cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/3088
title: Zimbabwe friction surface

description: The friction (cost allocation/effort) surface was assembled using three primary input datasets on land surface characteristics that help or hinder travel speeds: land cover, roads and topography. Landcover data were from the ESA CCI Landcover map for Africa 2016, roads data were merged from Open-Street Map (OSM) and the MapwithAi project and topography was taken from the SRTM Digital Elevation Model. The costs for travel consider walking/pedestrian travel in this data, but the software is supplied with an easy to change set of travel speeds so they can be adapted easily to consider travel speeds reflecting motorised transportation use. We have reduced the walking speeds to reflect the fact that adults walking with children move approximately 22% slower. There are two friction surfaces provided, the first defines open water as a barrier to travel and so the speed allocated to this landcover is NA. The second defines open water with an associated speed (1 km/hr). To create a walking speed array, first the road walking speeds were used and then missing values were filled with landcover walking speed values. This walking speed array was multiplied by the slope impact grid. The speed for each cell was converted from kilometers per hour to meters per second. Finally, the time (in seconds) to walk across each cell was calculated. The outputs are 20-m spatial resolution geotiffs indicating the time to walk across each cell. They are subsequently used in the least cost path analysis to estimate travel time to the nearest health facilities. However,these friction surfaces can be used by others to estimate travel speed to other destinations in a GIS.
description: cost_surface_water_Zim.tif - friction surface with water assigned a travel speed; cost_surface_Zim.tif - friction surface with water masked as a travel option.
DOI: 10.7488/ds/3093
title: Tanzania travel time to nearest hospital

description: Travel time surface was estimated using the cost allocation (friction surfaces) which used three primary input datasets on land surface characteristics that help or hinder travel speeds: land cover, roads and topography. This Geotiff is a 20-m spatial resolution surface where each pixel has a value which is the time in seconds to travel to the nearest hospital documented in the paper by Maina et al. (2020) doi: 10.1038/s41597-019-0142. According to the United Republic of Tanzania Ministry of Health and Social Welfare Health sector strategic plan (http://www.tzdpg.or.tz/fileadmin/documents/dpg_internal/dpg_working_groups_clusters/cluster_2/health/Key_Sector_Documents/Induction_Pack/Final_HSSP_IV_Vs1.0_260815.pdf) hospitals include (district hospital, designated hospital, regional and national referral hospitals) are found at the district level they can admit patients and provide basic medical services as well as advanced medical cares.
description: service_area_Tanz_Hosp.tif - travel time in seconds to the nearest dispensary facility from every pixel. Travel_Time_Hospitals.jpg - jpeg image of the geotiff file service_area_Tanz_Hosp.tif to demonstrate what the file should look like.
DOI: 10.7488/ds/3802
title: TestEd Survey of Staff and Student Experiences and Perceptions of Novel Covid-19 Testing Platform

description: Survey of staff and students at the University of Edinburgh related to their participation in a routine, asymptomatic Covid-19 workplace testing pilot. 522 participants completed a pilot survey in April 2021 and 1,750 completed the main survey (November 2021). Surveys explored: the acceptability of regular PCR testing among students and staff, particularly involving an approach that was less invasive than nasopharyngeal swabbing; barriers and facilitators to participating in a regular university testing programme, including in the context of other testing methods being available; and whether participation in such a programme changed adherence to public health guidelines.
DOI: 10.7488/ds/3493
title: A dataset on Voice Quality, Tone, and Vowel Quality in the Bor South dialect of Dinka

description: This document describes a dataset designed to examine Voice Quality (Modal vs. Breathy) and Tone (Low vs. High) in the Bor South dialect of Dinka. The materials consists of 29 minimal sets in which these two factors are orthogonally crossed, across all seven of the Dinka vowels (/i, e, ɛ, a, ɔ, o, u/). They were elicited in utterance-final position and in isolation, from eight speakers of the Bor South variety of Dinka. The archive includes 2157 sound files ( wav format, recorded digitally at 48kHz and 16 bit using a headset-mounted microphone), plus Praat TextGrid annotation files for 1724 of the wav files. See DescriptionOfTheDataset.pdf for a detailed description.
DOI: 10.7488/ds/3816
title: Development and Application of Desorption Electrospray Ionization Mass Spectrometry for Historical Dye Analysis
title: Development and Application of Desorption Electrospray Ionization Mass Spectrometry for Historical Dye Analysis

description: Primary data files for the data presented in upcoming publication E. Sandström, C. Vettorazzo, C.L. Mackay, L.G. Troalen and A.N. Hulme. 'Development and Application of Desorption Electrospray Ionization Mass Spectrometry for Historical Dye Analysis.' Analytical Chemistry (in submission).
DOI: 10.7488/ds/3108
title: Micellar catalysis of the Suzuki Miyaura reaction using biogenic Pd nanoparticles from Desulfovibrio alaskensis

description: NMR data supporting the paper "Micellar catalysis of the Suzuki Miyaura reaction using biogenic Pd nanoparticles from Desulfovibrio alaskensis".
DOI: 10.7488/ds/3113
title: Double double to double perovskite transformations in quaternary manganese oxides

description: CIF and raw data files from publication in Angew Chem 2021. DOI: 10.1002/anie.202108586
DOI: 10.7488/ds/3115
title: Gold precipitation by diamides - ICP-OES and NMR data

description: The efficient separation of gold and other metals from their ores and composite secondary sources such as electronic waste is necessary to realising circularity in metal supply chains. Processes based on precipitation are becoming increasingly popular and their development is reliant on designing and understanding chemical recognition to achieve selectivity. Here we show that the simple tertiary diamide PhC(O)NMe(CH2CH2)NMeC(O)Ph (L) precipitates gold selectively and directly from aqueous acidic solutions as the ion pair [HL][AuCl4], including from aqua regia solutions of electronic waste. The X-ray crystal structure of the precipitate displays an infinite chain of diamide cations, formed through an intermolecular proton chelate, interleaved with tetrachloridoaurate. Gold is released quantitatively from the isolated precipitate as HAuCl4 on contact with water, enabling ligand recycling. The diamide is highly selective, with its addition to a mixture of 29 metals in 2 M HCl resulting in 70% gold uptake and minimal removal of all other metals. Increasing the HCl concentration to 6 M allows complete collection of gold, iron, tin, and platinum, demonstrating that L is an adaptable selective metal precipitant controlled by just one variable. Thus, this discovery could be exploited in metal refining and recycling processes due to its tuneable selectivity under different metal leaching conditions, the avoidance of organic solvents inherent to biphasic extraction, and the straightforward recycling of the precipitant.
DOI: 10.7488/ds/3105
title: Wave buoy in current - experimental data

description: This dataset records experimental outputs (motions and mooring loads) from a scale model wave measurement buoy deployed in the FloWave Ocean Energy Research Facility. This work was part of the "Accounting for Current in Wave Buoy Measurements" project and was funded by the EPSRC Supergen ORE hub. The experimental data provided here relates to wave buoy tests with a taut and flexible (elastic) mooring under current and regular wave conditions. The six degree of freedom motions and mooring loads are provided for current-only, wave-only and combined wave-current over a range of directions and wave frequencies. The dataset was generated to provide improved tools to extend the ability of wave buoys to operate in areas subjected to waves and currents. The simple sphere form of the buoy also lends itself well to the validation of numerical modelling studies.
description: Wave_buoys_in_current_data_desciption.pdf - Provides a description of the experimental setup; test programme; instrumentation types; data file structure and measurement units; and test/filename list. Wave_buoys_in_current.zip - Packaged ASCII .csv data files as documented in Wave_buoys_in_current_data_desciption.pdf
DOI: 10.7488/ds/3116
title: Supporting data for: "The properties of human disease mutations at protein interfaces"

description: ABSTRACT: The assembly of proteins into complexes and interactions with other biomolecules are often vital for their biological function. While it is known that mutations at protein interfaces have a high potential to be damaging and cause human genetic disease, there has been relatively little consideration for how this varies between different types of interfaces. Here we investigate the properties of human pathogenic and putatively benign missense variants at homomeric (isologous and heterologous), heteromeric, DNA, RNA and other ligand interfaces, and at different regions with respect to those interfaces. We find that different types of interfaces vary greatly in their propensity to be associated with pathogenic mutations, with homomeric heterologous and DNA interfaces being particularly enriched in disease. We also find that residues that do not directly participate in an interface, but are close in 3D space, also show a significant disease enrichment. Finally, we show that mutations at different types of interfaces tend to have distinct property changes when undergoing amino acid substitutions associated with disease, and that this is linked to substantial variability in their identification by computational variant effect predictors.
description: * "annotation.out": Interface residue classifications (core/support/rim) from PDB structures. * "clinvar_set_VEPs.csv" and "gnomad_set_VEPs.csv": Pathogenic and putatively benign SNV datasets including uniprot and PDB mappings, relative protein location and VEP predictions. * "full_ints2.out": List of all interfaces and involved residues within the clinvar and gnomAD datasets. * "membrane_proteins.list": list of membrane protein uniprot IDs which were excluded from some analyses (plain text format). * "Ribosomal_proteins.list": list of ribosomal protein uniprot IDs which were excluded from some analyses (plain text format). * "Table_S1.csv": Full dataset of protein property changes by location.
DOI: 10.7488/ds/3156
title: Supplementary Tables for David W Clark's PhD Thesis "Inbreeding depression on human complex traits"

description: Appendix tables from the doctoral thesis of David W Clark "Inbreeding depression on human complex traits".
DOI: 10.7488/ds/3805
title: Interfacial adsorption kinetics of methane in microporous kerogen

description: This data folder contains the LAMMPS input files for running the molecular dynamics (MD) simulations in the paper Wang R., Datta S., Li J., Al-Afnan S. F.K., Gibelli L., Borg. M.K., 'Interfacial adsorption kinetics of methane in microporous kerogen.' Langmuir (in submission). It also contains the raw MD data for the adsorption simulations carried out on 6 different kerogen types.
DOI: 10.7488/ds/3096
title: Shock-induced collapse of surface nanobubbles

description: This dataset contains all the initial molecular configurations required to run some of the LAMMPS molecular dynamics simulations of shock induced collapse of nanobubbles that we present in our paper.
DOI: 10.7488/ds/3097
title: RESTART trial main results dataset

description: Analysis dataset used for the RESTART main results and imaging sub-study results papers in 2019
description: Protocol, SAP, data dictionary, sharing dataset, annotated CRFs
DOI: 10.7488/ds/3109
title: Absolute units in Arabidopsis clock models up to U2020.3
title: Testing the inferred transcription rates of a dynamic, gene network model in absolute units

description: Starting from the P2011 model of the circadian clock in Arabidopsis thaliana, this project corrects theoretical issues (steady-state binding assumption for the Evening Complex, EC) to form an intermediate model (published as U2019.1), rescales parameters to match absolute RNA levels from the TiMet WP1a RNA dataset of Flis et al. 2015 in U2019.2, then reoptimises model parameters globally to match RNA timeseries, period and amplitude constraints to produce the U2019.3 model. This project then replaces regulation of the PRRs with repression by later-expressed genes (instead of activation by earlier ones, as in P2011/P2012/U2019) in the U2019.2 model, to create the U2020.1 model, then also rescales to match the protein levels that were independently predicted by a simple translation model from those RNA levels, in the U2020.2 model, and performs a global reoptimisation as above to form U2020.3. The input data files, the computational environment for model development (a Docker image in the 'Reproducibility Toolset' assay) and the relevant model files and documentation are included here, as published in Urquiza and Millar, In Silico Plants, 2021. The biorXiv preprint version of the publication is linked here. The DOI for the publication was not yet available. The work was funded by a PhD scholarship from Conacyt, Mexico to U. Urquiza Garcia.
description: The input data files, the computational environment for model development (a Docker image in the 'Reproducibility Toolset' assay) and the relevant model files and documentation are included here, as published in Urquiza and Millar, In Silico Plants, 2021. The biorXiv preprint version of the publication is linked here. The DOI for the publication was not yet available. The files are provided within a structured hierarchy derived from SEEK software at the FAIRDOMHub.org repository. SEEK uses the standard ISA format, with metadata and external links at several levels, in addition to file metadata. The ISA files can be read using software available here https://isa-tools.org/software-suite.html. They are mirrored by the folder structure within the .ZIP archive file.
DOI: 10.7488/ds/3107
title: Extended Supplementary Tables for Thesis: "Omics Measures of Ageing and Disease Susceptibility" by Erin Macdonald-Dunlop

description: Extended supplementary tables from the thesis entitled "Omics Measures of Ageing and Disease Susceptibility" by Erin Macdonald-Dunlop. Supplementary tables for the three results chapters are in the corresponding folders. The enclosed tables match the links in the thesis appendix.
DOI: 10.7488/ds/3110
title: Complex small-world regulatory networks emerge from the 3D organisation of the human genome

description: The discovery that overexpressing one or a few critical transcription factors can switch cell state suggests that gene regulatory networks are relatively simple. In contrast, genome-wide association studies (GWAS) point to complex phenotypes being determined by hundreds of loci that rarely encode transcription factors and which individually have small effects. Here, we use computer simulations and a simple fitting-free polymer model of chromosomes to show that spatial correlations arising from 3D genome organisation naturally lead to stochastic and bursty transcription as well as complex small-world regulatory networks (where the transcriptional activity of each genomic region subtly affects almost all others). These effects require factors to be present at sub-saturating levels; increasing levels dramatically simplifies networks as more transcription units are pressed into use. Consequently, results from GWAS can be reconciled with those involving overexpression. We apply this pan-genomic model to predict patterns of transcriptional activity in whole human chromosomes, and, as an example, the effects of the deletion causing the diGeorge syndrome. ## Software ## For information on the LAMMPS see https://www.lammps.org .
DOI: 10.7488/ds/3106
title: Data supporting "Ultraviolet radiation drives emission of climate-relevant gases from marine phytoplankton"

description: This dataset comprises results contained in a manuscript entitled "Ultraviolet radiation drives emission of climate-relevant gases from marine phytoplankton" that describes an investigation of the production of carbon monoxide, carbon dioxide, methane, ethene, ethane, and nitrous oxide from cell suspensions of 16 marine phytoplankton species and their filtrates when exposed to ultraviolet radiation under controlled experimental conditions.
DOI: 10.7488/ds/3111
title: Self-diffusivity of dense confined fluids

description: Diffusion measurements using Event Driven Molecular Dynamics simulations in slit geometries. The parametric space covers confinement, and Knudsen number (or reduced fluid densities) for a rough surface.
DOI: 10.7488/ds/3419
title: Rare-earth precipitation by capsule formation

description: Quantitative ICP-MS data for rare-earth precipitations, nuclear magnetic resonance (NMR) spectroscopic data, infrared and Raman spectroscopic data, electrospray-ionisation mass spectrometry (ESI-MS) data.
DOI: 10.7488/ds/2972
title: Mendelian randomization of genetically independent aging phenotypes identifies LPA and VCAM1 as biological targets for human aging
title: Mendelian randomisation of genetically independent ageing phenotypes identifies LPA and VCAM1 as drug targets for human ageing

description: Genome-wide association summary statistics supporting the article Timmers et. al (2022) Nature Aging https://doi.org/10.1038/s43587-021-00159-8.
DOI: 10.7488/ds/3119
title: Translanguaging and product-oriented drama: Full Transcript
title: Translanguaging and product-oriented drama: Appendix II Full Transcript

description: Foreign language theatre groups are extra-curricular projects for students aiming to develop their language skills by staging performances of authentic plays. The current study investigated the translanguaging practices of 12 students and a teacher rehearsing a German play as part of a UK university theatre group comprising different European nationalities. Our aim was to understand how these practices can support foreign language and literacy development in the context of a script-based, product-oriented approach to drama. Three group rehearsals were audio-recorded and transcribed. Following identification of translanguaging instances, discourse analysis was applied to extracts selected for their relevance to the research questions. The findings revealed that rehearsals provided a rich learning environment in which participants were affectively engaged, with specific opportunities for contextualised language learning and literacy development. Translanguaging enhanced these learning opportunities, enabling students to engage with the German script and its language as bilinguals, and drawing on both their linguistic and multimodal repertoires to learn. The study concluded that the integration of translanguaging and product-oriented drama offers a linguistically diverse and embodied pedagogical approach to language education, which offers a wealth of learning affordances that are less readily accessed in monolingual environments.
DOI: 10.7488/ds/3103
title: Data supporting the thesis "The Evolutionary Genomics of Chlamydomonas"
title: transposable elements

description: Files from the PhD thesis "The Evolutionary Genomics of Chlamydomonas" by Rory Craig. Appendix C: Supplementary Material for Chapter 3: Note S1. High molecular weight DNA extraction protocol for Chlamydomonas. Dataset S1: Annotation notes for curated transposable elements from Chlamydomonas incerta, Chlamydomonas schloesseri, Edaphochlamys debaryana, Eudorina sp. and Volvox carteri. See Appendix E, Dataset S1 for Chlamydomonas reinhardtii transposable element annotation notes. Dataset S2: Assembly metrics for genome assemblies of all available Reinhardtinia species and selected outgroups. Dataset S3: Gene model annotation metrics for all available Reinhardtinia species and selected outgroups. Dataset S4. List of contigs terminating in telomeric repeats. Dataset S5. Orthogroup and InterPro domain annotation for Chlamydomonas-specific orthogroups with annotated domains. Dataset S6: Orthogroup and InterPro domain annotation for E. debaryana gene family expansions (log2-transformed ratios &gt;1) and contractions (ratios &lt;-1) . Dataset S7: Presence-absence of C. reinhardtii MT– genes in C. incerta, C. schloesseri and E. debaryana. Dataset S8: New genes identified with significant blastp homology to proteins from the C. reinhardtii v4.3 annotation. Dataset S9: Core-Reinhardtinia ultraconserved elements (elements &gt;=50 bp, 100% conservation within Chlamydomonas and &gt;=95% conservation across eight core-Reinhardtinia species). Appendix D: Supplementary Material for Chapter 4: Dataset S1: Metrics and sequence context of all CC-503 v6 assembly gaps. Dataset S2: Curated structural mutations unique to the CC-503 v6 assembly. Dataset S3: Curated structural mutations unique to the CC-4532 v6 assembly. Dataset S4. Metrics and sequence context of all CC-4532 v6 assembly gaps. Dataset S5. Curated TE transposition events unique to the CC-503 v6 assembly. Dataset S6: Curated TE transposition events unique to the CC-4452 v6 assembly. Appendix E: Supplementary Material for Chapter 5: Dataset S1: Annotation notes for the updated transposable element library for Chlamydomonas reinhardtii. Dataset S2: Chlamys annotation notes. Dataset S3: Naiad annotation notes. Dataset S4. Chlamys-like annotation notes. Dataset S5. Hydra annotation notes.
DOI: 10.7488/ds/3118
title: Translanguaging and product-oriented drama: Eight extracts for discourse analysis
title: Translanguaging and product-oriented drama: Appendix I Extracts Dataset

description: Foreign language theatre groups are extra-curricular projects for students aiming to develop their language skills by staging performances of authentic plays. The current study investigated the translanguaging practices of 12 students and a teacher rehearsing a German play as part of a UK university theatre group comprising different European nationalities. Our aim was to understand how these practices can support foreign language and literacy development in the context of a script-based, product-oriented approach to drama. Three group rehearsals were audio-recorded and transcribed. Following identification of translanguaging instances, discourse analysis was applied to extracts selected for their relevance to the research questions. The findings revealed that rehearsals provided a rich learning environment in which participants were affectively engaged, with specific opportunities for contextualised language learning and literacy development. Translanguaging enhanced these learning opportunities, enabling students to engage with the German script and its language as bilinguals, and drawing on both their linguistic and multimodal repertoires to learn. The study concluded that the integration of translanguaging and product-oriented drama offers a linguistically diverse and embodied pedagogical approach to language education, which offers a wealth of learning affordances that are less readily accessed in monolingual environments.
DOI: 10.7488/ds/3114
title: Terrestrial LiDAR of southern African woodland vegetation, Bicuar National Park (Angola), Mtarure Forest Reserve (Tanzania)

description: Terrestrial LiDAR point clouds and hemispherical photographs from 1 ha plots in southern African woodlands. 15 plots in Bicuar National Park, Angola, and 7 plots in Mtarure Forest Reserve, Tanzania. Scans were located to maximise woodland tree canopy penetration.