cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/3453
title: Prediction and analysis of phenotypes in the Arabidopsis clock mutant prr7prr9 using the Framework Model v2 (FMv2)
title: The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation

description: This upload contains or links to the biological data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), updated 2022 as bioRxiv https://doi.org/10.1101/105437v2, mostly testing and simulating the effect of a slow circadian clock in the prr7prr9 double mutant compared to the Col wild type plants, with controls in lsf1 and prr7 single mutants. Effects tested comprise gene expression, hypocotyl elongation, flowering time, major carbon metabolite levels, gas exchange and growth in terms of leaf number, area and biomass. This is one of the outputs from the EU TiMet project, https://fairdomhub.org/projects/92. Several data files contain results generated in the same studies, but not covered by the publication. For example, additional time points (18 or 21 days of growth), many additional metabolites, and additional genotypes including pgm, lhy cca1, and in one case, toc1 and gi. This data archive was updated during submisson to the journal _in Silico _Plants in 2022, and is formatted as a Research Object, generated by the Snapshot function of FairdomHub, based on Investigation https://fairdomhub.org/investigations/123. The same Snapshot is shared on FairdomHub and Zenodo. We request that users gives appropriate credit to the authors of any data released here, as a norm of academic practice, including data released under CC-0 licence on the FairdomHub. CC-0 was not available on Zenodo or DataShare.
description: This data archive is formatted as a Research Object, generated by the Snapshot function of FairdomHub, based on Investigation https://fairdomhub.org/investigations/123. It is a single .ZIP format file, with internal directories that follow the Investigation/Study/Assay (ISA) hierarchy of FairdomHub and metadata on each level in JSON and RDF files, linked to Data and Model files. Further detail is provided in the ReadMe.txt file and the .PNG image of the ISA hierarchy.
DOI: 10.7488/ds/3461
title: Identification and characterisation of immunoreactive fungal proteins recognised by sera from Zimbabweans sensitised to fungi

description: Exposure and sensitisation to fungal allergens poses a serious threat to human health. The prevalence of fungal allergic disease is increasing globally but is poorly studied in Africa. This study aimed to identify and characterise fungal proteins that were immunoreactive against serum samples from fungal-sensitised Zimbabweans. A pool of eight sera (3-5 years old) from fungi (Aspergillus fumigatus, Alternaria alternata, Cladosporium herbarum, Epicoccum nigrum, Penicillium chrysogenum, Rhizopus nigricans and Saccharomyces cerevisiae) sensitive Zimbabwean children (as determined by Skin prick tests) was used to screen proteins for immunoreactivity. Protein bands recognised by the sera were identified via mass spectrometry and bioinformatic analysis. The data on the identified proteins and the metadata of the eight children are presented here.
DOI: 10.7488/ds/3457
title: High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights on proto-oncogene deregulation

description: Simulation and experimental data and related scripts associated with the paper "High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights on proto-oncogene deregulation".
DOI: 10.7488/ds/3459
title: Breakup of a laminar liquid jet by coaxial non-swirling and swirling air streams

description: The dataset includes the drawings of the air swirlers, non-dimensional breakup lengths, first droplet locations, vector fields of the annular air flows, vorticity maps, POD modes, frequencies of the flapping instabilities, and 2D spectra.
DOI: 10.7488/ds/3844
title: Resonant noise amplification in a predator-prey model with quasi-discrete generations

description: Predator-prey models have been shown to exhibit resonance-like behaviour, in which random fluctuations in the number of organisms (demographic noise) are amplified when their frequency is close to the natural oscillatory frequency of the system. This behaviour has been traditionally studied in models with exponentially distributed replication and death times. Here we consider a biologically more realistic model, in which organisms replicate quasi-synchronously such that the distribution of replication times has a narrow maximum at some T&gt;0 corresponding to the mean doubling time. We show that when the frequency of replication f=1/T is tuned to the natural oscillatory frequency of the predator-prey model, the system exhibits oscillations that are much stronger than in the model with Poissonian (non-synchronous) replication and death. The effect can be explained by resonant amplification of coloured noise generated by quasi-synchronous replication events. To show this, we consider a single-species model with quasi-synchronous replication. We calculate the spectrum and the amplitude of demographic noise in this model, and use these results to obtain these quantities for the two-species model. The dataset is related to the publication M. Giannakou and B. Waclaw, Resonant noise amplification in a predator-prey model with quasi-discrete generations, arxiv:2301.13290 . The research is funded by the Max Planck Society and the Polish National Science Centre, both contributing through the Dioscuri Programme.
DOI: 10.7488/ds/3507
title: Inertio-Thermal Vapour Bubble Growth

description: This data folder contains the bubble growth data obtained from literature, MD simulation, and the IT model predictions presented in the paper. LAMMPS input files are provided for running the molecular dynamics simulations. Simulations were performed with LAMMPS version 29 Sep 2021.
DOI: 10.7488/ds/3788
title: Edinburgh Castle cloud burst data

description: Data for paper entitled "The impact of an extreme cloud burst on Edinburgh Castle" by Simon F. B. Tett, YoungHwa Cha, Kate Donovan, Gina-Maria Geffers and Ed Hawkins. This includes seasonal maximum rainfall from the UKCP18 CPM simulations for a roughly 200x200 km region centred on Edinburgh, and 15-minute radar maxima. Also includes parameters from GEV fits.
description: CPM_data -- seasonal maximum rainfall, seasonal mean and time of max for CPM simulations within about 200 km of Edinburgh. Sub directories contain data for each ensemble and for each time period. gev_fits_roll -- GEV fits to the CPM data images -- various images used nimrod_data -- samples of Nimrod radar data for July 4th 2021 (1km data) and summer 2021 & 2020 (5km data) radar_precip -- processed Nimrod data -- monthly max, mean and time of max for 1km 15 minute data (and some other data) ratios_roll -- computed distributions, intensity ratios and probability ratios. Not too hard to generate but saves time when plotting covariates -- covariate data from CPM data. orog_land-cpm_BI_2.2km.nc -- orographic data for the CPM. Contains height on rotated long/lat grid. * u2018_clc2018_v2020_20u1_ratster100m -- Corine Land Cover. Obtained from https://land.copernicus.eu/pan-european/corine-land-cover/clc-2000/view * uk_strm -- DEM regridded to OS GB grid at resoln of circa 100m. Obtained from https://doi.org/10.7488/ds/1928 * bdline_essh_gb -- boundary line data from the OS. Available from https://osdatahub.os.uk/downloads/open/BoundaryLine * GB_OS_boundaries -- created from bdline_essh_gb data using create_counties.py * GEBCO_topog_bathy_scotland.nc -- BEBCO topographic & bathy data. Extracted from 10.5285/c6612cbe-50b3-0cff-e053-6c86abc09f8f * -- files/directories not present as user should get those themselves.
DOI: 10.7488/ds/3799
title: Compressive properties of parametrically optimised mechanical metamaterials based on 3D projections of 4D geometries

description: This data set includes raw data with explantory text and diagrams for the engrXiv preprint, "Compressive properties of parametrically optimised mechanical metamaterials based on 3D projections of 4D geometries" by Gabrielis Cerniauskas and Parvez Alam (https://doi.org/10.31224/2796). The abstract for this paper is as follows: The design process of 3D mechanical metamaterials is still an emerging field and in this paper, we propose for the first time, a new design and optimisation approach based on 3D projections of 4D geometries (4-polytopes) and evolutionary algorithms. We find that through iterative parametric optimisation, 4-polytope projected mechanical metamaterials can be optimised to achieve both high specific stiffness and high specific yield strengths. Samples manufactured using a low-stereolithography method were tested in compression. We find that optimised tesseracts (8-cell structures) had a higher specific yield strength (22.8 kNm/kg) than that of honeycomb structures tested out-of-plane (19.4 kNm/kg) and a specific stiffness of (0.68 MNm/kg) which is more than 3-fold that of gyroid structures. The compressive strength to solid-modulus ratio of the 8-cell tesseract is very high (3×10−3), exceeding that of out-of-plane honeycombs, which are themselves closer in value to 5-cell pentatopes (2×10−3). 8-cell and 5-cell structures are in the region of one order of magnitude higher than 16-cell and 24-cell structures (∼ 2 × 10−4 − 8 × 10−4) and are hence comparable to nanostructured metamaterials. The 8-cell tesseracts are 18% stiffer, 43% stronger, and 19% tougher in compression than out-of-plane honeycomb structures, but unlike honeycombs, 8-cell tesseracts are 3D structures with cubic symmetry. Architecture has a profound effect on the relative consistency of properties with cubically symmetric structures displaying the greatest levels of consistency in terms of both strength and stiffness reduction as a function of pore space. The results presented in this paper showcase the potential of this new class of mechanical metamaterial based on 3D projected 4-polytopes.
DOI: 10.7488/ds/3482
title: REMOVED: Shifting the Narrative: Exploring the role of arts interventions in supporting communities in working across sectors to achieve place-based climate action.

description: REMOVED: This dataset has been removed from datashare as consent was revoked by the participants. This dataset is a collection of interview transcripts, survey results and field notes for a project investigating the role and challenges storytelling can play for shifting towards a sustainable society. At this critical point in human history, the efforts of all sectors are needed to help society move towards net-zero in the face of the twin crises of biodiversity loss and climate change. Funding from the British Academy’s Shared Understandings stream enabled us to explore what the community-based storytelling sector is contributing to shifting narratives towards sustainability. Our focus is to give voice to what informed advocates of traditional and performance storytelling have learned from the work they have been doing across the UK and beyond. Our findings also inform work with stories in other contexts and mediums, formal and informal.
DOI: 10.7488/ds/3487
title: SUPERSEDED - FLEGT Agreement Document Coding

description: ## This item has been replaced by the one which can be found at https://datashare.ed.ac.uk/handle/10283/4473 ## This data set contains an NVivo 11 coding file for 161 documents covering the EU's FLEGT Action Plan and Voluntary Partnership Agreement negotiations with partner countries. It was coded as part of an SRSF grant funded research project and focuses on the applicability of the Market Power Europe framework to the FLEGT Action Plan.
DOI: 10.7488/ds/3786
title: Structure of SALL4 zinc-finger domain reveals link between AT-rich DNA binding and Okihiro syndrome

description: Spalt-like 4 (SALL4) maintains vertebrate embryonic stem cell identity and is required for the development of multiple organs, including limbs. Mutations in SALL4 are associated with Okihiro syndrome and SALL4 is also a known target of thalidomide. SALL4 protein has a distinct preference for AT-rich sequences, recognised by a pair of zinc fingers at the C-terminus. However, unlike many characterised zinc finger proteins, SALL4 shows flexible recognition with many different combinations of AT-rich sequences being targeted. SALL4 interacts with the NuRD corepressor complex which potentially mediates repression of AT-rich genes. We present a crystal structure of SALL4 C-terminal zinc fingers with an AT-rich DNA sequence, which shows that SALL4 uses small hydrophobic and polar side chains to provide flexible recognition in the major groove. Missense mutations reported in patients that lie within the C-terminal zinc fingers reduced overall binding to DNA but not the preference for AT-rich sequences. Furthermore, these mutations altered association of SALL4 with AT-rich genomic sites, providing evidence that these mutations are likely pathogenic. ## Complementary datasets ## Datasets in this repository complement additional datasets that are deposited in public databases: * Coordinates and structure factors are deposited in the Protein Data Bank: accession 8A4I; * SAXS data are deposited in the small angle scattering database (SASDB): accessions SASDP64 (SALL4 ZFC4); SASDP74 (DNA); SASDP84 (SALL4 ZFC4 + DNA); * HT-SELEX data are deposited at Array express: accession E-MTAB-11519.
description: Datasets in this repository complement additional datasets that are deposited in public databases: Coordinates and structure factors are deposited in the Protein Data Bank: accession 8A4I SAXS data are deposited in the small angle scattering database (SASDB): accessions SASDP64 (SALL4 ZFC4); SASDP74 (DNA); SASDP84 (SALL4 ZFC4 + DNA) HT-SELEX data are deposited at Array express: accession E-MTAB-11519.
DOI: 10.7488/ds/3488
title: A dataset on vowel quality and Advanced Tongue Root in Shilluk

description: This document describes a dataset designed to investigate vowel quality and ATR in Shilluk. The primary data are sound files, digitally recorded at 48kHz using a Marantz PMD 660 recorder and a Shure SM10A microphone. The recordings were made in December 2008 and January 2009, with nine native speakers of Shilluk (three women, six men) who resided in Khartoum, the capital of Sudan. It includes 1105 files - 562 wav files and 543 Praat TextGrid files. See DescriptionOfTheDataset.pdf for a detailed description.
description: See DescriptionOfTheDataset.pdf
DOI: 10.7488/ds/3490
title: Inertia-gravity wave energy in 2D spectral space from a high-resolution Boussinesq simulation

description: This dataset is the end result of a high-resolution three-dimensional Boussinesq simulation allowed to run until its statistics are approximately stationary. It contains 3 CSV files. Ew.csv, a 406 X 575 matrix, is the IGW energy spectrum across a grid of 406 horizontal and 575 vertical wavenumbers. kh.csv and kz.csv are meshgrid values of the horizontal and vertical wavenumbers respectively, both the same size as Ew.csv. Details of the simulation and figures produced from this data can be found in "Inertia-gravity-wave diffusion by geostrophic turbulence: the impact of flow time dependence" (to be submitted) by Michael R. Cox, Hossein A. Kafiabad & Jacques Vanneste.
DOI: 10.7488/ds/3491
title: FLEGT Agreement Document Coding

description: This data set contains an NVivo 11 coding file for 164 documents covering the EU's FLEGT Action Plan and Voluntary Partnership Agreement negotiations with partner countries. It was coded as part of an SRSF grant funded research project and focuses on the applicability of the Market Power Europe framework to the FLEGT Action Plan. The data set contains the NVivo 11 coding file (Windows and Mac versions) and, contained within the .zip file, the 164 documents, in either PDF or Word format. These documents cover the following country cases: Cameroon (7), Central African Republic (8), Côte d'Ivoire (1), Democratic Republic of the Congo (1), Gabon (4), Ghana (17), Guyana (6), Honduras (9), Indonesia (21), Laos (36), Liberia (8), Republic of the Congo (21), Thailand (19), and Vietnam (5).
DOI: 10.7488/ds/3483
title: Dataset for paper "Model-scale experiments of passive pitch control for tidal turbines"

description: This dataset contains the raw data used to generate the anaysis and figures of the paper "Model-scale experiments of passive pitch control for tidal turbines", authored by Stefano Gambuzza, Gabriele Pisetta, Thomas Davey, Jeffrey Steynor, and Ignazio Maria Viola. This dataset also contains all scripts necessary to replicate the figures presented in the paper. Raw data is contained in the folder "datazet.zip/data/", Matlab functions to process the raw data are contained in the folder "dataset.zip/private/", and scripts that generate the plots are contained directly in the archive.
DOI: 10.7488/ds/3489
title: Quantification of Macrophage-Driven Inflammation During Myocardial Infarction with 18F-LW223, a Novel TSPO Radiotracer with Binding Independent of the rs6971 Human Polymorphism

description: Myocardial infarction (MI) is one of the leading causes of death worldwide, and inflammation is central to tissue response and patient outcomes. The 18-kDa translocator protein (TSPO) has been used in PET as an inflammatory biomarker. The aims of this study were to screen novel, fluorinated, TSPO radiotracers for susceptibility to the rs6971 genetic polymorphism using in vitro competition binding assays in human brain and heart; assess whether the in vivo characteristics of our lead radiotracer, 18F-LW223, are suitable for clinical translation; and validate whether 18F-LW223 can detect macrophage- driven inflammation in a rat MI model. Methods: Fifty-one human brain and 29 human heart tissue samples were screened for the rs6971 polymorphism. Competition binding assays were conducted with 3H-PK11195 and the following ligands: PK11195, PBR28, and our novel compounds (AB5186 and LW223). Na¨ıve rats and mice were used for in vivo PET kinetic studies, radiometabolite studies, and dosimetry experiments. Rats underwent permanent coronary artery ligation and were scanned using PET/CT with an invasive input function at 7 d after MI. For quantification of PET signal in the hypoperfused myocardium, K1 (rate constant for transfer from arterial plasma to tissues) was used as a surrogate marker of perfusion to correct the binding potential for impaired radiotracer transfer from plasma to tissue (BPTC). Results: LW223 binding to TSPO was not susceptible to the rs6971 genetic polymorphism in human brain and heart samples. In rodents, 18F-LW223 displayed a specific uptake consistent with TSPO expression, a slow metabolism in blood (69% of parent at 120 min), a high plasma free fraction of 38.5%, and a suitable dosimetry profile (effective dose of 20.5–24.5 μSv/MBq). 18F-LW223 BPTC was significantly higher in the MI cohort within the infarct territory of the anterior wall relative to the anterior wall of na¨ıve animals (32.7 ± 5.0 vs. 10.0 ± 2.4 cm3/mL/min, P # 0.001). Ex vivo immunofluorescent staining for TSPO and CD68 (macrophage marker) resulted in the same pattern seen with in vivo BPTC analysis. Conclusion: 18FLW223 is not susceptible to the rs6971 genetic polymorphism in in vitro assays, has favorable in vivo characteristics, and is able to accurately map macrophage-driven inflammation after MI. Mark G. MacAskill, Agne Stadulyte, Lewis Williams, Timaeus E.F. Morgan, Nikki L. Sloan, Carlos J. Alcaide- Corral, Tashfeen Walton, Catriona Wimberley, Chris-Anne McKenzie, Nick Spath, William Mungall, Ralph BouHaidar, Marc R. Dweck, Gillian A. Gray, David E. Newby, Christophe Lucatelli, Andrew Sutherland, Sally L. Pimlott, and Adriana A.S. Tavares
DOI: 10.7488/ds/3484
title: Development of an in vivo radiographic method with potential for use in improving bone quality and the welfare of laying hens through genetic selection.

description: Data from the measurement of bone density of laying hens using post mortem density and quasi static material testing and live bird x-ray derived density estimates. This is for the validation of live bird x-ray as a potential tool for genetic selection. A reproducability/repeatability study and a manipulation of skeletal quality experiment are included and a SOP for the performance of the technique to allow replication and to give more data than in the paper this accompanies.
description: CBPS_P172_DensityBS.csv Body weight, Post mortem tibia breaking strength, stiffness and density, live bird tibia density estimate, a key is included CBPS_P172_DensityBS.xslx Body weight, Post mortem tibia breaking strength, stiffness and density, live bird tibia density estimate, a key is included CBPS_P172_RepeatabilityReproducability.csv Body weight, Post mortem tibia breaking strength, stiffness and density, live bird tibia density estimate made on successive days and measured by two operators CBPS_P172_RepeatabilityReproducability.xslx RepeatabilityReproducability.csv Body weight, Post mortem tibia breaking strength, stiffness and density, live bird tibia density estimate made on successive days and measured by two operators CBPS_P180_Tibia.csv Body weight, Post mortem tibia breaking strength, stiffness and density, live bird tibia density estimate for hens fed with diets differing in calcium and phosphorous content, a key is included CBPS_P180_Tibia.xslx Body weight, Post mortem tibia breaking strength, stiffness and density, live bird tibia density estimate for hens fed with diets differing in calcium and phosphorous content, a key is included SOP-X-Ray.docx Detailed methodology to carry out live bird x-ray.
DOI: 10.7488/ds/3492
title: 3 T BOLD CVR data from healthy volunteers suitable for within-day repeatability analyses

description: We aimed to assess the repeatability of CVR measurements using 3 T BOLD MRI and a fixed CO2 inspired gas challenge. Therefore, we recruited healthy volunteers. Each had two CVR scans in two separate within-day MRI sessions. Between sessions, the participants came out of the scanner and scanner room. In the first MRI session, we also acquired anatomical brain scans. The dataset contains data from the 15 healthy volunteers: anatomical images (T1w, T2w), CVR-BOLD images. End-tidal CO2 and O2 traces acquired during the CVR scans can also be found along with the heart and respiration rates. # Associated publication # Sleight et al. "Cerebrovascular reactivity measurements using 3 T BOLD MRI and a fixed inhaled CO2 gas challenge: repeatability and impact of processing strategy" (accepted manuscript) Frontiers in Physiology