cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/1451
title: Small interfering RNAs (siRNA) genome-scale screen data for investigating host factors (HFs) involved in Herpes Simplex Virus Type 1 Replication

description: Small interfering RNA (siRNA) data associated with the following manuscript by Griffiths et al.(2013): A Systematic Analysis of Host Factors Reveals a Med23-Interferon-l Regulatory Axis against Herpes Simplex Virus Type 1 Replication. Herpes simplex virus type 1 (HSV-1) is a neurotropic virus causing vesicular oral or genital skin lesions, meningitis and other diseases particularly harmful in immunocompromised individuals. To comprehensively investigate the complex interaction between HSV-1 and its host we combined two genome-scale screens for host factors (HFs) involved in virus replication. A yeast two-hybrid screen for protein interactions and a RNA interference (RNAi) screen with a druggable genome small interfering RNA (siRNA) library confirmed existing and identified novel HFs which functionally influence HSV-1 infection. Hela cells were reverse-transfected with siRNA SMARTpools (4 siRNAs per gene). After 48 h the siRNAs were tested for cytotoxicity (3 replicates) or the capacity to influence replication of the HSV-1 GFP reporter virus C12 (6 replicates) from 24 to 80 h post-infection. Virus replication slopes during the linear phase were calculated and normalized to mock-transfected cells. Replication slopes were then compared to replication upon knockdown of essential (ICP4, VP16) or non-essential (VP11/12) viral genes, a cellular receptor for HSV-1 (HVEM) or control RISC-free siRNA (RSCF).
DOI: 10.7488/ds/1487
title: Specific heat and SQUID data for the compounds in the paper "The structurally flexible and solution stable [Ln4TM8(OH)8(L)8(O2CR)8(MeOH)y](ClO4)4: a playground for magnetic refrigeration" By Euan Brechin and co-workers, accepted for publication in the journal Inorganic Chemistry.
DOI: 10.7488/ds/1995
title: Ancillary data used for global GPP simulations by the JULES land surface model for 2001-2010

description: This dataset contains the ancillary data (soil, vegetation, etc) used for simulations of Gross Primary Productivity (GPP) by the Joint UK Land Environment Simulator (JULES) Land Surface Model (LSM) at global scales for 2001--2010 (https://doi.org/10.7488/ds/1461). Data is available at 3 different horizontal spatial resolutions (0.5x0.5, 1x1 and 2x2 degrees). The data is organised on a 2D grid. All files are in netCDF format. To briefly view information regarding the files, there is software on Linux called ncdump (to read the data and metadata) and ncview (to plot the data without writing computer code).
description: The dataset contains ancillary data (soil, vegetation, etc) at 3 different horizontal spatial resolutions (0.5x0.5, 1x1 and 2x2 degrees). For each spatial resolution, there are 6 files, which are described as follows: 1. EI-Halfdeg-land-elevation2d Contains the latitudes and longitudes of the points at which JULES is run globally. 2. hydro1k_topo_watch_0p5deg2d Contains the spatially varying parameter values for the TOPMODEL-type parameterisation of runoff. 3. qrparm.soil_HWSD_class3_van_genuchten2d Contains the spatially varying soil property values. 4. qrparm.veg.frac2d Contains the fraction of the land area in each gridbox that is covered by each of the surface types. 5. WATCHEI_initial_conditions2d Contains the initial state of prognostic variables which must be set at the start of a run. 6. WFD-EI-LandFraction2d Contains the landmask of the points at which JULES is run globally. Also included in the dataset is the annual CO2 concentrations (parts per million by volume) required by JULES. The data covers the time period from 1765-2013. More detailed information on the ancilary data required by JULES can be found in the documentation (http://jules-lsm.github.io/).
DOI: 10.7488/ds/1460
title: Eye-movement data for visually guided and memory-guided saccades

description: Please see ReadMe.txt.
description: A description of the dataset and files are provided in the file ReadMe.txt.
DOI: 10.7488/ds/1403
title: FitQuest Qualitative DataSet

description: This dataset contains qualitative interview and observation notes from the pilot FitQuest randomised controlled trial. The overall aim of the trial was to evaluate whether a theory based location-based exergame (FitQuest) could increase exercise self-efficacy and physical activity (PA) at school compared to standard provision in physical education (PE) classes. The cluster randomised controlled trial (RCT) was conducted among children aged 10-11 years attending 10 state-funded primary schools in Scotland. One class in each school was randomly allocated to intervention (n=5, 111 children) or control (n=5, 104 children). The qualitative dataset archived here was also gathered during the pilot RCT in order to explore whether the programme theory for FitQuest was correct with respect to how and why it would change children’s perceptions of physical activity (PA) and exercise self-efficacy in the school setting. A further aim was to investigate the features of the school setting (context) that may impact on FitQuest’s implementation and effectiveness. The dataset has transcripts of 6 paired interviews with children and three interviews with teachers. It also has researchers' notes from 19 observation sessions. The trial was registered as ISRCTN11693550.
description: See readme.txt
DOI: 10.7488/ds/2481
title: GWAS summary statistics for UPLC IgG N-glycosylation traits
title: Glycosylation of immunoglobulin G is a complex trait regulated by a large network of genes

description: The majority of proteins undergo post-translational glycosylation, in which complex carbohydrates are attached to the surface of proteins. However, when studying glycoproteins, the glycan component is often neglected. Glycosylation can affect protein structure and function, as is the case with Immunoglobulin G, the most abundant antibody in human blood and an important component of the immune system. Effector functions of IgG require the addition of a glycan moiety and are regulated by the composition of the carbohydrate, thus affecting activity of the immune system. Aberrant glycosylation of IgG has been observed in many diseases, but little is understood about the mechanisms behind these changes. Here we show that the synthesis of the glycan fraction is under control of an interconnected set of genes. We performed the largest genome-wide association study of IgG N-glycosylation to date (N=8,090) and found 27 associated loci (15 novel) that explain up to 22% of variance in glycosylation level. We developed a data-driven network approach to propose how these genes form a functional network regulating glycosylation of IgG. From this network we confirmed in-vitro that the transcription factor IKZF1 regulates the expression of glycosyltransferase FUT8, resulting in increased levels of fucosylated glycans. We also found strong in-silico evidence that RUNX1 and RUNX3 transcription factors, together with SMARCB1 chromatin remodelling protein, regulate expression of glycosyltransferase MGAT3. We showed that glycosylation variants supporting this network are pleiotropic with inflammatory and autoimmune diseases, suggesting how variants with an effect on both IgG glycosylation levels and disease risk could influence glycosyltransferases and result in aberrant IgG glycosylation profiles observed in these diseases.
DOI: 10.7488/ds/1445
title: Tunable Shear Thickening in Suspensions

description: Shear thickening, an increase of viscosity with shear rate, is a ubiquitous phenomena in suspended materials that has implications for broad technological applications. Controlling this thickening behavior remains a major challenge and has led to empirical strategies ranging from altering the particle surfaces and shape to modifying the solvent properties. However, none of these methods allow for active control of flow properties during shear itself. Here, we demonstrate that by strategic imposition of a high-frequency and low-amplitude shear perturbation orthogonal to the primary shearing flow, we can largely eradicate shear thickening. The orthogonal shear effectively becomes a regulator for controlling thickening in the suspension, allowing the viscosity to be reduced by up to two decades on demand. In a separate setup, we show that such effects can be induced by simply agitating the sample transversely to the primary shear direction. Overall, the ability of in situ manipulation of shear thickening paves a route towards creating materials whose mechanical properties can be actively controlled.
DOI: 10.7488/ds/1393
title: DATA: Unsteady flow and particle migration in dense, non-Brownian suspensions

description: We present experimental results on dense corn-starch suspensions as examples of non-Brownian, nearly-hard particles that undergo continuous and discontinuous shear thickening (CST and DST) at intermediate and high densities respectively. Our results offer strong support for recent theories involving a stress-dependent effective contact friction among particles. We show however that in the DST regime, where theory might lead one to expect steady-state shear bands oriented layerwise along the vorticity axis, the real flow is unsteady. To explain this, we argue that steady-state banding is generically ruled out by the requirement that, for hard non-Brownian particles, the solvent pressure and the normal-normal component of the particle stress must balance separately across the interface between bands. (Otherwise there is an unbalanced migration flux.) However, long-lived transient shear bands remain possible. For further information, see the related pre-print: Hermes et al (2015) "Unsteady flow and particle migration in dense, non-Brownian suspensions" at http://arxiv.org/pdf/1511.08011v1.pdf (N.B. figure numbers in the pre-print are not necessarily the same as those on the filenames in this dataset).
DOI: 10.7488/ds/2060
title: Data supporting Cachat et al. (2017): "Synthetic self-patterning and morphogenesis in mammalian cells: a proof-of-concept step towards synthetic tissue development"

description: These are raw image datasets used in a manuscript (Cachat et al., 2017: Synthetic self-patterning and morphogenesis in mammalian cells: a proof-of-concept step towards synthetic tissue development) with the following abstract: This paper reports a proof-of-concept study as a step toward synthetic-biological morphogenesis of tissues. Events in normal animal development usually follow the sequence: patterning → differential gene expression → morphogenesis. A synthetic biological approach to development might follow a similar sequence, with each stage under the control of synthetic biological modules. We have constructed and published a synthetic module that drives self-organised patterning of mammalian cell populations into patches of different cell types. Here, as a proof of concept, we extend the self-patterning module with a morphogenetic effector that drives elective cell death in just one cell type. The result is a self-constructing pattern of two cell types, one of which can be selectively eliminated to leave remaining cells as a monolayer with a net-like structure. This simple device demonstrates and validates the idea of coupling synthetic biological morphogenetic effectors to synthetic biological patterning devices. It opens the path to engineering more sophisticated structures and, perhaps eventually, tissues
description: There is one zipped file containing original images included in Cachat et al. (2017) Synthetic self-patterning and morphogenesis in mammalian cells: a proof-of-concept step towards synthetic tissue development (submitted).
DOI: 10.7488/ds/1371
title: Property trends in simple metals: An empirical potential approach
DOI: 10.7488/ds/1929
title: Scotland Land-Form PANORAMA® DTM

description: Land-Form PANORAMA® DTM from Ordnance Survey Open Data, mosaiced and clipped to a country boundary (derived from OS Open Boundary data) using ArcGIS. 1:50,000 scale DTM. Digital Terrain Model. This dataset was first accessioned in the EDINA ShareGeo Open repository on 2010-07-14 and migrated to Edinburgh DataShare on 2017-02-22.
description: ArcInfo GRID
DOI: 10.7488/ds/1928
title: GB SRTM Digital Elevation Model (DEM) 90m

description: This Shuttle Radar Topography Mission (SRTM) DEM was created from level 1 data which was cleaned and had holes patched. The data does not incluse the Shetland Islands as SRTM data becomes unreliable at 60N. The cell size is close to 90m. It covers the whole of the UK. The data is presented in OSGB coords and is free to use and distribute. Acknowdgement of NASA/NGA/DLR/ASI as originating agencies for the data is appreciated. Please acknowledge ShareGeo as the source of this derived dataset. See NASA JPL website for more information: http://www2.jpl.nasa.gov/srtm/index.html. Digital Terrain Model. This dataset was first accessioned in the EDINA ShareGeo Open repository on 2010-06-09 and migrated to Edinburgh DataShare on 2017-02-22.
description: ArcInfo GRID
DOI: 10.7488/ds/1970
title: Wikimedia Europe History Map

description: Various Atlas illustration from 264BC - present | Mostly WR Shepherd upload by Roke | From Wikimedia Commons (c) expired. http://commons.m.wikimedia.org/wiki/Atlas_of_European_history. Scanned map. This dataset was first accessioned in the EDINA ShareGeo Open repository on 2015-05-10 and migrated to Edinburgh DataShare on 2017-02-22.
description: ESRI Shapefile
DOI: 10.7488/ds/1765
title: Gower Peninsula Footpaths

description: A Kingston University first year undergraduate fieldtrip to the Welsh Gower Peninsula involving a Global Positioning System (GPS) survey of footpaths. This file was orignally a raw (unedited) tracklog from the Garmin Gecko GPS receivers, which was provided in a GPX (GPS exchange file) format and converted to an ESRI point shapefile using the Minnesota Department of Resouce's (MN DNR) Garmin conversion software. GIS vector data. This dataset was first accessioned in the EDINA ShareGeo Open repository on 2010-09-14 and migrated to Edinburgh DataShare on 2017-02-21.
description: ESRI Shapefile
DOI: 10.7488/ds/1971
title: Glasgow Campus Map Exercise

description: An exercise to create a campus web map using OpenStream, QGIS and OpenLayers. GIS vector data. This dataset was first accessioned in the EDINA ShareGeo Open repository on 2016-02-16 and migrated to Edinburgh DataShare on 2017-02-22.
description: ESRI Shapefile
DOI: 10.7488/ds/1349
title: RCrO3-xNx ChemComm 2016

description: Low temperature powder neutron diffraction data files and cif files used for crystal and magnetic structure refinements for RCrO3-xNx materials where R = La, Pr, Nd.
DOI: 10.7488/ds/1730
title: Victims of Sheffield Flood 1864

description: This dataset shows the locations where victims were found after the Sheffield Flood of 1864. Information adapted from: Machan, Peter. 'The Dramatic Story of The Sheffield Flood?' 1999 ISBN 1-901587-05-3. GIS vector data. This dataset was first accessioned in the EDINA ShareGeo Open repository on 2010-06-30 and migrated to Edinburgh DataShare on 2017-02-21.
description: ESRI Shapefile
DOI: 10.7488/ds/2559
title: 'DAVIES_NC_2018' - Data supporting paper Davies et al. "Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function."

description: Data supporting paper Davies et al. "Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function." Nature Communications DOI: 10.1038/s41467-018-04362-x . UK Biobank only summary results; Reaction Time N = 330,069; Verbal Numerical Reasoning N = 168,033. ## Note ## The files "Davies2018_UKB_RT_summary_results_29052018.txt" and "Davies2018_UKB_VNR_summary_results_29052018.txt" are identical to the two files of the same names previously available on the website of the Centre for Cognitive Ageing and Cognitive Epidemiology (CCACE) http://www.ccace.ed.ac.uk/node/335 as part of the zip archive "Davies_NC_2018.zip".
description: The files "Davies2018_UKB_RT_summary_results_29052018.txt" and "Davies2018_UKB_VNR_summary_results_29052018.txt" are identical to the two files of the same names previously available on the website of the Centre for Cognitive Ageing and Cognitive Epidemiology (CCACE) http://www.ccace.ed.ac.uk/node/335 as part of the zip archive "Davies_NC_2018.zip".
DOI: 10.7488/ds/1458
title: Stimulation of canine joint cells to model osteoarthritis

description: Canine chondrocytes and osteoblasts were embedded in an agarose matrix and simultaneously stimulated with cytokines whilst being cyclically compressed. Both cell types were compressed for 4 hours at 1 Hz followed by a 24 hour recovery incubation. The chondrocytes were stimulated with 5 ng/mL of IL8 for the duration of compression, but removed for the recovery phase. Osteoblasts were stimulated with 0.5 ng/mL IL8 and 0.5 ng/mL IL1b for the duration of the compression and for the entirety of the 24 hour incubation step.
DOI: 10.7488/ds/1453
title: How does grid-resolution modulate geomorphic processes: data

description: In many locations, our ability to study the processes which shape the Earth are greatly enhanced through the use of high resolution digital topographic data. However, although the availability of such datasets has markedly increased in recent years, many locations of significant geomorphic interest still do not have high resolution topographic data available. Here, we aim to constrain how well we can understand surface processes through topographic analysis performed on lower resolution data. We generate digital elevation models from point clouds at a range of grid resolutions from 1 to 30 meters, which covers the range of widely used data resolutions available globally, at three locations in the United States. Using these data, the relationship between curvature and grid resolution is explored, alongside the estimation of the hillslope sediment transport coefficient ($D$, in m$^2$ yr$^{-1}$) for each landscape. Curvature, and consequently $D$, values are shown to be generally insensitive to grid resolution, particularly in landscapes with broad hilltops and valleys. Curvature distributions, however, become increasingly condensed around the mean, and theoretical considerations suggest caution should be used when extracting curvature from landscapes with sharp ridges. The sensitivity of curvature and topographic gradient to grid resolution are also explored through analysis of one dimensional approximations of curvature and gradient, providing a theoretical basis for the results generated using two dimensional topographic data. Two methods of extracting channels from topographic data are tested. A geometric method of channel extraction that finds channels by detecting threshold values of planform curvature is shown to perform well at resolutions up to 30 meters in all three landscapes. The landscape parameters of hillslope length and relief are both successfully extracted at the same range of resolutions. These parameters can be used to detect landscape transience and our results suggest that such work need not be confined to high resolution topographic data. A synthesis of the results presented in this work indicate that although high resolution (e.g., 1 m) topographic data does yield exciting possibilities for geomorphic research, many key parameters can be understood in lower resolution data, given careful consideration of how analyses are performed. Data sourced from OpenTopography.org.
description: See README.txt
DOI: 10.7488/ds/1461
title: Global GPP simulated by the JULES land surface model for 2001-2010

description: This study evaluates the ability of the Joint UK Land Environment Simulator (JULES) Land Surface Model (LSM), the land surface scheme of the UK Met Office Unified Model (MetUM), to simulate Gross Primary Productivity (GPP) at regional and global scales for 2001--2010. Model simulations were driven with a variety of meteorological datasets and at various spatial resolutions (0.5x0.5, 1x1, 2x2 degree resolution). The meteorological datasets include: 1. WFDEI-GPCC The WATCH Forcing Data methodology was applied to the ERA-Interim reanalysis data (WFDEI) for the 1979--2012 period (Weedon et al., 2014. https://doi.org/10.1002/2014WR015638 ). WFDEI has two precipitation products, corrected using either CRU (Climate Research Unit at the University of East Anglia) or GPCC (Global Precipitation Climatology Centre) precipitation totals and are referred to as WFDEI-CRU and WFDEI-GPCC, respectively. 2. WFDEI-CRU See above. 3. PRINCETON The PRINCETON dataset is a global 62 year near-surface meteorological dataset used for driving land surface models and was created by Princeton University's Terrestrial Hydrology Group ( http://hydrology.princeton.edu/home.php ) (Sheffield et al., 2006. https://doi.org/10.1175/JCLI3790.1 ). JULES GPP was then compared to spatially gridded estimates of GPP from the upscaling of GPP from the FLUXNET network (FLUXNET-MTE), the MODIS sensor and the CARDAMOM framework. GPP, Gross Primary Productivity, is the total amount of carbon uptake by plants (per unit area in unit time) and used in photosynthesis. All files are in netCDF format. There is metadata in the files. To briefly view information regarding the files, there is software on Linux called ncdump (to read the data and metadata) and ncview (to plot the data without writing computer code).
DOI: 10.7488/ds/1428
title: Temporal analysis of RNA turnover in Interferon Gamma treated bone marrow-derived macrophages

description: Two data sets with transcript ratios associated with the manuscript:An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway. The full data set is on NCBI, gene expression omnibus (GEO) accession number GSE63290.
DOI: 10.7488/ds/2062
title: DFE-alpha data tables

description: Tables in binary format used by the software DFE-alpha. Reference: Keightley, P. D. and Eyre-Walker, A. (2007). Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177: 2251-2261.
DOI: 10.7488/ds/1580
title: Regional brain atlas for assessment of white matter hyperintensities
title: Regional brain atlas for assessment of white matter hyperintensities

description: This dataset contains a reference brain-extracted T1-weighted structural magnetic resonance image, representative of a normal brain from an individual in the first half of the 80th decade of life (70 to 75 years old), and the correspondent binary masks of the regions identified as relevant for studying white matter hyperintensities.
description: Please see "Regional_brain_atlas_for_assessing_WMH.pdf".