cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2300
title: Optimization of sprayer for matrix application in MALDI mass spectrometry imaging

description: Successful matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) relies on the selection of the most appropriate matrix and optimization of the matrix application parameters. In order to achieve reproducible high spatial-resolution imaging data, several commercially available automated matrix application platforms have become available. However, the high cost of these commercial matrix sprayers is restricting access into this emerging research field. Here, we report an automated platform for matrix deposition, employing a converted commercially-available 3D printer ($300) and other parts commonly found in an analytical chemistry lab as a low-cost alternative to commercial sprayers. Using printed fluorescent rhodamine B microarrays and employing experimental design, the matrix deposition parameters were optimized to minimize surface analyte diffusion. Finally, the optimized matrix application method was applied to image 3-dimensional MCF-7 cell culture spheroid sections (ca. 500 µm diameter tissue samples). Using this system, we demonstrate robust and reproducible observation of endogenous metabolite distributions with high spatial resolution.
description: Datasets archived as .imzML and .ibd raw files (suitable for viewing on multiple platforms - for .imzML, some examples of free software are described at https://en.wikipedia.org/wiki/Mass_spectrometry_imaging .) 1. Imaging file of sectioned spheroids coated using the converted 3D printer without optimization of application parameters (3D_printer_No_Optimization.imzml) 2. Imaging file of sectioned spheroids coated using the converted 3D printer with optimization of application parameters (3D_printer_ Optimized.imzml) 3. Imaging file of sectioned spheroids coated using the commercial sprayer with optimization of application parameters (Commercial_Printer.imzml)
DOI: 10.7488/ds/2221
title: Ca Double Double and Double Triple Perovskites

description: Complex Ferrimagnetism and Magnetoresistance Switching in Ca-based Double Double and Triple Double Perovskites. We have used high pressures and temperatures to synthesize the cation ordered AA′BB′O6 perovskites CaMnFeReO6, CaMnMnReO6, and Ca(Mn0.5Cu0.5)FeReO6. Neutron diffraction reveals complex ferrimagnetic orders in all three materials; CaMnFeReO6 and Ca(Mn0.5Cu0.5)FeReO6 have large room temperature magnetizations with low temperature switching of magnetoresistance in the latter material, and CaMnMnReO6 displays a high coercivity of 1.3 T at low temperatures.
DOI: 10.7488/ds/1697
title: Development of an Advanced System for Automated 200 mm Wafer Mapping of Stress Using Test Structures S. Lokhandwala, J. Murray, S. Smith, A.R. Mount†, J.G. Terry, A.J. Walton

description: Controlling and understanding the stress in materials is of major importance in the successful fabrication of MEMS devices. Failure to properly account for stress related effects can lead to the substrate warping and layer delamination, both of which are detrimental to the performance and reliability of components. Hence, it is desirable to have reliable and automated technology to spatially monitor both stress and strain on silicon wafers. This paper reports in detail an integrated measurement system that has been specifically designed to semi-automatically wafer map stress, strain and Young’s modulus. The measurement system is designed to determine the rotation of a test structure automatically and then calculate the strain. Young’s modulus is then determined using a nanoindenter running customised software and the combination of the two measurements from the same location is used to calculate and map the spatial stress in the film. This data is the set used in the results presented in "Development of an Advanced System for Automated 200 mm Wafer Mapping of Stress Using Test Structures", associated with ICMTS 2017
DOI: 10.7488/ds/2050
title: Quantum and isotope effects in lithium metal
title: Computational data for "Quantum and isotope effects in lithium metal"

description: The crystal structure of elements at zero pressure and temperature is the most fundamental information in condensed matter physics. For decades it has been believed that lithium, the simplest metallic element, has a complicated ground-state structure. Using synchrotron X-ray diffraction in diamond-anvil-cells and multiscale simulations with density functional theory and molecular dynamics we show that the previously accepted martensitic ground-state is metastable. The actual ground-state is face-centered-cubic. We find that isotopes of lithium, under identical thermal paths, exhibit a large difference in martensitic transition temperature. Lithium exhibits large quantum mechanical effects, serving as a metallic intermediate between helium, with its quantum-effect-dominated structures, and the higher mass elements. By disentangling the quantum-kinetic complexities, we prove that fcc lithium is the groundstate, and we synthesize it by decompression.
DOI: 10.7488/ds/364
title: Theory of high pressure hydrogen, made simple / AIRAPT 2015 data
title: High pressure AIMD runs for hydrogen – trajectories

description: We report molecular dynamics calculations for Phase I of hydrogen which show that all the phase transitions can be understood in a classical model with simple treatment of exchange-correlation. We present code for a simple thermodynamic model of high pressure hydrogen which allows us to discuss the thermodynamics of the phase boundaries of Phase I. - This dataset includes code for extracting figures/movies in xyz format, phase diagram code in octave. The work was undertaken at the ARCHER facility at the University of Edinburgh.
DOI: 10.7488/ds/2005
title: Scenarios of shifts in GEnS bioclimate strata based on CIMP5 climate change scenarios for 2050

description: This dataset provides an alternative representation of global climate change projections based on shifts in the 125 multivariate strata of the Global Environmental Stratification (Metzger et al. 2013), which are characterised by relatively homogeneous climate. These strata form climate analogues that help in the interpretation of climate change impacts. A Random Forest classifier was calculated and applied to 63 Coupled Model Intercomparison Project Phase 5 (CMIP5) climate scenarios at 5 arcmin resolution. The dataset summarises future environmental change for 2050 and forms a middle ground, conveniently integrating current knowledge of climate change impact with the interpretation advantages of categorical data but with a level of detail that resembles a continuous surface at global and regional scales.
description: See datadescription.txt file.
DOI: 10.7488/ds/2055
title: [[SUPERSEDED - this dataset is replaced by a later version: https://doi.org/10.7488/ds/2109]] Accounting for the Complex Hierarchical Topology of EEG Functional Connectivity in Network Binarisation

description: [[SUPERSEDED - this dataset is replaced by a later version: https://doi.org/10.7488/ds/2109]] Research into binary network analysis of brain function faces a methodological challenge in selecting an appropriate threshold to binarise edge weights. For EEG, such binarisation should take into account the complex hierarchical structure found in functional connectivity. We explore the density range suitable for such structure and provide a comparison of state-of-the-art binarisation techniques, the recently proposed Cluster-Span Threshold (CST), minimum spanning trees and union of shortest path graphs, with arbitrary proportional thresholds and weighted networks. We test these techniques on weighted complex hierarchy models by contrasting model realisations with small parametric differences. We also test the robustness of these techniques to random and targeted topological attacks. We reveal that complex hierarchical topology requires a medium-density range binarisation solution, such as the CST which proves near maximal for distinguishing differences when compared with arbitrary proportional thresholding. Simulated results are validated with the analysis of three relevant EEG datasets: eyes open and closed resting states; visual short-term memory tasks; and resting state Alzheimer's disease with a healthy control group. The CST consistently outperforms other state-of-the-art binarisation methods for topological accuracy and robustness in both synthetic and real data. We provide insights into how the complex hierarchical structure of functional networks is best revealed in medium density ranges and how it safeguards against targeted attacks. These EEG PLI connnectivity data sets are used in the analysis of our submitted manuscript: https://arxiv.org/abs/1610.06360.
description: EyesOpenClosedData.mat contains the adjacency matrices of data processed as in the manuscript. The data comes from the Neurophysiological Biomarker Toolbox, available from www.nbtwiki.net. SpainADdata.mat contains the adjacency matrices of data processed as in the manuscript. The description of the signals can be found in Escudero J, Abasolo D, Hornero R, Espino P, Lopez M. Analysis of electroencephalograms in Alzheimer's disease patients with multiscale entropy. Physiological Measurement. 2016;27(11):1091-1106. YHAshapeBindData.mat contains the adjacency matrices of data processed as in the manuscript. The signals are described in Smith K, Azami H, Escudero J, Parra MA, Starr JM. Comparison of network analysis approaches on EEG connectivity in beta during Visual Short-term Memory binding tasks. IEEE Proc. EMBC 2015. 2015;doi:10.1109/EMBC.2015.7318829. They were provided by Mario A. Parra, supported by the Alzheimer's Society, grant # AS-R42303 and MRC grant # MRC-R42552.
DOI: 10.7488/ds/83
title: Snapshots of an N-body model of M4

description: 326 snapshots of an N-body model of the Galactic globular cluster M4. Each snapshot consists of a list of all the particles in the simulation at one time.
description: The snapshots are listed in "files.dat". Each line of this file gives the time (Myr), the total number of particles (N + Npairs, where Npairs is the number of KS regularised pairs), Npairs, and the three coordinates of the density centre (pc). The name of each snapshot is of the form .dat, where is as listed in the first column of files.dat. The first N lines give data on all particles, and the last Npairs lines give data on the barycentres of all KS pairs. Each line of a snapshot gives particle mass (Msun), three coordinates of position (pc), three components of velocity (km/s), the type of the star (Hurley, Pols & Tout 2000, MNRAS, 315, pp.546-7), the luminosity (Lsun), the stellar radius (Henon units), M_V, B-V.
DOI: 10.7488/ds/1481
title: SUPERSEDED - Emergent eddy saturation diagnostic data
title: Fluid Dynamics
title: Mesoscale parameterisation

description: Dataset for the article "Emergent eddy saturation from an energy constrained eddy parameterisation". Superseded by: http://datashare.is.ed.ac.uk/handle/10283/2365
DOI: 10.7488/ds/2241
title: Code and Data accompanying "pH sensing through a single optical fibre using SERS and CMOS SPAD line arrays"

description: Full exploitation of fibre Raman probes has been limited by the obstruction of weak Raman signals by background fluorescence of the sample and the intrinsic Raman signal of the delivery fibre. Here we utilised functionalised gold nanoshells (NS) to take advantage of the surface-enhanced Raman spectroscopy (SERS) effect to enhance the pH responsive spectrum of 4-mercaptobenzoic acid (MBA), however fibre background is still dominant. Using the photon arrival time-resolving capability of a CMOS single photon avalanche diode (SPAD) based line sensor we recover the SERS spectrum without fibre background in a 10 s measurement. In this manner, pH sensing through a multimode fibre at a low excitation power, that is safe for future in vivo applications, with short acquisition times (10 or 60 s) is demonstrated. A measurement precision of ±0.07 pH units is thus achieved.
description: data and code.txt - describes contents of archive Data-OE-TG-SERS.zip - archive of data and code
DOI: 10.7488/ds/2090
title: Dataset pertaining to the publication “Polymorphisms in B3GAT1, SLC9A9 and MGAT5 are associated with variation within the human plasma N-glycome of 3533 European adults.”

description: The majority of human proteins are post-translationally modified by covalent addition of one or more complex oligosaccharides (glycans). Alterations in glycosylation processing are associated with numerous diseases and glycans are attracting increasing attention both as disease biomarkers and as targets for novel therapeutic approaches. Using a recently developed high-throughput high-performance liquid chromatography (HPLC) analysis method, we have reported, in a pilot genome-wide association study of 13 glycan features in 2705 individuals from three European populations, that polymorphisms at three loci (FUT8, FUT6/FUT3 and HNF1A) affect plasma levels of N-glycans. Here, we extended the analysis to 33 directly measured and 13 derived glycosylation traits in 3533 individuals and identified three novel gene association (MGAT5, B3GAT1 and SLC9A9) as well as replicated the previous findings using an additional European cohort. MGAT5 (meta-analysis association P-value = 1.80 × 10−10 for rs1257220) encodes a glycosyltransferase which is known to synthesize the associated glycans. In contrast, neither B3GAT1 (rs7928758, P = 1.66 × 10−08) nor SLC9A9 (rs4839604, P = 3.50 × 10−13) had previously been associated functionally with glycosylation of plasma proteins. Given the glucuronyl transferase activity of B3GAT1, we were able to show that glucuronic acid is present on antennae of plasma glycoproteins underlying the corresponding HPLC peak. SLC9A9 encodes a proton pump which affects pH in the endosomal compartment and it was recently reported that changes in Golgi pH can impair protein sialylation, giving a possible mechanism for the observed association.
description: Please see PlasmaGlycansGWAS_README_DATASHARE.pdf
DOI: 10.7488/ds/2129
title: Nonequilibrium chromosome looping via molecular slip links

description: We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of cohesinlike molecules, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred 'loading site'. This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.
description: Data corresponding to Figures 1 and 2 in the paper.
DOI: 10.7488/ds/2239
title: Edinburgh_NIH10

description: This data set contains 10 normal healthy subjects ('sub-001' to 'sub-010') from a larger NIH funded project (NIH grant R01 EB004155) investigating changes in water diffusion parameters with age. Subjects underwent structural and diffusion MRI at 1.5 T and provided images suitable for a wide range of analyses, e.g. tractography, connectome etc.
DOI: 10.7488/ds/2124
title: Osmotaxis in E. coli through changes in motor speed - 3 minute recordings for long term CW Bias characterization

description: 3 minute recordings of (single cell) single motor rotation in Volume Recovery Buffer (VRB) and VRB supplemented with 200 mM sucrose. These measurements were used to construct Figure 2 B and C of the paper "Osmotaxis in E. coli through changes in motor speed" (in press). Additional values for Fig. 2 B and C were taken from the 'Osmotic shock' dataset, also in this repository. The data are raw (X,Y) voltages from the position sensitive detector as decribed in the Methods section of the paper.
description: Dataset contains 119 .zip archives, each containing a single cell (single motor) rotation measurement. A single measurement contains 36 text files ordered chronologically, in order of an ascending integer count. Out of the 119 files, 48 begin with a prefix 'VRB' and correspond to Volume Recovery Buffer measurements, and 71 with the prefix 200 correspond to measurements performed 12 or more minutes after osmotic upshift using VRB+200 mM Sucrose. Sampling rate was 10kHz, the (X,Y) bead position pairs are separated into columns and the duration of a single .txt file is 5 seconds.
DOI: 10.7488/ds/2746
title: Instances for "Increasing electric vehicle adoption through the optimal deployment of fast-charging stations for local and long-distance travel"

description: Two networks representing possible locations for electric vehicle charging stations in the province of Quebec in Canada, and in the state of California in the U.S.A. This data was created by the authors of the paper "Increasing electric vehicle adoption through the optimal deployment of fast-charging stations for local and long-distance travel".
description: The data files are described in the READ_ME.txt file.
DOI: 10.7488/ds/2452
title: Bismuth titanate modified and immobilized TiO2 photocatalysts for water purification: broad pollutant scope, ease of re-use and mechanistic studies

description: Deposition of titanium dioxide (TiO2) coatings onto glass beads from a P25 enriched sol of titanium butoxide is described. This method gives a robust and stable covering, to which small bismuth containing clusters of 1-5 nm have been introduced using a simple and scalable sequential ionic layer adsorption reaction (SILAR) method. This bismuth-modified TiO2 coating has been proven to show significant improvements over the pristine TiO2 samples for a variety of different pollutants including intermediates in consumer product manufacture, pesticides, drugs and explosives. Using scavenger tests, the mechanism of degradation for each of the pollutant molecules tested has been probed, and a thorough discussion of the differences presented. The applicability of the system has also been assessed, with ease of re-use of the photocatalyst-bead apparatus investigated through recycling tests.
DOI: 10.7488/ds/2305
title: Model output relating to HCHO columns over India

description: Model input and output for the publication "Which processes drive observed variations of HCHO columns over India?", which, at the time of writing, is in Atmospheric Chemistry and Physics Discussions with DOI 10.5194/acp-2017-1017. HCHO: formaldehyde. ## Box model (CABBA/MECCA)## Contained in BOX.zip: The contents of this are the output from each run of the model, which includes a .zip of the model code. The file caaba.log in each contains all of the namelist options. For the isoprene-related runs listed in table 1, there exists two folders for each, one base run with no isoprene injection and a second (suffixed with ""_9i"") for the run with the injection. These are written out in full, i.e. SOUTH_01 and SOUTH_01_9i relate to S_01. For the D_05 runs, "D_hold_base" contains the unperturbed run, "D_hold_C3H6" contains the run with an injection of propene, "D_hold_C3H8" contains the run with the injection of propane, and "D_hold_C4H10" contains the run with an injection of n-butane. ## GEOS-Chem ## Contained in GEOS_CHEM.zip: * GEOS_CHEM/ts_omi.YYYYMMDD.bpch' - ND51 output from the GEOS-Chem model * GEOS_CHEM/trac_avg_2014isop.bpch' - Contains monthly averages of the isoprene emissions calculated by MEGAN * GEOS_CHEM/input.geos' - is the main input file used for the GEOS-Chem run (reconstructed as original file had been edited) * GEOS_CHEM/HEMCO_Config.rc' - is the input file for the HEMCO component (reconstructed as original file had been edited)
description: The .geos and .rc files are simply text files that can be read by gedit or similar. They are model input files. The .bpch files are output from the GEOS-Chem simulation (GEOS-Chem v10-01). This is the “binary punch” format, which is pretty antiquated by now but can still be read by a variety of programmes. http://acmg.seas.harvard.edu/gamap/doc/Chapter_6.html#6.2 might be the best documentation of it. The community of GEOS-Chem users (which is a few hundred people) is necessarily very familiar with data in this format. The most widely-used viewing program for GEOS-Chem output is GAMAP (an IDL utility) http://acmg.seas.harvard.edu/gamap/ . GAMAP download and installation instructions are at: http://acmg.seas.harvard.edu/gamap/doc/Chapter_2.html .
DOI: 10.7488/ds/2560
title: "DAVIES_MP_2016.zip" - Data supporting Davies et al. Genome-wide association study of cognitive functions and educational attainment in UK Biobank (N=112 151).

description: Data supporting the paper Davies et al. Genome-wide association study of cognitive functions and educational attainment in UK Biobank (N=112 151). Molecular Psychiatry (2016). ## Note re working with data ## Each of the four data files contains over seventeen million rows. Users will encounter difficulties if they attempt to view the contents of these files using Notepad++ or Notepad. Microsoft Excel 2016 will not display all rows, only the first one million or so rows. These are space-delimited files.
DOI: 10.7488/ds/2102
title: Patchy promiscuity: machine learning applied to predict the host specificity of Salmonella enterica and Escherichia coli

description: Salmonella enterica and Escherichia coli are bacterial species that colonise different animal hosts with sub-types that can cause life-threatening infections in humans. Source attribution of zoonoses is an important goal for infection control as is identification of isolates in reservoir hosts that represent a threat to human health. In this study, host specificity and zoonotic potential were predicted using machine learning in which Support Vector Machine (SVM) classifiers were built based on whole genome sequence content. Analysis of over 1000 S. enterica genomes allowed the correct prediction (67% - 90% accuracy) of the source host for S. Typhimurium isolates and the same classifier could then differentiate the source host for alternative serovars such as S. Dublin. A key finding from both phylogeny and SVM methods was that the majority of isolates were assigned to host-specific sub-clusters and had high host-specific SVM scores. Moreover, only a minor subset of isolates had high probability scores for multiple hosts, indicating generalists with genetic content that may facilitate transition between hosts. The same approach correctly identified human versus bovine E. coli isolates (83% accuracy) and the potential of the classifier to predict a zoonotic threat was demonstrated using E. coli O157. The research indicates marked host restriction for both S. enterica and E. coli, with only limited isolate subsets exhibiting host promiscuity by gene content. Machine learning can be successfully applied to interrogate source attribution of bacterial isolates and has the capacity to predict zoonotic potential.
description: * Salmonella enterica data is provided in the supplementary data file: salmonella_data.tgz . The file includes isolates IDs, proteins variants (PVs) and their annotations. * Escherichia coli data which includes IDs, protein variants (PVs) and their annotations are provided in supplementary data file: ecoli_data.tgz * Descriptive PVs for each model are provided as supplementary files. The name of the file describes the model for which these PVs were used. So salmonella_PV_30_AO_annotations.csv means these are the PVs that describe Salmonella Typhimurium avian isolates vs. all others isolates. * Supplementary file HB_Stm_PVs.csv provides PVs that were used in the training model with only human and bovine STm isolates. * Supplementary files HB_ecoli_PVs_with.stx and HB_ecoli_PVs_without.stx provide PVs that were used in the models to test E. coli O157 isolates.