cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2741
title: St Cecilias Concert Hall

description: A Scan of the Concert Hall at St. Cecilia's Hall, 13 Scan locations, captured with a BLK 360, registered using Autodesk Recap Pro, exported to .e57 file format.
DOI: 10.7488/ds/2818
title: Multi-method genome and epigenome wide studies of inflammatory protein levels in healthy older adults - Linear Regression EWAS Proteins

description: This dataset represents one of five datasets which correspond to the study: "Multi-method genome and epigenome wide studies of inflammatory protein levels in healthy older adults". These datasets represent association studies on the levels of the same set of 70 inflammatory proteins. Each dataset represents one of five distinct methods used to perform genome-wide and epigenome-wide association studies on these protein levels. These methods are: Linear Regression GWAS, Linear Regression EWAS, OSCA EWAS, BayesR+ GWAS and BayesR+ EWAS. These analyses were performed as part of the Lothian Birth Cohort 1936 Study. This data relates to summary statistics for EWAS of 70 Olink inflammation proteins - performed by OLS regression EWAS.
DOI: 10.7488/ds/2222
title: SUPERSEDED - Hi-C genomes from "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism"

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2296. ## The cow rumen is a specialised organ adapted for the efficient breakdown of plant material into energy and nutrients, and it is largely the rumen microbiome that encodes the enzymes responsible. Many of these enzymes are of significant industrial interest. Despite this, rumen microbes are under-represented in public databases. Here we present 283 draft bacterial and archaeal genomes assembled directly from over 800 gigabases of rumen metagenomic sequence data and 43 samples, using both metagenomic binning and Hi-C-based Proximity-Guided Assembly. Comparative analysis with current publicly available genomes reveals that the majority of these represent previously unsequenced strains and species of bacteria and archaea. The genomes contain over 16,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in public databases. Inclusion of the 283 genomes presented here improves metagenomic read classification by 2-3-fold, both in our data and in other publicly available rumen datasets. This release improves the coverage of rumen microbes in the public databases, and represents a highly valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome.
DOI: 10.7488/ds/2088
title: Segmentation of the 4DL Connectome 2: YFP-H 1.3-19.3

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). This dataset is the outcome of Yellow Fluorescent Protein H (YFP-H) expression in numerous muscles of the mouse footpad. The zip archive contains subdirectories numbered according to the muscles ("1.3-3L", "8.6-2", "14.6-2" etc). The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/2089
title: Segmentation of the 4DL Connectome 3: YFP-H 9.6

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). This dataset is the outcome of Yellow Fluorescent Protein H (YFP-H) expression in muscle 9.6 of the mouse footpad. The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/2086
title: Segmentation of the 4DL Connectome 4: YFP-16, 19.8

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) the data creators performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). This dataset is the outcome of Yellow Fluorescent Protein 16 (YFP-16) expression in muscle 19.8 of the mouse footpad. This zip archive contains three subdirectories containing primary images and data on axon segmentation and endplate analysis respectively. The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/2083
title: Segmentation of the 4DL Connectome 5: YFP-16, 19.11-1L – primary images and endplate analysis

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). This dataset is the outcome of Yellow Fluorescent Protein 16 (YFP-16) expression in muscle 19.11-1L of the mouse footpad. The zip archive contains two subdirectories containing data from the endplate analysis and the primary images respectively. The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/2084
title: Segmentation of the 4DL Connectome 6: YFP-16, 19.11-1L – axon segmentation

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). This dataset is the outcome of Yellow Fluorescent Protein 16 (YFP-16) expression in muscle 19.11-1L; specifically the axon segmentation. The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/2085
title: Segmentation of the 4DL Connectome 7: YFP-16, 19.11-1R

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). This dataset is the outcome of Yellow Fluorescent Protein 16 (YFP-16) expression in muscle 19.11-1R of the mouse footpad. This zip archive contains three subdirectories containing primary images and data on axon segmentation and endplate analysis respectively. The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/2082
title: Segmentation of the 4DL Connectome 8: YFP-16, 13.9 (incomplete)

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). This dataset is the outcome of Yellow Fluorescent Protein 16 (YFP-16) expression in muscle 13.9 of the mouse footpad. This zip archive contains three subdirectories containing primary images and data on axon segmentation and endplate analysis respectively. The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/2078
title: Segmentation of the 4DL Connectome 10: CFP 14.3.11-1L

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). This dataset is the outcome of Cyan Fluorescent Protein (CFP) expression in muscle 14.3.11-1L of the mouse footpad. This zip archive contains three subdirectories containing primary images and data on axon segmentation and endplate analysis respectively. The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/2087
title: Segmentation of the 4DL Connectome 9: YFP-16, 21.9-2L (incomplete)

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). This dataset contains microscopy images which show Yellow Fluorescent Protein 16 (YFP-16) expression in muscle 21.9-2L of the mouse footpad. The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/2079
title: Segmentation of the 4DL Connectome 11: CFP 14.3.11-2R

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). This dataset is the outcome of Cyan Fluorescent Protein (CFP) expression in muscle 14.3.11-2R of the mouse footpad. This zip archive contains three subdirectories containing primary images and data on axon segmentation and endplate analysis respectively. The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/2081
title: Segmentation of the 4DL Connectome 12: Deconvolution PSFs (calibration information)

description: Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. In Hirst et al (2013) we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). The remainder of the data relating to this study can be found grouped together in the "Connectomic analysis of the mouse fourth deep lumbrical muscle connectome" DataShare Collection at http://datashare.is.ed.ac.uk/handle/10283/2657.
DOI: 10.7488/ds/2326
title: Matlab codes for "Amplitude- and Fluctuation-based Dispersion Entropy"

description: Dispersion entropy (DispEn) is a recently introduced entropy metric to quantify the uncertainty of time series. It is fast and, so far, it has demonstrated very good performance in the characterisation of time series. It includes a mapping step, but the effect of different mappings has not been studied yet. Here, we investigate the effect of linear and nonlinear mapping approaches in DispEn. We also inspect the sensitivity of different parameters of DispEn to noise. Moreover, we develop fluctuation-based DispEn (FDispEn) as a measure to deal with only the fluctuations of time series. Furthermore, the original and fluctuation-based forbidden dispersion patterns are introduced to discriminate deterministic from stochastic time series. Finally, we compare the performance of DispEn, FDispEn, permutation entropy, sample entropy, and Lempel–Ziv complexity on two physiological datasets. The results show that DispEn is the most consistent technique to distinguish various dynamics of the biomedical signals. Due to their advantages over existing entropy methods, DispEn and FDispEn are expected to be broadly used for the characterization of a wide variety of real-world time series. The Matlab codes used in this paper are freely available here.
DOI: 10.7488/ds/1405
title: Inferring time derivatives, including cell growth rates, using Gaussian processes

description: Often the time-derivative of a measured variable is of as much interest as the variable itself. For a growing population of biological cells, for example, the population’s growth rate is typically more important than its size. Here we introduce a non-parametric method to infer first and second time-derivatives as a function of time from time-series data. Our approach is based on established properties of Gaussian processes and therefore applies to a wide range of data. In tests, the method is at least as accurate as others, but has several advantages: it estimates errors both in the inference and in any summary statistics, such as lag times, allows interpolation with the corresponding error estimation, and can be applied to any number of experimental replicates. As illustrations, we infer growth rate from measurements of the optical density of populations of microbial cells and estimate the rate of in vitro assembly of an amyloid fibril and both the speed and acceleration of two separating spindle pole bodies in a single yeast cell. Being accessible through both a GUI and from scripts, our algorithm should have broad application across the sciences.
description: Data from Figures 2 and 3, see readme.txt
DOI: 10.7488/ds/2096
title: Supersaturation dependence of glycine polymorphism using laser-induced nucleation, sonocrystallization and nucleation by mechanical shock

description: The nucleation of glycine from aqueous supersaturated solution has been studied using nonphotochemical laser-induced nucleation (NPLIN), ultrasound (sonocrystallization), and mechanical shock of sample vials. It was found that at higher supersaturation, samples were more susceptible to nucleation and produced more of the γ-glycine polymorph. The results are described in terms of a mechanism common to all three nucleation methods, involving the induction of cavitation events and pressure shockwaves. The switch in preference from α- to γ-glycine was observed to occur over a narrower range of supersaturation values for NPLIN. We attribute this to induction of cavitation events with higher energies, which result in higher localized pressures and supersaturations. Experiments on NPLIN using circularly versus linearly polarized light showed no evidence for binary polarization switching control of glycine polymorphism.
description: Raw and processed data used to produce Figures and Tables in the corresponding article. Contents of files are described in the file 'README.txt'.
DOI: 10.7488/ds/2092
title: Supporting material for "Importance of the Pre-Industrial Baseline in Determining the Likelihood of Exceeding the Paris Limits"

description: During the Paris Conference in 2015, nations of the world strengthened the United Nations Framework Convention on Climate Change by agreeing to holding ‘the increase in the global average temperature to well below 2C above pre-industrial levels and pursuing efforts to limit the temperature increase to 1.5C’. However, ‘pre-industrial’ was not defined. Here we investigate the implications of different choices of the pre-industrial baseline on the likelihood of exceeding these two temperature thresholds. We find that for the strongest mitigation scenario RCP2.6 and a medium scenario RCP4.5, the probability of exceeding the thresholds and timing of exceedance is highly dependent on the pre-industrial baseline; for example, the probability of crossing 1.5C by the end of the century under RCP2.6 varies from 61% to 88% depending on how the baseline is defined. In contrast, in the scenario with no mitigation, RCP8.5, both thresholds will almost certainly be exceeded by the middle of the century with the definition of the pre-industrial baseline of less importance. Allowable carbon emissions for threshold stabilization are similarly highly dependent on the pre-industrial baseline. For stabilization at 2C, allowable emissions decrease by as much as 40% when earlier than nineteenth-century climates are considered as a baseline. # Funding # Data produced as part of the ERC funded project (EC-320691), Transition into the Anthopocene (TITAN) at the School of GeoSciences.
DOI: 10.7488/ds/2098
title: Images used to calculate the pressure dependence of the saturated methane concentration in water as a function of pressure
title: methane Water Images

description: We have measured the maximum concentration of methane dissolved in water as a function of pressure using a diamond anvil cell. These images show the sample space with regions of methane (darker) and water+methane (lighter). From the relative areas of these regions we estimated the concentration.
description: Dataset consists of images and metadata (time, temperature etc.) in the form of an open office document. Images can be cut and pasted if needed.
DOI: 10.7488/ds/2263
title: Painting with bacteria: Smart templated self assembly using motile bacteria

description: Dataset supporting the manuscript entitled 'Painting with bacteria: Smart templated self assembly using motile bacteria': External control of the swimming speed of ‘active particles’ can be used to self assemble designer structures in situ on the µm to mm scale. We demonstrate such reconﬁgurable templated active self assembly in a ﬂuid environment using light powered strains of Escherichia coli. The physics and biology controlling the sharpness and formation speed of patterns is investigated using a bespoke fast-responding strain.