Wellcome Open Research最新文献

{"title":"A range of voltage-clamp protocol designs for rapid capture of hERG kinetics.","authors":"Chon Lok Lei, Dominic J Whittaker, Monique J Windley, Matthew D Perry, Adam P Hill, Gary R Mirams","doi":"10.12688/wellcomeopenres.23319.2","DOIUrl":"10.12688/wellcomeopenres.23319.2","url":null,"abstract":"<p><p>We provide details of a series of short voltage-clamp protocols designed for gathering a large amount of information on hERG (K _v11.1) ion channel gating. The protocols have a limited number of steps and consist only of steps and ramps, making them easy to implement on any patch clamp setup, including automated platforms. The primary objective is to assist with parameterisation, selection and refinement of mathematical models of hERG gating. We detail a series of manual and automated model-driven designs, together with an explanation of their rationale and design criteria. Experimental data under all these protocols is available in a partner publication. Although the protocols are intended to study hERG1a currents, the approaches could be easily extended and generalised to other ion channel currents.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"673"},"PeriodicalIF":0.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12334913/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817633","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 chromosomal genome sequence of the giant barrel sponge, <i>Xestospongia muta</i> Schmidt 1870 and its associated microbial metagenome sequences.","authors":"Jose Victor Lopez, Shirley A Pomponi, Ute Hentschel, Dirk Erpenbeck, Nina Pruzinsky, Cara Fiore, Rebecca Mulheron, Graeme Oatley, Elizabeth Sinclair, Eerik Aunin, Noah Gettle, Camilla Santos, Michael Paulini, Haoyu Niu, Victoria McKenna, Rebecca O'Brien","doi":"10.12688/wellcomeopenres.24173.1","DOIUrl":"10.12688/wellcomeopenres.24173.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Xestospongia muta</i> (Caribbean barrel sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence has a total length of 158.52 megabases. Most of the assembly (99.56%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.99 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs, including <i>Candidatus</i> Poribacteria species, Candidatus Latescibacteria, Acidobacteriota, Actinomycetota Gemmatimonadota, multiple Chloroflexota and the archaeon Nitrosopumilus. Gene annotation of this assembly on Ensembl identified 20,220 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"336"},"PeriodicalIF":0.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12398682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144971034","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 eyed flat-backed millipede, <i>Nanogona polydesmoides</i> (Leach, 1814).","authors":"Christian Owen, Olga Sivell, Duncan Sivell, Richard J Twitchett, Gregory D Edgecombe","doi":"10.12688/wellcomeopenres.24341.1","DOIUrl":"10.12688/wellcomeopenres.24341.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Nanogona polydesmoides</i> (eyed flat-backed millipede; Arthropoda; Diplopoda; Chordeumatida; Craspedosomatidae). The genome sequence has a total length of 406.26 megabases. Most of the assembly (95.49%) is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.55 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"332"},"PeriodicalIF":0.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12334921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817638","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 zebra danio, <i>Danio rerio</i> (Hamilton, 1822) (Cypriniformes: Danionidae).","authors":"Kerstin Howe, Caroline Howard, Shane A McCarthy, Jonathan M D Wood","doi":"10.12688/wellcomeopenres.24569.1","DOIUrl":"10.12688/wellcomeopenres.24569.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Danio rerio</i> (zebra danio; Chordata; Actinopteri; Cypriniformes; Danionidae). The genome sequence has a total length of 1 413.66 megabases. Most of the assembly (99.85%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome was also assembled, with a length of 16.6 kilobases. Gene annotation of this assembly on Ensembl identified 25 582 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"330"},"PeriodicalIF":0.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145001177","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 Little Snipefly, <i>Chrysopilus asiliformis</i> (Preyssler, 1791).","authors":"Liam M Crowley, Susan C Taylor","doi":"10.12688/wellcomeopenres.24326.1","DOIUrl":"10.12688/wellcomeopenres.24326.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Chrysopilus asiliformis</i> (Little Snipefly; Arthropoda; Insecta; Diptera; Rhagionidae). The genome sequence has a total length of 429.05 megabases. Most of the assembly (99.58%) is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.38 kilobases. Gene annotation of this assembly on Ensembl identified 14,233 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"329"},"PeriodicalIF":0.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12371324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144971054","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":"Digital mental health interventions for adolescents and young people (10-24 years) in Africa: A protocol for a systematic review of mental health outcomes, engagement, and equity considerations.","authors":"Aggrey Gisiora Mokaya, Nondumiso Michelle Dlamini, Syethemba Nkosi, Mpilonhle Thembinkosi Nzuza, Thandeka Smith, Grace Nduku Wambua, Xanthe Hunt, Alan Stein, Nothando Ngwenya","doi":"10.12688/wellcomeopenres.24117.1","DOIUrl":"10.12688/wellcomeopenres.24117.1","url":null,"abstract":"<p><strong>Background: </strong>Adolescents and young people (AYP) aged 10-24 years in Africa experience a high burden of mental health disorders but face significant barriers to accessing care, including a severe shortage of mental health professionals, stigma, and limited integration of mental health services into primary healthcare. Digital mental health interventions (DMHIs) offer a promising avenue to bridge these gaps by providing accessible, scalable, and potentially equitable support. However, little is known about the effectiveness, acceptability, and equity impacts of these interventions among African AYP.</p><p><strong>Objective: </strong>This systematic review aims to identify, characterize, and synthesize evidence on DMHIs targeting adolescents and young people in Africa, focusing on mental health outcomes, engagement, feasibility, and equity considerations.</p><p><strong>Methods: </strong>We will search PubMed, Scopus, Web of Science, and EBSCOhost databases, as well as the PsyberGuide repository, for empirical studies published between January 1, 2015, and April 3, 2025. Eligible studies must evaluate a digital mental health intervention among AYP aged 10-24 years living in Africa. Study designs will include randomized controlled trials, quasi-experimental studies, observational studies, and mixed-methods studies. Outcomes of interest include mental health symptom reduction (depression, anxiety, stress), psychological well-being, engagement, feasibility, acceptability, and equity-related factors such as gender inclusivity and digital access. Risk of bias will be assessed using RoB 2 and ROBINS-I tools, and evidence quality will be rated using the GRADE approach. Quantitative synthesis will be conducted where feasible, otherwise narrative synthesis will be employed.</p><p><strong>Conclusion: </strong>This review will provide a comprehensive synthesis of available evidence on DMHIs for adolescents and young people in Africa, offering critical insights into their effectiveness, feasibility, and contribution to promoting mental health equity. The findings aim to inform the development, implementation, and policy integration of digital mental health strategies tailored to young populations in diverse African contexts.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"331"},"PeriodicalIF":0.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145001127","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":"An ontological framework for organising and describing behaviours: The Human Behaviour Ontology.","authors":"Paulina M Schenk, Robert West, Oscar Castro, Emily Hayes, Janna Hastings, Marie Johnston, Marta M Marques, Elizabeth Corker, Alison J Wright, Gabriella Stuart, Lisa Zhang, Micaela Santilli, Susan Michie","doi":"10.12688/wellcomeopenres.21252.2","DOIUrl":"10.12688/wellcomeopenres.21252.2","url":null,"abstract":"<p><strong>Background: </strong>Human behaviours have been classified in domains such as health, occupation and sustainability. We aimed to develop a broadly applicable behavioural framework to facilitate integrating evidence across domains.</p><p><strong>Methods: </strong>The Human Behaviour Ontology (HBO), a part of the Behaviour Change Intervention Ontology (BCIO), was developed by: (1) specifying its scope, (2) identifying candidate classes from existing classifications, (3) refining it by annotating behaviours in relevant literature, (4) a stakeholder review with behavioural and ontology experts, (5) testing the inter-rater reliability of its use in annotating research reports, (6) refining classes and their relations, (7) reviewing its coverage of behaviours in theories and (8) publishing its computer-readable version.</p><p><strong>Results: </strong>The initial ontology contained 128 classes (Steps 1-4), achieving an inter-rater reliability of 0.63 for familiar researchers and 0.74 after minor adjustments (to the ontology and guidance) for unfamiliar researchers. Following Steps 6-7, the published ontology included 230 classes, with six upper-level behavioural classes: human behaviour, individual human behaviour, individual human behaviour pattern, individual human behaviour change, population behaviour and population behaviour pattern. 'Individual human behaviour' was defined as \" <i>a bodily process of a human that involves co-ordinated contraction of striated muscles controlled by the brain</i>\", with its 159 subclasses organised across high-level classes relating to: experiences (e.g., playing); expression (e.g., laughing); reflectiveness; harm (e.g., self-injury behaviour); harm prevention; coping; domestic activities; goals; habits; health (e.g., undergoing vaccination); life-function (e.g., breathing behaviour); interactions with materials (e.g., consumption); bodily care (e.g., washing); position (e.g., postural behaviour); social environments (e.g., communication); and behavioural substitution. Additional classes needed for characterising behaviours (e.g., frequency and duration), their attributes and behavioural abstinence were included. Relations were defined for timings, locations, participants, mental processes, functions, goals and outcomes.</p><p><strong>Conclusions: </strong>The HBO provides an extensive and detailed framework for describing human behaviours.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"237"},"PeriodicalIF":0.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12334917/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817634","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 Protocol to examine the needs and experiences of autistic children/young people or children/young people with an intellectual disability when receiving support for mental health difficulties from child and adolescent mental health services.","authors":"Naomi Williams, Julie Taylor, Helena Tuomainen","doi":"10.12688/wellcomeopenres.23597.2","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23597.2","url":null,"abstract":"<p><strong>Background: </strong>Studies indicate a high prevalence of co-occurring mental health conditions in autistic children and young people (CYP) and CYP with intellectual disability (ID), with approximately 25% experiencing mental health conditions compared to 17.2% of their non-autistic or non-ID counterparts. Delivering psychological therapies to autistic CYP and CYP with ID proves challenging due to inaccessible mental health provision. Further research is necessary to comprehend autistic CYP and CYP with ID and their parent/carers needs and experiences within mental health services and identify barriers to access and engagement. The perspectives of autistic CYP or CYP with ID and their parent/carers should be incorporated into treatment planning to enhance psychological therapies.</p><p><strong>Methods: </strong>We will conduct between 1-3 Narrative Interviews per participant, lasting up to 1.5 hours per 'sitting'. Narrative interviews are a qualitative research method used to collect detailed and thorough information from individuals about their life events, insights, and perspectives. The study will involve CYP creating metaphors, allowing them to share their story. The study will use alternative methods of communication specific to their needs to allow the research team to explore the complexities of autistic CYP and CYP with ID needs and experiences. Additionally, parents/carers of autistic CYP and CYP with ID will tell their story of the needs and experiences of their child verbally.</p><p><strong>Results: </strong>This study results will help to share the needs and experiences of the autistic CYP and CYP with ID, or a co-occurrence of both diagnoses and expose the barriers to accessing mental health services for autistic CYP and CYP with ID.</p><p><strong>Conclusions: </strong>Recommendations will include guidance on decision-making for referrals, assessment, and treatment provision for autistic CYP and CYP with ID and co-occurring mental health difficulties.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"143"},"PeriodicalIF":0.0,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12501585/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145252960","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.23338.3","DOIUrl":"10.12688/wellcomeopenres.23338.3","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 from tradition and damage community cohesion. Younger participants were positive about the benefits of 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":"2025-06-09","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":"Study protocol for the Bio-HEAT study: Investigating the Biological pathways from HEAT exposure to preterm birth and other adverse maternal and child health outcomes in South Africa.","authors":"Ijeoma Solarin, Darshnika Pemi Lakhoo, Kimberly Mc Alpine, Margaret M Brennan, Admire Chikandiwa, Nicholas B Brink, Lebohang Radebe, Marié Landsberg, Clive Gray, G Justus Hofmeyr, Howard Chang, Robyn Hetem, Sibusisiwe Makhanya, Phelelani T Mpangase, Shane Norris, Michael Urban, Valerie Vannevel, Amy Wise, Matthew F Chersich, Karl-Gunter Technau, Renate Strehlau","doi":"10.12688/wellcomeopenres.23616.2","DOIUrl":"10.12688/wellcomeopenres.23616.2","url":null,"abstract":"<p><strong>Introduction: </strong>Epidemiological evidence linking heat exposure to adverse maternal and child health outcomes is compelling. However, the biological and social mechanisms underlying these associations remain poorly understood. Understanding the pathways explaining these associations is important given rising global temperatures, and the urgent need for developing and testing adaptive interventions.</p><p><strong>Methods: </strong>This transdisciplinary study in Johannesburg, South Africa, will monitor a cohort of 200 women from their second trimester until one-year postpartum, alongside their infants. Heat exposure and environmental factors will be tracked using personal, community and facility-level temperature monitors and geospatial data. Data will be collected on social conditions, medical and obstetric history, heat stress and adaptation, hydration, mental wellbeing, and sleep quality. Clinical data includes physical measurements, ultrasound, cardiotocography, and biological specimens (blood, urine, saliva) analysed for inflammatory markers, RNA, metabolic indicators, renal function and hormonal levels. Placental and cord blood analyses will assess foetal stress. Infant data will include medical history, hospital visits, neurodevelopment, anthropometric measurements, vital signs, and urine analysis. Three nested sub-studies (20-50 participants) will explore specific aspects: Sub-study 1 will use wearable devices to monitor sleep, activity, and heart rate in high-risk women; Sub-study 2 will involve qualitative interviews; and Sub-study 3 will assess breastmilk composition and volume.</p><p><strong>Planned analyses: </strong>Our primary aim is to document linkages between heat exposure and inflammatory pathways that precede preterm birth. The hypothesis that heat exposure triggers maternal inflammation will be tested by analysing epigenetic changes associated with inflammatory cytokine protein and gene expression. We will investigate thermoregulation and hydration during labour. Using isotope techniques, we assess whether heat exposure alters breastmilk composition and volume. Conceptual frameworks and graphical causal models will be developed to delineate pathways of vulnerability and protective mechanisms.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"121"},"PeriodicalIF":0.0,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12209768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545064","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}