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cmmid/reconnect_uk_social_contact_survey
No full textThis repository contains the code and analysis for the Reconnect study, a comprehensive study designed to understand patterns of social interactions across different age groups and settings in the United Kingdom. This repository reproduces the analyses which can be carried out on the survey datasets, which can be found on Zenodo at 10.5281/zenodo.16845075
Analysis dataset for: "Support To Rural India’s Public Education System (STRIPES2) and impact on numeracy and literacy scores: A cluster randomized trial in rural villages of Madhya Pradesh, India"
No full textIntroduction: Rates of primary school enrolment have improved in India, but levels of learning achievement remain low. In the Support To Rural India’s Public Education System (STRIPES) trial, a para-instructor intervention improved numeracy and literacy levels in Telangana, India (2008−10). The STRIPES2 trial was designed to assess whether a similar intervention in a younger cohort of children would have similar effects in Satna and Maihar districts of Madhya Pradesh, India, and be cost-effective.
Methods: In this Madhya Pradesh cluster-randomized controlled trial, 196 villages (clusters) were randomized to receive either a health (CHAMPION2: community health promotion and medical provision and impact on neonates) or education (STRIPES2) intervention. Villages receiving the health intervention were controls for the education intervention and vice versa . For children newly enrolled in primary school, the STRIPES2 intervention comprised before/after-school classes (2 hours per day, 6 days a week) given by trained para-instructors from the local community, frequent monitoring, and engagement with caregivers to motivate children, delivered by the Pratham Education Foundation. STRIPES2 activities had to be suspended twice for around ten and a half months, and some components of the intervention modified due to the COVID-19 pandemic. The period of the trial was extended with the primary outcome (a composite literacy and numeracy score of Early Grade Reading and Mathematics Assessments) assessed around 30 months after classes started.
Results: Composite test scores were significantly higher in the intervention arm (98 villages; 3054 children) than in the control arm (98 villages; 3275 children) at the end of the trial. The mean difference on a percentage point scale was 14.17; 95% CI 11.36 to 16.97; p < 0.001, equating to a 0.58 (95% CI 0.47 to 0.71) standard deviation difference. The cost per child per 0.1 SD increase in composite test score was INR 2476 (US$33.5).
Conclusion: Despite COVID-19 interruptions and disruptions, STRIPES2 resulted in a major improvement in children’s literacy and numeracy. However, the cost of achieving such benefits was substantial
Target population estimate methods
No full textThis Excel file contains country-level data on annual live births from 1999 -2023 in Kenya derived from Cohort Component Projections method, BCG and DTP1 doses as denominators method, Population growth rate method and ANC1 Visits method. The file supports analysis comparing the 4 target population estimation methods
Additional file 2 of A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission
No full textSupplementary tables of the masked genomic regions, mixed infections identified in the Moldova dataset, and genomic clusters with information on the predicted number of sequences and constituent sequences of mixed infections
thegargiulian/GRDM
No full textReplication materials for: "Can we estimate crisis death tolls by subtracting total population estimates? A critical review and appraisal" by Hampton Gaddy and Maria Gargiulo and published in Demographic Research (https://www.demographic-research.org/articles/volume/52/23/). These materials are also accessible via the web page of the article linked above. All analyses are replicable in R (version 4.2.2). The code and data files needed to reproduce the main and supplementary figures of the paper are as follows. For each data files that cannot be redistributed is noted, the access procedure used and variable metadata is described
Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics
No full textOBJECTIVES: Although taxonomic variations in chicken gut microbiota have been previously documented, their functional capacity remain poorly understood. To gain a better understanding, we incorporated whole genome shotgun metagenomics to analyse microbial communities of two different organs: the caeca and the large intestine. RESULTS: Using 24 samples obtained from the caeca and the large intestine of commercial chickens, we assembled Metagenome-Assembled Genomes (MAGs) and characterise their functional profiles. Afterwards, using 8 samples, we integrated this sequencing data with chicken performance metadata body weight (BW), weight gain, feed intake (FI), feed conversion ratio (FCR) and age. MAGs belonging to specific families were found to be positively associated with changes in performance parameters. Functional analyses suggest changes in nutrient geochemical cycles including hydrogen generation within the carbon-cycle. Furthermore, 108 CAZymes were identified for MAGs belonging to two major families - glycoside hydrolase (GH) and polysaccharide lyase (PL), which are important for breakdown of dietary carbohydrates and fibres. A total of 13 polysaccharide lyases were identified functioning on day 20 with enzymes were specific to organs. Overall, our results provide a deeper understanding of microbial-mediated metabolism concerning key performance parameters in chicken production
GIS data for "Prevalence and characteristics of dengue virus co-infection in patients and mosquitoes collected from patients’ houses"
No full textCo-infection with multiple DENV serotypes can affect human immune status and complicate the clinical presentation and management of dengue patients, so understanding the prevalence and dynamics of co-infection is important for effective dengue control. We aimed to identify and characterize DENV co-infection patterns in field-caught mosquitoes and dengue patients. This study was conducted in northeastern Thailand between June 2016 to August 2019. Female Aedes mosquitos collected from and around dengue patient’s houses were analyzed for DENV infection and presence of serotypes using RT-PCR. DENV serotyping was successful in 154 (39.49%) of human and 165 (14.26%) of mosquito samples. Prevalence of DENV co-infection in patients and mosquitoes was 22.73% (35 cases) and 28.48% (47 samples), respectively. Co-infection with multiple serotypes were double (human 88.57%, mosquito 89.36%), triple (human 5.72%, mosquito 10.64%) and quadruple (human 5.72%, mosquito 0%) infections. Concurrent infection was different between hosts and concurrence patterns of DENV serotype in each host mostly composed of the predominant serotype of the detected year. This is the first report that show DENV co-infection patterns in field-caught mosquito and in dengue fever patients with combinations of triple and quadruple serotypes in Thailand. These finding are potentially useful for understanding shifts in serotypes, concurrent DENV infection patterns, vaccine development, and further research on the ability of vectors to transmit multiple serotypes
Quantitative bias analysis for mismeasured variables in health research: a review of software tools
No full textAbstract Background Measurement error and misclassification can cause bias or loss of power in epidemiological studies. Software performing quantitative bias analysis (QBA) to assess the sensitivity of results to mismeasurement are available. However, QBA is still not commonly used in practice, partly due to a lack of knowledge of these software implementations. The features and particular use cases of these tools have not been systematically evaluated. Methods We reviewed and summarised the latest available software tools for QBA in relation to mismeasured variables in health research. We searched the electronic database Web of Science for studies published between January 2014 and May 2024 (inclusive). We included epidemiological studies that described the use of software tools for QBA in relation to mismeasurement. We also searched for tools catalogued on the CRAN archive, in Stata manuals, and via Stata’s net command, available from within Stata or from the IDEAS/RePEc database. Tools were included if they were purpose-built, had documentation, and were applicable to epidemiological research. Data on the tools’ features and use cases were then extracted from the full article texts and software documentation. Results 17 publicly available software tools for QBA were identified, accessible via R, Stata, and online web tools. The tools cover various types of analysis, including regression, contingency tables, mediation analysis, longitudinal analysis, survival analysis and instrumental variable analysis. However, there is a lack of software tools performing QBA for misclassification of categorical variables and measurement error outside of the classical model. Additionally, the existing tools often require specialist knowledge. Conclusions Despite the availability of several software tools, there are still gaps in the existing collection of tools that need to be addressed to enable wider usage of QBA in epidemiological studies. Efforts should be made to create new tools to assess multiple mismeasurement scenarios simultaneously, and also to increase the clarity of documentation for existing tools, and provide tutorials and examples for their usage. By doing so, the uptake of QBA techniques in epidemiology can be improved, leading to more accurate and reliable research findings
JAN-Filipe/scfr-influenza
No full textCode and data to support a literature review of symptomatic-case fatality risk (sCFR) for seasonal influenza. This article reviews studies published between 2009 and 2024
Empirical treatment with valganciclovir in African infants living with HIV hospitalised with severe pneumonia: a randomised factorial controlled trial
No full textData for: "Empirical treatment with valganciclovir in African infants living with HIV hospitalised with severe pneumonia: a randomised factorial controlled trial"