cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6834965.v1
title: Fig. S9b from Tensile fracture of a single crack in first-year sea ice

description: The breakup of sea ice in the Arctic and Antarctic has been studied during three field trips in the spring of 1993 at Resolute, N.W.T. and the fall of 2001 and 2004 on McMurdo Sound via <i>in situ</i> cyclic loading and fracture experiments. In this paper, the back-calculated fracture information necessary to the specification of an accurate viscoelastic fictitious (cohesive) crack model is presented. In particular, the changing shape of the stress separation curve with varying conditions and loading scenarios is revealed.This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
DOI: 10.6084/m9.figshare.6834956
title: Fig. S9a from Tensile fracture of a single crack in first-year sea ice

description: The breakup of sea ice in the Arctic and Antarctic has been studied during three field trips in the spring of 1993 at Resolute, N.W.T. and the fall of 2001 and 2004 on McMurdo Sound via <i>in situ</i> cyclic loading and fracture experiments. In this paper, the back-calculated fracture information necessary to the specification of an accurate viscoelastic fictitious (cohesive) crack model is presented. In particular, the changing shape of the stress separation curve with varying conditions and loading scenarios is revealed.This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
DOI: 10.6084/m9.figshare.6834959
title: Fig. S7b from Tensile fracture of a single crack in first-year sea ice

description: The breakup of sea ice in the Arctic and Antarctic has been studied during three field trips in the spring of 1993 at Resolute, N.W.T. and the fall of 2001 and 2004 on McMurdo Sound via <i>in situ</i> cyclic loading and fracture experiments. In this paper, the back-calculated fracture information necessary to the specification of an accurate viscoelastic fictitious (cohesive) crack model is presented. In particular, the changing shape of the stress separation curve with varying conditions and loading scenarios is revealed.This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
DOI: 10.6084/m9.figshare.6834956.v1
title: Fig. S9a from Tensile fracture of a single crack in first-year sea ice

description: The breakup of sea ice in the Arctic and Antarctic has been studied during three field trips in the spring of 1993 at Resolute, N.W.T. and the fall of 2001 and 2004 on McMurdo Sound via <i>in situ</i> cyclic loading and fracture experiments. In this paper, the back-calculated fracture information necessary to the specification of an accurate viscoelastic fictitious (cohesive) crack model is presented. In particular, the changing shape of the stress separation curve with varying conditions and loading scenarios is revealed.This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
DOI: 10.6084/m9.figshare.6834950
title: Supplementary tables from Signatures of human-commensalism in the house sparrow genome

description: Supplementary tables in an Excel spreadsheet
DOI: 10.6084/m9.figshare.6834959.v1
title: Fig. S7b from Tensile fracture of a single crack in first-year sea ice

description: The breakup of sea ice in the Arctic and Antarctic has been studied during three field trips in the spring of 1993 at Resolute, N.W.T. and the fall of 2001 and 2004 on McMurdo Sound via <i>in situ</i> cyclic loading and fracture experiments. In this paper, the back-calculated fracture information necessary to the specification of an accurate viscoelastic fictitious (cohesive) crack model is presented. In particular, the changing shape of the stress separation curve with varying conditions and loading scenarios is revealed.This article is part of the theme issue ‘Modelling of sea-ice phenomena’.
DOI: 10.6084/m9.figshare.6834950.v1
title: Supplementary tables from Signatures of human-commensalism in the house sparrow genome

description: Supplementary tables in an Excel spreadsheet
DOI: 10.6084/m9.figshare.6834935
title: Intertidal clams exhibit population synchrony across spatial and temporal scales

description: This repository includes detailed code and raw data for reproducing analyses in <i>Intertidal clams exhibit population synchrony across spatial and temporal scales </i>(Barber et al. 2019). Files include readme.doc containing metadata, detailed R code, and two .csv files with clam and environmental data needed for the analysis.<br>
DOI: 10.6084/m9.figshare.6834935.v1
title: Intertidal clams exhibit population synchrony across spatial and temporal scales

description: This repository includes detailed code and raw data for reproducing analyses in <i>Intertidal clams exhibit population synchrony across spatial and temporal scales </i>(Barber et al. 2019). Files include readme.doc containing metadata, detailed R code, and two .csv files with clam and environmental data needed for the analysis.<br>
DOI: 10.6084/m9.figshare.6834878
title: An Asynchronous Distributed Expectation Maximization Algorithm for Massive Data: The DEM Algorithm

description: The family of expectation--maximization (EM) algorithms provides a general approach to fitting flexible models for large and complex data. The expectation (E) step of EM-type algorithms is time-consuming in massive data applications because it requires multiple passes through the full data. We address this problem by proposing an asynchronous and distributed generalization of the EM called the distributed EM (DEM). Using DEM, existing EM-type algorithms are easily extended to massive data settings by exploiting the divide-and-conquer technique and widely available computing power, such as grid computing. The DEM algorithm reserves two groups of computing processes called <i>workers</i> and <i>managers</i> for performing the E step and the maximization step (M step), respectively. The samples are randomly partitioned into a large number of disjoint subsets and are stored on the worker processes. The E step of DEM algorithm is performed in parallel on all the workers, and every worker communicates its results to the managers at the end of local E step. The managers perform the M step after they have received results from a γ-fraction of the workers, where γ is a fixed constant in (0, 1]. The sequence of parameter estimates generated by the DEM algorithm retains the attractive properties of EM: convergence of the sequence of parameter estimates to a local mode and linear global rate of convergence. Across diverse simulations focused on linear mixed-effects models, the DEM algorithm is significantly faster than competing EM-type algorithms while having a similar accuracy. The DEM algorithm maintains its superior empirical performance on a movie ratings database consisting of 10 million ratings. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.6834878.v1
title: An Asynchronous Distributed Expectation Maximization Algorithm For Massive Data: The DEM Algorithm

description: The family of Expectation-Maximization (EM) algorithms provides a general approach to fitting flexible models for large and complex data. The expectation (E) step of EM-type algorithms is time consuming in massive data applications because it requires multiple passes through the full data. We address this problem by proposing an asynchronous and distributed generalization of the EM called the Distributed EM (DEM). Using DEM, existing EM-type algorithms are easily extended to massive data settings by exploiting the divide-and-conquer technique and widely available computing power, such as grid computing. The DEM algorithm reserves two groups of computing processes called <i>workers</i> and <i>managers</i> for performing the E step and the maximization step (M step), respectively. The samples are randomly partitioned into a large number of disjoint subsets and are stored on the worker processes. The E step of DEM algorithm is performed in parallel on all the workers, and every worker communicates its results to the managers at the end of local E step. The managers perform the M step after they have received results from a γ-fraction of the workers, where γ is a fixed constant in (0, 1]. The sequence of parameter estimates generated by the DEM algorithm retains the attractive properties of EM: convergence of the sequence of parameter estimates to a local mode and linear global rate of convergence. Across diverse simulations focused on linear mixed-effects models, the DEM algorithm is significantly faster than competing EM-type algorithms while having a similar accuracy. The DEM algorithm maintains its superior empirical performance on a movie ratings database consisting of 10 million ratings.
DOI: 10.6084/m9.figshare.6834872.v1
title: Extremiles: A new perspective on asymmetric least squares

description: Quantiles and expectiles of a distribution are found to be useful descriptors of its tail in the same way as the median and mean are related to its central behavior. This paper considers a valuable alternative class to expectiles, called extremiles, which parallels the class of quantiles and includes the family of expected minima and expected maxima. The new class is motivated via several angles, which reveals its specific merits and strengths. Extremiles suggest better capability of fitting both location and spread in data points and provide an appropriate theory that better displays the interesting features of long-tailed distributions. We discuss their estimation in the range of the data and beyond the sample maximum. A number of motivating examples are given to illustrate the utility of estimated extremiles in modeling noncentral behavior. There is in particular an interesting connection with coherent measures of risk protection.
DOI: 10.6084/m9.figshare.6834872.v2
title: Extremiles: A new perspective on asymmetric least squares

description: Quantiles and expectiles of a distribution are found to be useful descriptors of its tail in the same way as the median and mean are related to its central behavior. This paper considers a valuable alternative class to expectiles, called extremiles, which parallels the class of quantiles and includes the family of expected minima and expected maxima. The new class is motivated via several angles, which reveals its specific merits and strengths. Extremiles suggest better capability of fitting both location and spread in data points and provide an appropriate theory that better displays the interesting features of long-tailed distributions. We discuss their estimation in the range of the data and beyond the sample maximum. A number of motivating examples are given to illustrate the utility of estimated extremiles in modeling noncentral behavior. There is in particular an interesting connection with coherent measures of risk protection.
DOI: 10.6084/m9.figshare.6834872.v3
title: Extremiles: A New Perspective on Asymmetric Least Squares

description: Quantiles and expectiles of a distribution are found to be useful descriptors of its tail in the same way as the median and mean are related to its central behavior. This article considers a valuable alternative class to expectiles, called extremiles, which parallels the class of quantiles and includes the family of expected minima and expected maxima. The new class is motivated via several angles, which reveals its specific merits and strengths. Extremiles suggest better capability of fitting both location and spread in data points and provide an appropriate theory that better displays the interesting features of long-tailed distributions. We discuss their estimation in the range of the data and beyond the sample maximum. A number of motivating examples are given to illustrate the utility of estimated extremiles in modeling noncentral behavior. There is in particular an interesting connection with coherent measures of risk protection. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6834866.v1
title: Selection Corrected Statistical Inference for Region Detection with High-throughput Assays

description: Scientists use high-dimensional measurement assays to detect and prioritize regions of strong signal in spatially organized domain. Examples include finding methylation enriched genomic regions using microarrays, and active cortical areas using brain-imaging. The most common procedure for detecting potential regions is to group neighboring sites where the signal passed a threshold. However, one needs to account for the selection bias induced by this procedure to avoid diminishing effects when generalizing to a population. This paper introduces pin-down inference, a model and an inference framework that permit population inference for these detected regions. Pin-down inference provides non-asymptotic point and confidence interval estimators for the mean effect in the region that account for local selection bias. Our estimators accommodate non-stationary covariances that are typical of these data, allowing researchers to better compare regions of different sizes and correlation structures. Inference is provided within a conditional one-parameter exponential family per region, with truncations that match the selection constraints. A secondary screening-and-adjustment step allows pruning the set of detected regions, while controlling the false-coverage rate over the reported regions. We apply the method to genomic regions with differing DNA-methylation rates across tissue. Our method provides superior power compared to other conditional and non-parametric approaches.
DOI: 10.6084/m9.figshare.6834803
title: Functional response data from Resistance is futile: lack of predator switching and a preference for native prey predict the success of an invasive prey species

description: Underlying raw consumption data for Experiment 1
DOI: 10.6084/m9.figshare.6834803.v1
title: Functional response data from Resistance is futile: lack of predator switching and a preference for native prey predict the success of an invasive prey species

description: Underlying raw consumption data for Experiment 1
DOI: 10.6084/m9.figshare.6834797
title: Rstudio scripts

description: In here all R scipts, each corresponding a different statiscal analysis used for the report.<br>All csv and Excel files containing a corrosponding name were used for the R-scripts.
DOI: 10.6084/m9.figshare.6834800
title: Prey switching data from Resistance is futile: lack of predator switching and a preference for native prey predict the success of an invasive prey species

description: Underlying raw consumption data for Experiment 2
DOI: 10.6084/m9.figshare.6834800.v1
title: Prey switching data from Resistance is futile: lack of predator switching and a preference for native prey predict the success of an invasive prey species

description: Underlying raw consumption data for Experiment 2
DOI: 10.6084/m9.figshare.6834797.v1
title: Rstudio scripts

description: In here all R scipts, each corresponding a different statiscal analysis used for the report.<br>All csv and Excel files containing a corrosponding name were used for the R-scripts.
DOI: 10.6084/m9.figshare.6834788
title: Data and CSV files

description: In here all csv files and excel sheets used for statistical analyses are stored.The Excel file 'Raw data' contains a description of each varable in the tab 'metadata'.The second tab contains all the obtained raw data.<br>
DOI: 10.6084/m9.figshare.6834794
title: Figures

description: All figures obtained when carrying out the statiscal analyses. The names indicate which statistical analysis was used.
DOI: 10.6084/m9.figshare.6834794.v1
title: Figures

description: All figures obtained when carrying out the statiscal analyses. The names indicate which statistical analysis was used.
DOI: 10.6084/m9.figshare.6834770
title: File S3: Saccharomyces cerevisiae predicted protein connectivity distribution data.

description: Saccharomyces cerevisiae predicted protein connectivity distribution data.
DOI: 10.6084/m9.figshare.6834755
title: File S2: Phylogenetic analysis of additional three HGTs (HGT-1, HGT-3 & HGT6) where targeted single gene analysis of publicly accessible genome data identified additional putative recipient taxa.m

description: <b>Phylogenetic analysis of additional three HGTs (HGT-1, HGT-3 & HGT6) where targeted single gene analysis of publicly accessible genome data identified additional putative recipient taxa.</b>
DOI: 10.6084/m9.figshare.6834749
title: Table 2: data processing steps

description: Overview of processing steps that have been performed on each individual collected dataset to obtain the normalized hg19 data available on GEO.
DOI: 10.6084/m9.figshare.6834746
title: Table 3: Segmented copy number data

description: Segmented copy number data containing log2 ratios and gain/loss/amplification/homozygous deletion annotation per segment.
DOI: 10.6084/m9.figshare.6834749.v1
title: Table 2: data processing steps

description: Overview of processing steps that have been performed on each individual collected dataset to obtain the normalized hg19 data available on GEO.
DOI: 10.6084/m9.figshare.6834743
title: Table 1: Patient annotations

description: Sample annotations of the 556 high-risk neuroblastoma samples in the dataset, including clinical information and other information such as array platform and MYCN amplification status.
DOI: 10.6084/m9.figshare.6834725
title: File S1: Phylogenetic data supporting seven cases of ascomycete-basidiomycete HGT and including comparisons of phylogenetic ancestry of genes in high linkage to the HGT genes.

description: <b>Phylogenetic data supporting seven cases of ascomycete-basidiomycete HGT and including comparisons of phylogenetic ancestry of genes in high linkage to the HGT genes.</b>
DOI: 10.6084/m9.figshare.6834725.v1
title: File S1: Phylogenetic data supporting seven cases of ascomycete-basidiomycete HGT and including comparisons of phylogenetic ancestry of genes in high linkage to the HGT genes.

description: <b>Phylogenetic data supporting seven cases of ascomycete-basidiomycete HGT and including comparisons of phylogenetic ancestry of genes in high linkage to the HGT genes.</b>
DOI: 10.6084/m9.figshare.6834539
title: MATLAB Code from The auxiliary region method: a hybrid method for coupling PDE- and Brownian-based dynamics for reaction–diffusion systems

description: Zip file containing all of the code required to run the ARM.
DOI: 10.6084/m9.figshare.6834536
title: Data matrix from New highly pachyostotic nothosauroid interpreted as a filter-feeding Triassic marine reptile

description: Two well-preserved specimens of a new eosauropterygian from the Upper Triassic of Central Spain are attributed to a new taxon, <i>Paludidraco multidentatus</i> gen. et sp. nov. It is a member of Simosauridae that presents several exclusive characters suggesting a highly specialized trophic adaptation. This discovery increases the already high ecological disparity of the Triassic marine reptiles.
DOI: 10.6084/m9.figshare.6834536.v1
title: Data matrix from New highly pachyostotic nothosauroid interpreted as a filter-feeding Triassic marine reptile

description: Two well-preserved specimens of a new eosauropterygian from the Upper Triassic of Central Spain are attributed to a new taxon, <i>Paludidraco multidentatus</i> gen. et sp. nov. It is a member of Simosauridae that presents several exclusive characters suggesting a highly specialized trophic adaptation. This discovery increases the already high ecological disparity of the Triassic marine reptiles.
DOI: 10.6084/m9.figshare.6834539.v1
title: MATLAB Code from The auxiliary region method: a hybrid method for coupling PDE- and Brownian-based dynamics for reaction–diffusion systems

description: Zip file containing all of the code required to run the ARM.
DOI: 10.6084/m9.figshare.6834518
title: Supplementary Material for: Thyroid Hemiagenesis in a Thyroiditis Prone Mouse Strain

description: <b><i>Background:</i></b> Thyroid hemiagenesis, a rare congenital condition detected by ultrasound screening of the neck, is usually not manifested clinically in humans. This condition has been reported in mice with hypothyroidism associated with induced deficiency in paired box 8 and NK2 homeobox 1, sonic hedgehog, or T-box 1. Unexpectedly, we observed thyroid hemiagenesis in NOD.H2<sup>h4</sup> mice, an unusual strain that spontaneously develops iodide enhanced thyroid autoimmunity but remains euthyroid. <b><i>Objectives and Methods:</i></b> First, to compare mice with thyroid hemiagenesis versus bilobed littermates for serum T4, autoantibodies to thyroglobulin (ELISA) and thyroid peroxidase (TPO; flow cytometry with eukaryotic cells expressing mouse TPO), gross anatomy, and thyroid histology; second, to estimate the percentage of mice with thyroid hemiagenesis in the NOD.H2<sup>h4</sup> mice we have studied over 6 years. <b><i>Results:</i></b> Thyroid hemiagenesis was observed in 3 of 1,025 NOD.H2<sup>h4</sup> mice (2 females, 1 male; 0.3%). Two instances of hemiagenesis were in wild-type females and one in a transgenic male expressing the human TSHR A-subunit in the thyroid. Two mice had very large unilobed glands, as in some human cases with this condition. Thyroid lymphocytic infiltration, serum T4, and the levels of thyroid autoantibodies were similar in mice with thyroid hemiagenesis and bilobed littermates. <b><i>Conclusions:</i></b> Unlike hypothyroidism associated with hemiagenesis in transcription factor knockout mice, hemiagenesis in euthyroid NOD.H2<sup>h4</sup> mice occurs spontaneously and is phenotypically similar to that occasionally observed in humans.
DOI: 10.6084/m9.figshare.6834518.v1
title: Supplementary Material for: Thyroid Hemiagenesis in a Thyroiditis Prone Mouse Strain

description: <b><i>Background:</i></b> Thyroid hemiagenesis, a rare congenital condition detected by ultrasound screening of the neck, is usually not manifested clinically in humans. This condition has been reported in mice with hypothyroidism associated with induced deficiency in paired box 8 and NK2 homeobox 1, sonic hedgehog, or T-box 1. Unexpectedly, we observed thyroid hemiagenesis in NOD.H2<sup>h4</sup> mice, an unusual strain that spontaneously develops iodide enhanced thyroid autoimmunity but remains euthyroid. <b><i>Objectives and Methods:</i></b> First, to compare mice with thyroid hemiagenesis versus bilobed littermates for serum T4, autoantibodies to thyroglobulin (ELISA) and thyroid peroxidase (TPO; flow cytometry with eukaryotic cells expressing mouse TPO), gross anatomy, and thyroid histology; second, to estimate the percentage of mice with thyroid hemiagenesis in the NOD.H2<sup>h4</sup> mice we have studied over 6 years. <b><i>Results:</i></b> Thyroid hemiagenesis was observed in 3 of 1,025 NOD.H2<sup>h4</sup> mice (2 females, 1 male; 0.3%). Two instances of hemiagenesis were in wild-type females and one in a transgenic male expressing the human TSHR A-subunit in the thyroid. Two mice had very large unilobed glands, as in some human cases with this condition. Thyroid lymphocytic infiltration, serum T4, and the levels of thyroid autoantibodies were similar in mice with thyroid hemiagenesis and bilobed littermates. <b><i>Conclusions:</i></b> Unlike hypothyroidism associated with hemiagenesis in transcription factor knockout mice, hemiagenesis in euthyroid NOD.H2<sup>h4</sup> mice occurs spontaneously and is phenotypically similar to that occasionally observed in humans.
DOI: 10.17028/rd.lboro.6834488
title: Tissue Engineered Skeletal Muscle Scaffold

description: Modular tissue engineered scaffold for insertion into 3D printed bioreactor.
DOI: 10.6084/m9.figshare.6834515
title: Experiment 4 - Moving Cursor

description: Data from Experiment 4 from Wiener, Zhou, Bader, & Joiner.
DOI: 10.6084/m9.figshare.6834482
title: Experiment 2 - Hold

description: Experiment 2 data from Wiener, Zhou, Bader, & Joiner.
DOI: 10.6084/m9.figshare.6834515.v1
title: Experiment 4 - Moving Cursor

description: Data from Experiment 4 from Wiener, Zhou, Bader, & Joiner.
DOI: 10.6084/m9.figshare.6834482.v1
title: Experiment 2 - Hold

description: Experiment 2 data from Wiener, Zhou, Bader, & Joiner.