cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5483527.v1
title: Ecological risk assessment of metals in roadside agricultural soils: A modified approach

description: The threat of metal contamination of roadside agricultural soils poses severe ecological risks throughout the globe due to dual contamination by intensive agriculture and traffic-related activities. Therefore, the present study was conducted to assess ecological risks posed by metals (Cd, Co, Cr, Cu, Fe, Mn, Pb, and Zn) in intensively cultivated roadside agricultural soils of Punjab, India. The results of the contamination assessment factors <i>i.e.</i> Contamination Factor (CF) and Enrichment Factor (EF) indicated that the studied soils were moderately to highly contaminated with metals. It was observed that the Modified Risk Index (MRI), which is based upon EF, indicated the ecological risks of metals more efficiently than the traditional Ecological Risk Index (RI), which is based upon CF in the present study. The MRI values indicated that the metals posed considerable to high risk in 67.86% samples as compared to only 7.14% samples based upon RI values. Thus, MRI can be considered as a more efficient risk indicator in comparison to RI. Spatial distribution maps of MRI indicated to higher metal contamination in inner urban parts of study area due to higher traffic and industrial activities.
DOI: 10.6084/m9.figshare.5483461
title: 'Which tree' simulations

description: This archive contains simulation parameters, simulated genomes and alignments as well as assemblies and annotations from simulated error-prone reads from a known phylogeny.
DOI: 10.6084/m9.figshare.5483473.v2
title: Extending​ ​Gateways​ ​into​ ​the​ ​Field: Geospatial​ ​Extensions​ ​and​ ​Remote​ ​Data​ ​Services

description: Science gateways are generally accessed via web browsers from workstation or laptop computers. However, activities such as fieldwork and data collection have prompted an increasing call for new methods of access using a wide range of mobile and specialized devices. Our work to extend the HUBzero gateway framework with new access routes is described. Specifically, an emphasis is placed on enabling the flow of geospatial data and metadata between geo-enhanced HUBzero hubs and devices in the field.
DOI: 10.6084/m9.figshare.5483464.v1
title: 'Which tree' trees

description: Contains an archive with trees inferred from simulated data by various methods
DOI: 10.6084/m9.figshare.5483473.v3
title: Extending​ ​Gateways​ ​into​ ​the​ ​Field: Geospatial​ ​Extensions​ ​and​ ​Remote​ ​Data​ ​Services

description: Science gateways are generally accessed via web browsers from workstation or laptop computers. However, activities such as fieldwork and data collection have prompted an increasing call for new methods of access using a wide range of mobile and specialized devices. Our work to extend the HUBzero gateway framework with new access routes is described. Specifically, an emphasis is placed on enabling the flow of geospatial data and metadata between geo-enhanced HUBzero hubs and devices in the field.
DOI: 10.6084/m9.figshare.5483464.v2
title: 'Which tree' trees

description: Contains an archive with trees inferred from simulated data by various methods
DOI: 10.6084/m9.figshare.5483473.v4
title: Extending​ ​Gateways​ ​into​ ​the​ ​Field: Geospatial​ ​Extensions​ ​and​ ​Remote​ ​Data​ ​Services

description: Science gateways are generally accessed via web browsers from workstation or laptop computers. However, activities such as fieldwork and data collection have prompted an increasing call for new methods of access using a wide range of mobile and specialized devices. Our work to extend the HUBzero gateway framework with new access routes is described. Specifically, an emphasis is placed on enabling the flow of geospatial data and metadata between geo-enhanced HUBzero hubs and devices in the field.
DOI: 10.6084/m9.figshare.5481565
title: Dataset 1: Anti-H3 Stalk Reactive Antibodies in Human Plasma

description: Plasma was obtained from 13 donors, 12 of which had been previously vaccinated within the past 5 years with trivalent or quadrivalent seasonal influenza vaccines. Plasma baseline anti-influenza IgG was measured by mPlex-Flu assay. (A) Levels of IgG against distinct H3N2 strains. Each column depicts mean fluorescence intensity (MFI), representing an individual donor. (B) Levels of H3 stalk-reactive IgG. Each symbol and line represents one donor. (C) IgG-binding to chimeric cH5/1 and cH5/3 proteins. This analysis was performed at a 1:5000 dilution.
DOI: 10.6084/m9.figshare.5481529
title: Supplementary Tables S2, S14, and S15

description: Perofmance of fast phylogenetic programs in likelihood score maximization on single-gene alignments. Likelihood scores in these tables were calculated using RAxML (Table S2), IQ-TREE (Table S14), and phangorn (Table S15), respectively.
DOI: 10.6084/m9.figshare.5481565.v1
title: Dataset 1: Anti-H3 Stalk Reactive Antibodies in Human Plasma

description: Plasma was obtained from 13 donors, 12 of which had been previously vaccinated within the past 5 years with trivalent or quadrivalent seasonal influenza vaccines. Plasma baseline anti-influenza IgG was measured by mPlex-Flu assay. (A) Levels of IgG against distinct H3N2 strains. Each column depicts mean fluorescence intensity (MFI), representing an individual donor. (B) Levels of H3 stalk-reactive IgG. Each symbol and line represents one donor. (C) IgG-binding to chimeric cH5/1 and cH5/3 proteins. This analysis was performed at a 1:5000 dilution.
DOI: 10.6084/m9.figshare.5481205
title: Data and code from: Assessing the relative influences of abiotic and biotic factors on American Eel (Anguilla rostrata) distribution using hydrologic, physical habitat, and functional trait data

description: This fileset contains three files from "Assessing the relative influences of abiotic and biotic factors on American Eel (<i>Anguilla rostrata</i>) distribution using hydrologic, physical habitat, and functional trait data".(1) A1_rawData. Excel file containing the subwatershed x predictor variable matrix. Sheet 1 contains the raw data for all predictor variables across all data classes. Sheet 2 contains a description and data source for each variable in the matrix. Data sources are detailed in the main text.(2) A2_traitData. Excel file containing the fish species x trait matrix. Sheet 1 contains raw data for the 139 species included in the analysis. Sheet 2 contains descriptions for each trait in the matrix. Sheet 3 contains the references used to assemble the traits database.(3) A3_Code. Text file containing code used in the analysis and data collection. This text file contains Python code to compute subwatershed trait summaries and R code for the null model analysis including sample-background overlap (SBO).
DOI: 10.6084/m9.figshare.5481205.v1
title: Data and code from: Non-modeling applications of MaxEnt logic can identify abiotic and biotic determinants of species’ distributions: a case study with the American Eel (Anguilla rostrata)

description: This fileset contains three files from "Non-modeling applications of MaxEnt logic can identify abiotic and biotic determinants of species’ distributions: a case study with the American Eel (<i>Anguilla rostrata</i>)".(1) A1_rawData. Excel file containing the subwatershed x predictor variable matrix. Sheet 1 contains the raw data for all predictor variables across all data classes. Sheet 2 contains a description and data source for each variable in the matrix. Data sources are detailed in the main text.(2) A2_traitData. Excel file containing the fish species x trait matrix. Sheet 1 contains raw data for the 139 species included in the analysis. Sheet 2 contains descriptions for each trait in the matrix. Sheet 3 contains the references used to assemble the traits database.(3) A3_Code. Text file containing code used in the analysis and data collection. This text file contains Python code to compute subwatershed trait summaries and R code to compute observed sample-background overlap (SBO) and permutations for significance of observed SBO.
DOI: 10.6084/m9.figshare.5481139
title: Disgust responses to disease related stimuli.

description: Disgust responses to disease related stimuli. R analysis syntax.
DOI: 10.6084/m9.figshare.5481205.v2
title: Data and code from: Non-modeling applications of MaxEnt logic can identify abiotic and biotic determinants of species’ distributions: a case study with the American Eel (Anguilla rostrata)

description: This fileset contains three files from "Non-modeling applications of MaxEnt logic can identify abiotic and biotic determinants of species’ distributions: a case study with the American Eel (<i>Anguilla rostrata</i>)".(1) A1_rawData. Excel file containing the subwatershed x predictor variable matrix. Sheet 1 contains the raw data for all predictor variables across all data classes. Sheet 2 contains a description and data source for each variable in the matrix. Data sources are detailed in the main text.(2) A2_traitData. Excel file containing the fish species x trait matrix. Sheet 1 contains raw data for the 139 species included in the analysis. Sheet 2 contains descriptions for each trait in the matrix. Sheet 3 contains the references used to assemble the traits database.(3) A3_Code. Text file containing code used in the analysis and data collection. This text file contains Python code to compute subwatershed trait summaries and R code to compute observed sample-background overlap (SBO) and permutations for significance of observed SBO.
DOI: 10.6084/m9.figshare.5481205.v3
title: Data and code from: A framework to assess the relative influences of abiotic and biotic factors on a species’ distribution using pseudo-absence and functional trait data: a case study with the American Eel (Anguilla rostrata)

description: This fileset contains three files from "Non-modeling applications of MaxEnt logic can identify abiotic and biotic determinants of species’ distributions: a case study with the American Eel (<i>Anguilla rostrata</i>)".(1) A1_rawData. Excel file containing the subwatershed x predictor variable matrix. Sheet 1 contains the raw data for all predictor variables across all data classes. Sheet 2 contains a description and data source for each variable in the matrix. Data sources are detailed in the main text.(2) A2_traitData. Excel file containing the fish species x trait matrix. Sheet 1 contains raw data for the 139 species included in the analysis. Sheet 2 contains descriptions for each trait in the matrix. Sheet 3 contains the references used to assemble the traits database.(3) A3_Code. Text file containing code used in the analysis and data collection. This text file contains Python code to compute subwatershed trait summaries and R code to compute observed sample-background overlap (SBO) and permutations for significance of observed SBO.
DOI: 10.6084/m9.figshare.5481088.v1
title: Relationship of chlorophyll to phosphorus and nitrogen in nutrient-rich lakes

description: Nitrogen (N) and phosphorus (P) commonly co-limit primary productivity in lakes, and chlorophyll <i>a</i> (Chl-<i>a</i>) is predicted to be greatest under high N, high P regimes. Because land use practices can alter N and P biogeochemical cycles in watersheds, it is unclear whether previously documented phytoplankton–nutrient relationships apply where landscapes are highly disturbed. Here, we analyzed a lake water quality database from an agricultural region to explore relationships among Chl-<i>a</i>, total N (TN), and total P (TP) under extreme nutrient concentrations. Chl-<i>a</i> was weakly related to TN when TP was ≤100 μg L<sup>−1</sup> but displayed a stronger response to TN at higher TP. When TP exceeded 100 μg L<sup>−1</sup>, Chl-<i>a</i> increased with increasing TN until reaching a TN threshold of ~3 mg L<sup>−1</sup> and decreased thereafter, resulting in a high nutrient, low Chl-<i>a</i> region that did not coincide with shifts in nutrient limitation, light availability, cellular Chl-<i>a</i> content, phytoplankton composition, or zooplankton grazing pressure. Beyond the threshold, nitrate comprised most of TN and occurred with reduced dissolved organic matter (DOM). These observations suggest that photolysis of nitrate may produce reactive oxygen species that damage DOM and phytoplankton. Reduction in N loading at high P could therefore increase Chl-<i>a</i> and decrease water clarity, resulting in an apparent worsening of water quality. Our data suggest that monitoring Chl-<i>a</i> or Secchi depth may fail to indicate water quality degradation by extreme nutrient concentrations. These findings highlight how extreme nutrient regimes in lakes can produce novel relationships between phytoplankton and nutrients.
DOI: 10.6084/m9.figshare.5481139.v1
title: Disgust responses to disease related stimuli.

description: Disgust responses to 72 disease related stimuli.
DOI: 10.6084/m9.figshare.5481139.v2
title: Disgust responses to disease related stimuli.

description: Disgust responses to disease related stimuli. R analysis syntax.
DOI: 10.17045/sthlmuni.5480962
title: Phylogenetic Tree from the BEAST analysis of Dytiscidae

description: Phylogenetic Tree from the BEAST analysis of the Dytiscidae family. (http://beast.community), (Drummond AJ, Suchard MA, Xie D & Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7 Molecular Biology And Evolution 29: 1969-1973)<br>The file can be viewed as a txt or can be opened in FigTree (http://tree.bio.ed.ac.uk/software/figtree/)
DOI: 10.6084/m9.figshare.5480989
title: Phylogenetic data of Zucchini et al., 2017. Nature Microbiology

description: Multiple alignment and phylogeny of PASTA domains of 30 Streptococcaceae strains (PASTA_domains). <br>Multiple alignments and phylogenies of A/B/C-types PASTA domains and Pkinase domains of 30 Streptococcaceae strains (A-Type, B-Type, C-Type, Pkinase).<br>Multiple alignment and phylogeny of 30 Streptococcaceae strains based on ribosomal proteins (Streptococcaceae).
DOI: 10.6084/m9.figshare.5480908
title: R code from Re-evaluating the link between brain size and behavioural ecology in primates

description: R code used to execute PGLS and model comparisons
DOI: 10.6084/m9.figshare.5480905
title: Dataset 1 from Re-evaluating the link between brain size and behavioural ecology in primates

description: Dataset referred to as "Dataset 1" in text containing primate behavioural-ecological and brain size information
DOI: 10.6084/m9.figshare.5480896
title: Tree from Do extra-group fertilizations increase the potential for sexual selection in male mammals?

description: Tree used to construct evolutionary relationships for species in our comparative analyses
DOI: 10.6084/m9.figshare.5480890
title: R Script from Do extra-group fertilizations increase the potential for sexual selection in male mammals?

description: R Script for running the main statistical analyses reported in the paper
DOI: 10.6084/m9.figshare.5480875
title: The effect of leg-to-body ratio on male attractiveness depends on the ecological validity of the figures

description: The data that are reported in the paper "The effect of leg-to-body ratio on male attractiveness depends on the ecological validity of the figures" by Versluys, T.M.M., & Skylark, W.J.
DOI: 10.6084/m9.figshare.5480878
title: Data from Do extra-group fertilizations increase the potential for sexual selection in male mammals?

description: Data for statistical analyses reported in the paper
DOI: 10.6084/m9.figshare.5480848
title: qPCR primer sequences. from A pronounced uterine pro-inflammatory response at parturition is an ancient feature in mammals

description: Regulating maternal immunity is necessary for successful human pregnancy. Whether this is needed in mammals with less invasive placentation is subject to debate. Indeed, the short gestation times in marsupials have been hypothesized to be due to a lack of immune regulation during pregnancy. Alternatively, the maternal marsupial immune system may be unstimulated in the absence of a highly invasive placenta. Transcripts encoding pro-inflammatory cytokines were found to be overrepresented in the whole uterine transcriptome at terminal pregnancy in the opossum, <i>Monodelphis domestica</i>. To investigate this further, immune gene transcripts were quantified throughout opossum gestation. Transcripts encoding pro-inflammatory cytokines remained relatively low during pre- and peri-attachment pregnancy stages. Levels dramatically increased late in gestation, peaking within 12 h prior to parturition. These results mirror the spike of inflammation seen at eutherian parturition but not at attachment or implantation. Our results are consistent with the role of pro-inflammatory cytokines at parturition being an ancient and conserved birth mechanism in therian mammals.
DOI: 10.6084/m9.figshare.5480848.v1
title: qPCR primer sequences. from A pronounced uterine pro-inflammatory response at parturition is an ancient feature in mammals

description: Regulating maternal immunity is necessary for successful human pregnancy. Whether this is needed in mammals with less invasive placentation is subject to debate. Indeed, the short gestation times in marsupials have been hypothesized to be due to a lack of immune regulation during pregnancy. Alternatively, the maternal marsupial immune system may be unstimulated in the absence of a highly invasive placenta. Transcripts encoding pro-inflammatory cytokines were found to be overrepresented in the whole uterine transcriptome at terminal pregnancy in the opossum, <i>Monodelphis domestica</i>. To investigate this further, immune gene transcripts were quantified throughout opossum gestation. Transcripts encoding pro-inflammatory cytokines remained relatively low during pre- and peri-attachment pregnancy stages. Levels dramatically increased late in gestation, peaking within 12 h prior to parturition. These results mirror the spike of inflammation seen at eutherian parturition but not at attachment or implantation. Our results are consistent with the role of pro-inflammatory cytokines at parturition being an ancient and conserved birth mechanism in therian mammals.
DOI: 10.6084/m9.figshare.5480839
title: Raw data from Sleep macrostructure is modulated by positive and negative social experience in adult pet dogs

description: All raw data analysed for the manuscript is provided
DOI: 10.6084/m9.figshare.5480839.v1
title: Raw data from Sleep macrostructure is modulated by positive and negative social experience in adult pet dogs

description: All raw data analysed for the manuscript is provided
DOI: 10.6084/m9.figshare.5480785
title: Electronic Supplementary material S1 Sample location from Genetic signature of Last Glacial Maximum regional refugia in a circum-Antarctic sea spider

description: Supplementary material S1. Details of DNA vouchers (sample) including station number, latitude, longitude, average bottom depth (m), cruise or expedition and repository institution.
DOI: 10.6084/m9.figshare.5480785.v1
title: Electronic Supplementary material S1 Sample location from Genetic signature of Last Glacial Maximum regional refugia in a circum-Antarctic sea spider

description: Supplementary material S1. Details of DNA vouchers (sample) including station number, latitude, longitude, average bottom depth (m), cruise or expedition and repository institution.
DOI: 10.6084/m9.figshare.5480767
title: Electronic Supplementary material S2 Regions and haplotypes from Genetic signature of Last Glacial Maximum regional refugia in a circum-Antarctic sea spider

description: Supplementary material S2. Data for each region (AP, Antarctic Peninsula; EA, East Antarctica; WED, Weddell Sea; SAI, sub-Antarctic islands) including number of individuals per station, the haplotype number (Hap) related to the network (Fig. 3) and number of individuals per haplotype (N/Hap) for each sampling site.
DOI: 10.6084/m9.figshare.5480767.v1
title: Electronic Supplementary material S2 Regions and haplotypes from Genetic signature of Last Glacial Maximum regional refugia in a circum-Antarctic sea spider

description: Supplementary material S2. Data for each region (AP, Antarctic Peninsula; EA, East Antarctica; WED, Weddell Sea; SAI, sub-Antarctic islands) including number of individuals per station, the haplotype number (Hap) related to the network (Fig. 3) and number of individuals per haplotype (N/Hap) for each sampling site.
DOI: 10.6084/m9.figshare.5480752
title: Host, Infection, and Clinical Signs Data from Co-infection does not predict disease signs in <i>Gopherus</i> tortoises

description: Spreadsheet and column descriptions including unique identifiers; host species, sex, and size; sampling year; qPCR infection data; and clinical signs data.
DOI: 10.6084/m9.figshare.5480758
title: Electronic Supplementary material S3 Genebank accession numbers from Genetic signature of Last Glacial Maximum regional refugia in a circum-Antarctic sea spider

description: Supplementary material table 3. Genbank accession numbers of each haplotype of the Nymphon australe used in this study.
DOI: 10.6084/m9.figshare.5480752.v1
title: Host, Infection, and Clinical Signs Data from Co-infection does not predict disease signs in <i>Gopherus</i> tortoises

description: Spreadsheet and column descriptions including unique identifiers; host species, sex, and size; sampling year; qPCR infection data; and clinical signs data.
DOI: 10.6084/m9.figshare.5480758.v1
title: Electronic Supplementary material S3 Genebank accession numbers from Genetic signature of Last Glacial Maximum regional refugia in a circum-Antarctic sea spider

description: Supplementary material table 3. Genbank accession numbers of each haplotype of the Nymphon australe used in this study.
DOI: 10.6084/m9.figshare.5480740
title: Gruber et al. 2017 Data of behavioural measures from captive-raised and wild-caught cane toads from exploration, risk-taking and neophilia trials from Is the behavioural divergence between range-core and range-edge populations of cane toads (<i>Rhinella marina</i>) due to evolutionary change or developmental plasticity?

description: Data of behavioural measures collected from captive-raised and wild-caught cane toads during exploration, risk-taking and neophilia trials
DOI: 10.6084/m9.figshare.5480737
title: Electronic Supplementary material S4 AMOVA results from Genetic signature of Last Glacial Maximum regional refugia in a circum-Antarctic sea spider

description: Pairwise COI FST distance and analysis of molecular variance (AMOVA) among the N. australe populations within the Antarctic regions
DOI: 10.6084/m9.figshare.5480740.v1
title: Gruber et al. 2017 Data of behavioural measures from captive-raised and wild-caught cane toads from exploration, risk-taking and neophilia trials from Is the behavioural divergence between range-core and range-edge populations of cane toads (<i>Rhinella marina</i>) due to evolutionary change or developmental plasticity?

description: Data of behavioural measures collected from captive-raised and wild-caught cane toads during exploration, risk-taking and neophilia trials
DOI: 10.6084/m9.figshare.5480737.v1
title: Electronic Supplementary material S4 AMOVA results from Genetic signature of Last Glacial Maximum regional refugia in a circum-Antarctic sea spider

description: Pairwise COI FST distance and analysis of molecular variance (AMOVA) among the N. australe populations within the Antarctic regions
DOI: 10.6084/m9.figshare.5480716
title: Nature Graduate Survey 2017

description: Anonymised raw data and questionnaire from Springer Nature's 2017 Graduate survey
DOI: 10.6084/m9.figshare.5480701
title: BARM gene sequences

description: The proteins.faa.gz file contains amino-acid sequences for the genes present on contigs longer than 1 Kb contained in the Baltic Sea reference metagenome assembly. The proteins.ffn.gz file contains the nucleotide sequences for the same genes.<br>The proteins.bed.gz file contains the position on the assembly file for each gene.
DOI: 10.6084/m9.figshare.5480710
title: State of Open Data survey 2017

description: Anonymised raw data from Digital Science Open Data survey 2017