cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/3796
title: Impact of granular inclusions on the phase behaviour of colloidal gels

description: This dataset accompanies the article "Impact of granular inclusions on the phase behaviour of colloidal gels" by Li, Royer, Sun and Ness (arXiv:2207.03864, to appear in Soft Matter). It contains the raw data for generating the plots therein, as described in README.txt. The data represent measurements of the isostatic length and viscoelastic moduli of filled and unfilled colloidal gels (Figs 1a-2d); probability distributions of the colloid-colloid contact number and void volumes (Figs 2e-3b); and phase diagrams depicting the liquid-gel boundary of filled and unfilled gels (Fig 4). Colloidal gels formed from small attractive particles are commonly used in formulations to keep larger components in suspension. However, despite extensive work characterizing unfilled gels, little is known about how larger inclusions alter the phase behavior and microstructure of the colloidal system. Here we use numerical simulations to examine how larger `granular' particles can alter the gel transition phase boundaries. We find two distinct regimes depending on both the filler size and native gel structure: a `passive' regime where the filler fits into already-present voids, giving little change in the transition, and an `active' regime where the filler no longer fits in these voids and instead perturbs the native structure. In this second regime the phase boundary is controlled by an effective colloidal volume fraction given by the available free volume.
description: Raw data associated with each of the figures in the article "Impact of granular inclusions on the phase behaviour of colloidal gels"
DOI: 10.7488/ds/3166
title: Laser-induced nucleation of supersaturated aqueous sodium bromide

description: This dataset comprises original images and videos collected during experiments on the nucleation and crystal growth from supersaturated aqueous solutions of sodium bromide. Different methods were used to induce nucleation: mechanical shock-induced nucleation, nucleation by ultrasound (sonocrystallization), non-photochemical laser-induced nucleation (NPLIN) and laser-trapping nucleation. The most stable crystal form at room temperature is known to be sodium bromide dihydrate (DH) and this form was favoured (&gt; 95%) through spontaneous nucleation or mechanical shock. Sonocrystallization favoured DH crystals (74%). Remarkably both laser-induced nucleation methods showed a strong preference (&gt; 90%) for anhydrous (AH) crystals.
description: Please see text file README.txt included with the dataset.
DOI: 10.7488/ds/3162
title: Compositional modelling of immune response and virus transmission dynamics – Supplementary data

description: This repository contains calibration and simulation data accompanying the paper of the same title about the interaction of the adaptive immune response and transmission of SARS-CoV-2. All data is reproducible from the software at https://git.sr.ht/~wwaites/immune-transmission however reproduction is computationally expensive. For this reason the data is made available separately here.
description: This dataset contains three types of files. Calibration data (.db) are SQLite databases in the format of the PyABC programme. Sampled trajectories from the model (.h5) are in HDF5 format. Post-processed data (.tsv) is in tab-separated value format. These are described in detail in the README file in the source code repository https://git.sr.ht/~wwaites/immune-transmission.
DOI: 10.7488/ds/3163
title: SUPERSEDED - GWAS summary statistics pertaining to the publication "Same role but different actors: genetic regulation of post-translational modification of two distinct proteins"

description: ## This item has been replaced by the one which can be found at https://datashare.ed.ac.uk/handle/10283/4088 ## Post-translational modifications (PTMs) diversify protein functions and dynamically coordinate their signalling networks, influencing most aspects of cell physiology. Nevertheless, their genetic regulation or influence on complex traits is not fully understood. Here, we compare for the first time the genetic regulation of the same PTM of two proteins – glycosylation of transferrin and immunoglobulin G (IgG). By performing genome-wide association analysis of transferrin glycosylation, we identified 10 significantly associated loci, all novel. Comparing these with IgG glycosylation-associated genes, we note protein-specific associations with genes encoding glycosylation enzymes (transferrin - MGAT5, ST3GAL4, B3GAT1; IgG - MGAT3, ST6GAL1) as well as shared associations (FUT6, FUT8). Colocalisation analyses of the latter suggest that different causal variants in the FUT genes regulate fucosylation of the two proteins. We propose that they affect the binding of different transcription factors in different tissues, with fucosylation of IgG being regulated by IKZF1 in B-cells and of transferrin by HNF1A in liver.
description: Please see readme.txt for details.
DOI: 10.7488/ds/3797
title: EBV serostatus and total number of siblings GWAS summary statistics

description: GWAS on EBV serostatus/total number of siblings on UKBiobank participants Mendelian randomisation identifies priority groups for prophylactic EBV vaccination. Marisa D. Muckian, MSc; James. F Wilson, DPhil; Graham S. Taylor, PhD; Helen R. Stagg, PhD; Nicola Pirastu, PhD We mapped the complex evidence from the literature prior to this study factors associated with EBV serostatus (as a proxy for infection) into a causal diagram to determine putative risk factors for our study. Using data from the UK Biobank of 8,422 individuals genomically deemed to be of white British ancestry between the ages of 40 and 69 at recruitment between the years 2006 and 2010, we performed a genome wide association study (GWAS) of EBV serostatus and total number of sibligns, followed by a Two Sample MR to determine which putative risk factors were causal.
description: GWAS on EBV serostatus/total number of siblings on UKBiobank participants Mendelian randomisation identifies priority groups for prophylactic EBV vaccination. Marisa D. Muckian, MSc; James. F Wilson, DPhil; Graham S. Taylor, PhD; Helen R. Stagg, PhD; Nicola Pirastu, PhD We mapped the complex evidence from the literature prior to this study factors associated with EBV serostatus (as a proxy for infection) into a causal diagram to determine putative risk factors for our study. Using data from the UK Biobank of 8,422 individuals genomically deemed to be of white British ancestry between the ages of 40 and 69 at recruitment between the years 2006 and 2010, we performed a genome wide association study (GWAS) of EBV serostatus and total number of sibligns, followed by a Two Sample MR to determine which putative risk factors were causal.
DOI: 10.7488/ds/3004
title: Stakeholders' views of asthma and school-based asthma programme for primary school children: A qualitative study in Malaysia
title: CuT-AsthMa - Phase 1b (Qualitative study among stakeholders)

description: This is a qualitative study conducted among 52 stakeholders in the education and health sectors in Malaysia. We explored the views of school staff, healthcare professionals and policymakers, about asthma and school asthma programmes for primary school children to inform the development of a Culturally Tailored school-based intervention for Asthma in Malaysia (CuT-AsthMa) programme. The documents consist of the participant information sheet and consent form, the background questionnaire, topic guides and a coding tree. This study is to support part of the PhD work at the Usher Institute, the University of Edinburgh (PhD title: Culturally Tailored school-based intervention for Asthma in Malaysia (CuT-AsthMa)) 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/3164
title: Additional files for 'The evolution of nitrogen fixation in cyanobacteria'

description: Supplementary data for Latysheva N, Junker VL, Palmer WJ, Codd GA and Barker D, 'The evolution of nitrogen fixation in cyanobacteria' (2012, Bioinformatics 28:603-606, doi:10.1093/bioinformatics/bts008). This supplementary data is the corrected version of March 2012, which supersedes the version on the Web site of the journal Bioinformatics. For further details, see 'README.pdf' within the zipfile.
description: See 'README.pdf' within the zipfile.
DOI: 10.7488/ds/3843
title: CARDAMOM driving data and C-cycle model outputs to accompany "Scale-variance in the carbon dynamics of fragmented, mixed-use landscapes estimated using Model-Data Fusion"

description: This archive contains the driving data and selected model outputs to accompany the manuscript: Milodowski, D.T., Smallman, T.L., Williams, M. (in submission), "Scale-variance in the carbon dynamics of fragmented, mixed-use landscapes estimated using Model-Data Fusion", Biogeosciences Discussions. Many terrestrial landscapes are heterogeneous. Mixed land cover and land-use generate a complex mosaic of fragmented ecosystems at fine spatial resolutions with contrasting ecosystem stocks, traits and processes, each differently sensitive to environmental and human factors. Representing spatial complexity within terrestrial ecosystem models is a key challenge for understanding regional carbon dynamics, their sensitivity to environmental gradients, and their resilience in the face of climate change. Heterogeneity underpins this challenge due to the trade-off between the fidelity of ecosystem representation within modelling frameworks and the computational capacity required for fine-scale model calibration and simulation. We directly address this challenge by quantifying the sensitivity of simulated carbon fluxes in a mixed-use landscape in the UK to the spatial resolution of the model analysis.
description: The archive contains two zip files containing: (i) the observations and driving data assimilated into CARDAMOM; and (ii) a selection of model output, including the carbon (C) stocks for each DALEC pool, and a compilation of key C fluxes. Data and model output are stored as netcdf files. The xarray package (https://docs.xarray.dev/en/stable/index.html) provides a convenient starting point for using netcdf files within python environments. More details are provided in the document "Milodowski_etal_dataset_description.pdf" See also the document: "Milodowski_etal_dataset_description.pdf"
DOI: 10.7488/ds/2999
title: Central complex EPG-PFL3 modulation model simulation data

description: Central complex model simulations data. This dataset regroups the different experiment conducted on an EPG-PFL3 synaptic modulation model of the insect central complex to explain landmark guidance behaviour. Each folder includes all the XY-theta data and the neuron activity for the different condition tested.
DOI: 10.3886/e183804
title: Data and Code for: The Health of Democracies during the Pandemic: Results from a Randomized Survey Experiment

description: Concerns have recently been raised about the potential demise of democracy – although there was a perceived slide in the strength of democratic institutions even before the pandemic – this was possibly accelerated by restrictions on movement and other public health regulations. Using in-depth survey experiments of 8,000 responses from several Western democracies, we find that, following the treatment providing information on restrictions and infringements by China and South Korea to contain the COVID-19 pandemic, subjects become less willing to sacrifice specific and generic rights and more worried about long-term erosion relative to the control group, but there was no effect of our treatment on support for democratic procedures. Taken together, the results suggest that support for democratic processes was inelastic to concerns about the freedoms it enabled very early in the pandemic and might have been a moment of particular vulnerability.
description: We use the unweighted results in our main analysis and provide nationally representative weights in the dataset.
description: Individuals older than 18 living in France, Germany, Italy, the United Kingdom, and the United States in March-April 2020. Smallest Geographic Unit: Principal (largest) administrative divisions
DOI: 10.7488/ds/3045
title: Deciding on Personalized Ads: Nudging Developers About User Privacy

description: Online experiment survey data associated with the below paper. The survey-based online experiment was conducted with 400 participants with experience in mobile app development. There were six conditions where the framing around advertisement tracking choices was varied in terms of options and text. The dataset contains the full text of the survey, and the redacted data set where data such as unique ID from Prolific have been removed. Mohammad Tahaei, Alisa Frik, and Kami Vaniea "Deciding on Personalized Ads: Nudging Developers About User Privacy". In proceedings of the Symposium on Usable Privacy and Security (SOUPS). 2021
DOI: 10.3886/e183804v1
title: Data and Code for: The Health of Democracies during the Pandemic: Results from a Randomized Survey Experiment

description: Concerns have recently been raised about the potential demise of democracy – although there was a perceived slide in the strength of democratic institutions even before the pandemic – this was possibly accelerated by restrictions on movement and other public health regulations. Using in-depth survey experiments of 8,000 responses from several Western democracies, we find that, following the treatment providing information on restrictions and infringements by China and South Korea to contain the COVID-19 pandemic, subjects become less willing to sacrifice specific and generic rights and more worried about long-term erosion relative to the control group, but there was no effect of our treatment on support for democratic procedures. Taken together, the results suggest that support for democratic processes was inelastic to concerns about the freedoms it enabled very early in the pandemic and might have been a moment of particular vulnerability.
description: We use the unweighted results in our main analysis and provide nationally representative weights in the dataset.
description: Individuals older than 18 living in France, Germany, Italy, the United Kingdom, and the United States in March-April 2020. Smallest Geographic Unit: Principal (largest) administrative divisions
DOI: 10.7488/ds/3000
title: CARDAMOM Brazil C-cycle multi-DALEC, multi-CMIP6 scenarios (1x1 degree; monthly; 2001-2017)

description: Dataset continues CARDAMOM output for the calibration of 5 DALEC C-cycle models (M1-5) across Brazil for a 17 year period (2001-2017) at a monthly time step and 1 x 1 degree spatial resolution. The calibration used Earth Observation derived estimates of leaf area, above ground woody biomass and databased soil carbon stocks. The calibrated models were then projected to 2100 using 4 climate change scenarios drawn from the UKESM submission to CMIP6. The dataset includes C-stocks, fluxes and ecosystem properties along with their associated parameteric uncertainties. Separate files exist for each model, calibration period and climate change scenario. The multi-model ensemble provides a quantification of the role of model structural uncertainty allowing partitioning of the relative importance of parametric, model structure and climate change scenario uncertainties. This dataset is associated with a paper intended for submission to Earth System Dynamics. Smallman et al., (in prep) Parameter uncertainty dominates forecast error across Brazil for much of the 21st Century.
description: A brief description of differences between each DALEC model are outlined in the M1_M5_summary_description.txt file. The output files include MOHC indicating the scenario was drawn from the Meteorological Office Handley Centre (MOHC). The following scenarios are used SSP1-2.6 W/m2, SSP2-4.5 W/m2, SSP37.0 W/m2 and SSP5-8.5 W/m2. The file name structure is: [Model]_[DATATYPE]_MOHC_[SSPcode]_climate_change_[startyear]_[endyear].nc Specific files are provided per model, per scenario with files separately containing stocks, fluxes and ecosystem properties.
DOI: 10.7488/ds/3003
title: Antigenic diversity in Theileria parva populations from cattle and African buffalo analysed using long read sequencing

description: East Coast fever (ECF) in cattle is caused by the tick-borne protozoan Theileria parva, and is transmitted by the three-host tick Rhipicephalus appendiculatus. The African buffalo (Syncerus caffer) is the natural host for T. parva but does not suffer disease, whereas ECF is often fatal in cattle. The genetic relationship between T. parva populations circulating in cattle and buffalo is poorly understood, and has not been studied in sympatric buffalo and cattle. The study aimed to determine the genetic diversity of T. parva populations in cattle and buffalo, in an area where livestock co-exist with buffalo adjacent to the Serengeti National Park, Tanzania. Three T. parva antigens known to be recognized by CD8+ and CD4+ T cells in immunized cattle, were used to characterize genetic diversity in T. parva cattle (n=149) and buffalo samples (n=22). Long read (Pacbio) sequencing was used to generate full length or near-full length allelic sequences. Patterns of diversity were similar across all three antigens, with allelic diversity being significantly greater in buffalo-derived parasites compared to cattle-derived (e.g. median cattle allele count for Tp1 was 9, compared to 81.5 for buffalo), with very few alleles shared between species (8 of 651 alleles were shared for Tp1). Most alleles were unique to buffalo with a smaller proportion unique to cattle (412 buffalo-unique vs 231 cattle-unique for Tp1). There were indications of genetic substructuring of the population, with one allelic cluster representing alleles found in both cattle and buffalo (including the TpM reference genome allele), and another containing predominantly only alleles deriving from buffalo. These data illustrate the complex interplay between T. parva populations in buffalo and cattle, revealing the significant genetic diversity in the buffalo T. parva population, the limited sharing of parasite genotypes between the host species, and highlight that a subpopulation of T. parva is maintained by transmission within cattle. The data indicate that fuller understanding of buffalo T. parva population dynamics in particular is needed, as only a comprehensive understanding of the population genetics of T. parva populations will enable assessment of buffalo-derived infection risk in cattle, and how this may impact upon control measures such as vaccination.
DOI: 10.7488/ds/3005
title: SUPERSEDED - Data supporting "Ultraviolet photochemical production of climate-relevant gases from marine phytoplankton"

description: ## SUPERSEDED - This dataset has been replaced by the one which can be found at: https://doi.org/10.7488/ds/3106 ## This dataset comprises results contained in a manuscript entitled "Ultraviolet photochemical production of climate-relevant gases from marine phytoplankton" that describes an investigation of the production of carbon monoxide, carbon dioxide, methane, ethene, ethane, and nitrous oxide from cell suspensions of 16 marine phytoplankton species and their exudates when exposed to ultraviolet radiation under controlled experimental conditions.
description: This dataset contains one Excel file "Phytoplankton-UV.xlsx" structured with individual sheets corresponding to the Figures and Tables within the manuscript.
DOI: 10.7488/ds/3399
title: RESTART Extended Follow Up Dataset

description: Analysis dataset used for the RESTART extended follow up results paper in 2021 (doi:10.1001/jamaneurol.2021.2956). This dataset contains the data dictionary and statistical analysis plan form the RESTART extended follow up. It also contains the Data sharing description and Request form that should be used to obtain a copy of the data. Additional information about the data (trial protocol, annotated CRFs) can be found with the RESTART main results dataset ( https://doi.org/10.1016/S0140-6736(19)30840-2 ).
description: SOP, Data dictionary, request form, data sharing process. Annotated CRFs are available via RESTART trail main results dataset.
DOI: 10.7488/ds/3401
title: Diagnostic availability survey, Sierra Leone, 2019

description: Between February 2019 and September 2019, a cross-sectional mixed-methods survey was conducted in all 40 Community Health Centres (CHCs) in Western Area, one of five principal divisions in Sierra Leone. All CHCs in Western Area Rural District (n = 15) and Urban District (n = 25) were included in the survey, totalling 40 CHCs. The survey was based on the Basic Package of Essential Health Services as the national benchmark for essential tests that match the disease profile and meet the needs and priorities of the country. The Basic Package included 27 tests for the CHC level, 17 of which were RDTs in the form of lateral flow dipsticks, cassettes or handheld devices. In addition to the tests listed in the Basic Package, the survey included two tests (the manual Widal test and the Cholera RDT), which were of interest to the MOHS because of their perceived high popularity and availability in Sierra Leone, despite having limited sensitivity. We did observational checks of the equipment, consumables and reagents needed to carry out the five manual assays with the highest reported availability. In addition, the survey included questions about supply sources for tests and reagents, staffing, and availability of essential infrastructure and systems (electrification, water supply, maintenance, biosafety, and waste management).
description: Diagnostic availability survey Sierra Leone 2019 (anonymised).xlsx
DOI: 10.7488/ds/3400
title: SoSTART trial main results dataset: documentation and request form

description: Analysis dataset for the SoSTART trial main results (https://doi.org/10.1016/S1474-4422(21)00264-7). This dataset contains all the descriptive information about the data. Including protocol, statistical analysis plan, data dictionary, annotated case reporting forms, data sharing description and data request form. The data have been archived in the DataVault under the deposit title "SoSTART Annonymised Analysis dataset" within the vault "Start or STop Anticoagulants Randomised Trial (SoSTART) archive" https://doi.org/10.7488/c5e0a535-76a8-4c23-b455-108eb7c4d918. Please review the descriptive documents, complete and submit a data request form in order to obtain a copy of the data.
DOI: 10.7488/ds/3398
title: Participation, performance, and outcomes in an undergraduate physics degree: Perspectives on gender and socioeconomic factors

description: Data for Figures 1-8 in the paper "Participation, performance, and outcomes in an undergraduate physics degree: Perspectives on gender and socioeconomic factors" by Rachel E Harrington, Job HJ Thijssen and Judy Hardy, to appear in Physical Review Physics Education Research.
DOI: 10.7488/ds/3409
title: SUPERSEDED - Breakup of a laminar liquid jet by coaxial non-swirling and swirling air streams

description: '## This item has been replaced by the one which can be found at https://datashare.ed.ac.uk/handle/10283/4435 ## The dataset includes the drawings of the air swirlers, non-dimensional breakup lengths, first droplet locations, the vector fields of the annular air flows, vorticity maps, POD modes, the frequencies of the flapping instabilities, and 2D spectra.
description: The file descriptions are included in Readme.txt.