Wellcome Open Research最新文献

{"title":"The genome sequence of the whiskered bat, <i>Myotis mystacinus</i> (Kuhl, 1817).","authors":"Hazel Ryan, Sonja C Vernes, Emma C Teeling, Meike Mai","doi":"10.12688/wellcomeopenres.23345.1","DOIUrl":"10.12688/wellcomeopenres.23345.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual male <i>Myotis mystacinus</i> (whiskered bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence has a total length of 2,081.20 megabases. Most of the assembly (97.52%) is scaffolded into 23 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.93 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"684"},"PeriodicalIF":0.0,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11615438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781285","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 white-beaked dolphin, <i>Lagenorhynchus albirostris</i> (Gray, 1846).","authors":"Nicholas J Davison, Phillip Morin","doi":"10.12688/wellcomeopenres.23369.1","DOIUrl":"10.12688/wellcomeopenres.23369.1","url":null,"abstract":"<p><p>We present a genome assembly from a juvenile female <i>Lagenorhynchus albirostris</i> (the white-beaked dolphin; Chordata; Mammalia; Artiodactyla; Delphinidae). The genome sequence has a total length of 2,544.80 megabases. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.39 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"687"},"PeriodicalIF":0.0,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11615437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781286","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 reference microRNAs in skeletal muscle of a canine model of Duchenne muscular dystrophy.","authors":"Dominique O Riddell, John C W Hildyard, Rachel C M Harron, Dominic J Wells, Richard J Piercy","doi":"10.12688/wellcomeopenres.22481.2","DOIUrl":"10.12688/wellcomeopenres.22481.2","url":null,"abstract":"<p><strong>Background: </strong>Duchenne muscular dystrophy (DMD) is a fatal muscle wasting disease caused by mutations in the dystrophin gene. DE50-MD dogs are an animal model of DMD used as a final translational model for evaluation of promising treatments. MicroRNA (miR) expressions in the muscle of DE50-MD dogs represent potential biomarkers, but stable reference miRs must first be identified. The aim of this paper was to establish a panel of reference miRs for WT and DE50-MD dogs over a range of ages and muscle groups.</p><p><strong>Methods: </strong>RNA was extracted from WT and DE50-MD dog (N=6 per genotype) vastus lateralis muscle samples collected longitudinally at 3, 6, 9, 12, 15 and 18 months of age, and from muscles collected post-mortem (N=3 per genotype; cranial tibial, semimembranosus, lateral triceps and diaphragm). 87 RNAs were quantified in a subset of 6-month-old WT and DE50-MD muscles (N=4 per genotype) using the QIAcuity miFinder panel. GeNorm, BestKeeper and Normfinder were used to identify a candidate panel of the 8 most stable small RNAs, which were then quantified in all RNA samples, alongside the commonly used reference RNA snRNA U6.</p><p><strong>Results: </strong>The most stable miRs of this subset were used to normalise quantities of dystromiRs miR-1, miR-133a and miR-206, and fibromiR miR-214. MicroRNAs miR-191, let-7b, miR-125a and miR-15a were the most stable miRs tested, while snRNA U6 performed poorly. DystromiR expression, normalised to the geometric mean of the panel of reference miRs, was lower for miR-1 and miR-133a in DE50-MD compared to WT muscles, while miR-206 levels did not significantly differ between genotypes. FibromiR miR-214 was 2- to 4-fold higher in DE50-MD versus WT muscles.</p><p><strong>Conclusions: </strong>A normalisation factor derived from miR-191, let-7b, miR-125a and miR-15a is suitable for normalising miR expression data from WT and DE50-MD muscle over a range of ages and muscle types.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"362"},"PeriodicalIF":0.0,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11621615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801679","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":"Organophosphate and carbamate susceptibility profiling of Anopheles gambiae sl. across different ecosystems in southern Benin.","authors":"Camille Dossou, Genevieve Tchigossou, Massioudou Koto, Seun Michael Atoyebi, Eric Tossou, Danahé Adanzounon, Sandra Ateutchia Ngouanet, Haziz Sina, Innocent Djègbè, Adam Gbankoto, Charles Wondji, Rousseau Djouaka","doi":"10.12688/wellcomeopenres.21452.2","DOIUrl":"10.12688/wellcomeopenres.21452.2","url":null,"abstract":"<p><strong>Background: </strong>To overcome the spread of high pyrethroid resistance in the main malaria vectors and malaria disease persistence, it is crucial to look for effective and better resistance management strategies. Understanding the phenotypic profile of <i>Anopheles gambiae sl.</i> against alternatives insecticides like organophosphates and carbamates is crucial.</p><p><strong>Methods: </strong><i>Anopheles</i> larvae and pupae were collected from the breeding sites in rice fields, pineapple crop areas, and peri-urban areas. WHO susceptibility tests were conducted on unfed female mosquitoes aged 3-5 days old. Mosquitoes were exposed to malathion 5%, pirimiphos-methyl 0.25%, and bendiocarb 0.1% using the standard WHO protocol. Polymerase chain reaction (PCR) techniques were used to detect species, <i>kdr</i> and <i>Ace-1</i> mutations.</p><p><strong>Results: </strong><i>Anopheles gambiae sl.</i> from Sèdjè-Dénou rice field population was resistant to bendiocarb (0.1%) with a mortality rate of 72.2% whereas <i>Anopheles gambiae sl.</i> populations from Zinvié-Dokomey (rice field), Zè-Tozounmè (pineapple field), and Adjagbo (peri-urban area) were suspected to be resistant with mortality rates of 90%, 93.5%, 95.4% respectively. However, all of them were susceptible to organophosphates (malathion and pirimiphos-methyl) with a mortality rate of 100%. PCR assay revealed that 100% of the mosquitoes tested were <i>Anopheles coluzzii</i>. The frequencies of <i>Ace-1R</i> mutation in all <i>Anopheles coluzzii</i> populations tested were low (3-27%).</p><p><strong>Conclusions: </strong>Organophosphates (malathion and pirimiphos-methyl) have maintained their efficacy against <i>Anopheles coluzzii</i> populations from Sèdjè-Dénou (rice field), Zè Tozounmè (pineapple field), Zinvié Dokomey (rice field), or Adjagbo (peri-urban area). The good efficacy of these organophosphates against <i>Anopheles coluzzii</i> populations from the southern part of Benin are observed in the current study. The use of pirimiphos-methyl for IRS in this part of the country would be a successful alternative for malaria control in this area.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"424"},"PeriodicalIF":0.0,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11599805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740527","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 glistening inkcap, <i>Coprinellus micaceus Coprinellus</i>; <i>Coprinellus micaceus</i> ((Bull.) Vilgalys, Hopple & Jacq. Johnson, 2001).","authors":"Richard Wright, Kieran Woof","doi":"10.12688/wellcomeopenres.23349.1","DOIUrl":"10.12688/wellcomeopenres.23349.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Coprinellus micaceus</i> (the glistening inkcap; Basidiomycota; Agaricomycetes; Agaricales; Psathyrellaceae). The genome sequence is 52.0 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 54.99 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"677"},"PeriodicalIF":0.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11617826/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787209","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":"\"Transgenders are not dinosaurs!\" Stigma faced by transgender women in their daily lives in India: implications for research and policy.","authors":"Sandhya Kanaka Yatirajula, Ankita Mukherjee, Santosh Giri, Pallab K Maulik","doi":"10.12688/wellcomeopenres.22658.1","DOIUrl":"10.12688/wellcomeopenres.22658.1","url":null,"abstract":"<p><strong>Background: </strong>Transgender women face stigma that adversely impacts their mental wellbeing. The stigma can be self-directed (internal), discrimination, violence and hatred directed towards them by others, mostly cis-gender persons (interpersonal stigma) and discrimination faced at the level of institutional arrangements (structural stigma).</p><p><strong>Methods: </strong>This was an exploratory study that used qualitative methods of data collection (focused group discussions and in-depth interviews) to gather data from consenting adult trans women who lived in the city of Kolkata situated in the eastern state of West Bengal in India.</p><p><strong>Results: </strong>The findings showed that trans women faced the trauma of non-acceptance and even rejection by their families when they began to express their chosen gender. Their gender non-conforming behaviour made them the butt of ridicule and harassment in school, resulting in many of them not finishing school. This made finding employment difficult. The trans women study participants also faced harassment at the hands of the police and from hospital staff, making them reluctant to approach the police for help and seek treatment from health providers for their physical as well as mental health concerns.</p><p><strong>Conclusions: </strong>It is important for researchers to be cognizant of the challenges faced by trans women/transgender people while designing and conducting research. It is also important for policymakers to make gender affirming policies to mitigate and eliminate the stigma that transgender people are subject to thereby promoting their wellbeing.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"496"},"PeriodicalIF":0.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11541070/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605136","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 sycamore periphyllus aphid, <i>Periphyllus acericola</i> (Walker, 1848).","authors":"Liam M Crowley","doi":"10.12688/wellcomeopenres.23341.1","DOIUrl":"10.12688/wellcomeopenres.23341.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual female <i>Periphyllus acericola</i> (the sycamore periphyllus aphid; Arthropoda; Insecta; Hemiptera; Aphididae). The genome sequence has a total length of 405.30 megabases. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 33.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,463 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"676"},"PeriodicalIF":0.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11612552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142772806","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 for linking participants' retailer 'loyalty card' records into the Avon Longitudinal Study of Parents and Children (ALSPAC).","authors":"Anya Skatova, Andy Boyd","doi":"10.12688/wellcomeopenres.18900.1","DOIUrl":"10.12688/wellcomeopenres.18900.1","url":null,"abstract":"<p><p>Longitudinal population studies (LPS) have a long history of providing insights into how individual consumption patterns and other lifestyle choices affect health and socio-economic outcomes. LPS typically operate as research databanks, integrating rich and deep phenotypic data - covering diverse aspects of individual, family and household status - with genomic data and linked records on health and socio-economic outcomes. However, individual consumption and behavioural choices are traditionally studied solely using self-report methods which are prone to known biases. We propose to enrich LPS databanks with a new form of digital footprint data - individual shopping history records. These are collected by supermarkets through \"loyalty\" card schemes and can provide a new perspective on real world behaviours and history of consumption. However, as a novel class of data in the context of longitudinal research, our ability to assess the quality and completeness of the data is unknown, as is our ability to effectively triangulate between self-reported and linked data. This paper describes a protocol for linking individual level shopping history data into a LPS using Avon Longitudinal Study of Parents and Children (ALSPAC) as a testbed. The protocol covers the process of establishing participant fair processing, an ethical and legal basis for the linkage framework itself, and how these data will be integrated into the ALSPAC databank. It does not cover the subsequent research use of these data. The protocol was built on an extensive participant engagement and acceptability work and has been approved by the ALSPAC Law and Ethics committee.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"8 ","pages":"99"},"PeriodicalIF":0.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10474335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10151905","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":"Improving health outcomes among older adults in India: effectiveness and implementability of a novel comprehensive geriatric assessment based intervention.","authors":"Jaya Singh Kshatri, Susan Shenkin, Stewart Mercer, David Weller, Subrata Kumar Palo, Sandipana Pati, Daisy Janssen, Sanghamitra Pati","doi":"10.12688/wellcomeopenres.19796.3","DOIUrl":"10.12688/wellcomeopenres.19796.3","url":null,"abstract":"<p><strong>Background: </strong>There is significant evidence on the benefits of comprehensive assessment in older adults. But this evidence is primarily from western countries and in secondary care settings. National policies in India recognize this need and envision community-based screening and facility-based assessment programs integrated into the care pathways for the elderly. However, this is yet to translate into specific interventions, primarily due to lack of complex interventions necessary and evidence of their effectiveness. This study aims to design and pilot an integrated (Community + Facility) Elderly Health Status Assessment and Screening (EHSAS) intervention to improve health outcomes of older adults and assess its feasibility for implementation in Indian rural settings.</p><p><strong>Methods: </strong>We propose a hybrid design where we will build the complex intervention, develop and validate the tools needed, pilot it using an exploratory cluster randomized trial and evaluate its implementatbility using the Exploration-Preparation-Implementation-Sustainment (EPIS) framework.</p><p><strong>Conclusions: </strong>This study will fill critical gaps in evidence regarding the effectiveness of geriatric screening and assessment in community and primary care settings in low-middle income countries and provide validated tools and implementation models for adoption into national programs.</p><p><strong>Registration: </strong>CTRI/2023/07/055661.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"8 ","pages":"414"},"PeriodicalIF":0.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11564926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648815","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 influence of maternal long term health conditions including multimorbidity on child oral health: A scoping review and evidence gap map protocol.","authors":"Faith Campbell, Scott McGregor, Louise Marryat, Ryan Stewart, Jan Clarkson, Heather Cassie","doi":"10.12688/wellcomeopenres.21725.2","DOIUrl":"10.12688/wellcomeopenres.21725.2","url":null,"abstract":"<p><strong>Objective: </strong>This scoping review will map the extent and type of evidence in relation to the association between maternal long term health conditions (LTCs), including multimorbidity, and child oral health.</p><p><strong>Introduction: </strong>Newer theories are emerging that detail the many factors that can influence child oral health at child, family and community levels. More recently, the association between maternal general health and child oral health has been explored, with preliminary evidence suggesting a link between shared environmental factors and diet/substance use during pregnancy causing childhood caries.</p><p><strong>Inclusion criteria: </strong>All published studies that describe the relationship between maternal LTCs (including multimorbidity) and child oral health. There will be no limitation on the date of publication due to the limited number of studies available from the initial search of PubMed. The review will exclude case studies, abstracts, and grey literature. Literature must be in English language.</p><p><strong>Methods: </strong>The following databases will be searched; CINAHL, Cochrane Library, Maternity and Infant Care, Medline via PubMed, Scopus, Web of Science. The search will include sources in English only and will be undertaken between April and July 2024. Studies to be included will be of any type of study design that describe a relationship between maternal long term health conditions, including maternal long term oral health conditions, and child oral health. Data extraction will be undertaken using tabulation of results by at least two independent reviewers. Narrative analysis of the evidence will be undertaken, and results will be presented in a narrative and tabular manner due to the heterogenous and limited evidence base found in the test search. This review has been registered prospectively on Open Science Framework, ( https://doi.org/10.17605/OSF.IO/ECSWJ). The review will also inform an Evidence Gap Map (EGM) to illustrate the current evidence base regarding maternal health factors that influence child oral health.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"299"},"PeriodicalIF":0.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568369/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648819","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}