Wellcome Open Research最新文献

{"title":"The genome sequence of long-finned pilot whale, <i>Globicephala melas</i> (Traill, 1809).","authors":"Nicholas J Davison, Phillip A Morin","doi":"10.12688/wellcomeopenres.23919.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23919.1","url":null,"abstract":"<p><p>We present a genome assembly from a male specimen of <i>Globicephala melas</i> (long-finned pilot whale; Chordata; Mammalia; Artiodactyla; Delphinidae). The genome sequence has a total length of 2,651.28 megabases. Most of the assembly (89.15%) is scaffolded into 23 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.39 kilobases. Gene annotation of this assembly on Ensembl identified 17,911 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"180"},"PeriodicalIF":0.0,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12009481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144026122","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 European ground squirrel, <i>Spermophilus citellus</i> (Linnaeus, 1766).","authors":"Dimitra-Lida Rammou, Dionisios Youlatos, Alexandros Triantafyllidis","doi":"10.12688/wellcomeopenres.23974.1","DOIUrl":"10.12688/wellcomeopenres.23974.1","url":null,"abstract":"<p><p>We present a genome assembly from a female <i>Spermophilus citellus</i> (European ground squirrel; Chordata; Mammalia; Rodentia; Sciuridae). The genome sequence has a total length of 3,090.03 megabases. Most of the assembly (95.47%) is scaffolded into 20 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.45 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"184"},"PeriodicalIF":0.0,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144162507","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 <i>Glossophaga mutica</i> (Chiroptera, Phyllostomidae, Glossophaginae; Merriam, 1898).","authors":"Nancy B Simmons, Melissa R Ingala, Brian P O'Toole, Linelle Abueg, Kirsty McCaffrey, Bonhwang Koo, Giulio Formenti, Erich D Jarvis, Myrtani Pieri, Meike Mai, Larry N Singh, Philge Philip, Laramie L Lindsey, Ning Zhang, Jonathan L Gray, Emma C Teeling, Sonja C Vernes","doi":"10.12688/wellcomeopenres.23611.1","DOIUrl":"10.12688/wellcomeopenres.23611.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual female <i>Glossophaga mutica</i> (Chordata; Mammalia; Chiroptera; Phyllostomidae). The genome sequence is 2.13 in span. The majority of the assembly is scaffolded into 32 chromosomal pseudomolecules, with the X sex chromosome assembled.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"174"},"PeriodicalIF":0.0,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144095331","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":"Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024.","authors":"Arnold W Lambisia, John Mwita Morobe, Edidah Moraa, Salim Mwarumba, Fredrick K N Korir, Raila Seif Athman, Rebecca Kiptui, Micheal Mbee, Nelly Mugo, Patrick Amoth, Penny Muange, Charlotte J Houldcroft, Edwine Barasa, Joseph Mwangangi, George Githinji, Edward C Holmes, Lynette Isabella Ochola-Oyier, Charles N Agoti","doi":"10.12688/wellcomeopenres.23522.2","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23522.2","url":null,"abstract":"<p><strong>Background: </strong>In early 2024, a surge in acute hemorrhagic conjunctivitis (AHC), also referred as \"red eye\" disease, was observed in coastal Kenya, prompting the Ministry of Health to issue an outbreak alert. Herein, we investigated the etiology of this outbreak.</p><p><strong>Methods: </strong>Ocular swabs were obtained from 13 individuals presenting with AHC at a Mombasa clinic in early February 2024. Ten of these were analyzed using bacterial cultures, and all 13 using a pan-adenovirus quantitative PCR (qPCR) and metagenomic sequencing. Potential viral etiology was confirmed by a specific qPCR, amplicon sequencing and phylogenetic analysis.</p><p><strong>Results: </strong>Bacterial cultures yielded no growth except in three samples where non-pathogenic bacteria were detected. All 13 samples were adenovirus qPCR negative. Metagenomic sequencing detected coxsackievirus A24 variant (CA24v) in three of the 13 samples. CV-A24v detections were confirmed by both CV-A24v specific qPCR and amplicon sequencing of an approximately 450 nucleotide long VP4/2 junction genomic region. Phylogenetic analysis of the VP4/2 sequences showed that they were closely related to CV-A24v genotype IV.</p><p><strong>Conclusion: </strong>The AHC epidemic in coastal Kenya in early 2024 was likely caused by CA24v. Metagenomic sequencing is a powerful tool for identifying potential causative agents of new disease outbreaks.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"28"},"PeriodicalIF":0.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11992516/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052432","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":"Experiences with the Implementation of Cuban Health Cooperation Programs in Low and Middle-Income Countries: A Scoping Review.","authors":"Faith Njiriri, Moriasi Nyanchoka, Jacinta Nzinga, Benjamin Tsofa","doi":"10.12688/wellcomeopenres.23844.1","DOIUrl":"10.12688/wellcomeopenres.23844.1","url":null,"abstract":"<p><strong>Background: </strong>Health systems in low and middle-income countries (LMICs) face chronic Human Resources for Health (HRH) shortages. This is especially worse in rural and primary healthcare settings. The Cuban government since 1960s has been implementing a policy strategy for producing healthcare workers for export, to boost their economy. Several LMICs have since established health cooperation programs with Cuba to import health workers to address their shortages. This review aimed to examine the emergence, design, utility, outcomes, and lessons learned from the implementation of these programs.</p><p><strong>Methods: </strong>We conducted a scoping review using the Joanna Briggs Institute (JBI) methodology and searched for literature across four databases. Two independent reviewers screened the articles and selected relevant articles based on pre-defined criteria. We extracted data and synthesized findings using thematic analysis.</p><p><strong>Results: </strong>We included 71 articles after screening 3509 articles. Cuban health cooperation programs have been implemented in many LMICs in South America, Africa, Southeast Asia, and the Pacific region. These programs are formalized primarily through bilateral agreements and implemented as exchange initiatives. This involves importing Cuban healthcare workers and sending collaborating country students to study in Cuba. These programs aimed to address HRH shortages and maldistribution, inadequate training capacity, and respond to medical emergencies in the host countries. Cuban healthcare workers, primarily family physicians, within the host countries; are deployed in primary healthcare settings, increasing the rural health workforce, and improving healthcare access and outcomes. These programs have faced several challenges including opposition from local medical professionals, underutilization due to poorly coordinated recruitment, and language barrier.</p><p><strong>Conclusion: </strong>Cuban health cooperations in LMICs have shown diverse results based on their structures. Long-term comprehensive programs have proven to be more successful in boosting the healthcare workforce and enhancing health outcomes. Key factors for optimizing HRH health cooperation include effective collaborative decision-making and need-based deployment.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"167"},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144162451","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":"Changing patterns in marriage choice and related health risk in the Pakistani heritage community in Bradford UK: a qualitative study.","authors":"Neil Small, Rifat Razaq, Vishal Sharma, Alice Cunningham, Zuneera Khurshid, Shahid Islam","doi":"10.12688/wellcomeopenres.23338.2","DOIUrl":"10.12688/wellcomeopenres.23338.2","url":null,"abstract":"<p><strong>Background: </strong>Children born to blood relations (consanguineous parents), primarily cousins, have higher mortality and morbidity than children born to non-consanguineous parents. Consanguinity is low in the UK but high in some communities, including the Pakistani heritage community in Bradford. There has been a marked decrease in consanguinity in the last decade and that is likely to result in reductions in excess mortality and morbidity.</p><p><strong>Methods: </strong>Drawing on patterns of child health reported by the Born in Bradford study, augmented with a summary of the literature on motivations for choosing consanguineous unions and on the shifting characteristics of those who make this choice, questions about marriage choice and knowledge of allied health risk were devised. They were explored in four focus groups with self-identified members of the Pakistani heritage community. Groups were divided by age and gender. Discussions were analysed using Thematic Analysis.</p><p><strong>Results: </strong>There was agreement that rates of consanguinity were declining. Older group members were concerned this might indicate a shift away from tradition and damage community cohesion. Younger participants were positive about the benefits of a shift towards individual choice. They felt this could be achieved without damaging community strengths. Reasons for the fall in numbers were attributed to changes within the community, including higher numbers of people staying in education beyond school. External factors, including new immigration rules, were also considered.There was not a consensus about health risks, some older respondents were sceptical of links between marriage choice and child health and concerned about how health risks were communicated. All were concerned that marriage choice should not be used to demonise this community.</p><p><strong>Conclusion: </strong>A commitment to sustaining community cohesion is shared by all groups. Younger people think this can be achieved despite falls in consanguinity. There are continuing challenges in communicating health risk.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"690"},"PeriodicalIF":0.0,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144180257","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":"From smoking cessation to physical activity: Can ontology-based methods for automated evidence synthesis generalise across behaviour change domains?","authors":"Oscar Castro, Emma Norris, Alison J Wright, Emily Hayes, Ella Howes, Candice Moore, Robert West, Susan Michie","doi":"10.12688/wellcomeopenres.21664.2","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21664.2","url":null,"abstract":"<p><strong>Background: </strong>Developing behaviour change interventions able to tackle major challenges such as non-communicable diseases or climate change requires effective and efficient use of scientific evidence. The Human Behaviour-Change Project (HBCP) aims to improve evidence synthesis in behavioural science by compiling intervention reports and annotating them with an ontology to train information extraction and prediction algorithms. The HBCP used smoking cessation as the first 'proof of concept' domain but intends to extend its methodology to other behaviours. The aims of this paper are to (i) assess the extent to which methods developed for annotating smoking cessation intervention reports were generalisable to a corpus of physical activity evidence, and (ii) describe the steps involved in developing this second HBCP corpus.</p><p><strong>Methods: </strong>The development of the physical activity corpus involved: (i) reviewing the suitability of smoking cessation codes already used in the HBCP, (ii) defining the selection criteria and scope, (iii) identifying and screening records for inclusion, and (iv) annotating intervention reports using a code set of 200+ entities from the Behaviour Change Intervention Ontology.</p><p><strong>Results: </strong>Stage 1 highlighted the need to modify the smoking cessation behavioural outcome codes for application to physical activity. One hundred physical activity intervention reports were reviewed, and 11 physical activity experts were consulted to inform the adapted code set. Stage 2 involved narrowing down the scope of the corpus to interventions targeting moderate-to-vigorous physical activity. In stage 3, 111 physical activity intervention reports were identified, which were then annotated in stage 4.</p><p><strong>Conclusions: </strong>Smoking cessation annotation methods developed as part of the HBCP were mostly transferable to the physical activity domain. However, the codes applied to behavioural outcome variables required adaptations. This paper can help anyone interested in building a body of research to develop automated evidence synthesis methods in physical activity or for other behaviours.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"402"},"PeriodicalIF":0.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11992510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144017018","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 a cave beetle, <i>Leptodirus hochenwartii</i> F.J.Schmidt, 1832.","authors":"Teo Delić","doi":"10.12688/wellcomeopenres.23959.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23959.1","url":null,"abstract":"<p><p>We present a genome assembly from a male specimen of <i>Leptodirus hochenwartii</i> (cave beetle; Arthropoda; Insecta; Coleoptera; Leiodidae). The genome sequence has a total length of 492.36 megabases. Most of the assembly (98.03%) is scaffolded into 14 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 22.01 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"159"},"PeriodicalIF":0.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11992515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144064883","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 Four-spotted Footman moth, <i>Lithosia quadra</i> (Linnaeus, 1758).","authors":"Finley Hutchinson, Liam M Crowley","doi":"10.12688/wellcomeopenres.23788.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23788.1","url":null,"abstract":"<p><p>We present a genome assembly from a male <i>Lithosia quadra</i> (Four-spotted Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence has a total length of 456.27 megabases. Most of the assembly (99.91%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"146"},"PeriodicalIF":0.0,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12038344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144056144","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 Straw-barred Pearl moth, <i>Pyrausta despicata</i> Scopoli, 1763.","authors":"Gavin R Broad, David C Lees, Douglas Boyes","doi":"10.12688/wellcomeopenres.23902.1","DOIUrl":"10.12688/wellcomeopenres.23902.1","url":null,"abstract":"<p><p>We present a genome assembly from a male specimen of <i>Pyrausta despicata</i> (Straw-barred Pearl; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 481.83 megabases. Most of the assembly (99.61%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.29 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"151"},"PeriodicalIF":0.0,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182406","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}