cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/1370
title: Dataset pertaining to the publication “Loci Associated with N-Glycosylation of Human Immunoglobulin G Show Pleiotropy with Autoimmune Diseases and Haematological Cancers”

description: Dataset pertaining to the publication “Loci Associated with N-Glycosylation of Human Immunoglobulin G Show Pleiotropy with Autoimmune Diseases and Haematological Cancers”. The files are comma separated and contain genome wide association meta-analysis data for the discovery studies. Summary data are given for the meta-analyses of over 2 million directly genotyped or imputed single variant polymorphisms corresponding to the HAPMAP2 release 22 reference panel : allele2, effallele, allele for which effect (beta) is reported, allele1, alternate allele. chromosome and position are position of the SNP on NCBI36/hg18 build. Meta-analysis mean effect size (beta) is the inverse-variance weighted estimate derived from individual discovery study; sebeta is its standard error. p is meta-analysis P-value; npops is the number of populations used for meta-analysis at that locus; n is the total number of samples used in individual level GWASs. Meta-analysis estimates are corrected for inflation of test statistics using genomic control at the individual study level. The archive IgGGlycans_GWAMA_2013.tar.gz contains seventy-seven gzipped files corresponding to genome-wide association meta-analysis (GWAMA) of seventy-seven IgG glycans traits.
description: The archive IgGGlycans_GWAMA_2013.tar.gz contains seventy-seven gzipped files corresponding to genome-wide association meta-analysis (GWAMA) of seventy-seven IgG glycans traits.
DOI: 10.7488/ds/2115
title: Dataset 1 pertaining to the publication "Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants"

description: The Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based population cohort with DNA, biological samples, socio-demographic, psychological and clinical data from ~24,000 adult volunteers across Scotland. Although data collection was cross-sectional, GS:SFHS became a prospective cohort due to the ability to link to routine Electronic Health Record (EHR) data. Over 20,000 participants were selected for genotyping using a genome-wide array. Genome-wide association studies (GWAS) were used to test the effects of a spectrum of variants, imputed using the Haplotype Research Consortium (HRC) dataset, on medically relevant traits measured directly or obtained from EHRs. The HRC dataset allowed investigation of variants with low minor allele frequencies in the entire GS:SFHS genotyped cohort. Genome-wide associations were run on 20,032 individuals using both genotyped and HRC imputed data. Results replicated known associations and additionally revealed novel findings, mainly with rare variants. The dataset contains genome-wide association summary statistics for this project. The remaining 5 data files can be found here: http://datashare.is.ed.ac.uk/handle/10283/2788
description: README.txt
DOI: 10.7488/ds/2114
title: SUPERSEDED - Dataset 2 pertaining to the publication "Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants"

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2602 ## The Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based population cohort with DNA, biological samples, socio-demographic, psychological and clinical data from ~24,000 adult volunteers across Scotland. Although data collection was cross-sectional, GS:SFHS became a prospective cohort due to the ability to link to routine Electronic Health Record (EHR) data. Over 20,000 participants were selected for genotyping using a genome-wide array. Genome-wide association studies (GWAS) were used to test the effects of a spectrum of variants, imputed using the Haplotype Research Consortium (HRC) dataset, on medically relevant traits measured directly or obtained from EHRs. The HRC dataset allowed investigation of variants with low minor allele frequencies in the entire GS:SFHS genotyped cohort. Genome-wide associations were run on 20,032 individuals using both genotyped and HRC imputed data. Results replicated known associations and additionally revealed novel findings, mainly with rare variants. The dataset contains genome-wide association summary statistics for this project. The other 11 data files can be found here: http://datashare.is.ed.ac.uk/handle/10283/2789
DOI: 10.7488/ds/212
title: Modulation of Genetic Associations with Serum Urate Levels by Body-Mass-Index in Humans

description: Full lists of genome-wide association results for urate level as analysed in the PLOS-ONE manuscript "Modulation of Genetic Associations with Serum Urate Levels by Body-Mass-Index in Humans”. Please read the READ_DATASHARE.txt for full description.
DOI: 10.7488/ds/2125
title: GWAS summary statistics for uric acid in GS:SFHS

description: The Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based population cohort with DNA, biological samples, socio-demographic, psychological and clinical data from ~24,000 adult volunteers across Scotland. Although data collection was cross-sectional, GS:SFHS became a prospective cohort due to the ability to link to routine Electronic Health Record (EHR) data. Over 20,000 participants were selected for genotyping using a genome-wide array. Genome-wide association studies (GWAS) were used to test the effects of variants on the uric acid phenotype from the EHR. Results replicated a known association and the dataset contains genome-wide association summary statistics for this project.
DOI: 10.7488/ds/104
title: International Stroke Trial database (version 2)

description: The International Stroke Trial (IST) was one of the biggest randomised trials in acute stroke. Methods: Available data on variables assessed at randomisation, at the early outcome point (14-days after randomisation or prior discharge) and at 6-months were extracted and made publically available. Results and Conclusions: The IST provides an excellent source of primary data easy-to-use for sample size calculations and preliminary analysis necessary for planning a good quality trial. # Associated publications # * The erratum paper explains the difference between this version ie version 2, and the previous version: Sandercock, P.A.G., Niewada, M., Członkowska, A. et al. Erratum to: The International Stroke Trial database. Trials 13, 24 (2012). https://doi.org/10.1186/1745-6215-13-24 . * Main results paper for the trial: International Stroke Trial Collaborative Group 1997, 'The International Stroke Trial (IST): A randomised trial of aspirin, subcutaneous heparin, both, or neither among 19 435 patients with acute ischaemic stroke', The Lancet, vol. 349, no. 9065, pp. 1569-1581. https://doi.org/10.1016/S0140-6736(97)04011-7 .
description: International Stroke Trial database unicode data file International Stroke Trial database csv data file
DOI: 10.7488/ds/105
title: International Stroke Trial database (superseded)

description: ## This dataset has been replaced by the one which can be found at https://doi.org/10.7488/ds/104 . ## The International Stroke Trial (IST) was one the biggest randomised trials in acute stroke. Methods: Available data on variables assessed at randomisation, at the early outcome point (14-days after randomisation or prior discharge) and at 6-months were extracted and made publically available. Results and Conclusions: The IST provides an excellent source of primary data easy-to-use for sample size calculations and preliminary analysis necessary for planning a good quality trial.
description: International Stroke Trial database unicode data file International Stroke Trial database csv data file
DOI: 10.7488/ds/2951
title: Medication-Wide Association Study of Dementia

description: Dataset and code list from medication-wide association study of dementia, using the Secure Anonymised Information Linkage databank Dementia electronic Cohort (SAIL-DeC). The dataset contains the hazard ratios and p-values for all medications included in the analysis (744 drugs in total). These results are from the full study population (n=551,344), of whom 16,998 developed dementia during follow-up. Numbers &lt;10 have been masked to preserve de-identification of study participants. The code list contains Read version 2 and ICD-10 codes used to identify medications and dementia outcomes in the study.
DOI: 10.7488/ds/2969
title: SUPERSEDED - Supplementary File 1: Key findings from downloaded COVID-19 information for those categorised as high-risk (20 April 2020)

description: ## SUPERSEDED - this item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2982 . ## Data supporting McClatchey et al "COVID-19 information for people living with asthma: A rapid review of publicly available information" JACI: In practice (accepted manuscript). Abstract: In 2020, COVID-19 was declared a pandemic, posing risk to high-risk communities, such as people living with severe asthma. We rapidly reviewed COVID-19 information available online for people with asthma, to assess whether information aligns with risk communication and asthma self-management guidelines. Information from five English-speaking countries and global websites providing COVID-19 information for people with asthma (including those at high-risk of severe disease) were downloaded. Informed by the World Health Organization (WHO) emergency risk communication guideline and the National Institute for Health and Care Excellence asthma guidelines, 102 webpages from 43 unique organisations that provided asthma-related health information were analysed. We found that COVID-19 online information for people with asthma largely followed the WHO emergency risk communication guideline and provided some asthma self-management strategies.
DOI: 10.7488/ds/3037
title: Global hospital admissions and in-hospital mortality associated with all-cause and virus-specific acute lower respiratory infections in children and adolescents aged 5-19 years between 1995 and 2019

description: This dataset includes the data for the paper entitled "Global hospital admissions and in-hospital mortality associated with all-cause and virus-specific acute lower respiratory infections in children and adolescents aged 5-19 years between 1995 and 2019: a systematic review and modelling study" (accepted in May 2021). Most of the data used in the paper are uploaded in the supplementary appendix with the paper. Here, we provide more details for each outcome.
DOI: 10.7488/ds/2540
title: Data for re-evaluation of the causes of variation among mouse aggregation chimaeras

description: The data are numerical data used to produce Figs. 2 & 5, Supplementary Figs. S3–S6 and Supplementary Table S2 in a manuscript entitled “Re-evaluation of the causes of variation among mouse aggregation chimaeras” by West JD, Tang P-C, Everett, CA, Mackay GE, Flockhart JH and Keighren MA. The study seeks to understand why the composition of mouse aggregation chimaeras, comprising two genetically distinct cell populations, varies much more widely than that of X-inactivation mosaics. Analysis of published results for chimaeric blastocysts suggests that some variation already exists among aggregates before segregation of the ICM and TE. This would include both biological variation between aggregated embryos and experimental variation introduced by the chimaera production procedures. Variation among chimaeric ICMs was greater than among whole blastocysts, implying that significant additional variation arises when cells are allocated to the ICM or trophectoderm (TE). Moreover, in mid-gestation chimaeras, the compositions of the epiblast derivatives were not negatively correlated with the PrE derivatives, again suggesting that significant variation existed among ICMs before epiblast formation. The composition of samples from postimplantation stage chimaeras were more strongly correlated within the epiblast lineage or within the PrE lineage than between the two lineages, implying that the second allocation step, involving the segregation of the epiblast and PrE lineages, is also a significant source of variation among chimaeric epiblasts. Computer simulation results were consistent with the conclusion that the wide variation in chimaeric epiblast composition arises by two stochastic allocation steps, during the formation of the ICM and epiblast respectively. Later allocation events will cause variation among both chimaeras and X-inactivation mosaics. We also suggest that previously published U-shaped frequency distributions for chimaeric placenta composition might be explained by how TE cells are allocated to the polar TE and the subsequent movement of TE cells from the polar TE to the mural TE.
DOI: 10.7488/ds/2753
title: Phase 2: The views and experiences of people with limited health literacy and asthma on managing their condition: a qualitative study
title: Qualitative study

description: We used a method called photovoice, an arts-based qualitative method by which people can identify, represent and express their life experience through photographs. The photographs were used to stimulate discussion during a subsequent interview. To enact social change, some photographs which had been consented by participants were put up in an exhibition attended by local and international stakeholder. The idea is to create awareness of what it is like to be a person with asthma. The first document is the codebook of the overall analysis of the qualitative interview. In total, we had 26 in-depth interviews and 8 photovoice interviews. The process that took place to create this codebook includes: 1) initial open coding 2) collation of open codings to form categories and 3) formation of themes. The codebook is used to organise the themes in a systematic manner, to aid mapping of themes for further latent analysis and to aid write-up. Other documents include the flyer to invite participants to this study, infographic materials to aid photovoice training and two sets of the participants information sheet and consent (i) in-depth interview (ii) photovoice training and interviews Both documents are information to support part of the PhD work at the Usher Institute, the University of Edinburgh (PhD title: Developing and piloting an ICT-based intervention for adult asthma with limited health literacy to improve asthma self-management) Due to the sensitivity of the data and to protect the confidentiality of the participants involved in this study, the raw data will be deposited in DataVault at the University of Edinburgh.
DOI: 10.7488/ds/2455
title: SUPERSEDED - Photometric stereo dataset with annotated leaf masks

description: ## This item has been replaced by the one which can be found at: https://doi.org/10.7488/ds/2514 ## Automated leaf segmentation is a challenging area in computer vision. Recent advances in machine learning approaches allowed to achieve better results than traditional image processing techniques (Scharr et al., 2016; Mengye and Zemel, 2016); however, training such systems often require large annotated datasets (Giuffrida et al., 2017). To contribute with annotated datasets and help to overcome this bottleneck in plant phenotyping research, here we provide a novel photometric stereo (PS) dataset with annotated leaf masks. This dataset forms part of work done in the BBSRC Tools and Resources Development project BB/N02334X/1.
description: Please see the "Dataset description.docx" file
DOI: 10.7488/ds/3181
title: Synaptic and non synaptic proteome in ageing murine cortical isolates

description: Label free proteomic analysis of "synaptic" and "non-synaptic" mitochondrial subpopulations isolated from murine cortex throughout the process of "normal healthy" ageing. These are sub populations of mitochondria as isolated and defined by Lai JC, Walsh JM, Dennis SC, Clark JB. Synaptic and non-synaptic mitochondria from rat brain: isolation and characterization. J Neurochem. 1977;28(3):625-31. Files attached include synaptic or non-synaptic mitochondrial time course data output from Progenesis software. This data is an update with additional content (superseding https://doi.org/10.7488/ds/2333).
description: 1.Graham et al_Raw MS data archive: This is approximately 14GB of raw mass spec files for young, mid and old age isolates of synaptic and non synaptic mitochondrial fractions. 2. Graham et al_Progenesis analysis output: This is the data output following analysis of the raw files from 1. (above) with Progenesis software. 3. Graham et al_Mitocarta overlap: This is a list with the candidates identified which overlap with aspects of the Mitocarta dataset (freely available from here: https://www.broadinstitute.org/mitocarta/mitocarta30-inventory-mammalian-mitochondrial-proteins-and-pathways). 4. Graham et al_Clusters of expression correlates: This is a multi tabbed file with the outputs of proteomic data clustering with specific expression trends following analysis with BioLayout software (available from here: http://biolayout.org/). 5. Graham et al_Heatmap components: This is a list of the filtered data which was used to generate a heatmap of candidates whose expression alters in a biologically relevant manner with advancing age.
DOI: 10.7488/ds/2881
title: Staphylococcus aureus secreted lipases do not inhibit innate immune killing mechanisms: Extended Figure 1

description: Staphylococcus aureus pathogenesis is mediated by a plethora of secreted proteins, many of which remain incompletely characterised. For example, S. aureus abundantly secretes two isoforms of the enzyme lipase into the extracellular milieu, where they scavenge upon polymeric triglycerides. To analyse the role of lipases in host-pathogen interactions, recombinant S. aureus lipase 1 and 2 were purified from a ClearColi® BL21 (DE3). To confirm recombinant lipase 1 and 2 were functional proteins, a turbiometric assay was employed. Functional recombinant lipases were used in our studies to help broaden our understanding of the interaction of S. aureus lipases with the innate immune system.
DOI: 10.7488/ds/2074
title: Data from the study "Fine-mapping host genetic variation underlying outcomes to Mycobacterium bovis infection in dairy cows"

description: This dataset derives form a study on the host genetic variation in resistance to bovine tuberculosis (bTB) in dairy cattle. It is well established that host genetic variation in resistance to bTB exists in dairy cattle. However, cattle diagnosed as infected with M. bovis display varying signs of pathology. The variation in host response to infection could represent a continuum since time of exposure or distinct outcomes due to differing pathogen handling. To investigate this 1966 Holstein-Friesian dairy cows were genotyped using the the BovineHD SNP chip. Three distinct phenotypes were defined in the study single intradermal cervical comparative tuberculin (SICCT) test positives with visible lesions (VLs), SICCT-positives with undetected visible lesions (NVLs) and matched controls SICCT-negative on multiple occasions. Up to 15 of the 29 chromosomes of the bovine genome were found to harbour heritable variation. By case phenotype, 4 of 5 chromosomes explaining heritable variation in the VLs were also found for NVLs, but an additional 10 chromosomes were unique to NVLs. Furthermore, five different genomic regions with heritable variation were found for the two case phenotypes. A genomic region of interest detected in NVLs, but not VLs, was on chromosome 23 located near the bovine leukocyte antigen (BoLA) class IIb region. BoLA is the bovine version of the Major Histocompatibility Complex, a family of genes which encode cell surface molecules involved in the immune system, playing an important role in disease resistance. The results suggest some differing underlying genetics governing observed versus non-observed pathology for bTB infected animals, supporting the notion of a bTB infection spectrum. The implications of complex genetic control of bTB susceptibility may need to be considered in disease control.
DOI: 10.7488/ds/2232
title: CAD files for constructing the image capture system

description: Improvements in high-throughput phenotyping technologies are rapidly expanding the scope and capacity of plant biology studies to measure growth traits. Nevertheless, the costs of commercial phenotyping equipment and infrastructure remain prohibitively expensive for wide-scale uptake, while academic solutions can require significant local expertise. Here a low-cost methodology for plant biologists to build their own phenotyping system for quantifying growth rates and phenotypic characteristics of Arabidopsis thaliana rosettes throughout the diel cycle is presented. The group constructed an image capture system consisting of a near infra-red (NIR, 940 nm) LED panel with a mounted Raspberry PI NoIR camera and developed a MatLab-based software module (iDIEL Plant) to characterise rosette expansion. The software was able to accurately segment and characterise multiple rosettes within an image, regardless of plant arrangement or genotype, and batch process image sets. To further validate the system, wild-type Arabidopsis plants (Col-0) and two mutant lines with reduced Rubisco contents, pale leaves and slow growth phenotypes (1a3b and 1a2b) were grown on a single plant tray. Plants were imaged from 9 to 24 days after germination every 20 minutes throughout the 24 hour light-dark growth cycle (i.e. the diel cycle). The resulting dataset provided a dynamic and uninterrupted characterisation of differences in rosette growth and expansion rates over time for the three lines tested. The methodology offers a straightforward solution for setting up automated, scalable and low-cost phenotyping facilities in a wide range of lab environments that could greatly increase the processing power and scalability of Arabidopsis soil growth experiments. iDIEL Plant software and CAD files for image capture system (ICS).
DOI: 10.7488/ds/3274
title: SUPERSEDED - GenOMICC WGS summary statistics
title: GWAS and TWAS GenOMICC summary statistics

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/3411 ## GWAS summary statistics from 7,491 critically ill patients from COVID-19 and 48,400 population controls: European(EUR) 5,989/42,891; South Asian(SAS) 788/3,793; African(AFR) 440/1,350; East Asian(EAS) 274/366. GWAS models were calculated with SAIGE using a logisitic mixed-model regression. A trans-ancestry meta-analysis was performed using inverse-variant weighted fixed-effects. Ancestry-specific and trans-ancestry summary statistics are available. TWAS was performed using GTEx v8 gene expression data for lung and blood and an all-tissue meta-analysis. Summary statistics for tissue-specific and meta-TWAS are available.