and outside of the natal home range smoothed over a 30 day period to assign the point of emigration. We used the latter as the standard against which we compared the ten published methods.

RESULTS: The start of golden eagle dispersal occurred from 39 until 250 days after fledging (based on method 12). Previously published methods provided very different estimates of the point of emigration with a general tendency for most to apparently assign it prematurely. By contrast the two methods we proposed provided very similar estimates for the point of emigration that under visual examination appeared to fit the definition of emigration much better.

CONCLUSIONS: We have used simple methods to decide when an individual has dispersed - they are rigorous and repeatable. Despite one method requiring much more information, both methods provided robust estimates for when individuals emigrated at the start of natal dispersal. Considerable individual variation in recorded behaviour appears to account for the difficulty capturing the point of emigration and these results demonstrate the potential pitfalls associated with species exhibiting complex dispersal behaviour. We anticipate that coupled with the rapidly increasing availability of tracking data, our new methods will, for at least some species, provide a far simpler and more biologically representative approach to determine the timing of emigration.},
}

*Animal Distribution
Animals
Geographic Information Systems
Raptors/*physiology
Scotland

@article {pmid23587026,
year = {2013},
author = {Hardisty, A and Roberts, D and , and Addink, W and Aelterman, B and Agosti, D and Amaral-Zettler, L and Ariño, AH and Arvanitidis, C and Backeljau, T and Bailly, N and Belbin, L and Berendsohn, W and Bertrand, N and Caithness, N and Campbell, D and Cochrane, G and Conruyt, N and Culham, A and Damgaard, C and Davies, N and Fady, B and Faulwetter, S and Feest, A and Field, D and Garnier, E and Geser, G and Gilbert, J and Grosche, and Grosser, D and Hardisty, A and Herbinet, B and Hobern, D and Jones, A and de Jong, Y and King, D and Knapp, S and Koivula, H and Los, W and Meyer, C and Morris, RA and Morrison, N and Morse, D and Obst, M and Pafilis, E and Page, LM and Page, R and Pape, T and Parr, C and Paton, A and Patterson, D and Paymal, E and Penev, L and Pollet, M and Pyle, R and von Raab-Straube, E and Robert, V and Roberts, D and Robertson, T and Rovellotti, O and Saarenmaa, H and Schalk, P and Schaminee, J and Schofield, P and Sier, A and Sierra, S and Smith, V and van Spronsen, E and Thornton-Wood, S and van Tienderen, P and van Tol, J and Tuama, ÉÓ and Uetz, P and Vaas, L and Vignes Lebbe, R and Vision, T and Vu, D and De Wever, A and White, R and Willis, K and Young, F},
title = {A decadal view of biodiversity informatics: challenges and priorities.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {16},
pmid = {23587026},
issn = {1472-6785},
mesh = {Animals ; *Biodiversity ; Computational Biology/*instrumentation/*methods ; Ecosystem ; Humans ; Information Dissemination ; },
abstract = {Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.},
}

Animals
*Biodiversity
Computational Biology/*instrumentation/*methods
Ecosystem
Humans
Information Dissemination

@article {pmid23497177,
year = {2013},
author = {Tonk, L and Bongaerts, P and Sampayo, EM and Hoegh-Guldberg, O},
title = {SymbioGBR: a web-based database of Symbiodinium associated with cnidarian hosts on the Great Barrier Reef.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {7},
pmid = {23497177},
issn = {1472-6785},
mesh = {Animals ; Anthozoa/*microbiology ; Australia ; *Coral Reefs ; DNA, Ribosomal Spacer/genetics ; *Databases, Genetic ; Dinoflagellida/classification/*genetics ; Genetic Markers ; Internet ; Sequence Analysis, DNA ; Symbiosis ; User-Computer Interface ; },
abstract = {BACKGROUND: The algal endosymbionts (genus Symbiodinium) associated with scleractinian corals (and other reef invertebrates) have received a lot of research attention in the past decade, particularly as certain host-symbiont associations appear more affected by increasing seawater temperatures than others. With the rapid accumulation of information on the diversity of Symbiodinium, it is becoming increasingly difficult to compare newly acquired Symbiodinium data with existing data to detect patterns of host-symbiont specificity on broader spatial scales. The lack of a general consensus on the classification of Symbiodinium species coupled with the variety of different markers used to identify the genus Symbiodinium (ITS1, ITS2, LSU D1/D2, chloroplast 23S rDNA and psbA minicircle) further complicate direct comparison.

DESCRIPTION: The SymbioGBR database compiles all currently available Symbiodinium sequences and associated host information of data collected from the Great Barrier Reef into a single relational database that is accessible via a user-friendly, searchable web-based application (http://www.SymbioGBR.org). SymbioGBR allows users to query Symbiodinium types or sequences sourced from various genetic markers (e.g. ITS1, ITS2, LSU D1/D2 and chloroplast 23S) and invertebrate host species to explore their reported associations. In addition, as the database includes sequence information of multiple genetic markers, it allows cross-referencing between conventional (e.g. ITS2 region) and novel markers that exhibit low intragenomic variability (e.g. psbA region). Finally, the database is based on the collection details of individual specimens. Such host-symbiont associations can be assessed quantitatively and viewed in relation to their environmental and geographic context.

CONCLUSIONS: The SymbioGBR database provides a comprehensive overview of Symbiodinium diversity and host-associations on the Great Barrier Reef. It provides a quick, user-friendly means to compare newly acquired data on Symbiodinium (e.g. raw sequences or characterized Symbiodinium types) with previous data on the diversity of invertebrate host-symbiont associations on the GBR. The inclusion of psbAncr sequence information allows for validation of widely used ITS1/ITS2 markers and their ability to accurately identify relevant sequences. Most importantly, centralization of sequence information from multiple genetic markers will aid the classification of Symbiodinium species diversity and allow researchers to easily compare patterns of host-Symbiodinium associations.},
}

Animals
Anthozoa/*microbiology
Australia
*Coral Reefs
DNA, Ribosomal Spacer/genetics
*Databases, Genetic
Dinoflagellida/classification/*genetics
Genetic Markers
Internet
Sequence Analysis, DNA
Symbiosis
User-Computer Interface

@article {pmid23173946,
year = {2012},
author = {Renaud, AK and Savage, J and Adamowicz, SJ},
title = {DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits.},
journal = {BMC ecology},
volume = {12},
number = {},
pages = {24},
pmid = {23173946},
issn = {1472-6785},
mesh = {Animals ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Female ; Genes, Insect ; Male ; Muscidae/*classification/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate "species" diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues.

RESULTS: Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected.

CONCLUSIONS: Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.},
}

Animals
Cluster Analysis
*DNA Barcoding, Taxonomic
*Databases, Genetic
Female
Genes, Insect
Male
Muscidae/*classification/genetics
Sequence Analysis, DNA
Species Specificity

@article {pmid23095476,
year = {2012},
author = {Sherwood, AR and Wang, N and Carlile, AL and Neumann, JM and Wolfgruber, TK and Presting, GG},
title = {The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource.},
journal = {BMC ecology},
volume = {12},
number = {},
pages = {22},
pmid = {23095476},
issn = {1472-6785},
mesh = {*Biodiversity ; *Chlorophyta ; *Clinical Laboratory Information Systems ; *Cyanobacteria ; *Databases, Factual ; *Diatoms ; Fresh Water ; Hawaii ; Internet ; *Rhodophyta ; User-Computer Interface ; },
abstract = {BACKGROUND: Biodiversity databases serve the important role of highlighting species-level diversity from defined geographical regions. Databases that are specially designed to accommodate the types of data gathered during regional surveys are valuable in allowing full data access and display to researchers not directly involved with the project, while serving as a Laboratory Information Management System (LIMS). The Hawaiian Freshwater Algal Database, or HfwADB, was modified from the Hawaiian Algal Database to showcase non-marine algal specimens collected from the Hawaiian Archipelago by accommodating the additional level of organization required for samples including multiple species.

DESCRIPTION: The Hawaiian Freshwater Algal Database is a comprehensive and searchable database containing photographs and micrographs of samples and collection sites, geo-referenced collecting information, taxonomic data and standardized DNA sequence data. All data for individual samples are linked through unique 10-digit accession numbers ("Isolate Accession"), the first five of which correspond to the collection site ("Environmental Accession"). Users can search online for sample information by accession number, various levels of taxonomy, habitat or collection site. HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011. At the present time the database houses data for over 2,825 samples of non-marine algae from 1,786 collection sites from the Hawaiian Archipelago. These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages.

CONCLUSIONS: HfwADB is a digital repository that acts as a Laboratory Information Management System for Hawaiian non-marine algal data. Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and micrographs, and DNA sequences. It is publicly available at http://algae.manoa.hawaii.edu/hfwadb/.},
}

*Biodiversity
*Chlorophyta
*Clinical Laboratory Information Systems
*Cyanobacteria
*Databases, Factual
*Diatoms
Fresh Water
Hawaii
Internet
*Rhodophyta
User-Computer Interface

@article {pmid21929792,
year = {2011},
author = {Gonzalez, SC and Soto-Centeno, JA and Reed, DL},
title = {Population distribution models: species distributions are better modeled using biologically relevant data partitions.},
journal = {BMC ecology},
volume = {11},
number = {},
pages = {20},
pmid = {21929792},
issn = {1472-6785},
mesh = {Animals ; Geographic Information Systems ; Mice/genetics/*physiology ; *Models, Biological ; *Population Dynamics ; ROC Curve ; Southeastern United States ; Statistics as Topic ; },
abstract = {BACKGROUND: Predicting the geographic distribution of widespread species through modeling is problematic for several reasons including high rates of omission errors. One potential source of error for modeling widespread species is that subspecies and/or races of species are frequently pooled for analyses, which may mask biologically relevant spatial variation within the distribution of a single widespread species. We contrast a presence-only maximum entropy model for the widely distributed oldfield mouse (Peromyscus polionotus) that includes all available presence locations for this species, with two composite maximum entropy models. The composite models either subdivided the total species distribution into four geographic quadrants or by fifteen subspecies to capture spatially relevant variation in P. polionotus distributions.

RESULTS: Despite high Area Under the ROC Curve (AUC) values for all models, the composite species distribution model of P. polionotus generated from individual subspecies models represented the known distribution of the species much better than did the models produced by partitioning data into geographic quadrants or modeling the whole species as a single unit.

CONCLUSIONS: Because the AUC values failed to describe the differences in the predictability of the three modeling strategies, we suggest using omission curves in addition to AUC values to assess model performance. Dividing the data of a widespread species into biologically relevant partitions greatly increased the performance of our distribution model; therefore, this approach may prove to be quite practical and informative for a wide range of modeling applications.},
}

Animals
Geographic Information Systems
Mice/genetics/*physiology
*Models, Biological
*Population Dynamics
ROC Curve
Southeastern United States
Statistics as Topic

@article {pmid17900366,
year = {2007},
author = {Blundell, AG and Burkey, TV},
title = {A database of schemes that prioritize sites and species based on their conservation value: focusing business on biodiversity.},
journal = {BMC ecology},
volume = {7},
number = {},
pages = {10},
pmid = {17900366},
issn = {1472-6785},
mesh = {Animals ; *Biodiversity ; Birds ; Conservation of Natural Resources/*methods ; *Databases, Factual ; Plants ; Wetlands ; },
abstract = {BACKGROUND: Biodiversity offsets are conservation projects used mainly by business to counterbalance the environmental impacts of their operations, with the aim of achieving a net neutral or even beneficial outcome for biodiversity. Companies considering offsets need to know: (1) if there are areas of such biological importance that no impact is acceptable, and outside of these no-go areas, (2) the relative importance of biodiversity in the impacted site versus the site(s) proposed for protection, to ensure that the offset is of equal or greater status than that lost through the company's operations. We compiled a database of 40 schemes that use various methods to assess conservation priorities, and we examined if the schemes would allow companies to answer the above questions.

DESCRIPTION: Overall, schemes tend to be designed to guide conservation organizations in their own priority setting or they categorize species based on conservation status. Generally, the schemes do not provide all the necessary information for offsets because they operate at a broad spatial scale or with low spatial resolution, which make it difficult to assess sites at the project level. Furthermore, most schemes do not explicitly incorporate threat, which we consider key to assessing whether offsets protect habitats or species that would otherwise be lost (i.e., provide additionality). The schemes are useful, however, for identifying the major conservation issues in different ecosystems around the globe.

CONCLUSION: Companies can proceed by first avoiding, reducing, and mitigating impacts, and then using existing schemes to identify i) no-go areas and ii) appropriate offsets to compensate for any unavoidable loss in biodiversity. If existing schemes are inadequate, then companies should use integrated conservation planning techniques to define offset options within the region of their operations.},
}

Animals
*Biodiversity
Birds
Conservation of Natural Resources/*methods
*Databases, Factual
Plants
Wetlands

@article {pmid17144922,
year = {2006},
author = {Johnson, K and Neville, TB and Neville, P},
title = {GIS habitat analysis for lesser prairie-chickens in southeastern New Mexico.},
journal = {BMC ecology},
volume = {6},
number = {},
pages = {18},
pmid = {17144922},
issn = {1472-6785},
mesh = {Agriculture ; Animals ; *Conservation of Natural Resources ; *Ecosystem ; *Galliformes ; *Geographic Information Systems ; Herbicides ; New Mexico ; },
abstract = {BACKGROUND: We conducted Geographic Information System (GIS) habitat analyses for lesser prairie-chicken (LPCH, Tympanuchus pallidicinctus) conservation planning. The 876,799 ha study area included most of the occupied habitat for the LPCH in New Mexico. The objectives were to identify and quantify: 1. suitable LPCH habitat in New Mexico, 2. conversion of native habitats, 3. potential for habitat restoration, and 4. unsuitable habitat available for oil and gas activities.

RESULTS: We found 16% of suitable habitat (6% of the study area) distributed in 13 patches of at least 3,200 ha and 11% of suitable habitat (4% of the study area) distributed in four patches over 7,238 ha. The area converted from native vegetation types comprised 17% of the study area. Ninety-five percent of agricultural conversion occurred on private lands in the northeastern corner of the study area. Most known herbicide-related conversions (82%) occurred in rangelands in the western part of the study area, on lands managed primarily by the US Bureau of Land Management (BLM). We identified 88,190 ha (10% of the study area) of habitats with reasonable restoration potential. Sixty-two percent of the primary population area (PPA) contained occupied, suitable, or potentially suitable habitat, leaving 38% that could be considered for oil and gas development.

CONCLUSION: Although suitable LPCH habitat appears at first glance to be abundant in southeastern New Mexico, only a fraction of apparently suitable vegetation types constitute quality habitat. However, we identified habitat patches that could be restored through mesquite control or shin-oak reintroduction. The analysis also identified areas of unsuitable habitat with low restoration potential that could be targeted for oil and gas exploration, in lieu of occupied, high-quality habitats. Used in combination with GIS analysis and current LPCH population data, the habitat map represents a powerful conservation and management tool.},
}

Agriculture
Animals
*Conservation of Natural Resources
*Ecosystem
*Galliformes
*Geographic Information Systems
Herbicides
New Mexico

@article {pmid40088887,
year = {2025},
author = {Hartley, GA and Okhovat, M and Hoyt, SJ and Fuller, E and Pauloski, N and Alexandre, N and Alexandrov, I and Drennan, R and Dubocanin, D and Gilbert, DM and Mao, Y and McCann, C and Neph, S and Ryabov, F and Sasaki, T and Storer, JM and Svendsen, D and Troy, W and Wells, J and Core, L and Stergachis, A and Carbone, L and O'Neill, RJ},
title = {Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100808},
doi = {10.1016/j.xgen.2025.100808},
pmid = {40088887},
issn = {2666-979X},
abstract = {Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here, we characterize fully assembled centromeres in the eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha-satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence that this epigenetic feature is conserved in the absence of satellite arrays. We uncovered a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, we identify duplications and deletions in HLE centromeres that distinguish them from other gibbons. Finally, we observed differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, and thus propose that a combination of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.},
}

@article {pmid40087683,
year = {2025},
author = {Mbuba, E and Mañas-Chavernas, N and Moore, SJ and Ruzige, PD and Kobe, D and Moore, J and Philipo, R and Kisoka, N and Pontiggia, G and Chacky, F and Mwalimu, CD and Cattin, PC and Wolleb, J and Sandkuehler, R and Ross, A},
title = {Estimating the hole surface area of insecticide-treated nets using image analysis, manual hole counting and exact hole measurements.},
journal = {Malaria journal},
volume = {24},
number = {1},
pages = {82},
pmid = {40087683},
issn = {1475-2875},
mesh = {*Image Processing, Computer-Assisted/methods ; *Insecticide-Treated Bednets/statistics & numerical data ; Mosquito Control/methods ; Animals ; Insecticides ; },
abstract = {BACKGROUND: The physical integrity of insecticidal-treated nets (ITNs) is important for creating a barrier against host-seeking mosquitoes and, therefore, influences people's perception of the net's effectiveness and their willingness to use it. Monitoring the physical integrity of ITNs over time provides information for replenishment schedules and purchasing decisions. Currently, the assessment of physical integrity of ITNs is conducted by manually counting holes and estimating their size to class the net as functional or not. This approach is laborious to routinely conduct during field surveys of ITNs. Automated image analysis may provide a rapid assessment of the physical integrity of ITNs but it is not known if the images can capture sufficient information. As a first step, this study aimed to assess the agreement between estimated hole surface areas derived from (1) manually segmented images, (2) manual hole counting compared to (3) ground truth obtained by calibrated close-up shots of individual holes.

METHODS: The physical integrity of 75 ITNs purposely selected from an ongoing study was assessed by manual hole counting, image analysis and ground truth. For the image analysis, a graphical user interface was developed and used for the segmentation of holes visible in photographs taken from each side of the net. The hole surface area was then computed from this data. The agreement between the estimates from image analysis and manual hole counting was compared to the ground truth using the Bland-Altman method.

RESULTS: There was substantial agreement between the manually segmented image analysis estimates and the ground truth hole surface areas. The overall bias was small, with a mean ratio of the hole surface area from image analysis to the ground truth of 0.70, and the 95% limits of agreement ranging from 0.35 to 1.38. Manual hole counting underestimated the hole surface area compared to the ground truth, particularly among nets with holes above 10 cm in diameter.

CONCLUSION: Images coupled with manual segmentation contain sufficient information to calculate hole surface area. This lays the groundwork for incorporating automatic hole detection, and then assessing whether this method will offer a fast and objective method for routine assessment of physical integrity of ITNs. While the WHO method underestimated the hole surface area, it remains useful in classifying nets as either serviceable or too torn because the cut-off is specific to this method.},
}

*Image Processing, Computer-Assisted/methods
*Insecticide-Treated Bednets/statistics & numerical data
Mosquito Control/methods
Animals
Insecticides

@article {pmid40086213,
year = {2025},
author = {Dong, L and Mu, L and Huang, X},
title = {Exploring lipid remodeling and antioxidant responses in Chlorella pyrenoidosa exposed to streptomycin sulfate stress.},
journal = {Food chemistry},
volume = {478},
number = {},
pages = {143565},
doi = {10.1016/j.foodchem.2025.143565},
pmid = {40086213},
issn = {1873-7072},
abstract = {Microalgae, particularly Chlorella pyrenoidosa, are valuable for bioactive compounds and biofuel production, but antibiotic use in large-scale cultivation can impact growth and biochemical productivity. This study examines the physiological and molecular responses of C. pyrenoidosa to streptomycin sulfate (STRS) stress. STRS exposure significantly reduced cell density (15.31 × 10[6] to 11.20 × 10[6] cells/mL, p < 0.001) and photosynthetic efficiency (Fv/fm from 0.45 to 0.15). Multi-omics analysis revealed a dual adaptive strategy: (1) activation of antioxidant defenses, including upregulated superoxide dismutase (SOD, 19-fold) and ascorbate peroxidase (APX, 32-fold); (2) lipid remodeling, with increased α-linolenic acid (ALA) content (17.43 % to 21.25 %, p < 0.001) due to β-oxidation downregulation. These findings enhance understanding of microalgal stress adaptation and highlight potential applications in biofuel and food/feed industries. Future studies should optimize genetic and cultivation strategies to enhance these adaptive traits while ensuring ecological sustainability.},
}

@article {pmid40074806,
year = {2025},
author = {Tang, Y and Hu, H and Chen, S and Hao, B and Xu, X and Zhu, H and Zhan, W and Zhang, T and Hu, H and Chen, G},
title = {Multi-omics analysis revealed the novel role of NQO1 in microenvironment, prognosis and immunotherapy of hepatocellular carcinoma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8591},
pmid = {40074806},
issn = {2045-2322},
support = {24B0413//the Scientific Research Project of the Hunan Provincial Department of Education/ ; 2024JJ7455//Natural Science Foundation of Hunan Province/ ; 20224310NHYCG04//University of South China Clinical Research 4310 Program/ ; 20224310NHYCG01//University of South China Clinical Research 4310 Program/ ; 82473965//National Natural Science Foundation of China/ ; 2023JJ50156//the Natural Science Foundation of Hunan Province/ ; 202250045223//Science and technology innovation Program of Hengyang City/ ; ZYYD2024CG17//Central Government Guided Local Science and Technology Development Fund Project in Xinjiang Uygur Autonomous Region/ ; 2024WK4008//Hunan Province Innovation Ecological Construction Plan Science and Technology Assistance Project in Xinjiang Uygur Autonomous Region/ ; SYTG-Y202429//Health Technology Promotion Project in Xinjiang Uygur Autonomous Region/ ; },
mesh = {*Carcinoma, Hepatocellular/therapy/genetics/immunology/pathology ; *NAD(P)H Dehydrogenase (Quinone)/genetics/metabolism ; Humans ; *Liver Neoplasms/therapy/genetics/immunology/pathology ; *Tumor Microenvironment/immunology ; Prognosis ; *Immunotherapy/methods ; Gene Expression Regulation, Neoplastic ; Biomarkers, Tumor/genetics ; Male ; Female ; Nomograms ; Tumor-Associated Macrophages/immunology/metabolism ; Middle Aged ; Multiomics ; },
abstract = {NAD(P)H dehydrogenase quinone 1 (NQO1) is overexpressed in various cancers and is strongly associated with an immunosuppressive microenvironment and poor prognosis. In this study, we explored the role of NQO1 in the microenvironment, prognosis and immunotherapy of Hepatocellular carcinoma (HCC) using multi-omics analysis and machine learning. The results revealed that NQO1 was significantly overexpressed in HCC cells. NQO1[+]HCC cells were correlated with poor prognosis and facilitated tumor-associated macrophages (TAMs) polarization to M2 macrophages. We identified core NQO1-related genes (NRGs) and developed the NRGs-related risk-scores in hepatocellular carcinoma (NRSHC). The comprehensive nomogram integrating NRSHC, age, and pathological tumor-node-metastasis (pTNM) Stage achieved an area under the curve (AUC) above 0.7, demonstrating its accuracy in predicting survival outcomes and immunotherapy responses of HCC patients. High-risk patients exhibited worse prognoses but greater sensitivity to immunotherapy. Additionally, a web-based prediction tool was designed to enhance clinical utility. In conclusion, NQO1 may play a critical role in M2 polarization and accelerates HCC progression. The NRSHC model and accompanying tools offer valuable insights for personalized HCC treatment.},
}

*Carcinoma, Hepatocellular/therapy/genetics/immunology/pathology
*NAD(P)H Dehydrogenase (Quinone)/genetics/metabolism
Humans
*Liver Neoplasms/therapy/genetics/immunology/pathology
*Tumor Microenvironment/immunology
Prognosis
*Immunotherapy/methods
Gene Expression Regulation, Neoplastic
Biomarkers, Tumor/genetics
Male
Female
Nomograms
Tumor-Associated Macrophages/immunology/metabolism
Middle Aged
Multiomics

@article {pmid40074756,
year = {2025},
author = {Wei, P and Song, Y and Tian, R and Wang, Y and Chen, J and Yuan, Z and Zhou, W},
title = {CaecilianTraits, an individual level trait database of Caecilians worldwide.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {428},
pmid = {40074756},
issn = {2052-4463},
support = {32170445//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Amphibians/classification ; Animals ; *Databases, Factual ; Biodiversity ; Biological Evolution ; },
abstract = {Functional traits differ among species, which determine the ecological niche a species occupies and its ability to adapt to environment. However, differences in traits also exist at intraspecific level. Such variations shape differences in individual survival capabilities. Investigating intraspecific differences of functional traits is important for ecology, evolutionary biology and biodiversity conservation. Individual trait-based approaches have been applied in plant ecology. But for animals, most databases only provide data at the species level. In this study, we presented a global database of morphological traits for caecilians (Amphibia, Gymnophiona) at both species and individual level. Caecilians are a unique group of amphibians characterized by their secretive habits, which have limited our understanding of this taxon. We compiled the most comprehensive database covering 218 out of 222 known species, with 215 of them have individual level data. This database will facilitate research in the ecology, evolutionary biology, conservation biology, and taxonomy of caecilians. Furthermore, this dataset can be utilized to test ecological and evolutionary hypotheses at the individual level.},
}

*Amphibians/classification
Animals
*Databases, Factual
Biodiversity
Biological Evolution

@article {pmid40070804,
year = {2025},
author = {Vršanský, P and Sendi, H and Kotulová, J and Szwedo, J and Havelcová, M and Palková, H and Vršanská, L and Sakala, J and Puškelová, L and Golej, M and Biroň, A and Peyrot, D and Quicke, D and Néraudeau, D and Uher, P and Maksoud, S and Azar, D},
title = {Jurassic Park approached: a coccid from Kimmeridgian cheirolepidiacean Aintourine Lebanese amber.},
journal = {National science review},
volume = {12},
number = {3},
pages = {nwae200},
pmid = {40070804},
issn = {2053-714X},
abstract = {With the exception of a fly and a mite from the Triassic of Italy, all Mesozoic amber arthropods are from the Cretaceous. Late Jurassic Lebanese amber from Aintourine revealed a completely preserved adult coccid male (wing length 0.8 mm), Jankotejacoccus libanogloria gen. et sp. n., the earliest record of a plant sucking scale insect. Associated plant material included the cheirolepidiaceans Protopodocarpoxylon, Brachyphyllum and Classostrobus, plus Classopolis pollen, suggesting a forested temporary swamp habitat with ferns, tree ferns, water ferns, tall araucarian and ginkgoacean trees and shrubs. (Sub)tropic lateritic soil with vegetation debris underwent incomplete microbial decomposition in an anoxic water environment of peat swamp development. Strata-associated marine organisms support the Kimmeridgian age revealed by zircons. The discovery opens a new field of research in Jurassic amber fossils.},
}

@article {pmid40069723,
year = {2025},
author = {Pieroni, A and Zocchi, DM and Alrhmoun, M and Sulaiman, N and Bavorova, M and Sõukand, R},
title = {Not "just necessity"? Two-x-eco-cultural dilemmas and the ethnobiological importance of the informal grannies' markets in Moldova.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {21},
number = {1},
pages = {17},
pmid = {40069723},
issn = {1746-4269},
support = {714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; },
mesh = {Moldova ; Humans ; Female ; *Commerce ; Food Supply ; Conservation of Natural Resources ; Middle Aged ; Agriculture ; Rural Population ; Culture ; Anthropology, Cultural ; Aged ; Biodiversity ; },
abstract = {Informal food markets, particularly those managed by (elderly) women in post-communist Eastern Europe, represent a biocultural phenomenon of profound significance since globalisation and increasingly strict legal frameworks often threaten these reservoirs of biocultural food heritage. In the fall of 2022 and 2023, a preliminary field study was conducted by visiting the informal markets of six Moldovan centres: Chișinău, Orhei, Bălți, Călărași, Comrat, and Taraclia, and conversing with approximately 40 mid-aged and elderly sellers. We argue that these markets are crucial in sustaining small-scale farming, preserving biodiversity, and maintaining a connection between urban communities and rural communities and, ultimately, between these rural citizens and their nature, keeping small-scale family farming and domestic traditional gastronomic activities alive. By trading fresh, homegrown, and homemade food and goods (including handicrafts), these mid-aged and elderly vendors support local economies, promote environmental sustainability, and safeguard traditional ecological knowledge and cultural heritage. This paper explores how grannies' markets contribute to biocultural diversity and sustainable food practices, especially amid the country's recent turbulent political, socioeconomic, and demographic challenges. The analysis advocates for the survival rights of these ecological, economic, and cultural (2-x-eco-cultural) refugia and invites ethnobiologists, food studies and cultural heritage scholars, rural sociologists, and agricultural economists to defend the biocultural diversity of informal food markets, moving them from an "out of necessity" status to a solid pillar of a possible future, new, family farming and small-scale ecological and gastronomic (conscientious) tourism. Policymakers should protect and enhance these informal spaces, especially the socioecological farming systems behind them, as essential socioeconomic and environmental assets. They should emphasise their importance as hubs for biological diversity, cultural preservation, community cohesion, and ecological sustainability.},
}

Moldova
Humans
Female
*Commerce
Food Supply
Conservation of Natural Resources
Middle Aged
Agriculture
Rural Population
Culture
Anthropology, Cultural
Aged
Biodiversity

@article {pmid40066908,
year = {2025},
author = {Weeks, F and Myerson, R and Gangnon, R and Dykema, J and Cornelius, C and Green, T},
title = {Intrapartum Care Experiences Associated With Postpartum Visit Attendance.},
journal = {Birth (Berkeley, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1111/birt.12910},
pmid = {40066908},
issn = {1523-536X},
support = {//Wisconsin Alumni Research Foundation/ ; },
abstract = {INTRODUCTION: The postpartum visit is an important opportunity to prevent pregnancy-related morbidity and mortality; however, about 1 in 10 birthing people do not attend this visit. Intrapartum care experiences are an understudied factor that may contribute to postpartum healthcare engagement.

MATERIALS AND METHODS: We analyze data from a novel survey supplement on intrapartum care experiences administered to a probability-based population sample of people who have recently given birth through the Wisconsin Pregnancy Risk Assessment Monitoring System.

RESULTS: In regression models adjusting for a robust set of individual characteristics and birth hospital clustering, we find that lower provider responsiveness during intrapartum care is associated with increased odds of forgoing the postpartum visit (aOR 1.4, 95% CI 1.0-2.0).

DISCUSSION: The quality of care received during the birth hospitalization may shape how birthing people feel about health care providers and their willingness to attend future visits. Experiences of care during the intrapartum period may contribute to future health care utilization. Improving these experiences is an opportunity to promote long-term health.},
}

@article {pmid40064850,
year = {2025},
author = {Roman, J and Abraham, AJ and Kiszka, JJ and Costa, DP and Doughty, CE and Friedlaender, A and Hückstädt, LA and Marcondes, M and Wetsel, E and Pershing, AJ},
title = {Migrating baleen whales transport high-latitude nutrients to tropical and subtropical ecosystems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2125},
pmid = {40064850},
issn = {2041-1723},
mesh = {Animals ; *Animal Migration/physiology ; *Ecosystem ; *Whales/physiology/metabolism ; *Nutrients/metabolism ; Tropical Climate ; Seasons ; Nitrogen/metabolism ; Biomass ; Female ; },
abstract = {Baleen whales migrate from productive high-latitude feeding grounds to usually oligotrophic tropical and subtropical reproductive winter grounds, translocating limiting nutrients across ecosystem boundaries in their bodies. Here, we estimate the latitudinal movement of nutrients through carcasses, placentas, and urea for four species of baleen whales that exhibit clear annual migration, relying on spatial data from publicly available databases, present and past populations, and measurements of protein catabolism and other sources of nitrogen from baleen whales and other marine mammals. Migrating gray, humpback, and North Atlantic and southern right whales convey an estimated 3784 tons N yr[-1] and 46,512 tons of biomass yr[-1] to winter grounds, a flux also known as the "great whale conveyor belt"; these numbers might have been three times higher before commercial whaling. We discuss how species recovery might help restore nutrient movement by whales in global oceans and increase the resilience and adaptative capacity of recipient ecosystems.},
}

Animals
*Animal Migration/physiology
*Ecosystem
*Whales/physiology/metabolism
*Nutrients/metabolism
Tropical Climate
Seasons
Nitrogen/metabolism
Biomass
Female

@article {pmid40064777,
year = {2025},
author = {Crespo-Bellido, A and Martin, DP and Duffy, S},
title = {Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2912},
number = {},
pages = {125-143},
pmid = {40064777},
issn = {1940-6029},
mesh = {*Geminiviridae/genetics ; *Recombination, Genetic ; Software ; Algorithms ; Sequence Alignment ; Genome, Viral ; Evolution, Molecular ; Computational Biology/methods ; Phylogeny ; },
abstract = {Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.},
}

*Geminiviridae/genetics
*Recombination, Genetic
Software
Algorithms
Sequence Alignment
Genome, Viral
Evolution, Molecular
Computational Biology/methods
Phylogeny

@article {pmid40063696,
year = {2025},
author = {Smith, LB and Ahlich, E and Lang, B and Bollepalli, S and Prioleau, T and Bartolome, A and Hughes Lansing, A and Rancourt, D},
title = {Glycemic variability and weight-focused eating behaviors among adolescents and young adults with type 1 diabetes†.},
journal = {Journal of pediatric psychology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpepsy/jsaf009},
pmid = {40063696},
issn = {1465-735X},
support = {//Dexcom, Inc/ ; },
abstract = {OBJECTIVE: Type 1 diabetes (T1D) disease management and associated glycemic fluctuations can disrupt experiences of hunger and satiety, which may increase risk for disordered eating behaviors. Glycemic variability may be a useful trigger for just-in-time interventions for disordered eating behaviors. In this exploratory study, we hypothesized that two metrics of glycemic variability would be associated with greater hunger and predict eating behaviors for weight loss or maintenance in adolescents and young adults with T1D.

METHODS: Individuals with T1D were recruited from a university diabetes clinic (N = 34; 50% female, Mage = 19.53 years, MHbA1c = 7.98%; 29% Hispanic/Latinx; 79% White). Participants wore a blinded continuous glucose monitor for 5 days, and completed ecological momentary assessments (four prompts per day) that included measures of hunger and eating behaviors for weight loss or maintenance purposes. Generalized and linear mixed models were used to test hypotheses.

RESULTS: Approximately 30% of participants were at risk for an eating disorder based on Diabetes Eating Problem Survey-Revised scores. Greater glycemic variability did not predict hunger, but was associated with increased odds of endorsing any eating behavior for weight loss or maintenance purposes within-person (ps<.05). Greater hunger was associated with increased odds of endorsing disordered eating behavior within-person (p<.05).

CONCLUSIONS: This exploratory study provides some preliminary evidence that times of greater hunger and glycemic variability may be when individuals with T1D may be at higher risk of engaging in behaviors to lose or maintain weight.},
}

@article {pmid39823836,
year = {2025},
author = {Li, Z and Meng, C and Azad, MAK and Zhu, Q and Lin, W and Cui, Y and Lan, W and He, Q and Kong, X},
title = {Effects of the Salvia miltiorrhiza, Ligustrum lucidum, and Taraxacum mongolicum ultra-fine powder formula on meat quality of aged layers by multi-omics.},
journal = {Poultry science},
volume = {104},
number = {2},
pages = {104783},
pmid = {39823836},
issn = {1525-3171},
mesh = {*Taraxacum/chemistry ; Animals ; *Ligustrum/chemistry ; *Salvia miltiorrhiza/chemistry ; *Meat/analysis ; *Drugs, Chinese Herbal/pharmacology/administration & dosage/chemistry ; *Diet/veterinary ; *Animal Feed/analysis ; *Dietary Supplements/analysis ; *Chickens/physiology ; Female ; Powders/chemistry ; Aging/drug effects ; Multiomics ; },
abstract = {This study was aimed to identify the targets of 1% ultra-fine Chinese medicine formula (UCMF, 0.5% Salvia miltiorrhiza Bge. + 0.25% Ligustrum lucidum Ait. + 0.25% Taraxacum mongolicum Hand.-Mazz.) in delaying aging and explore its impacts on meat quality of aged layers. The effective components of the above three Chinese herbs were screened, and the network pharmacology analysis identified 91 common targets and enriched pathways between herbs and aging. The results showed that cellular response to chemical stimulus, response to oxidative stress, and response to oxygen-containing compound pathways were crucial for UCMF to resist aging. Further in vivo analyses confirmed that UCMF supplementation enhanced the antioxidant function in breast muscles of aged layers by upregulating (P < 0.05) the SOD2 gene expression. Meanwhile, UCMF supplementation reduced (P < 0.05) yellowness (b* value) and drip loss while enhancing (P < 0.05) cooked meat percentage of aged layers. For the health lipid indices in breast muscles, UCMF supplementation increased (P < 0.05) polyunsaturated fatty acids/saturated fatty acids and hypocholesterolemic/hypercholesterolemic ratios and decreased (P < 0.05) the thrombogenic index. The UCMF supplementation optimized the cecal microbiota of aged layers by enhancing the relative abundance of Firmicutes and reducing the relative abundances of Bacteroidetes and Spirochaetes (P < 0.05), which may be related to improving meat quality. In conclusion, dietary UCMF supplementation may be an effective strategy for improving antioxidant function and the meat quality of aged layers.},
}

*Taraxacum/chemistry
Animals
*Ligustrum/chemistry
*Salvia miltiorrhiza/chemistry
*Meat/analysis
*Drugs, Chinese Herbal/pharmacology/administration & dosage/chemistry
*Diet/veterinary
*Animal Feed/analysis
*Dietary Supplements/analysis
*Chickens/physiology
Female
Powders/chemistry
Aging/drug effects
Multiomics

@article {pmid39752826,
year = {2025},
author = {Zhao, X and Jiang, WY and Liu, JJ and Yan, WJ and Zhang, YH and Zhang, Z and Zhang, PD},
title = {Unraveling the impact of PFOA toxicity on Zostera marina using a multi-omics approach: Insights from growth, physiological, transcriptomic, and metabolomic signatures.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {137024},
doi = {10.1016/j.jhazmat.2024.137024},
pmid = {39752826},
issn = {1873-3336},
mesh = {*Caprylates/toxicity ; *Water Pollutants, Chemical/toxicity ; *Transcriptome/drug effects ; *Zosteraceae/genetics/drug effects/metabolism ; *Fluorocarbons/toxicity ; *Metabolomics ; Photosynthesis/drug effects ; Gene Expression Profiling ; Multiomics ; },
abstract = {Perfluorooctanoic acid (PFOA), an anthropogenic organic pollutant known for its persistence, resistance to degradation, and toxicity, has raised significant concerns about its potential ecological impacts. Zostera marina, a common submerged seagrass species in temperate offshore areas, is highly vulnerable to pollutant stressors. However, the impact of PFOA on Z. marina remains unclear. In this study, Z. marina was exposed to different concentrations of PFOA (0, 0.5, 1, 5, 10, and 20 μg/L) for 14 days. We subsequently assessed survival rates, growth patterns, physiological indices, transcriptomic profiles, and metabolomic characteristics. The results revealed dose-dependent PFOA accumulation in Z. marina tissues and significant growth inhibition. Furthermore, exposure to PFOA resulted in a significant reduction in photosynthetic pigment content (IBRv2 indices: 2.78-10.29) and elevated enzyme activity (IBRv2 indices: 2.90-8.96). Transcriptomic analysis identified 1511 differentially expressed genes associated with 11 KEGG pathways predominantly affected by PFOA exposure. Weighted gene co-expression network analysis highlighted the crucial role of the hydroxyphenylpyruvate reductase (hppr) gene in antioxidant defense mechanisms and detoxification processes against PFOA-induced stress. Metabolomics identified 412 differentially expressed metabolites, mainly consisting of flavonoids, organic acids, and lipids. In summary, PFOA exposure resulted in the down-regulation of gene expression related to photosynthesis and energy metabolism while also affecting metabolite synthesis. The response of Z. marina to PFOA stress involves modulation of the cytoskeletal dynamics and signal transduction pathways, as well as activation of a suite of genes and metabolites to initiate defense mechanisms.},
}

*Caprylates/toxicity
*Water Pollutants, Chemical/toxicity
*Transcriptome/drug effects
*Zosteraceae/genetics/drug effects/metabolism
*Fluorocarbons/toxicity
*Metabolomics
Photosynthesis/drug effects
Gene Expression Profiling
Multiomics

@article {pmid39724715,
year = {2025},
author = {Zhang, L and Du, Y and Li, Y and Wang, T and Pan, Y and Xue, X and Mu, X and Qiu, J and Qian, Y},
title = {Mitochondrial mechanism of florfenicol-induced nonalcoholic fatty liver disease in zebrafish using multi-omics technology.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {136958},
doi = {10.1016/j.jhazmat.2024.136958},
pmid = {39724715},
issn = {1873-3336},
mesh = {Animals ; *Zebrafish ; *Non-alcoholic Fatty Liver Disease/chemically induced/metabolism/pathology ; *Thiamphenicol/analogs & derivatives/toxicity ; *Anti-Bacterial Agents/toxicity ; Mitochondria/drug effects/metabolism ; Oxidative Stress/drug effects ; Liver/drug effects/metabolism/pathology ; Metabolomics ; Water Pollutants, Chemical/toxicity ; Energy Metabolism/drug effects ; Lipidomics ; Multiomics ; },
abstract = {Florfenicol (FF), a third-generation chloramphenicol antibiotic widely used in food-producing animals, has become a "pseudopersistent" environmental contaminant, raising concerns about its potential ecological and human health impacts. However, its bioaccumulation behavior and hepatotoxic mechanisms remain poorly understood. This study aims to address these gaps with a 28-day exposure experiment in adult zebrafish at 0.05 and 0.5 mg/L FF. Multiomic analyses (metabolomics, lipidomics, and transcriptomics), combined with histological and mitochondrial function assessments, were employed. Higher bioaccumulation was observed at 0.05 mg/L, potentially due to metabolic saturation at higher concentrations. Histological analysis revealed significant hepatic steatosis (>5 % steatosis area), indicative of moderate nonalcoholic fatty liver disease (NAFLD). Multiomic data demonstrated global dysregulation in energy metabolism, including marked alterations in lipids (accumulation of toxic sphingolipids, excessive fatty acids, and acylglycerol), amino acids, tricarboxylic acid cycle intermediates, and nucleotides. Crucially, mitochondrial dysfunction was identified as a central mechanism, with impaired respiratory chain activities, adenosine triphosphate depletion, elevated reactive oxygen species, and oxidative stress promoting NAFLD progression. These findings highlight mitochondrial impairment and oxidative stress as key drivers of FF-induced hepatotoxicity, providing novel insights into its toxicological mechanisms and emphasizing the ecological risks posed by antibiotic pollution in aquatic systems.},
}

Animals
*Zebrafish
*Non-alcoholic Fatty Liver Disease/chemically induced/metabolism/pathology
*Thiamphenicol/analogs & derivatives/toxicity
*Anti-Bacterial Agents/toxicity
Mitochondria/drug effects/metabolism
Oxidative Stress/drug effects
Liver/drug effects/metabolism/pathology
Metabolomics
Water Pollutants, Chemical/toxicity
Energy Metabolism/drug effects
Lipidomics
Multiomics

@article {pmid40062320,
year = {2025},
author = {Boyes, D and Davis, J and , and , and , and , and , and , },
title = {The genome sequence of the Sandy Carpet moth, Perizoma flavofasciatum (Thunberg, 1792).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {40},
pmid = {40062320},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Perizoma flavofasciatum (Sandy Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 369.30 megabases. Most of the assembly (99.88%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,915 protein-coding genes.},
}

@article {pmid40062319,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Alder Moth, Acronicta alni (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {68},
pmid = {40062319},
issn = {2398-502X},
abstract = {We present a genome assembly from a male Acronicta alni (Alder Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 470.37 megabases and 472.86 megabases. Most of haplotype 1 (98.95%) is scaffolded into 31 chromosomal pseudomolecules, including the Z chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 15.38 kilobases in length.},
}

@article {pmid40061226,
year = {2025},
author = {Ab Kadir, MA and Abdul Manaf, R and Mokhtar, SA and Ismail, LI},
title = {Identifying leptospirosis hotspots in Selangor: uncovering climatic connections using remote sensing and developing a predictive model.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18851},
pmid = {40061226},
issn = {2167-8359},
mesh = {*Leptospirosis/epidemiology ; Humans ; Cross-Sectional Studies ; Malaysia/epidemiology ; *Remote Sensing Technology/methods ; *Geographic Information Systems ; Male ; Female ; Adult ; Adolescent ; Incidence ; Machine Learning ; Middle Aged ; Child ; Young Adult ; Climate Change ; Aged ; Rain ; Child, Preschool ; },
abstract = {BACKGROUND: Leptospirosis is an endemic disease in countries with tropical climates such as South America, Southern Asia, and Southeast Asia. There has been an increase in leptospirosis incidence in Malaysia from 1.45 to 25.94 cases per 100,000 population between 2005 and 2014. With increasing incidence in Selangor, Malaysia, and frequent climate change dynamics, a study on the disease hotspot areas and their association with the hydroclimatic factors could enhance disease surveillance and public health interventions.

METHODS: This ecological cross-sectional study utilised a geographic information system (GIS) and remote sensing techniques to analyse the spatiotemporal distribution of leptospirosis in Selangor from 2011 to 2019. Laboratory-confirmed leptospirosis cases (n = 1,045) were obtained from the Selangor State Health Department. Using ArcGIS Pro, spatial autocorrelation analysis (Moran's I) and Getis-Ord Gi* (hotspot analysis) was conducted to identify hotspots based on the monthly aggregated cases for each subdistrict. Satellite-derived rainfall and land surface temperature (LST) data were acquired from NASA's Giovanni EarthData website and processed into monthly averages. These data were integrated into ArcGIS Pro as thematic layers. Machine learning algorithms, including support vector machine (SVM), Random Forest (RF), and light gradient boosting machine (LGBM) were employed to develop predictive models for leptospirosis hotspot areas. Model performance was then evaluated using cross-validation and metrics such as accuracy, precision, sensitivity, and F1-score.

RESULTS: Moran's I analysis revealed a primarily random distribution of cases across Selangor, with only 20 out of 103 observed having a clustered distribution. Meanwhile, hotspot areas were mainly scattered in subdistricts throughout Selangor with clustering in the central region. Machine learning analysis revealed that the LGBM algorithm had the best performance scores compared to having a cross-validation score of 0.61, a precision score of 0.16, and an F1-score of 0.23. The feature importance score indicated river water level and rainfall contributes most to the model.

CONCLUSIONS: This GIS-based study identified a primarily sporadic occurrence of leptospirosis in Selangor with minimal spatial clustering. The LGBM algorithm effectively predicted leptospirosis hotspots based on the analysed hydroclimatic factors. The integration of GIS and machine learning offers a promising framework for disease surveillance, facilitating targeted public health interventions in areas at high risk for leptospirosis.},
}

*Leptospirosis/epidemiology
Humans
Cross-Sectional Studies
Malaysia/epidemiology
*Remote Sensing Technology/methods
*Geographic Information Systems
Male
Female
Adult
Adolescent
Incidence
Machine Learning
Middle Aged
Child
Young Adult
Climate Change
Aged
Rain
Child, Preschool

@article {pmid40055331,
year = {2025},
author = {Guerrero, PC and Contador, T and Díaz, A and Escobar, C and Orlando, J and Marín, C and Medina, P},
title = {Southern Islands Vascular Flora (SIVFLORA) dataset: A global plant database from Southern Ocean islands.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {397},
pmid = {40055331},
issn = {2052-4463},
mesh = {*Biodiversity ; *Islands ; *Plants ; Databases, Factual ; Ecosystem ; Climate Change ; Oceans and Seas ; },
abstract = {The Southern Islands Vascular Flora (SIVFLORA) dataset is a globally significant, open-access resource that compiles essential biodiversity data on vascular plants from islands across the Southern Ocean. The SIVFLORA dataset was generated through five steps: study area delimitation, compiling the dataset, validating and harmonizing taxonomy, structuring dataset attributes, and establishing file format and open access. Covering major taxonomic divisions, SIVFLORA offers a comprehensive overview of plant occurrences, comprising 14,589 records representing 886 species, 95 families, and 42 orders. This dataset documents that 58.62% of the taxa are native, 9.61% are endemic, and 31.77% are alien species. The Falkland/Malvinas Archipelago, the most species-rich, contrast sharply with less diverse islands like the South Orkney Archipelago. SIVFLORA serves as a taxonomically harmonized, interoperable resource for investigating plant diversity patterns, ecosystem responses to climate change in extreme environments, island biogeography, endemism, and the effects of anthropogenic pressures on Southern Ocean flora.},
}

*Biodiversity
*Islands
*Plants
Databases, Factual
Ecosystem
Climate Change
Oceans and Seas

@article {pmid40055329,
year = {2025},
author = {Ferrer-Paris, JR and Sánchez-Mercado, A and Cornwell, WK and Ooi, M and Tozer, M and Mackenzie, BDE and Woodward, R and Denham, AJ and Auld, TD and Keith, DA},
title = {Fire ecology database for documenting plant responses to fire events in Australia.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {399},
pmid = {40055329},
issn = {2052-4463},
mesh = {*Databases, Factual ; *Fires ; *Plants ; Biodiversity ; Australia ; New South Wales ; },
abstract = {An understanding of fire-response traits is essential for predicting how fire regimes structure plant communities and for informing fire management strategies for biodiversity conservation. Quantification of these traits is complex, encompassing several levels of data abstraction scaling up from field observations of individuals, to general categories of species responses. We developed the Fire Ecology Database to accommodate this complexity. Its conceptual framework is underpinned by a flexible data pipeline enabling links between fire-related trait data and event information at individual, population, and community levels. Key features include: (a) concise and documented trait and method vocabularies; (b) documented uncertainty in observations and aggregation; and (c) documented origin of data including field observations, laboratory experiments, and expert elicitation. We demonstrated application of our framework using data from new field surveys and existing data sets in New South Wales, Australia. The database includes 14 traits for 6,287 plant species derived from 8,936 field work records from 2007 to 2018, 7,054 field records from surveys after 2019, and 48,306 records from 301 existing sources.},
}

*Databases, Factual
*Fires
*Plants
Biodiversity
Australia
New South Wales

@article {pmid40054299,
year = {2025},
author = {Guarischi, M and Montagnani, E and Catalano, G and Saligari, E and Signorini, S and Gori, M},
title = {From motion to interaction: How multisensory information shapes motor behaviors in children with visual impairment.},
journal = {Research in developmental disabilities},
volume = {159},
number = {},
pages = {104956},
doi = {10.1016/j.ridd.2025.104956},
pmid = {40054299},
issn = {1873-3379},
abstract = {BACKGROUND: The ability to move independently enables children to develop perceptual, cognitive, and social interaction skills. Concerning this, vision holds a key role. As a result, children with visual impairment (VI) might be more challenged in their ability to move within their surroundings and interact with their caregivers.

AIM: This study investigated whether the use of multisensory stimuli could influence the motor exploration of children with VI and shape their interaction with the caregivers. For this, the present work examined the variability of children's motor trajectory and the distance between children and caregivers in a setting with and without multisensory cues.

METHODS AND PROCEDURES: A Motion Capture System was used within an ecological playroom environment. The Strange Situation paradigm was simplified and adapted by placing three TechARMs in the corners of the playroom to deliver audio-visual stimuli, used instead of the stranger.

OUTCOMES AND RESULTS: Children with VI showed larger variability within their motor trajectory and kept a shorter distance from the caregivers when multisensory cues were introduced in the playroom.

CONCLUSIONS AND IMPLICATIONS: Multisensory signals were considered unusual and influenced the kinematic parameters. Motor control of the environment was achieved by managing attention flexibility. WHAT DOES THIS PAPER ADD?: This study enriches available evidence about the study of motor and social interaction in children with VI, highlighting how multisensory stimuli could either support or hinder social and motor behaviors. Moreover, enhancing ecological validity could drive progress in the development and application of technological devices to clinical and research setting.},
}

@article {pmid40045231,
year = {2025},
author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD},
title = {Cross-validation for training and testing co-occurrence network inference algorithms.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {74},
pmid = {40045231},
issn = {1471-2105},
support = {2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; },
mesh = {*Algorithms ; *Microbiota ; Computational Biology/methods ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.

RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.

CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.},
}

*Algorithms
*Microbiota
Computational Biology/methods
Bacteria/genetics/classification

@article {pmid39749403,
year = {2025},
author = {Bougiouri, K},
title = {Mind the Gap: A Neural Network Framework for Imputing Genotypes in Non-Model Species.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14066},
doi = {10.1111/1755-0998.14066},
pmid = {39749403},
issn = {1755-0998},
mesh = {*Neural Networks, Computer ; *Genotype ; Genotyping Techniques/methods ; Haplotypes/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Reduced representation sequencing (RRS) has proven to be a cost-effective solution for sequencing subsets of the genome in non-model species for large-scale studies. However, the targeted nature of RRS approaches commonly introduces large amounts of missing data, leading to reduced statistical power and biased estimates in downstream analyses. Genotype imputation, the statistical inference of missing sites across the genome, is a powerful alternative to overcome the caveats associated with missing sites. Typically, genotype imputation requires the presence of a reference panel of haplotypes, however, this is not always feasible for non-model species. In this issue of Molecular Ecology Resources, Mora-Márquez et al. (2024) develop gtImputation, an unsupervised machine learning imputation tool with an interactive GUI, which leverages information from the underlying data structure itself, without the need for a reference panel. They showcase that their method performs equally well and even surpasses existing haplotype-clustering and unsupervised machine learning algorithms, particularly for sites with low minor allele frequency (MAF) and for data sets with strong underlying population structure. This innovative framework adds to the ongoing efforts to expand the applicability of imputation to non-model species, offering the opportunity to apply varied types of analyses requiring dense sets of markers, while also maintaining lower sequencing costs.},
}

*Neural Networks, Computer
*Genotype
Genotyping Techniques/methods
Haplotypes/genetics
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid39739202,
year = {2025},
author = {Bard, NW and Davies, TJ and Cronk, QCB},
title = {Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14056},
doi = {10.1111/1755-0998.14056},
pmid = {39739202},
issn = {1755-0998},
support = {RGPIN-2019-04041//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04439//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Fungi/genetics/classification/isolation & purification ; *Genome, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Plants/microbiology ; DNA, Fungal/genetics ; Endophytes/genetics/classification/isolation & purification ; DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Relatively little is known of the host associations and compatibility of fungal plant pathogens and endophytes. Publicly available plant genomic DNA can be mined to detect incidental fungal DNA, but taxonomic assignment can be challenging due to short lengths and variable discriminative power among different genomic regions and taxa. Here, we introduce a computationally lightweight and accessible Snakemake pipeline for rapid detection and classification (identification and assignment to taxonomic rank) of pathogenic and endophytic fungi (and other fungi associated with plants) that targets the internal transcribed spacer (ITS) region, a fungal barcode standard. We include methods for maximising query sequence length, which gives higher support for ITS1 and ITS2 taxonomic classifications by extending to other fragments of the ITS region and providing taxon-specific local cut-off and confidence scores. We demonstrate our pipeline with a case study using public genomic sequence data for six diverse plant species, including four species within Betula, an ecologically and economically important broadleaved forest tree genus, a shrub and a grass. Our pipeline classified fungi within minutes to a few hours per host individual, with 204 different fungal genera identified at high confidence (≥ 70%). Our pipeline detected and classified pathogenic and endophytic genera known to associate with Betula, and many others with no prior record of association. Our pipeline, leveraging existing sequence data, has several potential applications, including detecting cryptic fungal pathogens and helping characterise the endophytic fungal microbiome, bioprospecting commercially useful fungal species, and determining the plant host range of fungi.},
}

*Fungi/genetics/classification/isolation & purification
*Genome, Plant/genetics
DNA, Ribosomal Spacer/genetics
Plants/microbiology
DNA, Fungal/genetics
Endophytes/genetics/classification/isolation & purification
DNA Barcoding, Taxonomic/methods
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid39611246,
year = {2025},
author = {Armstrong, EE and Li, C and Campana, MG and Ferrari, T and Kelley, JL and Petrov, DA and Solari, KA and Mooney, JA},
title = {A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14048},
doi = {10.1111/1755-0998.14048},
pmid = {39611246},
issn = {1755-0998},
mesh = {*Polymorphism, Single Nucleotide ; *Genetics, Population/methods ; Genotyping Techniques/methods ; Computational Biology/methods ; Animals ; },
abstract = {Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user-friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for a diploid species of conservation concern.},
}

*Polymorphism, Single Nucleotide
*Genetics, Population/methods
Genotyping Techniques/methods
Computational Biology/methods
Animals

@article {pmid39552382,
year = {2025},
author = {Beemelmanns, A and Bouchard, R and Michaelides, S and Normandeau, E and Jeon, HB and Chamlian, B and Babin, C and Hénault, P and Perrot, O and Harris, LN and Zhu, X and Fraser, D and Bernatchez, L and Moore, JS},
title = {Development of SNP Panels from Low-Coverage Whole Genome Sequencing (lcWGS) to Support Indigenous Fisheries for Three Salmonid Species in Northern Canada.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14040},
doi = {10.1111/1755-0998.14040},
pmid = {39552382},
issn = {1755-0998},
support = {//Genome Canada/ ; //Génome Québec/ ; //Ontario Genomics/ ; NST-1718-0036//Polar Knowledge Canada/ ; //Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; IT16149//Mitacs/ ; //Fisheries and Oceans Canada (DFO)/ ; //Ressources Aquatiques Québec (RAQ)/ ; },
mesh = {Animals ; *Polymorphism, Single Nucleotide ; *Fisheries ; *Salmonidae/genetics/classification ; Whole Genome Sequencing/methods ; Genotyping Techniques/methods ; Genotype ; Trout/genetics/classification ; Canada ; Genetics, Population/methods ; Nunavut ; Quebec ; Northwest Territories ; Computational Biology/methods ; },
abstract = {Single nucleotide polymorphism (SNP) panels are powerful tools for assessing the genetic population structure and dispersal of fishes and can enhance management practices for commercial, recreational and subsistence mixed-stock fisheries. Arctic Char (Salvelinus alpinus), Brook Trout (Salvelinus fontinalis) and Lake Whitefish (Coregonus clupeaformis) are among the most harvested and consumed fish species in Northern Indigenous communities in Canada, contributing significantly to food security, culture, tradition and economy. However, genetic resources supporting Indigenous fisheries have not been widely accessible to northern communities (e.g. Inuit, Cree, Dene). Here, we developed Genotyping-in-Thousands by sequencing (GT-seq) panels for population assignment and mixed-stock analyses of three salmonids, to support fisheries stewardship or co-management in Northern Canada. Using low-coverage Whole Genome Sequencing data from 418 individuals across source populations in Cambridge Bay (Nunavut), Great Slave Lake (Northwest Territories), James Bay (Québec) and Mistassini Lake (Québec), we developed a bioinformatic SNP filtering workflow to select informative SNP markers from genotype likelihoods. These markers were then used to design GT-seq panels, thus enabling high-throughput genotyping for these species. The three GT-seq panels yielded an average of 413 autosomal loci and were validated using 525 individuals with an average assignment accuracy of 83%. Thus, these GT-seq panels are powerful tools for assessing population structure and quantifying the relative contributions of populations/stocks in mixed-stock fisheries across multiple regions. Interweaving genomic data derived from these tools with Traditional Ecological Knowledge will ensure the sustainable harvest of three culturally important salmonids in Indigenous communities, contributing to food security programmes and the economy in Northern Canada.},
}

Animals
*Polymorphism, Single Nucleotide
*Fisheries
*Salmonidae/genetics/classification
Whole Genome Sequencing/methods
Genotyping Techniques/methods
Genotype
Trout/genetics/classification
Canada
Genetics, Population/methods
Nunavut
Quebec
Northwest Territories
Computational Biology/methods

@article {pmid39545396,
year = {2025},
author = {Li, J and Gao, Y and Shu, G and Chen, X and Zhu, J and Zheng, S and Chen, T},
title = {HMicroDB: A Comprehensive Database of Herpetofaunal Microbiota With a Focus on Host Phylogeny, Physiological Traits, and Environment Factors.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14046},
doi = {10.1111/1755-0998.14046},
pmid = {39545396},
issn = {1755-0998},
support = {2021YFF1201300//National Key Research and Development Program of China/ ; 2021YFF1201303//National Key Research and Development Program of China/ ; 2022YFC2703105//National Key Research and Development Program of China/ ; 2023M731976//Postdoctoral Research Foundation of China/ ; },
mesh = {*Microbiota/genetics ; Animals ; *Phylogeny ; *Amphibians/microbiology ; *Symbiosis/genetics ; Reptiles/microbiology ; Host Microbial Interactions/genetics ; Databases, Factual ; },
abstract = {Symbiotic microbiota strongly impact host physiology. Amphibians and reptiles occupy a pivotal role in the evolutionary history of Animalia, and they are of significant ecological, economic, and scientific value. Many prior studies have found that symbiotic microbiota in herpetofaunal species are closely associated with host phylogeny, physiological traits, and environmental factors; however, insufficient integrated databases hinder researchers from querying, accessing, and reanalyzing these resources. To rectify this, we built the first herpetofaunal microbiota database (HMicroDB; https://herpdb.com/) that integrates 11,697 microbiological samples from 337 host species (covering 23 body sites and associated with 23 host phenotypic or environmental factors), and we identified 11,084 microbial taxa by consistent annotation. The standardised analysis process, cross-dataset integration, user-friendly interface, and interactive visualisation make the HMicroDB a powerful resource for researchers to search, browse, and explore the relationships between symbiotic microbiota, hosts, and environment. This facilitates research in host-microbiota coevolution, biological conservation, and resource utilisation.},
}

*Microbiota/genetics
Animals
*Phylogeny
*Amphibians/microbiology
*Symbiosis/genetics
Reptiles/microbiology
Host Microbial Interactions/genetics
Databases, Factual

@article {pmid40044867,
year = {2025},
author = {Aguirre-Gutiérrez, J and Rifai, SW and Deng, X and Ter Steege, H and Thomson, E and Corral-Rivas, JJ and Guimaraes, AF and Muller, S and Klipel, J and Fauset, S and Resende, AF and Wallin, G and Joly, CA and Abernethy, K and Adu-Bredu, S and Alexandre Silva, C and de Oliveira, EA and Almeida, DRA and Alvarez-Davila, E and Asner, GP and Baker, TR and Benchimol, M and Bentley, LP and Berenguer, E and Blanc, L and Bonal, D and Bordin, K and Borges de Lima, R and Both, S and Cabezas Duarte, J and Cardoso, D and de Lima, HC and Cavalheiro, L and Cernusak, LA and Dos Santos Prestes, NCC and da Silva Zanzini, AC and da Silva, RJ and Dos Santos Alves da Silva, R and de Andrade Iguatemy, M and De Sousa Oliveira, TC and Dechant, B and Derroire, G and Dexter, KG and Rodrigues, DJ and Espírito-Santo, M and Silva, LF and Domingues, TF and Ferreira, J and Simon, MF and Girardin, CAJ and Hérault, B and Jeffery, KJ and Kalpuzha Ashtamoorthy, S and Kavidapadinjattathil Sivadasan, A and Klitgaard, B and Laurance, WF and Dan, ML and Magnusson, WE and Campos-Filho, EM and Manoel Dos Santos, R and Manzatto, AG and Silveira, M and Marimon-Junior, BH and Martin, RE and Vieira, DLM and Metzker, T and Milliken, W and Moonlight, P and Moraes de Seixas, MM and Morandi, PS and Muscarella, R and Nava-Miranda, MG and Nyirambangutse, B and Silva, JO and Oliveras Menor, I and Francisco Pena Rodrigues, PJ and Pereira de Oliveira, C and Pereira Zanzini, L and Peres, CA and Punjayil, V and Quesada, CA and Réjou-Méchain, M and Riutta, T and Rivas-Torres, G and Rosa, C and Salinas, N and Bergamin, RS and Marimon, BS and Shenkin, A and Silva Rodrigues, PM and Figueiredo, AES and Garcia, QS and Spósito, T and Storck-Tonon, D and Sullivan, MJP and Svátek, M and Vieira Santiago, WT and Arn Teh, Y and Theruvil Parambil Sivan, P and Nascimento, MT and Veenendaal, E and Zo-Bi, IC and Dago, MR and Traoré, S and Patacca, M and Badouard, V and de Padua Chaves E Carvalho, S and White, LJT and Zhang-Zheng, H and Zibera, E and Zwerts, JA and Burslem, DFRP and Silman, M and Chave, J and Enquist, BJ and Barlow, J and Phillips, OL and Coomes, DA and Malhi, Y},
title = {Canopy functional trait variation across Earth's tropical forests.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40044867},
issn = {1476-4687},
abstract = {Tropical forest canopies are the biosphere's most concentrated atmospheric interface for carbon, water and energy[1,2]. However, in most Earth System Models, the diverse and heterogeneous tropical forest biome is represented as a largely uniform ecosystem with either a singular or a small number of fixed canopy ecophysiological properties[3]. This situation arises, in part, from a lack of understanding about how and why the functional properties of tropical forest canopies vary geographically[4]. Here, by combining field-collected data from more than 1,800 vegetation plots and tree traits with satellite remote-sensing, terrain, climate and soil data, we predict variation across 13 morphological, structural and chemical functional traits of trees, and use this to compute and map the functional diversity of tropical forests. Our findings reveal that the tropical Americas, Africa and Asia tend to occupy different portions of the total functional trait space available across tropical forests. Tropical American forests are predicted to have 40% greater functional richness than tropical African and Asian forests. Meanwhile, African forests have the highest functional divergence-32% and 7% higher than that of tropical American and Asian forests, respectively. An uncertainty analysis highlights priority regions for further data collection, which would refine and improve these maps. Our predictions represent a ground-based and remotely enabled global analysis of how and why the functional traits of tropical forest canopies vary across space.},
}

@article {pmid40041564,
year = {2025},
author = {Zhang, J and Qian, H and Wang, X},
title = {An online version and some updates of R package U.Taxonstand for standardizing scientific names in plant and animal species.},
journal = {Plant diversity},
volume = {47},
number = {1},
pages = {166-168},
pmid = {40041564},
issn = {2468-2659},
abstract = {•We present 'U.Taxonstand Online', a user-friendly web application for scientific name matching of both plants and animals.•U.Taxonstand Online provides a solution for the users with limited abilities of programming and data mining.•We add several new functions to clean and format the data for R package U.Taxonstand.},
}

@article {pmid40038315,
year = {2025},
author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C},
title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {378},
pmid = {40038315},
issn = {2052-4463},
support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//École Nationale d'Ingénieurs de Saint-Etienne (National Engineering School of Saint-Étienne)/ ; },
mesh = {China ; *Microbiota ; *Archaea/genetics ; *Bacteria/genetics/classification ; *Bays ; Seawater/microbiology ; Metagenome ; Multiomics ; },
abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.},
}

China
*Microbiota
*Archaea/genetics
*Bacteria/genetics/classification
*Bays
Seawater/microbiology
Metagenome
Multiomics

@article {pmid39990470,
year = {2025},
author = {Edwards, SV and Fang, B and Khost, D and Kolyfetis, GE and Cheek, RG and DeRaad, DA and Chen, N and Fitzpatrick, JW and McCormack, JE and Funk, WC and Ghalambor, CK and Garrison, E and Guarracino, A and Li, H and Sackton, TB},
title = {Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39990470},
issn = {2692-8205},
support = {R01 GM123489/GM/NIGMS NIH HHS/United States ; R01 HG011485/HG/NHGRI NIH HHS/United States ; R35 GM133412/GM/NIGMS NIH HHS/United States ; U01 DA047638/DA/NIDA NIH HHS/United States ; },
abstract = {Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including ~100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.},
}

@article {pmid40034275,
year = {2025},
author = {Veneros, J and Hansen, AJ and Jantz, P and Roberts, D and Noguera-Urbano, E and García, L},
title = {Analysis of changes in temperature and precipitation in South American countries and ecoregions: Comparison between reference conditions and three representative concentration pathways for 2050.},
journal = {Heliyon},
volume = {11},
number = {4},
pages = {e42459},
pmid = {40034275},
issn = {2405-8440},
abstract = {Climate change is a global concern, and its impact on environmental variables such as temperature and annual precipitation is unknown spatially in the desert, andes, and rainforest ecoregions of Peru, Ecuador, and Colombia. In this study, we conducted a general review of climate drivers for South America (SA) and explored climate data using the GCM compareR package (General Circulation Models) and average ensembles for temperature and precipitation. Our results showed that all GCMs demonstrated increases in the annual mean temperature (BIO1) and in the mean temperature of the driest quarter (BIO9) for Peru, Ecuador, and Colombia for 2050 in three RCPs (2.6, 4.5, and 8.5). Also, most of the GCMs showed increases in the annual precipitation (BIO12) and the precipitation in the driest quarter (BIO17). We conducted non-parametric tests (Kruskal-Wallis Test) to assess if the medians of temperature and precipitation in the three ecoregions are equal for both the baseline and the climate change scenarios. We rejected the null hypothesis that the medians are equal for both temperatures and precipitation in the baseline vs. 2050 RCPs (2.6, 4.5, and 8.5). A spatial analysis was conducted to visualize the variations in temperature and precipitation between the RCPs versus the baseline, and the spatial variation at the country or ecoregion level can be observed. The annual mean temperature (°C) or annual precipitation (mm) divided by its standard deviation for each ecoregion (M metric) was analyzed to see how much the average temperature or the annual precipitation is relatively large compared to the variability or dispersion of temperatures or precipitation respectively; the average temperature and the annual precipitation for the baseline and the three RCPs are relatively large and associated with the variability or dispersion of their temperatures in the Napo moist forest compared to the other ecoregions. Our study provides important insights into the potential impacts of climate change on these ecosystems. Prospects in the Napo moist forest ecoregion, where significant changes in temperature and humidity have already occurred, and new species have invaded or evolved in the western Amazon rainforest, are particularly highlighted and reflected in terms of risk mitigation, ecosystem restoration, surveillance, and monitoring.},
}

@article {pmid40033715,
year = {2025},
author = {Gorné, LD and Hendry, AP and Pelletier, F and Sanderson, S and Correa, C and Arias, C and Beausoleil, MO and Boisjoly, M and Crispo, E and Berner, D and De León, LF and DiBattista, JD and Haines, GE and Haller, BC and Kinnison, MT and Muttalib, S and McKellar, AE and O'Dea, RE and Reyes-Corral, WD and Ritchot, Y and Oke, KB and Wood, ZT and Farrugia, T and Gotanda, KM},
title = {PROCEED v6.1: Phenotypic rates of change evolutionary and ecological database.},
journal = {Ecology},
volume = {106},
number = {3},
pages = {e70009},
doi = {10.1002/ecy.70009},
pmid = {40033715},
issn = {1939-9170},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Le Fonds Québécois de la Recherche sur la Nature et les Technologies/ ; //McGill University/ ; //National Science Foundation/ ; //Brock University/ ; },
mesh = {*Biological Evolution ; Animals ; *Phenotype ; *Databases, Factual ; Ecosystem ; },
abstract = {Populations must continuously respond to environmental change or risk extinction. These responses can be measured as phenotypic rates of change, which allow researchers to predict their contemporary evolutionary responses. In 1999, a database of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this database to examine the phenotypic responses as a function of the features of the study system (i.e., the population or set of populations, of a given species, that experienced a specific driver or disturbance), the measured traits, and methodological approaches. Therefore, PROCEED (Phenotypic Rates of Change Evolutionary and Ecological Database) is an ongoing compilation of rates of phenotypic change, typically calculated as Haldanes and Darwins, published in peer-reviewed literature (but also including data from theses and technical reports). Studies in this database measure the intraspecific change in quantitative (continuous or discrete) traits and report either the time elapsed from the onset of environmental novelty, or reference a historical or biological event reported in other sources (e.g., a mine opening or a well-documented biological invasion). Included studies either follow a single population through time (allochronic design) or compare two or more populations that diverged at a known time (synchronic design). Some included studies account for the total phenotypic variability in the field (i.e., phenotypic studies), while others employed common-garden or other quantitative genetic approaches to account for the heritable component of the phenotypic change (i.e., genetic studies). PROCEED includes systems in both natural and experimental conditions, provided that reproduction was not manipulated (i.e., artificial selection experiments were excluded). In the included experimental systems, the environment of the focal populations was manipulated (e.g., an herbivory exclusion experiment, where the type and load of herbivory are manipulated) but the studies did not deliberately select for trait values in the study population (e.g., the plant height). PROCEED does not include systems where the phenotypic change is presumably due to interspecific hybridization, polyploidy, or other chromosomal alterations. Here, we present the most recently updated PROCEED (Version 6.1). This new, curated version has 9263 records (n) collated from 326 studies, 1801 systems, and 428 species. The database includes records belonging to mammals (n = 686), birds (n = 1475), reptiles (n = 96), amphibians (n = 23), fishes (n = 3671), invertebrates (n = 1141, mostly arthropods), and plants (n = 2171). The maximum elapsed time between the environmental change and the sampling is 500 years but is typically less than 100 years (third quartile 89.5; median 45 years). The database also includes a set of variables describing biological and methodological aspects of the study system and measured traits, along with features of the sampling design in the primary source of information. This new version of PROCEED also includes a time series dataset comprising a subset of records included in the general dataset. These are allochronic studies with three or more sampling times throughout the entire study period. The time series dataset contains 655 time series (s)-belonging to 61 studies, from 156 systems, and 77 species-including mammals (s = 140), birds (s = 77), reptiles (s = 4), amphibians (s = 8), fishes (s = 404), and plants (s = 22). The data are released under a Creative Commons CC0 1.0 Universal Public Domain Dedication license.},
}

*Biological Evolution
Animals
*Phenotype
*Databases, Factual
Ecosystem

@article {pmid38995706,
year = {2024},
author = {Dietrich, SW and Ma, W and Ding, Y and Watanabe, KH and Zelinski, MB and Sluka, JP},
title = {MOTHER-DB: A Database for Sharing Nonhuman Ovarian Histology Images.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {21},
number = {6},
pages = {2598-2603},
pmid = {38995706},
issn = {1557-9964},
support = {P51 OD011092/OD/NIH HHS/United States ; },
mesh = {Female ; *Databases, Factual ; *Ovary/pathology ; Animals ; Metadata ; Information Dissemination/methods ; Image Processing, Computer-Assisted/methods ; Computational Biology/methods ; },
abstract = {The goal of the Multispecies Ovary Tissue Histology Electronic Repository (MOTHER) project is to establish a collection of nonhuman ovary histology images for multiple species as a resource for researchers and educators. An important component of sharing scientific data is the inclusion of the contextual metadata that describes the data. MOTHER extends the Ecological Metadata Language (EML) for documenting research data, leveraging its data provenance and usage license with the inclusion of metadata for ovary histology images. The design of the MOTHER metadata includes information on the donor animal, including reproductive cycle status, the slide and its preparation. MOTHER also extends the ezEML tool, called ezEML+MOTHER, for the specification of the metadata. The design of the MOTHER database (MOTHER-DB) captures the metadata about the histology images, providing a searchable resource for discovering relevant images. MOTHER also defines a curation process for the ingestion of a collection of images and its metadata, verifying the validity of the metadata before its inclusion in the MOTHER collection. A Web search provides the ability to identify relevant images based on various characteristics in the metadata itself, such as genus and species, using filters.},
}

Female
*Databases, Factual
*Ovary/pathology
Animals
Metadata
Information Dissemination/methods
Image Processing, Computer-Assisted/methods
Computational Biology/methods

@article {pmid40030035,
year = {2025},
author = {Jin, J and Zhang, R and Li, J and Gao, F and Liao, Z and Yu, Y and Wang, Y and Bucci, D and Xiao, M and Ma, R and Ma, Q and Gao, S and Lio, J and Novais, F and Huang, SC and Zhu, J and Ghoneim, H and Wen, H and Li, Z and Sun, N and Xin, G},
title = {The NAE1-mediated neddylation operates as an essential post-translational modification checkpoint for effector CD8[+] T cells.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {10},
pages = {e2424061122},
doi = {10.1073/pnas.2424061122},
pmid = {40030035},
issn = {1091-6490},
support = {1R01CA269984//HHS | NIH | National Cancer Institute (NCI)/ ; CCR231013713//Susan G. Komen (SGK)/ ; RSG-23-1036499-01//American Cancer Society (ACS)/ ; },
mesh = {*CD8-Positive T-Lymphocytes/immunology/metabolism ; Humans ; *Protein Processing, Post-Translational ; Animals ; Mice ; *NEDD8 Protein/metabolism/genetics ; Ubiquitin-Activating Enzymes/metabolism/genetics ; NFATC Transcription Factors/metabolism/genetics ; Lymphocyte Activation ; Receptors, Antigen, T-Cell/metabolism ; Colonic Neoplasms/immunology/metabolism/genetics/pathology ; Signal Transduction ; Mice, Inbred C57BL ; },
abstract = {Optimal activation of CD8+ T cells is crucial for immunity-mediated destruction of cancer, requiring a substantial amount of proteins involved in metabolism, proliferation, and effector function. Despite extensive studies emphasizing the role of transcriptional regulation in this process, paired transcriptomic and proteomic analyses reveal that the RNA profile is poorly correlated with protein levels. This discrepancy underscores the importance of post-translational modifications (PTMs) in controlling protein abundance during activation. However, the impact of PTMs on the CD8+ T cell protein dynamic remains underexplored. We identify that neddylation, a recently discovered PTM, is activated in response to T cell receptor (TCR) stimulation and enriched in effector CD8+ T cells from colon cancer patients. Mechanistically, we found the rate-limiting enzyme of neddylation, neural precursor cell expressed developmentally down-regulated protein 8 activating enzyme E1 (NAE1), is induced by the NFATc1, a critical transcription factor downstream of TCR signaling. Our observation revealed that genetic ablation of NAE1 significantly disturbed the proteomic landscape related to activation and mitochondrial function. As a result, CD8+ T cells lacking NAE1 exhibited severely compromised activation, proliferation, and survival, which was accompanied by impaired mitochondrial function. Consistently, deletion of NAE1 in CD8+ T cells abolished their antitumor function and promoted tumor progression. By contrast, the overexpression of NAE1 significantly improved the function of tumor-infiltrating CD8+ T cells. Overall, we uncovered neddylation, a previously underappreciated PTM, as a proteomic checkpoint for CD8+ T cell activation. Enforced expression of NAE1 offers promising therapeutic potential for boosting the antitumor CD8+ T cell responses.},
}

*CD8-Positive T-Lymphocytes/immunology/metabolism
Humans
*Protein Processing, Post-Translational
Animals
Mice
*NEDD8 Protein/metabolism/genetics
Ubiquitin-Activating Enzymes/metabolism/genetics
NFATC Transcription Factors/metabolism/genetics
Lymphocyte Activation
Receptors, Antigen, T-Cell/metabolism
Colonic Neoplasms/immunology/metabolism/genetics/pathology
Signal Transduction
Mice, Inbred C57BL

@article {pmid40029426,
year = {2025},
author = {Zhang, J and Wang, Q and Gao, H and Qi, Q and He, W and Li, J and Yao, S and Li, W},
title = {Ecological suitability distribution of hop based on MaxEnt modeling.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {4},
pages = {346},
pmid = {40029426},
issn = {1573-2959},
mesh = {China ; *Environmental Monitoring ; *Humulus/growth & development ; *Ecosystem ; Geographic Information Systems ; Climate ; Soil/chemistry ; },
abstract = {Hop has been widely utilized in both food production and traditional medicine owing to their distinctive flavor and various pharmacological effects. In recent years, the increasing demand for hop has led to their cultivation in many regions across China. However, hops require specific ecological conditions, including climate, soil, precipitation, and temperature, which significantly affect their distribution and growth. To facilitate the standardization and scientific cultivation of hops, it is essential to clarify the distribution of their ecological suitability. In this study, we collected data from 95 hops distribution locations and 115 ecological factors to determine the areas suitable for hops cultivation using the Maximum Entropy (MaxEnt) model and Geographic Information System (GIS). The highly suitable areas are primarily located in the northwestern part of the Xinjiang Uygur Autonomous Region, the eastern part of Gansu Province, Shaanxi Province, the southwestern part of Shanxi Province, and parts of Ningxia Hui Autonomous Region and Yunnan Province. These findings provide valuable guidance for the scientific cultivation of hops, ensuring the efficient use of ecological resources and promoting sustainable cultivation practices.},
}

China
*Environmental Monitoring
*Humulus/growth & development
*Ecosystem
Geographic Information Systems
Climate
Soil/chemistry

@article {pmid40028932,
year = {2025},
author = {Eisaguirre, JM and Lohman, MG and Frye, GG and Johnson, HE and Riecke, TV and Williams, PJ},
title = {Estimating Spatially Explicit Survival and Mortality Risk From Telemetry Data With Thinned Point Process Models.},
journal = {Ecology letters},
volume = {28},
number = {3},
pages = {e70092},
doi = {10.1111/ele.70092},
pmid = {40028932},
issn = {1461-0248},
support = {//U.S. Geological Survey/ ; //National Science Foundation Graduate Research Fellowship Program/ ; //Institute for Wetland and Waterfowl Research Bonnycastle Fellowship for Wetland and Waterfowl Research/ ; },
mesh = {Animals ; *Telemetry ; Alaska ; Ecosystem ; Models, Biological ; Mortality ; Geographic Information Systems ; },
abstract = {Mortality risk for animals often varies spatially and can be linked to how animals use landscapes. While numerous studies collect telemetry data on animals, the focus is typically on the period when animals are alive, even though there is important information that could be gleaned about mortality risk. We introduce a thinned spatial point process (SPP) modelling framework that couples relative abundance and space use with a mortality process to formally treat the occurrence of mortality events across the landscape as a spatial process. We show how this model can be embedded in a hierarchical statistical framework and fit to telemetry data to make inferences about how spatial covariates drive both space use and mortality risk. We apply the method to two data sets to study the effects of roads and habitat on spatially explicit mortality risk: (1) VHF telemetry data collected for willow ptarmigan in Alaska, and (2) hourly GPS telemetry data collected for black bears in Colorado. These case studies demonstrate the applicability of this method for different species and data types, making it broadly useful in enabling inferences about the mechanisms influencing animal survival and spatial population processes while formally treating survival as a spatial process, especially as the development and implementation of joint analyses continue to progress.},
}

Animals
*Telemetry
Alaska
Ecosystem
Models, Biological
Mortality
Geographic Information Systems

@article {pmid40028774,
year = {2025},
author = {Fuzessy, L and Pizo, MA},
title = {NeoFrugivory: A comprehensive database for frugivory interactions and functional traits in the Neotropics.},
journal = {Ecology},
volume = {106},
number = {3},
pages = {e70049},
doi = {10.1002/ecy.70049},
pmid = {40028774},
issn = {1939-9170},
support = {2023/12469-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 21/02943-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 151167/2023-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 304742/2019-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; *Fruit/physiology ; Vertebrates/physiology ; Databases, Factual ; Tropical Climate ; Plants/classification ; Feeding Behavior ; Herbivory ; Ecosystem ; },
abstract = {Frugivory plays a crucial role in shaping Neotropical ecosystems, influencing plant dispersal, community dynamics, and ecosystem function. Despite its ecological significance, a systematic understanding of frugivore-fruit interactions spanning the entire Neotropical realm has been lacking. Therefore, we compiled the NeoFrugivory database, which addresses this gap by synthesizing data from a wide range of sources, including peer-reviewed literature, field studies, and existing databases. NeoFrugivory represents a comprehensive compilation of 10,175 unique frugivory interactions across the Neotropical region, the most diverse in terms of vertebrate frugivores, and consolidates information from 419 studies spanning from 1967 to 2023. It includes 2375 plant species and 758 terrestrial vertebrate species. In addition to documenting frugivory interactions, NeoFrugivory includes information on functional traits for both plants and vertebrates, such as body mass, diet, fruit morphology, and seed characteristics. The database encompasses diverse terrestrial vertebrate taxa, including species belonging to taxonomic groups such as Primates, Chiroptera, Birds, Artiodactyla/Perissodactyla, Reptilia, Carnivora, Marsupialia, and Rodentia. By providing a centralized repository of frugivory interactions, NeoFrugivory facilitates comprehensive analyses of ecological networks, evolutionary patterns, and ecosystem dynamics across the Neotropics, and NeoFrugivory provides a unique resource for researchers interested in exploring the intricate dynamics of plant-animal frugivory interactions in the Neotropics. This database enables researchers to explore the ecological roles of different frugivore taxa, identify keystone species, assess the resilience of mutualistic networks, and evaluate the impacts of environmental change on fruit-frugivore interactions. Furthermore, NeoFrugivory serves as a valuable resource for conservation practitioners, supporting the design and implementation of targeted conservation strategies aimed at preserving biodiversity and ecosystem function in the Neotropical region. Overall, NeoFrugivory represents a significant advancement in our understanding of frugivory dynamics in the Neotropics and provides a foundation for future research and conservation efforts in this ecologically diverse and critically important region. There are no copyright restrictions on the data; this paper should be cited when data are used in publications.},
}

Animals
*Fruit/physiology
Vertebrates/physiology
Databases, Factual
Tropical Climate
Plants/classification
Feeding Behavior
Herbivory
Ecosystem

@article {pmid40027489,
year = {2025},
author = {Bai, D and Chen, T and Xun, J and Ma, C and Luo, H and Yang, H and Cao, C and Cao, X and Cui, J and Deng, YP and Deng, Z and Dong, W and Dong, W and Du, J and Fang, Q and Fang, W and Fang, Y and Fu, F and Fu, M and Fu, YT and Gao, H and Ge, J and Gong, Q and Gu, L and Guo, P and Guo, Y and Hai, T and Liu, H and He, J and He, ZY and Hou, H and Huang, C and Ji, S and Jiang, C and Jiang, GL and Jiang, L and Jin, LN and Kan, Y and Kang, D and Kou, J and Lam, KL and Li, C and Li, C and Li, F and Li, L and Li, M and Li, X and Li, Y and Li, ZT and Liang, J and Lin, Y and Liu, C and Liu, D and Liu, F and Liu, J and Liu, T and Liu, T and Liu, X and Liu, Y and Liu, B and Liu, M and Lou, W and Luan, Y and Luo, Y and Lv, H and Ma, T and Mai, Z and Mo, J and Niu, D and Pan, Z and Qi, H and Shi, Z and Song, C and Sun, F and Sun, Y and Tian, S and Wan, X and Wang, G and Wang, H and Wang, H and Wang, H and Wang, J and Wang, J and Wang, K and Wang, L and Wang, SK and Wang, X and Wang, Y and Xiao, Z and Xing, H and Xu, Y and Yan, SY and Yang, L and Yang, S and Yang, Y and Yao, X and Yousuf, S and Yu, H and Lei, Y and Yuan, Z and Zeng, M and Zhang, C and Zhang, C and Zhang, H and Zhang, J and Zhang, N and Zhang, T and Zhang, YB and Zhang, Y and Zhang, Z and Zhou, M and Zhou, Y and Zhu, C and Zhu, L and Zhu, Y and Zhu, Z and Zou, H and Zuo, A and Dong, W and Wen, T and Chen, S and Li, G and Gao, Y and Liu, YX},
title = {EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.},
journal = {iMeta},
volume = {4},
number = {1},
pages = {e70001},
pmid = {40027489},
issn = {2770-596X},
abstract = {Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in-depth analysis of microbial communities at both the high-resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user-friendly pipeline that supports multiple analysis methods, including quality control and host removal, read-based, assembly-based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third-generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.},
}