Wellcome Open Research最新文献

{"title":"The Ebola Data Platform: A prospective, standardised, clinical dataset collected during the 2013-2016 West African Ebola outbreak.","authors":"Laura Merson, Trokon Omarley Yeabah, Samantha Strudwick, Tamba Fayiah, Jennifer H Lee, Musa Martin Feika, Gemma Buck, Kwame Oneill, Kalynn Kennon, Mahamoud Sama Cherif","doi":"10.12688/wellcomeopenres.22483.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22483.1","url":null,"abstract":"<p><p>The Ebola Data Platform (EDP) was developed to strengthen knowledge and capacity across health, research, and humanitarian communities to reduce the impact of Ebola through responsible data use. This collaborative initiative was established by West African governments, NGOs, academic organisations, and intra-governmental health organisations directly involved in the 2013-2016 West African Ebola outbreak. The platform was established to provide a centralised, standardised dataset of individual patient data collected during the outbreak for the purpose of research to improve Ebola treatment and control, and includes over 13,600 patient records of individuals infected and treated from 22 different Ebola treatment centres across Guinea, Sierra Leone, Liberia, and Nigeria. Patient data are available from treatment centre triage and admission, inpatient clinical observations, and outcomes, with outpatient follow-up available for some datasets. Data include signs and symptoms, pre-existing comorbidities, vital signs, laboratory testing, treatments, complications, dates of admission and discharge, mortality, viral strains, and other data. This publication describes characteristics of the EDP dataset, its architecture, methods for data access and tools for utilising the dataset.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"548"},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11499738/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509139","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":"A chromosomal reference genome sequence for the malaria mosquito, <i>Anopheles marshallii</i>, Theobald, 1903.","authors":"Boris K Makanga, Diego Ayala, Nil Rahola, Lemonde B A Bouafou, Harriet F Johnson, Haynes Heaton, Martin G Wagah, Joanna C Collins, Ksenia Krasheninnikova, Sarah E Pelan, Damon-Lee B Pointon, Ying Sims, James W Torrance, Alan Tracey, Marcela Uliano-Silva, Jonathan M D Wood, Katharina von Wyschetzki, Shane A McCarthy, Daniel E Neafsey, Alex Makunin, Mara K N Lawniczak","doi":"10.12688/wellcomeopenres.22989.1","DOIUrl":"10.12688/wellcomeopenres.22989.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual female <i>Anopheles marshallii</i> (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae) from Lopé, Gabon. The genome sequence is 225.7 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"554"},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11538599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142592481","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":"Mortality, morbidity and educational outcomes in children of consanguineous parents in the Born in Bradford cohort.","authors":"Neil Small, Brian Kelly, Daniel S Malawsky, Rajib Lodh, Sam Oddie, John Wright","doi":"10.12688/wellcomeopenres.22547.2","DOIUrl":"10.12688/wellcomeopenres.22547.2","url":null,"abstract":"<p><strong>Background: </strong>Children of consanguineous parents have a higher risk of infant and childhood mortality, morbidity and intellectual and developmental disability.</p><p><strong>Methods: </strong>Using a UK based longitudinal cohort study we quantify differences according to the consanguinity status of children from birth to 10 in mortality, health care usage, two health and three educational outcomes. The cohort comprises 13727 children; 35.7% White British, 43.7% Pakistani heritage, and 20.8% are from other ethnic groups.</p><p><strong>Results: </strong>Compared to children whose parents were not related children whose parents were first cousins were more likely to die by age 10 (odds ratio 2.81, 95% CI 1.82-4.35) to have higher rates of primary care appointments (incident rate ratio 1.39, 95% CI 1.34-1.45) and more prescriptions (incident rate ratio 1.61, 95% CI 1.50-1.73). Rates of hospital accident and emergency attendance (incident rate ratio 1.21,95% CI 1.12-1.30) and hospital outpatients' appointments (incident rate ratio 2.21,95% CI 1.90-2.56) are higher. Children of first cousins have higher rates of speech/ language development difficulties (odds ratio 1.63, 95% CI 1.36-1.96) and learning difficulties (odds ratio 1.89, 95% CI 1.28-2.81). When they begin school they are less likely to reach phonics standards (odds ratio 0.73, 95% CI 0.63-0.84) and less likely to show a good level of development (odds ratio 0.61, 95% CI 0.54-0.68). At age 10 there are higher numbers with special educational needs from first cousin unions compared to all children whose parents are not blood relations (odds ratio 1.38, 95% CI 1.20-1.58). Effect sizes for consanguinity status are similar in univariable and multivariable models where a range of control variables are added.</p><p><strong>Conclusions: </strong>There is higher childhood mortality and greater use of health care as well as higher rates of learning difficulties, speech and language development challenges and substantive differences in education outcomes in children whose parents are first cousins.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"319"},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381756","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 mottled worm, <i>Allolobophora</i> <i>icterica</i> (formerly <i>Aporrectodea</i> <i>icterica <i>)</i> </i> (Savigny, 1826).","authors":"Emma Sherlock, Chris Fletcher","doi":"10.12688/wellcomeopenres.23066.1","DOIUrl":"10.12688/wellcomeopenres.23066.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual mottled worm, <i>Allolobophora icterica</i> (Annelida; Clitellata; Crassiclitellata; Lumbricidae). The genome sequence has a total length of 1,117.80 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.33 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"556"},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11530748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569746","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":"Nested case control study of prevalence and aetiology of dementia in a rural Ugandan population, and a situational analysis of services available for affected families: a protocol. <i>Part of the DEPEND Uganda study (Dementia EPidemiology, unmet Need and co-Developing Solutions)</i>.","authors":"Josephine Prynn, Racheal Alinaitwe, Beatrice Kimono, Tunde Peto, Nicholas J Ashton, Claire J Steves, Joseph Mugisha, Martin Prince","doi":"10.12688/wellcomeopenres.22944.1","DOIUrl":"10.12688/wellcomeopenres.22944.1","url":null,"abstract":"<p><strong>Background: </strong>The prevalence of dementia in low- and middle-income countries is increasing, yet epidemiological data from African populations remain scarce. Crucial risk factors differ in Africa from more intensively studied global areas, including a high burden of cerebrovascular disease and HIV, but lower rates of other risk factors like physical inactivity.Understanding dementia aetiology in African settings has been limited by the expensive and invasive nature of biomarker testing. This study leverages developments in blood-based and retinal imaging biomarker technology to examine the drivers of dementia in older Ugandans.People with dementia have complex needs benefiting from multi-dimensional support. Understanding current services will allow identification of barriers and opportunities to strengthen support available to people with dementia and their families.</p><p><strong>Methods: </strong>The study is nested within the existing General Population Cohort run by the MRC/UVRI & LSHTM Research Unit. Currently, all adults aged 60+ (around 1400) are undergoing brief cognitive screening.In Part 1, cohort participants will be selected based on cognitive screening scores to undergo detailed cognitive assessment, using methods developed by the 10/66 Dementia Research Group. Part 2 is a case control study of people with and without dementia using antecedent data, questionnaires, physical assessment, retinal imaging, and Alzheimer's blood-based biomarkers. We will also compare disability, frailty, quality of life, and social engagement in people with and without dementia.Part 3 assesses current provision of formal support for people with dementia through review of publicly available literature and expert interviews.</p><p><strong>Conclusions: </strong>This is the first study in Africa using blood-based and retinal imaging biomarkers to examine the pathological processes underlying dementia, and it will systematically map services available for people with dementia. This paves the way for effective policy strategies for both dementia prevention and support for people with dementia and their families.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"544"},"PeriodicalIF":0.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11490832/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476098","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 Brindled Ochre moth, <i>Dasypolia templi</i> (Thunberg, 1792).","authors":"Andy Griffiths","doi":"10.12688/wellcomeopenres.23054.1","DOIUrl":"10.12688/wellcomeopenres.23054.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual male Brindled Ochre moth, <i>Dasypolia templi</i> (Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 855.30 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"542"},"PeriodicalIF":0.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11525101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142558952","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 Pale November moth, <i>Epirrita christyi</i> (Allen, 1906).","authors":"Douglas Boyes, Liam M Crowley, Clare Boyes","doi":"10.12688/wellcomeopenres.23060.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23060.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual female Pale November moth, <i>Epirrita christyi</i> (Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 474.20 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.99 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,983 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"540"},"PeriodicalIF":0.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142628873","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 Broom moth, <i>Ceramica pisi</i> Linnaeus, 1758.","authors":"Andy Griffiths, Denise C Wawman, Liam M Crowley","doi":"10.12688/wellcomeopenres.23050.1","DOIUrl":"10.12688/wellcomeopenres.23050.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual male <i>Ceramica pisi</i> (the Broom moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence spans 732.70 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,916 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"539"},"PeriodicalIF":0.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648817","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 ruby bryozoan, <i>Bugula neritina</i> (Linnaeus, 1758).","authors":"Rebekka Uhl, John Bishop, Helen Jenkins, Christine Wood, Patrick Adkins, Freja Azzopardi","doi":"10.12688/wellcomeopenres.23056.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23056.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Bugula neritina</i> (the ruby bryozoan; Bryozoa; Gymnolaemata; Cheilostomatida; Bugulidae). The genome sequence has total length of 216.00 megabases. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,264 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"533"},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480708/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476046","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 conger eel, <i>Conger conger</i> (Linnaeus, 1758).","authors":"Patrick Adkins, Rachel Brittain, Joanna Harley, Vengamanaidu Modepali","doi":"10.12688/wellcomeopenres.23052.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23052.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual <i>Conger conger</i> (the European conger eel; Chordata; Actinopteri; Anguilliformes; Congridae). The genome sequence spans 1,136.40 megabases. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"532"},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476043","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}