2671 research outputs found
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typhoidgenomics/TyphoidGenomicsConsortiumMykrobe
No full textThis repository holds the tabulated data and code behind the paper of the Global Typhoid Genomics Consortium, "Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi" published in Genome Medicine, 2025 (preprint available in BioRxiv). Note that Typhi Mykrobe is not a QC tool. It is recommended that users continue to undertake their own QC on short and long read data
Systematic review of risk assessment tools for post-discharge mortality among children in sub-Saharan Africa
No full textPost-discharge mortality is increasingly recognized as a major contributor to the high burden of childhood mortality in sub-Saharan Africa. Accurate identification of children at risk for post-discharge mortality is critically important to inform interventions to reduce deaths following hospital discharge. Our objective was to describe the current state of development, validation, or implementation for risk assessment tools for post-hospital discharge mortality (PDM) in sub-Saharan Africa. We conducted a systematic review of publications on risk assessment tools for PDM among children aged 0–18 years in sub-Saharan Africa. We searched CABI Global Health, Cochrane Reviews, Cochrane Trials, ProQuest Dissertations and Theses, Embase, PubMed, and Web of Science with no date or language restriction. We included publications if they described a tool/model with weights assigned to variables to quantify risk of PDM, included children, and were conducted in sub-Saharan Africa. We determined the level of evidence for tools using the Evidence-Based-Medicine Working Group hierarchy. Of 4,893 publications screened, 289 full texts were reviewed, and seven publications that reported 23 risk assessment tools for PDM among children in sub-Saharan Africa were identified. These studies enrolled 49,669 total participants (3.6%, n = 1,795 experienced PDM). There was substantial heterogeneity in identified risk factors, although all identified malnutrition as a risk factor for PDM. All risk assessment tools had fair (i.e., area under the receiver operating characteristic curve [AUC] ≥0.70) or good (AUC ≥ 0.80) discriminatory value in internal validation. Only two risk assessment tools had been externally validated, and none were implemented. Existing risk assessment tools to identify children at risk for PDM in sub-Saharan Africa lack broad validation and implementation. Malnutrition is a common risk factor for PDM. Further studies are needed to validate and implement such tools to reduce PDM among children
“If we lose it, we are worried”: Individual and provider level perceptions towards weight change among people living with HIV who undergo TB screening in routine health care settings in Gauteng Province, South Africa
No full textBACKGROUND: HIV weakens the immune system, increasing the risk of tuberculosis (TB) in people with living HIV (PLHIV). People living with HIV and on antiretroviral treatment (ART) often experience physical body size changes. Studies have found a significant discrepancy between PLHIV’s self-reported weight loss and their measured weight loss when being screened for TB using the WHO tool. To understand this inconsistency, a qualitative sub-study was conducted to explore perceptions and attitudes towards weight change among adults attending HIV care, as well as health care workers in public clinics in Gauteng, South Africa. METHODS: Our qualitative study was nested within the XPHACTOR study. A total of seven focus group discussions were conducted, five with adult participants attending for HIV care and two with health care workers and research staff in clinics around Gauteng. Inductive thematic analysis was used to analyse the data. FINDINGS: The majority of PLHIV preferred to gain weight due to fear of stigma associated with weight loss. Weight loss is associated with HIV/AIDS, suggesting that people attending HIV care may underreport weight loss in the context of a TB symptoms screening tool because they fear stigma. Participants reported that weight changes impacted their daily lives and had psychological effects on them. Some PLHIV described lipodystrophy as disproportional weight gain. Culture and media have an influence on the perception of ideal body size and shape for both men and women. CONCLUSIONS: Underreporting weight loss might result in poor sensitivity of the WHO TB screening tool and suggests that we need either alternative ways to determine weight loss or screening tools for TB that are less dependent on reported symptoms
DidDrog11/land-use-lassa-hosts
No full textThis repository contains the code and data used for the analysis presented in "Land use gradients drive spatial variation in Lassa fever host communities in the Eastern Province of Sierra Leone." The study examines the impact of land use and species interactions on rodent community composition and Lassa fever spillover risk using hierarchical occupancy models
julianmatthewman/Eczema_hospital_outcomes_public
No full textCode and codelists for "Mapping risks of hospital-recorded health conditions in people with eczema
Data and R-code to accompany 'Modelling the impact of climate and the environment on the spatiotemporal dynamics of Lyme borreliosis in Germany'
No full textData and R code to support Lotto Batista et al., (2025). Modelling the impact of climate and the environment on the spatiotemporal dynamics of Lyme borreliosis in Germany
Dataset for "EDTA tubes are suitable for insulin and C-peptide measurement in resource-limited settings and can be stored at room temperature for up to 24 hours"
No full textDataset for the publication, "EDTA tubes are suitable for insulin and C-peptide measurement in resource-limited settings and can be stored at room temperature for up to 24 hours". It contains 5 variables - sample ID, time points, results, PTID condition, and anlyte
Code for Cascades of effectiveness of next-generation insecticide-treated nets against malaria, from entomological trials to real-life conditions
No full textThis code is associated with the following manuscript: "Cascades of effectiveness of new-generation insecticide-treated nets against malaria, from entomological trials to real-life conditions"
NaomiWaterlow/Future_projections_AMR
No full textR code written to calculate future burden projections of antimicrobial resistance (AMR) based on changing demography and varying incidence and resistance prevalence levels by age and gender
EmilieFinch/dengue-singapore
No full textThis repo contains code and data to support Finch et al "Climate variation and serotype competition drive dengue outbreak dynamics in Singapore". This study quantifies the role of climate variation and serotype competition in shaping dengue risk in Singapore using over 20 years of weekly case data, and integrates these findings into an early warning system framework able to predict dengue outbreaks up to 2 months ahead. Model fitting is performed in INLA. Climate and dengue case data are available in the data folder. Note that data on dengue serotype frequencies shown in Figure 1 are not included in this repo as they are not publicly available