bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of
Streptococcus pyogenes
Authors: Hirose Yujiro , Zielinski Daniel C. , Poudel Saugat , Rychel Kevin , Baker Jonathon L. , Toya Yoshihiro , Yamaguchi Masaya , Heinken Almut , Thiele Ines , Kawabata Shigetada , Palsson Bernhard O. , Nizet Victor 
Published: August 2024

ABSTRACT

Streptococcus pyogenes
is responsible for a range of diseases in humans contributing significantly to morbidity and mortality. Among more than 200 serotypes of
S. pyogenes
, serotype M1 strains hold the greatest clinical relevance due to their high prevalence in severe human infections. To enhance our understanding of pathogenesis and discovery of potential therapeutic approaches, we have developed the first genome-scale metabolic model (GEM) for a serotype M1
S. pyogenes
strain, which we name iYH543. The curation of iYH543 involved cross-referencing a draft GEM of
S. pyogenes
serotype M1 from the AGORA2 database with gene essentiality and autotrophy data obtained from transposon mutagenesis-based and growth screens. We achieved a 92.6% (503/543 genes) accuracy in predicting gene essentiality and a 95% (19/20 amino acids) accuracy in predicting amino acid auxotrophy. Additionally, Biolog Phenotype microarrays were employed to examine the growth phenotypes of
S. pyogenes,
which further contributed to the refinement of iYH543. Notably, iYH543 demonstrated 88% accuracy (168/190 carbon sources) in predicting growth on various sole carbon sources. Discrepancies observed between iYH543 and the actual behavior of living
S. pyogenes
highlighted areas of uncertainty in the current understanding of
S. pyogenes
metabolism. iYH543 offers novel insights and hypotheses that can guide future research efforts and ultimately inform novel therapeutic strategies.

IMPORTANCE

Genome-scale models (GEMs) play a crucial role in investigating bacterial metabolism, predicting the effects of inhibiting specific metabolic genes and pathways, and aiding in the identification of potential drug targets. Here, we have developed the first GEM for the
S. pyogenes
highly virulent serotype, M1, which we name iYH543. The iYH543 achieved high accuracy in predicting gene essentiality. We also show that the knowledge obtained by substituting actual measurement values for iYH543 helps us gain insights that connect metabolism and virulence. iYH543 will serve as a useful tool for rational drug design targeting
S. pyogenes
metabolism and computational screening to investigate the interplay between inhibiting virulence factor synthesis and growth.
Low levels and determinants of appropriate complementary feeding practices among children aged 6–23 months from Tigray, Ethiopia: a community-based cross-sectional study
Authors: Mulugeta Afework , Abebe Haftom Temesgen , Redae Getachew , Gebremariam Mebrahten , Abay Meseret , Yohannes Desta Berhe , Bazzano Alessandra N 
Published: August 2024

IntroductionComplementary feeding is considered appropriate when introduced timely at 6 months of age, and where it fulfils the minimum meal frequency, minimum dietary diversity and minimum acceptable diet. Sufficient evidence is available on the different individual indicators of appropriate complementary feeding.ObjectiveThis study was conducted to assess the prevalence and determinants of appropriate complementary feeding practices among children aged 6–23 months in Tigray, Northern Ethiopia.Design and settingA community-based cross-sectional study was conducted in 52 districts of Tigray.ParticipantsA total of 5321 children aged 6–23 months were included using stratified two-stage random sampling.ResultsApproximately 19% of children received appropriate complementary feeding. Maternal residence in urban areas (adjusted OR (AOR) 1.26; 95% CI 1.062 to 1.489), maternal education (AOR 1.34; 95% CI 1.111 to 1.611), antenatal care (ANC) visits (AOR 1.75; 95% CI 1.343 to 2.281), household food security (AOR 2.81; 95% CI 2.367 to 3.330) and provision of colostrum to newborns (AOR 1.76; 95% CI 1.139 to 2.711) were found predictors of appropriate complementary feeding. Moreover, children in the 12–17 and 18–23 months age groups were 1.3 (AOR 1.30; 95% CI 1.083 to 1.551) and 1.7 (AOR 1.73; 95% CI 1.436 to 2.072) times more likely to receive appropriate complementary feeding respectively, compared with children aged 6–11 months.ConclusionsAppropriate complementary feeding practices among children aged 6–23 months remain unacceptably low in Tigray. Recommendations to improve nutrition outcomes include counselling on age-appropriate complementary feeding, education for girls and women, targeting families through food security initiatives, provision of nutrition education on appropriate complementary feeding practices during ANC visits, supporting mothers to initiate breastfeeding within the first hour of delivery and crafting context-based messaging for rural families.
Exploring the efficacy and safety of acupuncture versus sham acupuncture for diminished ovarian reserve: study protocol for a multicentre randomised controlled trial
Authors: Xiao Qiwei , Wu Yumi , Su Chenchen , Yang Jie , Wang Jian , Pei Lixia , Wang Yang , Hu Jie , Chen Li , Yang Li , Li Jiashan , Li Weixin , Gou Minghui , Feng Yixuan , Xu Huanfang , Fang Yigong 
Published: August 2024

IntroductionThe therapeutic needs of women with diminished ovarian reserve (DOR), coupled with the increasing application of acupuncture in improving ovarian function, have highlighted the need to verify the efficacy and safety of acupuncture for DOR. This study aims to provide high-quality evidence by evaluating both ovarian reserve and in vitro fertilisation (IVF) outcomes.Methods and analysisA large-scale, multicentre, randomised controlled trial will be carried out across seven hospitals in China. 400 women with DOR will be randomised in a 1:1 ratio to an acupuncture group or a sham acupuncture group. Acupuncture or sham acupuncture will consist of 36 sessions per participant over 12 weeks. The primary outcome will be the change in antral follicle count (AFC) at week 12 from baseline. Secondary outcomes are AFC at week 24, the serum levels of basal follicle-stimulating hormone and anti-Mullerian hormone at weeks 12 and 24, the scores of the Self-Rating Anxiety Scale at weeks 12 and 24, clinical pregnancy rate, and IVF embryo transfer related outcomes. Any adverse events during treatment will be documented.Ethics and disseminationThe study protocol has been approved by all the participating institutions. Written informed consent will be obtained prior to participant enrolment. The results of this study will be published in peer-reviewed publications.Trial registration numberChiCTR2200062295Protocol versionV2.0-20220317
Evaluating the gap in rapid diagnostic testing: insights from subnational Kenyan routine health data
Authors: Robert Bibian N. , Moturi Angela K. , Bahati Felix , Macharia Peter M. , Okiro Emelda A. 
Published: August 2024

BackgroundUnderstanding diagnostic capacities is essential to addressing healthcare provision and inequity, particularly in low-income and middle-income countries. This study used routine data to assess trends in rapid diagnostic test (RDT) reporting, supplies and unmet needs across national and 47 subnational (county) levels in Kenya.MethodsWe extracted facility-level RDT data for 19 tests (2018–2020) from the Kenya District Health Information System, linked to 13 373 geocoded facilities. Data quality was assessed for reporting completeness (ratio of reports received against those expected), reporting patterns and outliers. Supply assessment covered 12 RDTs reported by at least 50% of the reporting facilities (n=5251), with missing values imputed considering reporting trends. Supply was computed by aggregating the number of tests reported per facility. Due to data limitations, demand was indirectly estimated using healthcare-seeking rates (HIV, malaria) and using population data for venereal disease research laboratory test (VDRL), with unmet need computed as the difference between supply and demand.ResultsReporting completeness was under 40% across all counties, with RDT-specific reporting ranging from 9.6% to 89.6%. Malaria RDTs showed the highest annual test volumes (6.3–8.0 million) while rheumatoid factor was the lowest (0.5–0.7 million). Demand for RDTs varied from 2.5 to 11.5 million tests, with unmet needs between 1.2 and 3.5 million. Notably, malaria testing and unmet needs were highest in Turkana County, as well as the western and coastal regions. HIV testing was concentrated in the western and central regions, with decreasing unmet needs from 2018 to 2020. VDRL testing showed high volumes and unmet needs in Nairobi and select counties, with minimal yearly variation.ConclusionRDTs are crucial in enhancing diagnostic accessibility, yet their utilisation varies significantly by region. These findings underscore the need for targeted interventions to close testing gaps and improve data reporting completeness. Addressing these disparities is vital for equitably enhancing diagnostic services nationwide.
Exploring the water, sanitation and hygiene status and health outcomes in Zimbabwe: a scoping review protocol
Authors: Betera Same , Wispriyono Bambang , Nunu Wilfred Njabulo 
Published: August 2024

BackgroundThe sixth United Nations Sustainable Development Goal emphasises universal access to clean water, sanitation and hygiene (WASH) to ensure human well-being as a fundamental human right for sustainable development. In Zimbabwe, WASH reforms began more than a century ago from the preindependence to postindependence era. However, countries face pressing challenges in improving their related health outcomes. Therefore, this scoping review aims to explore WASH status and how it influences health outcomes in Zimbabwe.Methods and analysisThe leading databases to be searched for relevant sources published in English with an unrestricted search back until May 2024 include PubMed, EBSCO, SAGE, SpringerLink, Cochrane Library, ScienceDirect, Scopus, Web of Science and African Journals Online. A search string was developed for retrieving literature, and reports from key stakeholders in the WASH sector will be included in this study as grey literature. The study will employ a two-step screening process for identifying relevant literature incorporating Cohen’s kappa coefficient statistics to estimate the inter-rater reliability between two independent reviewers using Mendeley and Rayyan software. The Strengthening the Reporting of Observational Studies in Epidemiology checklist for observational studies and the Consolidated Standards of Reporting Trials checklist for randomised controlled trials will be used for the quality checks. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews will guide this study in terms of data collection, extraction and analysis from relevant literature. Data charting was used to present and interpret the findings. The entire process is scheduled to commence in June 2024, with the manuscript anticipated to be submitted to a journal in October 2024.Ethics and disseminationThis review will use only published data; therefore, no ethical clearance is required. The findings will be disseminated to relevant stakeholders through peer-reviewed journals, meetings, conferences, seminars and forums.
Spatial-temporal analysis of climate and socioeconomic conditions on cholera incidence in Mozambique from 2000 to 2018: an ecological longitudinal retrospective study
Authors: Armando Chaibo Jose , Rocklöv Joacim , Sidat Mohsin , Tozan Yesim , Mavume Alberto Francisco , Bunker Aditi , Sewe Maquins Odhiambo 
Published: August 2024

ObjectivesThis study aims to assess both socioeconomic and climatic factors of cholera morbidity in Mozambique considering both spatial and temporal dimensions.DesignAn ecological longitudinal retrospective study using monthly provincial cholera cases from Mozambican Ministry of Health between 2000 and 2018. The cholera cases were linked to socioeconomic data from Mozambique Demographic and Health Surveys conducted in the period 2000–2018 and climatic data; relative humidity (RH), mean temperature, precipitation and Normalised Difference Vegetation Index (NDVI). A negative binomial regression model in a Bayesian framework was used to model cholera incidence while adjusting for the spatiotemporal covariance, lagged effect of environmental factors and the socioeconomic indicators.SettingEleven provinces in Mozambique.ResultsOver the 19-year period, a total of 153 941 cholera cases were notified to the surveillance system in Mozambique. Risk of cholera increased with higher monthly mean temperatures above 24°C in comparison to the reference mean temperature of 23°C. At mean temperature of 19°C, cholera risk was higher at a lag of 5–6 months. At a shorter lag of 1 month, precipitation of 223.3 mm resulted in an 57% increase in cholera risk (relative risk, RR 1.57 (95% CI 1.06 to 2.31)). Cholera risk was greatest at 3 lag months with monthly NDVI of 0.137 (RR 1.220 (95% CI 1.042 to 1.430)), compared with the reference value of 0.2. At an RH of 54%, cholera RR was increased by 62% (RR 1.620 (95% CI 1.124 to 2.342)) at a lag of 4 months. We found that ownership of radio RR 0.29, (95% CI 0.109 to 0.776) and mobile phones RR 0.262 (95% CI 0.097 to 0.711) were significantly associated with low cholera risk.ConclusionThe derived lagged patterns can provide appropriate lead times in a climate-driven cholera early warning system that could contribute to the prevention and management of outbreaks.
Transition from rehabilitation hospital to the National Disability Insurance Scheme (NDIS) for people with brain injury and spinal cord injury: a data linkage protocol
Authors: Guthrie Simon Andrew John , Alexander Tara , Tickle Leonie , Winkler Di , Walsh John Ernest 
Published: August 2024

IntroductionTraumatic brain injury (TBI) and spinal cord injury (SCI) are both major contributors to permanent disability globally, with an estimated 27 million new cases of TBI and 0.93 million new cases of SCI globally in 2016. In Australia, the National Disability Insurance Scheme (NDIS) provides support to people with disability. Reports from the NDIS suggest that the cost of support for people with TBI and SCI has been increasing dramatically, and there is a lack of independent analysis of the drivers of these increases. This data linkage seeks to better understand the participant transition between rehabilitation hospitals and the NDIS and the correlation between functional independence in rehabilitation and resource allocation in the NDIS.Methods and analysisThis is a retrospective, population-based cohort study using Australia-wide NDIS participant data and rehabilitation hospital episode data. The linked dataset provides a comparison of functional independence against which to compare the NDIS resource allocation to people with TBI and SCI. This protocol outlines the secure and separated data linkage approach employed in linking partially identified episode data from the Australasian Rehabilitation Outcomes Centre (AROC) with identified participant data from the NDIS. The linkage employs a stepwise deterministic linkage approach. Statistical analysis of the linked dataset will consider the relationship between the functional independence measure score from the rehabilitation hospital and the committed funding supports in the NDIS plan. This protocol sets the foundation for an ongoing data linkage between rehabilitation hospitals and the NDIS to assist transition to the NDIS.Ethics and disseminationEthics approval is from the Macquarie University Human Research Ethics Committee. AROC Data Governance Committee and NDIS Data Management Committee have approved this project. Research findings will be disseminated to key stakeholders through peer-reviewed publications in scientific journals and presentations to clinical and policy audiences via AROC and NDIS.
Efficacy of high-flow nasal oxygen therapy started in the emergency room versus conventional oxygen therapy in patients with acute hypoxaemic respiratory distress: protocol for a French multicentric, prospective, open and randomised superiority study protocol (HIFLOWED)
Authors: Pretalli Jean Baptiste , Parmentier Anne-Laure , Mauny Frederic , Desmettre Thibaut , Marjanovic Nicolas , Capellier Gilles , Khoury Abdo 
Published: August 2024

IntroductionAcute respiratory failure is a life-threatening condition frequently found in the emergency department. High-flow nasal oxygen (HFNO) is increasingly used in emergency departments for patients with hypoxaemic acute respiratory failure. However, despite the increasing number of studies, its potential advantages regarding the need for therapeutic escalation and mortality have not been precisely evaluated. Our objective is to compare conventional oxygen therapy to HFNO when they are initiated during the first hour following the patient’s arrival at the emergency department, with the hypothesis that HFNO would reduce the need for ventilatory therapy escalation.Methods and analysisThis is a multicentric, prospective, open and randomised superiority study. 500 inpatients will be randomised (1:1) to receive conventional oxygen therapy or HNFO. The primary outcome is a failure in the oxygen therapy defined as the need for a therapeutic escalation within 4 hours after therapy initiation.Ethics and disseminationThe study has been submitted and approved by the Comité de Protection des Personnes Nord Ouest IV (20 October 2020). As required, a notification was sent to the Agence nationale de sécurité du médicament et des produits de santé (22 October 2020). The research results will be published in peer-reviewed publications and presented at international conferences.Trial registration numberNCT04607967.
Assessment of the understanding and awareness of bioethics among healthcare professionals in all public and private hospitals of Haripur district, Pakistan: a multicentre cross-sectional study
Authors: Ateeb Muhammad , Haq Ijaz ul , Zakki Shahbaz Ahmad , Altaf Ehtisham , Junaid Muhammad , Ali Mustafa , Rehman Atif Ur , Wajid Daniyal , Fareed Abdullah , Mehmood Asad 
Published: August 2024

ObjectiveTo assess the level of bioethics awareness among healthcare professionals in Pakistan, focusing on the associations with sociodemographic characteristics, training and teaching of ethics, medical ethics practice and specific ethical issues.DesignCross-sectional study.SettingPublic and private hospitals in Haripur, Pakistan.ParticipantsA total of 647 healthcare professionals participated in this study.MethodsThis study was conducted between March and May 2023, following Strengthening the Reporting of Observational Studies in Epidemiology checklist criterion, involving healthcare professionals with at least 6 months of experience in patient care practice. Providers under close supervision are advised not to respond to the bioethics knowledge, attitudes and practices survey form due to potential ethical dilemmas.ResultsBoth physicians and non-physicians need to know more about bioethics. There was a significant difference (p<0.05) in ethical training and teaching based on job categories/designations, with ethical views differing greatly by job designation. Specific ethical issues, such as accepting gifts from patients and pharmaceutical companies, referral fees, advising specific products, disclosure of medical errors, patient confidentiality, not informing patients fully about treatment and performing tasks for financial gain, showed significant associations (p<0.05) with healthcare professional’s designation. Ethical awareness scores also showed significant differences (p<0.05) based on age, ethnicity, place of posting, professional experience and the organisation’s ethical guidelines.ConclusionThis study highlighted a notable gap in the understanding of certain ethical concerns among healthcare professionals, with nurses showing relatively lower awareness of healthcare practice compared with other professionals. Addressing these issues through targeted training and robust ethical guidelines is critical to improving patient care in Pakistan’s healthcare system.
Understanding how traumatic brain injury-related changes in fluid biomarkers affect quality of life outcomes in veterans: a prospective observational trial protocol (UNTANGLE)
Authors: Metry Youstina , McMullan Christel , Upthegrove Rachel , Belli Antonio , Gomes Renata S M , Blanch Richard J , Ahmed Zubair 
Published: August 2024

IntroductionTraumatic brain injury (TBI) is a major cause of disability, with annual global incidence estimated as 69 million people. Survivors can experience long-term visual changes, altered mental state, neurological deficits and long-term effects that may be associated with mental illness. TBI is prevalent in military personnel due to gunshot wounds, and blast injury. This study aims to evaluate the relationship between evolving visual, biochemical and mental health changes in both military veterans and civilians, suffering from TBI, and detect preliminary indicators of prognosis for TBI recovery, and quality-of-life outcomes.Methods and analysisUNTANGLE is a 24-month prospective observational pilot study recruiting three patient groups: civilians with acute moderate-severe TBI, military veterans with diagnosis of a previous TBI and a control group of civilians or veterans with no history of a previous TBI. Patients will undergo visual, biochemical and mental health assessments, as well as patient-reported quality of life outcome measures over the course of a 1-year follow-up period.Ethics and disseminationEthical approval has been obtained from the Health Research Authority and Health and Care Research Wales with a REC reference number of 23/NW/0203. The results of the study will be presented at scientific meetings and published in peer-reviewed journals, including both civilian and military-related publications. We will also present our findings at national and international meetings of learnt neuroscience and neuropsychiatry and military societies. We anticipate that our pilot study will inform a larger study on the long-term outcomes of TBI and quality of life, specific to military veterans, such that potential interventions may be accessed as quickly as possible.Trial registration numberISRCTN13276511.