Wellcome Open Research最新文献

{"title":"The genome sequence of <i>Glacies alpinata</i> (Scopoli, 1763) (Lepidoptera: Geometridae).","authors":"Paula Escuer, Kay Lucek, Charlotte J Wright, Joana I Meier, Mark L Blaxter","doi":"10.12688/wellcomeopenres.24664.1","DOIUrl":"10.12688/wellcomeopenres.24664.1","url":null,"abstract":"<p><p>We present a genome assembly from a male specimen of <i>Glacies alpinata</i> (Arthropoda; Insecta; Lepidoptera; Geometridae). The assembly contains two haplotypes with total lengths of 575.96 megabases and 573.82 megabases. Most of haplotype 1 (99.77%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.2 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"392"},"PeriodicalIF":0.0,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12417988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145034313","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":"Systems Policy Analysis for Antimicrobial Resistance Targeted Action (SPAARTA): A Research Protocol.","authors":"Raheelah Ahmad, Nina Zhu, Rishabh Jain, Jyoti Joshi, Mirfin Mpundu, Paola Amigo Gutierrez, Alison Holmes, Tillman Weyde, Rifat Atun","doi":"10.12688/wellcomeopenres.22923.2","DOIUrl":"10.12688/wellcomeopenres.22923.2","url":null,"abstract":"<p><strong>Background: </strong>The majority of countries (88%) have an Antimicrobial Resistance (AMR) National Action Plan (NAP V.1.0), but many remain unimplemented, and lack funding for interventions. Intervention selection requires a systematic approach to explain and predict progress. Looking beyond AMR is important to ensure the capture of systemic factors at the country level, which can impede or accelerate success.</p><p><strong>Aim: </strong>To provide innovative policy analysis to allow country comparison and refine targeted action, while developing and implementing NAPs (V.2.0).</p><p><strong>Methods: </strong>Mixed-method multi-country case study of policies and implementation strategies to address AMR across One Health. Starting with 17 countries, the sample includes each WHO region and emerging economies.This investigation of structures, processes, and outcomes has three components:a. Textual analysis of peer-reviewed literature, policy documents, global, national and state level progress reports, validated by global and in-country experts. An all-language article search conducted for 2000-2024, using broad search terms: 'Antimicrobial resistance policies', 'national action plan', 'surveillance', 'AMR systems' supplemented by hand searches. Deductive analysis using multi-disciplinary frameworks including the Expert Consensus for Implementation Research (ERIC). b. Longitudinal quantitative analysis assessing country contextual determinants and Antimicrobial Use (AMU) and AMR outcomes. Data from global health indicator repositories and international and national AMU and AMR surveillance networks are analysed using econometrics and machine learning approaches.c. Interactive Tableau dashboard development to display insights from a & b to allow visualisation and comparison of case-country AMR intervention context and components.</p><p><strong>Discussion: </strong>This protocol provides a systematic, transparent approach for countries to benchmark their own AMR strategies. The interactive dashboard will allow comparisons between country clusters by geography or economy, and enable rapid knowledge mobilisation among strategic and operational stakeholders including policy makers and planners. This protocol facilitates others to perform this structured assessment and nominate their country for the next wave of analysis.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"700"},"PeriodicalIF":0.0,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12332476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817635","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 Lesser Mountain Ringlet, <i>Erebia melampus</i> Füssly, 1775 (Lepidoptera: Nymphalidae).","authors":"Selim Bouaouina, Kay Lucek, Charlotte J Wright, Joana I Meier, Mark L Blaxter","doi":"10.12688/wellcomeopenres.24659.1","DOIUrl":"10.12688/wellcomeopenres.24659.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Erebia melampus</i> (Lesser Mountain Ringlet; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The assembly contains two haplotypes with total lengths of 479.19 megabases and 424.26 megabases. Most of haplotype 1 (99.7%) is scaffolded into 21 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.2 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"394"},"PeriodicalIF":0.0,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145138982","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 Cranberry Fritillary, <i>Boloria aquilonaris</i> (Stichel, 1908) (Lepidoptera: Nymphalidae).","authors":"Hans-Peter Wymann, Alena Suchackova Bartonova, Kay Lucek, Charlotte J Wright, Joana I Meier, Mark L Blaxter","doi":"10.12688/wellcomeopenres.24620.1","DOIUrl":"10.12688/wellcomeopenres.24620.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Boloria aquilonaris</i> (Cranberry Fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The assembly contains two haplotypes with total lengths of 415.84 megabases and 390.14 megabases. Most of haplotype 1 (99.86%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.17 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"378"},"PeriodicalIF":0.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12334919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817637","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 Mountain Clouded Yellow, <i>Colias phicomone</i> (Esper, 1780) (Lepidoptera: Pieridae).","authors":"Daniel Linke, Irena Klečková, Pavel Matos-Maraví, Charlotte J Wright, Joana I Meier, Mark L Blaxter","doi":"10.12688/wellcomeopenres.24625.1","DOIUrl":"10.12688/wellcomeopenres.24625.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Colias phicomone</i> (Mountain Clouded Yellow; Arthropoda; Insecta; Lepidoptera; Pieridae). The assembly contains two haplotypes with total lengths of 420.60 megabases and 355.84 megabases. Most of haplotype 1 (99.03%) is scaffolded into 31 chromosomal pseudomolecules, including the W, Z ₁, and Z ₂ sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.15 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"379"},"PeriodicalIF":0.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145132025","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":"Comparative performance of the InBios SCoV-2 Detect ^TM IgG ELISA and the in-house KWTRP ELISA in detecting SARS-CoV-2 spike IgG antibodies in Kenyan populations.","authors":"Bernadette Kutima, Eunice Wageci Kagucia, Kennedy Mwai, Makobu Kimani, Antipa Sigilai, Daisy Mugo, Henry Karanja, John N Gitonga, Angela Karani, Donald Akech, Monica Toroitich, Boniface Karia, James Tuju, Abdhalah K Ziraba, Godfrey Bigogo, Caroline Ochieng, Clayton Onyango, Shirley Lidechi, Patrick K Munywoki, Sophie Uyoga, Ifedayo M O Adetifa, Lynette I Ochola Oyier, Philip Bejon, J Anthony G Scott, Ambrose Agweyu, George M Warimwe, James Nyagwange","doi":"10.12688/wellcomeopenres.20240.2","DOIUrl":"10.12688/wellcomeopenres.20240.2","url":null,"abstract":"<p><strong>Background: </strong>The InBios SCoV-2 Detect™ IgG ELISA (InBios) and the in-house KWTRP ELISA (KWTRP) have both been used in the estimation of SARS-CoV-2 seroprevalence in Kenya. Whereas the latter has been validated extensively using local samples, the former has not. Such validation is important for informing the comparability of data across the sites and populations where seroprevalence has been reported.</p><p><strong>Methods: </strong>We compared the assays directly using pre-pandemic serum/plasma collected in 2018 from 454 blood donors and 173 malaria cross-sectional survey participants, designated gold standard negatives. As gold standard SARS-CoV-2 positive samples: we assayed serum/plasma from 159 SARS-CoV-2 PCR-positive patients and 166 vaccination-confirmed participants.</p><p><strong>Results: </strong>The overall agreement on correctly classified samples was >0.87 for both assays. The overall specificity was 0.89 (95% CI, 0.87-0.91) for InBios and 0.99 (95% CI, 0.97-0.99) for KWTRP among the gold standard negative samples while the overall sensitivity was 0.97 (95% CI, 0.94-0.98) and 0.93 (95% CI, 0.90- 0.95) for InBios and KWTRP ELISAs respectively, among the gold standard positive samples. In all, the positive predictive value for InBios was 0.83 (95% CI, 0.79-0.87) and 0.98 (95% CI, 0.96-0.99) for KWTRP while the negative predictive value was 0.98 (95% CI, 0.97- 0.99) and 0.97 (95% CI, 0.95-0.98) for InBios and KWTRP respectively.</p><p><strong>Conclusions: </strong>Overall, both assays showed sufficient sensitivity and specificity to estimate SARS-CoV-2 antibodies in different populations in Kenya.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"349"},"PeriodicalIF":0.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12368485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144971306","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 bronze bream, <i>Abramis brama</i> (Linnaeus, 1758) (Cypriniformes: Leuciscidae).","authors":"Andy D Nunn, Bernd Hänfling, Richard Pitman","doi":"10.12688/wellcomeopenres.24606.1","DOIUrl":"10.12688/wellcomeopenres.24606.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Abramis brama</i> (bronze bream; Chordata; Actinopteri; Cypriniformes; Leuciscidae). The genome sequence has a total length of 1 108.20 megabases. Most of the assembly (99.13%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.61 kilobases. Gene annotation of this assembly on Ensembl identified 25 268 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"371"},"PeriodicalIF":0.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12441676/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145087529","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 Black Hairstreak, <i>Satyrium pruni</i> (Linnaeus, 1758) (Lepidoptera: Lycaenidae).","authors":"Jaakko Pohjoismaki, Marko Mutanen, Charlotte J Wright, Joana I Meier, Mark L Blaxter","doi":"10.12688/wellcomeopenres.24619.1","DOIUrl":"10.12688/wellcomeopenres.24619.1","url":null,"abstract":"<p><p>We present a genome assembly from a male specimen of <i>Satyrium pruni</i> (Black Hairstreak; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The assembly contains two haplotypes with total lengths of 869.86 megabases and 870.75 megabases. Most of haplotype 1 (99.02%) is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.46 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"377"},"PeriodicalIF":0.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12417987/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145034266","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 Marsh Pennywort, <i>Hydrocotyle vulgaris</i> L. (Apiales: Araliaceae).","authors":"Markus Ruhsam, Peter M Hollingsworth","doi":"10.12688/wellcomeopenres.24582.1","DOIUrl":"10.12688/wellcomeopenres.24582.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Hydrocotyle vulgaris</i> (Marsh Pennywort; Streptophyta; Magnoliopsida; Apiales; Araliaceae). The assembly contains two haplotypes with total lengths of 870.40 megabases and 862.86 megabases. Most of haplotype 1 (97.78%) is scaffolded into 48 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial and plastid genome assemblies have lengths of 562.52 kilobases and 153.03 kilobases, respectively.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"370"},"PeriodicalIF":0.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12421231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145041476","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 White-barred Clearwing, <i>Synanthedon spheciformis</i> (Denis & Schiffermüller), 1775 (Lepidoptera: Sesiidae).","authors":"Jaakko Pohjoismaki, Marko Mutanen, Charlotte J Wright, Joana I Meier, Mark L Blaxter","doi":"10.12688/wellcomeopenres.24613.1","DOIUrl":"10.12688/wellcomeopenres.24613.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Synanthedon spheciformis</i> (White-barred Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The assembly contains two haplotypes with total lengths of 388.57 megabases and 372.40 megabases. Most of haplotype 1 (99.88%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 19.11 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"373"},"PeriodicalIF":0.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12449690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145114084","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}