cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2712
title: Insights into the genetic basis of retinal detachment

description: Dataset of genome-wide association meta-analysis summary statistics associated with the publication “Insights into the genetic basis of retinal detachment” available at HMG: DOI: 10.1093/hmg/ddz294. If you use this dataset, please cite the manuscript.
description: This dataset encloses a single tab-delimited compressed file rd_meta.tbl.gz containing the individual summary statistic of over 7.5 million SNPs imputed with the Haplotype Reference Consortium (HRCr1-1). These results were obtained by conducting an inverse variance weighted meta-analysis of the effect of the genome-wide association studies of retinal detachment case-control sets from the UK Biobank or clinically ascertained as described in the manuscript. File header description: MarkerName is the unique variant name chromosome_position; CHR the chromosome number; BP is the physical location (bp) based on the genome build GRCh37; Allele1 is the effect allele for which the effect of retinal detachment has been reported (Effect); Allele2 the alternate allele; Freq1 is the mean frequency of the effect allele (Allele1); Effect is the meta-analysis effect size; StdErr is the standard error of the effect; Pvalue the P-value of the test; ID the rsid (dbSNP).
DOI: 10.7488/ds/2544
title: Dataset for "Real-time measurement of tumour hypoxia using an implantable microfabricated oxygen sensor"
title: Dataset for "An implantable microfabricated sensor for real-time measurement of tissue oxygenation"

description: Dataset for "Real-time measurement of tumour hypoxia using an implantable microfabricated oxygen sensor" by Marland et al. (2020) https://doi.org/10.1016/j.sbsr.2020.100375. # Change to title # The original title of this dataset was: 'Dataset for "An implantable microfabricated sensor for real-time measurement of tissue oxygenation"' reflecting the title of the original associated manuscript. The manuscript title changed as a result of the publication process. On 6 November 2020 the title of the dataset was subsequently changed to match the title of the associated journal article, to become 'Dataset for "Real-time measurement of tumour hypoxia using an implantable microfabricated oxygen sensor"'.
DOI: 10.7488/ds/2871
title: Insulation wall informal settlement fire experiment (Test 11)

description: This dataset presents Test 11 (insulation wall experiment). Different from Baseline experiment, the interior walls are insulated, and the other conditions are totally the same with Baseline.
DOI: 10.7488/ds/2220
title: The Blizzard Challenge 2017

description: WITHDRAWN: This item has been withdrawn from DataShare at the request of Professor Simon King and is no longer available.The Blizzard Challenge 2017 was the thirteenth annual Blizzard Challenge and was once again organised by Simon King at the University of Edinburgh, with support from the other members of the Blizzard Challenge committee – Keiichi Tokuda and Alan Black. The task this year was the same as in 2016, using a slightly expanded single-speaker English corpus, comprising around 6.5 hours of audio from 56 professionally-produced children’s audiobooks. We hereby provide the data that was used for building Merlin benchmark.
DOI: 10.7488/ds/2848
title: Interaction between Nearly Hard Colloidal Spheres at an Oil-Water Interface v2

description: We show that the interaction potential between sterically stabilised, nearly hard-sphere (PMMA-PLMA) colloids at a water-oil interface has a negligible unscreened-dipole contribution, suggesting that models previously developed for charged particles at liquid interfaces are not necessarily applicable to sterically stabilised particles. Interparticle potentials, U(r), are extracted from radial distribution functions (g(r), measured by fluorescence microscopy) via Ornstein-Zernike (OZ) inversion and via a reverse Monte Carlo scheme. The results are then validated by particle tracking in a blinking optical trap. Using a Bayesian model comparison, we find that our PMMA-PLMA data is better described by screened monopole only rather than a functional form having a screened monopole plus an unscreened dipole term. We postulate that the long range repulsion we observe arises mainly through interactions between neutral holes on a charged interface i.e. the charge of the liquid interface cannot, in general, be ignored. In agreement with this interpretation, we find that the interaction can be tuned by varying salt concentration in the aqueous phase. Inspired by recent theoretical work on point charges at dielectric interfaces, which we explain is relevant here, we show that a screened 1/r^2 term can also be used to fit our data. Finally, we present measurements for PMMA-PHSA particles at a water-oil interface. These suggest that, for PMMA-PHSA particles, there is an additional contribution to the interaction potential. This is in line with our optical-tweezer measurements for PMMA-PHSA colloids in bulk oil, which indicate that they are slightly charged.
DOI: 10.7488/ds/2873
title: Horizontal window informal settlement fire experiment (Test 13)

description: This dataset presents Test 13. Different from Baseline experiment, the window width has been increased, and the other conditions are totally the same with Baseline.
DOI: 10.7488/ds/2243
title: Structural basis for DNA 3'-end processing by human Tyrosyl-DNA phosphodiesterase 1

description: Tyrosyl-DNA phosphodiesterase (Tdp1) is a DNA 3'-end processing enzyme that repairs topoisomerase 1B-induced DNA damage. We use a new tool combining site-specific DNA-protein cross-linking with mass spectrometry to identify Tdp1 interactions with DNA. A conserved phenylalanine (F259) of Tdp1, required for efficient DNA processing in biochemical assays, cross-links to defined positions in DNA substrates. Crystal structures of Tdp1-DNA complexes capture the DNA repair machinery after 3'-end cleavage; these reveal how Tdp1 coordinates the 3'-phosphorylated product of nucleosidase activity and accommodates duplex DNA. A hydrophobic wedge splits the DNA ends, directing the scissile strand through a channel towards the active site. The F259 side-chain stacks against the -3 base pair, delimiting the junction of duplexed and melted DNA, and fixes the scissile strand in the channel. Our results explain why Tdp1 cleavage is non-processive and provide a molecular basis for DNA 3'-end processing by Tdp1.
description: Most of the data files are mass spectrometry datasets which are organised according to the figure panels in the manuscript that they feed into. ## Zip files ## The .zip files contain .d directories in Bruker format, produced by mass spectrometry equipment; these directories (once unzipped) can be opened using Bruker DataAnalysis, which is commercial software widely used by mass spectrometry research groups. ### Figure 3C + D ### * For control oligo - Filename: "Hei62-3 trunk H263A xlink_RG6_01_3508.d.zip" * For -2 5IdU oligo - Filename: "Hei66-4 trunk H263A xlink_RG7_01_3491.d.zip" * For -3 5IdU oligo - Filename: "Hei77-1 trunk H263A xlink_RG8_01_3495.d.zip" ### Figure 3E ### * For control oligo - Filename: "Hei62A16_000001.d.zip" * For -2 5IdU oligo - Filename: "Hei66A16_000001.d.zip" * For -3 5IdU oligo - Filename: "Hei77A 16_000002.d.zip" ### Figure 3F ### * For -2 5IdU oligo - Filename: "Hei66A16 iso 740 cid 20 V_000002.d.zip" * For -3 5IdU oligo - Filename: "Hei77A 16 iso 740 cid 20V_000001.d.zip" ## Image files ## In addition there are a few image files, again organised by figure panel: ### Figure 3B ### * Upper panel - Filename: "ff161214 Gels 1-2-3-4.png" * Lower panel - Filename: "ff161214 Coomassie.JPG" ### Figure 6B ### * "Figure 6B.png" (image file derived from ff020715.gel) * "ff020715.gel" (Original ImageQuant file, used for quantitation of data)
DOI: 10.7488/ds/2260
title: Code and data accompanying "Cell geometry across the ring structure of Sitka Spruce"

description: Micro computed x-ray tomography scans of Sitka spruce wood at two scales: one overview scan of three 7mm by 7mm by 70mm specimens with a voxel size of 52.7 micron, showing the ring structure of the wood, and seven scans of smaller parts of those specimens with voxel sizes ranging from 1.05 micron to 2.49 micron, showing the geometry of the cells. The location of each high resolution scan is identified within the overview scan to allow comparison and correlation of the data at these two scales. # Funding # The depositor would like to acknowledge the following support: * Leverhulme Trust Programme Grant: ’Natural Material Innovation’; * EPSRC Grant No. EP/M028267/1: The Advanced Imaging of Materials (AIM) facility.
description: # File listing # (1) "Readme.txt" - documentation (2) "LargeScale_Locations.mat" - 'LargeScale' array is the overview scan as a 3D uint8 array at 52.7 micron resolution, and 'Specimen...' are 3D logical arrays indicating the location of each sub-specimen. (3) "Specimen X Number X.zip" - Each of these zip files contains: * 'Header.txt' - Details of the scan, including resolution in microns * 'scandata.mat' - A 3D uint8 array of the subspecimen scan * 'segment.m' - A script to binarize, smooth and segment the scan data, giving a 3D array with each cell identified by an index number (may be 'segmentearly.m' and 'segmentlate.m' for scans with a hard transition between earlywood and latewood).
DOI: 10.7488/ds/2438
title: Open prediction of polysaccharide utilisation loci (PUL) in 5414 public Bacteroidetes genomes using PULpy

description: Polysaccharide utilisation loci (PUL) are regions within the genomes of Bacteroidetes that encode all the necessary machinery for the cleavage of particular carbohydrates. Prediction of PUL from genomic data alone involves the identification of carbohydrate-active enzymes (CAZymes) co-localised with susCD gene pairs. Here we present the open prediction of PUL in 5414 public Bacteroidetes genomes, and an open-source pipeline to reproduce or extend the results. The PULpy code "Open prediction of Polysaccharide Utilisation Loci (PUL)" can be obtained via GitHub as documented in the attached README.txt file.
description: samples.tsv describes the 5414 genomes used in the analysis all.pul.tsv is a data table providing one row of information for each gene within each PUL prediction sum.pul.tsv is a data table providing one row of information for each PUL
DOI: 10.7488/ds/2608
title: Alkyne-tagged PLGA allows direct visualisation of nanoparticles in vitro and ex vivo by stimulated Raman scattering microscopy

description: Polymeric nanoparticles (NPs) are attractive candidates for the controlled and targeted delivery of therapeutics in vitro and in vivo. However, detailed understanding of the uptake, location and ultimate cellular fate of the NPs is necessary in order to satisfy safety concerns, which is difficult because of the nanoscale size of these carriers. In this work, we show how small chemical labels can be appended to poly(lactic acid-co-glycolic acid) (PLGA) in order to synthesise NPs that can then be imaged by stimulated Raman scattering (SRS) microscopy, a vibrational imaging technique which can elucidate bond specific information in biological environments, such as the identification of alkyne signatures in modified PLGA terpolymers. We show that both deuterium and alkyne labelled NPs can be imaged within primary rat microglia, and the alkyne NPs can also be imaged ex vivo cortical mouse brain tissue. Immunohistochemical analysis confirms that the NPs localize in microglia in the mouse brain tissue, demonstrating that these NPs have the potential to deliver therapeutics selectively to microglia.
DOI: 10.7488/ds/2732
title: ECA Casting Workshop

description: A Scan of Edinburgh College of Art Casting Workshop, 2 Scan locations, captured with a BLK 360, registered using Autodesk Recap Pro, exported to .e57 file format.
DOI: 10.7488/ds/2324
title: Understanding the adsorption process in ZIF-8 using high pressure crystallography and computational modelling

description: Supporting data for our publication "Understanding the adsorption process in ZIF-8 using high pressure crystallography and computational modelling' to be published in Nature Comm.
DOI: 10.7488/ds/2627
title: Experimental Data of a Floating Cylinder in a Wave Tank – Comparison Solid and Water Ballast

description: The experimental set-up allows for the comparison of two different ballast options of a floating cylinder in a wave tank. Four different internal water drafts are tested as well as an equivalent solid ballast option. The model is excited by regular waves which are characterised with five wave gauges in front of the floating cylinder and two behind. Additionally, the time series of the six-degree of freedom response of the floating structure is made available. Regular waves with an initial amplitude of 0.05 m and frequencies over the range 0.3 to 1.1 Hz are investigated. This results in a wide range of different responses of the floating structure as well as very big rotations of up to 20 degrees. This data-set allows for identification of the influence caused by the sloshing of the interior water volume and can be used to validate numerical models of fluid-structure-fluid interaction. 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/2612
title: Genetic and epigenetic architectures of neurological protein biomarkers in the Lothian Birth Cohort 1936 - GWAS Proteins

description: Data supporting the paper Hillary, R et al. "Genome and epigenome wide studies of neurological etc" https://doi.org/10.1038/s41467-019-11177-x . Specifically: GWAS proteins (Genome Wide Association Study).
DOI: 10.7488/ds/2466
title: Complex cation and spin orders in the high pressure ferrite CoFe3O5

description: Data are for the paper 'Complex cation and spin orders in the high pressure ferrite CoFe3O5' by Ka. Hong et al, Inorg. Chem. (2018) Details of the files are in README.txt
DOI: 10.7488/ds/2766
title: Conceptual risk model for fire risk in informal settlements of Cape Town

description: This dataset contains fire risk data for informal settlements in Cape Town, South Africa. The geographic dataset in shapefile format consists of polygons of informal settlements in the City of Cape Town with attributable risk metrics. The risk metrics were calculated from the dwelling outline dataset also available in this collection (available at https://datashare.is.ed.ac.uk/handle/10283/3560). The aerial photography from which the digitised dwelling outlines were produced was captured in February 2018 and thus the shapefile of informal settlement fire risk captured conditions of settlements for February 2018. The dataset is also presented in table format (.xlsx, .pdf, .csv) for use in a non-GIS workspace. 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/2381
title: Single-cell bacterial electrophysiology reveals mechanisms of stress induced damage - Butanol
title: Figure 3

description: Dataset supporting Figure 3 of the paper "Single-cell bacterial electrophysiology reveals mechanisms of stress induced damage" (E. Krasnopeeva et al, 2018). Recording of the motor speed of the E.coli cells treated with 5 different concentrations of butanol in MM9 medium or PBS buffer. The motor speed is recorded for 2~min, then 20 ul of MM9 (or PBS) supplemented with a given concentration of butanol is flushed into the tunnel-slide. The shock motor speed is recorded for 10 min, followed by a flush back into MM9 (or PBS). Postshock speed is recorded for 5 min. The motor speed recording is uninterrupted for the duration of the experiment (total of 17 min). The data are raw (X,Y) voltages from the position sensitive detector sampled at 10 kHz frequency as decribed in the Methods section of the paper. The archive contains folders named "MM9" and "PBS" denoting the medium used in the experiments, each of which containing folders named according to the butanol concentration used for the treatment. Each .txt file contains a recording of an individual cell motor speed. Additional DataShare items related to this paper can be accessed: https://doi.org/10.7488/ds/2382, https://doi.org/10.7488/ds/2383, https://doi.org/10.7488/ds/2567.
DOI: 10.7488/ds/2382
title: Single-cell bacterial electrophysiology reveals mechanisms of stress induced damage - Indole
title: Figure 1 and 2

description: Data supporting figures 1 and 2 of the paper "Single-cell bacterial electrophysiology reveals mechanisms of stress induced damage". Text files contain the (x,y) voltages recieved from the position sensitive detector with 10 kHz frequency (see Materials and Methods section of the paper). Fig 1.txt supports figure 1C and contains an E. coli motor speed recording in MM9 medium when no stress is applied. Indole.zip archive supports Figure 2 and contains motor speed recordings during treatment with different indole concentrations. The motor speed is recorded for 2 min, then 20 ul of MM9 supplemented with a given concentration of indole is flushed into the tunnel-slide. The shock motor speed is recorded for 10 min, followed by a flush back into MM9 medium. Postshock speed is recorded for 5 min. The motor speed recording is uninterrupted for the duration of the experiment (total of 17 min). Folders in the archive are named according to the indole concentration used for the treatment, each text file correspond to an individual cell. Additional DataShare items related to this paper can be accessed: https://doi.org/10.7488/ds/2381, https://doi.org/10.7488/ds/2383, https://doi.org/10.7488/ds/2567.
DOI: 10.7488/ds/2383
title: Single-cell bacterial electrophysiology reveals mechanisms of stress induced damage - Light
title: Figure 4

description: Dataset supporting figure 4 of the paper "Single-cell bacterial electrophysiology reveals mechanisms of stress induced damage" (Krasnopeeva et al, 2018). The archive contains folders named "MM9" and "PBS" denoting the medium used for the experiment. Each of the two contains folder named according to the effective power applied to the cells. Each text file corresponds to a single cell and contains (x,y) voltages recieved from the position sensitive detector at 10 kHz frequency. Photodamage experiments are performed as follows: using the flow-cell MM9 or PBS is constantly supplied at 10 ul/min rate with a syringe pump. Cells are sequentially exposed to the light of 395~nm and 475~nm wavelength. Speed recording starts simultaneously with the light exposure. 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/2567.
DOI: 10.7488/ds/2574
title: Co-emergence of magnetic order and structural fluctuations in magnetite

description: Data are to accompany the publication 'Co-emergence of magnetic order and structural fluctuations in magnetite' by G. Perversi et al, Nature Communications 2019. Data are; .dat files, intensity vs. two theta for input into standard Rietveld programs such as Fullprof. .gr files, PDFs generated from above files, suitable for standard PDF analysis packages. Low temperature data are in Cryo directory. High temperature data are in Furnace directory. Background .dat files are in Backgrounds directory. Temperatures of datasets are shown in the filenames.
DOI: 10.7488/ds/2778
title: Global burden of respiratory infections associated with seasonal influenza in young children in 2018: a systematic review and modelling study

description: # Background # Seasonal influenza virus is a common cause of acute lower respiratory infection (ALRI) in young children. In 2008, we estimated that 20 million influenza-virus-associated ALRI and 1 million influenza-virus-associated severe ALRI occurred in children under 5 years globally. Despite this substantial burden, only a few low-income and middle-income countries have adopted routine influenza vaccination policies for children and, where present, these have achieved only low or unknown levels of vaccine uptake. Moreover, the influenza burden might have changed due to the emergence and circulation of influenza A/H1N1pdm09. We aimed to incorporate new data to update estimates of the global number of cases, hospital admissions, and mortality from influenza-virus-associated respiratory infections in children under 5 years in 2018. # Methods # We estimated the regional and global burden of influenza-associated respiratory infections in children under 5 years from a systematic review of 100 studies published between Jan 1, 1995, and Dec 31, 2018, and a further 57 high-quality unpublished studies. We adapted the Newcastle-Ottawa Scale to assess the risk of bias. We estimated incidence and hospitalisation rates of influenza-virus-associated respiratory infections by severity, case ascertainment, region, and age. We estimated in-hospital deaths from influenza virus ALRI by combining hospital admissions and in-hospital case-fatality ratios of influenza virus ALRI. We estimated the upper bound of influenza virus-associated ALRI deaths based on the number of in-hospital deaths, US paediatric influenza-associated death data, and population-based childhood all-cause pneumonia mortality data in six sites in low-income and lower-middle-income countries. # Findings # In 2018, among children under 5 years globally, there were an estimated 109·5 million influenza virus episodes (uncertainty range [UR] 63·1–190·6), 10·1 million influenza-virus-associated ALRI cases (6·8–15·1); 870 000 influenza-virus-associated ALRI hospital admissions (543 000–1 415 000), 15 300 in-hospital deaths (5800–43 800), and up to 34 800 (13 200–97 200) overall influenza-virus-associated ALRI deaths. Influenza virus accounted for 7% of ALRI cases, 5% of ALRI hospital admissions, and 4% of ALRI deaths in children under 5 years. About 23% of the hospital admissions and 36% of the in-hospital deaths were in infants under 6 months. About 82% of the in-hospital deaths occurred in low-income and lower-middle-income countries. # Interpretation # A large proportion of the influenza-associated burden occurs among young infants and in low-income and lower middle-income countries. Our findings provide new and important evidence for maternal and paediatric influenza immunisation, and should inform future immunisation policy particularly in low-income and middle-income countries.
DOI: 10.7488/ds/2756
title: Experimental data for the article "Predictable Properties of Fitness Landscapes Induced by Adaptational Tradeoffs"
title: Inhibition curves of sensitive and resistant E. coli mutants at different concentrations of ciprofloxacin

description: We used strains from Marcusson et al. (2009) (courtesy of Douglas Huseby and Diarmaid Hughes). The strains are isogenic derivatives of MG1655, a K12 strain of the bacterium E. coli, with specific point mutations or gene deletions in five different loci: gyrA:S83L, gyrA:D87N, parC:S80I, ΔmarR, and ΔacrR. There are 32 possible combinations of these alleles, but we only used the wild type, single mutants (5 strains) and double mutants (8 strains of 10 possible combinations): LM179 (00000), LM378 (10000), LM534 (01000), LM792 (00100), LM202 (00010), LM351 (00001), LM625 (11000), LM862 (10100), LM421 (10010), LM647 (10001), LM1124 (01100), LM538 (01010), LM592 (01001), LM367 (00011). A binary sequence after the strain’s name represents the presence/absence of a particular mutated allele (order as in the above list of genetic alterations). Reference: Marcusson, Linda L., Niels Frimodt-Møller, and Diarmaid Hughes. "Interplay in the selection of fluoroquinolone resistance and bacterial fitness." PLoS pathogens 5.8 (2009).