cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2229
title: Persistent three- and four-atom orbital molecules in the spinel AlV2O4

description: Electronic instabilities in transition metal compounds may lead to ground states containing orbital molecules when direct metal-metal orbital interactions occur. The spinel AlV2O4 was reported to contain V717+ orbital heptamers that emerge below a 700 K charge ordering transition. Our X-ray total scattering analysis of AlV2O4 between 300 and 1100 K reveals a very different picture as the postulated heptamers are found to be pairs of spin-singlet V39+ trimers and V48+ tetramers, and these orbital molecules persist to at least 1100 K in a disordered high temperature cubic phase. PDF and crystallographic data files and cif files for AlV2O4 at various temperatures.
DOI: 10.7488/ds/2742
title: Dynamic Earth

description: A Scan of the Dynamic Earth interior, 22 Scan locations, captured with a BLK 360, registered using Autodesk Recap Pro, exported to .e57 file format.
DOI: 10.7488/ds/2534
title: Datasets of journal paper "Electrical impedance tomography for real-time and label-free cellular viability assays of 3D tumour spheroids"

description: This dataset comprises raw voltage measurement data to reconstruct images in Fig 6 in paper "Electrical impedance tomography for real-time and label-free cellular viability assays of 3D tumour spheroids". ABSTRACT: There is currently a need to culture cells in 3D to better mimic the behaviour of cells growing in the natural environment. In parallel, this calls for novel technologies to assess cell growth in 3D cell culture. In this study, we demonstrated both in silico and in vitro that cell viability inside large cell spheroids could be monitored in real time and label-free with electrical impedance tomography (EIT). Simulations using a single shell model and the effective media approximation (EMA) method were performed to prove the performance of EIT on spheroid imaging and viability monitoring. Then in vitro experiments were conducted to measure in real time a loss of cell viability in MCF-7 breast cancer spheroids when exposed to Triton X-100 and validate with conventional biochemical assays. It is shown that EIT has a spatial resolution of 1.14% and it could monitor the cell mortality over 20% of a spheroid under laboratory noise level. The reconstructed conductivity images for cell mortality induced by the chemical are clear and match the result in the cellular metabolic viability assay. Furthermore, the image reconstruction speed in the experiment was less than 0.3 seconds. Taken together, the results show the potential of EIT for non-destructive real-time and label-free cellular assays in the miniature sensor, providing physiological information in the applications of 3D drug screening and tissue engineering.
DOI: 10.7488/ds/1715
title: Emergent eddy saturation diagnostic data
title: Mesoscale parameterisation
title: Fluid Dynamics

description: Dataset for the article "Emergent eddy saturation from an energy constrained eddy parameterisation".
DOI: 10.7488/ds/2515
title: Conching chocolate is a prototypical transition from frictionally jammed solid to flowable suspension with maximal solid content

description: The mixing of a powder of 10-50μm primary particles into a liquid to form a dispersion with the highest possible solid content is a common industrial operation. Building on recent advances in the rheology of such 'granular dispersions', we study a paradigmatic example of such powder incorporation: the conching of chocolate, in which a homogeneous, flowing suspension is prepared from an inhomogeneous mixture of particulates, triglyceride oil and dispersants. Studying the rheology of a simplified formulation, we find that the input of mechanical energy and staged addition of surfactants combine to effect a considerable shift in the jamming volume fraction of the system, thus increasing the maximum flowable solid content. We discuss the possible microscopic origins of this shift, and suggest that chocolate conching exemplifies a ubiquitous class of powder-liquid mixing.
description: The dataset comprises 4 .zip files which contain tab-delimited data for Figures 3, 4, 5a and 7 respectively. A readme file with a description of the data relating to each figure is included inside each of the relevant .zip files.
description: Funded in part through the MRSEC Program of the National Science Foundation under Award Number DMR-1420073.
DOI: 10.7488/ds/2103
title: Structural evidence for the covalent modification of FabH by 4,5-dichloro-1,2-dithiol-3-one (HR45)

description: We use mass spectrometry analysis and molecular modelling to show the established antimicrobial inhibitor 4,5-dichloro-1,2-dithiol-3-one (HR45) acts by forming a covalent adduct with the target β-ketoacyl-ACP synthase III (FabH). The 5-chloro substituent directs attack of the essential active site thiol (C112) via a Michael-type addition elimination reaction mechanism.
DOI: 10.7488/ds/2077
title: Multiscale simulation of dynamic wetting

description: This data set contains the output data from all molecular dynamics and multiscale simulations carried out in the paper entitled: "Multiscale simulation of dynamic wetting" submitted to the International Journal of Heat and Mass Transfer. All data is organised according to the Figure numbers in this paper.
DOI: 10.7488/ds/2867
title: Window west side (opposite to the door wall) informal settlement fire experiment (Test 7)

description: This dataset presents Test 7 (window west side experiment). Different from Baseline experiment, the window location was changed from front long wall to the opposite long wall, and the other conditions are totally the same with Baseline.
DOI: 10.7488/ds/2107
title: Data set for "Self-similar Properties of Decelerating Turbulent Jets."

description: The flow in a decelerating turbulent round jet is investigated using direct numerical simulation. The simulations are initialised with a flow field from a statistically-stationary turbulent jet. Upon stopping the inflow, a deceleration wave passes through the jet, behind which the velocity field evolves towards a new statistically-unsteady self-similar state. Assumption of unsteady self-similar behaviour leads to analytical relations concerning the evolution of the centreline mean axial velocity and the shapes of the radial profiles of the velocity statistics. Consistency between these predictions and the simulation data supports the use of the assumption of self-similarity. The mean radial velocity is predicted to reverse in direction near to the jet centreline as the deceleration wave passes, contributing to an approximately three-fold increase in the normalised mass entrainment rate. The shape of the mean axial velocity profile undergoes a relatively small change across the deceleration transient, and this observation provides direct evidence in support of previous models that have assumed that the mean axial velocity profile, and in some cases also the jet spreading angle, remain approximately constant within unsteady jets.
DOI: 10.7488/ds/2509
title: Lion range changes through the late Quaternary, modelled using Global Environmental Stratification

description: This dataset projects the Global Environmental Stratification (GEnS) (Metzger, 2013) onto palaeoclimatic models of the mid-Holocene and Last Glacial Maximum. A Random Forest Classifier was applied to nine PMIP3 climate scenarios for the mid-Holocene, and three scenarios for the Last Glacial Maximum at a 5 arc-minute resolution following the methodology of Soteriades et al., (2017). This dataset summarises palaeo-environmental change for the mid-Holocene and Last Glacial Maximum using categorical classes of Environmental Zones and Strata.
DOI: 10.7488/ds/2225
title: NAI Yeast Transcriptome Wide Data
title: NAI Yeast Transcriptome Wide Data Selega et al Nature Methods 2017

description: These are fasta files containing collapsed read data from of our NAI yeast transcriptome data from the Selega et al Nature Methods paper published in 2017 ( https://doi.org/10.1038/nmeth.4068 ). Abbreviation: NAI: 2-methylnicotinic acid imidazolide.
description: Control_1_1.fasta Forward collapsed read data of the first negative control dataset Control_1_2.fasta Reverse collapsed read data of the first negative control dataset Control_2_1.fasta Forward collapsed read data of the second negative control dataset Control_2_2.fasta Reverse collapsed read data of the second negative control dataset NAI_1_1.fasta Forward collapsed read data of the first NAI dataset NAI_1_2.fasta Reverse collapsed read data of the first NAI dataset NAI_2_1.fasta Forward collapsed read data of the second NAI dataset NAI_2_2.fasta Reverse collapsed read data of the second NAI dataset
DOI: 10.7488/ds/2446
title: Isotope Depletion Mass Spectrometry (ID MS) for Enhanced Top-Down Protein Fragmentation - Datasets

description: Top-down mass spectrometry has become an important technique for the identification of proteins and characterisation of chemical and posttranslational modifications. However, as the molecular mass of proteins increases intact mass determination and top-down fragmentation efficiency become more challenging due to the partitioning of the mass spectral signal into many isotopic peaks. In large proteins, this results in reduced sensitivity and increased spectral complexity and signal overlap. This phenomenon is a consequence of the natural isotopic heterogeneity of the elements which comprise proteins (notably 13C). Here we present a bacterial recombinant expression system for the production of proteins depleted in 13C and 15N and use this strategy to prepare a range of isotopically depleted proteins. High resolution MS of isotope depleted proteins reveal dramatically reduced isotope distributions, which results in increases in sensitivity and deceased spectral complexity. We demonstrate that the monoisotopic signal is observed in mass spectra of proteins up to ~50 kDa. This allows confidant assignment of accurate molecular mass, and facile detection of low mass modifications (such as deamidation). We outline the benefits of this isotope depletion strategy for top-down fragmentation. The reduced spectral complexity alleviates problems of signal overlap; the presence of monoisotopic signals allow more accurate assignment of fragment ions; and the dramatic increase in single-to-noise ratio (up to 7-fold increases) permits vastly reduced data acquisition times. Together, these compounding benefits allow the assignment of ca. 3-fold more fragment ions than analysis of proteins with natural isotopic abundances. Thus, more comprehensive sequence coverage can be achieved; we demonstrate near single amino-acid resolution of the 29 kDa protein carbonic anhydrase from a single top-down MS experiment. Finally, we demonstrate that the ID-MS strategy allows far greater sequence coverage to be obtained in time limited top-down data acquisitions – highlighting potential advantages for top-down LC-MS/MS workflows and top-down proteomics.
description: Please refer to Readme file for full details. All data files are .baf format and can be opened with DataAnalysis (Bruker Daltonics).
DOI: 10.7488/ds/1464
title: Influence of dipolar interactions on the magnetic susceptibility spectra of ferrofluids

description: These files contain original simulation data for Figures 1, 3, 4, 5, and 7; the theoretical lines can be generated from the formulae given in the paper. The simulation data and formulae for Figures 2 and 6 are given in the paper.
description: These files contain original simulation data for Figures 1, 3, 4, 5, and 7; the theoretical lines can be generated from the formulae given in the paper. The simulation data and formulas for Figures 2 and 6 are given in the paper.
DOI: 10.7488/ds/2418
title: Onset pitch perturbations and the cross-linguistic implementation of voicing: supplementary materials

description: This dataset contains supplementary materials to the paper "Onset pitch perturbations and the cross-linguistic implementation of voicing: evidence from tonal and non-tonal languages", published in the Journal of Phonetics. It contains CSV data files and R code necessary to replicate the analyses reported in the paper, along with a PDF containing plots and post-hoc comparisons.
description: The out/ directories contain the output for each language; there are separate files for durations; spectral measures (f0, H1, H2...) taken at 10 msec intervals beginning 40 msec before closure release and ending at 100 msec following closure release; and f0 of the sonorant preceding the closure, with 1 measure taken every millisecond (these are later binned). bkk = Thai pnh = Khmer han = Vietnamese The scripts/ directories for each language contain the scripts that are called by seaAnalyze-revision.R. You shouldn't need to run these individually, but you can. The main scripts/ directory includes the seaAnalyze-revision.R script, which calls the other scripts and can be used to generate all figures and tables in the paper.
DOI: 10.7488/ds/127
title: Wally Referring Expression Corpus (WREC) v0.1.0
title: Release version 0.1.0

description: The data in this corpus consists of descriptions of individuals in visually complex scenes. The descriptions were collected and annotated as part of the Wally project, an ongoing research project between collaborators at the University of Edinburgh and the Ohio State University. The project aims to combine insights from the research domains of vision and language in order to better model the way language is used to describe entities in visually complex scenes. In this context, we used crowd-sourcing techniques to collect a large number of descriptions of individuals in scenes. The individuals appeared in scenes from the book 'Where's Wally' (known in the US as 'Where's Waldo') and participants wrote descriptions to identify for a naive listener which individual was the target (indicated to the participant with a box around the target individual). A subset of those descriptions were annotated (1672 out of 4256 total descriptions, representing 11 of the 28 total scenes). Descriptions were annotated to indicate which words referenced the target and which words were used to introduce other entities as landmarks and mark relationships between entities in the scene. Further details can be found in the README file.
description: The description of the dataset is to be found in WREC_v0.1.0_README
DOI: 10.7488/ds/2119
title: Orthogonality and burden of a heterologous AND gate gene circuit in E. coli host
title: RNA-Seq sample dataset for studying gene circuit host interaction

description: RNA-Seq sample preparation and sequencing E. coli NCM3722 cultures were grown and growth stopped 4 hrs post day dilution by adding 1/10 volume of 5% phenol 95% ethanol (v/v). Cells were harvested by centrifugation (4500 x g for 30 min). Supernatants were discarded and pellets drained by gravity flow for 5 min. Pellets wet weights were measured by subtracting the weights of cognate empty tubes. There are 7 samples in total containing 6 different plasmid constructs in the E. coli host. Samples 1 and 2 are biological replicates of the same construct (AND gate in pSB3K3), Sample 3 (Inputs-gfp in pSB3K3), Sample 4 (empty pSB3K3), Sample 5 (AND gate in pSB4K5), Sample 6 (Inputs-gfp in pSB4K5), Sample 7 (empty pSB4K5). The pellet cell samples were frozen at -80 °C before sent out on dry ice to vertis Biotechnologie AG for RNA-Seq. In brief, the cell pellets were incubated with lysozyme for 15 min at room temperature. The total RNA was then isolated using the mirVana RNA isolation kit (Invitrogen) including DNase treatment. Primary transcript enrichment was achieved by rRNA depletion and treatment with Terminator exonuclease (Epicentre) to remove other processed RNAs. RNA was fragmented using RNaseIII and cDNA libraries were built including PCR amplification with barcoded sequencing adaptors. Samples were pooled in approximately equimolar amounts to form one cDNA pool. The cDNA pool was sequenced on an Illumina HiSeq 2000 machine. The short sequence alignment software "Bowtie" (19) was used to map RNA-Seq reads (about 20 million each sample) on the E. coli MG1655 annotated genome (NCBI accession number NC_000913) and the cognate plasmid circuit sequences of each sample. The number of mapped reads for each gene was determined according to their annotated location features (NCBI gff format). The expression levels of genes were subsequently determined using the normalized measure of RPKM (Reads Per Kilobase of transcript per Million mapped reads). Read mapping were visualized using the Integrative Genomics Viewer tool (IGV).
description: RNA-Seq dataset for 7 cell samples, sequenced on Illumina 2500 platform.
DOI: 10.7488/ds/2227
title: Code and datasets for structural analyses in Natan et al, "Assembly in the translation milieu imposes evolutionary constraints on homomeric proteins"

description: This contains datasets and Perl scripts needed to reproduce the figures in Natan et al "Assembly in the translation milieu imposes evolutionary constraints on homomeric proteins". Specifically, it can be used to calculate the N- vs C-terminal interface enrichment for sets of homomeric or heteromeric structures, as in Figs 1B-C, and Figs S1-S3. The archive should only be extracted on a case-sensitive file system. The scripts have been tested on Mac and Linux systems.
description: See README file in archive
DOI: 10.7488/ds/2236
title: Stacking characteristics of close packed materials

description: It is shown that the enthalpy of any close packed structure for a given element can be characterized as a linear expansion in a set of continuous variables α_n, which describe the stacking configuration. This enables us to represent the infinite, discrete set of stacking sequences within a finite, continuous space of the expansion parameters H_n. These H_n determine the stable structure and vary continuously in the thermodynamic space of pressure, temperature, or composition. The continuity of both spaces means that only transformations between stable structures adjacent in the H_n space are possible, giving the model predictive as well as descriptive ability. We calculate the H_n using density functional theory and interatomic potentials for a range of materials. Some striking results are found: e.g. the Lennard-Jones potential model has 11 possible stable structures and over 50 phase transitions as a function of cutoff range. The very different phase diagrams of Sc, Tl, Y, and the lanthanides are understood within a single theory. We find that the widely reported 9R-fcc transition is not allowed in equilibrium thermodynamics, and in cases where it has been reported in experiments (Li, Na), we show that DFT theory is also unable to predict it.
description: Some files in the LJ_Data subdirectory end in a string of the form "." followed by a combination of the letters 'a', 'b' and 'c' indicating the stacking configuration (i.e. not a filename extension as such). These files are plain text.
DOI: 10.7488/ds/2340
title: Characterisation of time-dependent mechanical behaviour of trabecular bone samples
title: uCT images and mechanical test data for trabecular bone samples

description: Twenty (n=20) untreated bovine trabecular bone cylindrical samples (without any chemical treatment) were scanned by suing uCT at high resolution (17.22 µm), before mechanical tests. The bone volume ratio (BV/TV) ranged from 15% to 54%. The provided uCT images can be used for the development of finite element models of the bone microstructure and for evaluating indices of bone microstructure (e.g. bone volume ratio, fabric tensors). Samples were subjected to compressive multiple-load-creep-unload-recovery experiments, the raw experimental data is provided for any possible further analysis. This innovative creep-recovery experiments at multiple load levels, which considered compression force equivalent to different strain levels (from 2000 με to 25000 με), investigated the time-dependent behaviour of trabecular bone in pre- and post-yield regimes. The detailed experiment methodology can be found from related thesis chapter and the cited journal papers.
description: Please refer to readme file within this dataset.
DOI: 10.7488/ds/2137
title: An mRNA expression atlas for the domestic chicken generated by the meta-analysis of RNA-seq datasets

description: The chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We have created an mRNA expression atlas for the domestic chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues. Randomly down-sampling each dataset to a common depth and quantifying expression against a reference transcriptome using the probabilistic mRNA quantitation tool Kallisto ensures that each dataset explores comparable transcriptomic space, despite methodological differences between laboratories. The network analysis tool Miru was used to extract robust clusters of co-expressed genes from the atlas. Many clusters were strongly tissue or cell-type restricted, including a set of macrophage-specific transcripts. Other co-expression clusters were clearly associated with processes, including the cell division cycle and the formation and function of motile cilia. In many cases, the clusters contain transcription factors that have previously been implicated in their regulation. For example, the macrophage cluster includes BATF3, CEBPB, IRF1, NFE2L2, NRR1H3, SPI1, STAT1, and TFEC, each of which is also macrophage-enriched in mammals. Likewise, the cell cycle cluster contains FOXM1 and the motile cilia cluster contains FOXJ1. The atlas therefore provides a resource for the annotation of genes that currently have only a locus ID based upon the principle of ‘guilt by association’. The approach we have developed can be extended with new datasets from novel tissues, and is applicable to any species.
description: 18 RNA-sequencing datasets, of chicken (Gallus gallus) bone marrow derived macrophages (BMDMs), both unstimulated and 24 hours after stimulation with lipopolysaccharide (LPS), are available from the European Nucleotide Archive under study accession PRJEB22373 (http://www.ebi.ac.uk/ena/data/view/PRJEB22373). These samples are derived from 3 male and 3 female broilers (Ross 308), and 3 female layers (CSF1R-MacApple transgenic NOVOgen Brown), all 8 weeks of age. The dataset attached here contains expression level estimates per gene (as transcripts per million), generated after randomly down-sampling each of the 18 BMDM +/- LPS datasets to 10 million reads 100 times (using seqtk seeded with a random integer between 0 and 10,000). It may be seen that the random sampling used to down-size each dataset does not substantially alter the relative expression estimates of any two genes within any given sample, with equivalent expression profiles reconstructed for each of 100 random samples.