cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/324
title: Hydrodynamic and Contact Contributions to Continuous Shear Thickening in Colloidal Suspensions

description: Shear thickening is a widespread phenomenon in suspension flow that, despite sustained study, is still the subject of much debate. The longstanding view that shear thickening is due to hydrodynamic clusters has been challenged by recent theory and simulations suggesting that contact forces dominate, not only in discontinuous, but also in continuous shear thickening. Here, we settle this dispute using shear reversal experiments on micron-sized silica and latex particles to measure directly the hydrodynamic and contact force contributions to shear thickening. We find that contact forces dominate even continuous shear thickening. Computer simulations show that these forces most likely arise from frictional interactions.
description: This item contains six zipped folders. Each folder contains spreadsheet(s) and readme file(s).
DOI: 10.7488/ds/360
title: Relative Photoionization Cross Sections of Super-Atom Molecular Orbitals (SAMOs) in C60

description: Photoelectron VMI (Velocity Map Imaging) images of C60 using femtosecond laser pulses at different wavelengths.
description: This data is supporting information relating to: Bohl, E., Sokół, K. P., Mignolet, B., Thompson, J. O. F., Johansson, J. O., Remacle, F. & Campbell, E. E. B. Relative Photoionization Cross Sections of Super-Atom Molecular Orbitals (SAMOs) in C60. J. Phys. Chem. A (2015). doi:10.1021/acs.jpca.5b10339
DOI: 10.7488/ds/235
title: Characterizing pressure-induced uranium C-H agostic bonds

description: Under pressure: The diuranium(III) compound [UN''2]2(μ-η6:η6-C6H6) (N''=N(SiMe3)2) has been studied using variable, high-pressure single-crystal X-ray crystallography, and density functional quantum chemistry. In this compound, the low-coordinate metal cations are coupled through π- and δ-symmetric arene overlap and show close metalCH contacts with the flexible methyl CH groups of the sterically encumbered amido ligands. The metal-metal separation decreases with increasing pressure, but the most significant structural changes are to the close contacts between different ligand CH bonds and the U centers. Although X-ray crystallographic software suggests agostic-type interactions between the U and ligand peripheral CH groups, QTAIM (quantum theory of atoms-in-molecules) computational analysis suggests that there is no such interaction at ambient pressure. However, at the highest pressure studied (3.2 GPa), interactions with the U centers, assigned as agostic, are evidenced by QTAIM.
description: Most of the files in this dataset are in .cif format, reflecting the Crystallographic Information Framework which is a standard documented and maintained by the International Union of Crystallography – see http://www.iucr.org/resources/cif .
DOI: 10.7488/ds/304
title: Swimming In a Crystal

description: We study catalytic Janus particles and Escherichia coli bacteria swimming in a two-dimensional colloidal crystal. The Janus particles orbit individual colloids and hop between colloids stochastically, with a hopping rate that varies inversely with fuel (hydrogen peroxide) concentration. At high fuel concentration, these orbits are stable for 100s of revolutions, and the orbital speed oscillates periodically as a result of hydrodynamic, and possibly also phoretic, interactions between the swimmer and the six neighbouring colloids. Motile E. coli bacteria behave very differently in the same colloidal crystal: their circular orbits on plain glass are rectified into long, straight runs, because the bacteria are unable to turn corners inside the crystal.
DOI: 10.7488/ds/250
title: Self-organization and transition to turbulence in isotropic fluid motion driven by negative damping at low wavenumbers

description: We observe a symmetry-breaking transition from a turbulent to a self-organized state in direct numerical simulation of the Navier-Stokes equation at very low Reynolds number. In this self-organised state the kinetic energy is contained only in modes at the lowest resolved wavenumber, the skewness vanishes, and visualization of the flows shows a lack of small-scale structure, with the vorticity and velocity vectors becoming aligned (a Beltrami flow).
description: This item contains: 14 tar.gz zipped folders containing the core data and 1 README.txt file.
DOI: 10.7488/ds/2465
title: Structural and electronic properties of the alkali metal incommensurate phases

description: Under pressure, the alkali elements sodium, potassium, and rubidium adopt nonperiodic structures based on two incommensurate interpenetrating lattices. While all elements form the same “host” lattice, their “guest” lattices are all distinct. The physical mechanism that stabilizes these phases is not known, and detailed calculations are challenging due to the incommensurability ofthe lattices. Using a series of commensurate approximant structures, we tackle this issue using density functional theory calculations. In Na and K, the calculations prove accurate enough to reproduce not only the stability of the host-guest phases, but also the complicated pressure dependence of the host-guest ratio and the two guest-lattice transitions. We find Rb-IV to be metastable at all pressures, and suggest it is a high-temperature phase. The electronic structure of these materials is unique: they exhibit two distinct, coexisting types of electride behavior, with both fully localized pseudoanions and electrons localized in 1D wells in the host lattice, leading to low conductivity. While all phases feature pseudogaps in the electronic density of states, the perturbative free-electron picture applies to Na, but not to K and Rb, due to significant d-orbital population in the latter.
description: See README.txt.
DOI: 10.7488/ds/3049
title: Sex-stratified logistic mixed models: 42 binary traits

description: Sex-stratified GWAS can help shed light on sexual differences in genetic architecture. In Bernabeu et al (2021) we fit sex-stratified logistic mixed models (using REGENIE) across a total of 42 binary traits for which we’d found evidence of sexual differences for at least one genetic variant. Here, the results of said models, as well as the comparison statistics between male and female genetic effects, are included. Each file contains the results for a single binary trait, as stated in the file name, using its corresponding UK Biobank trait code. Trait descriptions, including their respective UK Biobank codes, are stated in the “trait_description_binary.tsv” file. For each trait (each .gz file), GWAS summary statistics obtained for over 9 million genetic variants across the autosomal genome and circa 450K individuals, as well as the results of the t-test comparing genetic effect estimates between the sexes, are included.
description: This DataShare deposit includes GWAS datasets for 42 binary traits. Each file represents a trait, as stated in the file title. A table is also included which matches each trait code with a description. Fields include those returned by REGENIE for each sex: chromosome, position, ID, reference allele (allele 0), alternative allele (allele 1), frequency of the alternative allele, sample size, SNP imputation score and the test performed (additive). These are followed by the estimated effect sizes (first order approximation), standard errors (first order approximation), chi-square test statistic and -log10 p value. Finally, sex comparison statistics are included, including the t-statistic [STAT-Comp_REGENIE], as calculated on effects transformed on linear scale using FOA transformation, p-value [PVAL-Comp_REGENIE] and FDR corrected p-value [PVAL-Comp_REGENIE_FDR].
DOI: 10.7488/ds/204
title: Lagging strand replication shapes the mutational landscape of the genome

description: The origin of mutations is central to understanding evolution and of key relevance to health. Variation occurs non-randomly across the genome, and mechanisms for this remain to be defined. Here we report that the 5' ends of Okazaki fragments have significantly increased levels of nucleotide substitution, indicating a replicative origin for such mutations. Using a novel method, emRiboSeq, we map the genome-wide contribution of polymerases, and show that despite Okazaki fragment processing, DNA synthesized by error-prone polymerase-alpha (Pol-alpha) is retained in vivo, comprising ~1.5% of the mature genome. We propose that DNA-binding proteins that rapidly re-associate post-replication act as partial barriers to Pol-delta-mediated displacement of Pol-alpha-synthesized DNA, resulting in incorporation of such Pol-alpha tracts and increased mutation rates at specific sites. We observe a mutational cost to chromatin and regulatory protein binding, resulting in mutation hotspots at regulatory elements, with signatures of this process detectable in both yeast and humans.
description: See dataShareREADME.txt
DOI: 10.7488/ds/302
title: Construction of a modular arsenic resistance operon in E. coli and the production of arsenic nanoparticles: Figure 4 original images

description: Original EM images and EDX data for pEC20 & pArsRBCC E. coli cells incubated with sodium arsenate. (A): TEM image of cell with bound arsenic; (B): close-up of analysed area; (C): green box indicates where beam was placed, red box indicates where background reading was taken; (D): atomic % from X-ray spectra; (E): summed X-ray spectrum from the analysed region showing all elements present.
DOI: 10.7488/ds/312
title: Somatic Cell Nuclear Transfer (Cloning) Efficiency

description: Cloning by nuclear transfer from adult somatic cells is a remarkable demonstration of developmental plasticity. When a nucleus is placed in oocyte cytoplasm, the changes in chromatin structure that govern differentiation can be reversed, and the nucleus can be made to control development to term. The overall efficiency of cloning is typically between 0 and 3 % (number of live offspring as a percentage of the number of nuclear transfer embryos), irrespective of the species, the donor cell type or technique. However, this is the cumulative result of losses at each stage of the cloning process. The tables in the PDF provide a summary of the data for each report published by the Data Creators on somatic cell (fetal to adult cells) nuclear transfer up until the time of its compilation, in July 2002. Where the appropriate data was made available, the table provides cloning efficiency for each major stage of the process.
DOI: 10.7488/ds/164
title: Simulation data: Experiments in Globalisation, Food Security and Land Use Decision Making

description: This zip file contains all simulation data produced for the publication Calum Brown, Dave Murray-Rust, Jasper van Vliet, Shah Jamal Alam, Peter H Verburg, Mark D Rounsevell (2014) Experiments in globalisation, food security and land use decision making. Once unzipped, the folder has the following structure: every sub-experiment (regionalisation) of the 19 experiments described in the text has its own folder. Within each, 30 simulations of each sub-experiment has a further folder and within each of these, csv files give the coordinates of modelled cells, capital values for each cell, agent type owning each cell, the individual agent's competitiveness on that cell, and the quantities of services produced. There is one csv file for each timestep of the simulation. All analyses in the above publication were based on this data. For any enquiries, please contact Calum Brown: calum.brown@ed.ac.uk.
DOI: 10.7488/ds/221
title: ARCHER Annual Survey Report 2014

description: Report and data from ARCHER (UK National HPC Service) annual user survey
DOI: 10.7488/ds/39
title: Repeated Harvard Sentence Prompts corpus version 0.5
title: REHASP 0.5

description: Studio recording of female native British English talker producing three sets of Harvard sentences (thirty prompts), each prompt repeated forty times. Available both as unprocessed 96 kHz recordings and standardised 16 kHz files.
DOI: 10.7488/ds/277
title: DNA modulates solvent isotope effects in a nanopore

description: Here we investigate the modulation of solvent isotope effects by the entry of DNA molecules into individual α-haemolysin nanopores. Solvent isotope effects in D2O versus H2O were enhanced (kH/kD ≈ 1.6) compared to the bulk (kH/kD ≈ 1.2), except when the pore was most blocked (kH/kD ≤ 1.1).
description: Ion current recordings, raw data as recorded in PClamp 10.2 software. NOTE: Some files are in Axon(TM) Binary Format (ABF), a format proprietary to Molecular Devices.
DOI: 10.7488/ds/275
title: How focussing on hydrogen bonding interactions in amino acids can miss the bigger picture: a high-pressure neutron powder diffraction study of epsilon-glycine.

description: Data associated with the paper: Parsons et al (2015) "How focussing on hydrogen bonding interactions in amino acids can miss the bigger picture: a high-pressure neutron powder diffraction study of epsilon-glycine", CrystEngComm, DOI: 10.1039/C5CE00327J.
DOI: 10.7488/ds/279
title: Analysis of the Thermal Degradation of the Individual Anthocyanin Components of Black Carrot (Daucus carota L.) – A New Approach Using High-Resolution 1H NMR Spectroscopy
DOI: 10.7488/ds/292
title: ARCHER CSE Performance Data and Service Report: Q2 2015

description: Data from SAFE (https://www.archer.ac.uk/safe) and Quarter 2 2015 Service Report from ARCHER Computational Science and Engineering Service. These contain data on usage and performance of the ARCHER CSE Service for Quarter 2 2015 (April - June 2015).
DOI: 10.7488/ds/291
title: ARCHER CSE Performance Data and Service Report: Q1 2015

description: Data from SAFE (https://www.archer.ac.uk/safe) and Quarter 1 2015 Service Report from ARCHER Computational Science and Engineering Service. These contain data on usage and performance of the ARCHER CSE Service for Quarter 1 2015 (January - March 2015).
DOI: 10.7488/ds/326
title: Can dispersion forces govern aromatic stacking in an organic solvent?

description: Experimental support for the dominance of van der Waals dispersion forces in aromatic stacking interactions occurring in organic solution is surprisingly limited. Here, we have examined the size-dependence of aromatic stacking in an organic solvent. The interaction energy was found to vary by ~7.5 kJ mol–1 on going from a phenyl-phenyl to an anthracene-pyrene stack. Strikingly, the experimental data were highly correlated with dispersion energies determined using symmetry-adapted perturbation theory (SAPT), while the induction, exchange, electrostatic and solvation energy components correlated poorly. Both the experimental data and the SAPT-dispersion energies gave high-quality correlations with the change in solvent accessible area upon complexation. Thus, the size-dependence of aromatic stacking interactions is consistent with the dominance of van der Waals dispersion forces even in the presence of a competing polarizable solvent.
description: .xyx coordinates of minimised complex geometries, NMR characterisation and titration data.
DOI: 10.7488/ds/276
title: Simulations of dipolar fluids using effective many-body isotropic interactions

description: These files contain original simulation data for Figures 4, 5, 6, 7, 9, and 11, and PDF versions of Figures 3, 8, and 10. All theoretical lines (including those in Figures 1 and 2) can be generated from the formulas given in the paper.
description: Please see README.txt.
DOI: 10.7488/ds/282
title: Listening test materials for "Multiple Feed-forward Deep Neural Networks for Statistical Parametric Speech Synthesis"

description: In the paper which this data accompanies, we investigate a combination of several feed-forward deep neural networks (DNNs) for a high-quality statistical parametric speech synthesis system. Recently, DNNs have significantly improved the performance of essential components in the statistical parametric speech synthesis, e.g. spectral feature extraction, acoustic modelling and spectral post-filter. In this paper our proposed technique combines these feed-forward DNNs so that the DNNs can perform all standard steps of the statistical speech synthesis from end to end, including the feature extraction from STRAIGHT spectral amplitudes, acoustic modelling, smooth trajectory generation and spectral post-filter. The proposed DNN-based speech synthesis system is then compared to the state-of-the-art speech synthesis systems, i.e. conventional HMM-based, DNN-based and unit selection ones.
DOI: 10.7488/ds/141
title: Dinka_LuanyjangDialect_Jan-May2007_controlled_NounsSingularAndPural

description: The data are elicited Dinka utterances: collected through controlled elicitation, using English to convey the utterances to be translated to the speaker. The dialect is the Luanyjang variety, which is part of the Rek cluster. In total, the dataset contains 1096 sound files, with one utterance per sound file. In most cases, the target word in the utterance is a noun, elicited in one or more of a small number of sentence frames. These noun data were recorded so that listening to them and inspecting their acoustic representations could be used to help in determining the correct phonological transcription. The resulting transcriptions of noun forms are recorded in the table in nounnumber_dataset.pdf. This pdf is included in this dataset, and also includes nouns for which the transcription was determined purely based on auditory impressions. The nouns in nounnumber_dataset.pdf form the basis of a published paper: Ladd, D. Robert, Bert Remijsen & Caguor A. Manyang (2009). On the distinction between regular and irregular inflectional morphology: evidence from Dinka. Language 85(3), 659-670. In addition, this archived dataset also includes evidence of a) the construct state of some nouns, as it presents itself on nouns modified by a possessor or a demonstrative; b) forms from the paradigm of the verb {mel} ‘soil, make dirty’. The structure of the file names is explained in the readme.
description: See explanation in readme.pdf
DOI: 10.7488/ds/313
title: Polarization Reconfigurable Antennas Using Graphene For Microwave Applications
title: Results

description: Simulation data obtained from commercial software "Computer Simulation Technology - CST: CST STUDIO SUITE 2014" exported to Excel format .xlsx.
DOI: 10.7488/ds/203
title: Quasi-geostrophic double gyre force function data
DOI: 10.7488/ds/361
title: Two-scale evolution during shear reversal in dense suspensions

description: Matlab data files used to plot the figures in a paper titled "Two-scale evolution during shear reversal in dense suspensions".
DOI: 10.7488/ds/299
title: Edwin: a robotic platform for automated RNA extraction and analysis during reporter gene-based dynamic characterisation of bacterial promoters

description: Please see info.txt (contained in the zip file).
DOI: 10.7488/ds/233
title: Constrained interpolation data (superseded)

description: # This data item has been replaced by the one which can be found at https://doi.org/10.7488/ds/1362. #
DOI: 10.7488/ds/305
title: BaCrO3-x JSSC 2015
DOI: 10.7488/ds/289
title: ThBisImido https://doi.org/10.1021/jacs.5b06630

description: Molecules containing actinide-nitrogen multiple bonds are of current interest as simple models for new actinide nitride nuclear fuels, and potential catalytic activation of inert hydrocarbon C-H bonds. Molecules with uranium-nitrogen multiple bonds are now being widely studied, yet thorium nitrogen multiple bonds remain extremely rare. Calculations suggest that thorium nitrogen double bonds should display significant polarity, unlike U=N bonds, but like early transition metal analogues, many of which react with alkanes. Arguments over whether thorium should be considered more like these latter elements than an actinide are receiving increasing attention with reports of new reduced thorium complexes with d-electron configurations, and proposals that a bis(imido) thorium complex should be cis (transition metal–like), rather than trans, as is the norm for uranium. Sterically protecting cyclopentadienyl-based ligands that enabled the first molecular Th=N bonds to be isolated also constrain their reactivity and flexibility. Here, simple mono(imido), and the first bis(imido) thorium complexes K[Th(=NAr)N"3] and K2[Th(=NAr)2(N")2] are readily made from insertion reactions (Ar = aryl, N" = N(SiMe3)2). X-ray and computational structural analyses show a cis-bis(imido) geometry, and polarised double bonds, in line with the more ‘transition metal-like’ nature, and hinting at the possibility for further reactivity with small inert molecules such as hydrocarbons.
DOI: 10.7488/ds/130
title: Wellcome Trust Gold OA fees - University of Edinburgh 2007-2012

description: This spreadsheet is a summary of Gold OA fees paid for by the Wellcome Trust under a block grant awarded to the University of Edinburgh between 2007-2012.
description: WT_data_ariadne_v3.csv
DOI: 10.7488/ds/1735
title: Archaeological Site Dataset for the Jazira Region of Syria

description: This archaeological dataset complements 13 other datasets as part of a study that compared ancient settlement patterns with modern environmental conditions in the Jazira region of Syria. This study examined settlement distribution and density patterns over the past five millennia using archaeological survey reports and French 1930s 1:200,000 scale maps to locate and map archaeological sites. An archaeological site dataset was created and compared to and modelled with soil, geology, terrain (contour), surface and subsurface hydrology and normal and dry year precipitation pattern datasets; there are also three spreadsheet datasets providing 1963 precipitation and temperature readings collected at three locations in the region. The environmental datasets were created to account for ancient and modern population subsistence activities, which comprise barley and wheat farming and livestock grazing. These environmental datasets were subsequently modelled with the archaeological site dataset, as well as, land use and population density datasets for the Jazira region. Ancient trade routes were also mapped and factored into the model, and a comparison was made to ascertain if there was a correlation between ancient and modern settlement patterns and environmental conditions; the latter influencing subsistence activities. This archaeological dataset was generated to show settlement distribution patterns in the Jazira region of Syria. The sites were mapped using publications of surveys conducted and the French 1:200,000 maps. The French maps include the identification of sites using toponyms called 'Tells'. The temporal extent of the archaeological sites in this dataset span from the Neolithic to Islamic periods of Syria. The extent of the archaeological site dataset comprises an area within the Syrian Jazira, which lies between the Syrian and Turkish border in the north; the Syrian and Iraqi border to the east, including the River Tigris; and to the River Euphrates to the south and west. All related data collected was confined within this area with the exception of this archaeological dataset. Archaeological sites were identified and mapped along both banks of the River Euphrates. Derived from 1:200,000 French maps comprising the 1:200,000 French Levant Map Series sheets (Further Information element in this metadata record provides list of sheets). Data also extracted from numerous archaeological survey reports and publications dating back to the 1930s. GIS vector data. This dataset was first accessioned in the EDINA ShareGeo Open repository on 2010-07-01 and migrated to Edinburgh DataShare on 2017-02-21.
description: ESRI Shapefile
DOI: 10.7488/ds/260
title: 4-PAM Visible Light Communications with a XOR-tree Digital Silicon Photomultiplier
DOI: 10.7488/ds/209
title: ARCHER CSE Performance Data and Service Report: Q2 2014

description: Data from SAFE (https://www.archer.ac.uk/safe) and Quarter 2 2014 Service Report from ARCHER Computational Science and Engineering Service. These contain data on usage and performance of the ARCHER CSE Service for Quarter 2 2014 (April - June 2014).