cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2786
title: APP NL/F - 1 year rodent EEG and video recordings. Cerebellum reference
title: APP_1yr_Cerebellum

description: This dataset relates to the rodent data reported in the manuscript "Circadian and brain state modulation of network hyperexcitability in Alzheimer's disease". (Brown et al., (2018) 27 April 2018, 5 (2) ENEURO.0426-17.2018. DOI: 10.1523/ENEURO.0426-17.2018). These data were previously archived in the interim DataVault. Please see the Collection page https://datashare.is.ed.ac.uk/handle/10283/3586 for several other data filesets supporting the same publication. The repository contains EEG data from 12 month old APP NL/F+/+ and age matched C57Bl6J wild-type (WT) control mice. Data acquired using Opensource Instruments EEG data acquisition system, and LWDAQ/Neuroarchiver software. The data are saved in .ndf format and can be viewed using Neuroarchiver tool in LWDAQ, available here: http://alignment.hep.brandeis.edu/Software/Download/ Recording electrode coordinates: x: -2.25; y: -2.46 Reference electrode: Cerebellum The repository contains: - This README_APP_1yr_Cerebellum.txt file - "RecordingInfo_APP_1yr_Cerebellum.csv" with variables: - Mouse: The mouse ID - DOB: Date of birth in format dd/mm/yyyy - Sex - Genotype - Transmitter: The ID of transmitter. The number after the "." indicates the channel number relating to the data as stored in the .ndf data file - surgery date in format dd/mm/yyyy - first file: name of the first file - last file - last recording date in format dd/mm/yyyy - Reference: Location of reference electrode - Subfolder: Name of subfolder within "Neuroarchiver data" subfolder that contains the EEG data - An archive, "APP_1yr_Cerebellum.zip" which contains: - A folder "Neuroarchiver data". This contains subfolders labelled by start_date_to_end_date of recordings. Each subfolder contains data files saved in .ndf format. The .ndf files are named are named Mxxxxxxxxxx.ndf, where xxxxxxxxxx indicates the Unix time stamp (i.e. number of seconds after 00:00:00 on 1/1/1970) for the start of the file acquisition. The relevant channel number for the specified mouse ID is noted in RecordingInfo_APP_1yr_Cerebellum.csv - Transmitter. - A folder "Video", containing subfolders named by date (dd-mm-yyy)_mouseID. Each subfolder contains video data saved in .avi. Data acquired on webcams.
DOI: 10.7488/ds/2956
title: Associations between alcohol use and accelerated biological ageing

description: Data supporting the manuscript "Associations between alcohol use and accelerated biological ageing". Specifically: Genome Wide Association Study of brain age.
DOI: 10.7488/ds/2415
title: Acoustothermal atomization of water nanofilms

description: This data folder contains the output data from all molecular dynamics simulations carried out in this paper: Pillai et al. https://doi.org/10.1103/PhysRevLett.121.104502 .
DOI: 10.7488/ds/2950
title: Supplemental data table for Isolating lithologic versus tectonic signals of river profiles to test orogenic models for the Eastern and Southeastern Carpathians

description: This dataset contains a table of Schmidt Hammer data points acquired during a field campaign in the Eastern Carpathians in 2018. It is a supplemental material to the manuscript Isolating "lithologic versus tectonic signals of river profiles to test orogenic models for the Eastern and Southeastern Carpathians" submitted to JGR-Earth Surface. Abstract of the paper: Fluvial morphology is affected by a wide range of forcing factors, which can be external, such as faulting and changes in climate, or internal, such as variations in rock hardness or degree of fracturing. It is a challenge to separate internal and external forcing factors when they are co-located or occur coevally. Failure to account for both factors leads to potential misinterpretations. For example, steepening of a channel network due to lithologic contrasts could be misinterpreted as a function of increased tectonic displacements. These misinterpretations are enhanced over large areas, where landscape properties needed to calculate channel steepness (\textit{e.g.} channel concavity) can vary significantly in space. In this study, we investigate relative channel steepness over the Eastern Carpathians, where it has been proposed that active rock uplift in the Southeastern Carpathians gives way N- and NW-wards to ca. 8 Myrs of post-orogenic quiescence. We develop a technique to quantify relative channel steepness based on a wide range of concavities, and show that the main signal shows an increase in channel steepness from east to west across the range. Rock hardness measurements and geological studies suggest this difference is driven by lithology. When we isolate channel steepness by lithology to test for ongoing rock uplift along the range, we find steeper channels in the south of the study area compared to the same units in the North. This supports interpretations from longer timescale geological data that active rock uplift is fastest in the southern Southeastern Carpathians.
DOI: 10.7488/ds/2505
title: SAIL dementia e-cohort (SAIL-DeC)

description: These files contain details on the creation of the Secure Anonymised Information Linkage (SAIL) databank dementia e-cohort (SAIL-DeC).
DOI: 10.7488/ds/2797
title: Peptide occurrences dataset from UniProt Feb 2018

description: Peptide occurences at different lengths, found in UniProt Feb 2018 release (UniProtKB/Swiss-Prot 2018_02 - February 28, 2018). An output of the Leverhulme funded project: Understanding the biological ramifications of a ‘forbidden’ tetramer peptide nullomer. The dataset was generated using version 1.0.0 of the NullPeptides software (Git Hub repo: https://github.com/stevenshave/NullomerPeptides)
DOI: 10.7488/ds/2858
title: PROTOCOL: Quantitative Fibronectin to help Decision-making in women with Symptoms of Preterm Labour – Comparison with Partosure and Actim Partus QUIDS 2
title: QUIDS 2 Protocol

description: Study protocol for QUIDS 2
DOI: 10.7488/ds/2935
title: Preparation of iron(IV) nitridoferrate Ca4FeN4 through azide-mediated oxidation under high-pressure conditions

description: Data from characterisation of the title compound; Magnetic, Mossbauer, Neutron and X-ray diffraction results
DOI: 10.7488/ds/2064
title: NMR of Scotch Whisky Dataset

description: This dataset contains a number of NMR spectra for a sample of Scotch Whisky. The acquisition methodology is laid out in a recent paper, "Advanced Solvent Signal Suppression for the Acquisition of 1D and 2D NMR Spectra of Scotch Whisky", in Magnetic Resonance in Chemistry - DOI: 10.1002/mrc.4621. Data are for one sample of Scotch Whisky, a 12-year-old Highland Single Malt matured in a Sherry cask. The "1DOnly.zip" file includes only the first four experiments. The experiments included are as follows: Expno 10 - 1D 1H with water suppression Expno 11 - 1D 1H reverse inept of ethanol CH2/CH3 signals Expno 12 - 1D 13C inverse gated decoupling spectrum Expno 13 - 1D 1H NMR spectrum with water and ethanol suppression. The following were acquired with solvent suppression as described in the paper, and are only included in the larger .zip file. Expno 20 - 1D CSSF-TOCSY NMR spectrum Expno 30 - BASHD-TOCSY Expno 31 - BASHD-TOCSY Expno 40 - J-Resolved Expno 50 - 1H,1H COSY Expno 60 - 1H,1H TOCSY Expno 70 - 1H,13C HSQC Expno 80 - 1H,13C HSQC-TOCSY Expno 90 - 1H,13 HMBC Data are provided in Bruker TopSpin 3.x compatible format, with all original metadata. All data acquired on a Bruker Avance III HD 600 MHz spectrometer with TCI cryoprobe using TopSpin 3.2.
DOI: 10.7488/ds/2953
title: Archival Metadata Descriptions from the University of Edinburgh Centre for Research Collections - Extracted October 2020

description: The dataset includes metadata descriptions extracted from the Centre for Research Collections' online archival catalog using OAI-PMH EAD harvesting. Metadata descriptions were extracted from four metadata fields: an identifier (), Biographical / Historical (), Scope and Contents (), and Processing Information (). The descriptions were extracted in October 2020. The dataset includes five files that will be annotated for instances of gender bias, in an effort to create a gold standard dataset on which an algorithm can be trained to identify and classify gender bias in text. ## Acknowledgments ## This dataset has been created for a PhD project conducted in collaboration with Beatrice Alex, Benjamin Bach, and Melissa Terras (PhD supevisors); and with Rachel Hosker and the Centre for Research Collections (CRC). This group of collaborators will be involved in future uses of the data as this PhD project continues; specifically, for determining how to annotate the data for gender bias. Thanks are due to Scott Renton for his guidance in using the Open Archives Initiative - Protocol for Metadata Harvesting (OAI-PMH), which was necessary to extract selections of metadata in Encoded Archival Description (EAD) XML format from the CRC's online archives' catalog, ArchivesSpace.
description: Dataset created to annotate and train a classification algorithm on, in an effort to automate the identification and classification of types of gender bias in text. From the start of the first file to the end of the last file, the descriptions are in the same order they appeared when harvested using OAI-PMH. The descriptions were transformed from EAD, format to TXT format.
DOI: 10.7488/ds/2548
title: Dataset for "Helical and oscillatory microswimmer motility statistics from differential dynamic microscopy"

description: Raw data (i.e. simulated videos) supporting the manuscript "Helical and oscillatory microswimmer motility statistics from differential dynamic microscopy" published in New Journal of Physics. Research grant: ERC-AdG-340877 PHYSAPS .
description: See Readme file.
DOI: 10.7488/ds/2385
title: An ADAMTS3 Missense Variant is Associated with Norwich Terrier Upper Airway Syndrome - Supporting Data

description: This dataset comprises of Variant Call Format (VCF) files associated with the BAM files in this publication. The full BAM files will be submitted to European Nucleotide Archive.
DOI: 10.7488/ds/2572
title: De novo gene and transcript models created for a gene expression atlas of the domestic water buffalo (Bubalus bubalis)

description: The domestic water buffalo (Bubalus bubalis) makes a major contribution to the global agricultural economy in the form of milk, meat, hides and draught power. The global water buffalo population is predominantly found in Asia, and per head of population more people depend upon the buffalo than on any other livestock species. Despite its agricultural importance, there are comparatively fewer genomic and transcriptomic resources available for buffalo than for other livestock species. We have generated a large-scale gene expression atlas covering multiple tissue and cell types from all major organ systems collected from three breeds of riverine water buffalo (Mediterranean, Pandharpuri and Bhadawari), and used the network analysis tool Graphia Professional to identify clusters of genes with similar expression profiles. Alongside similar data we and others have generated for ruminants as part of the Functional Annotation of Animal Genomes Consortium, this comprehensive transcriptome supports functional annotation and comparative analysis of the water buffalo genome. This dataset contains, in GTF format, the full set of gene and transcript models assembled across all tissues and cell types comprising the water buffalo (Bubalus bubalis) expression atlas.
description: This dataset contains, in GTF format, the full set of gene and transcript models assembled across all tissues and cell types comprising the water buffalo (Bubalus bubalis) expression atlas. The atlas constitutes 220 tissue and cell samples collected from ten river buffalo of three different breeds (Mediterranean, Pandharpuri and Bhadawari). For each sample, reads were aligned to the draft buffalo assembly (UMD_CASPUR_WB_2.0) and de novo transcripts assembled using a HISAT/StringTie pipeline. This generates a sample-specific transcriptome for each set of mapped reads. In order to create a uniform, non-redundant set of transcripts for comparative purposes, these individual GTFs were then merged using StringTie --merge, producing the output file "merged.gtf". This dataset contains that file.
DOI: 10.7488/ds/2954
title: SUPERSEDED - Source data and scripts for "Intein-assisted bisection mapping systematically splits proteins for Boolean logic and inducibility engineering"

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/3001 ## Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augmented a mini-Mu transposon-based screening approach and devised the intein-assisted bisection mapping (IBM) method. IBM robustly revealed clusters of split sites on four proteins, converting them into AND or NAND logic gates. We further showed that the use of inteins expands functional sequence space for splitting a protein. We also demonstrated the utility of our approach over rational inference of split sites from structural alignment of homologous proteins. Furthermore, the intein inserted at an identified site could be engineered by the transposon again to become partially chemically inducible, and to some extent enabled post-translational tuning on host protein function. Our work offers a generalizable and systematic route towards creating split protein-intein fusions and conditional inteins for protein activity control.
DOI: 10.7488/ds/2932
title: CANTERA Reduced Chemical Mechanism for Dimethyl Ether Combustion

description: The file contains a reduce chemical mechanism for Dimethyl ether-air combustion. It is a reduced mechanism containing 31 species and 82 reactions, converted from the CHEMKIN input file of Pan et al. [1]. The mechanism is derived from the detailed Dymethyl ether-air chemistry of Burke et al. [2]. ## Format ## The .cti file is a plain text file in the Cantera Thermodynamic Input format for use with the open-source Cantera chemical kinetics tools, see https://cantera.org . ## References ## [1] Pan, L., Kokjohn, S., & Huang, Z. (2015). Development and validation of a reduced chemical kinetic model for dimethyl ether combustion. Fuel, 160, 165-177. [2] Burke, U., Somers, K.P., O’Toole, P., Zinner, C.M., Marquet, N., Bourque, G., Petersen, E.L., Metcalfe, W.K., Serinyel, Z. and Curran, H.J., 2015. An ignition delay and kinetic modeling study of methane, dimethyl ether, and their mixtures at high pressures. Combustion and flame, 162(2), pp.315-330.
DOI: 10.7488/ds/2934
title: Supplementary material for paper "Time-resolved spectroscopy of fluorescence quenching in optical fibre-based pH sensors"

description: Abstract: Numerous optodes, with fluorophores as the chemical sensing element and optical fibres for light delivery and collection, have been fabricated for minimally invasive endoscopic measurements of key physiological parameters such as pH. These flexible miniaturised optodes have typically attempted to maximize signal-to-noise through the application of high concentrations of fluorophores. We show that high-density attachment of carboxyfluorescein onto silica microspheres, the sensing elements, results in fluorescence energy transfer, manifesting as reduced fluorescence intensity and lifetime in addition to spectral changes. We demonstrate that the change in fluorescence intensity of carboxyfluorescein with pH in this “high-density” regime is opposite to that normally observed, with complex variations in fluorescent lifetime across the emission spectra of coupled fluorophores. Improved understanding of such highly loaded sensor beads is important as it leads to large increases in photostability and will aid the development of compact fibre probes, suitable for clinical applications. The time resolved spectral measurement techniques presented here can be further applied to similar studies of other optodes.
description: Supplementary material for paper "Time-resolved spectroscopy of fluorescence quenching in optical fibre-based pH sensors" contains the following folders: - 'rawData' contains the steady-state (sometimes refered to as intensity-based) and time-resolved data sets taken and analysed in the paper, and a txt file describing the data sets in detail. - 'scripts' contains the analysis scripts used to generate the plots and figures in the paper. The steady-state analysis was done in Matlab, while the time-resolved analysis was performed in python 2.7. - 'figures' contains the figures included in the paper.
DOI: 10.7488/ds/2938
title: Data and code for Core crosstalk in ordered imaging fibre bundles

description: Data and code for the paper: "Core crosstalk in ordered imaging fibre bundles" Parker, H, et al. (Accepted manuscript).
DOI: 10.7488/ds/2931
title: Changes of Fermi Surface Topology due to the Rhombohedral Distortion in SnTe

description: Stoichiometric SnTe is theoretically a small gap semiconductor that undergoes a ferroelectric distortion on cooling. In reality however, crystals are always nonstoichiometric and metallic; the ferroelectric transition is therefore, more accurately described as a polar structural transition. Here, we study the Fermi surface using quantum oscillations as a function of pressure. We find the oscillation spectrum changes at high pressure due to the suppression of the polar transition and less than 10 kbars is sufficient to stabilize the undistorted cubic lattice, this is accompanied by a large decrease in the Hall and electrical resistivities. Combined with our density functional theory calculations and angle-resolved photoemission spectroscopy measurements, this suggests the Fermi surface L pockets have lower mobility than the tubular Fermi surfaces that connect them. Additionally, we find the unusual phenomenon of a linear magnetoresistance that exists irrespective of the distortion that we attribute to regions of the Fermi surface with high curvature.
DOI: 10.7488/ds/2874
title: Understanding high pressure molecular hydrogen with a hierarchical machine-learned potential
title: DFT trajectory dataset for "Understanding high pressure molecular hydrogen with a hierarchical machine-learned potential"

description: The hydrogen phase diagram has several unusual features which are well reproduced by density functional calculations. Unfortunately, these calculations do not provide good physical insights into why those features occur. Here, we present a fast interatomic potential, which reproduces the molecular hydrogen phases: orientationally disordered Phase I; broken-symmetry Phase II, efficiently-packed Phase III and reentrant melt curve. The H2 vibrational frequency drops at high pressure because of increased coupling between neighbouring molecules, not bond weakening. Liquid H2 is denser than coexisting close-packed solid at high pressure because the favored molecular orientation switches from quadrupole-energy-minimizing to steric-repulsion-minimizing. The latter allows molecules to get closer together, without the atoms getting closer, but cannot be achieved within in a close-packed layer due to frustration. A similar effect causes negative thermal expansion. At high pressure, rotation is hindered in Phase I, such that it cannot be regarded as a molecular rotor phase. This dataset contains DFT trajectory data used for fitting the machine learned interatomic potential.
DOI: 10.7488/ds/2781
title: A hybrid model for seasonal forecast of Indonesian fire risk ​

description: Documentation for the dataset is provided in the README file. List of files: 1. Readme.txt 2. A hybrid model code in the NCL language (seasonalforecasting.ncl.txt) 3. Equatorial Asian monthly total burned area (ba_eqa.data) 4. Sea Surface Temperature (SST) prediction data (model_aug_l1to3.data, model_sep_l1to3.data, model_oct_l1to3.data) 5. Sea Surface Temperature (SST) prediction data (model_aug_l1to3.txt, model_sep_l1to3.txt, model_oct_l1to3.txt)
DOI: 10.7488/ds/2952
title: Listening-test materials for "Where do the improvements come from in sequence-to-sequence neural TTS?"

description: This data release contains listening-test materials associated with the paper "Where do the improvements come from in sequence-to-sequence neural TTS?", presented at SSW10 (the 10th ISCA Speech Synthesis Workshop) in Vienna, Austria, 2019.
description: See readme.txt
DOI: 10.7488/ds/2946
title: Search strategies designed to retrieve all references on coronavirus (COVID-19) and stroke healthcare

description: These search strategies were designed and constructed between May and July 2020. They are designed to retrieve all potential references in stroke healthcare and medicine (including transient ischaemic attack, cerebral small vessel disease, and subarachnoid haemorrhage) and coronavirus (COVID-19) on in the MEDLINE database on the Ovid platform, CENTRAL in The Cochrane Library, PubMed, US National Institutes of Health Ongoing Trials Register ClinicalTrials.gov (www.clinicaltrials.gov), and Google Scholar using the 2dSearch interface. The MEDLINE Ovid search strategy was written as a protocol and all additional searches were based on it. This high sensitivity search strategy contains 21 separate search lines and incorporates a combination of Medical Subject Headings (MeSH) from the National Library of Medicine, uncontrolled vocabulary/keywords in the Text Word (.tw) field, and Boolean operators to maximise sensitivity and recall. This search is divided into two components: 1. terms relevant to stroke healthcare and medicine; and 2. terms relevant to Coronavirus (COVID-19) which were based on the Ovid expert search for COVID-19 (Ovid MEDLINE(R) All 1946 to present) which can be viewed here: https://tools.ovid.com/coronavirus/Covid-19%20search%20notes.pdf.
description: Search strategy originally designed to retrieve all Coronavirus (COVID-19) references in MEDLINE Ovid. This search strategy was originally designed in January 2020 and optimised over subsequent months to achieve better balance of sensitivity and specificity.
description: Text file (UTF-8 coding) containing 5 separate search strategies.
DOI: 10.7488/ds/2725
title: Data for "Pathogen transmission from vaccinated hosts can cause dose-dependent reduction in virulence"
title: Previously titled - Data for "Transmission from vaccinated hosts can cause dose-dependent reduction in pathogen virulence"

description: # Abstract # Many livestock and increasingly human vaccines are leaky, blocking symptoms without preventing infection or onward transmission. Leakiness is concerning as it increases vaccination coverage required to prevent disease spread, and can promote evolution of increased pathogen virulence. Despite leakiness, vaccination may reduce pathogen load, affecting disease transmission dynamics. However, the impacts on post-transmission disease development and infectiousness in contact individuals are unknown. Here, we use transmission experiments involving Marek’s disease virus in chickens to show that vaccination with a leaky vaccine substantially reduces viral load in both vaccinated individuals and unvaccinated contact individuals they infect. Consequently, contact birds are less likely to develop disease symptoms or die, show less severe symptoms when these are present, and shed less infectious virus themselves, when infected by vaccinated birds. These results highlight that even partial vaccination with a leaky vaccine can have unforeseen positive consequences in controlling the spread and symptoms of disease.
description: * "MD_analysis_data_filtering_details.R" R code file identifying which datasets used for which analyses, and describing pre-analysis filtering. * "Contact_2018.csv" * "ContactDiseaseS_2018.csv" * "ContactDiseaseSEM_2018.csv" * "ContactInfection_2018.csv" * "ContactMort_2018.csv" * "HVT_qPCR_summary_RB18Nov2019.csv" Vaccine virus transmission qPCR results. * "Shedder_2018.csv" * "ViralLoadFile_2017_2018.csv"