cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2944
title: Cornea resistance factor GWAS in the UK Biobank

description: Summary statistics from the genome-wide association study (GWAS) of cornea resistance factor (CRF) of 76,029 UK Biobank samples of British ancestry obtained through the application number 19655. The CRF analysis was performed on the average of the left and right eye measurements. Any outliers (i.e. CRF greater than population mean difference + 3 standard deviations) were removed. Further phenotypic filtering was applied by removing samples linked to, or self-reporting, ocular conditions that could affect the measurements accuracy such as eye surgery, refractive laser surgery, cataract surgery, glaucoma high pressure surgery or laser treatment, corneal graft surgery, eye injury , keratoconus or cornea disorders. A total of 102490 samples were kept. Using the genetic quality control of the UK Biobank the 76318 samples of British ancestry with imputed data failing heterozygosity or/and missingness, or having a mismatch between self-reported and genotype-derived gender or showing putative sex chromosome aneuploidy as well as individuals who have withdrawn from the study at the time of analysis were removed. An total of N-76029 were included in the GWAS. The GWAS was performed on common and low-frequency (MAF &gt; 0.5%) well imputed (INFO &gt; 0.6) variants using a linear mixed model accounting for population structure and (cryptic) relatedness, implemented in the software BOLT_LMM v1.3. Covariates fitted in the model were: age, sex, assessment centre, genotyping array, genotyping batch and the 20 first principal components of ancestry provided by the UK Biobank.
description: The dataset enclose gwas summary statistic with the following fields: SNP: variant rsID or chr:bp_allele1_allele0 CHR: chromosome BP: genome position (bp) ALLELE1: effect allele ALLELE0: non effect allele A1FREQ: effect allele frequency BETA: effect SE: effect standard error P_BOLT_LMM: association pvalue
DOI: 10.7488/ds/2100
title: Potentially serious incidental findings on brain and body magnetic resonance imaging conducted among apparently healthy adults: a systematic review and meta-analysis

description: Data related to manuscript titled 'Potentially serious incidental findings on brain and body magnetic resonance imaging conducted among apparently healthy adults: a systematic review and meta-analysis'.
DOI: 10.7488/ds/2422
title: Supplemental materials: ALS-specific cognitive and behavior changes associated with advancing disease stage in ALS

description: These files are supplemental tables and figures for the following open access publication: Crockford et al., (2018) ALS-specific cognitive and behavior changes associated with advancing disease stage in ALS. Neurology. 91:1-11. doi:10.1212/WNL.0000000000006317 Please refer to this publication in interpreting the dataset.
DOI: 10.7488/ds/147
title: A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci

description: Background Chromatin structure at a given site can differ between chromosome copies in a cell, and such imbalances in chromatin structure have been shown to be important in understanding the molecular mechanisms controlling several disease loci. Human genetic variation, DNA methylation, and disease have been intensely studied, uncovering many sites of allele-specific DNA methylation (ASM). However, little is known about the genome-wide occurrence of sites of allele-specific histone modification (ASHM) and their relationship to human disease. The aim of this study was to investigate the extent and characteristics of sites of ASHM in human embryonic stem cells (hESCs). Results Using a statistically rigorous protocol, we investigated the genomic distribution of ASHM in hESCs, and their relationship to sites of allele-specific expression (ASE) and DNA methylation. We found that, although they were rare, sites of ASHM were substantially enriched at loci displaying ASE. Many were also found at known imprinted regions, hence sites of ASHM are likely to be better markers of imprinted regions than sites of ASM. We also found that sites of ASHM and ASE in hESCs colocalize at risk loci for developmental syndromes mediated by deletions, providing insights into the etiology of these disorders. Conclusion These results demonstrate the potential importance of ASHM patterns in the interpretation of disease loci, and the protocol described provides a basis for similar studies of ASHM in other cell types to further our understanding of human disease susceptibility.
description: 1756-8935-5-6-s1.xls: Number of mapped reads for each dataset used in this study. 1756-8935-5-6-s1.xls: Read counts for each allele and each histone modification at the sites of ASHM identified in this study. 1756-8935-5-6-s1.xls: Sites of ASHM and their distance to corresponding annotations. 1756-8935-5-6-s4.pdf: Location of ASE and ASHM sites at the 17q12 locus. 1756-8935-5-6-s5.xls: H1 Bisulfite sequencing dataset comparison. 1756-8935-5-6-s6.xls: Datasets used in this analysis. 1756-8935-5-6-s5.pdf: Description of method for calling sites of ASHM. 1756-8935-5-6-s5.pdf: ASHM site quality control (A) Coverage of Bisulfite sequencing reads across the whole genome and at sites of ASHM only. 0.26% of sites in the whole genome analysis had coverages of greater than 100, but these have been excluded from this plot. The mean coverage at sites of ASHM was 23x as opposed to the genome-wide mean coverage of 32 x. (B) Hardy-Weinberg equilibrium (HWE) P-values at 54 ASHM site polymorphisms (i.e. before HWE filtering) and at all high-coverage sites.
DOI: 10.7488/ds/236
title: Preservation status of Knowledge Base+ packages

description: An analysis of how well packages described in Jisc KB+ are preserved by archiving agencies, as measured by The Keepers Registry.
description: See README
DOI: 10.7488/ds/82
title: Visual and Linguistic Treebank

description: The Visual and Linguistic Treebank is a data set of images annotated with human-written descriptions, object boundaries, and Visual Dependency Representations. The images are freely available from the Action Recognition Task in the PASCAL VOC 2010 data set; our annotations are available for only the trainval data. Descriptions are available for all 2,424 images in the trainval data, and object annotations and Visual Dependency Representations are available for a subset of 341 images.
description: N.B. the URL where the source PASCAL images may be obtained was changed. To provide the new URL, a new version of the readme file, "README_v2.md" was added to this item.
DOI: 10.7488/ds/162
title: Refractive indices (500-3500 cm-) and emissivity (600-3350 cm-1) of pure water and seawater

description: Tables of infrared refractive indices have been compiled and calculations made of emissivity for pure water and seawater (35 PSU), suitable for radiative transfer simulation of observations of thermal imagers, such as the series of Along Track Scanning Radiometers. The refractive indices are tabulated as a function of wave number (500–3500 cm-1) and temperature (274, 287, and 300 K). The emissivities are tabulated as a function of wave number (600–3350 cm-1), view angle (0–85°), temperature (270–310 K), and wind speed (0–25 m s-1 at 12.5 m).
description: Dataset is documented in the file 'readme'. Files in dataset are: ARCForwardEmissivityPureWater.nc, ARCForwardEmissivitySeawater.nc, ARCNadirEmissivityPureWater.nc, ARCNadirEmissivitySeawater.nc, ARCWideangleEmissivityPureWater.nc, ARCWideangleEmissivitySeaWater.nc, nk274_287_300_purewater.txt, nk274_287_300_seawater.txt, nk3Sigma.txt, readme
DOI: 10.7488/ds/274
title: Experiment materials for "Disfluencies in change detection in natural, vocoded and synthetic speech."

description: The current dataset is associated with the DiSS paper "Disfluencies in change detection in natural, vocoded and synthetic speech." In this paper we investigate the effect of filled pauses, a discourse marker and silent pauses in a change detection experiment in natural, vocoded and synthetic speech. In natural speech change detection has been found to increase in the presence of filled pauses, we extend this work by replicating earlier findings and explore the effect of a discourse marker, like, and silent pauses. Furthermore we report how the use of "unnatural" speech, namely synthetic and vocoded, affects change detection rates.
DOI: 10.7488/ds/101
title: IRI-Scotland Technical Staff survey

description: IRIS Technical Staff survey:Survey Overview. Number of respondents: 12 Expected number of respondents: 20 Response rate: 60.0% Launch date: 26 Apr 2006 Close date: 28 May 2006
description: The IRI-Scotland project (http://www.iriscotland.lib.ed.ac.uk/) carried out a series of online questionnaires in 2006 to assess the attitudes towards open access and institutional repositories within the higher education community in Scotland. In total, three questionnaires were targeted at different stakeholder groups within the community - academic authors, technical staff responsible for repository development, and senior management from academic libraries. The second IRI-Scotland survey was targeted at technical staff, usually based in academic libraries or aligned information services support groups, who would be responsible for developing a digital repository in their institution. The questions were aimed to help determine the functional requirements needed to build a national hosted repository service that would be suitable for the current and future repository infrastructure in Scotland. We present here anonymous data from the technical staff survey in comma separated value format.
DOI: 10.7488/ds/294
title: Particle-size effects in the formation of bicontinuous Pickering emulsions

description: We demonstrate that the formation of bicontinuous emulsions stabilized by interfacial particles (bijels) is more robust when nanoparticles rather than microparticles are used. Emulsification via spinodal demixing in the presence of nearly neutrally wetting particles is induced by rapid heating. Using confocal microscopy, we show that nanospheres allow successful bijel formation at heating rates two orders of magnitude slower than is possible with microspheres. In order to explain our results, we introduce the concept of mechanical leeway i.e. nanoparticles benefit from a smaller driving force towards disruptive curvature. Finally, we suggest that leeway mechanisms may benefit any formulation in which challenges arise due to tight restrictions on a pivotal parameter, but where the restrictions can be relaxed by rationally changing the value of a more accessible parameter.
DOI: 10.7488/ds/102
title: IRI-Scotland senior management survey

description: IRIS senior management survey: Survey Overview Number of respondents: 25 Expected number of respondents: 35 Response rate: 71.4% Launch date: 15 Mar 2006 Close date: 25 Apr 2006
description: The IRI-Scotland project (http://www.iriscotland.lib.ed.ac.uk/) carried out a series of online questionnaires in 2006 to assess the attitudes towards open access and institutional repositories within the higher education community in Scotland. In total, three questionnaires were targeted at different stakeholder groups within the community – academic authors, technical staff responsible for repository development, and senior management from academic libraries. The third IRI-Scotland survey was targeted at senior management with the intent to identify the level of repository adoption in the community, assess policies relating to open access, and to identify suitable institutional contacts for the project. We present here anonymous data from the senior management survey in comma separated value format.
DOI: 10.7488/ds/1306
title: Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

description: The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the observed interactions are still largely obscure. We present a polymer modelling scheme based on the assumption that chromosome architecture is maintained by protein bridges which form chromatin loops. To test the model we perform FISH experiments and also compare with Capture-C data. Starting merely from the locations of protein binding sites, our model accurately predicts the experimentally observed chromatin interactions, revealing a population of 3D conformations.
description: Experimental data sets, simulation data sets and files used to perform simulations are provided in gzipped tarballs. The README gives brief details of each zipped file, and each of these contains a further README with full details.
DOI: 10.7488/ds/257
title: Superseded - Human vs Machine Spoofing

description: This Item has been replaced. Please see Wester, M; Wu, Z; Yamagishi, J. (2015). Human vs Machine Spoofing, [dataset]. University of Edinburgh. https://doi.org/10.7488/ds/258.
DOI: 10.7488/ds/1507
title: Human tau increases amyloid beta plaque size but not amyloid beta-mediated synapse loss in a novel mouse model of Alzheimer’s disease: Data set from Jackson et al 2016 EJN

description: Alzheimer’s disease is characterized by the presence of aggregates of amyloid beta (Aβ) in senile plaques and tau in neurofibrillary tangles, as well as marked neuron and synapse loss. Of these pathological changes, synapse loss correlates most strongly with cognitive decline. Synapse loss occurs prominently around plaques due to accumulations of oligomeric Aβ. Recent evidence suggests that tau may also play a role in synapse loss but the interactions of Aβ and tau in synapse loss remain to be determined. In this study, we generated a novel transgenic mouse line, the APP/PS1/rTg21221 line, by crossing APP/PS1 mice, which develop Aβ-plaques and synapse loss, with rTg21221 mice, which overexpress wild-type human tau. When compared to the APP/PS1 mice without human tau, the cross-sectional area of ThioS+ dense core plaques was increased by ~50%. Along with increased plaque size, we observed an increase in plaque-associated dystrophic neurites containing misfolded tau, but there was no exacerbation of neurite curvature or local neuron loss around plaques. Array tomography analysis similarly revealed no worsening of synapse loss around plaques, and no change in the accumulation of Aβ at synapses. Together, these results indicate that adding human wild-type tau exacerbates plaque pathology and neurite deformation but does not exacerbate plaque-associated synapse loss. This dataset includes data associated with this manuscript along with custom analysis macros. The raw images are too large to upload to our limited repository system, at over 300 GB total, but are available upon request tara.spires-jones@ed.ac.uk
DOI: 10.7488/ds/1577
title: SUPERSEDED - Tidal turbine model external geometry CAD files

description: ## THIS ITEM HAS BEEN REPLACED BY THE ONE AT http://datashare.is.ed.ac.uk/handle/10283/2356 . ## Laboratory testing of tidal turbine models is an essential tool to investigate hydrodynamic interactions between turbines and the flow. Such tests can be used to calibrate numerical models and to estimate rotor loading and wake development to inform the design of full scale machines and array layout. These CAD files provide the outer geometry of a highly instrumented turbine model developed as part of the X-MED project funded by the EPSRC (EP/ J010235/1). The model has a 1.2m diameter, three bladed horizontal axis rotor and is bottom mounted. These two STL files provide the external geometry of a tidal turbine model. Nacelle_and_tower.stl corresponds to the stationary part and rotor.stl is the rotating part, including the blades.
DOI: 10.7488/ds/1485
title: Gene trees for orthologous groups from "The evolution of nitrogen fixation in cyanobacteria"

description: Phylogenetic trees for the orthologous groups predicted across 49 taxa of Cyanobacteria and 16 Proteobacteria by Latysheva et al. (2012, Bioinformatics 28:603-606; doi:10.1093/bioinformatics/bts008) are provided here. For the 13854 groups containing at least three protein sequences, phylogenies were reconstructed as follows. Multiple alignment of protein sequences was performed using MAFFT (Katoh and Toh 2008, doi:10.1093/bib/bbn013), in "E-INS-I" mode with 1000 iterations. A phylogenetic model was selected for each protein multiple alignment by the Bayesian Information Criterion in MODELGENERATOR (Keane et al. 2006, doi:10.1186/1471-2148-6-29), with four Gamma-distributed rate categories for "+G" models. 200 bootstrap replicates of the multiple alignment were generated using seqboot in the PHYLIP package (Felsenstein, J. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle). Using the selected model, phylogeny was reconstructed by maximum likelihood with PhyML (Guindon et al. 2010, doi:10.1093/sysbio/syq010), both for the original alignment and for the bootstrap replicates.
description: mltrees.zip: 13584 unrooted ML trees in PHYLIP format. The start of each filename gives the orthologous group number. Tip labels in trees consist of the protein accession, followed by an underscore, then the three-letter abbreviation for the taxon. Orthologous group numbers and taxon abbreviations are as in Latysheva et al. (2012, 10.1093/bioinformatics/bts008). bstrees.zip: 13584 bootstrap samples, each of 200 trees, in PHYLIP format. The start of each filename gives the orthologous group number. Tips are labelled as in mltrees.zip.
DOI: 10.7488/ds/286
title: Towards a unified description of the rheology of hard-particle suspensions

description: The rheology of suspensions of Brownian, or colloidal, particles (diameter~$d \lesssim 1~\mu$m) differs markedly from that of larger grains ($d \gtrsim 50~\mu$m). Each of these two regimes has been separately studied, but the flow of suspensions with intermediate particle sizes ($1~\mu\textrm{m} \lesssim d \lesssim 50~\mu$m), which occur ubiquitously in applications, remains poorly understood. By measuring the rheology of suspensions of hard spheres with a wide range of sizes, we show experimentally that shear thickening drives the transition from colloidal to granular flow across the intermediate size regime. This insight makes possible a unified description of the (non-inertial) rheology of hard spheres over the full size spectrum. Moreover, we are able to test a new theory of friction-induced shear thickening, showing that our data can be well fitted using expressions derived from it.
DOI: 10.7488/ds/1503
title: Preprocessed gene trees from "Xenolog Classification"

description: Preprocessed gene trees from 49 taxa of Cyanobacteria and 16 Proteobacteria used by Darby et al. (2017, Bioinformatics 33:640-649; doi:10.1093/bioinformatics/btw686) are provided here. These consist of trees for 13623 of the gene families of Latysheva et al. (2012, doi:10.1093/bioinformatics/bts008). Using Notung-2.8.1.7 (Stolzer et al. 2012, doi:10.1093/bioinformatics/bts386), unrooted trees with bootstrap support (out of 200; doi:10.7488/ds/1485) were preprocessed with the following steps: (1) root with DTL (duplication, transfer, loss) model --costdup 3 --costtrans 2.5 --costloss 2; (2) rearrange with DL model --costdup 3 --costloss 2 --threshold 90%; (3) reroot with DTL model --costdup 3 --costtrans 2.5 --costloss 2. Both zip files contain the output from this pipeline. The Newick format trees reflect the tree topology after this process. The Notung format trees also include the reconciliation, and other meta data. The Notung format is described in detail in Appendix A (File Formats) of the Notung manual (http://www.cs.cmu.edu/~durand/Notung). ## Acknowledgment ## This work was funded by the National Science Foundation grant DBI-1262593. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
description: alltreesNewick.zip: 13623 preprocessed trees in Newick format. The start of each filename gives the orthologous group number. Tip labels in trees consist of the protein accession, followed by an underscore, then the three-letter abbreviation for the taxon. Orthologous group numbers and taxon abbreviations are as in Darby et al. (2016, "Xenolog classification", Bioinformatics, submitted) and Latysheva et al. (2012, 10.1093/bioinformatics/bts008). alltreesNotung.zip: 13623 preprocessed trees in Notung format. The start of each filename gives the orthologous group number. Tips are labelled as in alltreesNewick.zip.
DOI: 10.7488/ds/1359
title: Mn2MnReO6 ChemComm2016

description: Structural and magnetic data for Mn2MnReO6, supporting a paper submitted to Chemical Communications.
DOI: 10.7488/ds/1982
title: Matlab codes for "Refined Composite Multiscale Dispersion Entropy and its Application to Biomedical Signals"

description: Multiscale entropy (MSE) is a widely-used tool for the analysis of biomedical signals. It was proposed to overcome the deficiencies of conventional entropy methods when quantifying the complexity of time series. However, MSE is undefined for very short signals and slow for real-time applications as a result of using sample entropy (SampEn). To overcome these shortcomings, we introduce multiscale dispersion entropy (DisEn - MDE) as a very fast and powerful method to quantify the complexity of signals. MDE is based on our recently developed DisEn, which has a computation cost of O(N), compared with O(N^2) for SampEn. We also propose the refined composite MDE (RCMDE) to improve the stability of MDE. We evaluate MDE, RCMDE, and refined composite MSE (RCMSE) on synthetic signals and find that these methods show similar results but the MDE and RCMDE are significantly faster than MSE and RCMSE, respectively. The results also show that RCMDE is more stable than MDE and RCMSE for short and noisy signals, which are common in biomedical applications. To evaluate the proposed methods on real signals, three biomedical datasets, including focal and non-focal electroencephalograms (EEGs), blood pressure recordings in Fantasia database, and resting-state EEGs activity in Alzheimer's disease, are used. The results again show similar trends of RCMSE, MDE, and RCMDE, although the RCMDE and MDE are significantly faster and lead to larger differences between physiological conditions known to alter the complexity of the physiological recordings. To sum up, MDE and RCMDE are expected to be useful for the analysis of physiological signals thanks to their ability to distinguish different types of dynamics. The Matlab codes used in this paper are freely available here.
DOI: 10.7488/ds/248
title: UK Statutory Instruments
title: uk_statutoryinstruments

description: This dataset contains all national level UK statutory instruments from 1987 to 2008 coded according to the Comparative Agendas Project (CAP) content coding scheme (www.comparativeagendas.info). The data is a pilot of the project "Bureaucratic Agendas: The Responsiveness of Secondary Legislation in a Comparative Perspective" that is currently being developed (see http://sbevan.com/projects--data.html). Please cite the following article when using this data: Bevan, Shaun. 2015. “Bureaucratic Responsiveness: The Effects of Government, Public and European Attention on the UK Bureaucracy.” Public Administration, 93(1): 139-158. (doi: 10.1111/padm.12113).