cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2568
title: Supplementary data for the manuscript "Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic"

description: Patterns of gene expression are primarily determined by proteins that locally enhance or repress transcription. While many transcription factors target a restricted number of genes, others appear to modulate transcription levels globally. An example is MeCP2, an abundant methylated-DNA binding protein that is mutated in the neurological disorder Rett Syndrome. Despite much research, the molecular mechanism by which MeCP2 regulates gene expression is not fully resolved. Here we integrate quantitative, multi-dimensional experimental analysis and mathematical modelling to show that MeCP2 is a novel type of global transcriptional regulator whose binding to DNA creates "slow sites" in gene bodies. Waves of slowed-down RNA polymerase II formed behind these sites travel backward and indirectly affect initiation, reminiscent of defect-induced shock waves in non-equilibrium physics transport models. This mechanism differs from conventional gene regulation mechanisms, which often involve direct modulation of transcription initiation. Our findings point to a genome-wide function of DNA methylation that may account for the reversibility of Rett syndrome in mice. Moreover, our combined theoretical and experimental approach provides a general method for understanding how global gene expression patterns are choreographed.
description: See Readme.txt
DOI: 10.7488/ds/2393
title: Dynamical analysis of bacteria in microscopy movies

description: This repository contains data and code related to the manuscript "Dynamical analysis of bacteria in microscopy movies", PloS One, 14, 6, e0217823, 2019 (https://doi.org/10.1371/journal.pone.0217823). Please find more information on the contents and structure of the files in the corresponding readme files.
description: See readme_rawdata.txt and readme_figuredata.txt files for more details.
DOI: 10.7488/ds/2495
title: UltraSuite Repository - sample data

description: UltraSuite is a repository of ultrasound and acoustic data from child speech therapy sessions. The current release includes three data collections, one from typically developing children -- Ultrax Typically Developing (UXTD) -- and two from children with speech sound disorders -- Ultrax Speech Sound Disorders (UXSSD) and UltraPhonix (UPX). This dataset contains a small sample from each of the three datasets in the UltraSuite repository, as well as their accompanying documentation. This is convenient for users who are unable or unwilling to download the entirety of the repository. Note that the sample data provided here is only a small subset of the repository. For additional details and instructions on getting UltraSuite data, please see http://www.ultrax-speech.org/ultrasuite
description: The UPX, USSD and UXTD samples are contained in separate .zip archives. Each archive file contains sample data from two speakers ('core' folder), and the documentation relating to the respective full repository ('doc' folder). The four core data types are as follows: *.wav - speech waveform; *.ult - raw ultrasound data; *.param - ultrasound parameters; *.txt - prompt text with utterance recording date/time.
DOI: 10.7488/ds/2361
title: Fully-resolved array of simulations investigating the influence of the magnetic Prandtl number

description: This dataset is for a paper which is currently in submission. We explore the effect of the magnetic Prandtl number Pr_M on energy and dissipation in fully-resolved direct numerical simulations of steady-state, mechanically-forced homogeneous magnetohydrodynamic turbulence in the range Pr_M=1/32 to 32. We compare the spectra and show that if the simulations are not fully-resolved, the steepness of the scaling of the kinetic-to-magnetic dissipation ratio with Pr_M is overestimated. We also present results of decaying turbulence with helical and nonhelical magnetic fields, where we find nonhelical reverse spectral transfer for Pr_M&lt;1 for the first time. The results of this systematic analysis have applications ranging from tokamak reactors to black hole accretion disks.
description: See README.txt for description of dataset. See the PhD theses of Sam Yoffe (https://arxiv.org/abs/1306.3408) and Moritz Linkmann (https://www.era.lib.ed.ac.uk/handle/1842/19572) for a description of the code.
DOI: 10.7488/ds/2493
title: Supplementary data to "Ligand binding site structure shapes allosteric signal transduction and the evolution of allostery in protein complexes" by G. Abrusan and J.A. Marsh

description: The structure of ligand binding sites has been shown to profoundly influence the evolution of function in homomeric protein complexes. Complexes with multi-chain binding sites (MBSs) have more conserved quaternary structure, more similar binding sites and ligands between homologues, and evolve new functions slower than homomers with single-chain binding sites (SBSs). Here, using in silico analyses of protein dynamics, we investigate whether ligand binding-site structure shapes allosteric signal transduction pathways (STPs), and whether the structural similarity of binding sites influences the evolution of allostery. Our analyses show that: 1) allostery is more frequent among MBS complexes than in SBS complexes, particularly in homomers; 2) in MBS homomers, semi-rigid communities and critical residues frequently connect interfaces and thus they are characterized by STPs that cross protein-protein interfaces, while SBS homomers usually not; 3) ligand binding alters community structure differently in MBS and SBS homomers; 4) allosteric proteins are more likely to have homologs with similar binding site than non-allosteric proteins, suggesting that binding site similarity is an important factor driving the evolution of allostery.
DOI: 10.7488/ds/2598
title: SUPERSEDED - Data for "Transmission from vaccinated hosts can cause dose-dependent reduction in pathogen virulence"

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2725 . ## # Abstract # Many livestock and increasingly human vaccines are leaky, blocking symptoms without preventing infection or onward transmission. Leakiness is concerning as it increases vaccination coverage required to prevent disease spread, and can promote evolution of increased pathogen virulence. Despite leakiness, vaccination may reduce pathogen load, affecting disease transmission dynamics. However, the impacts on post-transmission disease development and infectiousness in contact individuals are unknown. Here, we use transmission experiments involving Marek’s disease virus in chickens to show that vaccination with a leaky vaccine substantially reduces viral load in both vaccinated individuals and unvaccinated contact individuals they infect. Consequently, contact birds are less likely to develop disease symptoms or die, show less severe symptoms when these are present, and shed less infectious virus themselves, when infected by vaccinated birds. These results highlight that even partial vaccination with a leaky vaccine can have unforeseen positive consequences in controlling the spread and symptoms of disease.
description: Data descriptions are all in the file "MD analysis data filtering details.R". Names of all files: * "MD analysis data filtering details.R " * "ContactMort_2018.csv " * "Shedder_2018.csv " * "ContactDiseaseSEM_2018.csv " * "ContactDiseaseS_2018.csv " * "Contact_2018.csv " * "ContactInfection_2018.csv " * "ViralLoadFile_2017_2018.csv"
DOI: 10.7488/ds/2752
title: Data for "A smartphone-based test for the assessment of attention deficits in delirium: a case-control diagnostic test accuracy study in older hospitalised patients."

description: Paper: A smartphone-based test for the assessment of attention deficits in delirium: a case-control diagnostic test accuracy study in older hospitalised patients. ABSTRACT ## Background ## Delirium is a common and serious acute neuropsychiatric syndrome which is often missed in routine clinical care. Inattention is the core cognitive feature. Diagnostic test accuracy (including cut-points) of a smartphone Delirium App (DelApp) for assessing attention deficits was assessed in older hospital inpatients. ## Methods ## This was a case-control study of hospitalised patients aged ≥65 years with delirium (with or without pre-existing cognitive impairment), who were compared to patients with dementia without delirium, and patients without cognitive impairment. Reference standard delirium assessment, which included a neuropsychological test battery, was based on Diagnostic and Statistical Manual of Mental Disorders-5 criteria. A separate blinded assessor administered the DelApp arousal assessment (score 0-4) and attention task (0-6) yielding an overall score of 0 to 10 (lower scores indicate poorer performance). Analyses included receiver operating characteristic curves and sensitivity and specificity. Optimal cut-points for delirium detection were determined using Youden's index. ## Results ## A total of 187 patients were recruited, mean age 83.8 (range 67-98) years, 152 (81%) women; n=61 with delirium; n=61 with dementia without delirium; and n=65 without cognitive impairment. Patients with delirium performed poorly on the DelApp (median score=4/10; inter-quartile range 3.0, 5.5) compared to patients with dementia (9.0; 5.5, 10.0) and those without cognitive impairment (10.0; 10.0, 10.0). Area under the curve for detecting delirium was 0.89 (95% Confidence Interval 0.84, 0.94). At an optimal cut-point of &lt;8, sensitivity was 91.7% (84.7%, 98.7%) and specificity 74.2% (66.5%, 81.9%) for discriminating delirium from the other groups. Specificity was 68.3% (56.6%, 80.1%) for discriminating delirium from dementia (cut-point &lt;6). ## Conclusion ## Patients with delirium (with or without pre-existing cognitive impairment) perform poorly on the DelApp compared to patients with dementia and those without cognitive impairment. A cut-point of &lt;8/10 is suggested as having optimal sensitivity and specificity. The DelApp is a promising tool for assessment of attention deficits associated with delirium in older hospitalised adults, many of whom have prior cognitive impairment, and should be further validated in representative patient cohorts.
DOI: 10.7488/ds/2339
title: Characterisation of mechanical behaviour of demineralised and deproteinised trabecular bone samples
title: uCT images and mechanical test data for demineralised and deproteinised trabecular bone samples.

description: Nineteen (n=19) bovine trabecular bone samples were scanned before chemical treatment by using Skyscan at high resolution (17.22 µm). The chemical treatment was to either demineralise or deproteinise the samples. Thirteen (n=13) trabecular bone cylindrical samples were successfully demineralised. The mechanical tests included fully reversed cyclic loading experiment (n=5) to investigate bone’s asymmetric mechanical behaviour in tension and compression. Tests were also conducted to evaluate the timedependent behaviour of demineralised trabecular bone through tensile multiple-load-creep-unload-recovery (MLCUR) experiments (n=8). The original uCT, undertaken before chemical treatment, bone volume ratio (BV/TV) of samples for fully reversed cyclic experiment was found to be in the range of 21% - 32%; and BV/TV for MLCUR experiment samples were found in the range of 16% - 38%. Other six (n=6) trabecular bone cylindrical samples were deproteinised and subjected to monotonic loading. The bone volume ratio range from 22% to 32%. The detailed experiment methodologies can be found in related thesis chapter and/or cited journal papers.
description: Please refer to readme file within this dataset.
DOI: 10.7488/ds/2553
title: Data and figures for the publication "Analysis of two partially-saturated-cell methods for lattice Boltzmann simulation of granular suspension rheology"

description: Data supporting the published paper "Analysis of two partially-saturated-cell methods for lattice Boltzmann simulation of granular suspension rheology" (authors: Tim Najuch and Jin Sun) in Computers and Fluids (May, 2019) https://doi.org/10.1016/j.compfluid.2019.05.004 ABSTRACT: The lattice Boltzmann method (LBM) has been widely used to simulate fluid–solid flows with various approaches to couple the two phases. We study the partially-saturated-cell (PSC) approach proposed by Nobel and Torcznski [A lattice-Boltzmann method for partially saturated computational cells. International Journal of Modern Physics, 9(8):1189–1201, 1998], which modifies the LB equation by an additional solid collision term weighted by the lattice solid fraction. We analyse two different PSC schemes with regard to its capability of accurately computating the hydrodynamic stresslet, which is essential to computing the stress, hence the rheology of suspensions of granular particles. Through simulations of single and pair particles in a simple shear flow field, we show that a commonly used solid collision term based on non-equilibrium bounce-back fails to correctly capture the stresslet, although can result in a numerically accurate hydrodynamic torque, when compared to the analytical solutions. In contrast, a model using superposition, which has neither hitherto been analysed nor extensively applied, is demonstrated to be able to accurately calculate both the stresslet and the torque. We finally highlight the importance of using the correct model when simulating suspension rheology, showing the viscosity obtained in simulations of hundreds of mono-disperse particles at various solid fractions sheared homogeneously using the Lees-Edwards boundary condition.
DOI: 10.7488/ds/2730
title: 55 George Square during Edinburgh Festival

description: A Scan of 55 George Square during Edinburgh Festival, 8 Scan locations, captured with a BLK 360, registered using Autodesk Recap Pro, exported to .e57 file format. At the time of scanning this building was the location for The College Office for the College of Arts, Humanities and Social Sciences (CAHSS).
DOI: 10.7488/ds/2889
title: ATEC manuscript 2 - supporting data: "Quantifying Uncertainty and Bridging the Scaling Gap in the Retrieval of Leaf Area Index by Coupling Sentinel-2 and UAV Observations"

description: Leaf area index (LAI) estimates can inform decision-making in crop management. The European Space Agency’s Sentinel-2 satellite, with observations in the red-edge spectral region, can monitor crops globally at sub-field spatial resolutions (10–20 m). However, satellite LAI estimates require calibration with ground measurements. Calibration is challenged by spatial heterogeneity and scale mismatches between field and satellite measurements. Unmanned Aerial Vehicles (UAVs), generating high-resolution (cm-scale) LAI estimates, provide intermediary observations that we use here to characterise uncertainty and reduce spatial scaling discrepancies between Sentinel-2 observations and field surveys. We use a novel UAV multispectral sensor that matches Sentinel-2 spectral bands, flown in conjunction with LAI ground measurements. UAV and field surveys were conducted on multiple dates—coinciding with different wheat growth stages—that corresponded to Sentinel-2 overpasses. We compared chlorophyll red-edge index (CIred-edge) maps, derived from the Sentinel-2 and UAV platforms. We used Gaussian processes regression machine learning to calibrate a UAV model for LAI, based on ground data. Using the UAV LAI, we evaluated a two-stage calibration approach for generating robust LAI estimates from Sentinel-2. The agreement between Sentinel-2 and UAV CIred-edge values increased with growth stage—R2 ranged from 0.32 (stem elongation) to 0.75 (milk development). The CIred-edge variance between the two platforms was more comparable later in the growing season due to a more homogeneous and closed wheat canopy. The single-stage Sentinel-2 LAI calibration (i.e., direct calibration from ground measurements) performed poorly (mean R2 = 0.29, mean NRMSE = 17%) when compared to the two-stage calibration using the UAV data (mean R2 = 0.88, mean NRMSE = 8%). The two-stage approach reduced both errors and biases by &gt;50%. By upscaling ground measurements and providing more representative model training samples, UAV observations provide an effective and viable means of enhancing Sentinel-2 wheat LAI retrievals. We anticipate that our UAV calibration approach to resolving spatial heterogeneity would enhance the retrieval accuracy of LAI and additional biophysical variables for other arable crop types and a broader range of vegetation cover types.
DOI: 10.7488/ds/2724
title: Structural study of the pressure-induced metal-insulator transition in LiV2O4

description: .xy files (intensity vs. 2theta) for the diffraction patterns of LiV2O4. Temperature and pressure for each datset are shown in the file title. Data is support of manuscript: Structural study of the pressure-induced metal-insulator transition in LiV2O4 Alexander J. Browne and J. Paul Attfield, Physical Review Materials, 2020.​
DOI: 10.7488/ds/2471
title: Mechanical stability of surface nanobubbles

description: This data folder contains example 2D and 3D cases for the Molecular Dynamics (MD) simulations, including data from post-processing for the results plotted in the paper: Dockar et al. "Mechanical stability of surface nanobubbles” (in press). MD simulatons were run with LAMMPS version 30 July 2016 (https://lammps.sandia.gov). Each folder starting with the word 'Figure' is linked with the actual Figure in the journal paper, and contains the data used to plot each figure.
DOI: 10.7488/ds/2468
title: Parallel Audiobook Corpus

description: The Parallel Audiobook Corpus (version 1.0) is a collection of parallel readings of audiobooks. The corpus consists of approximately 121 hours of speech at 22.05KHz across 4 books and 59 speakers. The data is provided in two formats. Chapter data contains the audiobook recording at the chapter level. Each chapter-level waveform is accompanied by the text and its respective word-level alignment. This format can be used if you are looking for a segmentation that does not correspond to utterance-level units. Segmented data provides a more traditional format for the corpus. The chapter-level alignment was segmented into utterances with waveforms organized by speaker. Note that, within each book, utterance identifiers are consistent across speakers, making it simple to find parallel data.
description: Please see readme.txt file for information about these data. Information about this dataset can also be found at the following URL: https://msamribeiro.github.io/parallel-corpus/
DOI: 10.7488/ds/2636
title: Timeseries used in Zielinski et al. Strengths and Limitations of Period Estimation Methods
title: Strengths and Limitations of Period Estimation Methods for Circadian Data
title: Circadian timeseries data for testing methods of periods analysis

description: Dataset contains timeseries data used for testing period analysis methods. The full details of the data are described in the actual paper, here there is only a short summary of methods generation. The synthetic test signals comprise: - a pure cosine of known frequency, and hence known period; - a pulsed waveform which comprises pulses of a Gaussian waveform with a standard deviation of (period/7); - a double pulsed waveform which comprises two periodic Gaussian waveforms; - simulated clock data generated using a delayed negative feedback loop (DNFL) model. Here we use parameter sets identical to those used in Costa MJ et al. Biostatistics 2013 to produce two sets with moderate level of asymmetry or a moderate shoulder. Once the basic time series had been generated, noise was added. The noise was additive and was either uniform noise or walking noise. Uniform noise is drawn from a uniform distribution and the amplitude of the noise is defined as a percentage of the amplitude of the original time-series. This would be characteristic of the noise in a measurement system. Walking noise is additive and uniform, but this time the distribution of the noise is restricted so that the current data point lies within a limited range of the previous data point. To assess applicability of the methods to the analysis of real biological systems, we also tested data sets obtained by in vivo imaging of transgenic Arabidopsis thaliana plants.
description: * "synthetic data noise.zip" - generated data with uniform noise added. Each signal waveform is in a separate subfolder, which then contain data groups but noise level and timeseries duration (in days) ; * "synthetic data wnoise.zip" - generated data with "walking" noise added. Each signal waveform is in a separate subfolder, which then contain data groups but noise level and timeseries duration (in days) ; * "bio data.zip" - examples of biological data ; * "amp trends.zip" - data with amplitude dampening, organized in subfolders by signal waveform and dampening pattern ; * "base trends.zip" - data with baseline trends added, organized in subfolders by trend pattern. The files with suffix "results" contains results of period analysis for the datasets with BioDare methods.
DOI: 10.7488/ds/2377
title: Images for "Functional Transport of Organic Anions and Cations in the Murine Mesonephros"

description: The mesonephros of mammals is a transient renal structure that contributes to various aspects of mammalian fetal development including the male reproductive system, hematopoietic stem cells and vascular endothelial cells. The mesonephros develops from the intermediate mesoderm and forms tubules that are segmented in a similar way to the nephrons of the permanent kidney (but lacking loops of Henle). Early studies have suggested that the mesonephros in marsupials and some placental mammals may perform an excretory function, but these studies have not directly shown active transport of organic anions and cations. Excretory function in the rodent mesonephros has not been investigated. Here, we use live uptake and efflux assays in vitro to show that the murine mesonephros is able to transport organic anions and cations through specific transporters from early in its development. Transcript analysis suggests that there are subtle differences between the transporters involved in uptake and efflux by the murine permanent, metanephric tubules and by the mesonephric tubules. These data suggest that the mammalian mesonephros can provide an excretory function for the early developing embryo, in addition to the excretory function provided by the placenta.
description: Images taken by either Jamie Smith or Melanie Lawrence each in their own subfolder. Within these subfolders, each has a second subfolder with the gestational age at which the mesoephros was studied. Each age has its own third subfolder with each assay type and number of the assay. In each separate assay subfolder are located the images for that assay as a raw data file with both the control or inhibitor-treated image. All the files including can be opened with Fiji or Image J software.