cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5353573.v1
title: Dataset for: Complex restitution behavior and reentry in a cardiac tissue model for neonatal mice

description: Spatio-temporal dynamics in cardiac tissue emerging from the coupling of individual cardiomyocytes underlie the heart’s normal rhythm as well as undesired and possibly life-threatening arrhythmias. While single cells and their transmembrane currents have been studied extensively, systematically investigating spatio-temporal dynamics is complicated by the non-trivial relationship between single-cell and emergent tissue properties. Mathematical models have been employed to bridge this gap and contribute to a deepened understanding of the onset, development and termination of arrhythmias. However, no such tissue-level model currently exists for neonatal mice. Here, we build on a recent single-cell model of neonatal mouse cardiomyocytes by Wang & Sobie (40) to predict properties that are commonly used to gauge arrhythmogenicity of cardiac substrates. We modify the model to yield well-defined behavior for common experimental protocols and construct a spatially extended version to study emergent tissue dynamics. We find a complex action potential duration (APD) restitution behavior characterized by a non-monotonic dependence on pacing frequency. Electrotonic coupling in tissue leads not only to changes in action potential morphology but can also induce spatially concordant and discordant alternans not observed in the single-cell model. In two-dimensional tissue, our results show that the model supports stable functional reentry, whose frequency is in good agreement with that observed in adult mice. Our results can be used to further constrain and validate the mathematical model of neonatal mouse cardiomyocytes with future experiments.
DOI: 10.6084/m9.figshare.5353549
title: Spatial patterns of cryptobenthic coral reef fishes in the Red Sea

description: Images of reef fishes collected in the Red Sea<br>Coker, D. J., DiBattista, J. D., Sinclair-Taylor, T. H., & Berumen, M. L. (2018). Spatial patterns of cryptobenthic coral-reef fishes in the Red Sea. <i>Coral Reefs</i>, <i>37</i>(1), 193-199.<br>
DOI: 10.6084/m9.figshare.5353540
title: genotype.RData

description: This RData contains the genotypes of 2510 dairy cows after quality control and filtering. The dataset consisted of 364 cases and 2, 146 controls genotyped for 44, 046 SNPs.
DOI: 10.6084/m9.figshare.5353501
title: Local groundwater balance model: stakeholders’ efforts to address groundwater monitoring and literacy

description: Understanding groundwater systems is crucial to ensure their monitoring and protection. Global groundwater models and predictive tools exist to better understand them. In view of scarce groundwater data, especially in developing countries, the question of how to model these systems and make them usable for groundwater management is crucial. Herein, we demonstrate how a transdisciplinary process can overcome the data scarcity problem and lead to the development of a local groundwater balance model (LGBM). Over 50 actors from more than 15 disciplines and groundwater-related sectors were involved for the case of Yucatan, Mexico. Results revealed high wastewater emissions to the aquifer discharged without treatment and poor recycling practices. The method can be adapted to specific regions, can be used to address methodological challenges for monitoring, and can contribute to the achievement of the 2030 Development Agenda by addressing Sustainable Development Goal 6-related Targets (6.3, 6.4, 6.5, 6.6(a, b)).
DOI: 10.6084/m9.figshare.5353498
title: genotype data of 2510 dairy cows

description: Genotype data of 2510 dairy cows. The dataset consisted of 364 cases and 2, 146 controls genotyped for 44, 046 SNPs
DOI: 10.6084/m9.figshare.5353501.v1
title: Local groundwater balance model: stakeholders’ efforts to address groundwater monitoring and literacy

description: Understanding groundwater systems is crucial to ensure their monitoring and protection. Global groundwater models and predictive tools exist to better understand them. In view of scarce groundwater data, especially in developing countries, the question of how to model these systems and make them usable for groundwater management is crucial. Herein, we demonstrate how a transdisciplinary process can overcome the data scarcity problem and lead to the development of a local groundwater balance model (LGBM). Over 50 actors from more than 15 disciplines and groundwater-related sectors were involved for the case of Yucatan, Mexico. Results revealed high wastewater emissions to the aquifer discharged without treatment and poor recycling practices. The method can be adapted to specific regions, can be used to address methodological challenges for monitoring, and can contribute to the achievement of the 2030 Development Agenda by addressing Sustainable Development Goal 6-related Targets (6.3, 6.4, 6.5, 6.6(a, b)).
DOI: 10.6084/m9.figshare.5353486
title: Horse data Plos One 2017.xlsx

description: This data file accompanies the Plos One publication:Low plasma cortisol and fecal cortisol metabolite measures as indicators of compromised welfare in domestic horses (<i>Equus caballus</i>) Jodi Pawluski<sup>1*</sup>, Patrick Jego<sup>2</sup>, Séverine Henry<sup>2</sup>, Anaelle Bruchet<sup>2</sup>, Rupert Palme<sup>3</sup>, Caroline Coste<sup>2</sup>, & Martine Hausberger<sup>4*</sup> <sup> </sup> <sup>1 </sup>Institut de recherche en santé, environnement et travail (Irset), U1085 INSERM, Université de Rennes 1, Rennes, France <sup>2 </sup>Université de Rennes 1, UMR 6552 CNRS Ethologie Animale et Humaine, Station Biologique de Paimpont, France <sup>3</sup>University of Veterinary Medicine, Department of Biomedical Sciences, Vienna, Austria <sup>4</sup>CNRS, UMR 6552 Ethologie animale et humaine, Université de Rennes 1, Rennes, France *Corresponding authors Email : j.pawluski@gmail.com/jodi-lynn.pawluski@univ-rennes1.fr Email : martine.hausberger@univ-rennes1.fr
DOI: 10.6084/m9.figshare.5353480
title: Result of analysis with Metascape (Gene List)

description: Metascape (http://metascape.org/) was used for the gene set enrichment analysis. A gene list for metascape analysis was generated from the output of cuffdiff program, in which 235 genes judged as ‘significantly differentially expressed’ (p&lt;0.05) in cuffdiff output (gene_exp.diff) were indicated.
DOI: 10.6084/m9.figshare.5353462
title: Results of Data analysis of RNA-Seq

description: <b>Data analysis of RNA-Seq</b> FASTQ files for RCC4-EV cells (DRR100656) and RCC4-VHL cells (DRR100657) were evaluated by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) after the trimming process by FASTX-Toolkit v0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit/). The human reference sequence file (hs37d5.fa) was downloaded from the 1000 genome ftp site (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/), and the annotated general feature format (gff) file was downloaded from the Illumina iGenome ftp site (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/NCBI/build37.2/). The human genome index was constructed with bowtie-build in Bowtie v.2.2.9. The fastq files were aligned to the reference genomic sequence by TopHat v.2.1.1 with default parameters. Bowtie2 v2.2.9 and Samtools v.1.3.1 was used with the TopHat program47. Estimation of transcript abundance was calculated, and the count values were normalized to the upper quartile of the fragments per kilobase of transcript per million fragments mapped reads (FPKM) using Cufflinks (cuffdiff) v2.1.1. cuffdiff output (gene_exp. diff) was presentated (gene_exp.diff.txt).
DOI: 10.6084/m9.figshare.5353393
title: Quantification of edematous changes by diffusion magnetic resonance imaging in gastrocnemius muscles after spinal nerve ligation

description: Using a rat spinal nerve ligation-induced CRPS model, we show that edematous changes in gastrocnemius muscle can be detected quantitatively by diffusion magnetic resonance imaging (MRI). Using the line-scan diffusion spectrum on a 1.5 T clinical MR imager, we demonstrate significant elevation of the apparent diffusion coefficient (ADC) ratios in gastrocnemius muscle on the ligated versus the sham-operated rats by one day after surgery, those ratios gradually decreased over time. Meanwhile, T2 ratios in gastrocnemius muscle on the ligated rats increased gradually and significantly, peaking two weeks after surgery, and those ratios remained high and were consistent with edema. Expression of vascular endothelial growth factor (VEGF), a key regulator of blood vessel formation and function, was significantly lower in gastrocnemius muscle on the ligated versus non-ligated side, suggesting that nerve ligation promotes edematous changes and perturbs VEGF expression in target muscle.
DOI: 10.6084/m9.figshare.5353399
title: STRetch CI test data

description: Simulated STR expansion at a single locus. For usage see:https://github.com/Oshlack/STRetch/wiki
DOI: 10.6084/m9.figshare.5353228
title: An Australian provenance for the eastern Otago Schist protolith, South Island, New Zealand: evidence from detrital zircon age patterns and implications for the origin of its gold

description: Uranium–lead age patterns of detrital zircons in Otago Schist meta-sandstones from eastern Otago, including areas of orogenic gold mineralisation, are mostly consistent with a Rakaia Terrane (Torlesse Composite Terrane) accretionary wedge protolith. Southwest of the Hyde-Macraes and Rise & Shine shear zones the depositional age is regarded as Middle–Late Triassic. At the south and west margins, there are two areas in the Late Triassic Waipapa Terrane protolith. Northeast of the Hyde-Macraes Shear Zone, the schist protolith has Middle to Late Triassic and middle to late Permian depositional ages of Rakaia Terrane affinity. At the northeastern margin of the Hyde-Macraes Shear Zone, there is a narrow strip with a mid-Carboniferous protolith, which may be a counterpart of the Carboniferous accretionary wedge in the New England Orogen, eastern Australia. Ordovician–Silurian zircons are a minor but distinctive feature in many of the protolith age patterns and form significant age components at hard-rock gold locations. These constrain the provenance of Rakaia Terrane protolith sediments to Late Triassic time and within the Permian–Triassic magmatic arcs at the northeastern Australian continental margin and partly within the Ordovician–Silurian granitoids of the Charters Towers Province hinterland and environs. The latter have extensive gold mineralisation and thus upon exhumation might be the origin of Otago gold.
DOI: 10.6084/m9.figshare.5353393.v1
title: Quantification of edematous changes by diffusion magnetic resonance imaging in gastrocnemius muscles after spinal nerve ligation

description: Using a rat spinal nerve ligation-induced CRPS model, we show that edematous changes in gastrocnemius muscle can be detected quantitatively by diffusion magnetic resonance imaging (MRI). Using the line-scan diffusion spectrum on a 1.5 T clinical MR imager, we demonstrate significant elevation of the apparent diffusion coefficient (ADC) ratios in gastrocnemius muscle on the ligated versus the sham-operated rats by one day after surgery, those ratios gradually decreased over time. Meanwhile, T2 ratios in gastrocnemius muscle on the ligated rats increased gradually and significantly, peaking two weeks after surgery, and those ratios remained high and were consistent with edema. Expression of vascular endothelial growth factor (VEGF), a key regulator of blood vessel formation and function, was significantly lower in gastrocnemius muscle on the ligated versus non-ligated side, suggesting that nerve ligation promotes edematous changes and perturbs VEGF expression in target muscle.
DOI: 10.6084/m9.figshare.5353399.v1
title: STRetch CI test data

description: Simulated STR expansion at a single locus. For usage see:https://github.com/Oshlack/STRetch/wiki
DOI: 10.6084/m9.figshare.5353228.v1
title: An Australian provenance for the eastern Otago Schist protolith, South Island, New Zealand: evidence from detrital zircon age patterns and implications for the origin of its gold

description: Uranium–lead age patterns of detrital zircons in Otago Schist meta-sandstones from eastern Otago, including areas of orogenic gold mineralisation, are mostly consistent with a Rakaia Terrane (Torlesse Composite Terrane) accretionary wedge protolith. Southwest of the Hyde-Macraes and Rise & Shine shear zones the depositional age is regarded as Middle–Late Triassic. At the south and west margins, there are two areas in the Late Triassic Waipapa Terrane protolith. Northeast of the Hyde-Macraes Shear Zone, the schist protolith has Middle to Late Triassic and middle to late Permian depositional ages of Rakaia Terrane affinity. At the northeastern margin of the Hyde-Macraes Shear Zone, there is a narrow strip with a mid-Carboniferous protolith, which may be a counterpart of the Carboniferous accretionary wedge in the New England Orogen, eastern Australia. Ordovician–Silurian zircons are a minor but distinctive feature in many of the protolith age patterns and form significant age components at hard-rock gold locations. These constrain the provenance of Rakaia Terrane protolith sediments to Late Triassic time and within the Permian–Triassic magmatic arcs at the northeastern Australian continental margin and partly within the Ordovician–Silurian granitoids of the Charters Towers Province hinterland and environs. The latter have extensive gold mineralisation and thus upon exhumation might be the origin of Otago gold.
DOI: 10.6084/m9.figshare.5353183
title: Data, plotting scripts, and figures for "Accelerating finite-rate chemical kinetics with coprocessors: comparing vectorization methods on GPUs, MICs, and CPUs"

description: This bundle of files contains all the data and plotting scripts "Accelerating finite-rate chemical kinetics with coprocessors: comparing vectorization methods on GPUs, MICs, and CPUs", as well as the figures themselves.<br>These results are part of the paper:Christopher P Stone, Andrew T Alferman, and Kyle E. Niemeyer, and Chih-Jen Sung. "Accelerating finite-rate chemical kinetics with coprocessors: comparing vectorization methods on GPUs, MICs, and CPUs," 2017. Under review, available via https://arxiv.org/abs/1608.05794
DOI: 10.17608/k6.auckland.5353204.v1
title: Incipits Nokki 05

description: Incipits for mass Nokki 05 in the new Wanhal catalogue.<br>
DOI: 10.6084/m9.figshare.5353171
title: Araucaria angustifolia Forest data.xlsx

description: Adults individuals genotypes and progenies from Araucaria angustifolia in forest and grassland landscape in Santa Catarina, Brazil using 7 microsatellites.
DOI: 10.6084/m9.figshare.5353171.v1
title: Araucaria angustifolia Forest data.xlsx

description: Adults individuals genotypes and progenies from Araucaria angustifolia in forest and grassland landscape in Santa Catarina, Brazil using 7 microsatellites.
DOI: 10.6084/m9.figshare.5352994
title: Nested Hierarchical Functional Data Modeling and Inference for the Analysis of Functional Plant Phenotypes

description: In a plant science Root Image Study, the process of seedling roots bending in response to gravity is recorded using digital cameras, and the bending rates are modeled as functional plant phenotype data. The functional phenotypes are collected from seeds representing a large variety of genotypes and have a three-level nested hierarchical structure, with seeds nested in groups nested in genotypes. The seeds are imaged on different days of the lunar cycle, and an important scientific question is whether there are lunar effects on root bending. We allow the mean function of the bending rate to depend on the lunar day and model the phenotypic variation between genotypes, groups of seeds imaged together, and individual seeds by hierarchical functional random effects. We estimate the covariance functions of the functional random effects by a fast penalized tensor product spline approach, perform multi-level functional principal component analysis (FPCA) using the best linear unbiased predictor of the principal component scores, and improve the efficiency of mean estimation by iterative decorrelation. We choose the number of principal components using a conditional Akaike information criterion and test the lunar day effect using generalized likelihood ratio test statistics based on the marginal and conditional likelihoods. We also propose a permutation procedure to evaluate the null distribution of the test statistics. Our simulation studies show that our model selection criterion selects the correct number of principal components with remarkably high frequency, and the likelihood-based tests based on FPCA have higher power than a test based on working independence. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5352991
title: Over-Dispersed Age-Period-Cohort Models

description: We consider inference and forecasting for aggregate data organized in a two-way table with age and cohort as indices, but without measures of exposure. This is modeled using a Poisson likelihood with an age-period-cohort structure for the mean while allowing for over-dispersion. We propose a repetitive structure that keeps the dimension of the table fixed while increasing the latent exposure. For this, we use a class of infinitely divisible distributions which include a variety of compound Poisson models and Poisson mixture models. This results in asymptotic <i>F</i> inference and <i>t</i> forecast distributions.
DOI: 10.6084/m9.figshare.5352994.v1
title: Nested Hierarchical Functional Data Modeling and Inference for the Analysis of Functional Plant Phenotypes

description: In a plant science Root Image Study, the process of seedling roots bending in response to gravity is recorded using digital cameras, and the bending rates are modeled as functional plant phenotype data. The functional phenotypes are collected from seeds representing a large variety of genotypes and have a three-level nested hierarchical structure, with seeds nested in groups nested in genotypes. The seeds are imaged on different days of the lunar cycle, and an important scientific question is whether there are lunar effects on root bending. We allow the mean function of the bending rate to depend on the lunar day and model the phenotypic variation between genotypes, groups of seeds imaged together, and individual seeds by hierarchical functional random effects. We estimate the covariance functions of the functional random effects by a fast penalized tensor product spline approach, perform multi-level functional principal component analysis (FPCA) using the best linear unbiased predictor of the principal component scores, and improve the efficiency of mean estimation by iterative decorrelation. We choose the number of principal components using a conditional Akaike information criterion and test the lunar day effect using generalized likelihood ratio test statistics based on the marginal and conditional likelihoods. We also propose a permutation procedure to evaluate the null distribution of the test statistics. Our simulation studies show that our model selection criterion selects the correct number of principal components with remarkably high frequency, and the likelihood-based tests based on FPCA have higher power than a test based on working independence. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5352988
title: A Simple and Effective Inequality Measure

description: Ratios of quantiles are often computed for income distributions as rough measures of inequality, and inference for such ratios has recently become available. The special case when the quantiles are symmetrically chosen; that is, when the <i>p</i>/2 quantile is divided by the (1 − <i>p</i>/2) quantile, is of special interest because the graph of such ratios, plotted as a function of <i>p</i> over the unit interval, yields an informative inequality curve. The area above the curve and less than the horizontal line at one is an easily interpretable measure of inequality. The advantages of these concepts over the traditional Lorenz curve and Gini coefficient are numerous: they are defined for all positive income distributions, they can be robustly estimated and large sample confidence intervals for the inequality coefficient are easily found. Moreover, the inequality curves satisfy a median-based transference principle and are convex for many commonly assumed income distributions.
DOI: 10.6084/m9.figshare.5352988.v1
title: A Simple and Effective Inequality Measure

description: Ratios of quantiles are often computed for income distributions as rough measures of inequality, and inference for such ratios has recently become available. The special case when the quantiles are symmetrically chosen; that is, when the <i>p</i>/2 quantile is divided by the (1 − <i>p</i>/2) quantile, is of special interest because the graph of such ratios, plotted as a function of <i>p</i> over the unit interval, yields an informative inequality curve. The area above the curve and less than the horizontal line at one is an easily interpretable measure of inequality. The advantages of these concepts over the traditional Lorenz curve and Gini coefficient are numerous: they are defined for all positive income distributions, they can be robustly estimated and large sample confidence intervals for the inequality coefficient are easily found. Moreover, the inequality curves satisfy a median-based transference principle and are convex for many commonly assumed income distributions.
DOI: 10.6084/m9.figshare.5352991.v2
title: Over-Dispersed Age-Period-Cohort Models

description: We consider inference and forecasting for aggregate data organized in a two-way table with age and cohort as indices, but without measures of exposure. This is modeled using a Poisson likelihood with an age-period-cohort structure for the mean while allowing for over-dispersion. We propose a repetitive structure that keeps the dimension of the table fixed while increasing the latent exposure. For this, we use a class of infinitely divisible distributions which include a variety of compound Poisson models and Poisson mixture models. This results in asymptotic <i>F</i> inference and <i>t</i> forecast distributions.
DOI: 10.23645/epacomptox.5352997.v1
title: The Chemical and Products Database (CPDat) MySQL Data File

description: Quantitative data on product chemical composition is a necessary parameter for characterizing near-field exposure. This data set comprises reported and predicted information on &gt;75,000 chemicals contained in &gt;15,000 consumer products. The data’s primary intended use is for exposure, risk, and safety assessments. The data set includes specific products with quantitative or qualitative ingredient information, which has been publicly disclosed through material safety data sheets (MSDS) and ingredient lists. A single product category from a refined and harmonized set of categories has been assigned to each product. The data set also contains information on the functional role of chemicals in products, which can inform predictions of the concentrations in which they occur. These data will be useful to exposure and risk assessors evaluating chemical and product safety. The data set presented here is in the form of a MySQL relational database, which mimics CPDat data available under the ‘Exposure’ tab of the CompTox Chemistry Dashboard (https://comptox.epa.gov/dashboard) as of August 2017.