cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2793
title: Multivariate genomic scan implicates novel loci and haem metabolism in human ageing

description: Ageing phenotypes, such as years lived in good health (healthspan), total years lived (lifespan), and survival until an exceptional old age (longevity), are of interest to us all but require exceptionally large sample sizes to study genetically. Here we combine existing genome-wide association summary statistics for healthspan, lifespan, and longevity in a multivariate framework, increasing statistical power, and identified 10 genomic loci which influence all three phenotypes, of which five (near FOXO3, SLC4A7, LINC02513, ZW10, and FGD6) have not been reported previously at genome-wide significance. The majority of these 10 loci are associated with cardiovascular disease and some affect the expression of genes known to change activity with age. In total, we implicate 78 genes, and find these to be enriched for ageing pathways previously highlighted in model organisms, such as the response to DNA damage, apoptosis, and homeostasis. Finally, we identify a pathway worthy of further study: haem metabolism.
description: See README.txt
DOI: 10.7488/ds/2537
title: Hfq CLASH and TEX processed data

description: The data contains bedgraph and GTF annotation files that were used for the Iosub et al paper describing Hfq CLASH data. Included as well are test files that will allow users to learn how to use the Granneman Lab GenomeBrowser classes for reproducing some of the plots provided in the paper or for making their own publication ready figures.
description: * "Bedgraph_and_GTF_files_for_genome_browser.zip" This zip file contains bedgraph and gene transfer format files (GTF) that can be used to visualise the data in a Genome Browser, such as Integrated Genome Browser or used with the Granneman Lab GenomeBrowser Python code. * "Genome_files.zip" Contains the E. coli reference genome and GTF annotation file used for this study. * "Granneman_Lab_GenomeBrowser_test_files.zip" Contains a Jupyter Notebook and test files that will allow people interested in trying our Python GenomeBrowser code to learn how to use it. * "TEX_data_analyses.zip" Contains code and the results of the data analyse performed on the Transcription Start Site mapping data from the Storz lab (Thomason et al Journal of Bacteriology 2015)
DOI: 10.7488/ds/2614
title: Force chains and networks: wet suspensions through dry granular eyes

description: Recent advances in shear-thickening suspension rheology suggest a relation between (wet) suspension flow below jamming and (dry) granular physics. To probe this connection, we simulated the contact force networks in suspensions of non-Brownian spheres using the discrete element method (DEM), varying the particle friction coefficient and volume fraction. We find that force networks in these suspensions show quantitative similarities to those in jammed dry grains. As suspensions approach the jamming point, the extrapolated volume fraction and coordination number at jamming are similar to critical values obtained for isotropically compressed spheres. Similarly, the shape of the distribution of contact forces in flowing suspensions is remarkably similar to that found in granular packings, suggesting potential refinements for analytical mean field models for the rheology of shear thickening suspensions.
description: README.md contains an overall description of the dataset in Markdown format. Descriptions of individual files are also given in the subfolders.
DOI: 10.7488/ds/2721
title: SUPERSEDED - Water buffalo and cattle XPEHH scores across breeds

description: ## SUPERSEDED - This dataset has been replaced by the one which can be found at https://doi.org/10.7488/ds/2849 . ## This dataset consists of XP-EHH scores calculated using the hapbin software (https://github.com/evotools/hapbin) with default parameters across 79 water buffalo and 294 cattle whole genome sequences. The breeds being compared and the chromosome number are indicated in each file name. The water buffalo positions are with respect to the UOA_WB_1 genome assembly and the cattle with respect to ARS-UCD1.2.
DOI: 10.7488/ds/2809
title: Diode pumping of liquid crystal lasers

description: Data files comprise unprocessed data for: efficiency measurements ("Efficiency Data") bandgap spectra ("Spectral Data") laser output spectra ("Spectral Data")
DOI: 10.7488/ds/2542
title: Cs3Bi2I9 as high-performance electrode material achieving high capacitance and stability in an economical supercapacitor

description: Supercapacitors are well-known as promising energy storage devices capable of bridging the gap between conventional electrolytic capacitors and batteries to deliver both high power and energy densities for applications in electric vehicles and a smart energy grid. However, many reported instances of high-capacitance pseudocapacitors employ strong Faradaic reactions that hinder fast charge-discharge cycles and long-term stability, limiting their commercial viability. In this study, we utilize an economical and solution-processable procedure to fabricate a Cs3Bi2I9-based symmetric supercapacitor employing both electric double layer capacitance and pseudocapacitance with an aqueous NaClO4 electrolyte to deliver an outstanding device areal capacitance of 2.4 F cm-2 and specific capacitance of 280 F g-1. The Cs3Bi2I9 device achieves an excellent 88% capacitance retention after 5000 charge-discharge cycles, proving its long-term cycle stability and promise as a practical supercapacitor. We characterize the time-dependent charge storage mechanisms through cyclic voltammetry and electrochemical impedance spectroscopy to find that electrostatic charge accumulation predominates at high potentials (0.3-0.6 V) whereas weak, Faradaic charge adsorption and pore penetration bolster charge storage at lower potentials (0.0-0.2 V).
description: See readme in the file upload
DOI: 10.7488/ds/2761
title: Turbine loading and performance data for three Supergen UKCMER Tidal Turbines in a closely spaced staggered array at FloWave

description: This dataset presents a set of turbine loading and performance measurements carried out at the FloWave Ocean Energy Research Facility, around a closely spaced staggered array of three nominally 1:15 scale tidal turbines, with a 1.2m rotor diameter. Measurements were made at different rotation speeds, with the three turbine array compared to just the single rear turbine, logging: streamwise root bending moment in each blade, drive shaft torque, thrust on the rotor, and angular velocity of the rotor.
description: Dataset and file format described in "Turbine loading and performance data for three SuperGen UKCMER Tidal Turbines in a closely spaced staggered array at FloWave.pdf"
DOI: 10.7488/ds/2762
title: Flow data around three Supergen UKCMER Tidal Turbines in a closely spaced staggered array at FloWave

description: This dataset presents a comprehensive set of flow measurements carried out at the FloWave Ocean Energy Research Facility, around a closely spaced staggered array of three nominally 1:15 scale tidal turbines, with a 1.2m rotor diameter, including empty tank baseline data.
description: Dataset and file format described in "Flow data around three SuperGen UKCMER Tidal Turbines in a closely spaced staggered array at FloWave.pdf"
DOI: 10.7488/ds/2400
title: Spatial computational model of calcium signalling in the dendritic spines and its relation to Alzheimer's Disease

description: Memory in its simplest forms involves plastic changes in synaptic strength. Synaptic long-term potentiation (LTP) and long-term depression (LTD) exist in a delicate balance, which is disturbed in a number of diseases. In Alzheimer’s Disease, the balance is skewed towards LTD, which results in cognitive impairments. Long-term synaptic plasticity relies on Calcium signalling in the postsynaptic neuron and the activation of calmodulin and, subsequently, of CaMKII or calcineurin, leading to the induction of LTP or LTD, respectively. In Alzheimer’s disease, basal Calcium levels are elevated because of changes in Ca release from intracellular stores, and in transmembrane receptor function. This results in increased activation of calcineurin and hence, increased LTD. We develop a spatial particle-based stochastic model of Ca signalling in the dendritic spine in early LTP and LTD. The model includes Calcium influx through, activation of calmodulin, activation of calmodulin-dependent kinases and phosphatases and their effect on AMPA receptor and NMDA receptor function. This model helps us understand downstream effects of Calcium dysregulation in Alzheimer’s disease. We tested the impact of different calcium levels on the molecular pathways of long term plasticity. The healthy version of the model shows how the calcium signalling works in the dendritic spine head. While disease model have impaired calcium pumps, which leads to a build up of calcium within the spine head. The dynamics of the calcium influx can be changed to test the reactivity of pathways in response to calcium signal. This can done by changing the quantity to release and release pattern in MCell.
description: There are two version of the model, a healthy version and a disease model. Both .blend and mdl files are included in the dataset.
DOI: 10.7488/ds/2433
title: Byzantine aqueducts of Constantinople outside the city

description: This dataset is related to the PhD research of Francesca Ruggeri, published in the thesis "Engineering the Byzantine Water Supply of Constantinople: mapping, hydrology and hydraulics of the long aqueducts outside the City" (2018) http://hdl.handle.net/1842/31521. This aims at providing additional material resulting from the GIS work presented in Chapter 5 of the thesis. Archaeological survey data were available from previous campaigns carried out by Prof. James Crow in the years 1995-2009 in Turkish Thrace. Such data were systematically reassessed and organised by the author to create a comprehensive database of the remains of the Byzantine aqueducts of Constantinople. This dataset includes: maps of the Byzantine aqueducts and related features, as image files [map]; map locations viewable in Google Earth/Google Maps, as .kmz files [kmz]; shapefiles of Water Supply route and features for GIS use [shp]; lists of features (bridges, tunnels, channels), as Excel files [excel]. All maps and GIS features were created in ESRI ArcMap by F Ruggeri.
description: This dataset includes: maps of the Byzantine aqueducts and related features, as image files [map]; map locations viewable in Google Earth/Google Maps, as .kmz files [kmz]; shapefiles of Water Supply route and features for GIS use [shp]; lists of features (bridges, tunnels, channels), as Excel files [excel]. All maps and GIS features were created in ESRI ArcMap by F Ruggeri.
DOI: 10.7488/ds/2547
title: MD simulations Phase IV-V H2

description: Data supporting the thesis "Theoretical investigation of solid hydrogen and deuterium" Magdau, Ioan-Bogdan (2016) [PhD thesis].
DOI: 10.7488/ds/2432
title: Dynamics of Nanodroplets on Vibrating Surfaces

description: This data folder contains the output data from all molecular dynamics simulations carried out in this paper: Pillai, R, Borg, M & Reese, J 2018, 'Dynamics of nanodroplets on vibrating surfaces' Langmuir. DOI: 10.1021/acs.langmuir.8b02066 .
description: This data folder contains the output data from all molecular dynamics simulations carried out in this paper.
DOI: 10.7488/ds/2530
title: Data supporting the manuscript "Effective radiative forcing and climate responses to 1970-2010 changes in greenhouse gases, anthropogenic aerosols and ozone"

description: This folder contains six files numbered in order. File01: The global mean surface temperature evolution from all the experiments analyzed File02; The CESM1 simulated aerosol burdens and AOD, used to plot both the bars and spatial maps in Figure 2 File03: The longitude, latitude grids, as well as the spatial map of 1970-2010 temperature and precipitation changes, used to plot the zonal mean and spatial maps. The observational and reanalysis data can be obtained from corresponding data sources cited in the paper File04: The spatial maps of effective radiative forcing and surface temperature responses to GHGs, aerosols and ozone. This dataset is used to plot both the spatial patterns in Figure 4, the regional mean ERF in Figure 5, the temperature sensitivity estimates in Figure 6, as well as the supporting Figure S2 and S3. File05:The spatial maps of precipitation responses to GHGs, aerosols and ozone, being used to plot the spatial patterns in Figure 7 and the zonal mean in Figure S4. File06: The probability distribution and the of global and regional mean daily precipitation. All these datasets are produced and can be read using the Python cPickle package.
DOI: 10.7488/ds/2527
title: PA-X Peace Agreement Database and Dataset Version 1
title: PA-X
title: Peace Agreement Database

description: The new PA-X Peace Agreement Database (www.peaceagreements.org) addresses a gap in the study of peace processes by archiving and coding all formal peace agreements signed since 1990. It currently contains more than 1500 agreements, coding conceptually for 225 substantive categories such as power-sharing or transitional justice and enabling search permutations which can disaggregate the data by country, entity, region, conflict type, and stage of agreement, and different combinations of issues addressed. The database is intended to support qualitative and quantitative research on peace agreements, enabling triangulation with existing peace agreement and conflict datasets, and support the study of sequencing and its relationship to substantive trade-offs within and across conflicts.
description: * "pax-export.csv" Main data file ; * "PA-X codebook Version1-Updated" Codebook for the main data file.
DOI: 10.7488/ds/2550
title: Dynamics-dependent density distribution in active suspensions

description: Dataset for the manuscript entitled 'Dynamics-dependent density distribution in active suspensions': Self-propelled colloids constitute an important class of intrinsically non-equilibrium matter. Typically, such a particle moves ballistically at short times, but eventually changes its orientation, and displays random-walk behaviour in the long-time limit. Theory predicts that if the velocity of non-interacting swimmers varies spatially in 1D, v(x), then their density ρ(x) satisﬁes ρ(x) = ρ(0)v(0)/v(x), where x = 0 is an arbitrary reference point. Such a dependence of steady-state ρ(x) on the particle dynamics, which was the qualitative basis of recent work demonstrating how to ‘paint’ with bacteria, is forbidden in thermal equilibrium. We verify this prediction quantitatively by constructing bacteria that swim with an intensity-dependent speed when illuminated and implementing spatially-resolved diﬀerential dynamic microscopy (sDDM) for quantitative analysis over ∼ mm length-scales. A spatial light pattern therefore creates a speed proﬁle, along which we ﬁnd that, indeed, ρ(x)v(x) = constant, provided that steady state is reached.
DOI: 10.7488/ds/2573
title: Competing Timescales Lead to Oscillations in Shear-Thickening Suspensions

description: Competing timescales generate novelty. Here, we show that a coupling between the timescales imposed by instrument inertia and the formation of interparticle frictional contacts in shear-thickening suspensions leads to highly asymmetric shear-rate oscillations. Experiments tuning the presence of oscillations by varying the two timescales support our model. The observed oscillations give access to a shear-jamming portion of the flow curve that is forbidden in conventional rheometry. Moreover, the oscillation frequency allows us to quantify an intrinsic relaxation time for particle contacts. The coupling of fast contact network dynamics to a slower system variable should be generic to many other areas of dense suspension flow, with instrument inertia providing a paradigmatic example. For further information see the related pre-print: Richards, J. A., et al. "Competing Time Scales Lead to Oscillations in Shear-Thickening Suspensions." arXiv preprint arXiv:1902.07655 (2019).
description: Data and Python plotting scripts are in folders for each Figure, 1 to 4, as numbered in the referencing paper, e.g. "Figure1.zip". A description of the data structure and format are included in a readme file for each figure, e.g., "README_fig1.txt" for Figure 1.
DOI: 10.7488/ds/2411
title: Gabapentin for the Management of Chronic Pelvic Pain in Women (GaPP1)

description: This is a pilot study looking at the effect of Gabapentin in women with chronic pelvic pain. Participants were assigned at random to the placebo or the drug group. The design follows procedure of double blinding, i.e. neither patients, nor people involved in data collection or analysis knew the participants group. There was two sessions on thermal stimulation, in which a thermal probe was applied to the abdomen or to the hand. After each stimulation are two rating scales were presentated in succession. In a third session, punctuations were applied to he hand and fMRI scans conducted. The full study (not fMRI) report has been published here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0153037 .
description: * The experiment was conducted using "Presentation" (NeuroBehavioural Systems www.neurobs.com) and the scripts are available in Experiment.zip (in the /stimuli directory of the Gapp1.zip archive). Files named *.sce and *.exp are for use with the package "Presentation"; they are plain text, so the contents may be read using any text editor. * There was two sessions on thermal stimulation, in which a thermal probe was applied to the abdomen or to the hand. After each stimulation are two rating scales were presentated in succession. In a third session, punctuations were applied to he hand. Files subxxxx_ThermalAbdomen.tsv and subxxxx_ThermalHand.tsv show the timing of the thermal probe, rating scales and volume acquisition. * Files subxxxx_ThermalAbdomen_scales.tsv and subxxxx_ThermalHand_scales.tsv report the answer of the subjects. * The file subxxxx_punctate.tsv reports the timing of the stimulation. * Participants.tsv contains the behavioural data collected for each participant.
DOI: 10.7488/ds/2734
title: ECA Textiles Workshop

description: A Scan of Edinburgh College of Art Textiles Workshop, 7 Scan locations, captured with a BLK 360, registered using Autodesk Recap Pro, exported to .e57 file format.
DOI: 10.7488/ds/2401
title: Critical mode and band-gap-controlled bipolar thermoelectric properties of SnSe

description: From the related article: The reliable calculation of electronic structures and understanding of electrical properties depends on an accurate model of the crystal structure. Here, we have reinvestigated the crystal structure of the high-zT thermoelectric material tin selenide, SnSe, between 4 and 1000 K using high-resolution neutron powder diffraction. Symmetry analysis reveals the presence of four active structural distortion modes, one of which is found to be active over a relatively wide range of more than ±200 K around the symmetry-breaking Pnma--Cmcm transition at 800~K. Density functional theory calculations on the basis of the experimental structure parameters show that the unusual, step-like temperature dependencies of the electrical transport properties of SnSe are caused by the onset of intrinsic bipolar conductivity, amplified and shifted to lower temperatures by a rapid reduction of the band gap between 700 and 800 K. The calculated band gap is highly sensitive to small out-of-plane Sn displacements observed in the diffraction experiments. SnSe with a sufficiently controlled acceptor concentration is predicted to produce simultaneously a large positive and a large negative Seebeck effect along different crystal directions. https://doi.org/10.1103/PhysRevMaterials.2.085405
description: See README.pdf.
DOI: 10.7488/ds/2486
title: Sampling order optimization preserves contrast and improves clinical diagnostic utility of accelerated prospective 3D brain MRI: a radiological assessment study on healthy volunteers

description: The code and data herein distributed reproduce the results published in the paper: Arnold JulianVinoj Benjamin, Wajiha Bano, Grant Mair, Mike Davies, and Ian. Marshall,“Sampling order optimization preserves contrast and improves clinical diagnostic utility of accelerated prospective 3D brain MRI: a radiological assessment study on healthy volunteers”. In: Proc Intl Soc Mag Reson Med 2018, #3189. The data comprises of 3D brain datasets from eight healthy volunteers. Each dataset contains raw data from a fully sampled scan and three accelerated scans that are described in the aforementioned paper.
DOI: 10.7488/ds/2765
title: Inter- and intra-animal variation in the integrative properties of stellate cells in the medial entorhinal cortex

description: The data are whole-cell patch-clamp recordings from neurons in the medial entorhinal cortex of adult mice. The data for each neuron is a series of voltage responses to current steps or ramps injected through the recording electrode.
description: There are two .tar.gz archive files. One contains stellate cell data and the other contains calbindin cell data. Each file has a similar folder structure when unzipped. The original data was recorded with Axograph and is in the folder 'multi_data'. The folder structure is '/multidata/slice/cell', where slice and cell are names specific to each experiment / recording. The electrophysiology data here is in .axgd format. To open .axgd files you can either use Axograph (available commerically from https://axograph.com/) or Neuromatic (http://www.neuromatic.thinkrandom.com/) which requires IGORpro (available commercially from (https://www.wavemetrics.com/). It should also be possible to open the data using the axographio Python package (https://pypi.org/project/axographio/) but we haven’t tested this. Most 'cell' level folders also contain an image of the slice in .jpg format. The electrophysiology data is also provided in hdf5 format in the folder name 'Database'. These files end in '.h5'. The folders also contain code to build the .h5 files from the .axgd files and then to automatically extract the parameters used for further analyses. This code should be sufficient to replicate the data processing. We plan to separately document and make this code available via our Github site (https://github.com/MattNolanLab).
DOI: 10.7488/ds/2578
title: Marioni_et_al_AD_GWAS_Sumstats_June2019_Correction - Data supporting Marioni et al. "GWAS on family history of Alzheimer's disease"

description: Data supporting the paper: Marioni, RE, Harris, SE, Zhang, Q, Mcrae, AF, Hagenaars, SP, Hill, WD, Davies, G, Ritchie, CW, Gale, CR, Starr, JM, Goate, AM, Porteous, DJ, Yang, J, Evans, KL, Deary, IJ, Wray, NR & Visscher, PM 2018, 'GWAS on family history of Alzheimer’s disease' Translational Psychiatry, vol. 8, no. 1. DOI: 10.1038/s41398-018-0150-6. ## Note about using the files ## Each of the .txt files contains over seven million rows. Users will encounter difficulties if they attempt to view the content using Notepad++ or Microsoft Notepad. Microsoft Excel 2016 will not display all rows. These space-delimited text files contains several columns, with a header row, which are listed in the readme file.