cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2843
title: Scripts - software suite, scores and documentary recordings

description: The files included here are a set of live performance recordings of Scripts, performed live at St Giles Cathedral in Edinburgh by the Quasar Sax Quartet with computer processing by Martin Parker. Quasar Saxophone Quartet are: Marie-Chantal Leclair, Jean-Marc Bouchard, Mathieu Leclair, Thomas Vachon-Croteau.
DOI: 10.7488/ds/2760
title: N2An2mTP2 open data
DOI: 10.7488/ds/2453
title: Characterisation of the UK honey bee metagenome

description: The European honey bee (Apis mellifera) plays a major role in pollination and food production, but is under threat from emerging pathogens and agro-environmental insults. As with other organisms, honey bee health is a complex product of environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of bee genetics and their molecular ecology can help manage modern challenges to bee health and production. Sampling bee and cobiont genomes, we characterised the metagenome of 19 honey bee colonies across Britain. Low heterozygosity was observed in bees from many Scottish colonies, sharing high similarity to the native dark bee, A. mellifera mellifera. Apiaries exhibited high diversity in the composition and relative abundance of individual microbiome taxa. Most non-bee sequences derived from known honey bee commensal bacteria or known pathogens, e.g. Lotmaria passim (Trypanosomatidae), and Nosema spp. (Microsporidia). However, DNA was also detected from numerous additional bacterial, plant (food source), protozoan and metazoan organisms. To classify sequences from cobionts lacking genomic information, we developed a novel network analysis approach clustering orphan contigs, allowing the identification of a pathogenic gregarine. Our analyses demonstrate the power of high-throughput, directed metagenomics in agroecosystems identifying potential threats to honey bees present in their microbiota.
description: Contains raw Illumina reads, assembled contigs, annotated clusters of contigs. View ReadMe.txt for description of files.
DOI: 10.7488/ds/2347
title: Computational Modelling of malaria diagnostic test

description: Early diagnosis of malaria is important for the prevention of malaria disease outbreak and providing an affected person with appropriate treatment early on. In malaria-endemic areas, where resources and access to health care are limited, the malaria rapid diagnostic test (mRDT) has widely been used because it is easy to use, cheap and fast. However, mRDT is prone to several limitations, such as inconsistent diagnostic specificity and sensitivity between different brands. Here, we build the first computational chemical kinetic model of mRDT which allows simulation of different parameter sets by using complex pathway simulator software (COPASI). Our model successfully reproduces in-vivo experimental results, confirming its validity. Using our model, we explore the principle of mRDT and demonstrate the potential for enhancing the diagnostic range of mRDT through parameter optimisation. Moreover, we use our model to investigate the prozone effect, the false negative response resulting from hyper-parasitaemia. This has previously been observed when using only the mRDT against Plasmodium histidine-rich protein-2 (pHRP-2) and not Plasmodium lactate dehydrogenase (pLDH). Our model can reproduce this result and is the first to provide a mechanistic explanation for why test differs in their susceptibility to the prozone effect. N.B. The COPAS software is open source and may be downloaded from: http://copasi.org/
DOI: 10.7488/ds/2490
title: Untargeted Metabolite Mapping in 3D Cell Culture Models using High Spectral Resolution FT-ICR Mass Spectrometry Imaging - Datasets

description: Mass spectrometry imaging (MSI) is an effective tool to investigate multicellular tumor spheroids (MTS) in a spatially-resolved manner. It has been used to study the distribution of lipids, post-translational modifications, metabolites and the time-dependent penetration of drugs. Using the high spectral resolution achievable with Fourier-transform ion cyclotron resonance (FT-ICR), here we use MSI to image 8-day-old MCF-7 spheroids. We show that specific metabolite markers (adenosine phosphates and glutathione) indicate that the central region of these cell culture models experience increased hypoxic and oxidative stress. By using discriminatory analysis, we have identified which m/z values localize towards the outer proliferative or central hypoxic regions of an MTS, and have assigned elemental formula with sub-ppm error. Using this information, we have mapped these metabolites back to distinct pathways to improve our understanding of the molecular environment of a tumor
description: See Readme.pdf for details. All MSI datafiles are uploaded as both .imzML and .ibd raw files (suitable for viewing on multiple platforms)
DOI: 10.7488/ds/2501
title: Thiourea Bismuth Iodide: Crystal structure, Characterization and High Performance as an Electrode Material for Supercapacitors

description: This paper reports on the synthesis, crystal structure and application of a novel hybrid bismuth-halide complex: (CN2SH5)3BiI6 (TBI) for supercapacitor applications, featuring merits including high areal capacitance, low cost, solution-processability and non-toxicity. Single crystal X-ray diffraction reveals that TBI crystallizes in the monoclinic system, with discrete [BiI6]3- octahedra as the inorganic motif. Utilizing TBI as the active supercapacitor electrode material with carbon cloth current collector and aqueous NaClO4 electrolyte, an electrode areal capacitance of 3.32 F/cm2 and a systemic specific capacitance of 1030 F/g was achieved when the device operates as an electric double-layer capacitor (EDLC). The supercapacitor device shows excellent capacitance retention even after 5,000 charge-discharge cycles. The powder XRD patterns, Raman spectroscopy and SEM images of TBI electrodes were compared before and after the cycling test to demonstrate the material stability and investigate the film morphology.
DOI: 10.7488/ds/2556
title: Lamin A conformation modelling

description: Data in support of manuscript: "Lamin A molecular compression and sliding as mechanisms behind nucleoskeleton elasticity" Lamin A is a nuclear intermediate filament protein critical for nuclear architecture and mechanics and mutated in a wide range of human diseases. Yet little is known about the molecular architecture of lamins and mechanisms of their assembly. Here we use cross-linking SILAC mass spectrometry to determine interactions within lamin dimers and between dimers in higher-order polymers. We find evidence for a compression mechanism where coiled coils in the lamin A rod can slide onto each other to contract rod length, likely driven by a wide range of electrostatic interactions with the flexible linkers between coiled coils. Similar interactions occur with unstructured regions flanking the rod domain during oligomeric assembly. Mutations linked to human disease block these interactions, suggesting that this spring-like contraction can explain in part the dynamic mechanical stretch and flexibility properties of the lamin polymer and other intermediate filament networks.
DOI: 10.7488/ds/2456
title: Lock-in spin structures and ferrimagnetism in polar Ni2-xCoxScSbO6 oxides

description: All data are for the paper published in Chem Comm 2018. Powder X-ray and neutron diffraction datasets and cif crystallographic files. Magnetisation vs temperature or field data.
DOI: 10.7488/ds/2359
title: Dimensional crossover of correlated anion disorder in oxynitride perovskites

description: Cif and data files (.gss format) for powder structure refinements of Ba1-xSrxTaO2N materials at 300 K using the GSAS software package. Ba/Sr contents are indicated in the file names.
DOI: 10.7488/ds/2634
title: The role of friction in the yielding of adhesive non-Brownian suspensions

description: Yielding behavior is well known in attractive colloidal suspensions. Adhesive non-Brownian suspensions, in which the interparticle bonds are due to finite-size contacts, also show yielding behavior. We use a combination of steady-state, oscillatory and shear-reversal rheology to probe the physical origins of yielding in the latter class of materials, and find that yielding is not simply a matter of breaking adhesive bonds, but involves unjamming from a shear-jammed state in which the micro-structure has adapted to the direction of the applied load. Comparison with a recent constraint-based rheology model shows the importance of friction in determining the yield stress, suggesting novel ways to tune the flow of such suspensions.
description: The dataset comprises six .zip files. Five files, Fig1.zip to Fig5.zip, that contain data and corresponding plotting for Figures 1 to 5 of the related paper "The role of friction in the yielding of adhesive non-Brownian suspensions" and an additional folder, Data.zip, containing data referenced in the paper, e.g. from which values have been extracted and used in other figures. All file formats and contents are described in the corresponding readme text files labelled e.g. README_fig1.txt for Figure 1.
DOI: 10.7488/ds/2751
title: Vibrational coherences in manganese single-molecule magnets after ultrafast photoexcitation

description: Data for the article "Vibrational coherences in manganese single molecule magnets after ultrafast photoexcitation". Raw transient absorption data for Mn(acac)3, Mn3 and Mn6. Data for three different pump/probe polarisation direction are provided (parallel, magic angle and perpendicular). The Raman and UV/Vis spectra and outputs from the computations are also included. See journal article for more information.
DOI: 10.7488/ds/2496
title: Listening test results of the Voice Conversion Challenge 2018

description: This dataset is associated with a paper and a dataset below: (1) Jaime Lorenzo-Trueba, Junichi Yamagishi, Tomoki Toda, Daisuke Saito, Fernando Villavicencio, Tomi Kinnunen, Zhenhua Ling, "The Voice Conversion Challenge 2018: Promoting Development of Parallel and Nonparallel Methods", Proc Speaker Odyssey 2018, June 2018. https://doi.org/10.21437/Odyssey.2018-28 (2) Lorenzo-Trueba, Jaime; Yamagishi, Junichi; Toda, Tomoki; Saito, Daisuke; Villavicencio, Fernando; Kinnunen, Tomi; Ling, Zhenhua. (2018). The Voice Conversion Challenge 2018: database and results, [sound]. The Centre for Speech Technology Research, The University of Edinburgh, UK. https://doi.org/10.7488/ds/2337 and includes lists of listening test raw scores given by subjects and corresponding audio files that they assessed. This was funded by The Japan Society for the Promotion of Science (Grant number: 15H01686, 16H06302, 17H04687, 17H06101)
DOI: 10.7488/ds/2494
title: Ferri- and ferro- magnetism in CaMnMReO6 double double perovskites of late transition metals M = Co and Ni

description: Magnetisation data, powder neutron diffraction, and powder x-ray diffraction results for the title compounds at variable temperatures.
DOI: 10.7488/ds/2633
title: Comparison of Escherichia coli surface attachment methods for single-cell microscopy

description: See readme file. ## Funding ## This research was funded by Human Frontier Science Program Grant (RGP0041/2015) and the Ministry of Science and Technology, Republic of China under contract No. MOST-107-2112-M-008-025-MY3.
DOI: 10.7488/ds/2644
title: Testing the Wyart-Cates model for non-Brownian shear thickening using bidisperse suspensions [Dataset]

description: Raw simulation data and processed simulation and experimental data to support the article "Testing the Wyart-Cates model for non-Brownian shear thickening using bidisperse suspensions" by Ben M. Guy et al, published in Soft Matter and available on arXiv: https://arxiv.org/abs/1901.02066. Further details are contained in the README files attached. ABSTRACT: There is a growing consensus that shear thickening of concentrated dispersions is driven by the formation of stress-induced frictional contacts. The Wyart-Cates (WC) model of this phenomenon, in which the microphysics of the contacts enters solely via the fraction f of contacts that are frictional, can successfully fit flow curves for suspensions of weakly polydisperse spheres. However, its validity for "real-life", polydisperse suspensions has yet to be seriously tested. By performing systematic simulations and experiments on bidisperse mixtures of spheres, we show that the WC model applies only in the monodisperse limit and fails when substantial bidispersity is introduced. Our results prompt new questions about the microphysics of thickening for both monodisperse and polydisperse systems. ## Acknowledgments ## The full list of funders is: &gt; EPSRC EP/J007404/1 &gt; EPSRC EP/N025318/1 &gt; Maudslay-Butler Research Fellowship at Pembroke College, Cambridge &gt; EPSRC SOFI CDT (EP/L015536/1) &gt; The Royal Academy of Engineering &gt; The Leverhulme Trust Senior Research Fellowship LTSRF1617/13/2
DOI: 10.7488/ds/2640
title: Metagenome assembled rumen-uncultured genomes (RUGs)

description: DNA was sequenced from rumen contents from cattle, sheep, red deer and reindeer. We constructed 391 metagenome assembled rumen-uncultured genomes (RUGs).
DOI: 10.7488/ds/2420
title: Probing the dynamics of crystal nucleation via measurements of emission lifetimes in crystalloluminescence of sodium chloride

description: The data consist of measurements of the time dependence of photoemission events in crystalloluminescence (XTL) of sodium chloride. Aqueous solutions of NaCl were intentionally doped with trace amounts of copper and silver ions, and crystallization was induced by mixing with HCl. The mean lifetime for solutions doped only with copper ions was 39.9 ± 0.8 microseconds, which is close to the ultraviolet photoluminescence lifetime of solid NaCl doped with Cu+. The rise time for emission events indicates that crystal nuclei are formed within 10 ns. The mean lifetime for solutions doped with a mixture of silver and copper ions was 12.7 ± 0.7 microseconds, which suggests that electronic energy transfer takes place between Ag+ and dimer (Ag+)2 species in the crystal lattice. Co-incident radiofrequency and acoustic signals were not detected, indicating that triboluminescence by crystal fracture is not a significant mechanism for XTL.
DOI: 10.7488/ds/2711
title: SUPERSEDED - Synaptome data with individual synapse parameters, types and subtypes for 10 representative sagittal mouse brain sections across the lifespan
title: A lifespan program of mouse synaptome architecture

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2796 ## How synapses change molecularly during the lifespan and across all brain circuits is unknown. We analyzed the protein composition of billions of individual synapses from birth to old age on a brain-wide scale in the mouse, revealing a program of changes in the lifespan synaptome architecture spanning individual dendrites to the systems level. Three major phases were uncovered, corresponding to human childhood, adulthood and old age. An arching trajectory of synaptome architecture drives the differentiation and specialization of brain regions to a peak in young adults before dedifferentiation returns the brain to a juvenile state. This trajectory underscores changing network organization and hippocampal physiology that may account for lifespan transitions in intellectual ability and memory, and the onset of behavioral disorders.
description: "The dataset is intended for use with the application Synaptome Explorer, whose binaries are provided in https://github.com/SynaptomeMapping/SynaptomeExplorerV2 The data are compressed in a single file, expanded to 11 folders (10 datasets and 1 for configurations) and 2 files: * 'masks.json': Delineation hierarchy for all datasets in JSON format. * 'masks.png': Color lookup table associated with masks.json. * 'synaptome_explorer_configs/_any_file_.json': configuration file provided as an argument for execution of the application Synaptome Explorer V2. * '_any_other_folder_/config.json': imaging configuration for the current dataset. * '_any_other_folder_/correction.dds': correction greyscale image as the DDS file format, used by the application for better display of the raw image data. * '_any_other_folder_/masks.png': image that stores RGBA-encoded delineation IDs. * '_any_other_folder_/montage.dds': low-resolution version of the raw image data. * '_any_other_folder_/puncta.hdf5': puncta parameters in the HDF5 format. * '_any_other_folder_/puncta_extrema_global_and_per_protein.cache': binary cache file storing the minimum and maximum values for all puncta, globally and by channel. * '_any_other_folder_/sparsetex.tex': Raw image data at various levels of detail stored as DDS tiles. * '_any_other_folder_/sparsetex.cfgp': Binary configuration data for raw image data. "
DOI: 10.7488/ds/2470
title: The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics
title: Rumen uncultured genomes (RUGs)

description: "Metagenomic and proteomic datasets from: The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics Rob. D. Stewart, Marc D. Auffret, Amanda Warr, Alan Walker, Rainer Roehe and Mick Watson (unpublished) The data contain: - genomes and predicted proteins for 4941 metagenome-assembled genomes - Polysaccharide utilisation loci (PUL) predictions - CAZy predictions - Annotation results against UniRef, Hungate collection, KEGG and CAZy - protein clusters at 100%, 90% and 50% identity - Oxford Nanopore assembly of one of the samples"
description: "dbcan2 - dbCAN2 CAZy predictions diamond - DIAMOND searches against public data mags - the metagenome-assembled genomes nanopore_assembly - the nanopore assembly proteins - the protein predictions PUL - prediction of polysaccharide utilisation loci rumiref - protein clusters"
DOI: 10.7488/ds/2296
title: Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

description: This dataset represents 913 draft bacterial and archaeal genomes assembled from over 800 gigabases of rumen metagenomic sequence data derived from 43 Scottish cattle, using both metagenomic binning and Hi-C-based proximity-guided assembly. Most of these genomes represent previously unsequenced strains and species. The draft genomes contain over 1.2 million predicted protein sequences, and 69,000 proteins predicted to be involved in carbohydrate metabolism. ## Relation to earlier versions ## This data is referenced by Watson et al. (In Submission). A previous paper, in bioRXiv, referenced the earlier dataset "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism" https://datashare.is.ed.ac.uk/handle/10283/2772. This in turn was superseded by the more recent version Hi-C genomes from "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism" https://datashare.is.ed.ac.uk/handle/10283/2911. The paper underwent many rounds of review, the first-round revised paper referenced the second (Hi-C) dataset and the final, accepted version will reference the DOI of this dataset. The datasets changed in nature and in name during this process.
DOI: 10.7488/ds/2964
title: Radio frequency-chain selection for energy and spectral efficiency maximization in hybrid beamforming under hardware imperfections

description: This dataset contains MATLAB functions to plot the main results for the following paper: Evangelos Vlachos, John Thompson, Aryan Kaushik and Christos Masouros,"Radio frequency-chain selection for energy and spectral efficiency maximization in hybrid beamforming under hardware imperfections", Accepted for Publication in Royal Society Proceedings Part A, November 2020. The code licence terms can be found in the file LICENCE and full details can be found in the file README.
DOI: 10.7488/ds/2328
title: PIV dataset for 'The leading-edge vortex of yacht sails' (OE, Arredondo-Galeana and Viola, 2018, Fig. 9, 10, 11, 12)
title: Flow around a spinnaker, dataset, (OE, Arredondo-Galeana and Viola, 2018, Fig. 9, 10, 11, 12)

description: Matlab files for Figures 9, 10 and 11 of journal paper "The leading-edge vortex of yacht sails" of article in press in Ocean Engineering. All velocity values to be normalised with Ufreestream = 0.114 m/s, x and y data in mm. 1) Fig9_Averaged_Flow_Fields data set contains the averaged velocity fields of planes A, B and C in x,y,u,v format (117649 rows, 1 column or a 343x343 matrix). 2) Fig10_Fig11_Instantaneous_Flow_Fields data set contains the instantaneous velocity fields of planes A, B and C in x,y,u,v format (117649 rows, 306 columns or a 343x343x306 matrix). 3) Fig10_Fig11_Gamma2_Contours contains the Gamma2 contours and the subtracted flow field for planes A, B and C, presented in Fig 10 and Fig 11. An additional XY dataset is provided for providing a reference plane. 4) Supplementary material in PDF format for Derivation_of_kappa. 5) Supplementary material in PDF format for Gamma2contours used for kappas used in Fig12. 6) Supplementary material in PDF.format for Fig12 calculated values
DOI: 10.7488/ds/2563
title: Data supporting Deary & Hagenaars et al. Genetic contributions to self-reported tiredness

description: Data supporting the paper Deary & Hagenaars et al. Genetic contributions to self-reported tiredness. Molecular Psychiatry (2017). doi:10.1038/mp.2017.5.
DOI: 10.7488/ds/2497
title: ParAlleL plasmid sequences in SBOL, GENBANK and FASTA format

description: Data supporting the paper "ParAlleL: a novel population-based approach to biological logic gates" (Under review manuscript). Abstract: In vivo logic gates have proven difficult to combine into larger devices. Our cell-based logic system, ParAlleL, decomposes a large circuit into a collection of small subcircuits working in parallel, each subcircuit responding to a different combination of inputs. A final global output is then generated by a combination of the responses. Using ParAlleL, for the first time a completely functional 3-bit full adder and full subtractor were generated using Escherichia coli cells; as well as a calculator-style display that shows a numeric result, from 0 to 7, when the proper 3 bit binary inputs are introduced into the system. ParAlleL demonstrates the use of a parallel approach for the design of cell-based logic gates that facilitates the generation and analysis of complex processes, without the need for complex genetic engineering.
DOI: 10.7488/ds/2507
title: Data and Code for "Fibre-based Spectral Ratio Endomicroscopy for Contrast Enhancement of Bacterial Imaging and Pulmonary Autofluorescence"

description: Fibre-based optical endomicroscopy (OEM) permits high resolution fluorescence microscopy in endoscopically accessible tissues. Fibred OEM has the potential to visualise pathologies targeted with fluorescent imaging probes and provide an in vivo in situ molecular pathology platform to augment disease understanding, diagnosis and stratification. Here we present an inexpensive widefield ratiometric fibred OEM system capable of enhancing the contrast between similar spectra of pathologically relevant fluorescent signals without the burden of complex spectral unmixing. As an exemplar, we demonstrate the potential of the platform to detect fluorescently labelled Gram-negative bacteria in the challenging environment of highly autofluorescent lung tissue in whole ex vivo human lungs.
description: Readme.txt