cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5033468
title: Bats and their ectoparasites of Coiba National Park, Panama. Raw data.xlsx

description: Please see paper for details regarding the methods.
DOI: 10.6084/m9.figshare.5033468.v1
title: Bats and their ectoparasites of Coiba National Park, Panama. Raw data.xlsx

description: Please see paper for details regarding the methods.
DOI: 10.6084/m9.figshare.5033414
title: Tonian to early Cryogenian synorogenic basin of the São Gabriel Terrane, Dom Feliciano Belt, southernmost Brazil

description: A provenance and stratigraphic study of the Neoproterozoic Pontas do Salso Complex (PSC), western portion of the Dom Feliciano Belt (DFB), was conducted with U–Pb zircon geochronological analysis of the metasediments and the host rocks. The U–Pb isotopic data from detrital zircon of the metasediments indicate the source from the latest Middle Tonian to Late Cryogenian (between 897 and 684 Ma) and maximum depositional age of 685 ± 18 Ma in an arc-related basin setting adjacent in the Sao Gabriel Arc. The metasediments of the PSC form an elongated body in the N35°E direction and occur in the central portion of the São Gabriel Terrane (SGT), which is constituted by ophiolitic complexes and arc-related rocks, generated probably during the final consolidation of Rodinia supercontinent, although this question is still open. Low- to medium-K calc-alkaline, metaluminous affinity, and trace-element geochemistry suggest that the chemical composition of the protoliths was generated from metasomatized mantle sources in subduction zones. The PSC is composed of meta-arkoses, with subordinate metaconglomerates and metapelites. The meta-arkoses are disposed in plane-parallel layers, which also internally feature small-scale cross-bedding structures. The matrix has a blastopsammitic, poorly selected, fine to coarse texture, and hexagonal quartz and plagioclase porphyroclasts with superimposed thermal metamorphism. The polymict metaconglomerates are matrix-supported, with 15–55% of clasts of metavolcanic rocks, metasediments, undeformed granites, and quartz veins. The metapelites comprise mainly muscovite phyllites with syn-tectonic garnet and chloritoid porphyroblasts. The PSC represents a sedimentary succession deposited on an arc-related basin formed during the collapse and uplift of the SGT.
DOI: 10.6084/m9.figshare.5033468.v3
title: Bats and their ectoparasites of Coiba National Park, Panama. Raw data.xlsx

description: Please see paper for details regarding the methods.
DOI: 10.6084/m9.figshare.5033414.v1
title: Tonian to early Cryogenian synorogenic basin of the São Gabriel Terrane, Dom Feliciano Belt, southernmost Brazil

description: A provenance and stratigraphic study of the Neoproterozoic Pontas do Salso Complex (PSC), western portion of the Dom Feliciano Belt (DFB), was conducted with U–Pb zircon geochronological analysis of the metasediments and the host rocks. The U–Pb isotopic data from detrital zircon of the metasediments indicate the source from the latest Middle Tonian to Late Cryogenian (between 897 and 684 Ma) and maximum depositional age of 685 ± 18 Ma in an arc-related basin setting adjacent in the Sao Gabriel Arc. The metasediments of the PSC form an elongated body in the N35°E direction and occur in the central portion of the São Gabriel Terrane (SGT), which is constituted by ophiolitic complexes and arc-related rocks, generated probably during the final consolidation of Rodinia supercontinent, although this question is still open. Low- to medium-K calc-alkaline, metaluminous affinity, and trace-element geochemistry suggest that the chemical composition of the protoliths was generated from metasomatized mantle sources in subduction zones. The PSC is composed of meta-arkoses, with subordinate metaconglomerates and metapelites. The meta-arkoses are disposed in plane-parallel layers, which also internally feature small-scale cross-bedding structures. The matrix has a blastopsammitic, poorly selected, fine to coarse texture, and hexagonal quartz and plagioclase porphyroclasts with superimposed thermal metamorphism. The polymict metaconglomerates are matrix-supported, with 15–55% of clasts of metavolcanic rocks, metasediments, undeformed granites, and quartz veins. The metapelites comprise mainly muscovite phyllites with syn-tectonic garnet and chloritoid porphyroblasts. The PSC represents a sedimentary succession deposited on an arc-related basin formed during the collapse and uplift of the SGT.
DOI: 10.6084/m9.figshare.5033468.v2
title: Bats and their ectoparasites of Coiba National Park, Panama. Raw data.xlsx

description: Please see paper for details regarding the methods.
DOI: 10.6084/m9.figshare.5033405
title: A Robust Model-Free Feature Screening Method for Ultrahigh-Dimensional Data

description: Feature screening plays an important role in dimension reduction for ultrahigh-dimensional data. In this article, we introduce a new feature screening method and establish its sure independence screening property under the ultrahigh-dimensional setting. The proposed method works based on the nonparanormal transformation and Henze–Zirkler’s test, that is, it first transforms the response variable and features to Gaussian random variables using the nonparanormal transformation and then tests the dependence between the response variable and features using the Henze–Zirkler’s test. The proposed method enjoys at least two merits. First, it is model-free, which avoids the specification of a particular model structure. Second, it is condition-free, which does not require any extra conditions except for some regularity conditions for high-dimensional feature screening. The numerical results indicate that, compared to the existing methods, the proposed method is more robust to the data generated from heavy-tailed distributions and/or complex models with interaction variables. The proposed method is applied to screening of anticancer drug response genes. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5033408
title: Large-Scale Structured Sparsity via Parallel Fused Lasso on Multiple GPUs

description: We present a massively parallel algorithm for the fused lasso, powered by a multiple number of graphics processing units (GPUs). Our method is suitable for a class of large-scale sparse regression problems on which a two-dimensional lattice structure among the coefficients is imposed. This structure is important in many statistical applications, including image-based regression in which a set of images are used to locate image regions predictive of a response variable such as human behavior. Such large datasets are increasingly common. In our study, we employ the split Bregman method and the fast Fourier transform, which jointly have a high data-level parallelism that is distinct in a two-dimensional setting. Our multi-GPU parallelization achieves remarkably improved speed. Specifically, we obtained as much as 433 times improved speed over that of the reference CPU implementation. We demonstrate the speed and scalability of the algorithm using several datasets, including 8100 samples of 512 × 512 images. Compared to the single GPU counterpart, our method also showed improved computing speed as well as high scalability. We describe the various elements of our study as well as our experience with the subtleties in selecting an existing algorithm for parallelization. It is critical that memory bandwidth be carefully considered for multi-GPU algorithms. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5033399
title: A meta-analytical comparison of atenolol with angiotensin-converting enzyme inhibitors on arterial stiffness, peripheral blood pressure and heart rate in hypertensive patients

description: <i>Objectives</i>: This meta-analysis of randomized parallel controlled trials was designed to compare the efficacy of atenolol with angiotensin-converting enzyme inhibitors (ACEIs) in changing pulse wave velocity (PWV), peripheral blood pressure and heart rate (HR) among patients with essential hypertension. <i>Methods</i>: This study was conducted according to the PRISMA guideline. Data collection was independently completed by two investigators. Statistical analyses were completed by Stata software (v12.0). <i>Results</i>: Eight clinical trials were meta-analyzed in this study. Overall changes in PWV (weighted mean difference or WMD = 0.068, 95% confidence interval or CI: −0.487 to –0.623, P = 0.811) and peripheral systolic blood pressure (PSBP) (WMD = −1.281 mmHg, 95% CI: −6.936 to 4.375, P = 0.657) did not differ significantly between atenolol and ACEIs treatment. Relative to ACEIs, atenolol had a more favorable impact on peripheral diastolic blood pressure (PDBP) (WMD = −1.912 mmHg, 95% CI: −3.732 to −0.091, P = 0.040) and HR (WMD = −9.23 bpm, 95% CI: −12.53 to −5.93, P &lt; 0.001). In stratified analyses, particularly by follow-up period, atenolol was observed to be superior over ACEIs within early 3-month treatment in PSBP (WMD = −4.097 mmHg, 95% CI: −6.589 to −1.605, P = 0.001), PDBP (WMD = −6.802 mmHg, 95% CI: −8.517 to −5.087, P &lt; 0.001) and HR (WMD = −14.242 bpm, 95% CI: −16.427 to −12.058, P = 0.028), without heterogeneity (<i>I</i><sup>2</sup> = 0.0%). There were low probabilities of publication bias for all comparisons. <i>Conclusions</i>: Our findings demonstrate that atenolol and ACEIs were equally effective in reducing PWV and PSBP, while atenolol was superior over ACEIs in improving PDBP and HR, especially within short-term treatment.
DOI: 10.6084/m9.figshare.5033399.v1
title: A meta-analytical comparison of atenolol with angiotensin-converting enzyme inhibitors on arterial stiffness, peripheral blood pressure and heart rate in hypertensive patients

description: <i>Objectives</i>: This meta-analysis of randomized parallel controlled trials was designed to compare the efficacy of atenolol with angiotensin-converting enzyme inhibitors (ACEIs) in changing pulse wave velocity (PWV), peripheral blood pressure and heart rate (HR) among patients with essential hypertension. <i>Methods</i>: This study was conducted according to the PRISMA guideline. Data collection was independently completed by two investigators. Statistical analyses were completed by Stata software (v12.0). <i>Results</i>: Eight clinical trials were meta-analyzed in this study. Overall changes in PWV (weighted mean difference or WMD = 0.068, 95% confidence interval or CI: −0.487 to –0.623, P = 0.811) and peripheral systolic blood pressure (PSBP) (WMD = −1.281 mmHg, 95% CI: −6.936 to 4.375, P = 0.657) did not differ significantly between atenolol and ACEIs treatment. Relative to ACEIs, atenolol had a more favorable impact on peripheral diastolic blood pressure (PDBP) (WMD = −1.912 mmHg, 95% CI: −3.732 to −0.091, P = 0.040) and HR (WMD = −9.23 bpm, 95% CI: −12.53 to −5.93, P &lt; 0.001). In stratified analyses, particularly by follow-up period, atenolol was observed to be superior over ACEIs within early 3-month treatment in PSBP (WMD = −4.097 mmHg, 95% CI: −6.589 to −1.605, P = 0.001), PDBP (WMD = −6.802 mmHg, 95% CI: −8.517 to −5.087, P &lt; 0.001) and HR (WMD = −14.242 bpm, 95% CI: −16.427 to −12.058, P = 0.028), without heterogeneity (<i>I</i><sup>2</sup> = 0.0%). There were low probabilities of publication bias for all comparisons. <i>Conclusions</i>: Our findings demonstrate that atenolol and ACEIs were equally effective in reducing PWV and PSBP, while atenolol was superior over ACEIs in improving PDBP and HR, especially within short-term treatment.
DOI: 10.6084/m9.figshare.5033405.v1
title: A Robust Model-Free Feature Screening Method for Ultrahigh-Dimensional Data

description: Feature screening plays an important role in dimension reduction for ultrahigh-dimensional data. In this article, we introduce a new feature screening method and establish its sure independence screening property under the ultrahigh-dimensional setting. The proposed method works based on the nonparanormal transformation and Henze–Zirkler’s test, that is, it first transforms the response variable and features to Gaussian random variables using the nonparanormal transformation and then tests the dependence between the response variable and features using the Henze–Zirkler’s test. The proposed method enjoys at least two merits. First, it is model-free, which avoids the specification of a particular model structure. Second, it is condition-free, which does not require any extra conditions except for some regularity conditions for high-dimensional feature screening. The numerical results indicate that, compared to the existing methods, the proposed method is more robust to the data generated from heavy-tailed distributions and/or complex models with interaction variables. The proposed method is applied to screening of anticancer drug response genes. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5033381
title: Radiation induced pulmonary fibrosis as a model of progressive fibrosis: Contributions of DNA damage, inflammatory response and cellular senescence genes

description: <b>Purpose/Aim of Study</b>: Studies of pulmonary fibrosis (PF) have resulted in DNA damage, inflammatory response, and cellular senescence being widely hypothesized to play a role in the progression of the disease. Utilizing these aforementioned terms, genomics databases were interrogated along with the term, “pulmonary fibrosis,” to identify genes common among all 4 search terms. Findings were compared to data derived from a model of radiation-induced progressive pulmonary fibrosis (RIPF) to verify that these genes are similarly expressed, supporting the use of radiation as a model for diseases involving PF, such as human idiopathic pulmonary fibrosis (IPF). <b>Materials and Methods</b>: In an established model of RIPF, C57BL/6J mice were exposed to 12.5 Gy thorax irradiation and sacrificed at 24 hours, 1, 4, 12, and 32 weeks following exposure, and lung tissue was compared to age-matched controls by RNA sequencing. <b>Results</b>: Of 176 PF associated gene transcripts identified by database interrogation, 146 (&gt;82%) were present in our experimental model, throughout the progression of RIPF. Analysis revealed that nearly 85% of PF gene transcripts were associated with at least 1 other search term. Furthermore, of 22 genes common to all four terms, 16 were present experimentally in RIPF. <b>Conclusions</b>: This illustrates the validity of RIPF as a model of progressive PF/IPF based on the numbers of transcripts reported in both literature and observed experimentally. Well characterized genes and proteins are implicated in this model, supporting the hypotheses that DNA damage, inflammatory response and cellular senescence are associated with the pathogenesis of PF.
DOI: 10.6084/m9.figshare.5033408.v2
title: Large-Scale Structured Sparsity via Parallel Fused Lasso on Multiple GPUs

description: We present a massively parallel algorithm for the fused lasso, powered by a multiple number of graphics processing units (GPUs). Our method is suitable for a class of large-scale sparse regression problems on which a two-dimensional lattice structure among the coefficients is imposed. This structure is important in many statistical applications, including image-based regression in which a set of images are used to locate image regions predictive of a response variable such as human behavior. Such large datasets are increasingly common. In our study, we employ the split Bregman method and the fast Fourier transform, which jointly have a high data-level parallelism that is distinct in a two-dimensional setting. Our multi-GPU parallelization achieves remarkably improved speed. Specifically, we obtained as much as 433 times improved speed over that of the reference CPU implementation. We demonstrate the speed and scalability of the algorithm using several datasets, including 8100 samples of 512 × 512 images. Compared to the single GPU counterpart, our method also showed improved computing speed as well as high scalability. We describe the various elements of our study as well as our experience with the subtleties in selecting an existing algorithm for parallelization. It is critical that memory bandwidth be carefully considered for multi-GPU algorithms. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5033408.v1
title: Large-scale Structured Sparsity via Parallel Fused Lasso on Multiple GPUs

description: We present a massively parallel algorithm for the fused lasso, powered by a multiple number of graphics processing units (GPUs). Our method is suitable for a class of large-scale sparse regression problems on which a two-dimensional lattice structure among the coefficients is imposed. This structure is important in many statistical applications, including image-based regression in which a set of images are used to locate image regions predictive of a response variable such as human behavior. Such large datasets are increasingly common. In our study, we employ the split Bregman method and the fast Fourier transform, which jointly have a high data-level parallelism that is distinct in a two-dimensional setting. Our multi-GPU parallelization achieves remarkably improved speed. Specifically, we obtained as much as 433 times improved speed over that of the reference CPU implementation. We demonstrate the speed and scalability of the algorithm using several datasets, including 8100 samples of 512×512 images. Compared to the single GPU counterpart, our method also showed improved computing speed as well as high scalability. We describe the various elements of our study as well as our experience with the subtleties in selecting an existing algorithm for parallelization. It is critical that memory bandwidth be carefully considered for multi-GPU algorithms.
DOI: 10.6084/m9.figshare.5033381.v1
title: Radiation induced pulmonary fibrosis as a model of progressive fibrosis: Contributions of DNA damage, inflammatory response and cellular senescence genes

description: <b>Purpose/Aim of Study</b>: Studies of pulmonary fibrosis (PF) have resulted in DNA damage, inflammatory response, and cellular senescence being widely hypothesized to play a role in the progression of the disease. Utilizing these aforementioned terms, genomics databases were interrogated along with the term, “pulmonary fibrosis,” to identify genes common among all 4 search terms. Findings were compared to data derived from a model of radiation-induced progressive pulmonary fibrosis (RIPF) to verify that these genes are similarly expressed, supporting the use of radiation as a model for diseases involving PF, such as human idiopathic pulmonary fibrosis (IPF). <b>Materials and Methods</b>: In an established model of RIPF, C57BL/6J mice were exposed to 12.5 Gy thorax irradiation and sacrificed at 24 hours, 1, 4, 12, and 32 weeks following exposure, and lung tissue was compared to age-matched controls by RNA sequencing. <b>Results</b>: Of 176 PF associated gene transcripts identified by database interrogation, 146 (&gt;82%) were present in our experimental model, throughout the progression of RIPF. Analysis revealed that nearly 85% of PF gene transcripts were associated with at least 1 other search term. Furthermore, of 22 genes common to all four terms, 16 were present experimentally in RIPF. <b>Conclusions</b>: This illustrates the validity of RIPF as a model of progressive PF/IPF based on the numbers of transcripts reported in both literature and observed experimentally. Well characterized genes and proteins are implicated in this model, supporting the hypotheses that DNA damage, inflammatory response and cellular senescence are associated with the pathogenesis of PF.
DOI: 10.6084/m9.figshare.5033378
title: <i>In situ</i> stress distribution and mechanical stratigraphy in the Bowen and Surat basins, Queensland, Australia

description: Database of additional wells with image log data.
DOI: 10.6084/m9.figshare.5033378.v1
title: <i>In situ</i> stress distribution and mechanical stratigraphy in the Bowen and Surat basins, Queensland, Australia

description: Database of additional wells with image log data.
DOI: 10.6084/m9.figshare.5032499
title: Effects of host species and environment on the skin microbiome of Plethodontid salamanders

description: Environmental metadata for 100 Plethodon salamanders of three species sampled in the Central Appalachian Mountains. We conducted a general descriptive analysis of the bacterial OTUs identified from the three host species (n = 100), including description of their core microbiome. Then, we examined microbiome structure<b> </b>in two subsets of the data: a co-occurring species dataset (n = 62) and an elevational dataset (n = 50). Twelve individuals were included in both analyses. <br>We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring <i>Plethodon</i> salamander species (35 <i>P. cinereus</i>, 17 <i>P. glutinosus</i>, 10 <i>P. cylindraceus</i>) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of <i>P. cinereus</i> along an elevational gradient (n = 50, 700 – 1000 masl) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. <br>Pyrosequencing runs have been deposited in the National Center for Biotechnology Information Sequence Read Archive (www.ncbi.nlm.nih.gov/sra) under accession number SUB2660574
DOI: 10.6084/m9.figshare.5032478
title: Combined tracking plot, camera trap and nest monitoring data

description: Combined tracking plot, camera trap and nest monitoring data in 2014-2015 and 2015-2016 nesting seasons
DOI: 10.6084/m9.figshare.5032481
title: Anthropogenic noise pollution disrupts the structure and dynamics of fish shoals

description: All variables for the measures analysed.
DOI: 10.6084/m9.figshare.5032499.v1
title: Effects of host species and environment on the skin microbiome of Plethodontid salamanders

description: Environmental metadata for 100 Plethodon salamanders of three species sampled in the Central Appalachian Mountains. We conducted a general descriptive analysis of the bacterial OTUs identified from the three host species (n = 100), including description of their core microbiome. Then, we examined microbiome structure<b> </b>in two subsets of the data: a co-occurring species dataset (n = 62) and an elevational dataset (n = 50). Twelve individuals were included in both analyses. <br>We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring <i>Plethodon</i> salamander species (35 <i>P. cinereus</i>, 17 <i>P. glutinosus</i>, 10 <i>P. cylindraceus</i>) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of <i>P. cinereus</i> along an elevational gradient (n = 50, 700 – 1000 masl) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. <br>Pyrosequencing runs have been deposited in the National Center for Biotechnology Information Sequence Read Archive (www.ncbi.nlm.nih.gov/sra) under accession number SUB2660574
DOI: 10.6084/m9.figshare.5032466
title: Microstructural controls on the pressure-dependent permeability of Whitby mudstone

description: A CSV file containing all experimental conditions and a tabulation of results
DOI: 10.6084/m9.figshare.5032442
title: Circulations in Our System

description: see also SSRN 2865571 "Einsteins Criterion Applied to Logical Macroeconomics Modeling"<br>
DOI: 10.6084/m9.figshare.5032478.v1
title: Combined tracking plot, camera trap and nest monitoring data

description: Combined tracking plot, camera trap and nest monitoring data in 2014-2015 and 2015-2016 nesting seasons