Wellcome Open Research最新文献

{"title":"The genome sequence of the particolored bat, Vespertilio murinus Linnaeus, 1758","authors":"Bob Vandendriessche, An Martel, Meike Mai, E. Teeling, Sonja C. Vernes","doi":"10.12688/wellcomeopenres.22606.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22606.1","url":null,"abstract":"We present a genome assembly from an individual male Vespertilio murinus (the particolored bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence is 1,925.6 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.96 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"31 38","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141800526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of the Hungarian meadow viper, Vipera ursinii rakosiensis Méhely, 1893","authors":"B. Halpern, Judit Vörös, Ann M. Mc Cartney, Giulio Formenti, Alice Mouton","doi":"10.12688/wellcomeopenres.22694.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22694.1","url":null,"abstract":"We present a genome assembly from an individual female Vipera ursinii rakosiensis (the Hungarian meadow viper; Chordata; Lepidosauria; Squamata; Viperidae). The genome sequence is 1,625.0 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.38 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141801425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of a jewel beetle, Agrilus biguttatus (Fabricius, 1776)","authors":"Steve Garland","doi":"10.12688/wellcomeopenres.22762.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22762.1","url":null,"abstract":"We present a genome assembly from an individual female Agrilus biguttatus (jewel beetle; Arthropoda; Insecta; Coleoptera; Buprestidae). The genome sequence spans 368.10 megabases. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.41 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"37 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141800248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Probing the functional magnetic resonance imaging response to psilocybin in functional neurological disorder (PsiFUND): study protocol","authors":"Matt Butler, Catherine Bird, Carolina Maggio, Amy Durden, N. Modlin, Kete Campbell-Coker, Mark J Edwards, Susannah Pick, L. M. Millman, Emily Lowery, C.S.K. Bhagavan, Richard Kanaan, Dawn Golder, Bridget Mildon, Mitul Mehta, James Rucker, Timothy Nicholson","doi":"10.12688/wellcomeopenres.22543.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22543.1","url":null,"abstract":"Background Functional neurological disorder (FND) is a common cause of neurological symptoms including paralysis, seizures, and movement disorders. It is often debilitating, is associated with high health and social care costs, and can have a poor prognosis. Functional magnetic resonance imaging (fMRI) has suggested FND is a multi-network disorder; the default mode network (DMN) may be specifically implicated. Converging evidence suggests that other variable mechanisms including dissociation, interoception, and motor agency may be differentially abnormal in people with FND. Psychedelics are currently under investigation for numerous neuropsychiatric disorders and have been shown to disrupt functional networks such as the DMN. Administering psychedelics to people with FND will help us to probe mechanistic theories of the disorder. Protocol In this open-label neuroimaging study, we will administer 25mg oral psilocybin with psychological support to people with chronic FND (target n = 24). Participants will undergo resting-state and task-based (Libet’s clock, a measure of motor agency) fMRI sequences which will be compared in a pre-post manner. Additional mechanistic outcomes including measures of interoception (heartbeat tracking task), somatisation, illness perceptions, imaginative suggestibility, and dissociation will be collected. Data on expectancy, preparedness, and subjective experience of the psychedelic experience will also be gathered. Participants will be followed up for three months following psilocybin administration. fMRI changes in networks such as the DMN will be analysed using seed-based approaches, and additional exploratory analysis of resting-state imaging will take place. Discussion The study will help us to probe the mechanisms thought to potentially underpin FND. As the first modern study of psychedelics in FND, it will also help us to understand whether psychedelic administration alongside psychological support might be safe and feasible in this patient population.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"19 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141806298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Creating a body of physical activity evidence to test the generalisation of annotation methods for automated evidence synthesis","authors":"Oscar Castro, E. Norris, Alison J. Wright, Emily Hayes, Ella Howes, Candice Moore, Robert West, Susan Michie","doi":"10.12688/wellcomeopenres.21664.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21664.1","url":null,"abstract":"Background The Human Behaviour-Change Project (HBCP) aims to improve evidence synthesis in behavioural science by compiling intervention reports, annotating them according to an ontology, and using the resulting data 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 evidence relating to a different behaviour, namely physical activity, and (ii) describe the steps involved in developing this second HBCP corpus. Methods The development of the physical activity corpus took place in four stages: (i) reviewing the suitability of smoking cessation codes already used in the HBCP, (ii) defining the selection criteria and scope of the corpus, (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. Results 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. Conclusions 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.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141806447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Power Relations in Optimisation of Therapies and Equity in Access to Antibiotics (PROTEA) Study: investigating the intersection of socio-economic and cultural drivers on antimicrobial resistance (AMR) and its influence on healthcare access and health-providing behaviours in India and South Africa","authors":"E. Charani, Sipho Dlamini, Anastasia Koch, Sanjeev Singh, Rebecca Hodes, Ramanan Laxminarayan, D. Batheja, Elelwani L. Ramugondo, A. S. Mukherjee, M. Mendelson","doi":"10.12688/wellcomeopenres.20193.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.20193.1","url":null,"abstract":"Across social structures within society, including healthcare, power relations manifest according to gender, socioeconomic status, race, ethnicity, and class influencing infection related healthcare access and health providing-behaviours. Therefore, accounting for sociocultural drivers, including gender, race, and class, and their influence on economic status can improve healthcare access and health-providing behaviours in infection prevention and control (IPC) as well as antibiotic use, which in turn helps mitigate the spread of antimicrobial resistance (AMR). This Wellcome funded research will investigate how and why the social determinants of health and economic status influence how people seek, experience, and provide healthcare for suspected or proven (bacterial) infections and how these factors influence antibiotic prescribing and use in South Africa (upper middle-income country) and India (lower middle-income country). The aim of this body of work is to, (1) define and estimate the sociocultural and economic drivers for AMR in different resource settings, (2) design, implement and evaluate context-sensitive IPC and antimicrobial stewardship (AMS) interventions, and (3) inform policy and strategy for AMR mitigation. The population will be healthcare workers (HCWs), patients, and their carers across acute medical and surgical pathways where IPC and antibiotic-related healthcare access and health-providing behaviours will be studied. Qualitative methods will include ethnographic research, semi-structured in-depth interviews, and focus groups with healthcare providers, patients and carers. Quantitative analysis of bedside observational data from hospitals and population level data on antibiotic use will study the various predictors of AMR using bivariable and multivariable regression analyses. The research will provide high-quality evidence on how social determinants intersect with health, social well-being, and vulnerability in IPC practices and antibiotic use. Using this knowledge we will: 1) design, implement, and measure effects of interventions accounting for these factors; 2) provide a toolkit for advocacy for actors in AMR, and healthcare to assist them to promote dialogue, including policy dialogue on this issue. This work directly benefits the target population and informs healthcare services and practice across the participating countries with potential for wider translation. The setting will be hospitals in South Africa (middle-income country) and India (lower middle-income country). The population will be healthcare workers (HCWs), patients, and their carers across acute medical and surgical pathways where IPC and antibiotic-related health-seeking and health-providing behaviours will be studied. These populations represent communities most affected by infections and AMR because existing interventions do not address a) differences in how surgical versus medical teams manage infections; b) the role of the wider social network of indi","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"38 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141807263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of the blue mussel, Mytilus edulis Linnaeus, 1758","authors":"Simon Taylor, Bas Payne, Vengamanaidu Modepalli","doi":"10.12688/wellcomeopenres.22704.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22704.1","url":null,"abstract":"We present a genome assembly from an individual Mytilus edulis (the blue mussel; Mollusca; Bivalvia; Mytilida; Mytilidae). The genome sequence is 1,368.4 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.75 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"67 24","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141817827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of the jumping weevil, Orchestes rusci (Herbst, 1795)","authors":"Stephen Moran","doi":"10.12688/wellcomeopenres.22745.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22745.1","url":null,"abstract":"We present a genome assembly from an individual female Orchestes rusci (the jumping weevil; Arthropoda; Insecta; Coleoptera; Curculionidae). The genome sequence spans 624.00 megabases. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.73 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"38 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141814917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of the European harvest mouse, Micromys minutus (Pallas, 1771)","authors":"Michelle F. O'Brien, Rosa Lopez Colom","doi":"10.12688/wellcomeopenres.22747.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22747.1","url":null,"abstract":"We present a genome assembly from an individual female Micromys minutus (the European harvest mouse; Chordata; Mammalia; Rodentia; Muridae). The genome sequence spans 2,651.80 megabases. Most of the assembly is scaffolded into 34 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.24 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"26 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141816858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genome sequence of the black-headed gull, Chroicocephalus ridibundus (Linnaeus, 1766)","authors":"Rosa Lopez Colom, Michelle F. O'Brien","doi":"10.12688/wellcomeopenres.22741.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22741.1","url":null,"abstract":"We present a genome assembly from an individual male Chroicocephalus ridibundus (the black-headed gull; Chordata; Aves; Charadriiformes; Laridae). The genome sequence spans 1,417.60 megabases. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.82 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"9 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141817393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}