cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11923545
title: Aoki_morphologydata.csv

description: This dataset contains morphological measurements, sample localities, sex, date of collection and age of two Japanese subspecies of the Eurasian Jay (<i>Garrulus glandarius japonicus </i>and <i>G. g. tokugawae</i>) for comparisons of their morphological characteristics.
DOI: 10.6084/m9.figshare.11923545.v2
title: Aoki_morphologydata.csv

description: This dataset contains morphological measurements, sample localities, sex, date of collection and age of two Japanese subspecies of the Eurasian Jay (<i>Garrulus glandarius japonicus </i>and <i>G. g. tokugawae</i>) for comparisons of their morphological characteristics.
DOI: 10.6084/m9.figshare.11923545.v1
title: Aoki_morphologydata.csv

description: This dataset contains morphological measurements, sample localities, sex, date of collection and age of two Japanese subspecies of the Eurasian Jay (<i>Garrulus glandarius japonicus </i>and <i>G. g. tokugawae</i>) for comparisons of their morphological characteristics.
DOI: 10.6084/m9.figshare.11923479
title: Eastern oyster (Crassostrea virginica) gonad DNA methylation data and analysis

description: Epigenetic modification, specifically DNA methylation, is one possible mechanism for transgenerational plasticity. Before inheritance of methylation patterns can be characterized we need a better understanding of how environmental change modifies the parental epigenome. Specifically, methylation patterns should be understood in reproductive tissue. We examined the effect of ocean acidification on Eastern oyster (<i>Crassostrea virginica</i>) reproductive tissue.<br>The associated Github repository can be found here: https://github.com/epigeneticstoocean/paper-gonad-meth<br>This repository is associated with the manuscript "General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (<i>Crassostrea virginica</i>)" on bioRXiv: https://www.biorxiv.org/content/10.1101/2020.01.07.897934v1
DOI: 10.6084/m9.figshare.11923479.v1
title: General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica)

description: Epigenetic modification, specifically DNA methylation, is one possible mechanism for intergenerational plasticity. Before inheritance of methylation patterns can be characterized, we need a better understanding of how environmental change modifies the parental epigenome. To examine the influence of experimental ocean acidification on eastern oyster (Crassostrea virginica) gonad tissue, oysters were cultured in the laboratory under control (491 ± 49 µatm) or high (2550 ± 211 µatm) pCO2 conditions for four weeks. DNA from reproductive tissue was isolated from five oysters per treatment, then subjected to bisulfite treatment and DNA sequencing. Irrespective of treatment, DNA methylation was primarily found in gene bodies with approximately 22% of CpGs (2.7% of total cytosines) in the C. virginica genome predicted to be methylated. In response to elevated pCO2, we found 598 differentially methylated loci primarily overlapping with gene bodies. A majority of differentially methylated loci were in exons (61.5%) with less intron overlap (31.9%). While there was no evidence of a significant tendency for the genes with differentially methylated loci to be associated with distinct biological processes, the concentration of these loci in gene bodies, including genes involved in protein ubiquitination and biomineralization suggests DNA methylation may be important for transcriptional control in response to ocean acidification. Changes in gonad methylation also indicate potential for these methylation patterns to be inherited by offspring. Understanding how experimental ocean acidification conditions modify the oyster epigenome, and if these modifications are inherited, allows for a better understanding of how ecosystems will respond to environmental change. <br>
DOI: 10.6084/m9.figshare.11923479.v3
title: Eastern oyster (Crassostrea virginica) gonad DNA methylation data and analysis

description: Epigenetic modification, specifically DNA methylation, is one possible mechanism for transgenerational plasticity. Before inheritance of methylation patterns can be characterized we need a better understanding of how environmental change modifies the parental epigenome. Specifically, methylation patterns should be understood in reproductive tissue. We examined the effect of ocean acidification on Eastern oyster (<i>Crassostrea virginica</i>) reproductive tissue.<br>The associated Github repository can be found here: https://github.com/epigeneticstoocean/paper-gonad-meth<br>This repository is associated with the manuscript "General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (<i>Crassostrea virginica</i>)" on bioRXiv: https://www.biorxiv.org/content/10.1101/2020.01.07.897934v1
DOI: 10.6084/m9.figshare.11923479.v2
title: General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica)

description: Epigenetic modification, specifically DNA methylation, is one possible mechanism for intergenerational plasticity. Before inheritance of methylation patterns can be characterized, we need a better understanding of how environmental change modifies the parental epigenome. To examine the influence of experimental ocean acidification on eastern oyster (Crassostrea virginica) gonad tissue, oysters were cultured in the laboratory under control (491 ± 49 µatm) or high (2550 ± 211 µatm) pCO2 conditions for four weeks. DNA from reproductive tissue was isolated from five oysters per treatment, then subjected to bisulfite treatment and DNA sequencing. Irrespective of treatment, DNA methylation was primarily found in gene bodies with approximately 22% of CpGs (2.7% of total cytosines) in the C. virginica genome predicted to be methylated. In response to elevated pCO2, we found 598 differentially methylated loci primarily overlapping with gene bodies. A majority of differentially methylated loci were in exons (61.5%) with less intron overlap (31.9%). While there was no evidence of a significant tendency for the genes with differentially methylated loci to be associated with distinct biological processes, the concentration of these loci in gene bodies, including genes involved in protein ubiquitination and biomineralization suggests DNA methylation may be important for transcriptional control in response to ocean acidification. Changes in gonad methylation also indicate potential for these methylation patterns to be inherited by offspring. Understanding how experimental ocean acidification conditions modify the oyster epigenome, and if these modifications are inherited, allows for a better understanding of how ecosystems will respond to environmental change. <br>
DOI: 10.6084/m9.figshare.11923419
title: Supporting Information-Knigge et al.,"Mandibular symphyseal fusion in fossil primates: Insights from correlated patterns of jaw shape and masticatory function in living primates"

description: These files contain raw data and supporting analyses and figures for Knigge et al., "Mandibular symphyseal fusion in fossil primates: Insights from correlated patterns of jaw shape and masticatory function in living primates."<br>Appendix 1: Includes a table of EMG data used in this study and supporting analyses and results<br>Appendix 2: Raw coordinate data for the full landmark dataset of extant primate specimens<br>Appendix 3: Raw coordinate data for the reduced landmark dataset that includes all extant and fossil primate specimens.
DOI: 10.6084/m9.figshare.11923302
title: DATA: Evaluation of the skill in monthly-to-seasonal soil moisture forecasting based on SMAP satellite observations over the southeastern US

description: Providing accurate soil moisture (SM) conditions is a critical step in model initialization in weather forecasting, agricultural planning, and water resources management. This study develops monthly-to-seasonal (M2S) top layer SM forecasts by forcing 1- to 3-month ahead precipitation forecasts with Noah3.2 Land Surface Model. The SM forecasts are developed over the southeastern US (SEUS), and the SM forecasting skill is evaluated in comparison with the remotely sensed SM observations collected by the Soil Moisture Active Passive (SMAP) satellite. Our results indicate potential in developing real-time SM forecasts. The retrospective 18-month (April 2015–September 2016) comparison between SM forecasts and the SMAP observations shows statistically significant correlations of 0.62, 0.57, and 0.58 over 1-, 2-, and 3-month lead times respectively.
DOI: 10.6084/m9.figshare.11923302.v2
title: DATA: Evaluation of the skill in monthly-to-seasonal soil moisture forecasting based on SMAP satellite observations over the southeastern US

description: Providing accurate soil moisture (SM) conditions is a critical step in model initialization in weather forecasting, agricultural planning, and water resources management. This study develops monthly-to-seasonal (M2S) top layer SM forecasts by forcing 1- to 3-month ahead precipitation forecasts with Noah3.2 Land Surface Model. The SM forecasts are developed over the southeastern US (SEUS), and the SM forecasting skill is evaluated in comparison with the remotely sensed SM observations collected by the Soil Moisture Active Passive (SMAP) satellite. Our results indicate potential in developing real-time SM forecasts. The retrospective 18-month (April 2015–September 2016) comparison between SM forecasts and the SMAP observations shows statistically significant correlations of 0.62, 0.57, and 0.58 over 1-, 2-, and 3-month lead times respectively.
DOI: 10.6084/m9.figshare.11923302.v1
title: DATA: Evaluation of the skill in monthly-to-seasonal soil moisture forecasting based on SMAP satellite observations over the southeastern US

description: Providing accurate soil moisture (SM) conditions is a critical step in model initialization in weather forecasting, agricultural planning, and water resources management. This study develops monthly-to-seasonal (M2S) top layer SM forecasts by forcing 1- to 3-month ahead precipitation forecasts with Noah3.2 Land Surface Model. The SM forecasts are developed over the southeastern US (SEUS), and the SM forecasting skill is evaluated in comparison with the remotely sensed SM observations collected by the Soil Moisture Active Passive (SMAP) satellite. Our results indicate potential in developing real-time SM forecasts. The retrospective 18-month (April 2015–September 2016) comparison between SM forecasts and the SMAP observations shows statistically significant correlations of 0.62, 0.57, and 0.58 over 1-, 2-, and 3-month lead times respectively.
DOI: 10.6084/m9.figshare.11923170
title: <i>Clitopilus, Clitocella</i>, and <i>Clitopilopsis</i> in China

description: Within the family Entolomataceae, many reports of <i>Entoloma</i> and <i>Rhodocybe</i> have been published, but few reports on <i>Clitopilus</i> and allied genera are available. In this study, <i>Clitopilus, Clitocella</i>, and <i>Clitopilopsis</i> from China were studied by morphological and phylogenetic methods. Portions of nuc 28S rDNA (28S), RNA polymerase II second largest subunit (<i>rpb2</i>), translation elongation factor 1-alpha (<i>tef1</i>), and ATPase subunit 6 (<i>atp6</i>), were employed to elucidate the relationships of <i>Clitopilus</i> and allies. Results indicate that <i>Clitopilus</i> should be divided into three sections, namely, sect. <i>Clitopilus</i>, sect. <i>Scyphoides</i>, and sect. <i>Crispi</i>, the last of which is newly described. In total, 17 species of <i>Clitopilus, Clitocella</i>, and <i>Clitopilopsis</i> are found in China; 14 species belong to <i>Clitopilus</i>, of which 5 are new: <i>C. yunnanensis, C. brunniceps, C. rugosiceps, C. sinoapalus</i>, and <i>C. umbilicatus</i>. Two species of <i>Clitocella</i>, including one new species, <i>Clitocella orientalis</i>, are described. One new species of <i>Clitopilopsis</i>, namely, <i>Clitopilopsis albida</i>, is proposed.
DOI: 10.6084/m9.figshare.11923170.v1
title: <i>Clitopilus, Clitocella</i>, and <i>Clitopilopsis</i> in China

description: Within the family Entolomataceae, many reports of <i>Entoloma</i> and <i>Rhodocybe</i> have been published, but few reports on <i>Clitopilus</i> and allied genera are available. In this study, <i>Clitopilus, Clitocella</i>, and <i>Clitopilopsis</i> from China were studied by morphological and phylogenetic methods. Portions of nuc 28S rDNA (28S), RNA polymerase II second largest subunit (<i>rpb2</i>), translation elongation factor 1-alpha (<i>tef1</i>), and ATPase subunit 6 (<i>atp6</i>), were employed to elucidate the relationships of <i>Clitopilus</i> and allies. Results indicate that <i>Clitopilus</i> should be divided into three sections, namely, sect. <i>Clitopilus</i>, sect. <i>Scyphoides</i>, and sect. <i>Crispi</i>, the last of which is newly described. In total, 17 species of <i>Clitopilus, Clitocella</i>, and <i>Clitopilopsis</i> are found in China; 14 species belong to <i>Clitopilus</i>, of which 5 are new: <i>C. yunnanensis, C. brunniceps, C. rugosiceps, C. sinoapalus</i>, and <i>C. umbilicatus</i>. Two species of <i>Clitocella</i>, including one new species, <i>Clitocella orientalis</i>, are described. One new species of <i>Clitopilopsis</i>, namely, <i>Clitopilopsis albida</i>, is proposed.
DOI: 10.6084/m9.figshare.11923122
title: Dunham et al "Asymmetrical gait kinematics of free-ranging callitrichines in response to changes in substrate diameter and orientation"

description: Dataset used to analyze the influence of substrate diameter and orientation on gait selection in free-ranging Saguinus and Cebuella.
DOI: 10.6084/m9.figshare.11923026
title: Dataset: Canopy Nitrogen addition promotes xylem formation of Castanopsis chinensis (Sprengel) Hance in a subtropical forest in China

description: Increased atmospheric nitrogen (N) deposition caused by intensive anthropogenic activities resulted in inconsistent effects on the xylem formation of trees, in N-limited boreal and temperate forests. However, the effects of N deposition on xylem formation of trees in subtropical forests, are still poorly understood. The aims of the study were to (i) characterize the dynamics of xylem formation in <i>C. chinensis</i> in a subtropical forest in China and (ii) determine the effect on xylem formation of adding N to the canopy. From 2013-2016, 50 kg N ha<sup>-1</sup> yr<sup>-1 </sup>was applied over the canopy of <i>C. chinensis </i>at the end of each month (April to October) in a subtropical forest in southern China. Then, the dynamics of xylem formation including the width of cambium cells, enlargement cells, wall-thickening cells and mature cells were monitored during 2015 and 2016 using a microcore sampling approach.
DOI: 10.6084/m9.figshare.11923122.v1
title: Dunham et al "Asymmetrical gait kinematics of free-ranging callitrichines in response to changes in substrate diameter and orientation"

description: Dataset used to analyze the influence of substrate diameter and orientation on gait selection in free-ranging Saguinus and Cebuella.
DOI: 10.6084/m9.figshare.11923017
title: Genetic and phenotypic evidence of a contact zone between divergent color morphs of the iconic red-eyed treefrog

description: individual_fastq.zipRaw fastq files for each individual. Libraries prepared using Best RADseq method<br>inputs-scripts.tar.gz<br>Scripts for generating input files from raw sequence data sample-info_phenotypes.xlsxLeg color data used for color similarity analysis (tab:all_phenotyped_RGB%) and for genome-wide association analysis (tab:genotyped&phenotyped). RGB values and percent of pixels in each color bin generated with colordistance package in R.<br>
DOI: 10.6084/m9.figshare.11923014
title: Prokka-annotated data of assemblies for BioProject PRJEB30858

description: BioProject
DOI: 10.6084/m9.figshare.11923026.v1
title: Canopy Nitrogen addition promotes xylem formation of Castanopsis chinensis (Sprengel) Hance in a subtropical forest in China

description: In this study, 50 kg N ha<sup>−1</sup> yr<sup>−1 </sup>was applied to the canopy of <i>C. chinensis</i> in a subtropical forest in south China from 2013‒2016. Then, the dynamics of xylem formation were monitored during 2015 and 2016 using microcore sampling. In the data set, the width of cambium cells, enlargment cells, wall-thickening cells and mature cells were recorded during 2015 and 2016.
DOI: 10.6084/m9.figshare.11923014.v1
title: Prokka-annotated data of assemblies for BioProject PRJEB30858

description: BioProject
DOI: 10.6084/m9.figshare.11923017.v1
title: Genetic and phenotypic evidence of a treefrog contact zone suggests the evolution of novel hybrid coloration

description: individual_fastq.zipRaw fastq files for each individual. Libraries prepared using Best RADseq method<br><br>sample-info_phenotypes.xlsxLeg color data used for color similarity analysis (tab:all_phenotyped_RGB%) and for genome-wide association analysis (tab:genotyped&phenotyped). RGB values and percent of pixels in each color bin generated with colordistance package in R.<br>
DOI: 10.6084/m9.figshare.11923026.v3
title: Dataset: Canopy Nitrogen addition promotes xylem formation of Castanopsis chinensis (Sprengel) Hance in a subtropical forest in China

description: Increased atmospheric nitrogen (N) deposition caused by intensive anthropogenic activities resulted in inconsistent effects on the xylem formation of trees, in N-limited boreal and temperate forests. However, the effects of N deposition on xylem formation of trees in subtropical forests, are still poorly understood. The aims of the study were to (i) characterize the dynamics of xylem formation in <i>C. chinensis</i> in a subtropical forest in China and (ii) determine the effect on xylem formation of adding N to the canopy. From 2013-2016, 50 kg N ha<sup>-1</sup> yr<sup>-1 </sup>was applied over the canopy of <i>C. chinensis </i>at the end of each month (April to October) in a subtropical forest in southern China. Then, the dynamics of xylem formation including the width of cambium cells, enlargement cells, wall-thickening cells and mature cells were monitored during 2015 and 2016 using a microcore sampling approach.
DOI: 10.6084/m9.figshare.11922966
title: Canopy Nitrogen addition promotes xylem formation of Castanopsis chinensis (Sprengel) Hance in a subtropical forest in China

description: In this study, 50 kg N ha<sup>−1</sup> yr<sup>−1 </sup>was applied to the canopy of <i>C. chinensis</i> in a subtropical forest in south China from 2013‒2016. Then, the dynamics of xylem formation were monitored during 2015 and 2016 using microcore sampling. In the data set, the width of cambium cells, enlargment cells, wall-thickening cells and mature cells were recorded during 2015 and 2016.
DOI: 10.6084/m9.figshare.11923005
title: MAGs.zip

description: Metagenome-assembled genomes generated in study from data of Ward et al. (2016).<br>Ward DV, Scholz M, Zolfo M, Taft DH, Schibler KR, Tett A, et al. Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants. Cell Rep. 2016 Mar 29;14(12):2912–24.<br>
DOI: 10.6084/m9.figshare.11923026.v2
title: Canopy Nitrogen addition promotes xylem formation of Castanopsis chinensis (Sprengel) Hance in a subtropical forest in China

description: In this study, 50 kg N ha<sup>−1</sup> yr<sup>−1 </sup>was applied to the canopy of <i>C. chinensis</i> in a subtropical forest in south China from 2013‒2016. Then, the dynamics of xylem formation were monitored during 2015 and 2016 using microcore sampling. In the data set, the width of cambium cells, enlargment cells, wall-thickening cells and mature cells were recorded during 2015 and 2016.
DOI: 10.6084/m9.figshare.11922966.v1
title: Canopy Nitrogen addition promotes xylem formation of Castanopsis chinensis (Sprengel) Hance in a subtropical forest in China

description: In this study, 50 kg N ha<sup>−1</sup> yr<sup>−1 </sup>was applied to the canopy of <i>C. chinensis</i> in a subtropical forest in south China from 2013‒2016. Then, the dynamics of xylem formation were monitored during 2015 and 2016 using microcore sampling. In the data set, the width of cambium cells, enlargment cells, wall-thickening cells and mature cells were recorded during 2015 and 2016.
DOI: 10.6084/m9.figshare.11922942
title: Life Experiences Dataset

description: Raw data of Life Experiences in Breast Cancer cross sectional study.
DOI: 10.6084/m9.figshare.11922942.v1
title: Life Experiences Dataset

description: Raw data of Life Experiences in Breast Cancer cross sectional study.
DOI: 10.6084/m9.figshare.11922924
title: Extinction risk at increasing levels of strategic protection

description: Data used to generate plots for Figure 1 in Hannah et al. 2020 30% land conservation and climate action reduces tropical extinction risk by more than 50%. Ecography
DOI: 10.6084/m9.figshare.11921253
title: TIES project

description: These data is from the Project TIES, includes R Script, TIFFs, and Datasets.
DOI: 10.6084/m9.figshare.11921253.v1
title: TIES project

description: These data is from the Project TIES, includes R Script, TIFFs, and Datasets.
DOI: 10.6084/m9.figshare.11921139
title: FXIa_NGS_raw_data

description: Next generation sequencing data for phage selection against FXIa
DOI: 10.6084/m9.figshare.11921139.v2
title: FXIa_NGS_raw_data

description: Next generation sequencing data for phage selection against FXIa
DOI: 10.6084/m9.figshare.11921139.v1
title: FXIa_IL_23R_NGS_raw_data

description: Next generation sequencing data for phage selection against FXIa and IL-23R
DOI: 10.6084/m9.figshare.11921082
title: Planilha Base - Monografia Bruno dos Santos Vieira.xlsx

description: Abstract: A pre-purchase financing pool (in Portuguese, “consórcio”) is a Brazilian financial product that, in its conception, was a Pareto optimal solution. As its market grew, however, the product went through a number of changes that made it more complex than common sense would suggest, still very much used to seeing it as a relatively simple product, in which administrative charges and other variables would accurately sum up its functioning. Using established investment analysis tools, this piece aims to carefully investigate the real nature of the pre-purchase financing pool system, particularly when it comes to when it is – or not – a competitive tools from the customer’s perspective. The main discussion topics have been put forward and, in its majority, rejected by data, which goes against what common sense seems to suggest on the matter. However, as well as pointing out mistakes, the main objective here is to establish a dialogue with society as a whole and, henceforth, to allow the consumer to use the data as an input for decision-making, reducing the information gap to which most people are currently subjected. <b>Keywords:</b> Consórcio; Pre-Purchase Financing Pool; Investment Analysis; Internal Rate of Return; Net Present Value; Contemplated Bonds.
DOI: 10.6084/m9.figshare.11920956
title: Stability analysis of cut slope with shear band propagation along a weak layer

description: Data presented here were used to analyse the initiation of retrogressive failure in cut slopes with shear band propagation in a weak layer, which is to be submitted to the Journal of Geophysical Research Solid Earth. Original data and also processed data for figures and tables are included here.<br>
DOI: 10.6084/m9.figshare.11920956.v1
title: Stability analysis of cut slope with shear band propagation along a weak layer

description: Data presented here were used to analyse the initiation of retrogressive failure in cut slopes with shear band propagation in a weak layer, which is to be submitted to the Journal of Geophysical Research Solid Earth. Original data and also processed data for figures and tables are included here.<br>