cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2218
title: MIKE 21 West Orkney Monthly Hs Summary Outputs

description: MIKE 21 WEST ORKNEY MONTHLY Hs SUMMARY OUTPUTS This collection of netCDF format files contains monthly summary outputs of significant wave height (Hs) from the West of Orkney MIKE 21 spectral wave model described in [1]. For each month the mean Hs and the values of the 5,10,20...,90,95th percentiles are given for each cell in the model. The model was designed to study the effects on wave height of both wave energy extraction and climate change. Four scenarios are included: Present day (2010) with and without wave energy convertors, and future climate (~2050) with and without wave energy convertors. See [1] for more detail on present-day; a future publication will describe the future version. This model was developed under the TeraWatt and EcoWatt2050 EPSRC projects (grant numbers EP/J010170/1 & EP/K012851/1 respectively). The data archived here are being used within the EcoWatt project for ongoing ecological studies. For the input files for the model used to produce these outputs, please see submission "WEST ORKNEY MIKE 21 MODEL INPUT FILES" in this repository. For further information please contact Dr. Vengatesan Venugopal, School of Engineering, University of Edinburgh (v.venugopal@ed.ac.uk). [1] V. Venugopal, R. Nemalidinne, and A. Vögler, ‘Numerical modelling of wave energy resources and assessment of wave energy extraction by large scale wave farms’, Ocean & Coastal Management, Mar. 2017.
DOI: 10.7488/ds/2451
title: The noun-verb distinction in silent gesture

description: This dataset comprises data collected in a silent gesture experiment, where participants where asked to communicate events using only gesture. Pairs of participants took part in the study in 3 stages. In stage 1, participants produced gestures for the events without a partner; in stage 2, they took turns to communicate about the events in pairs, using only gesture. In the final stage, participants produced gestures alone again. The events participants were asked to communicate showed objects being used in a typical fashion, designed to elicit verb-like gestures (e.g. a camera being used to take a photograph), or used in an atypical fashion, designed to elicit more noun-like gestures (e.g. someone digging with a camera).
description: Descriptions of the file structure and videos can be found in the file video_guide.pdf.
DOI: 10.7488/ds/2630
title: Mass Spectrometry Analysis of Encapsulated Ferritins from Haliangium ochraceum – Native IM-MS and HDX-MS

description: Encapsulated ferritins (EncFtn) are a recently characterised member of the ferritin superfamily. EncFtn are stored within encapsulin nanocompartments and together, they form an iron storage system. Here we elucidate the assembly pathway of EncFtn by studying its subcomplexes using native mass spectrometry and hydrogen-deuterium exchange mass spectrometry.
description: Mass Spectrometry Analysis of Wild-type and H63A Encapsulated Ferritins from Haliangium ochraceum. 1. LC-MS analysis of Hoch-WT and Hoch-H63A. 2. Native Mass Spectrometry datasets for Hoch-WT and Hoch-H6 3. Native Ion-mobility Mass Spectrometry datasets for Hoch-WT and Hoch-H63A 4. High Resolution FT-ICR Native Mass Spectrometry datasets for Hoch-WT and Hoch-H63A 5. HDX-MS datasets for Hoch-WT and Hoch-H63A. See attached data set notes pdf file for detailed information.
DOI: 10.7488/ds/2631
title: GWAS summary stats for meta-analysis of epigenetic age acceleration - Gibson et al, (2019)

description: 'Epigenetic age acceleration' is a valuable biomarker of ageing, predictive of morbidity and mortality, but for which the underlying biological mechanisms are not well established. Two commonly used measures, derived from DNA methylation, are Horvath-based (Horvath-EAA) and Hannum-based (Hannum-EAA) epigenetic age acceleration. We conducted genome-wide association studies of Horvath-EAA and Hannum-EAA in 13,493 unrelated individuals of European ancestry, to elucidate genetic determinants of differential epigenetic ageing. We identified ten independent SNPs associated with Horvath-EAA, five of which are novel. We also report 21 Horvath-EAA-associated genes including several involved in metabolism (NHLRC, TPMT) and immune system pathways (TRIM59, EDARADD). GWAS of Hannum-EAA identified one associated variant (rs1005277), and implicated 12 genes including several involved in innate immune system pathways (UBE2D3, MANBA, TRIM46), with metabolic functions (UBE2D3, MANBA), or linked to lifespan regulation (CISD2). Both measures had nominal inverse genetic correlations with father’s age at death, a rough proxy for lifespan. Nominally significant genetic correlations between Hannum-EAA and lifestyle factors including smoking behaviours and education support the hypothesis that Hannum-based epigenetic ageing is sensitive to variations in environment, whereas Horvath-EAA is a more stable cellular ageing process. We identified novel SNPs and genes associated with epigenetic age acceleration, and highlighted differences in the genetic architecture of Horvath-based and Hannum-based epigenetic ageing measures. Understanding the biological mechanisms underlying individual differences in the rate of epigenetic ageing could help explain different trajectories of age-related decline.
DOI: 10.7488/ds/2372
title: Comprehensive transcriptional profiling of the gastrointestinal tract of ruminants from birth to adulthood
title: RNASeq analysis of the ruminant GI tract

description: One of the most significant physiological challenges to neonatal and juvenile ruminants is the development and establishment of the rumen. Using a subset of RNA-Seq data from our high-resolution atlas of gene expression in sheep (Ovis aries) we have provided the first comprehensive characterisation of transcription of the entire gastrointestinal (GI) tract during the transition from pre-ruminant to ruminant. The dataset comprises 168 tissue samples from sheep at four different time points (birth, one week, 8 weeks and adult). Included here are the gene expression estimates as transcripts per million (TPM) for individual sheep (Table S4) and averaged across individuals (Table S1).
DOI: 10.7488/ds/2242
title: On the r&gt;h shift in Kiên Giang Khmer: supplementary materials

description: This dataset contains supplementary materials to the paper "On the r&gt;h shift in Kiên Giang Khmer" (Journal of the Southeast Asian Linguistics Society 10.2). It includes anonymised perception and production data (as CSV files) and R code to reproduce the figures and analyses described in the paper. The original anonymised audio recordings and associated Praat TextGrids are also available as a separate DataShare entry - https://doi.org/10.7488/ds/2075.
description: See README.txt
DOI: 10.7488/ds/2847
title: Comparative Genomics of Chlamydomonas

description: Files for "Comparative genomics of Chlamydomonas" manuscript.
description: See README. Please note information on two provisionally accepted file formats in the deposit: * GFF3 is General Feature Format 3. It is plain text, and is the standard file format used for gene annotations (gene coordinates, exon-intron structure, etc.). The format is described by NCBI here: https://www.ncbi.nlm.nih.gov/datasets/docs/about-ncbi-gff3/ * hal is hierarchical alignment format. It is an HDF5 file used for storing genome alignments. The format is described here (https://github.com/ComparativeGenomicsToolkit/hal) and in this publication (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654707/).
DOI: 10.7488/ds/2384
title: Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay

description: Supplementary data for Koszela et.al. Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay, BMC Biology, 2018
description: See README.txt file
DOI: 10.7488/ds/2308
title: Orbital molecules in the new spinel GaV2O4

description: Data to accompany; Orbital molecules in the new spinel GaV2O4 Alexander J. Browne, Calum Lithgow, Simon. A. J. Kimber, and J. Paul Attfield Inorg. Chem. 2018 Data are; cif files HRPD neutron data at various temperatures ID22 synchrotron data at various temperatures IN6 neutron data at various temperatures PDF synchrotron files at various temperatures Magnetisation data Resistivity data
DOI: 10.7488/ds/1992
title: Infrared peak splitting from phonon localization in solid hydrogen
title: Phonons for HD mixtures

description: Dataset contain CASTEP input and output for calculations of localization of phonons in C2c hydrogen under pressure. Also contains codes written in the project to extend the lattice dynamics calculation to large disordered unit cells representing post-DISREC hydrogen-deuterium mixtures as reported by Silvera in PRL (http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.145501).
DOI: 10.7488/ds/2284
title: Assembly and validation of conserved long non-coding RNAs in the ruminant transcriptome

description: mRNA-like long non-coding RNAs (lncRNA) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. This dataset demonstrates that few lncRNA are fully captured by biological replicates of the same RNA-seq library. In a transcriptional atlas of the domestic sheep (https://doi.org/10.1371/journal.pgen.1006997), 31 diverse tissues/cell types were sampled in each of 6 individual adults (3 females, 3 males, all unrelated virgin animals approximately 2 years of age). By taking a subset of 31 common tissues per individual, each of the 6 adults (f1, f2, f3, m1, m2, and m3) was represented by ~0.75 billion reads. In a typical lncRNA assembly pipeline, read alignments from all individuals are merged, to maximise the number of candidate gene models (using, for instance, StringTie --merge). With n = 6 adults (and ~0.75 billion reads per adult), there are (2^n)-1 = 63 possible combinations of data for which GTFs can be made with StringTie --merge. This dataset comprises those GTFs.
DOI: 10.7488/ds/2748
title: Dataset for: "A combined rheometry and imaging study of viscosity reduction in bacterial suspensions"

description: Dataset supporting the manuscript "A combined rheometry and imaging study of viscosity reduction in bacterial suspensions" accepted in PNAS.
DOI: 10.7488/ds/2587
title: Circuits! - Demonstrating the use of optical fibres in biomedical sciences
title: Circuits! - Light tool

description: The Circuits! - project, funded through the The Royal Academy of Engineering Ingenious Grant (ING1617/11/114), demonstrates how research at the intersection of physics, engineering, biology, and medicine can be presented in an interactive and educational way to a non-scientific audience. Respiratory diseases are significant contributors to avoidable morbidity and mortality and have a growing social and economic impact. With the aim of improving lung disease understanding, new techniques in fibre-based optical endomicroscopy have been recently developed. Interdisciplinary research with a focus on prevalent diseases provides a relatable context that can be used to enrich high school education. Here, we present a novel teaching methodology, developed between high school science teachers and researchers, that resembles a bench-to-bedside pathway. The methodology comprises an inexpensive educational tool (&lt; $ 70) adapted from a clinical optical endomicroscopy system and tutorials that cover state-of-the-art research. This data set contains STL files for the 3d printing parts, templates for graphs, an instructional video, teaching material and a detailed description and trouble shooting document for the education tool.
description: 3dPrinting-STL-files - folder containing the stl files needed to 3d print parts for the educational tool. Templates - folder containing templates for graphs to plot the recorded data. Instructional_Video.mp4 - video explaining in detail how to build and use the educational tool. Supplementary_Demonstrating_the_use_of_optical_fibres.pdf - Accompanying document to paper in submission including further details on the design of the educations tool, setting and troubleshooting, calibration procedure, variations of components and teaching aims. Teaching_Material.pdf - Accompanying teaching material that introduces the concept of diagnostic uncertainty, tells the story of a generalised but realistic clinical pathway and shows how current research aims to disrupt this pathway to improve clinical outcomes.
DOI: 10.7488/ds/2246
title: Data and movies accompanying 'Kinetic theory of pattern formation in mixtures of microtubules and molecular motors'

description: In this study we formulate a theoretical approach, based on a Boltzmann-like kinetic equation, to describe pattern formation in two-dimensional mixtures of microtubular filaments and molecular motors. Following the previous work by Aranson and Tsimring [Phys. Rev. E {\bf 74}, 031915 (2006) https://doi.org/10.1103/PhysRevE.74.031915 ] we model the motor-induced reorientation of microtubules as collision rules, and devise a semi-analytical method to calculate the corresponding interaction integrals. This procedure yields an infinite hierarchy of kinetic equations that we terminate by employing a well-established closure strategy, developed in the pattern-formation community and based on a power-counting argument. We thus arrive at a closed set of coupled equations for slowly varying local density and orientation of the microtubules, and study its behaviour by performing a linear stability analysis and direct numerical simulations. By comparing our method with the work of Aranson and Tsimring, we assess the validity of the assumptions required to derive their and our theories. We demonstrate that our approximation-free evaluation of the interaction integrals and our choice of a systematic closure strategy result in a rather different dynamical behaviour than was previously reported. Based on our theory, we discuss the ensuing phase diagram and the patterns observed.
description: See readme.txt file for details.
DOI: 10.7488/ds/2868
title: Window north side (side short wall that is close to the door) informal settlement fire experiment (Test 8))

description: This dataset presents Test 8 (window north side experiment). Different from Baseline experiment, the window location was changed from front long wall to the side short wall that is close to the door, and the other conditions are totally the same with Baseline.
DOI: 10.7488/ds/2586
title: Imaging Moving Targets for a Forward Scanning Automotive SAR

description: This dataset supports the following publication: Gishkori, S, Wright, D, Daniel, L, Gashinova, M & Mulgrew, B 2019, 'Imaging Moving Targets for a Forward Scanning Automotive SAR' IEEE Transactions on Aerospace and Electronic Systems, pp. 1-1. DOI: 10.1109/TAES.2019.2925446. In the paper, we extend the forward-scanning SAR methodology to reconstruct images of the moving targets, for a forward-looking automotive radar. This dataset is used to show the performance of our proposed algorithm. A *.mat file contains the data. The data can be read via the provided *.m file in Matlab.
DOI: 10.7488/ds/2380
title: A critical assessment of the line tension determined by the modied Young's equation

description: This dataset contains the output data (e.g. contact angle, contact base radius) from all molecular dynamics simulations of water nanodroplets carried out on different surfaces.
description: Please view README.txt file for more information about how the data set is divided.
DOI: 10.7488/ds/2594
title: Estimating numbers of intracellular molecules through analysing fluctuations in photobleaching

description: The impact of fluorescence microscopy has been limited by the difficulties of expressing measurements of fluorescent proteins in numbers of molecules. Absolute numbers enable the integration of results from different laboratories, empower mathematical modelling, and are the bedrock for a quantitative, predictive biology. Here we propose an estimator to infer numbers of molecules from fluctuations in the photobleaching of proteins tagged with Green Fluorescent Protein. Performing experiments in budding yeast, we show that our estimates of numbers agree, within an order of magnitude, with published biochemical measurements, for all six proteins tested. The experiments we require are straightforward and use only a wide-field fluorescence microscope. As such, our approach has the potential to become standard for those practising quantitative fluorescence microscopy.
description: * "README.txt " * "Def1_slide_1.csv" * "Gpm1_slide_1.csv" * "Guk1_slide_2.csv" * "Pgk1_slide_1.csv " * "Fus3_slide_1.csv" * "Gpm1_slide_2.csv" * "Hog1_slide_1.csv" * "Pgk1_slide_2.csv " * "Fus3_slide_2.csv" * "Guk1_slide_1.csv" * "Hog1_slide_2.csv"
DOI: 10.7488/ds/2373
title: Probing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy (Part 1)

description: Part 1 of datasets supporting the manuscript "Probing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy". Abstract: We demonstrate differential dynamic microscopy and particle tracking for the characterization of the spatiotemporal behavior of active Janus colloids in terms of the intermediate scattering function (ISF). We provide an analytical solution for the ISF of the paradigmatic active Brownian particle model and find striking agreement with experimental results from the smallest length scales, where translational diffusion and self-propulsion dominate, up to the largest ones, which probe effective diffusion due to rotational Brownian motion. At intermediate length scales, characteristic oscillations resolve the crossover between directed motion to orientational relaxation and allow us to discriminate active Brownian motion from other reorientation processes, e.g., run-and-tumble motion. A direct comparison to theoretical predictions reliably yields the rotational and translational diffusion coefficients of the particles, the mean and width of their speed distribution, and the temporal evolution of these parameters.
description: Please check the file readme_part_1.txt
DOI: 10.7488/ds/2869
title: Two windows (and one door) informal settlement fire experiment (Test 9)

description: This dataset presents Test 9 (two windows and one door). Different from Baseline experiment, one additional window is added at the short side wall that is far from the door, and the other conditions are totally the same with Baseline.
DOI: 10.7488/ds/2214
title: Distributed and dynamic intracellular organization of extracellular information in yeast

description: Data from single-cell microscopy experiments for "Distributed and dynamic intracellular organization of extracellular information" by Granados, Pietsch, Cepeda-Humerez, Tkačik and Swain. The data come from a microfluidics-based screening of the dynamics of nuclear translocation for 10 transcription factors (Msn2, Msn4, Dot6, Tod6, Sfp1, Maf1, Mig1, Mig2, Hog1, and Yap1), which are the endpoints of evolutionarily conserved signaling pathways (including protein kinase A (PKA), AMP kinase and TOR kinase pathways). The data set includes single-cell time series describing the response of each factor for environmental transitions from rich media (2% glucose) into three different stresses: carbon stress (low glucose), osmotic stress or oxidative stress. Responses to different magnitudes of each stress are also included.
description: All files in this dataset are documented in the attached README.txt file.
DOI: 10.7488/ds/2295
title: Wafer-Level Characterisation of Microelectrodes for Electrochemical Sensing Applications

description: This work presents a system for the in-line wafer-level characterisation of electrochemical sensors. Typically, such sensors are first diced and packaged before being electrochemically tested. By integrating their characterisation into the manufacturing process, the production of electrochemical sensors becomes more efficient and less expensive as they can be parametrically tested midway through the fabrication process, without the need to package them. This enables malfunctioning or failed devices to be identified before dicing and reduces costs as only functional devices are packaged (in many cases this can be more expensive than the sensor fabrication). This study describes wafer-level characterisation of a simple electrochemical sensor design using a photoresist hydrophobic corralling film for the electrolyte and a probe station for contacting to individual dies.
description: This dataset contains five .csv files and one readme file. Each .csv file is titled with the figure or table it relates to in the main paper. * "Read Me.txt" - Describes the data in this dataset relates to the experiments presented in the paper. * "Table 1.csv" - Contains contact angle measurements made on SPR 350 and SiN. * "Table 2.csv" - Contains five cyclic voltammetry measurements (changing voltage and measured current) made in the probe station and five made in a beaker, which gave the average limiting currents shown in the paper. * "Figure 5.csv" - Contains two cyclic voltammetry measurements, one made in the probe station and one in a beaker. * "Figure 6.csv" - Contains six cyclic voltammetry measurements made over a period of time in the probe station. * "Figure 7.csv" - Contains nine cyclic voltammetry measurements made on nine separate electrodes in the probe station.
DOI: 10.7488/ds/2319
title: Circadian and brain state modulation of network hyperexcitability in Alzheimer's disease - rodent datasets

description: Network hyperexcitability is a feature of Alzheimer's disease (AD) as well as numerous transgenic mouse models of AD. While hyperexcitability in AD patients and AD animal models share certain features, the mechanistic overlap remains to be established. We aimed to identify features of network hyperexcitability in AD models that can be related to epileptiform activity signatures in AD patients. We studied network hyperexcitability in mice expressing amyloid precursor protein (APP) with mutations that cause familial AD, and compared a transgenic model that overexpresses human APP (J20), to a knock-in model expressing APP at physiological levels (APPNL/F). We recorded continuous long-term electrocorticogram activity from mice, and studied modulation by circadian cycle, behavioural, and brain state. We report that while J20s exhibit frequent inter-ictal spikes (IIS), APPNL/F mice do not. In J20 mice, IIS were most prevalent during daylight hours and the circadian modulation was associated with sleep. Further analysis of brain state revealed that IIS in J20s are associated with features of rapid-eye movement (REM) sleep. We found no evidence of cholinergic changes that may contribute to IIS-circadian coupling in J20s. In contrast to J20s, intracranial recordings capturing IIS in AD patients demonstrated frequent IIS in non-REM sleep. The salient differences in sleep-stage coupling of IIS in APP overexpressing mice and AD patients suggests that different mechanisms may underlie network hyperexcitability in mice and humans. We posit that sleep-stage coupling of IIS should be an important consideration in identifying mouse AD models that most closely recapitulate network hyperexcitability in human AD. This repository contains the data relating to the rodent experiments.
DOI: 10.7488/ds/2297
title: GEOMETRIC (MITgcm) diagnostic data

description: Dataset for the article "Implementation of a geometrically and energetically constrained mesoscale eddy parameterisation in an ocean circulation model".
description: see the readme.txt