cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2458
title: Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions

description: Major depression is a debilitating psychiatric illness that is typically associated with low mood, anhedonia and a range of comorbidities. Depression has a heritable component that has remained difficult to elucidate with current sample sizes due to the polygenic nature of the disorder. To maximise sample size, we meta-analysed data on 807,553 individuals (246,363 cases and 561,190 controls) from the three largest genome-wide association studies of depression. We identified 102 independent variants, 269 genes, and 15 gene-sets associated with depression, including both genes and gene-pathways associated with synaptic structure and neurotransmission. Further evidence of the importance of prefrontal brain regions in depression was provided by an enrichment analysis. In an independent replication sample of 1,306,354 individuals (414,055 cases and 892,299 controls), 87 of the 102 associated variants were significant following multiple testing correction. Based on the putative genes associated with depression this work also highlights several potential drug repositioning opportunities. These findings advance our understanding of the complex genetic architecture of depression and provide several future avenues for understanding aetiology and developing new treatment approaches. The data contained in this item is described in a published manuscript located at https://doi.org/10.1038/s41593-018-0326-7.
description: See ReadMe.txt
DOI: 10.7488/ds/2884
title: Fire experiment of informal settlement dwelling without window (Test 1)

description: This link presents Test 1 of Phase 1. The fuel condition is different from that in Phase 2.
DOI: 10.7488/ds/2758
title: Dwelling outline - Informal Settlements of Cape Town

description: This data was generated under agreement by Centre for Geographical Analysis, Stellenbosch University. The geographic dataset in shapefile format consists of polygons of informal settlement dwelling in the City of Cape Town. The dwelling polygons were digitised from City of Cape Town aerial photography (available at http://web1.capetown.gov.za/web1/opendataportal/DatasetDetail?DatasetName=Aerial%20photography) at a scale of 1:200 using map projection WGS84 TM19. The aerial photography was captured in February 2018 and thus the shapefile of informal dwellings captured conditions on the ground for February 2018. This work is supported by IRIS-Fire project of UK (Engineering and Physical Sciences Research Council Grant no.: EP/P029582/1).
DOI: 10.7488/ds/1410
title: High Absorption Coefficient Cyclopentadithiophene Donor-free Dyes For Liquid and Solid-state dye-sensitized Solar Cells

description: We report a series of ‘donor-free’ dyes, featuring moieties of oligo(4,4-dihexyl-4H-cyclopenta[1,2-b:5,4-b’]dithiophene) (CPDT) functionalized with cyanoacrylic end groups for mesoscopic titania solar cells based on I-/I3- or Co(II)/Co(III) redox couple and spiro-OMeTAD hole transporter. These were compared with similar cells using an oligo(3-hexylthiophene) dye (5T) which we have reported before. Extending the CPDT moiety of the dye molecules from one to three (denoted as CPDT-1, CPDT-2 and CPDT-3) widens the photoresponse overlap with the solar spectrum, increases the molar absorption coefficient up to 75000 M-1cm-1 and improves the short-circuit current (JSC), open-circuit voltage (VOC) and power conversion efficiency (PCE) for all types of DSSCs. Among these sensitisers, CPDT-3 shows the highest PCE of 6.7%, 7.3% and 3.9% with I-/I3-, Co(II)/Co(III) redox couple and spiro-OMeTAD hole transporter, respectively, compared with 7.6%, 9.0% and 4.0% for 5T. Benefiting from the high absorption of CPDT-3, we demonstrate 900 nm-thick mesoporous TiO2 film with remarkable JSC of 10.9 mA cm-2 in solid-state DSCs.
DOI: 10.7488/ds/2769
title: Single-cell transcriptomics uncovers zonation of function in the mesenchyme during liver fibrosis - Seurat objects

description: We profile the transcriptomes of ~30,000 mouse single cells to deconvolve the hepatic mesenchyme in healthy and fibrotic liver at high resolution. We reveal spatial zonation of hepatic stellate cells across the liver lobule, designated portal vein-associated HSC and central vein-associated HSC, and uncover an equivalent functional zonation in a mouse model of centrilobular fibrosis. Our work illustrates the power of single-cell transcriptomics to resolve key collagen-producing cells driving liver fibrosis with high precision. We provide the contents of these data as Seurat R objects.
description: uninjured.rds: Seurat object in RDS format containing the raw, normalised, and scaled expression values for 12533 mouse single cell transcriptomes from healthy liver, corresponding to Figure 1. injured.rds: Seurat object in RDS format containing the raw, normalised, and scaled expression values for 23291 mouse single cell transcriptomes from healthy liver, corresponding to Figure 3. acute.rds: Seurat object in RDS format containing the raw, normalised, and scaled expression values for 7260 mouse single cell transcriptomes from healthy liver, corresponding to Figure 5. ss2.rds: Seurat object in RDS format containing the raw, normalised, and scaled expression values for 905 mouse single cell transcriptomes from healthy liver, corresponding to Figure S3. The Seurat objects contain metadata fields as follows: - various quality control metrics such as nGene, nUMI, percent.mito - enrichment: isolation protocol used, either PF (digestion protocol 1) or HSC (digestion protocol 2) - dataset: dataset of origin, i.e. HSC_Uninjured, PF_CCl4_Peak - condition: condition of liver of origin, i.e. Uninjured, Peak CCl4 - lineage: annotated mesenchymal lineage, either FB, HSC, or VSMC - hsc_zonation: annotated HSC zonation, either Portal or Central - pseudotime_central and pseudotime_portal (acute only): annotated pseudotemporal values
DOI: 10.7488/ds/2893
title: Synthetic building

description: Artificially generated point cloud (cloud_coloured.e57) of a one-storey facility with three spaces including openings in the walls. The IFC model (model.ifc) obtained from the cloud has been enriched with 2nd level space boundary (2LSB) information.
DOI: 10.7488/ds/2637
title: Resolving the fibrotic niche of human liver cirrhosis at single-cell level - Seurat RData object

description: We profile the transcriptomes of non-parenchymal cell types present in healthy and cirrhotic human liver. In particular, we uncover a novel scar-associated TREM2+CD9+ macrophage subpopulation, which expands in liver fibrosis, differentiates from circulating monocytes, has a corollary population in mouse liver fibrosis and is pro-fibrogenic. We also define novel ACKR1+ and PLVAP+ endothelial cells which expand in cirrhosis, are topographically scar-restricted and enhance leucocyte transmigration.
description: tissue.rdata: RData file containing a Seurat object "tissue", which in turn contains the raw and normalised expression values for 58,358 human single cell transcriptomes from healthy and cirrhotic liver. This represents the data after application of all relevant, stringent quality control and doublet removal steps, and thus while it does not wholly correlate to any figure shown in the related publication, may be thought of as the 'final' processed and annotated version of Figure 1. The Seurat object "tissue" also contains metadata fields as follows: - nGene, nUMI, percent.mito: quality control metrics - liver: liver of origin, i.e. Healthy1, Cirrhotic4 (see Extended Data Figure 2f) - dataset: dataset of origin, i.e. Healthy1_Cd45+, Cirrhotic4_Cd45+ - condition: condition of liver of origin, i.e. Uninjured, Cirrhotic - aetiology: aetiology of liver of origin, i.e. NAFLD, PBC - annotation_original: results of initial high-level clustering, i.e. 1-21 - annotation_lineage: results of lineage annotation, i.e. Endothelia, MPs - annotation_indepth: results of detailed low-level clustering, i.e. MPs (1), Endothelia (4)
DOI: 10.7488/ds/2338
title: SUPERSEDED - Load measurements on a 1.2m diameter three bladed horizontal axis tidal turbine tested in a recirculating flume

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2423 . ## Laboratory testing of tidal turbine models is an essential tool to investigate hydrodynamic interactions between turbines and the flow. This dataset provides load measurements time series for a three bladed horizontal axis tidal turbine model. The rotor is 1.2m in diameter and the measurements include rotor torque, thrust, absolute angular position, streamwise root bending moments of the blades and streamwise and transverse fundation loads. The turbine was developed and tested as part of the X-MED project funded by the EPSRC (EP/ J010235/1). The dataset is associated with the article XXXX details to come XXXX and the details of the turbine model can be found in 'Design and manufacture of a bed supported tidal turbine model for blade and shaft load measurement in turbulent flow and waves' by Payne, Stallard and Martinez published in 2017 in Renewable Energy (doi: https://doi.org/10.1016/j.renene.2017.01.068).
DOI: 10.7488/ds/2891
title: Quantitative magnetic resonance imaging predicts individual future liver performance after liver resection for cancer

description: The risk of poor post-operative outcome and the benefits of surgical resection as a curative therapy require careful assessment by the clinical care team for patients with primary and secondary liver cancer. Advances in surgical techniques have improved patient outcomes but identifying which individual patients are at greatest risk of poor post-operative liver performance remains a challenge. Here we report results from a multicentre observational clinical trial (ClinicalTrials.gov NCT03213314) which aimed to inform personalised pre-operative risk assessment in liver cancer surgery by evaluating liver health using quantitative multiparametric magnetic resonance imaging (MRI). We combined estimation of future liver remnant (FLR) volume with corrected T1 (cT1) of the liver parenchyma as a representation of liver health in 143 patients prior to treatment.
DOI: 10.7488/ds/2216
title: TeraWatt North Atlantic spectral wave model input files (for MIKE 21)

description: NORTH ATLANTIC MIKE 21 MODEL INPUT FILES This submission includes the input files for the North Atlantic spectral wave model that is described in [1,2]. It formed part of the TeraWatt and EcoWatt2050 EPSRC projects (grant numbers EP/J010170/1 & EP/K012851/1 respectively). The input files require the MIKE 21 modelling suite to run, available commercially from https://www.mikepoweredbydhi.com/; they were created and validated using the 2014 edition. Input files are being stored instead of outputs as per RCUK guidelines due to the size of the output files. For further information please contact Dr. Vengatesan Venugopal, School of Engineering, University of Edinburgh (v.venugopal@ed.ac.uk). [1] V. Venugopal and R. Nemalidinne, ‘Wave resource assessment for Scottish waters using a large scale North Atlantic spectral wave model’, Renewable Energy, vol. 76, no. Supplement C, pp. 503–525, Apr. 2015. [2] V. Venugopal, R. Nemalidinne, and A. Vögler, ‘Numerical modelling of wave energy resources and assessment of wave energy extraction by large scale wave farms’, Ocean & Coastal Management, Mar. 2017.
description: See readme.txt.
DOI: 10.7488/ds/2837
title: Additional Experimental Data of a Floating Cylinder in a Wave Tank - Verification Experiments

description: The presented experimental results provide additional data to a previously published investigation of a floating cylinder under regular wave conditions (https://doi.org/10.7488/ds/2627). Three test series are added to investigate the roll response of the water filled structure. This includes a change of the initial position of the cylinder in the wave tank as well as a rotation of the wave direction. The latter was also conducted for the solid ballast option to provide a direct comparison with the water filled cylinder. This research was carried out at the FloWave Ocean Energy Research Facility of the Institute for Energy Systems, University of Edinburgh.
DOI: 10.7488/ds/2643
title: Genome-wide analysis identifies molecular systems and 149 genetic loci associated with income

description: Data in support of manuscript : Hill, W.D. et al. (2019). Genome-wide analysis identifies molecular systems and 149 genetic loci associated with income. Nature Communications.
DOI: 10.7488/ds/2317
title: CARDAMOM pantropical retrievals 2000-2015

description: This dataset includes netCDF files reporting pantropical retrievals of the terrestrial carbon cycle using the CARDAMOM model-data fusion framework. Two experiments are included that alternatively include or omit fire disturbances. For each experiment, 4 files are included that report mean annual land-atmosphere carbon fluxes, carbon allocation to plant parts, vegetation and dead organic matter carbon pool sizes and transit times. Files include the pixel-wise uncertainty by reporting the median value as well as bounds of the 95%, 90% and 50% confidence intervals.
description: The dataset contains the following files corresponding to two model-data fusion experiment with CARDAMOM: - CARDAMOM_PanTropical_FIRE_allocation.nc: pantropical retrievals of carbon allocation in the FIRE experiment - CARDAMOM_PanTropical_FIRE_fluxes.nc: pantropical retrievals of land-atmosphere carbon fluxes in the FIRE experiment - CARDAMOM_PanTropical_FIRE_pools.nc: pantropical retrievals of carbon pools in the FIRE experiment - CARDAMOM_PanTropical_FIRE_transit_times.nc: pantropical retrievals of carbon transit times in the FIRE experiment - CARDAMOM_PanTropical_NOFIRE_allocation.nc: pantropical retrievals of carbon allocation in the NOFIRE experiment - CARDAMOM_PanTropical_NOFIRE_fluxes.nc: pantropical retrievals of land-atmosphere carbon fluxes in the NOFIRE experiment - CARDAMOM_PanTropical_NOFIRE_pools.nc: pantropical retrievals of carbon pools in the NOFIRE experiment - CARDAMOM_PanTropical_NOFIRE_transit_times.nc: pantropical retrievals of carbon transit times in the NOFIRE experiment
DOI: 10.7488/ds/2459
title: Characterisation of enzymatic processing of commercial (Kraft) lignin by high resolution FT-ICR mass spectrometry – Dataset.

description: High Resolution FT-ICR mass spectrometry datasets analysing the enzymatic processing of Kraft lignin.
DOI: 10.7488/ds/2567
title: Single-cell bacterial electrophysiology reveals mechanisms of stress induced damage - additional data (Figures 2D, 3D, 4D)

description: Dataset supporting figures 2D, 3D and 4D of the paper "Single-cell bacterial electrophysiology reveals mechanisms of stress induced damage" (Krasnopeeva et al, 2018). The archive contains excel spreadsheets with the data points plotted in figures 2D, 3D, 4D. For each point the mean and the standard error of the mean are given. The values are calculated as described in Krasnopeeva et al, 2018. Additional DataShare items related to this paper can be accessed: https://doi.org/10.7488/ds/2381, https://doi.org/10.7488/ds/2382, https://doi.org/10.7488/ds/2383.
DOI: 10.7488/ds/2250
title: Dirac cones in two-dimensional borane

description: We introduce two-dimensional borane, a single-layered material of BH stoichiometry, with promising electronic properties. We show that, according to Density Functional Theory calculations, two-dimensional borane is semimetallic, with two symmetry-related Dirac cones meeting right at the Fermi energy E_f. The curvature of the cones is lower than in graphene, thus closer to the ideal linear dispersion. Its structure, formed by a puckered trigonal boron network with hydrogen atoms connected to each boron atom, can be understood as distorted, hydrogenated borophene (Science {350}, 1513 (2015)). Chemical bonding analysis reveals the boron layer in the network being bound by delocalized four-center two-electron {\sigma} bonds. Finally, we suggest high-pressure could be a feasible route to synthesise two-dimensional borane.
DOI: 10.7488/ds/2355
title: Datasets for Low-Cost High Sensitivity Pulsed Endomicroscopy to Visualize Tri-Color Optical Signatures

description: A highly sensitive, modular three-color fluorescence endomicroscopy imaging platform spanning the visible to near-infrared (NIR) range is demonstrated. Light-emitting diodes (LEDs) were sequentially pulsed along with the camera acquisition to provide up to 20 frames per second (fps) three-color imaging performance or 60 fps single color imaging. The system was characterized for bacterial and cellular molecular imaging in ex vivo human lung tissue and for bacterial and indocyanine green imaging in ex vivo perfused sheep lungs. A practical method to reduce background tissue autofluorescence is also proposed. The platform was clinically translated into six patients with pulmonary disease to delineate healthy, cancerous, and fibrotic tissue autofluorescent structures. The instrument is the most broadband clinical endomicroscopy system developed to date (covering visible to the NIR, 500 to 900 nm) and demonstrates significant potential for future clinical utility due to its low cost and modular capability to suit a wide variety of molecular imaging applications.
DOI: 10.7488/ds/2557
title: Data from figures in 'Spatiotemporal Electrochemistry on Flexible Microelectrode Arrays: Progress Towards Smart Contact Lens Integration'

description: Data supporting Donora et al. 'Spatiotemporal Electrochemistry on Flexible Microelectrode Arrays: Progress Towards Smart Contact Lens Integration' (Accepted manuscript). Data tables are provided as tab-delimited text files.
DOI: 10.7488/ds/2628
title: ManySStuBs4J Dataset

description: The ManySStuBs4J corpus contains simple statement bugs mined from open-source Java projects hosted in GitHub. There are two variations of the dataset. One mined from the 100 Java Maven Projects and one mined from the top 1000 Java Projects. A project's popularity is determined by computing the sum of z-scores of its forks and watchers. See "README.txt" for further details.
DOI: 10.7488/ds/2723
title: Multi-beam Sonar Image Sequences

description: The dataset supports the following article: Diamantis K., Yaghoobi M., Davies M. and Hopgood J. 2019, 'A multi-frame resolution enhancement framework for multi-beam sonar systems' submitted for review to the IEEE Transactions of Geoscience and Remote Sensing. The article proposes a framework for the improvement of multi-beam echo-sounder image quality with the objective to facilitate real-time high-resolution applications. The framework relies on the fact that a large number of images are commonly acquired from different positions, during underwater scans. The dataset consists of seven different multi-beam sonar image sequences, used in the studies of improving sonar image resolution. The image sequences depict various underwater objects/structures and are converted to video-clips. Each video-clip includes from left to right: the standard sonar images, the images resulting from image registration and averaging, and the reconstructed images using the proposed high-resolution framework. All images have been processed using Matlab (The MathWorks, Inc., Natick, MA, USA) scripts.
DOI: 10.7488/ds/2639
title: Single cell transcriptional profiling of rat embryonic stem cells defined by Rex1-EGFP reporter expression

description: Rat embryonic stem cells exhibit basal levels of spontaneous differentiation in 2i+LIF (2iL) culture. Expression of a stem cell specific Rex1-EGFP knock-in reporter transgene in rat ESCs was used to isolate functionally distinct subsets of cells in rat ESC cultures, and determine their transcriptional profiles by single cell RNA sequencing.
description: Files included in this dataset: (1) Methodology (document including a diagram) (2) A tar file "plates.tar" containing 385 folders containing Single cell RNA sequencing fastq.gz files (to open, untar the .tar file, then gunzip the .gz files).
DOI: 10.7488/ds/2108
title: Code and Data accompanying "Ballistic and snake photon imaging for locating optical endomicroscopy fibres"

description: We demonstrate determination of the location of the distal-end of a fibre-optic device deep in tissue through the imaging of ballistic and snake photons using a time resolved single-photon detector array. The fibre was imaged with centimetre resolution, within clinically relevant settings and models. This technique can overcome the limitations imposed by tissue scattering in optically determining the in vivo location of fibre-optic medical instruments.
DOI: 10.7488/ds/2613
title: Cow genotypes before quality control in PLINK format. Dataset pertains to manuscript "Quantitative trait loci mapping for lameness associated phenotypes in Holstein Friesian dairy cattle"

description: Cow genotypes in PLINK format before quality control used for a GWAS study of lameness associated phenotypes in Holstein Friesian dairy cattle. Genotypes were merged from Affymetrix and Illumina SNP chips.
DOI: 10.7488/ds/2722
title: A putative genomic map for resistance of Bos indicus cattle in Cameroon to bovine tuberculosis

description: Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurisation of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding Bos taurus cattle for increased resistance to bTB is feasible. The utility of such an approach is still unknown for the Bos indicus cattle population. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture in Bos indicus breeds in Cameroon. We conducted a cross-sectional study of slaughter cattle in Cameroon and genotyped a sample of 213 cattle. Their genomic diversity was characterised using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci. Previous studies had found that breed was an important factor in explaining the epidemiology of bTB, with Fulani cattle appearing to be more susceptible than mixed breeds. However, we show that the apparent phenotypic differences in visual appearance between the breeds was not reflected by clear genomic differences. At the genetic level, cattle belonging to different hierarchical genomic clusters differed in their susceptibility to bTB. There was evidence of a genomic association between M. bovis infection status with specific SNPs. We highlight the need to understand the challenges faced by livestock in specific settings both in terms of pathogens and the environment, in addition to their intended purpose and how they fit into a defined management system. It is only at this point livestock keepers can then make informed breeding choices, not only for resistance to disease but also for increasing production.
description: The Illumina BovineHD 777K BeadChip (genome build Bos taurus UMD3.1) in PLINK format (.ped and .map files) is included. A phenotype file (.csv) stating the breed, sex, age and M. bovis status of the cattle samples involved in the study is also included. The files contain data on 228 Fulani and Mixed breed cattle from Cameroon and 216 reference cattle taken from Bovine HapMap Consortium (2009) and Bahbahani et al. (2017).
DOI: 10.7488/ds/2565
title: Data supporting Luciano et al. Association analysis in over 329,000 individuals identifies 116 independent variants influencing neuroticism

description: Data supporting the paper Luciano et al. Association analysis in over 329,000 individuals identifies 116 independent variants influencing neuroticism. Nature Genetics (2017). doi: 10.1038/s41588-017-0013-8