cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2918
title: "The genetic underpinnings of adiposity: from GWAS discovery to functional characterisation" extended supplementary data

description: Two extended supplementary tables, needed for the submission of a thesis in fulfilment of a PhD in Precision Medicine at the University of Edinburgh in 2020. This upload includes 2 files. The first file ("TableS1_iDXA_lm_outputs.txt") includes linear model summaries for GWAS models conducted within the thesis. The second ("TableS2_1251_SNP_info.xlsx") includes a list of significantly associated loci, resulting from said GWAS. This work used data from the UK Biobank cohort, under project number 19655.
DOI: 10.7488/ds/2047
title: Data extraction sheet for the systematic review of VARI-PD

description: Pneumococcal disease (PD) is a major cause of communicable disease burden globally. Evidence from animal and in vitro studies suggest viral acute respiratory infection (VARI) can predispose to pneumococcal infection. Evidence from population-based studies is conflicting, possibly due to a variety of methodological challenges and problems in these studies. We conducted a systematic review of population-based studies that analysed the association between preceding seasonal VARI and subsequent PD. In the current dataset, methods and findings were summarised for each included study in Sheet 2; additionally, reasons for exclusion were given in Sheet 1.
DOI: 10.7488/ds/1981
title: Data supporting Rubio et al on exacerbations of COPD

description: Please see the publication Rubio et al. ('Home monitoring of breathing rate in people with Chronic Obstructive Pulmonary Disease: observational study of feasibility, acceptability and change after exacerbation' International Journal of Chronic Obstructive Pulmonary Disease, vol 2017:12. DOI: 10.2147/COPD.S120706) on exacerbations of COPD (chronic obstructive pulmonary disease).
DOI: 10.7488/ds/2138
title: SUPERSEDED - Epidemiological characteristics of human-infective RNA viruses

description: ## This item has been superseded by the one which can be found at https://doi.org/10.7488/ds/2265 . ## RNA viruses are a major threat to human health. Here, based on extensive literature searches carried out over a period of 18 years, we provide a catalogue of all 214 known human-infective RNA virus species. We link these viruses to metadata for a number of traits that influence their epidemiology, including the date of the first report of human infection, transmissibility in human populations, transmission route(s) and host range. This database can be used in comparative studies of human-infective RNA viruses to identify the characteristics of viruses most likely to pose the greatest public health threat, both now and in the future.
description: Filename: Woolhouse and Brierley RNA virus database.xslx
DOI: 10.7488/ds/2802
title: National burden estimates of hospitalisations for acute lower respiratory infections due to respiratory syncytial virus in 2019: the Burden of Influenza and RSV Disease (BIRD) study

description: # Abstract # ## Background ## Respiratory syncytial virus (RSV) is the predominant viral pathogen associated with acute lower respiratory infection (ALRI) in children under five years of age (&lt;5y). Little is reported on the national estimates of RSV-ALRI hospital admissions in &lt;5y based on robust RSV epidemiology data. ## Methods ## We included data on RSV and ALRI hospital admission in &lt;5y from systematic literature reviews (including unpublished data) and from clinical databases. We used two different methods, namely the rate-based method and the proportion-based method, to estimate national RSV-ALRI admissions in &lt;5y in the year 2019 among countries with robust data. The rate-based method synthesized data on laboratory-confirmed RSV-ALRI hospitalisation rates using a spatiotemporal Gaussian process meta-regression (ST-GPR). The proportion-based method applied data on RSV positive proportions among ALRI to all-cause ALRI admission envelopes using a Bayesian regularized trimmed meta-regression (MR-BRT). Where applicable, we reported estimates by both methods in order to provide a plausible range for each included country. ## Findings ## A total of 334 studies and 1985 data points from 58 countries were included in the analysis, accounting for 58% of the &lt;5y population worldwide. The number of the annual national RSV-ALRI hospitalisations in &lt;5y ranged from 0·06 thousand (95% confidence interval [CI]: 0·02–0·14) in Iceland to 936·29 thousand (95% CI: 261·23–2151·83) in China. Despite great variation among countries, a high proportion of &lt;5 of RSV-ALRI hospitalisations were in infants &lt;1y in all countries (median proportion: 46%, interquartile range: 32–57). In most (76%) years, RSV-ALRI hospitalisation rate fluctuated between 80% and 120% of the country’s median yearly rate. General agreement was observed between estimates by the rate method and proportion method, with a few exceptions in India, Kenya, Norway and Philippines. The estimates by the rate-based method and by the proportion-based method could be extrapolated to a global estimate of 4·1 million (95% CI: 3·8–4·5) and 2·7 million 95% CI: 1·7–5·2) RSV-ALRI hospitalisations in &lt;5y, respectively. ## Interpretation ## By incorporating data from various sources, our study provides robust estimates on the national burden of RSV-ALRI admissions in &lt;5y. These estimates are important for informing policy for introduction of RSV immunisations and also serve as baseline data for assessing the effectiveness of implementing RSV immunisation programmes. ## Funding ## The Foundation for Influenza Epidemiology
DOI: 10.7488/ds/1491
title: Global, regional and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015

description: Background - We have previously estimated that respiratory syncytial virus (RSV) was associated with 22% of all episodes of (severe) acute lower respiratory infection (ALRI) resulting in 55000 to 199000 deaths in children younger than 5 years in 2005. In the past 5 years, major research activity on RSV has yielded substantial new data from developing countries. With a considerably expanded dataset from a large international collaboration, we aimed to estimate the global incidence, hospital admission rate, and mortality from RSV-ALRI episodes in young children in 2015. Methods - We estimated the incidence and hospital admission rate of RSV-associated ALRI (RSV-ALRI) in children younger than 5 years stratified by age and World Bank income regions from a systematic review of studies published between Jan 1, 1995, and Dec 31, 2016, and unpublished data from 76 high quality population-based studies. We estimated the RSV-ALRI incidence for 132 developing countries using a risk factor-based model and 2015 population estimates. We estimated the in-hospital RSV-ALRI mortality by combining in-hospital case fatality ratios with hospital admission estimates from hospital-based (published and unpublished) studies. We also estimated overall RSV-ALRI mortality by identifying studies reporting monthly data for ALRI mortality in the community and RSV activity. Findings - We estimated that globally in 2015, 33·1 million (uncertainty range [UR] 21·6–50·3) episodes of RSV-ALRI, resulted in about 3·2 million (2·7–3·8) hospital admissions, and 59 600 (48 000–74 500) in-hospital deaths in children younger than 5 years. In children younger than 6 months, 1·4 million (UR 1·2–1·7) hospital admissions, and 27 300 (UR 20 700–36 200) in-hospital deaths were due to RSV-ALRI. We also estimated that the overall RSV-ALRI mortality could be as high as 118 200 (UR 94 600–149 400). Incidence and mortality varied substantially from year to year in any given population. Interpretation Globally, RSV is a common cause of childhood ALRI and a major cause of hospital admissions in young children, resulting in a substantial burden on health-care services. About 45% of hospital admissions and in- hospital deaths due to RSV-ALRI occur in children younger than 6 months. An effective maternal RSV vaccine or monoclonal antibody could have a substantial effect on disease burden in this age group.
description: Data from systematic review and RSV GEN working group were collected, cleaned and combined in further analysis. Population data from UNICEF were used to generate population number of each variable of interest.
DOI: 10.7488/ds/2519
title: Global disease burden estimates of respiratory syncytial virus associated with acute respiratory infections in older adults in 2015: A systematic review and meta-analysis

description: Respiratory syncytial virus-associated acute respiratory infection (RSV-ARI) constitutes a substantial disease burden in older adults aged ≥65 years. We aimed to identify all studies worldwide investigating the disease burden of RSV-ARI in this population. We estimated the community incidence, hospitalization rate, and in-hospital case-fatality ratio (hCFR) of RSV-ARI in older adults, stratified by industrialized and developing regions, using data from a systematic review of studies published between January 1996 and April 2018 and 8 unpublished population-based studies. We applied these rate estimates to population estimates for 2015 to calculate the global and regional burdens in older adults with RSV-ARI in the community and in hospitals for that year. We estimated the number of in-hospital deaths due to RSV-ARI by combining hCFR data with hospital admission estimates from hospital-based studies. In 2015, there were about 1.5 million episodes (95% confidence interval [CI], .3 million-6.9 million) of RSV-ARI in older adults in industrialized countries (data for developing countries were missing), and of these, approximately 14.5% (214 000 episodes; 95% CI, 100 000-459 000) were admitted to hospitals. The global number of hospital admissions for RSV-ARI in older adults was estimated at 336 000 hospitalizations (uncertainty range [UR], 186 000-614 000). We further estimated about 14 000 in-hospital deaths (UR, 5000-50 000) related to RSV-ARI globally. The hospital admission rate and hCFR were higher for those aged ≥65 years than for those aged 50-64 years. The disease burden of RSV-ARI among older adults is substantial, with limited data from developing countries. Appropriate prevention and management strategies are needed to reduce this burden.
DOI: 10.7488/ds/2517
title: The etiological role of common respiratory viruses in acute respiratory infections in older adults: A systematic review and meta-analysis

description: Acute respiratory tract infections (ARI) constitute a substantial disease burden in adults and elderly individuals. We aimed to identify all case-control studies investigating the potential role of respiratory viruses in the etiology of ARI in older adults aged ≥65 years. We conducted a systematic literature review (across 7 databases) of case-control studies published from 1996 to 2017 that investigated the viral profile of older adults with and those without ARI. We then computed a pooled odds ratio (OR) with a 95% confidence interval and virus-specific attributable fraction among the exposed (AFE) for 8 common viruses: respiratory syncytial virus (RSV), influenza virus (Flu), parainfluenza virus (PIV), human metapneumovirus (HMPV), adenovirus (AdV), rhinovirus (RV), bocavirus (BoV), and coronavirus (CoV). From the 16 studies included, there was strong evidence of possible causal attribution for RSV (OR, 8.5 [95% CI, 3.9-18.5]; AFE, 88%), Flu (OR, 8.3 [95% CI, 4.4-15.9]; AFE, 88%), PIV (OR, not available; AFE, approximately 100%), HMPV (OR, 9.8 [95% CI, 2.3-41.0]; AFE, 90%), AdV (OR, not available; AFE, approximately 100%), RV (OR, 7.1 [95% CI, 3.7-13.6]; AFE, 86%) and CoV (OR, 2.8 [95% CI, 2.0-4.1]; AFE, 65%) in older adults presenting with ARI, compared with those without respiratory symptoms (ie, asymptomatic individuals) or healthy older adults. However, there was no significant difference in the detection of BoV in cases and controls. This review supports RSV, Flu, PIV, HMPV, AdV, RV, and CoV as important causes of ARI in older adults and provides quantitative estimates of the absolute proportion of virus-associated ARI cases to which a viral cause can be attributed. Disease burden estimates should take into account the appropriate AFE estimates (for older adults) that we report.
DOI: 10.7488/ds/2775
title: Cost of Respiratory Syncytial Virus-Associated Acute Lower Respiratory Infection Management in Young Children at the Regional and Global Level: A Systematic Review and Meta-Analysis

description: This is the first systematic review and meta-analysis summarizing the current evidence related to the cost of RSV disease among children below 5 years of age. It demonstrates that the economic burden associated with RSV disease is substantial. All data variables in the spreadsheet are documented in the publication, either in the main test or supplementary material.
DOI: 10.7488/ds/2541
title: Burden of RSV-associated ALRI in Children with Congenital Heart Disease

description: Introduction: Respiratory syncytial virus (RSV) is the most common viral cause of Acute Lower Respiratory Infections (ALRI) with significant childhood morbidity and mortality worldwide, especially among those with underlying diseases such as congenital heart disease (CHD). Estimates reporting RSV-ALRI severity in children with CHD are lacking, thus warranting the need to summarize the available data. Objectives: The aim of the current project was to identify relevant studies, to summarize the findings, and to conduct a meta-analysis of available data on RSV-associated ALRI hospitalizations in children under five years of age with underlying CHD compared to those without. Methods: Two authors conducted a systematic search of existing relevant literature. The populations of interest were hospitalized children less than five years old with RSV-associated ALRI and CHD (CHDRSV) and the comparison group was cases of RSV-associated ALRI hospitalizations without CHD (non-CHDRSV). We summarized the data and conducted a random effects meta-analysis for outcomes reported by two or more studies using median, mean difference, risk ratio (RR), odds ratio (OR), and incidence rate ratio (IRR).
DOI: 10.7488/ds/2518
title: Global and regional burden of hospital admissions for pneumonia in older adults: A systematic review and meta-analysis

description: Pneumonia constitutes a substantial disease burden among adults overall and those who are elderly. We aimed to identify all studies investigating the disease burden among older adults (age, ≥65 years) admitted to the hospital with pneumonia. We estimated the hospital admission rate and in-hospital case-fatality ratio (CFR) of pneumonia in older adults, stratified by age and economic status (industrialized vs developing), with data from a systematic review of studies published from 1996 through 2017 and from 8 unpublished population-based studies. We applied these rate estimates to population estimates for 2015 to calculate the global and regional burden in older adults who would have been admitted to the hospital with pneumonia that year. We estimated the number of in-hospital pneumonia deaths by combining in-hospital CFRs with hospital admission estimates from hospital-based studies. We identified 109 eligible studies; 73 used clinical pneumonia as the case definition, and 36 used radiologically confirmed pneumonia as the case definition. We estimated that, in 2015, 6.8 million episodes (uncertainty range [UR], 5.8-8.0 episodes) of clinical pneumonia resulted in hospital admissions of older adults worldwide. The hospital admission rate increased with advancing age and was higher in men. The total disease burden was likely underestimated when using the definition of radiologically confirmed pneumonia. Based on data from 52 hospital studies reporting data on pneumonia mortality, we estimated that about 1.1 million in-hospital deaths (UR, 0.9-1.4 in-hospital deaths) occurred among older adults. The burden of pneumonia requiring hospitalization among older adults is substantial. Appropriate prevention and management strategies should be developed to reduce its impact.
DOI: 10.7488/ds/2771
title: Respiratory Syncytial Virus-Associated Acute Lower Respiratory Infections in Children With Bronchopulmonary Dysplasia

description: Background Respiratory syncytial virus (RSV) is among the most important causes of acute lower respiratory tract infection (ALRI) in young children. We assessed the severity of RSV-ALRI in children less than 5 years old with bronchopulmonary dysplasia (BPD). Methods We searched for studies using EMBASE, Global Health, and MEDLINE. We assessed hospitalization risk, intensive care unit (ICU) admission, need for oxygen supplementation and mechanical ventilation, and in-hospital case fatality (hCFR) among children with BPD compared with those without (non-BPD). We compared the (1) length of hospital stay (LOS) and (2) duration of oxygen supplementation and mechanical ventilation between the groups. This dataset contains the full extraction records of the literature review.
DOI: 10.7488/ds/2526
title: The association between respiratory syncytial virus associated acute lower respiratory infection in early life and subsequent recurrent wheeze and asthma in later childhood
DOI: 10.7488/ds/2820
title: Global seasonality of human seasonal coronaviruses

description: Background It is speculated that the ongoing pandemic of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 virus could recur as seasonal outbreaks, a circulating pattern observed among other pre-existing human seasonal coronaviruses (sCoV). However, little is known about the seasonality of these sCoVs on a global scale. Methods We conducted a systematic review of existing data on the seasonality of human sCoV, including NL63, 229E, OC43 and HKU1. We searched four English databases and three Chinese databases for relevant publications between 1st January 2020 and 15th April 2020. We also searched online surveillance datasets and preprints. We extracted weekly or monthly number of sCoV from included studies and calculated the monthly annual average percentage (AAP) as the relative strength of virus activity. We compared the seasonality of sCoV with that of influenza virus and respiratory syncytial virus that we previously reported. We further modelled the monthly activity of sCoV using site-specific temperature, relative humidity and dew point.
DOI: 10.7488/ds/2880
title: Global burden of acute lower respiratory infection associated with human metapneumovirus in children under five years for 2018: a systematic review and modelling study

description: We provide datasets used in this study in this folder. The datasets include (1) the incidence rate of hMPV associated ALRI (see "ALRI" file); (2) hospitalisation rates of hMPV associated ALRI (see "Hos" file); (3) hospitalisation rates of hMPV with hypoxemia (see "sHos" file); (4) CFR of hMPV associated ALRI (see "CFR" file); (5) main table results (see "main table results" file); (6) proportion positives of hMPV in hospitalised ALRI (see "Prop" file). Background of this study: Acute lower respiratory infections (ALRI) are one of the leading causes of morbidity and mortality in children globally, accounting for 10% of mortality in children under five years in 2017.1 Human metapneumovirus (hMPV), first identified in 2001, is an important virus causing ALRI in young children. Previous evidence indicates that almost all children have been infected with hMPV by the age of five, and with most severe infections occurring in infants. Available pooled analyses among different populations have focused on broad age groups, and have shown that hMPV is associated with 6.1–6.4% of hospitalised ALRI among patients under 20 years of age worldwide. Incidence and mortality of hMPV–associated ALRI have only been available in a very limited number of published literature, especially for narrow age groups. There are no global or regional burden estimates for children under five years. Using the published and unpublished data on laboratory–confirmed (culture, immunofluorescence assay, or molecular test) hMPV morbidity and mortality, we sought to estimate the global and regional number of hMPV–associated ALRI cases, hospitalisations, and mortality by age strata in children under five years for 2018. Since the presence of hMPV in children’s upper respiratory tract does not imply causation, we estimated the global burden of ALRI that are attributable to hMPV by accounting for the causal attribution of hMPV.
DOI: 10.7488/ds/1704
title: SUPERSEDED - Data supporting Rubio et al on exacerbations of COPD

description: ## This dataset has been replaced by the one at https://doi.org/10.7488/ds/1981 . ##
DOI: 10.7488/ds/2823
title: Dementia risk prediction model - definitions of variables

description: List of ICD-10 and Read version 2 codes used to define predictor and outcome variables for dementia risk prediction model.
description: predictor_codes.xlsx dementia_codes.docx README.txt
DOI: 10.7488/ds/2049
title: Data for Comparison of two lines of tauGFP transgenic mice designed for lineage tracing

description: The data are numerical data used to produce some figures and tables for a manuscript comparing two lines of tauGFP transgenic mice designed for lineage tracing. Study Abstract: The tauGFP reporter fusion protein is produced nearly ubiquitously by the TgTP6.3 transgene in TP6.3 mice and its localisation to microtubules offers some advantages over soluble GFP as a lineage marker. However, TgTP6.3Tg/Tg homozygotes are not viable and TgTP6.3Tg/- hemizygotes are smaller than wild-type. TP6.4 mice carry the TgTP6.4 transgene, which was produced with the same construct used to generate TgTP6.3, so we investigated whether TgTP6.4 had any advantages over TgTP6.3. Although TgTP6.4Tg/Tg homozygotes died before weaning, TgTP6.4Tg/- hemizygotes were viable and fertile and only males were significantly lighter than wild-type. The TgTP6.4 transgene produced the tauGFP fusion protein by the 2-cell stage and it was widely expressed in adults but tauGFP fluorescence was weak or absent in several tissues, including some neural tissues. The TgTP6.4 transgene expression pattern changed over several years of breeding and mosaic transgene expression became increasingly common in all expressing tissues. Although mosaic expression makes the TgTP6.4 transgene unsuitable for use as a conventional cell lineage marker, mosaicism provides a useful system for visualising clonal lineages that arise during development or maintenance of adult tissues. Lineages in the adrenal cortex of TgTP6.4Tg/- hemizygotes were qualitatively and quantitatively comparable to lineages reported previously for other mosaic transgenic mice, X-inactivation mosaics and chimaeras. Mosaicism occurred less frequently in TP6.3 than TP6.4 mice and was only observed in the corneal epithelium and adrenal cortex. Such differences in the occurrence of mosaicism between related transgenic lines might provide a useful system for investigating the mechanism of transgene silencing.