Wellcome Open Research最新文献

{"title":"The genome sequence of <i>Inga laurina</i> (Sw.) Willd.","authors":"Rowan J Schley, R Toby Pennington, Alex D Twyford, Kyle G Dexter, Catherine Kidner, Todd P Michael","doi":"10.12688/wellcomeopenres.23057.1","DOIUrl":"10.12688/wellcomeopenres.23057.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual of <i>Inga laurina</i> (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 899.60 megabases. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, supporting the individual being an autotetraploid with 2 <i>n</i>=4 <i>x</i>=52. The mitochondrial and plastid genome assemblies have lengths of 1,261.88 kilobases and 176.27 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 33,101 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"567"},"PeriodicalIF":0.0,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11558168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142628826","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":"Investigating the feasibility and potential of combining industry AMR monitoring systems: a comparison with WHO GLASS.","authors":"Eve Rahbé, Aleksandra Kovacevic, Lulla Opatowski, Quentin J Leclerc","doi":"10.12688/wellcomeopenres.21181.2","DOIUrl":"10.12688/wellcomeopenres.21181.2","url":null,"abstract":"<p><strong>Background: </strong>Efforts to estimate the global burden of antimicrobial resistance (AMR) have highlighted gaps in existing surveillance systems. Data gathered from hospital networks globally by pharmaceutical industries to monitor antibiotic efficacy in different bacteria represent an underused source of information to complete our knowledge of AMR burden.. We analysed available industry monitoring systems to assess to which extent combining them could help fill the gaps in our current understanding of AMR levels and trends.</p><p><strong>Methods: </strong>We analysed six industry monitoring systems (ATLAS, GEARS, SIDERO-WT, KEYSTONE, DREAM, and SOAR) obtained from the Vivli platform and reviewed their respective isolates collection and analysis protocols. Using the R software, we designed a pipeline to harmonise and combine these into a single dataset. We assessed the reliability of resistance estimates from these sources by comparing the combined dataset to the publicly available subset of WHO GLASS for shared bacteria-antibiotic-country-year combinations.</p><p><strong>Results: </strong>Combined, the industry monitoring systems cover 18 years (4 years for GLASS), 85 countries (71), 412 bacterial species (8), and 75 antibiotics (25). Although all industry systems followed a similar centralised testing approach, the patient selection protocol and associated sampling period were unclear. Over all reported years and countries, E.coli, K. pneumoniae and S. aureus resistance rates were in >65% of cases within 0.1 of the corresponding estimate in GLASS. We did not identify systemic bias towards resistance in industry systems compared to GLASS.</p><p><strong>Conclusions: </strong>High agreement values for available comparisons with GLASS suggest that data for other bacteria-antibiotic-country-year combinations only present in industry systems could complement GLASS; however, for this purpose patient and isolate selection criteria must first be clarified to understand the representativeness of industry systems. This additional source of information on resistance levels could help clinicians and stakeholders prioritize testing and select appropriate antibiotics in settings with limited surveillance data.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"248"},"PeriodicalIF":0.0,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381755","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 does Public Financial Management (PFM) influence health system efficiency: A scoping review.","authors":"Anita Musiega, Benjamin Tsofa, Edwine Barasa","doi":"10.12688/wellcomeopenres.22533.1","DOIUrl":"10.12688/wellcomeopenres.22533.1","url":null,"abstract":"<p><strong>Background: </strong>Effective Public Financial Management (PFM) approaches are imperative in the quest for efficiency in health service delivery. Reviews conducted in this area have assessed the impact of PFM approaches on health system efficiency but have left out the mechanisms through which PFM influences efficiency. This scoping review aims to synthesize evidence on the mechanisms by which PFM influences health system efficiency.</p><p><strong>Methods: </strong>We searched databases of PubMed and Google Scholar and websites of the World Health Organization (WHO), World Bank and Overseas Development Institute (ODI) for peer-reviewed and grey literature articles that provided data on the relationship between PFM and health system efficiency. Three reviewers screened the articles for eligibility with the inclusion criteria. Data on PFM and health system efficiency was charted and summarized. We then reported the mechanisms by which PFM influence efficiency.</p><p><strong>Results: </strong>PFM processes and structures influence health system efficiency by influencing; the alignment of resources to health system needs, the cost of inputs, the motivation of health workers, and the input mix.</p><p><strong>Conclusion: </strong>The entire budget process influences health system efficiency. However, most of the findings are drawn from studies that focused on aspects of the budget process. Studies that look at PFM in totality will help explore other cross-cutting issues within sections of the budget cycle; they will also bring out the relationship between the different phases of the budget cycle.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"566"},"PeriodicalIF":0.0,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11502999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509138","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 a living mapping review of global research funding for infectious diseases with a pandemic potential - Pandemic PACT.","authors":"Olena Seminog, Rodrigo Furst, Thomas Mendy, Omid Rohanian, Shanthi Levanita, Zaharat Kadri-Alabi, Nusrat Jabin, Georgina Humphreys, Emilia Antonio, Adrian Bucher, Alice Norton","doi":"10.12688/wellcomeopenres.21202.2","DOIUrl":"10.12688/wellcomeopenres.21202.2","url":null,"abstract":"<p><p>The COVID CIRCLE initiative Research Project Tracker by UKCDR and GloPID-R and associated living mapping review (LMR) showed the importance of sharing and analysing data on research at the point of funding to improve coordination during a pandemic. This approach can also help with research preparedness for outbreaks and hence our new programme the Pandemic Preparedness: Analytical Capacity and Funding Tracking Programme (Pandemic PACT) has been established. The LMR described in this protocol builds on the previous UKCDR and GloPID-R COVID-19 Research Project database with addition of the priority diseases from the WHO Blueprint list plus initial additions of pandemic influenza, mpox and plague. We capture data on new funding commitments directly from funders and map these against a core ontology (aligned to existing research roadmaps). We will analyse regularly collated new research funding commitments to provide an open, accessible, near-real-time overview of the funding landscape for a wide range of infectious disease and pandemic preparedness research and assess gaps. The periodicity of updates will be increased in the event of a major outbreak. We anticipate that this LMR and the associated online tool will be a useful resource for funders, policy makers and researchers. In the future, our work will inform a more coordinated approach to research funding by providing evidence and data, including identification of gaps in funding allocation with a particular focus on low- and middle-income countries.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"156"},"PeriodicalIF":0.0,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11487232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476096","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":"\"Kuteteza\": A community-engaged COVID-19 Prevention and Protection Initiative in Southern Malawi.","authors":"Donnie Mategula, Ana Ibarz-Pavón, Melody Sakala, Marlen Chawani, Henry Sambakunsi, Mphatso D Phiri, Latif Ndeketa, Mwiza Sambo, Wisdom Shonga, Clara Sambani, Titus Divala, Steve Vinkhumbo, Dominic Nkhoma, Robert Mataya, Wongani Nyangulugu, Sepeedeh Saleh","doi":"10.12688/wellcomeopenres.20789.2","DOIUrl":"10.12688/wellcomeopenres.20789.2","url":null,"abstract":"<p><strong>Background: </strong>The COVID-19 epidemic in Malawi involved almost 90,000 recorded cases and 2,638 deaths. In response to early concerns about vulnerable older people in rural areas, we developed 'Kuteteza': a COVID-19 mitigation response project. Clinicians, public health professionals, and researchers collaborated with government and district-level staff in two Southern Malawi districts. Interventions included supported 'shielding' of older people - minimising social mixing whilst having their daily needs supported. Additional mitigation strategies included provision of masks, handwashing stations, and soap. Government partnerships allowed additional support for vulnerable groups. We present the findings of a realist project evaluation, assessing the feasibility of this approach.</p><p><strong>Methods: </strong>We collated anonymised descriptive data on Kuteteza procedures and conducted qualitative structured observations in villages involved in the initiative. We carried out three focus groups involving community members, frontline health staff, and volunteers in each setting. These provided deeper insights into experiences of the pandemic and impacts of the intervention, including suggested opportunities during future outbreaks.</p><p><strong>Results: </strong>The project involved 25 villages across two districts, with 1,087 people over the age of 60 voluntarily participating in 'shielding'. Supplies of food, water, and cooking fuel were mostly arranged within the family. In Kuteteza villages, the handwashing stations and soap were widely used, and there was awareness and some observance of COVID-19 prevention measures. The project, including the provision of supplies, was greatly appreciated by communities, but wider contextual constraints - namely widespread economic insecurity - presented persisting challenges. Suggestions for improvement largely concerned project enhancements and extensions.</p><p><strong>Conclusions: </strong>Through effective stakeholder engagement and contribution to national response strategy, the Kuteteza project helped raise COVID-19 awareness and supported populations at a critical time in the pandemic. Kuteteza approaches were welcomed locally and may be incorporated in future epidemic responses. Supported 'shielding' should be paired with government-led measures to mitigate economic hardship.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"24"},"PeriodicalIF":0.0,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11514378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142523227","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 Heart and Dart moth, <i>Agrotis exclamationis</i> (Linnaeus, 1758).","authors":"Ronald Forrester, Denise C Wawman","doi":"10.12688/wellcomeopenres.23042.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23042.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual female Heart and Dart moth, <i>Agrotis exclamationis</i> (Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 725.10 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,008 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"563"},"PeriodicalIF":0.0,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11496940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509144","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 yellow-girdled <i>Dasysyrphus</i>, <i>Dasysyrphus tricinctus</i> (Fallén, 1817).","authors":"Liam M Crowley, Katie J Woodcock","doi":"10.12688/wellcomeopenres.22892.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.22892.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual male <i>Dasysyrphus tricinctus</i> (the yellow-girdled <i>Dasysyrphus</i>; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence spans 1,054.90 megabases. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 18.39 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"561"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11499735/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509148","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 cuckoo wrasse, <i>Labrus mixtus</i> Linnaeus 1758.","authors":"Belle Heaton, Rachel Brittain, Patrick Adkins, Kesella Scott-Somme, Joanna Harley","doi":"10.12688/wellcomeopenres.23063.1","DOIUrl":"10.12688/wellcomeopenres.23063.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual <i>Labrus mixtus</i> (the cuckoo wrasse; Chordata; Actinopteri; Labriformes; Labridae). The genome sequence has a total length of 740.60 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.49 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"549"},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142628862","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 cephid sawfly, <i>Cephus spinipes</i> (Panzer, 1800).","authors":"Gavin R Broad, Laura Sivess, Stephanie Holt, Chris Fletcher, Inez Januszczak","doi":"10.12688/wellcomeopenres.23068.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.23068.1","url":null,"abstract":"<p><p>We present a genome assembly from an individual male cephid sawfly, <i>Cephus spinipes</i> (Arthropoda; Insecta; Hymenoptera; Cephidae). The genome sequence has a total length of 238.60 megabases. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.43 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"557"},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11494279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509142","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":"Chromosomal reference genome sequences for the malaria mosquito, <i>Anopheles coustani</i>, Laveran, 1900.","authors":"Lemonde B A Bouafou, Diego Ayala, Boris K Makanga, Nil Rahola, Harriet F Johnson, Haynes Heaton, Martin G Wagah, Joanna C Collins, Ksenia Krasheninnikova, Sarah E Pelan, Damon-Lee B Pointon, Ying Sims, James W Torrance, Alan Tracey, Marcela Uliano-Silva, Jonathan M D Wood, Katharina von Wyschetzki, Shane A McCarthy, Daniel E Neafsey, Alex Makunin, Mara K N Lawniczak","doi":"10.12688/wellcomeopenres.22983.1","DOIUrl":"10.12688/wellcomeopenres.22983.1","url":null,"abstract":"<p><p>We present genome assembly from individual female <i>An. coustani</i> (African malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae) from Lopé, Gabon. The genome sequence is 270 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled for both species. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"551"},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11490835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476097","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}