Wellcome Open ResearchPub Date : 2025-03-07eCollection Date: 2024-01-01DOI: 10.12688/wellcomeopenres.21010.4
Stephen Obol Opiyo, Racheal Nalunkuma, Stella Maris Nanyonga, Nathan Mugenyi, Andrew Marvin Kanyike
{"title":"Empowering Global AMR Research Community: Interactive GIS dashboards for AMR data analysis and informed decision-making.","authors":"Stephen Obol Opiyo, Racheal Nalunkuma, Stella Maris Nanyonga, Nathan Mugenyi, Andrew Marvin Kanyike","doi":"10.12688/wellcomeopenres.21010.4","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21010.4","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial Resistance (AMR) poses a global public health challenge, necessitating advanced tools to support data analysis, and visualization. This study introduces interactive Geographic Information System (GIS) dashboards as innovative platforms for AMR data analysis and visualization, offering comprehensive insights into resistance patterns, and geographic distribution across multiple countries, with a specific focus on Africa.</p><p><strong>Methods: </strong>Three GIS dashboards were developed to address key objectives. The first integrates over 860,000 ATLAS data points from 83 countries, providing an interactive platform. Users can filter data by variables such as country, year, and region, enhancing data accessibility and visualization. The second dashboard focuses on the ATLAS dataset for Kenya and Uganda, incorporating detailed variables such as species, sample sources, and resistance phenotypes. The third involves Kampala, Uganda, to fill data gaps, enabling localized analyses through interactive features like geographic mapping and sample breakdowns by year.</p><p><strong>Results: </strong>Sub-Saharan Africa faces three major challenges in handling antimicrobial resistance (AMR) data: limited accessibility for non-technical users, inefficiencies in processing large datasets, and insufficient longitudinal data for analysis. The introduction of interactive dashboards significantly improved AMR data visualization and interpretation across different scales. The global AMR dashboard effectively mapped geographical trends, uncovering critical data gaps, particularly the scarcity of AMR records from Africa. The Kenya and Uganda dashboard revealed key resistance patterns, highlighting the ineffectiveness of Ceftriaxone, Erythromycin, Levofloxacin, and Ampicillin against E. coli isolates. Additionally, the Kampala-specific dashboard, developed using simulated data, demonstrated the potential for localized AMR visualization, providing valuable insights where real-world data is limited. Across all platforms, the dashboards' interactive features enhanced data accessibility and streamlined trend identification, making AMR insights more interpretable, especially for researchers in Sub-Saharan Africa.</p><p><strong>Conclusions: </strong>Interactive GIS dashboards enhance AMR data analysis in Sub-Saharan Africa by improving accessibility, efficiently handling large datasets, and addressing data gaps. Unlike spreadsheets such as Excel, which struggle with large datasets due to computer constraints, dashboards offer dynamic visualization, real-time updates, and intuitive data exploration.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"234"},"PeriodicalIF":0.0,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11910713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143650938","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}
Wellcome Open ResearchPub Date : 2025-03-06eCollection Date: 2024-01-01DOI: 10.12688/wellcomeopenres.23135.2
Laura Merson, Karolina Witt, Arishay Hussaini, Ayesha Siddiqui, Eli Harriss, Steve Webb, Patricia Njuguna, Divya K Shah, An-Wen Chan, Robert Terry, Nandi Siegfried, Jeni Stolow, Emmanuelle Denis, Madiha Hashmi
{"title":"Infrastructure, capabilities, and capacities required for clinical trials design and delivery: A rapid scoping review of recommendations and regulations.","authors":"Laura Merson, Karolina Witt, Arishay Hussaini, Ayesha Siddiqui, Eli Harriss, Steve Webb, Patricia Njuguna, Divya K Shah, An-Wen Chan, Robert Terry, Nandi Siegfried, Jeni Stolow, Emmanuelle Denis, Madiha Hashmi","doi":"10.12688/wellcomeopenres.23135.2","DOIUrl":"10.12688/wellcomeopenres.23135.2","url":null,"abstract":"<p><strong>Objective: </strong>Synthesise the published literature and national regulations on infrastructure, capabilities and capacities required to manage and quality assure clinical research.</p><p><strong>Introduction: </strong>The World Health Assembly (WHA) resolution 75.8 (2022) called \"for a strengthened global architecture for coordinated and high-quality clinical trials\". For this remit, infrastructure, capabilities, and capacities needed to design and deliver high-quality clinical trials must be understood and advanced. This rapid scoping review aims to identify the breadth of requirements and recommendations for effective management of clinical trials in regulations, national legislation and the published literature. The findings will be summarised into themes. It will inform a framework for the assessment and development of units undertaking observational studies and interventional clinical trials.</p><p><strong>Inclusion criteria: </strong>Peer-reviewed literature, grey literature, and national legislation that recommends infrastructure, capabilities, and/or capacities needed to manage and quality assure clinical trials. Publications authored by those who design, manage, fund, sponsor, regulate or oversee clinical trials.</p><p><strong>Methods: </strong>Peer-reviewed and grey literature will be identified through Medline, Embase, PsycINFO, and Global Health via Ovid; SCOPUS; the Web of Science Core Collection; and the WHO Global Index Medicus using specific field codes to increase the specificity of the search strings. No date, language, or geographic limits will be applied. Deduplicated titles and abstracts will be screened by two blinded reviewers with discrepancies resolved by a third reviewer. Grey literature may be identified through the peer reviewed literature, supplemented with structured searches of Google and DynaMed. National regulations will be sourced online and from available summaries. Full text literature and regulations will be screened by a single reviewer, with proportionate verification by a second reviewer. Data will be extracted and coded for patterns in NVivo software. All items and codes will be summarised using a thematic framework analysis and identify core constructs within each theme.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"729"},"PeriodicalIF":0.0,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11923532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671163","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":"SAHELI: Study and Action on Hysterectomy: Evidence on women's health through the life course in India. Protocol for a mixed-methods study.","authors":"Sapna Desai, Dipti Govil, Devaki Nambiar, Hemali Heidi Sinha, Archana Roy, Kranti Vora, Josyula K Lakshmi, Archana Kumari, Gita D Mishra, Neerja Bhatla","doi":"10.12688/wellcomeopenres.23084.1","DOIUrl":"10.12688/wellcomeopenres.23084.1","url":null,"abstract":"<p><p>Hysterectomy, removal of the uterus, is a commonly performed surgery for gynaecological morbidities. Emerging evidence indicates that hysterectomy performed before age 45 (early hysterectomy), is associated with considerable risks to women's health. While most evidence on hysterectomy is from high-income settings, national surveys from India report high prevalence of early hysterectomy in specific regions, as well as higher prevalence amongst women in rural areas and with less education. The median age at hysterectomy in India is close to ten years before the onset of natural menopause. India has recently introduced national guidelines to address early hysterectomy, but large evidence gaps on the causes and consequences remain - which in turn limits the potential effectiveness of interventions at the clinical, health system and community level.</p><p><strong>Methods: </strong>SAHELI is a Team Science study that will examine: (i) individual, social and health system determinants of early hysterectomy; (ii) women's treatment pathways to hysterectomy and for gynaecological morbidity in general; and (iii) the consequences of undergoing hysterectomy on women's physical, mental, economic and social well-being across the life course. This mixed-methods study includes population surveys amongst women in ages 25-49 in three high-prevalence states; qualitative health systems research to trace treatment journeys with women, health care providers and other stakeholders; evidence syntheses; and knowledge translation activities to ensure findings inform co-produced strategies and interventions. The study is grounded in a feminist epidemiology approach, aiming to examine individual and structural causes of vulnerability and prioritising the views of women, particularly in knowledge translation.</p><p><strong>Conclusions: </strong>SAHELI, implemented by an all-women, multi-disciplinary team, is the first study in India to examine the causes and consequences of hysterectomy in a life course approach. We aim to influence interventions, policy and future research on women's health, particularly access to quality gynaecological care and comprehensive health services through the life course.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"584"},"PeriodicalIF":0.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11803392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143383391","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}
Wellcome Open ResearchPub Date : 2025-03-04eCollection Date: 2025-01-01DOI: 10.12688/wellcomeopenres.23797.1
Michelle F O'Brien, Rosa Lopez Colom
{"title":"The genome sequence of the common crane, <i>Grus grus</i> (Linnaeus, 1758).","authors":"Michelle F O'Brien, Rosa Lopez Colom","doi":"10.12688/wellcomeopenres.23797.1","DOIUrl":"10.12688/wellcomeopenres.23797.1","url":null,"abstract":"<p><p>We present a genome assembly from a male specimen of <i>Grus grus</i> (common crane; Chordata; Aves; Gruiformes; Gruidae). The assembly contains two haplotypes with total lengths of 1,352.26 megabases and 1,291.08 megabases. Most of haplotype 1 (91.85%) is scaffolded into 40 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 18.9 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"119"},"PeriodicalIF":0.0,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11953615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143754757","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}
Wellcome Open ResearchPub Date : 2025-03-04eCollection Date: 2025-01-01DOI: 10.12688/wellcomeopenres.23789.1
Chris Fletcher, David Alexander, Bethany Reed
{"title":"The genome sequence of the European smelt, <i>Osmerus eperlanus</i> (Linnaeus, 1758).","authors":"Chris Fletcher, David Alexander, Bethany Reed","doi":"10.12688/wellcomeopenres.23789.1","DOIUrl":"10.12688/wellcomeopenres.23789.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Osmerus eperlanus</i> (European smelt; Chordata; Actinopteri; Osmeriformes; Osmeridae). The genome sequence has a total length of 508.70 megabases. Most of the assembly (95.79%) is scaffolded into 28 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.61 kilobases.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"118"},"PeriodicalIF":0.0,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11966098/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143781282","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}
Wellcome Open ResearchPub Date : 2025-03-04eCollection Date: 2024-01-01DOI: 10.12688/wellcomeopenres.20080.2
Andreas Frølich, Rosamund E Dove, Maria Friberg, Annelie F Behndig, Thomas Sandström, Anders Blomberg, Ian S Mudway
{"title":"Respiratory tract lining fluid copper content contributes to pulmonary oxidative stress in patients with systemic sclerosis.","authors":"Andreas Frølich, Rosamund E Dove, Maria Friberg, Annelie F Behndig, Thomas Sandström, Anders Blomberg, Ian S Mudway","doi":"10.12688/wellcomeopenres.20080.2","DOIUrl":"10.12688/wellcomeopenres.20080.2","url":null,"abstract":"<p><strong>Background: </strong>Systemic sclerosis (SSc) is an autoimmune disease characterized by fibrosis of the skin and internal organs, mostly affecting young and middle-aged women. Significant questions remain as to its pathogenesis, especially the triggers for the associated interstitial lung disease (SSc-ILD). We examined the extent to which SSc and SSc-ILD were related to oxidative stress and altered metal homeostasis at the air-lung interface.</p><p><strong>Methods: </strong>In this case-control study, we recruited 20 SSc patients, of which 11 had SSc-ILD. Eighteen healthy individuals were recruited as age-matched healthy controls, for a total of 38 study participants. Low molecular weight antioxidants (ascorbate, urate and glutathione), metal transport and chelation proteins (transferrin and ferritin) and metals (Fe and Cu) concentrations, including a measure of the catalytically active metal pool, were determined in respiratory tract lining fluid (RTLF) collected by bronchoalveolar lavage from the SSc group and compared with healthy controls.</p><p><strong>Results: </strong>In the SSc group, 14 individuals were of female sex (70%) and the median age was 57 years (range 35-75). We observed evidence of oxidative stress in the RTLFs of SSc patients, characterised by increased concentrations of glutathione disulphide (GSSG, P<0.01), dehydroascorbate (DHA, P<0.05) and urate (P<0.01). This was associated with elevated RTLF Fe (P=0.07) and Cu (P<0.001), and evidence of a catalytic metal pool, demonstrated by an enhanced rate of ascorbate oxidation in the recovered lavage fluid (p<0.01). Cu concentrations were significantly associated with the ascorbate depletion rate (r=0.76, P<0.001), and GSSG (r=0.38, P<0.05) and protein carbonyl (r=0.44, P<0.01) concentrations. Whilst these markers were all increased in SSc patients, we found no evidence for an association with SSc-ILD.</p><p><strong>Conclusions: </strong>These data confirm the presence of oxidative stress in the airways of SSc patients and, for the first time, suggest that an underlying defect in metal homeostasis at the air-lung interface may play a role in disease progression.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"9 ","pages":"139"},"PeriodicalIF":0.0,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11923536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671078","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}
Wellcome Open ResearchPub Date : 2025-02-28eCollection Date: 2025-01-01DOI: 10.12688/wellcomeopenres.23764.1
Steven Falk, Liam M Crowley, James McCulloch, Ruth Y Akinmusola
{"title":"The genome sequence of a long-legged fly, <i>Scellus notatus</i> (Fabricius, 1781).","authors":"Steven Falk, Liam M Crowley, James McCulloch, Ruth Y Akinmusola","doi":"10.12688/wellcomeopenres.23764.1","DOIUrl":"10.12688/wellcomeopenres.23764.1","url":null,"abstract":"<p><p>We present a genome assembly from a female <i>Scellus notatus</i> (long-legged fly; Arthropoda; Insecta; Diptera; Dolichopodidae). The genome sequence has a total length of 446.83 megabases. Most of the assembly (99.72%) is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.7 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"117"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11914874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658870","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}
Wellcome Open ResearchPub Date : 2025-02-28eCollection Date: 2023-01-01DOI: 10.12688/wellcomeopenres.19340.1
Swagata Tripathy, Asha P Shetty, Upendra Hansda, Nanda Kumar P, Alok Kumar Sahoo, Mahalingam V, Sujata Mahapatra, Jayanta Kumar Mitra, P Bhaskar Rao, Kasturi Sanyal, Itimayee Panda, Guruprasad N, Jagannath Sahoo, Helen Eborral, Nazir Lone, Rashan Haniffa, Abi Beane
{"title":"AIIMS ICU Rehabilitation (AIR): development and description of intervention for home rehabilitation of chronically ill tracheostomized patients.","authors":"Swagata Tripathy, Asha P Shetty, Upendra Hansda, Nanda Kumar P, Alok Kumar Sahoo, Mahalingam V, Sujata Mahapatra, Jayanta Kumar Mitra, P Bhaskar Rao, Kasturi Sanyal, Itimayee Panda, Guruprasad N, Jagannath Sahoo, Helen Eborral, Nazir Lone, Rashan Haniffa, Abi Beane","doi":"10.12688/wellcomeopenres.19340.1","DOIUrl":"10.12688/wellcomeopenres.19340.1","url":null,"abstract":"<p><strong>Background: </strong>The paucity of state-supported rehabilitation for chronically ill patients with long-term tracheostomies has ramifications of prolonged hospital-stay, increased burden on acute-care resources, and nosocomial infections. Few interventions describe home rehabilitation of adult tracheostomized patients. Almost none involve stakeholders. This paper describes the All-India Institute of Medical Sciences (AIIMS) ICU rehabilitation (AIR) healthcare intervention developed to facilitate home rehabilitation of chronically ill tracheostomized patients.</p><p><strong>Methods: </strong>The AIR intervention development was based on the experience-based codesign theory (EBCD). A core research-committee studied prevalent knowledge and gaps in the area. Patients-carer and health-care stakeholders' experiences of barriers and facilitators to home care resulted in an intervention with interlinked components: family-carer training, equipment bank, m-health application, and follow-up, guided by the Medical Research Council (MRC) framework. Healthcare stakeholders (doctors, nurses, medical equipment vendors) and patient-carer dyads were engaged to gather experiences at various stages to form smaller codesign teams for each component. Multiple codesign meetings iteratively allowed refinement of the intervention over one year. The Template for Intervention Description and Replication (TIDieR) checklist was used to report the AIR intervention.</p><p><strong>Results: </strong>The first component comprised a minimum of three bedside hands-on training sessions for carers relating to tracheostomy suction, catheter care, monitoring oxygenation, enteral feeding, skincare, and physiotherapy, buttressed by pictorial-books and videos embedded in a mobile-application. The second was an equipment-bank involving a rental-retrieval model. The third component was a novel m-health tool for two-way communication with the core group and community of other patient-carers in the project for follow-up and troubleshooting. Home visits on days 7 and 21 post-discharge assessed patient hygiene, nutrition, physiotherapy, and established contact with the nearest primary healthcare facility for the future.</p><p><strong>Conclusions: </strong>Findings support the EBCD-based development using active feedback from stakeholders. Assessment of feasibility, process and effectiveness evaluation will follow.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":" ","pages":"285"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11399758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45243511","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}
Wellcome Open ResearchPub Date : 2025-02-28eCollection Date: 2023-01-01DOI: 10.12688/wellcomeopenres.18888.2
Nguyen Le Quang, Do Dang Anh Thu, Le Pham Tien Trieu, Nguyen Hong Hanh, Nguyen Huu Lan, Dang Thi Minh Ha, Guy Thwaites, Nguyen Thuy Thuong Thuong, Timothy M Walker
{"title":"A modified decontamination and storage method for sputum from patients with tuberculosis.","authors":"Nguyen Le Quang, Do Dang Anh Thu, Le Pham Tien Trieu, Nguyen Hong Hanh, Nguyen Huu Lan, Dang Thi Minh Ha, Guy Thwaites, Nguyen Thuy Thuong Thuong, Timothy M Walker","doi":"10.12688/wellcomeopenres.18888.2","DOIUrl":"10.12688/wellcomeopenres.18888.2","url":null,"abstract":"<p><strong>Background: </strong>Collecting and storing large number of sputum samples with a view to culturing these in the future requires an efficient initial handling method. We devised a modified sputum digestion and decontamination method that maximised storage capacity and <i>Mycobacterium tuberculosis</i> (M.tb) recovery from culture while minimising laboratory workload and risk of contamination.</p><p><strong>Methods: </strong>We collected smear microscopy positive sputum samples from patients with pulmonary tuberculosis (TB). The sputum samples were split and processed using both the standard N-Acetyl-L-cysteine and sodium hydroxide (NALC-NaOH) method and our modified method before freezing and later culturing in BD BACTEC 960 Mycobacterium Growth Indicator Tubes (MGIT) system. We assessed the Time to Positivity (TPP) and Growth Unit (GU) data.</p><p><strong>Results: </strong>We selected 22 sputum samples to compare two digestion and decontamination methods. The samples that underwent the modified method had longer TTP (p < 0.05) but similar GU in comparison to standard method. Overall, 1/22 samples failed to grow in MGIT after being processed by the modified method. We then applied the modified method to 348 sputum samples with Rifampicin resistance detected by GeneXpert MTB/RIF assay, which were frozen for between 1-25 months. The overall MGIT positive, negative, and contamination rate was 90.5%, 7.8%, and 1.7%, respectively. There was no significant difference in MGIT result when samples were grouped by duration of storage or positive smear grade.</p><p><strong>Conclusions: </strong>Our modified method yielded acceptable M.tb recovery rate and low contamination risk while allowing us to collect and store thousands of sputum samples over a long period of time for future tests.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"8 ","pages":"166"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11358684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142112575","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}
Wellcome Open ResearchPub Date : 2025-02-28eCollection Date: 2025-01-01DOI: 10.12688/wellcomeopenres.23763.1
James McCulloch, Liam M Crowley
{"title":"The genome sequence of a mirid bug, <i>Stenodema calcarata</i> (Fallen, 1807).","authors":"James McCulloch, Liam M Crowley","doi":"10.12688/wellcomeopenres.23763.1","DOIUrl":"10.12688/wellcomeopenres.23763.1","url":null,"abstract":"<p><p>We present a genome assembly from a specimen of <i>Stenodema calcarata</i> (mirid bug; Arthropoda; Insecta; Hemiptera; Miridae). The genome sequence has a total length of 575.35 megabases. Most of the assembly (98.42%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.31 kilobases in length.</p>","PeriodicalId":23677,"journal":{"name":"Wellcome Open Research","volume":"10 ","pages":"115"},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11950723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143754751","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}