Wellcome Open Research最新文献

{"title":"The genome sequence of the Antarctic lanternfish, <i>Electrona antarctica</i> (Günther, 1878).","authors":"Iliana Bista, Martin Collins","doi":"10.12688/wellcomeopenres.23803.2","DOIUrl":"10.12688/wellcomeopenres.23803.2","url":null,"abstract":"<p><p>We present a genome assembly from an individual female <i>Electrona antarctica</i> (the Antarctic lanternfish; Chordata; Actinopterigii; Myctophiformes; Myctophidae). The genome sequence has a total length of 1,427.40 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 20.02 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"89"},"PeriodicalIF":0.0,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606448","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":"(Un)timely care: findings from the Waiting Times project.","authors":"Lisa Baraitser, Kelechi Anucha, Jocelyn Catty, Stephanie Davies, Jordan Osserman, Laura Salisbury, Michael J Flexer, Martin D Moore","doi":"10.12688/wellcomeopenres.22556.2","DOIUrl":"10.12688/wellcomeopenres.22556.2","url":null,"abstract":"<p><p>There is a historic crisis in waiting times in the UK's National Health Service. Crisis brings both a call for judgement - a response to the question 'what has gone wrong?' - and a call to action, such as better management, more resources, strategies to mitigate staff burnout, or even a shift in access commitments to reduce demand. However, not all forms of waiting are a sign of service inefficiency or failure, or a form of abandonment or lack of care. Instead, we argue that all healthcare entails waiting, and other forms of elongated time such as pausing to observe, staying alongside patients at end of life, enduring or even encouraging the repeated presentations of those with medically unexplained symptoms, delaying treatment to see what time will bring the situation, or stopping treatment as an ethical intervention. In this paper, we offer three examples of care practices that require waiting, demanding considerable patience on the part of patients and healthcare workers: care for the chronically unwell in general practice; care of young people in mental health crisis; and care for trans and gender-questioning young people. When time is represented as a finite linear resource to be used efficiently, 'streamlining', speeding up systems, and making cuts to 'wasteful' practices seem like obvious solutions. But we argue that it is only by reckoning with the complex relationality and fundamental untimeliness of the care that runs alongside even the most timely interventions, that we can understand what it means to wait in and for the NHS, and what resources might be needed for the service and its users to flourish.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"490"},"PeriodicalIF":0.0,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145001132","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 Pearly Heath, <i>Coenonympha arcania</i> Linnaeus, 1761 (Lepidoptera: Nymphalidae).","authors":"Roger Vila, Sabina Vila, Paul Doniol-Valcroze, Charlotte J Wright, Joana I Meier, Mark L Blaxter","doi":"10.12688/wellcomeopenres.24624.1","DOIUrl":"10.12688/wellcomeopenres.24624.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Coenonympha arcania</i> (Pearly Heath; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The assembly contains two haplotypes with total lengths of 480.99 megabases and 458.33 megabases. Most of haplotype 1 (99.95%) is scaffolded into 29 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.28 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"364"},"PeriodicalIF":0.0,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145186913","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 Mountain Bumble Bee, <i>Bombus monticola</i> Smith, 1849 (Hymenoptera: Apidae).","authors":"Louise Hislop","doi":"10.12688/wellcomeopenres.24577.1","DOIUrl":"10.12688/wellcomeopenres.24577.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Bombus monticola</i> (Mountain Bumble Bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence has a total length of 306.99 megabases. Most of the assembly (90.92%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 24.12 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"367"},"PeriodicalIF":0.0,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12409256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145016269","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 Alpine Milkvetch, <i>Astragalus alpinus</i> L. (Fabales: Fabaceae).","authors":"Markus Ruhsam, Peter M Hollingsworth","doi":"10.12688/wellcomeopenres.24576.1","DOIUrl":"10.12688/wellcomeopenres.24576.1","url":null,"abstract":"<p><p>We present a genome assembly of <i>Astragalus alpinus</i> (Alpine Milkvetch; Streptophyta; Magnoliopsida; Fabales; Fabaceae). The assembly consists of two haplotypes with total lengths of 766.58 megabases and 749.43 megabases. Most of haplotype 1 (98.55%) and of haplotype 2 (99.06%) are each scaffolded into 8 chromosomal pseudomolecules. The mitochondrial sequence has a length of 313.83 kilobases and the plastid genome assembly has a length of 123.2 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"366"},"PeriodicalIF":0.0,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12398678/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144971067","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 SnackerTracker: A novel home-cage monitoring device for measuring food-intake and food-seeking behaviour in mice.","authors":"Marissa Mueller, Selma Tir, Carina Pothecary, Elise Meijer, Laurence Brown, Keiran Foster, Vladyslav Vyazovskiy, Stuart Peirson, Zoltán Molnár","doi":"10.12688/wellcomeopenres.23850.2","DOIUrl":"10.12688/wellcomeopenres.23850.2","url":null,"abstract":"<p><strong>Background: </strong>Accurately measuring activity and feeding is important in laboratory animal research, whether for welfare-monitoring or experimental recording. Quantification commonly involves manual pellet-weighing; however, this can physically disturb animals and cannot continuously assess both the amount and pattern of feeding over time. Improved means of food-intake measurement have been developed but can be costly and incompatible with many cage configurations.</p><p><strong>Methods: </strong>We developed the <i>SnackerTracker-</i>a novel home-cage monitoring system which continuously records food-intake, food-seeking activity, and ambient light conditions in laboratory mice. After benchtop validations, we tested this device by recording from C57BL/6J control mice under 12:12h light:dark (LD) and constant darkness (DD) to measure circadian rhythms in feeding behaviour. We then recorded from mice having disturbed circadian rhythms (cryptochrome 1 and 2 double-knockouts, <i>Cry1 ^-/-,Cry2 ^-/-</i> ), where irregular activity and feeding patterns were expected. Animals were individually housed with <i>SnackerTrackers</i> in Digital Ventilated Cages ^® (DVC, Tecniplast) to measure home cage activity. After habituation, 48-hour <i>SnackerTracker</i> and DVC recordings were collected and compared.</p><p><strong>Results: </strong>The <i>SnackerTracker</i> accurately measured food-masses throughout benchtop and <i>in vivo</i> validation tests. Time-course <i>SnackerTracker</i> feeding traces correlated well with DVC activity recordings, indicating that feeding reflects general cage locomotion in control and cryptochrome-deficient animals. In LD, <i>SnackerTracker</i> data showed expected feeding/fasting cycles in control and cryptochrome-deficient animals yet reduced dark-phase feeding in cryptochrome-deficient mice. In DD, increased feeding during the subjective nighttime was maintained in control animals but abolished in cryptochrome-deficient mice. Surprisingly, cryptochrome-deficient animals exhibited ultradian feeding rhythms.</p><p><strong>Conclusions: </strong>We validate the performance and value of monitoring home cage feeding using the <i>SnackerTracker</i>. Here we show that cryptochrome-deficient animals have decreased food-intake in LD, diurnal arrhythmicity in DD, and ultradian rhythms in feeding behaviour. The <i>SnackerTracker</i> provides a cost-effective, open-source, and user-friendly method of animal food intake and activity measurement.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"172"},"PeriodicalIF":0.0,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12375189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144971182","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":"Exploring mothers' and grandmothers' perceptions of animal-source complementary foods in the diets of young children in The Gambia: A qualitative study.","authors":"Emily Dawson, Ahmed Futa, Maaike Klappe, Carla Cerami, Hilary Davies-Kershaw","doi":"10.12688/wellcomeopenres.23090.2","DOIUrl":"10.12688/wellcomeopenres.23090.2","url":null,"abstract":"<p><strong>Background: </strong>In The Gambia, many children consume diets that are lacking in nutrients that are essential for their growth and development. This study aims to explore Gambian mothers' and grandmothers' perceptions around animal source foods (meat, eggs, milk etc.) in order to inform future interventions focused on improving child feeding practices.</p><p><strong>Methods: </strong>In July and August 2023, nine semi - structured focus group discussions were conducted with mothers and grandmothers in two settings in The Gambia. A purposeful sample of participants were recruited with the support of each local Medical Research Council clinic. Data were analysed using the framework method and thematic analysis. Participants included 19 mothers and 12 grandmothers in a semi-rural area and 12 mothers and 12 grandmothers in a rural area, caring for children 6-24 and grandmothers were in separate groups.</p><p><strong>Results: </strong>Knowledge gaps were identified in both settings regarding aspects of complementary feeding, such as the appropriate timing and methods for introducing animal source foods to children's diets. Differences were noted in the availability and dissemination of infant and young child feeding information in the two settings, emphasising the crucial role of contextual factors in shaping future programmes. The accessibility and affordability of animal source foods, was found to be a key determinant of their inclusion into children's diets. A reliance on commercially available complementary foods was common in both settings.</p><p><strong>Conclusion: </strong>This study reveals disparities between current complementary feeding practices and guidelines in this setting. It also underscores context-specific barriers caregivers encounter in offering diverse complementary foods, including animal source foods. A high reliance on commercially available complementary foods was also uncovered, particularly in Keneba. Further research is recommended to aid the development of context- specific interventions.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"65"},"PeriodicalIF":0.0,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12423624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145065610","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 scaffold-level genome sequence of an encrusting sponge, <i>Halisarca caerulea</i> Vacelet & Donadey, 1987, and its associated microbial metagenome sequences.","authors":"Jasper M de Goeij, Benjamin Mueller, Michelle Achlatis, Sara Campana, Meggie Hudspith, Niklas A Kornder, Ute Hentschel, Graeme Oatley, Elizabeth Sinclair, Eerik Aunin, Noah Gettle, Camilla Santos, Michael Paulini, Haoyu Niu, Victoria McKenna, Rebecca O'Brien","doi":"10.12688/wellcomeopenres.24281.1","DOIUrl":"10.12688/wellcomeopenres.24281.1","url":null,"abstract":"<p><p>We present a scaffold-level genome assembly from a <i>Halisarca caerulea</i> specimen (encrusting sponge; Porifera; Demospongiae; Chondrillida; Halisarcidae). The genome sequence is 195.70 megabases in span. The mitochondrial genome has also been assembled and is 19.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,722 protein-coding genes. The metagenome of the specimen was also assembled and four binned bacterial genomes related to the relevant sponge symbiont clades Alphaproteobacteria bacterium GM7ARS4 and Gammaproteobacteria bacterium <i>AqS2</i> ((Tethybacterales) were identified.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"344"},"PeriodicalIF":0.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12391866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144971223","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":"Decoding post-transcriptional gene expression controls in trypanosomatids using machine learning.","authors":"Michele Tinti, David Horn","doi":"10.12688/wellcomeopenres.23817.2","DOIUrl":"10.12688/wellcomeopenres.23817.2","url":null,"abstract":"<p><strong>Background: </strong>We recently described a pervasive cis-regulatory role for sequences in <i>Trypanosoma brucei</i> mRNA untranslated regions (UTRs). Specifically, increased translation efficiency (TE) was associated with the dosage and density of A-rich tracts. This finding raised three related questions: (1) What relative contributions do UTRs and codon usage bias make to TE in <i>T. brucei</i>? (2) What relative contributions do these sequences make to mRNA steady-state levels in <i>T. brucei</i>? (3) Do these sequences make substantial contributions to TE and/or mRNA steady-state levels in the related parasitic trypanosomatids, <i>T. cruzi</i> and <i>Leishmania</i>?</p><p><strong>Methods: </strong>To address these questions, we applied machine learning to analyze existing transcriptome, TE, and proteomics data.</p><p><strong>Results: </strong>Our predictions indicate that both UTRs and codon usage bias impact gene expression in all three trypanosomatids, but with substantial differences. In <i>T. brucei</i>, TE is primarily correlated with longer A-rich and C-poor UTRs. The situation is similar in <i>T. cruzi</i>, but codon usage bias makes a greater contribution to TE. In <i>Leishmania</i>, median TE is higher and is more strongly correlated with longer (A)U-rich UTRs and with codon usage bias. Codon usage bias has a major impact on mRNA abundance in all three trypanosomatids, while analysis of <i>T. brucei</i> proteomics data yielded results consistent with the view that this is due to differential translation elongation rates.</p><p><strong>Conclusions: </strong>Taken together, our findings indicate that gene expression control in trypanosomatids operates primarily at the point of translation, which is impacted by both UTRs and codon usage. We suggest a model whereby UTRs control the rate of translation initiation, while favoured codons increase the rate of translation elongation, thereby reducing mRNA turnover.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"173"},"PeriodicalIF":0.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12304876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144745291","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":"Strengthening Community Antimicrobial Stewardship in Africa: A Systematic Review of the Roles, Challenges, and Opportunities of Community Health and Animal Health Workers.","authors":"Conrad Tumwine, Reuben Kiggundu, Fahad Lwaigale, Herman Mwanja, Hannigton Katumba, Mackline Hope, J P Waswa, Flavia Dhikusooka, Vivian Twemanye, Andrew Kambugu, Francis Kakooza, Dathan Byonanebye","doi":"10.12688/wellcomeopenres.24387.1","DOIUrl":"10.12688/wellcomeopenres.24387.1","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) remains a critical global health challenge, and is mainly due to inappropriate antimicrobial use in human and animal health sectors. This systematic review examines the roles of Community Animal Health Workers (CAHWs) and Community Health Workers (CHWs) in antimicrobial stewardship (AMS) across Africa where AMR burden is highest and AMS programs are limited. Following PRISMA guidelines, this systematic review analyzed 16 studies (2017-2024) from nine African nations. We identified seven key roles of CAHWs and CHWs in AMS: 1) provision of clinical services (13 studies); 2) community mobilization (8 studies); 3) health promotion (7 studies); 4) provision of preventive services (5 studies); 5) epidemiological surveillance (4 studies); 6) advocacy (2 studies), and 7) medical waste management (2 studies). Despite their roles, challenges such as lack of supportive legislation (3 studies), inadequate remuneration (2 studies), and total reliance on foreign funding hinder AMS program sustainability. While most studies (14 studies) indicated that CAHWs and CHWs had received AMS training, their roles in the national AMR strategies remain unclear. CAHW and CHWs could be leveraged in advancing health promotion, raising AMR awareness, supporting AMR surveillance, enhancing integrated management of diseases, and improving waste management within One Health frameworks. To realize this potential, there is a need to formalize CAHW/CHW roles through targeted legislation, specialized training and sustainable funding. This evidence highlights the critical need for policy reforms to harness their potential in strengthening health systems and curbing AMR across Africa. PROSPERO registration number: CRD420251027215.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"346"},"PeriodicalIF":0.0,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12411836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145016216","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}