Wellcome Open Research最新文献

{"title":"The genome sequence of a weevil, <i>Hypera rumicis</i> (Linnaeus, 1758) (Coleoptera: Curculionidae).","authors":"Michael F Geiser, Clive R Turner, Maxwell V L Barclay","doi":"10.12688/wellcomeopenres.27925.1","DOIUrl":"10.12688/wellcomeopenres.27925.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual male <i>Hypera rumicis</i> (weevil; Arthropoda; Insecta; Coleoptera; Curculionidae). The assembly contains two haplotypes with total lengths of 1,773.45 megabases and 1,709.03 megabases. Most of the haplotype 1 assembly (99.72%) was scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. Most of haplotype 2 (99.63%) is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.55 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"11 ","pages":"744"},"PeriodicalIF":0.0,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220890","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 Toadflax Brocade, <i>Calophasia lunula</i> (Hufnagel, 1766) (Lepidoptera: Noctuidae).","authors":"Charlotte J Wright","doi":"10.12688/wellcomeopenres.27918.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.27918.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual male <i>Calophasia lunula</i> (Toadflax Brocade; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 585.35 megabases and 581.00 megabases. Most of the haplotype 1 assembly (99.85%) was scaffolded into 32 chromosomal pseudomolecules, including the Z sex chromosome and the B ₁ supernumerary chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.67 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"11 ","pages":"737"},"PeriodicalIF":0.0,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13650317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149168780","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":"Process mapping of a collaborative quality improvement study to optimise the use of antibiotics in intensive care units in Argentina: a Pathfinder study.","authors":"Javier Roberti, Ana Paula Rodríguez, Viviana Rodríguez, Facundo Jorro-Barón, Ezequiel Garcia-Elorrio","doi":"10.12688/wellcomeopenres.26970.2","DOIUrl":"10.12688/wellcomeopenres.26970.2","url":null,"abstract":"<p><strong>Objective: </strong>To systematically document the operational components, barriers, facilitators, and solutions of a quality improvement collaborative for antibiotic stewardship in intensive care units (ICUs) in the public sector of Argentina, using the Pathfinder methodological framework.</p><p><strong>Methods: </strong>Retrospective, descriptive observational study using mixed methods. Data sources included a documentary review of protocols, standard operating procedures, monitoring reports, and host study publications; an online survey with closed and open-ended questions administered to research team members; and triangulation with findings from the host study's previously published process evaluation, structured according to Normalisation Process Theory. Integration was performed using the Pathfinder Tracker. Analysis combined descriptive statistics with content analysis of open-ended responses.</p><p><strong>Results: </strong>Eleven stages of the research process were mapped, from question formulation to dissemination, with an estimated total effort of approximately 1,020 person-hours. The stages with the highest perceived difficulty (4/5) were ethical and institutional approvals, data collection, analysis, and dissemination, which together accounted for approximately 50% of the total estimated effort. Barriers were identified across three domains: institutional and regulatory (heterogeneity of ethical requirements, absence of stable local coordinators, publication costs); operational and technical (complex data collection forms, displacement of implementation focus due to the burden of data collection, variable connectivity); and human resources and capacity (clinical workload, staff turnover, insufficient training in implementation science). Solutions included a collaborative format with mentoring, agile communication via accessible digital tools (REDCap, WhatsApp, Zoom), and the use of theoretical frameworks for structuring (NPT, CFIR).</p><p><strong>Conclusions: </strong>The Pathfinder framework enabled a systematic and transferable reconstruction of the host study's processes, revealing barriers and solutions that conventional results reports do not capture. The findings are relevant for research teams in middle-income countries designing quality improvement collaboratives in complex hospital settings.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"11 ","pages":"522"},"PeriodicalIF":0.0,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13653102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149171711","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":"Surveillance-Driven Machine Learning for Prediction of Antimicrobial Susceptibility: An Explainable Modeling Framework using the Pfizer ATLAS Dataset (2004 - 2023).","authors":"Raphael Mutua, David Gichohi, Samuel K Ndegwa, Rahma O Golicha, Frida Njeru, Benson Kituku","doi":"10.12688/wellcomeopenres.26477.2","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.26477.2","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial resistance (AMR) is a growing global public health threat, particularly in low- and middle-income countries (LMICs), where delayed antimicrobial susceptibility testing (AST) and limited diagnostic capacity complicate timely treatment and antimicrobial stewardship (AMS). Although large-scale surveillance programmes routinely collect antimicrobial susceptibility data, these datasets remain underutilised for predictive analytics.</p><p><strong>Methods: </strong>We developed a surveillance-driven machine learning (ML) framework using isolate-level data from African sites participating in the Pfizer Antimicrobial Testing Leadership and Surveillance (ATLAS) programme between 2019 and 2023. Seven antibiotic-specific Extreme Gradient Boosting (XGBoost) models were developed to predict antimicrobial susceptibility using routinely collected microbiological, demographic, clinical, and geographical metadata. Model development included structured data preprocessing, RandomOverSampler-based class balancing restricted to the training data, hyperparameter optimisation using stratified cross-validation, and evaluation on a held-out test dataset. A rule-based MIC interpretation system and interactive dashboard were developed to demonstrate implementation of the analytical workflow.</p><p><strong>Results: </strong>The antibiotic-specific models demonstrated moderate predictive performance, with test accuracies ranging from 57% to 76%. Ceftazidime-Avibactam achieved the highest test accuracy (76%), followed by Gentamicin (65%) and Imipenem (64%), while Amikacin showed the lowest performance (57%). Feature-importance analysis identified bacterial species as consistently among the most influential predictors. In contrast, bacterial family, country of isolate collection, specimen source, clinical specialty, and demographic characteristics contributed to varying degrees across antibiotics. Performance was generally stronger for the more frequently represented susceptible class than for intermediate and resistant isolates.</p><p><strong>Conclusion: </strong>Routinely collected AMR surveillance data can support antibiotic-specific ML predictions without requiring genomic sequencing or detailed patient-level clinical information. This study provides a proof-of-concept framework for surveillance-driven predictive analytics that could complement conventional AMR surveillance and AMS. External validation, calibration, prospective clinical evaluation, and implementation studies are required before routine deployment.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"11 ","pages":"393"},"PeriodicalIF":0.0,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13624498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115462","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 sequences of the diplonemid protist <i>Diplonema japonicum</i> YPF1604 and its bacterial endosymbionts <i>Ca.</i> <i>Cytomitobacter primus</i> and <i>Ca.</i> <i>Nesciobacter abundans</i>.","authors":"Daria Tashyreva, Drahomíra Faktorová, Eva Stříbrná, Aleš Horák, Julius Lukeš, John M Archibald, Graeme Oatley, Elizabeth Sinclair, Eerik Aunin, Noah Gettle, Camilla Santos, Michael Paulini, Haoyu Niu, Victoria McKenna, Rebecca O'Brien","doi":"10.12688/wellcomeopenres.23917.3","DOIUrl":"10.12688/wellcomeopenres.23917.3","url":null,"abstract":"<p><p>We present a genome assembly of the diplonemid <i>Diplonema japonicum</i> YPF1604 (Discoba; Euglenozoa; Diplonemea; Diplonemidae). The genome sequence is 62.30 megabases in span. Most of the assembly is scaffolded into 118 chromosomal pseudomolecules. The multipartite mitochondrial genome was also assembled. The genome sequences of two bacterial endosymbionts, <i>Ca.</i> Cytomitobacter primus and <i>Ca.</i> Cytomitobacter primus, were also assembled.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"193"},"PeriodicalIF":0.0,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13598402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149040827","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 touch-me-not balsam, <i>Impatiens noli-tangere</i> L. (Ericales: Balsaminaceae).","authors":"Maarten J M Christenhusz","doi":"10.12688/wellcomeopenres.27873.1","DOIUrl":"10.12688/wellcomeopenres.27873.1","url":null,"abstract":"<p><p>We present a genome assembly of <i>Impatiens noli-tangere</i> (touch-me-not balsam; Streptophyta; Magnoliopsida; Ericales; Balsaminaceae). The assembly consists of two haplotypes with total lengths of 591.16 megabases and 584.76 megabases. Most of the haplotype 1 assembly (99.78%) was scaffolded into 10 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. Multiple mitochondrial sequences and a plastid genome were also assembled. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"11 ","pages":"718"},"PeriodicalIF":0.0,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220963","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 wall speedwell, <i>Veronica arvensis</i> L. (Lamiales: Plantaginaceae).","authors":"Maarten J M Christenhusz","doi":"10.12688/wellcomeopenres.27854.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.27854.1","url":null,"abstract":"<p><p>We present a genome assembly of <i>Veronica arvensis</i> (wall speedwell; Streptophyta; Magnoliopsida; Lamiales; Plantaginaceae). The assembly consists of two haplotypes with total lengths of 368.79 megabases and 369.14 megabases. Most of the haplotype 1 assembly (99.61%) was scaffolded into eight chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome assembly has a length of 280.62 kilobases and the plastid genome assembly has a length of 149.37 kilobases. Gene annotation of the haplotype 1 assembly by Ensembl identified 23,864 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"11 ","pages":"706"},"PeriodicalIF":0.0,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13620361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115428","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 Bastard Balm, <i>Melittis melissophyllum</i> L. (Lamiales: Lamiaceae).","authors":"Maarten J M Christenhusz, Sahr Mian, Ilia J Leitch","doi":"10.12688/wellcomeopenres.27850.1","DOIUrl":"10.12688/wellcomeopenres.27850.1","url":null,"abstract":"<p><p>We present a genome assembly of <i>Melittis melissophyllum</i> (Bastard Balm; Streptophyta; Magnoliopsida; Lamiales; Lamiaceae). The primary assembly has a total length of 436.70 megabases. Most of the primary assembly (97.71%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome assembly has a length of 366.69 kilobases and the plastid genome assembly has a length of 153.23 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"11 ","pages":"702"},"PeriodicalIF":0.0,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13654072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149171990","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 dewberry, <i>Rubus caesius</i> L. (Rosales: Rosaceae).","authors":"Maarten J M Christenhusz, José Ignacio Márquez-Corro, Isabel Larridon","doi":"10.12688/wellcomeopenres.27853.1","DOIUrl":"10.12688/wellcomeopenres.27853.1","url":null,"abstract":"<p><p>We present a genome assembly of the tetraploid <i>Rubus caesius</i> (dewberry; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The two assemblies, designated haplotype 1 and haplotype 2, have total lengths of 628.60 megabases and 633.30 megabases. Most of the haplotype 1 assembly (97.18%) was scaffolded into 14 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome assembly has a length of 423.35 kilobases and the plastid genome assembly has a length of 156.98 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"11 ","pages":"705"},"PeriodicalIF":0.0,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13662391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149196788","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 kidney vetch, <i>Anthyllis vulneraria</i> L. (Fabales: Fabaceae).","authors":"Markus Ruhsam, Peter M Hollingsworth","doi":"10.12688/wellcomeopenres.27830.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.27830.1","url":null,"abstract":"<p><p>We present a genome assembly of <i>Anthyllis vulneraria</i> (kidney vetch; Streptophyta; Magnoliopsida; Fabales; Fabaceae). The assembly consists of two haplotypes with total lengths of 334.47 megabases and 342.59 megabases. Most of the haplotype 1 assembly (92.49%) was scaffolded into six chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial sequences have lengths of 152.89, 53.26 and 83.2 kilobases and the plastid genome assembly has a length of 151.91 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"11 ","pages":"687"},"PeriodicalIF":0.0,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13650319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149168719","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}