Wellcome Open Research最新文献

{"title":"The emergence of common health conditions across the life course: evidence from the Born in Bradford family cohort.","authors":"Gillian Santorelli, Dan Lewer, Krishnarajah Nirantharakumar, Siang Ing Lee, Katherine Phillips, Rosemary R C McEachan, John Wright","doi":"10.12688/wellcomeopenres.20992.2","DOIUrl":"10.12688/wellcomeopenres.20992.2","url":null,"abstract":"<p><strong>Background: </strong>Born in Bradford (BiB) is a family cohort study with linked routine health records. We calculated the rates of common health conditions and explored differences between White European and South Asian participants.</p><p><strong>Methods: </strong>21 health conditions were identified using diagnostic codes and prescription records extracted from electronic health records. We calculated 2-year period prevalence before recruitment and incidence rates per 1000 person-years were calculated from recruitment to the end of 2021 (or censoring). Age-adjusted Cox proportional hazard models estimated hazard ratios (HR) by ethnicity.</p><p><strong>Results: </strong>The sample included 9,784 mothers, 52% were of South Asian heritage and 48% were White European. The highest prevalence and incidence rates were observed for common mental health disorders and eczema. South Asian women had higher incidence of 14 conditions, including diabetes (HR 3.94 [95% CI 3.15, 4.94]), chronic liver disease (2.98 [2.29, 3.88]) and thyroid disorders (1.87 [1.50, 2.33]), but lower incidence of cancer (0.51 [0.38, 0.68]), other and common mental health disorders (0.56 [0.45, 0.71] and 0.69 [0.64, 0.74] respectively), and other neuromuscular conditions (0.63 [0.49, 0.82]).</p><p><strong>Conclusions/discussion: </strong>This study reveals significant differences in the occurrence of several non-communicable health conditions between White European and South Asian women. The observed higher incidence of several conditions in South Asian women, consistent with established knowledge regarding elevated risks for diseases such as diabetes, likely reflects the complex interplay of social, cultural, lifestyle, environmental, and genetic determinants. These findings emphasise the need for culturally sensitive and targeted public health interventions aimed at addressing modifiable risk factors at both the individual and systemic levels to alleviate the burden of long-term health conditions and reduce existing health inequalities.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"210"},"PeriodicalIF":0.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226877","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":"How useful is Nanopore adaptive sampling for sequencing <i>Schistosoma mansoni</i> miracidia?","authors":"Rivka M Lim, Thomas M Arme, Moses Arinaitwe, Andrina Barungi, Thomas Crellen, Arne Jacobs, Amy B Pedersen, Joanne P Webster, Poppy H L Lamberton","doi":"10.12688/wellcomeopenres.24094.1","DOIUrl":"10.12688/wellcomeopenres.24094.1","url":null,"abstract":"<p><strong>Background: </strong>Whole-genome sequencing (WGS) is now widely used in <i>Schistosoma</i> genomics. Whilst adult worms typically provide sufficient DNA for molecular analyses, their inaccessibility in live definitive hosts presents a challenge for population studies. Larval stages, such as miracidia can be collected non-invasively and preserved on Whatman FTA cards, however these samples typically yield low quantities of DNA and have high levels of contamination, particularly when obtained from stool samples. To counteract contamination, multiple washing steps prior to placement onto Whatman FTA cards can be performed, but this is labour-intensive and can limit the number of larvae collected.</p><p><strong>Methods: </strong>Nanopore sequencing technologies includes an \"adaptive sampling\" feature, which enables selective enrichment or depletion of target DNA sequences during sequencing. In this study, we evaluated the potential of adaptive sampling to selectively enrich <i>S. mansoni</i> DNA from both washed and unwashed larval stage miracidia. We used Kraken2 to characterise sample contamination and assessed sequencing breadth and depth of genome coverage to determine whether adaptive sampling could provide sufficient <i>S. mansoni</i> DNA for WGS.</p><p><strong>Results and conclusion: </strong>Our results demonstrate that washed samples contained a higher proportion of <i>S. mansoni</i> DNA, validating the effectiveness of washing for contamination removal. However, adaptive sampling failed to generate sufficient <i>S. mansoni</i> reads for effective WGS. These findings suggest that, at present, washing remains critical for maximising <i>S. mansoni</i> DNA purity as adaptive sampling alone is insufficient for enrichment. Alternative enrichment strategies will be necessary to improve sequencing efficiency and data quality for <i>S. mansoni</i> WGS.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"239"},"PeriodicalIF":0.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12149812/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267303","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":"Expectations and Vietnam's responses during COVID-19: potential human rights violations and related propositions.","authors":"Hai Doan","doi":"10.12688/wellcomeopenres.18972.1","DOIUrl":"10.12688/wellcomeopenres.18972.1","url":null,"abstract":"<p><strong>Background: </strong>It appears that underneath many propositions or actions, there might have been certain expectations. The reality of the complexity of human beings and interactions within a society yields expectations which, in turn, further interact with each other.</p><p><strong>Methods: </strong>This paper offers the first in-depth study on 'expectations' in bioethical and health law studies, taking Vietnam's responses to coronavirus disease (COVID-19) as an illustration.</p><p><strong>Results: </strong>It defines 'expectations' as normative imaginaries that can induce or guide actions and inactions at individual and collective levels.</p><p><strong>Conclusions: </strong>It argues that violations of human rights and certain related propositions within the Vietnamese context can be understood in terms of expectations. Within such contexts as Vietnam, expectations account for behaviours, including human rights violations. It suggests that 'expectations' is a fruitful concept for bioethical and health law studies. Studying expectations thus has implications for governance and future research agendas.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":" ","pages":"147"},"PeriodicalIF":0.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12121475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47024419","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":"EFFICIENT RIBOSOMAL RNA DEPLETION FROM <i>DROSOPHILA</i> TOTAL RNA FOR NEXT-GENERATION SEQUENCING APPLICATIONS.","authors":"Omkar Koppaka, Shweta Tandon, Ankita Chodankar, Awadhesh Pandit, Baskar Bakthavachalu","doi":"10.12688/wellcomeopenres.23509.2","DOIUrl":"10.12688/wellcomeopenres.23509.2","url":null,"abstract":"<p><p>We developed a cost-effective enzyme-based rRNA-depletion method tailored for <i>Drosophila melanogaster</i>, addressing the limitations of existing commercial kits and the lack of peer-reviewed alternatives. Our method employs single-stranded DNA probes complementary to <i>Drosophila</i> rRNA, forming DNA-RNA hybrids. These hybrids are then degraded using the RNase H enzyme, effectively removing rRNA and enriching all non-ribosomal RNAs, including mRNA, lncRNA and small RNA. When compared to a commercial rRNA removal kit, our approach demonstrated superior rRNA removal efficiency and mapping percentage, confirming its effectiveness. Additionally, our method successfully enriched the non-coding transcriptome, making it a valuable tool for studying ncRNA in <i>Drosophila</i>. The probe sequences and rRNA-depletion protocol are made freely available, offering a reliable alternative for rRNA-depletion experiments.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"112"},"PeriodicalIF":0.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200156","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":"<i>\"I always wondered if my baby is able to feel my love for them\" -</i>  Development and pilot testing of two behavioural feedback strategies designed to improve maternal self-efficacy.","authors":"Alessandra Prioreschi, Deborah M James, Rebecca M Pearson, Antonia Smith, Shane A Norris, Kirsten L Rennie","doi":"10.12688/wellcomeopenres.23564.2","DOIUrl":"10.12688/wellcomeopenres.23564.2","url":null,"abstract":"<p><strong>Background: </strong>The aim of this pilot study was to describe the development of, and test the acceptability and feasibility of providing feedback on two behaviours in the context of supportive approaches to improve maternal self-efficacy. We hypothesised that providing individual behavioural feedback to mothers in a socially vulnerable context, when later embedded in supportive intervention approaches, may improve maternal self-efficacy and ultimately promote infant development.</p><p><strong>Methods: </strong>Feedback was developed following expert consultation with working groups, and included graphical feedback on mother and infant movement behaviours measured using accelerometry, as well as video feedback of mother-infant interactions using first person observation head cameras. Mothers wore the devices for one week, following which individual feedback on movement behaviours and mother-infant interactions was delivered at the Chris Hani Baragwanath Academic Hospital. We adapted an established and published strengths based approach as a guide for health workers to feedback video and accelerometer data. Feasibility and acceptability were tested by conducting focus group discussions with a sample of 8 mothers of infants aged 4-months from South Africa using a semi-structured interview guide.</p><p><strong>Results: </strong>Mothers included in this study were generally single, unemployed, and less than half had completed formal schooling. Most mothers had two or more children, and lived in informal housing (such as shacks and small, temporary prefabricated structures) with only outdoor toilet facilities available. The feedback was found to be both feasible, and largely acceptable in this context and compliance was 100%.</p><p><strong>Conclusion: </strong>We have been able to develop feedback with the potential to sensitise mothers to their infants' behaviours. When embedded in a supportive intervention, these feedback modalities have the potential to improve mother's self-efficacy through increasing feelings of competence and reflexive functioning.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"47"},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181607","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 Ibiza wall lizard, <i>Podarcis pityusensis</i> (Boscá, 1883).","authors":"Nathalie Feiner, Tobias Uller, Ferran de la Cruz, Roberto Garcia-Roa, Joana Meier","doi":"10.12688/wellcomeopenres.24143.1","DOIUrl":"10.12688/wellcomeopenres.24143.1","url":null,"abstract":"<p><p>Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Laterata; Lacertibaenia; Lacertidae; Lacertinae; <i>Podarcis</i>; <i>Podarcis pityusensis</i> (Boscá, 1883) (NCBI:txid74359).</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"235"},"PeriodicalIF":0.0,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12163369/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144302975","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>Rhynchopus euleeides</i> YPF1915 and its bacterial endosymbiont <i>Candidatus</i> Syngnamydia salmonis (Chlamydiota).","authors":"Daria Tashyreva, Drahomíra Faktorová, Aleš Horák, Julius Lukeš, John M Archibald, Graeme Oatley, Elizabeth Sinclair, Camilla Santos, Michael Paulini, Eerik Aunin, Noah Gettle, Haoyu Niu, Victoria McKenna, Rebecca O'Brien","doi":"10.12688/wellcomeopenres.24014.1","DOIUrl":"10.12688/wellcomeopenres.24014.1","url":null,"abstract":"<p><p>We present a genome assembly of the diplonemid <i>Rhynchopus euleeides</i> (Euglenozoa; Diplonemea; Diplonemea; Diplonemidae). The genome sequence is 199.0 megabases long, with most of the assembly scaffolded into 88 chromosomal pseudomolecules. The multipartite mitochondrial genome and the 2.0 megabase genome of <i>Ca.</i> Syngnamydia salmonis, a bacterial endosymbiont of <i>R. euleeides</i>, were also sequenced and assembled.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"233"},"PeriodicalIF":0.0,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12171722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318117","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 rove beetle, <i>Philonthus spinipes</i> Sharp, 1874.","authors":"Darren J Mann, Liam M Crowley","doi":"10.12688/wellcomeopenres.23996.1","DOIUrl":"10.12688/wellcomeopenres.23996.1","url":null,"abstract":"<p><p>We present a genome assembly from a female <i>Philonthus spinipes</i> (rove beetle; Arthropoda; Insecta; Coleoptera; Staphylinidae). The genome sequence has a total length of 671.10 megabases. Most of the assembly is scaffolded into 25 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 19.08 kilobases in length. Gene annotation of this assembly on Ensembl identified 30,004 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"217"},"PeriodicalIF":0.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134740/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226878","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":"<i>Drosophila</i> AHR limits tumor growth and stem cell proliferation in the intestine.","authors":"Minghua Tsai, Jiawei Sun, Cyrille Alexandre, Michael Shapiro, Adrien Franchet, Ying Li, Alex P Gould, Jean-Paul Vincent, Brigitta Stockinger, Nicola Laura Diny","doi":"10.12688/wellcomeopenres.23515.3","DOIUrl":"10.12688/wellcomeopenres.23515.3","url":null,"abstract":"<p><strong>Background: </strong>The aryl hydrocarbon receptor (AHR) plays important roles in intestinal homeostasis, limiting tumour growth and promoting differentiation in the intestinal epithelium. Spineless, the <i>Drosophila</i> homolog of AHR, has only been studied in the context of development but not in the adult intestine.</p><p><strong>Methods: </strong>The role of Spineless in the <i>Drosophila</i> midgut was studied by overexpression or inactivation of Spineless in infection and tumour models and RNA sequencing of sorted midgut progenitor cells.</p><p><strong>Results: </strong>We show that <i>spineless</i> is upregulated in the adult intestinal epithelium after infection with <i>Pseudomonas entomophila</i> ( <i>P</i>. <i>e</i>.). Spineless inactivation increased stem cell proliferation following infection-induced injury. Spineless overexpression limited intestinal stem cell proliferation and reduced survival after infection. In two tumour models, using either <i>Notch</i> RNAi or constitutively active Yorkie, Spineless suppressed tumour growth and doubled the lifespan of tumour-bearing flies. At the transcriptional level it reversed the gene expression changes induced in Yorkie tumours, counteracting cell proliferation and altered metabolism.</p><p><strong>Conclusions: </strong>These findings demonstrate a new role for Spineless in the adult <i>Drosophila</i> midgut and highlight the evolutionarily conserved functions of AHR/Spineless in the control of proliferation and differentiation of the intestinal epithelium.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"38"},"PeriodicalIF":0.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11982807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050398","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 petty spurge, <i>Euphorbia peplus</i> L. (Euphorbiaceae).","authors":"Maarten J M Christenhusz, Michael F Fay, Ilia J Leitch","doi":"10.12688/wellcomeopenres.24030.1","DOIUrl":"10.12688/wellcomeopenres.24030.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Euphorbia peplus</i> (petty spurge; Streptophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence has a total length of 277.10 megabases. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. We also assembled six multipartite mitochondrial molecules and one plastid genome.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"219"},"PeriodicalIF":0.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12125573/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200158","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}