Wellcome Open Research最新文献

{"title":"The genome sequence of the Eurasian Curlew, <i>Numenius arquata</i> (Linnaeus, 1758).","authors":"Grace Walsh, Barry O' Donoghue, Jacob Höglund, Barry John McMahon","doi":"10.12688/wellcomeopenres.24272.1","DOIUrl":"10.12688/wellcomeopenres.24272.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Numenius arquata</i> (Eurasian Curlew; Chordata; Aves; Charadriiformes; Scolopacidae). The assembly contains two haplotypes with total lengths of 1,348.86 megabases and 1,198.36 megabases. Most of haplotype 1 (89.99%) is scaffolded into 41 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.13 kilobases. Gene annotation of this assembly on Ensembl identified 15,412 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"298"},"PeriodicalIF":0.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12381557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144971091","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 Small Sallow Mining Bee, <i>Andrena praecox</i> (Scopoli, 1763).","authors":"Liam M Crowley","doi":"10.12688/wellcomeopenres.24301.1","DOIUrl":"10.12688/wellcomeopenres.24301.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Andrena praecox</i> (Small Sallow Mining Bee; Arthropoda; Insecta; Hymenoptera; Andrenidae). The genome sequence has a total length of 563.05 megabases. The assembly is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 20.36 kilobases. Gene annotation of this assembly on Ensembl identified 12,005 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"290"},"PeriodicalIF":0.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12344408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849236","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 Small Dotted Buff moth, <i>Photedes minima</i> Haworth, 1809.","authors":"Douglas Boyes, Liam M Crowley, Timilehin Adewumi","doi":"10.12688/wellcomeopenres.24264.1","DOIUrl":"10.12688/wellcomeopenres.24264.1","url":null,"abstract":"<p><p>We present a genome assembly from a male specimen of <i>Photedes minima</i> (Small Dotted Buff; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 694.66 megabases. Most of the assembly (99.95%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.38 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"299"},"PeriodicalIF":0.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12284473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699676","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 PAICE project: Integrating health and health equity into UK climate change policy.","authors":"Michael Davies, Charlie Dearman, Rosemary Green, Andrew Haines, Clare Heaviside, Filiz Karakas, Sudheer Kumar Kuppili, Susan Michie, James Milner, Gemma Moore, David Osrin, Silvia Pastorino, Giorgos Petrou, Irene Pluchinotta, Charles Simpson, Phil Symonds, Catalina Turcu, Ruth Unstead-Joss, Simon Vakeva-Baird, Sarah Whitmee, Ke Zhou, Nici Zimmermann","doi":"10.12688/wellcomeopenres.23431.2","DOIUrl":"10.12688/wellcomeopenres.23431.2","url":null,"abstract":"<p><p>This paper announces a new initiative - the research project <i>Policy and Implementation for Climate & Health Equity</i> (PAICE), which aims to investigate the complex systemic connections between climate change action, health and health equity, for translation of evidence into policy and practice in the UK. Using transdisciplinary approaches, PAICE will: (1) co-develop a programme theory and linked monitoring and evaluation plan, (2) work with the UK Climate Change Committee (CCC) and the Greater London Authority (GLA) using system dynamics to analyse national and local policy opportunities, (3) build an integrated model of the effects of these policies on population health, health equity and greenhouse gas emissions, (4) apply the findings to the CCC monitoring framework and GLA policy development, and (5) use the programme theory to help evaluate achievement of PAICE processes and objectives. If successful, PAICE will have helped to establish a systems capability to (i) monitor whether Government plans are on track to deliver their climate targets and associated health impacts and (ii) understand how relevant policy and implementation approaches could be enhanced.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"14"},"PeriodicalIF":0.0,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11947659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143732086","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 kidney sponge, <i>Chondrosia reniformis</i> Nardo, 1847, and its associated microbial metagenome sequences.","authors":"Lucia Pita, Manuel Maldonado, Vassiliki Koutsouveli, Ana Riesgo, 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.24166.1","DOIUrl":"10.12688/wellcomeopenres.24166.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Chondrosia reniformis</i> (kidney sponge; Porifera; Demospongiae; Chondrillida; Chondrillidae). The genome sequence has a total length of 117.37 megabases. Most of the assembly (99.98%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs. Gene annotation of the host organism assembly on Ensembl identified 17,340 protein-coding genes. The metagenome of the specimen was also assembled and 53 binned bacterial genomes were identified, including 40 high-quality MAGs that were representative of a typical high microbial abundance sponge and included three candiate phyla (Poribacteria, Latescibacteria, Binatota).</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"283"},"PeriodicalIF":0.0,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144476905","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 pragmatic randomized controlled trial of standard care versus corticosteroids plus standard care for treatment of pneumonia in adults admitted to Kenyan hospitals (SONIA).","authors":"Ruth Lucinde, Abdirahman Abdi, Benedict Orindi, Stella Mwakio, Henry Gathuri, Edwin Onyango, Salome Chira, Morris Ogero, Lynda Isaaka, Jimmy Shangala, Irene Njeri Oginga, Alvin Wachira, Evans Manuthu, Hazel Kariuki, Jared Nyikuli, Cyprian Wekesa, Amos Otedo, Hannah Bosire, Steve Biko Okoth, Winston Ongalo, David Mukabi, Wilber Lusamba, Beatrice Muthui, Nicholas Kirui, Isaac Adembesa, Caroline Mithi, Mohammed Sood, Nadia Ahmed, Bernard Gituma, Vera Bina Ongaki, Matiko Giabe, Charles Omondi, Loice Achieng Ombajo, Wangeci Kagucia, Mike English, Mainga Hamaluba, Lynette Isabella Ochola-Oyier, Dorcas Kamuya, Philip Bejon, Ambrose Agweyu, Samuel Akech, Anthony Oliwa Etyang","doi":"10.12688/wellcomeopenres.18401.2","DOIUrl":"10.12688/wellcomeopenres.18401.2","url":null,"abstract":"<p><strong>Background: </strong>Mortality among adults admitted to hospital with community acquired pneumonia in resource-limited settings is high. Recent studies conducted in high-income settings have demonstrated beneficial effects of low-dose corticosteroids in reducing mortality in patients with severe community acquired pneumonia. It is unknown whether these findings apply to low-income settings such as sub-Saharan Africa.This pragmatic randomized-controlled open-label trial will determine the effect of adjunctive low-dose corticosteroids in the management of adults admitted to hospital with community acquired pneumonia on mortality 30-days post-randomization.</p><p><strong>Methods: </strong>We will enroll and randomize 2180 patients admitted with a diagnosis of community acquired pneumonia into two arms: the control and intervention arm. Those in the control arm will receive standard care for the treatment of community acquired pneumonia i.e., combination therapy with a beta-lactam and macrolide antibiotic. Those in the intervention arm will receive up to 10-days treatment with low-dose oral corticosteroids in addition to standard care. All participants will be followed up to 30- days post randomization and their final status recorded (alive or dead).</p><p><strong>Discussion: </strong>If adjunctive low-dose oral corticosteroids are found to be beneficial, this easily scalable intervention would significantly reduce the currently high mortality associated with community acquired pneumonia.Pan-African Clinical Trials Registry: PACTR202111481740832; ISRCTRN registry: ISRCTN36138594.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"7 ","pages":"269"},"PeriodicalIF":0.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12177450/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144334002","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":"Multimorbidity in tuberculosis (TB) and its impact on patient care (MITICare): a cross-sectional study nested within a prospective cohort study protocol.","authors":"Katherine Hill, Rogers Owori, Molly Naisanga, Noela Owarwo, Sarah Mills, Helen R Stagg, Stellah Mpagama, Christine Sekaggya-Wiltshire, Derek Sloan","doi":"10.12688/wellcomeopenres.24237.1","DOIUrl":"10.12688/wellcomeopenres.24237.1","url":null,"abstract":"<p><p>Multimorbidity, defined as two or more co-existing long-term health conditions, is increasing in low- and middle-income countries, overlapping with ongoing high tuberculosis (TB) incidence. It is known that there is a high prevalence of multimorbidity in patients with TB in South Africa, but our understanding of how common TB-multimorbidity is in other African countries, and its effect on the trajectories of TB care, is limited. This cross-sectional study nested within a prospective cohort (co-designed between the Infectious Diseases Institute, Uganda and the University of St Andrews, United Kingdom) aims to describe the burden and evaluate the consequences of multimorbidity among patients with TB disease in Kampala, Uganda. The primary objective is to describe the prevalence of multimorbidity at the start of treatment for TB. The secondary objectives are to determine the effect of multimorbidity on clinical characteristics at the start of treatment, progress through TB care, and end of TB treatment outcomes. 254 adults commencing treatment for TB shall be recruited. Multimorbidity shall be assessed using structured questionnaires, simple examination and blood analysis. Th clinical characteristics of TB shall be determined using health and quality of life scores and, in patients with pulmonary TB, the degree of chest X-ray abnormalities and sputum bacillary burden. Patients shall be followed-up at two and six months and their response to treatment determined. The analysis of the prevalence of multimorbidity at baseline shall be reported using a proportion and 95% confidence interval. For the secondary objectives, regression models adjusting for confounders identified through directed acyclic graphs will be used. This study has been developed in close collaboration with a core patient and public involvement group, who will also be actively involved in the dissemination of study results. Ugandan and St Andrews University ethical approval has been prospectively granted (IDI-REC-2023-82, MD17720 and HS3888ES).</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"282"},"PeriodicalIF":0.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12335725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817636","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 therapeutic potential of exercise in post-traumatic stress disorder and its underlying mechanisms: A living systematic review of human and non-human studies.","authors":"Simonne Wright, Virginia Chiocchia, Olufisayo Elugbadebo, Ouma Simple, Toshi A Furukawa, Claire Friedrich, Charlotte Austin, Hossein Dehdarirad, David Gilbert, Jaycee Kennett, Edoardo G Ostinelli, Jennifer Potts, Fiona Ramage, Emily Sena, Spyridon Siafis, Claire Stansfield, James Thomas, Francesca Tinsdeall, Thomy Tonia, Malcolm Macleod, Andrea Cipriani, Georgia Salanti, Soraya Seedat","doi":"10.12688/wellcomeopenres.23033.4","DOIUrl":"10.12688/wellcomeopenres.23033.4","url":null,"abstract":"<p><strong>Background: </strong>Exercise for post-traumatic stress disorder (PTSD) is a potentially effective adjunct to psychotherapy. However, the biopsychosocial mechanisms of exercise are not well understood. This co-produced living systematic review synthesizes evidence from human and non-human studies.</p><p><strong>Methods: </strong>We Included controlled human and non-human studies involving searches of multiple electronic databases (until 31.10.23). Records were screened, extracted, assessed for risk of bias, and reconciled by two independent reviewers. The primary outcome for human studies was PTSD symptom severity, while outcomes of interest for non-human studies included freezing behaviour, fear memory, fear generalization, startle response, and locomotion. Data were synthesised with random-effects meta-analysis.</p><p><strong>Results: </strong>Eleven human studies and 14 non-human studies met the eligibility criteria. Results of human studies showed that exercise was not associated with symptom severity improvement compared to control (standardized mean difference [SMD] -0.08, 95% confidence interval [CI] -0.24 to 0.07). High-intensity exercise reduced PTSD symptoms scores more than moderate-intensity exercise. There was insufficient data to examine the effects of exercise on functional impairment, PTSD symptom clusters, and PTSD remission. Only three studies, all at high risk of bias, examined mechanisms of exercise with inconclusive results. Results of non-human studies showed that exercise was associated with improvement in all behavioural outcomes, including locomotor activity (SMD 1.30, 95% CI 0.74 to 1.87, 14 studies), and changes in several neurobiological markers, including increase in brain-derived neurotrophic factor (SMD 1.79, 95% CI 0.56 to 3.01).</p><p><strong>Conclusions: </strong>While non-human studies provide compelling evidence for the beneficial effects of exercise, human trials do not. Evidence from non-human studies suggest that exercise might increase the levels of brain-derived neurotrophic factor, enhance cognitive appraisal, and improve perceived exertion. Overall, the paucity of data on the effectiveness of exercise in PTSD and mechanisms of action underscore the need for rigorous trials.</p><p><strong>Registration: </strong>The protocol was registered with PROSPERO (ID:453615; 22.08.2023).</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"720"},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143765250","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 tongue-biting isopod, <i>Ceratothoa steindachneri</i> Koelbel, 1878.","authors":"Chris Fletcher, David Alexander, Bethany Reed, Jessica Thomas","doi":"10.12688/wellcomeopenres.24289.1","DOIUrl":"10.12688/wellcomeopenres.24289.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Ceratothoa steindachneri</i> (tongue-biting isopod; Arthropoda; Malacostraca; Isopoda; Cymothoidae). The genome sequence has a total length of 3,927.82 megabases. Most of the assembly (98.71%) is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 29.61 kilobases. Gene annotation of this assembly on Ensembl identified 13,816 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"278"},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12361884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144971226","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 solitary wasp, <i>Cerceris ruficornis</i> (Fabricius, 1793).","authors":"Olga Sivell, Clare Boyes","doi":"10.12688/wellcomeopenres.24270.1","DOIUrl":"10.12688/wellcomeopenres.24270.1","url":null,"abstract":"<p><p>We present a genome assembly from a female specimen of <i>Cerceris ruficornis</i> (solitary wasp; Arthropoda; Insecta; Hymenoptera; Crabronidae). The genome sequence has a total length of 566.08 megabases, of which 65.35% is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.07 kilobases. Gene annotation of this assembly on Ensembl identified 11,093 protein-coding genes.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"276"},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12411840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145016295","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}