Wellcome Open Research最新文献

{"title":"GRAPEVNE - Graphical Analytical Pipeline Development Environment for Infectious Diseases.","authors":"John-Stuart Brittain, Joseph Tsui, Rhys Inward, Bernardo Gutierrez, Gaspary Mwanyika, Houriiyah Tegally, Tuyen Huynh, George Githinji, Sofonias Kifle Tessema, John T McCrone, Samir Bhatt, Abhishek Dasgupta, Stephen Ratcliffe, Moritz U G Kraemer","doi":"10.12688/wellcomeopenres.23824.1","DOIUrl":"10.12688/wellcomeopenres.23824.1","url":null,"abstract":"<p><p>The increase in volume and diversity of relevant data on infectious diseases and their drivers provides opportunities to generate new scientific insights that can support 'real-time' decision-making in public health across outbreak contexts and enhance pandemic preparedness. However, utilising the wide array of clinical, genomic, epidemiological, and spatial data collected globally is difficult due to differences in data preprocessing, data science capacity, and access to hardware and cloud resources. To facilitate large-scale and routine analyses of infectious disease data at the local level (i.e. without sharing data across borders), we developed GRAPEVNE (Graphical Analytical Pipeline Development Environment), a platform enabling the construction of modular pipelines designed for complex and repetitive data analysis workflows through an intuitive graphical interface. Built on the <i>Snakemake</i> workflow management system, GRAPEVNE streamlines the creation, execution, and sharing of analytical pipelines. Its modular approach already supports a diverse range of scientific applications, including genomic analysis, epidemiological modeling, and large-scale data processing. Each module in GRAPEVNE is a self-contained Snakemake workflow, complete with configurations, scripts, and metadata, enabling interoperability. The platform's open-source nature ensures ongoing community-driven development and scalability. GRAPEVNE empowers researchers and public health institutions by simplifying complex analytical workflows, fostering data-driven discovery, and enhancing reproducibility in computational research. Its user-driven ecosystem encourages continuous innovation in biomedical and epidemiological research but is applicable beyond that. Key use-cases include automated phylogenetic analysis of viral sequences, real-time outbreak monitoring, forecasting, and epidemiological data processing. For instance, our dengue virus pipeline demonstrates end-to-end automation from sequence retrieval to phylogeographic inference, leveraging established bioinformatics tools which can be deployed to any geographical context. For more details, see documentation at: https://grapevne.readthedocs.io.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"279"},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12205304/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144529823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of the great crested newt, <i>Triturus cristatus</i> (Laurenti, 1768).","authors":"Jeffrey W Streicher, Stephanie Holt","doi":"10.12688/wellcomeopenres.24257.1","DOIUrl":"10.12688/wellcomeopenres.24257.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Triturus cristatus</i> (great crested newt; Chordata; Amphibia; Caudata; Salamandridae). The genome sequence has a total length of 22,324.62 megabases. Most of the assembly (98.78%) is scaffolded into 12 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.54 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"270"},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134737/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The chromosomal genome sequence of the sponge <i>Crambe crambe</i> (Schmidt, 1862) and its associated microbial metagenome sequences.","authors":"Manuel Maldonado, Lucia Pita, Ute Hentschel, Dirk Erpenbeck, Graeme Oatley, Elizabeth Sinclair, Eerik Aunin, Noah Gettle, Camilla Santos, Michael Paulini, Haoyu Niu, Victoria McKenna, Rebecca O'Brien","doi":"10.12688/wellcomeopenres.24154.1","DOIUrl":"10.12688/wellcomeopenres.24154.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual <i>Crambe crambe</i> (Porifera; Demospongiae; Poecilosclerida; Crambeidae). The host genome sequence is 143.20 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.53 kilobases in length. Several symbiotic prokaryotic genomes were assembled as MAGs, including two relevant sponge symbionts, the <i>Candidatus</i> Beroebacter blanensis/ <i>AqS2</i> clade (Tethybacterales, Gammaproteobacteria) of LMA sponges, and the widely distributed archaeal <i>Nitrosopumilus</i> sp. clade.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"275"},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166358/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144302972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of the Heath Bumblebee, <i>Bombus jonellus</i> (Kirby, 1802).","authors":"Gavin R Broad, Inez Januszczak, Chris Fletcher","doi":"10.12688/wellcomeopenres.24256.1","DOIUrl":"10.12688/wellcomeopenres.24256.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Bombus jonellus</i> (Heath Bumblebee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence has a total length of 357.90 megabases. Most of the assembly (78.06%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 24.83 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"269"},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144302974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of the Slender-footed Robberfly, <i>Leptarthrus brevirostris</i> (Meigen, 1804).","authors":"Robert Wolton","doi":"10.12688/wellcomeopenres.24277.1","DOIUrl":"10.12688/wellcomeopenres.24277.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Leptarthrus brevirostris</i> (Slender-footed Robberfly; Arthropoda; Insecta; Diptera; Asilidae). The assembly contains two haplotypes with total lengths of 850.81 megabases and 851.46 megabases. Most of haplotype 1 (99.05%) is scaffolded into 6 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 18.16 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"273"},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12254722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144627267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cognitive bias modification for social anxiety: protocol for a living systematic review of human studies and meta-analysis.","authors":"Jaycee Kennett, Claire Friedrich, Virginia Chiocchia, Simon E Blackwell, Toshi Furukawa, Per Carlbring, Thomy Tonia, Ava Homiar, Simonne Wright, Kelvin Opiepie, Richardson Mojica, Paulina Schenk, Susan Michie, Janna Hastings, Hossein Dehdarirad, Claire Stansfield, James Thomas, Jennifer Potts, Georgia Salanti, Andrea Cipriani","doi":"10.12688/wellcomeopenres.23278.2","DOIUrl":"10.12688/wellcomeopenres.23278.2","url":null,"abstract":"<p><strong>Background: </strong>Social anxiety is a heightened fear and discomfort in social situations. Cases of elevated distress and impaired functioning can lead to a clinical diagnosis of social anxiety disorder. Altering cognitive biases associated with social anxiety has been suggested as potentially beneficial; however, little is known about the comparative effectiveness of such interventions. The aim of this living systematic review is to examine the efficacy of cognitive bias modification for reducing social anxiety.</p><p><strong>Methods: </strong>We will search multiple electronic databases for randomised controlled trials evaluating the efficacy of cognitive bias modification for people diagnosed with social anxiety and people exposed to a social stressor. The primary outcome will be change in social anxiety related symptoms; secondary outcomes will be changes in social functioning and quality of life and adverse events. Study selection, data extraction and risk of bias assessment will be done by at least two reviewers using pre-defined tools. We will synthesise data from people with social anxiety diagnosis and those subjected to a simulated social stressor separately using random effects meta-analyses. Heterogeneity will be evaluated by investigating characteristics of included studies and we will conduct a network meta-analysis in order to compare the efficacy of subtypes of cognitive bias modification for social anxiety disorder. We will appraise the strength of the evidence for each outcome by reviewing the overall association, internal and external validity, and reporting biases. Where data allows, we will triangulate the evidence from both sources with a multidisciplinary group of experts. We will also descriptively report factors reported to mediate cognitive bias modification, The review will begin in living mode and the database search will be rerun every three months to identify potential new evidence. We will co-produce this review with members of a global lived experience advisory board. This protocol was registered on 15.10.2024 (CRD42024601380)..</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"657"},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12149809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of the Broad Centurion soldierfly, <i>Chloromyia formosa</i> (Scopoli, 1763).","authors":"Olga Sivell, Duncan Sivell","doi":"10.12688/wellcomeopenres.24255.1","DOIUrl":"10.12688/wellcomeopenres.24255.1","url":null,"abstract":"<p><p>We present a genome assembly from a male specimen of <i>Chloromyia formosa</i> (Broad Centurion soldierfly; Arthropoda; Insecta; Diptera; Stratiomyidae). The genome sequence has a total length of 790.81 megabases. Most of the assembly (98.79%) is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 17.69 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"266"},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12187159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144486041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Entomopathogenic fungi <i>Metarhizium pingshaense</i> increases susceptibility to insecticides in highly resistant malaria mosquitoes <i>Anopheles coluzzii</i>.","authors":"Doubé Lucien Lamy, Edounou Jacques Gnambani, Issiaka Sare, Souro Abel Millogo, Fatimata Aïcha Sodre, Moussa Namountougou, Mafalda Viana, Francesco Baldini, Abdoulaye Diabaté, Etienne Bilgo","doi":"10.12688/wellcomeopenres.21238.3","DOIUrl":"10.12688/wellcomeopenres.21238.3","url":null,"abstract":"<p><strong>Background: </strong><i>Metarhizium</i> spp. based mosquito control products are among the most investigated and could potentially serve as promising complements to chemical insecticides. However, limited knowledge exists on the implementation of this biocontrol tool in conjunction with primary insecticide-based strategies to achieve synergy.</p><p><strong>Methods: </strong>In laboratory bioassays, we combined 10 ⁷ conidia/ml native <i>Metarhizium pingshaense</i> strains with deltamethrin standard dose in two ways : before and after insecticide exposure. For comparison, some mosquitoes were exposed to deltamethrin or fungi alone. These combinations were tested on laboratory insecticide resistant <i>Anopheles coluzzii</i>.</p><p><strong>Results: </strong>We found that <i>Metarhizium pingshaense</i> and deltamethrin could be combined to achieve greater mortality against a highly insecticide resistance colony of <i>Anopheles coluzzii</i>. Specifically, when fungi were applied earlier than deltamethrin, mosquitoes became more sensitive to insecticide with a minimum Lethal Time to kill at least 50% of mosquito population (LT50) less than 8 days. In addition, when deltamethrin exposure was followed by <i>Metarhizium</i> infection, mosquito survival was similar to <i>Metarhizium</i> alone LT50 (LT50 ~11 days).</p><p><strong>Conclusion: </strong>These findings suggest that early mosquito infection to <i>Metarhizium pingshaense</i> followed by chemical insecticide exposure synergically increased mosquito susceptibility to the insecticide in the laboratory.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"290"},"PeriodicalIF":0.0,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144162462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of the Common Goldeneye, <i>Bucephala clangula</i> (Linnaeus, 1758).","authors":"Rosa Lopez Colom, Michelle F O'Brien","doi":"10.12688/wellcomeopenres.24275.1","DOIUrl":"10.12688/wellcomeopenres.24275.1","url":null,"abstract":"<p><p>We present a genome assembly from a male <i>Bucephala clangula</i> (Common Goldeneye; Chordata; Aves; Anseriformes; Anatidae). The genome sequence has a total length of 1,190.92 megabases. Most of the assembly (95.05%) is scaffolded into 40 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.63 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"258"},"PeriodicalIF":0.0,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12209769/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of an ichneumonid wasp, <i>Amblyjoppa proteus</i> (Christ, 1791).","authors":"Liam M Crowley, Gavin R Broad","doi":"10.12688/wellcomeopenres.24267.1","DOIUrl":"10.12688/wellcomeopenres.24267.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Amblyjoppa proteus</i> (ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence has a total length of 290.11 megabases. Most of the assembly (99.64%) is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 30.41 kilobases. Gene annotation of this assembly on Ensembl identified 12,770 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"262"},"PeriodicalIF":0.0,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12338164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144822741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}