cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9175157.v3
title: Sediment Oxygen and Sulfide Microprofiles in Extant and Restored Marshes of Jamaica Bay (New York, NY, USA)

description: This project contains field data from four restored marshes (restored 2003, 2006, 2010, and 2012) and two extant marshes in Jamaica Bay (New York, NY, USA). Methods used to collect and analyze these data are available in a manuscript, "Marsh plants enhance coastal marsh resilience by changing sediment redox conditions in an urban, eutrophic estuary," currently under review.<br>"20171016_O2Profiles_All.csv" and "20171016_H2SProfiles_All.csv" contain vertical microprofiles of O<sub>2</sub> and H<sub>2</sub>S concentrations in sediment cores from each sites. Microprofiles were measured using a motorized microprofiling system.<br>"h2s_parameters.csv" and "o2_parameters.csv" contain parameters from logistic fits of microprofile data. These parameters describe: (1) maximum concentrations, (2) rates of increase/decline, and (3) depths of maximum increase/decline.<br>"20180627_MicroprofileCores_SedimentData.csv" contains sediment characteristics (bulk density, porosity, organic content) for each sediment core.<br><br>"20180627_MicroprofileCores_PlantData.csv" contains aboveground and belowground plant characteristics for <i>Spartina alterniflora</i> in the cores.<br><br>"20180730_Inundation_summarydata.csv" contains daily tidal inundation data for each location.<br>"depthProfiler_app.R" is a shiny app that may be run locally to visualize logistic fits to all profile data. Running the app locally will require the <i>shiny</i>, <i>dplyr</i>, and <i>ggplot2 </i>packages.
DOI: 10.6084/m9.figshare.9175157.v2
title: Sediment Oxygen and Sulfide Microprofiles in Extant and Restored Marshes of Jamaica Bay (New York, NY, USA)

description: This project contains field data from four restored marshes (restored 2003, 2006, 2010, and 2012) and two extant marshes in Jamaica Bay (New York, NY, USA). Methods used to collect and analyze these data are available in a manuscript, "Marsh plants enhance coastal marsh resilience by changing sediment redox conditions in an urban, eutrophic estuary," currently under review.<br>"20171016_O2Profiles_All.csv" and "20171016_H2SProfiles_All.csv" contain vertical microprofiles of O<sub>2</sub> and H<sub>2</sub>S concentrations in sediment cores from each sites. Microprofiles were measured using a motorized microprofiling system.<br>"h2s_parameters.csv" and "o2_parameters.csv" contain parameters from logistic fits of microprofile data. These parameters describe: (1) maximum concentrations, (2) rates of increase/decline, and (3) depths of maximum increase/decline.<br>"20180627_MicroprofileCores_SedimentData.csv" contains sediment characteristics (bulk density, porosity, organic content) for each sediment core.<br><br>"20180627_MicroprofileCores_PlantData.csv" contains aboveground and belowground plant characteristics for <i>Spartina alterniflora</i> in the cores.<br><br>"20180730_Inundation_summarydata.csv" contains daily tidal inundation data for each location.
DOI: 10.6084/m9.figshare.9172628.v2
title: Bayesian model averaging over tree-based dependence structures for multivariate extremes

description: Describing the complex dependence structure of extreme phenomena is particularly challenging. To tackle this issue we develop a novel statistical method that describes extremal dependence taking advantage of the inherent tree-based dependence structure of the max-stable nested logistic distribution, and that identifies possible clusters of extreme variables using reversible jump Markov chain Monte Carlo techniques. Parsimonious representations are achieved when clusters of extreme variables are found to be completely independent. Moreover, we significantly decrease the computational complexity of full likelihood inference by deriving a recursive formula for the likelihood function of the nested logistic model. The method’s performance is verified through extensive simulation experiments which also compare different likelihood procedures. The new methodology is used to investigate the dependence relationships between extreme concentrations of multiple pollutants in California and how these concentrations are related to extreme weather conditions. Overall, we show that our approach allows for the representation of complex extremal dependence structures and has valid applications in multivariate data analysis, such as air pollution monitoring, where it can guide policymaking.
DOI: 10.6084/m9.figshare.9172628.v1
title: Bayesian Model Averaging Over Tree-based Dependence Structures for Multivariate Extremes

description: Describing the complex dependence structure of extreme phenomena is particularly challenging. To tackle this issue, we develop a novel statistical method that describes extremal dependence taking advantage of the inherent tree-based dependence structure of the max-stable nested logistic distribution, and which identifies possible clusters of extreme variables using reversible jump Markov chain Monte Carlo techniques. Parsimonious representations are achieved when clusters of extreme variables are found to be completely independent. Moreover, we significantly decrease the computational complexity of full likelihood inference by deriving a recursive formula for the likelihood function of the nested logistic model. The method’s performance is verified through extensive simulation experiments which also compare different likelihood procedures. The new methodology is used to investigate the dependence relationships between extreme concentrations of multiple pollutants in California and how these concentrations are related to extreme weather conditions. Overall, we show that our approach allows for the representation of complex extremal dependence structures and has valid applications in multivariate data analysis, such as air pollution monitoring, where it can guide policymaking. Supplementary materials for this article are available online.
DOI: 10.5517/ccdc.csd.cc24w2jn
title: CCDC 1992231: Experimental Crystal Structure Determination

description: Related Article: Laura Köttner, Monika Schildhauer, Sandra Wiedbrauk, Peter Mayer, Henry Dube|2020|Chem.-Eur.J.|26|10712|doi:10.1002/chem.202002176
DOI: 10.6084/m9.figshare.9172553
title: ROR Data Dump 1.0 (July 2019)

description: First ROR data download. Based on latest GRID release.
DOI: 10.6084/m9.figshare.9172439
title: MaizeTE_Seqs_12-Feb-2015.fasta.fa

description: This is .fasta file containing a list of sequences for 1526 canonical transposable elements (TE) in maize. This is a representation of every type of TE found in the maize genome as of B73 refseq version 3.This dataset was last updated on 02/12/2015 and downloaded from the Maize Transposable Element Database (http://maizetedb.org/∼maize/) on 01/23/2017.For reasons unknown, this database is no longer maintained and this dataset can no longer be accessed through the Maize TEDB website.<br><br><br>
DOI: 10.6084/m9.figshare.9172553.v1
title: ror.zip

description: First ROR data download. Based on latest GRID release.
DOI: 10.6084/m9.figshare.9172553.v2
title: ROR Data Dump

description: First ROR data download. Based on latest GRID release.
DOI: 10.6084/m9.figshare.9172553.v3
title: ROR Data Dump - July 2019

description: First ROR data download. Based on latest GRID release.
DOI: 10.6084/m9.figshare.9172553.v5
title: ROR Data Dump 1.0 (July 2019)

description: First ROR data download. Based on latest GRID release.
DOI: 10.6084/m9.figshare.9171974
title: Table S1: full dataset from Quantifying maladaptation during the evolution of sexual dimorphism

description: Females and males have distinct trait optima, resulting in selection for sexual dimorphism. However, most traits have strong cross-sex genetic correlations, which constrain evolutionary divergence between the sexes and lead to protracted periods of maladaptation during the evolution of sexual dimorphism. While such constraints are thought to be costly in terms of individual and population fitness, it remains unclear how severe such costs are likely to be. Building upon classical models for the ‘cost of selection’ in changing environments (<i>sensu</i> Haldane), we derived a theoretical expression for the analogous cost of evolving sexual dimorphism; this cost is a simple function of genetic (co)variances of female and male traits and sex differences in trait optima. We then conducted a comprehensive literature search, compiled quantitative genetic data from a diverse set of traits and populations, and used them to quantify costs of sexual dimorphism in the light of our model. For roughly 90% of traits, costs of sexual dimorphism appear to be modest, and comparable to the costs of fixing one or a few beneficial substitutions. For the remaining traits (approx. 10%), sexual dimorphism appears to carry a substantial cost—potentially orders of magnitude greater than costs of selection during adaptation to environmental changes.
DOI: 10.6084/m9.figshare.9172553.v4
title: ROR Data Dump 1.0 (July 2019)

description: First ROR data download. Based on latest GRID release.
DOI: 10.6084/m9.figshare.9171974.v1
title: Table S1: full dataset from Quantifying maladaptation during the evolution of sexual dimorphism

description: Females and males have distinct trait optima, resulting in selection for sexual dimorphism. However, most traits have strong cross-sex genetic correlations, which constrain evolutionary divergence between the sexes and lead to protracted periods of maladaptation during the evolution of sexual dimorphism. While such constraints are thought to be costly in terms of individual and population fitness, it remains unclear how severe such costs are likely to be. Building upon classical models for the ‘cost of selection’ in changing environments (<i>sensu</i> Haldane), we derived a theoretical expression for the analogous cost of evolving sexual dimorphism; this cost is a simple function of genetic (co)variances of female and male traits and sex differences in trait optima. We then conducted a comprehensive literature search, compiled quantitative genetic data from a diverse set of traits and populations, and used them to quantify costs of sexual dimorphism in the light of our model. For roughly 90% of traits, costs of sexual dimorphism appear to be modest, and comparable to the costs of fixing one or a few beneficial substitutions. For the remaining traits (approx. 10%), sexual dimorphism appears to carry a substantial cost—potentially orders of magnitude greater than costs of selection during adaptation to environmental changes.
DOI: 10.6084/m9.figshare.9171674
title: Additional data for: Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over seven years in a single center. Genome Research.

description: <b>Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over seven years in a single center. </b><b><br></b> Accession numbers and species/sub-species assignations given to the bacteria used in this study, represented as five collections in five tables. For bacteria sequenced in this study added associated metadata and key features (MLSTs and antimicrobial resistance gene detections) of the bacteria are given. <br> <b>Table S1. </b>Accession numbers, isolation site, study month of isolation, detected acquired resistance genes, antimicrobial resistance phenotypes, of <i>Klebsiella pneumoniae</i> in this study. <b><br></b><b>Table S2. </b>Accession numbers and metadata for the global <i>K. pneumoniae</i> collection (from: Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, <i>et al</i>. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in <i>Klebsiella pneumoniae</i>, an urgent threat to public health. Proc Natl Acad Sci U S A. 2015;112(27):E3574-81)<i>.</i> <b><br></b><b>Table S3. </b>Accession numbers and metadata for UK <i>K. pneumoniae </i>and <i>E. cloacae</i>(from: Moradigaravand D, Martin V, Peacock SJ, Parkhill J. Evolution and Epidemiology of Multidrug-Resistant <i>Klebsiella pneumoniae</i> in the United Kingdom and Ireland. MBio. 2017;8(1); Moradigaravand D, Reuter S, Martin V, Peacock SJ, Parkhill J. The dissemination of multidrug-resistant <i>Enterobacter cloacae</i> throughout the UK and Ireland. Nat Microbiol. 2016;1:16173)<i>.</i> <b><br></b><b>Table S4. </b>Accession numbers, isolation site, study month of isolation, detected acquired resistance genes, antimicrobial resistance phenotypes, of <i>Enterobacter cloacae </i>in this study. <b><br></b><b>Table S5. </b>Accession numbers and metadata for the global <i>E. cloacae </i>collection (from: Chavda KD, Chen L, Fouts DE, Sutton G, Brinkac L, Jenkins SG, <i>et al</i>. Comprehensive Genome Analysis of Carbapenemase-Producing <i>Enterobacter spp</i>.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms. MBio. 2016;7(6))<i>.</i> <b></b><i></i><sub></sub><sup></sup><br>
DOI: 10.6084/m9.figshare.9171674.v1
title: Additional data for: Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over seven years in a single center. Genome Research.

description: <b>Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over seven years in a single center. </b><b><br></b> Accession numbers and species/sub-species assignations given to the bacteria used in this study, represented as five collections in five tables. For bacteria sequenced in this study added associated metadata and key features (MLSTs and antimicrobial resistance gene detections) of the bacteria are given. <br> <b>Table S1. </b>Accession numbers, isolation site, study month of isolation, detected acquired resistance genes, antimicrobial resistance phenotypes, of <i>Klebsiella pneumoniae</i> in this study. <b><br></b><b>Table S2. </b>Accession numbers and metadata for the global <i>K. pneumoniae</i> collection (from: Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, <i>et al</i>. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in <i>Klebsiella pneumoniae</i>, an urgent threat to public health. Proc Natl Acad Sci U S A. 2015;112(27):E3574-81)<i>.</i> <b><br></b><b>Table S3. </b>Accession numbers and metadata for UK <i>K. pneumoniae </i>and <i>E. cloacae</i>(from: Moradigaravand D, Martin V, Peacock SJ, Parkhill J. Evolution and Epidemiology of Multidrug-Resistant <i>Klebsiella pneumoniae</i> in the United Kingdom and Ireland. MBio. 2017;8(1); Moradigaravand D, Reuter S, Martin V, Peacock SJ, Parkhill J. The dissemination of multidrug-resistant <i>Enterobacter cloacae</i> throughout the UK and Ireland. Nat Microbiol. 2016;1:16173)<i>.</i> <b><br></b><b>Table S4. </b>Accession numbers, isolation site, study month of isolation, detected acquired resistance genes, antimicrobial resistance phenotypes, of <i>Enterobacter cloacae </i>in this study. <b><br></b><b>Table S5. </b>Accession numbers and metadata for the global <i>E. cloacae </i>collection (from: Chavda KD, Chen L, Fouts DE, Sutton G, Brinkac L, Jenkins SG, <i>et al</i>. Comprehensive Genome Analysis of Carbapenemase-Producing <i>Enterobacter spp</i>.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms. MBio. 2016;7(6))<i>.</i> <b></b><i></i><sub></sub><sup></sup><br>
DOI: 10.6084/m9.figshare.9170981
title: Supplemental Material for AJP-Renal F00357-2019

description: Primer sequences and gene lists
DOI: 10.6084/m9.figshare.9170990
title: Glucose homeostasis is regulated by pancreatic β-cell cilia via endosomal EphA-processing

description: Abstract<i>Diabetes mellitus </i>affects one in eleven adults worldwide. Most suffer from Type 2 <i>Diabetes mellitus</i>which features elevated blood glucose levels, an inability to adequately respond to insulin and poor insulin secretion. Insulin producing β-cells have primary cilia and these have recently been implicated in the regulation of glucose metabolism, insulin signaling and islet integrity although their exact role is not clear. To investigate this role, we generated a β-cell-specific, inducible, cilia-less mouse by deleting a key cilia component, <i>Ift88</i>. After β-cell cilia were ablated glucose homeostasis and insulin secretion deteriorated leading to severe glucose intolerance over the course of twelve weeks. We screened 27 receptor protein-tyrosine kinases and found that EphA3 receptor was hyper-phosphorylated in islets from two different mouse models of ciliary dysfunction. Manipulating EphA/EphrinA signaling revealed that EphA hyper-phosphorylation blocks insulin secretion in a β-cell line and primary islets depleted of <i>Ift88</i>. EphA3 internalization is blocked by altered actin dynamics linked to epithelial-mesenchymal transition. Defects in insulin secretion from IFT88-depleted human islets and elevated pEPHA3 in islets from diabetic donors both point to a role for cilia/ basal body proteins in human glucose homeostasis<i>.</i>In conclusion, β-cell primary cilia play a novel role in actin remodeling and endocytosis.
DOI: 10.6084/m9.figshare.9170981.v1
title: Supplemental Material for AJP-Renal F00357-2019

description: Primer sequences and gene lists
DOI: 10.6084/m9.figshare.9170990.v1
title: Glucose homeostasis is regulated by pancreatic β-cell cilia via endosomal EphA-processing

description: Abstract<i>Diabetes mellitus </i>affects one in eleven adults worldwide. Most suffer from Type 2 <i>Diabetes mellitus</i>which features elevated blood glucose levels, an inability to adequately respond to insulin and poor insulin secretion. Insulin producing β-cells have primary cilia and these have recently been implicated in the regulation of glucose metabolism, insulin signaling and islet integrity although their exact role is not clear. To investigate this role, we generated a β-cell-specific, inducible, cilia-less mouse by deleting a key cilia component, <i>Ift88</i>. After β-cell cilia were ablated glucose homeostasis and insulin secretion deteriorated leading to severe glucose intolerance over the course of twelve weeks. We screened 27 receptor protein-tyrosine kinases and found that EphA3 receptor was hyper-phosphorylated in islets from two different mouse models of ciliary dysfunction. Manipulating EphA/EphrinA signaling revealed that EphA hyper-phosphorylation blocks insulin secretion in a β-cell line and primary islets depleted of <i>Ift88</i>. EphA3 internalization is blocked by altered actin dynamics linked to epithelial-mesenchymal transition. Defects in insulin secretion from IFT88-depleted human islets and elevated pEPHA3 in islets from diabetic donors both point to a role for cilia/ basal body proteins in human glucose homeostasis<i>.</i>In conclusion, β-cell primary cilia play a novel role in actin remodeling and endocytosis.
DOI: 10.6084/m9.figshare.9170975
title: DEMETER 2 Combined RNAi

description: Cancer cell line genetic dependencies estimated using the DEMETER2 model. DEMETER2 is applied to the combination of three large-scale RNAi screening datasets: the Broad Institute Project Achilles, Novartis Project DRIVE, and the Marcotte et al. breast cell line dataset. This dataset is derived from https://doi.org/10.6084/m9.figshare.6025238.v4 and formatted to more closely match quarterly releases. Specifically, the main matrices have been transposed so that they are indexed by cell line, cell lines are identified by DepMap IDs, and common dependencies and dependency probability estimated. Only select files are included. Refer to the original dataset for all files. See README for more information about files.<br>Visit the Cancer Dependency Map portal at https://depmap.org to explore related datasets. Email questions to depmap@broadinstitute.org<br>
DOI: 10.6084/m9.figshare.9170978
title: Processed acceleromter data

description: Attached are the processed accelerometer data for post stroke participants and hospital controls
DOI: 10.6084/m9.figshare.9170966
title: Supplementary Material for the Jaculus manuscript

description: This file contains all supplementary material and raw data to reproduce the analysis concerning the manuscript "Evolutionary history of two cryptic species of Northern African jerboas".
DOI: 10.6084/m9.figshare.9170978.v1
title: Processed acceleromter data

description: Attached are the processed accelerometer data for post stroke participants and hospital controls
DOI: 10.6084/m9.figshare.9170957
title: Demographics

description: Two files are uploaded that include the demographics data for both hospital controls and stroke participants.
DOI: 10.6084/m9.figshare.9170960
title: xxx
DOI: 10.6084/m9.figshare.9170957.v1
title: Demographics

description: Two files are uploaded that include the demographics data for both hospital controls and stroke participants.
DOI: 10.6084/m9.figshare.9170765
title: Data for: Genetics, morphology and diet of introduced populations of the ant-eating Texas Horned Lizard (Phrynosoma cornutum)

description: Data for: Genetics, morphology and diet of introduced populations of the ant-eating Texas Horned Lizard (Phrynosoma cornutum).
DOI: 10.6084/m9.figshare.9169997
title: Duxbury_Chapman_JGBS_2019_combined_raw_data_FIGSHARE.xlsx

description: Raw data associated with:<br>Duxbury, EML & Chapman T (2019).Sex-specific responses of life span and fitness to variation in developmental and adult diets in <i>Drosophila melanogaster</i>.<br><br>J. Gerontology, Biological Sciences<br>DOI: 10.1093/gerona/glz175<br> Sex-Specific Responses of Lifespan and Fitness to Variation in Developmental versus Adult Diets in D. melanogaster
DOI: 10.6084/m9.figshare.9170216
title: Comparison of DEKA Arm and body-powered prosthesis joint kinematics

description: Kinematic data set of the right shoulder, torso, and right elbow of users of a bypass body-powered upper-limb prosthesis and a bypass DEKA Arm prosthesis in MAT files. Kinematics were collected during completion of the Jebsen-Taylor Hand Function Test and the targeted Box and Blocks Test. Times for each task are contained in the excel spreadsheet.<br>Data contained in Angles structures...H = body-powered userL = DEKA Arm user<br>1st level:{1}=tBBT stand 1st trial, {2}=tBBT stand 2nd trial, {3}=JHFT 1 1st trial, {4}=JHFT 1 2nd trial,... {16}=JHFT 7 2nd trial, {17}=tBBT sit 1st trial, {18}=tBBT sit 2nd trial<br>2nd level:Angle selection<br>3rd level:1st column - raw data2nd column - segmented data (row = segment)3rd column - segmented and interpolated sample size match<br>4th level:Each column = 1 degree of freedom<br>
DOI: 10.6084/m9.figshare.9170216.v1
title: Comparison of DEKA Arm and body-powered prosthesis joint kinematics

description: Kinematic data set of the right shoulder, torso, and right elbow of users of a bypass body-powered upper-limb prosthesis and a bypass DEKA Arm prosthesis in MAT files. Kinematics were collected during completion of the Jebsen-Taylor Hand Function Test and the targeted Box and Blocks Test. Times for each task are contained in the excel spreadsheet.<br>Data contained in Angles structures...H = body-powered userL = DEKA Arm user<br>1st level:{1}=tBBT stand 1st trial, {2}=tBBT stand 2nd trial, {3}=JHFT 1 1st trial, {4}=JHFT 1 2nd trial,... {16}=JHFT 7 2nd trial, {17}=tBBT sit 1st trial, {18}=tBBT sit 2nd trial<br>2nd level:Angle selection<br>3rd level:1st column - raw data2nd column - segmented data (row = segment)3rd column - segmented and interpolated sample size match<br>4th level:Each column = 1 degree of freedom<br>
DOI: 10.6084/m9.figshare.9169997.v1
title: Duxbury_Chapman_JGBS_2019_combined_raw_data_FIGSHARE.xlsx

description: Raw data associated with:<br>Duxbury, EML & Chapman T (2019).Sex-specific responses of life span and fitness to variation in developmental and adult diets in <i>Drosophila melanogaster</i>.<br><br>J. Gerontology, Biological Sciences<br>DOI: 10.1093/gerona/glz175<br> Sex-Specific Responses of Lifespan and Fitness to Variation in Developmental versus Adult Diets in D. melanogaster