cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9985127.v1
title: Data from "Intraspecific variation shapes community-level behavioral responses to urbanization in spiders"

description: Data from Dahirel et al (2017) Ecology paper ( https://doi.org/10.1002/ecy.1915). See paper for full details (if access impossible due to paywall, contact author for a copy or access preprint version: https://www.biorxiv.org/content/10.1101/076497v1 )<br><br>The dataset comprises four csv files:Species_info: links species codenames used in other tables (Species_code) to full Family, Genus, and Species names<br>Site_info: links each of the 200x200m study sites unique ID (Site) to its 3x3km landscape unique ID (Landscape), its site-level and landscape-level urbanisation (% area occupied by buildings, Urba_site and Urba_landscape), its town, and its coordinates (latitude and longitude of site centroid)<br>spider_community: abundance by site for all 18 spider species found<br>spider_traits: phenotypic information for the 944 adults that were phenotyped, grouped by species and site. <br>Size_mm: cephalothorax width (mm); <br>CTL: capture thread length (cm, estimated); <br>Height: height from the ground to the center (hub) of the web (cm); <br>Mesh_width: average interval between two capture threads (cm); Effective_surface: web surface effectively occupied by capture threads (cm^2);Inclination: inclination of the web (degrees relative to the vertical)<br>
DOI: 10.6084/m9.figshare.9985085
title: Systematic revision of the <i>Tubifera casparyi–T</i>. <i>dictyoderma</i> complex: Resurrection of the genus <i>Siphoptychium</i> and introduction of the new genus <i>Thecotubifera</i>

description: The genus <i>Siphoptychium</i> is resurrected on the basis of comparative morphology and phylogeny of partial nuc 18S rDNA (18S) and translation elongation factor 1-alpha (<i>EF1A</i>) nucleotide sequences. The genus is characterized by the firm upper surface of the pseudoaethalium, accreted but easily separable sporothecae, a tubular or fibrous columella, and spores with a reticulate ornamentation consisting of 7–9 meshes across the diameter. In addition to the currently known single species <i>S. casparyi</i> (= <i>Tubifera casparyi</i>), two new members of <i>Siphoptychium</i> are described: <i>S. violaceum</i> from coniferous forests of Europe, east Asia, and southeast Asia, and <i>S. reticulatum</i> from temperate and subarctic regions of North America and alpine regions of Europe. A second genus, <i>Thecotubifera</i>, is described to accommodate <i>Tubifera dictyoderma</i>. The fruiting body of this species is transitional between a pseudoaethalium and a true aethalium. It is covered by a contiguous membranous cortex formed by the fused tips of the sporothecae, a feature typical for aethalia. However, the inner portions of sporothecae remain discernible, a feature more typical for pseudoaethalia. Columellae of <i>Th. dictyoderma</i> are formed by perforated plates, and the spores have a reticulate ornamentation consisting of 2–5 meshes across the diameter. For <i>Th. dictyoderma</i>, we could confirm records only for tropical regions and Japan, whereas all studied European specimens, including those mentioned in current monographs, represent species of <i>Siphoptychium</i>.
DOI: 10.6084/m9.figshare.9985085.v1
title: Systematic revision of the <i>Tubifera casparyi–T</i>. <i>dictyoderma</i> complex: Resurrection of the genus <i>Siphoptychium</i> and introduction of the new genus <i>Thecotubifera</i>

description: The genus <i>Siphoptychium</i> is resurrected on the basis of comparative morphology and phylogeny of partial nuc 18S rDNA (18S) and translation elongation factor 1-alpha (<i>EF1A</i>) nucleotide sequences. The genus is characterized by the firm upper surface of the pseudoaethalium, accreted but easily separable sporothecae, a tubular or fibrous columella, and spores with a reticulate ornamentation consisting of 7–9 meshes across the diameter. In addition to the currently known single species <i>S. casparyi</i> (= <i>Tubifera casparyi</i>), two new members of <i>Siphoptychium</i> are described: <i>S. violaceum</i> from coniferous forests of Europe, east Asia, and southeast Asia, and <i>S. reticulatum</i> from temperate and subarctic regions of North America and alpine regions of Europe. A second genus, <i>Thecotubifera</i>, is described to accommodate <i>Tubifera dictyoderma</i>. The fruiting body of this species is transitional between a pseudoaethalium and a true aethalium. It is covered by a contiguous membranous cortex formed by the fused tips of the sporothecae, a feature typical for aethalia. However, the inner portions of sporothecae remain discernible, a feature more typical for pseudoaethalia. Columellae of <i>Th. dictyoderma</i> are formed by perforated plates, and the spores have a reticulate ornamentation consisting of 2–5 meshes across the diameter. For <i>Th. dictyoderma</i>, we could confirm records only for tropical regions and Japan, whereas all studied European specimens, including those mentioned in current monographs, represent species of <i>Siphoptychium</i>.
DOI: 10.6084/m9.figshare.9983396
title: GBR_Whitsunday.csv

description: Time-Sampling years<br>Cyclone exposure-0 = No cyclone effects, 1 = Some cyclone effects<br>Bleaching exposure-0= No coral bleaching,1; 1% or more coral bleached<br>CoTS-Mean A.solaris densities<br>Shelf position-(1= inshore/inner shelf;2 = middle shelf;3 = outer shelf)<br>Bathymetry-Depth below sea level<br>Opened reef-Protected areas where no fishing is allowed. 1 = no-take, 0 = otherwise<br>Sea surface temperature anomaly (SSTA)-Difference between measured Sea Surface Temperature (SST) and the monthly long-term mean SST (°C)<br> Light attenuation-Attenuation coefficient (between 0 and 1): <br>Chlorophyll- Long term mean concentration (µg/m³) of chlorophyll A <br>CRS_T_AV-Temperature (mean ºC) at the sea surface<br>Primary-Primary flood plume frequency (weeks occurred/total weeks) during wet season (max = 26)<br>Secondary-Secondary flood plume<br>Tertiary-Representing further extent of plume
DOI: 10.6084/m9.figshare.9983390
title: Data files "Discovery of hyperstable carbohydrate‐active enzymes through metagenomics of extreme environments"

description: Data files from "Discovery of hyperstable carbohydrate‐active enzymes through metagenomics of extreme environments" https://doi.org/10.1111/febs.15080
DOI: 10.6084/m9.figshare.9983396.v1
title: GBR_Whitsunday.csv

description: Time-Sampling years<br>Cyclone exposure-0 = No cyclone effects, 1 = Some cyclone effects<br>Bleaching exposure-0= No coral bleaching,1; 1% or more coral bleached<br>CoTS-Mean A.solaris densities<br>Shelf position-(1= inshore/inner shelf;2 = middle shelf;3 = outer shelf)<br>Bathymetry-Depth below sea level<br>Opened reef-Protected areas where no fishing is allowed. 1 = no-take, 0 = otherwise<br>Sea surface temperature anomaly (SSTA)-Difference between measured Sea Surface Temperature (SST) and the monthly long-term mean SST (°C)<br> Light attenuation-Attenuation coefficient (between 0 and 1): <br>Chlorophyll- Long term mean concentration (µg/m³) of chlorophyll A <br>CRS_T_AV-Temperature (mean ºC) at the sea surface<br>Primary-Primary flood plume frequency (weeks occurred/total weeks) during wet season (max = 26)<br>Secondary-Secondary flood plume<br>Tertiary-Representing further extent of plume
DOI: 10.6084/m9.figshare.9983369
title: Humanity's Fundamental Environmental Limits -- model input files

description: These data constitute the spatially explicit input to our model of Earth's biophysical human carrying capacity (Binder et al 2020). They include average daily estimates of photosynthetically active radiation (PAR), light interception efficiency (EI) of crop canopy, and precipitation net of evapotranspiration (WATERFLUX); as well as land areas of each grid cell and the fractions currently farmed and irrigated. The data are made available here in a .mat (Matlab) file.<br>WATERFLUX is calculated as PRECIPITATION - PET, with negative values retained for purposes of the model. <br>PET is calculated with the Hargreaves (1985) equation using data for temperature and PAR (re-scaled by 1/0.487 to capture the full light spectrum). <br>Daily PAR for terrestrial areas are calculated from the high-frequency, instantaneous PAR values of the GLASS PAR product, using a generalized integration method developed by Holdahl (2019). For more detail, see: https://ethanholdahl.shinyapps.io/PAR_App/<br>Baseline daily interception efficiencies are calculated in two steps. First, growing periods are determined based on temperature data. All days with temperature minima in excess of 0 deg C (terrestrial) or with temperature means in excess of 10 deg C (ocean) are initially designated as eligible growing days. All eligible days that are part of a sequence of 30 or more consecutive eligible days (minimum season length) retain final designation as part of a growing period; other days are excluded. In the second step, light interception efficiencies of the crop canopy are calculated according to a quadratic equation fit to data reported in Dohleman and Long (2009). <br>AREA is calculated using the 'areaquad' function of Matlab's Mapping Toolbox. <br>FARMED is the percent of each grid cell dedicated to crop or pasture, based on data from Ramankutty et al (2008). <br>IRRIGATED is the percent of farmed land equipped for irrigation in each grid cell, based the Ramankutty data referenced above in conjunction with irrigation data from FAO's Aquastat (Siebert et al 2013). In the 1.7% of cases in which estimates of irrigated land exceed estimates of cultivated land, irrigation fractions are capped at 1. <br>UnitsPAR: MJ m-2 day-1WATERFLUX: mm m-2 day-1AREA: m2IRRIGATION, FARMED and EI are dimensionless.<br>All data have been resampled and aligned to a common 1-by-1 degree grid using Matlab's Mapping Toolbox. The upper left cell of each matrix (1, 1) corresponds to -179.5 deg E and 89.5 deg N. <br><br>For further information regarding the use and sources of these data, please consult our article, "Humanity's Fundamental Environmental Limits", in <i>Human Ecology</i>, available at:http://link.springer.com/article/10.1007/s10745-020-00140-w<br>
DOI: 10.6084/m9.figshare.9983390.v1
title: Data files "Discovery of hyperstable carbohydrate‐active enzymes through metagenomics of extreme environments"

description: Data files from "Discovery of hyperstable carbohydrate‐active enzymes through metagenomics of extreme environments" https://doi.org/10.1111/febs.15080
DOI: 10.6084/m9.figshare.9983369.v2
title: Humanity's Fundamental Environmental Limits -- model input files

description: These data constitute the spatially explicit input to our model of Earth's biophysical human carrying capacity (Binder et al 2020). They include average daily estimates of photosynthetically active radiation (PAR), light interception efficiency (EI) of crop canopy, and precipitation net of evapotranspiration (WATERFLUX); as well as land areas of each grid cell and the fractions currently farmed and irrigated. The data are made available here in a .mat (Matlab) file.<br>WATERFLUX is calculated as PRECIPITATION - PET, with negative values retained for purposes of the model. <br>PET is calculated with the Hargreaves (1985) equation using data for temperature and PAR (re-scaled by 1/0.487 to capture the full light spectrum). <br>Daily PAR for terrestrial areas are calculated from the high-frequency, instantaneous PAR values of the GLASS PAR product, using a generalized integration method developed by Holdahl (2019). For more detail, see: https://ethanholdahl.shinyapps.io/PAR_App/<br>Baseline daily interception efficiencies are calculated in two steps. First, growing periods are determined based on temperature data. All days with temperature minima in excess of 0 deg C (terrestrial) or with temperature means in excess of 10 deg C (ocean) are initially designated as eligible growing days. All eligible days that are part of a sequence of 30 or more consecutive eligible days (minimum season length) retain final designation as part of a growing period; other days are excluded. In the second step, light interception efficiencies of the crop canopy are calculated according to a quadratic equation fit to data reported in Dohleman and Long (2009). <br>AREA is calculated using the 'areaquad' function of Matlab's Mapping Toolbox. <br>FARMED is the percent of each grid cell dedicated to crop or pasture, based on data from Ramankutty et al (2008). <br>IRRIGATED is the percent of farmed land equipped for irrigation in each grid cell, based the Ramankutty data referenced above in conjunction with irrigation data from FAO's Aquastat (Siebert et al 2013). In the 1.7% of cases in which estimates of irrigated land exceed estimates of cultivated land, irrigation fractions are capped at 1. <br>UnitsPAR: MJ m-2 day-1WATERFLUX: mm m-2 day-1AREA: m2IRRIGATION, FARMED and EI are dimensionless.<br>All data have been resampled and aligned to a common 1-by-1 degree grid using Matlab's Mapping Toolbox. The upper left cell of each matrix (1, 1) corresponds to -179.5 deg E and 89.5 deg N. <br><br>For further information regarding the use and sources of these data, please consult our article, "Humanity's Fundamental Environmental Limits", in <i>Human Ecology</i>, available at:http://link.springer.com/article/10.1007/s10745-020-00140-w<br>
DOI: 10.6084/m9.figshare.9983369.v1
title: Humanity's Fundamental Environmental Limits -- model input files

description: These data constitute the spatially explicit input to our model of Earth's biophysical human carrying capacity. They include average daily estimates of photosynthetically active radiation (PAR), light interception efficiency (EI) of crop canopy, and precipitation net of evapotranspiration (WATERFLUX); as well as land areas of each grid cell and the fractions currently farmed and irrigated (Ramankutty et al 2008). The data are made available here in a .mat (Matlab) file.<br>WATERFLUX is calculated as PRECIPITATION - PET, with negative values retained for purposes of the model. <br>PET is calculated with the Hargreaves (1985) equation using data for temperature and PAR (re-scaled by 1/0.487 to capture the full light spectrum). <br>Daily PAR for terrestrial areas are calculated from the high-frequency, instantaneous PAR values of the GLASS PAR product, using a generalized integration method developed by Holdahl (2019). For more detail, see: https://ethanholdahl.shinyapps.io/PAR_App/<br>Baseline daily interception efficiencies are calculated in two steps. First, growing periods are determined based on temperature data. All days with temperature minima in excess of 0 deg C (terrestrial) or with temperature means in excess of 10 deg C (ocean) are initially designated as eligible growing days. All eligible days that are part of a sequence of 30 or more consecutive eligible days (minimum season length) retain final designation as part of a growing period; other days are excluded. In the second step, light interception efficiencies of the crop canopy are calculated according to a quadratic equation fit to data reported in Dohleman and Long (2009). <br>AREA is calculated using the 'areaquad' function of Matlab's Mapping Toolbox. UnitsPAR: MJ m-2 day-1WATERFLUX: mm m-2 day-1AREA: m2IRRIGATION, FARMED and EI are dimensionless.<br>All data have been resampled and aligned to a common 1-by-1 degree grid using Matlab's Mapping Toolbox. The upper left cell of each matrix (1, 1) corresponds to -179.5 deg E and 89.5 deg N. <br>
DOI: 10.6084/m9.figshare.9983006
title: Systematics of the Ameerega rubriventris complex (Anura: Dendrobatidae) with descriptions of two new cryptic species from the East-Andean versant of Peru

description: Aligned sequence data from the study Brown et al. 2019, "Systematics of the Ameerega rubriventris complex (Anura: Dendrobatidae) with descriptions of two new cryptic species from the East-Andean versant of Peru", Zootaxa. <br><br>The file concatenated_UCEs.phylip contains concatenated and aligned nuclear UCE for all relevant samples in the study in addition to a few outgroups. Individual loci are differentiated in the file concatenated_UCEs_charsets.nex, which contains partitions in case they are necessary.<br>The file mtDNA_aligned.fasta contains aligned mitochondrial genomes for all relevant samples, again in addition to a few outgroups. <br>
DOI: 10.6084/m9.figshare.9983006.v1
title: Systematics of the Ameerega rubriventris complex (Anura: Dendrobatidae) with descriptions of two new cryptic species from the East-Andean versant of Peru

description: Aligned sequence data from the study Brown et al. 2019, "Systematics of the Ameerega rubriventris complex (Anura: Dendrobatidae) with descriptions of two new cryptic species from the East-Andean versant of Peru", Zootaxa. <br><br>The file concatenated_UCEs.phylip contains concatenated and aligned nuclear UCE for all relevant samples in the study in addition to a few outgroups. Individual loci are differentiated in the file concatenated_UCEs_charsets.nex, which contains partitions in case they are necessary.<br>The file mtDNA_aligned.fasta contains aligned mitochondrial genomes for all relevant samples, again in addition to a few outgroups. <br>
DOI: 10.6084/m9.figshare.9982394
title: ECCO-Darwin V4

description: Monthly ECCO-Darwin V4 model output from Jan 1995 to December 2017. Model fields are bin averaged using a flux-conserving method.
DOI: 10.6084/m9.figshare.9982133
title: Final zone distribution of simulations

description: <b>For different (a, c), we simulate the model for two hours and report the final distribution of the zones</b><br><b>column1</b>: zones<b>column (a, c)</b>: pdf of the final occupation of the model with parameter (a, c)<br>
DOI: 10.6084/m9.figshare.9982076
title: Model with parameter (a,c)=(1,1)

description: <b>10,000 simulations of the model with parameter (a,c)=(1,1)</b><br><b>column1</b>: time (s)<b>column j</b>: occupied zones of the simulation j<br>
DOI: 10.6084/m9.figshare.9981833
title: Stopping durations

description: <b>column1</b>: id of the experiment<b>column2</b>: time (s), when the stopping period starts<b>column3</b>: duration (s)<br>
DOI: 10.6084/m9.figshare.9981800
title: Walking durations

description: <b>column1</b>: id of the experiment<b>column2</b>: time (s), when the walking period starts<b>column3</b>: duration (s)<br>
DOI: 10.6084/m9.figshare.9981791
title: Individual tree-ring width series

description: Individual tree-ring width series.
DOI: 10.6084/m9.figshare.9981797
title: Site characteristics

description: Site description including latitude, longitude and elevation.
DOI: 10.6084/m9.figshare.9982016.v1
title: Supplementary tables: Proteome of fluid from human ovarian antral follicles reveals insights in folliculogenesis and oocyte maturation

description: <b>Table S1. </b>Total identified proteins in Our study.<b> </b> <b>Table S2. </b>Identified proteins in Pool.<b> </b> <b>Table S3. </b>Identified proteins in Individual samples<b></b> <b>Table S4. </b>List of proteins identified in human ovarian follicular fluid (until 2018 and including our study).<b></b> <b>Table S5. </b>High abundant proteome of FF from hSAF compared with proteins identified by Pouslen L. et al.,2019 in big follicles. Non-depleted samples.<b></b> <b>Table S6. </b>Proteins potentially more concentrated or accessible by MS in FF from hSAF<b></b> <b>Table S7. </b>Functional annotation clustering carried out with 226 proteins<b></b>
DOI: 10.6084/m9.figshare.12866585.v2
title: Spatial density of adolescents aged 14 years old, victims of dental: a longitudinal study

description: <b>Abstract</b> <b>Background/Aim: </b>Knowledge about the spatial density of the domiciles of dental trauma victims can enable the identification of the most vulnerable areas and contribute to the planning of prevention, promotion, control and treatment actions, focusing on the most affected areas. The study aimed to analyze the spatial density of domiciles of 14-year-old adolescents, victims of dental trauma, in the city of Diamantina, southeastern Brazil, after two years of follow-up. <b></b> <b>Material and Methods: </b>This longitudinal study was carried out with 584 adolescents between 2013 and 2015. Dental trauma (Andreasen classification), overjet and lip protection (O'Mullane) were assessed by two examiners trained and calibrated (K&gt; 0.70). Information about binge drinking was collected among the adolescents through the Alcohol Use Disorders Identification Test and sociodemographic indicators were obtained through a questionnaire answered by the adolescent’s caregivers. The spatial analyses were performed to evaluate the spatial density of adolescents with dental trauma and the independent variables of interest according to the domicile using the Ripley’s K function and Kernel Map. <b>Results</b>: The Ripley's K function showed spatial aggregation of the domiciles of adolescent victims of dental trauma in relation to males, binge drinking and overjet, with a confidence level of 95%. The higher density of domiciles with adolescents with two or more traumatized teeth was found in the northeast region of the city. Boys were the most affected, their homes were located in the north, northwest and southeast regions at the baseline and follow-up. The largest density of domiciles of adolescents with overjet greater than 5 mm and inadequate lip protection was in the northeast region. Similar spatial distribution was identified for binge drinking for both years. <b>Conclusion: </b>The majority of adolescents with dental trauma lived in the northeast and southeast regions, characterized by high population density and higher social vulnerability.<br>
DOI: 10.6084/m9.figshare.9981791.v1
title: Individual tree-ring width series

description: Individual tree-ring width series.
DOI: 10.6084/m9.figshare.9981797.v1
title: Site characteristics

description: Site description including latitude, longitude and elevation.
DOI: 10.6084/m9.figshare.9981788
title: Tree-ring series in RWL format

description: Tree-ring width series grouped by site in RWL format.
DOI: 10.6084/m9.figshare.9982016.v2
title: Supplementary tables: Proteome of fluid from human ovarian antral follicles reveals insights in folliculogenesis and oocyte maturation

description: <b>Table S1. </b>Total identified proteins in Our study.<b> </b> <b>Table S2. </b>Identified proteins in Pool.<b> </b> <b>Table S3. </b>Identified proteins in Individual samples<b></b> <b>Table S4. </b>List of proteins identified in human ovarian follicular fluid (until 2018 and including our study).<b></b> <b>Table S5. </b>High abundant proteome of FF from hSAF compared with proteins identified by Pouslen L. et al.,2019 in big follicles. Non-depleted samples.<b></b> <b>Table S6. </b>Proteins potentially more concentrated or accessible by MS in FF from hSAF<b></b> <b>Table S7. </b>Functional annotation clustering carried out with 226 proteins<b></b><b>Table S8</b>. Proteins that correlated significatly with MDK or VIM.<br><b>Table S9. </b>MRM results<br>
DOI: 10.6084/m9.figshare.9981773
title: Estimation of the pheromone concentrations

description: <b>Total time spent previously in the neighbourhood of the ant</b><b><br></b><b>column1</b>: id of the experience<b>column2</b>: time (s)<b>column3</b>: total time spent walking<br><b>column4</b>: total time spent stopping<br><b>column5</b>: total time spent stopping over the total time<br>
DOI: 10.6084/m9.figshare.9981788.v1
title: Tree-ring series in RWL format

description: Tree-ring width series grouped by site in RWL format.
DOI: 10.6084/m9.figshare.9981746
title: Time series of the occupied zone

description: <b>In which zone the ants are</b><b>column 1</b>: id of the experiment<b>column 2</b>: time (s)<b>column 3</b>: zone number<br>
DOI: 10.6084/m9.figshare.9981746.v1
title: Time series of the occupied zone

description: <b>In which zone the ants are</b><b>column 1</b>: id of the experiment<b>column 2</b>: time (s)<b>column 3</b>: zone number<br>
DOI: 10.6084/m9.figshare.9981704
title: X,Y of the trajectories

description: <b>Coordinates of the trajectories of the 496 isolated ants<br></b><b>Column 1</b>: id of the experiment<b>Column 2</b>: time (s)<br><b>Column 3</b>: x<br><b>Column 4</b>: y<br><br>