cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6989267
title: Table S2 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Data used to convert length to ash-free dry mass (AFDM) for gastropods. Entries represent the minimum and maximum length values for each species in Eklöf et al. [46]. The scaling coefficient and exponent used in our analysis was determined via ordinary least squares linear regression on a log10-transformed version of this data, similar to the method used by Payne et al. [14]. min_length = smallest specimen of the relevant species; max_length = largest specimen of the relevant species; AFDW_min = ash-free dry mass for the smallest specimen of the relevant species; AFDM_max = ash-free dry mass for the largest specimen of the relevant species
DOI: 10.6084/m9.figshare.6989252
title: Table S1 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Basal metabolic rate and other pertinent data for 299 Neogene mollusc species from the Western Atlantic. Status = extinct or extant; distribution = broad or narrow as per Saupe et al. [33] and references therein; max_length = mean of maximum length for all measured individuals of the relevant species (in millimetres); B_species = mean BMR for species determined based upon Equation 1 and using mean temperature values; Bs_min_temp = mean BMR for species calculated using minimum temperature values; Bs_max_temp = mean BMR for species calculated using maximum temperature values; Bs_no_constant = mean BMR for species with the scaling constant excluded from Equation 1; and Bs_no_temp = mean BMR for species with temperature excluded from Equation 1.
DOI: 10.6084/m9.figshare.6989276.v2
title: Table S7 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Metabolic rates for fossil assemblages based upon fossil occurrence data from Supplementary Table 4 and calculated using Equation 2. B_assemblage = mean per capita BMR for relevant formation calculated using mean temperature values; Ba_min_temp = mean per capita BMR for relevant formation calculated using minimum temperature values; Ba_max_temp = mean per capita BMR for relevant formation calculated using maximum temperature values; Ba_no_temp = mean per capita BMR for relevant formation excluding temperature from calculation of BMR; Ba_no_constant = mean per capita BMR for relevant formation excluding the scaling constant from calculation of BMR; q0_obs = observed value for species richness; q0_est = maximum estimated species richness based upon rarefaction; q1_Obs = observed value for exponential of Shannon’s Entropy Index; q1_est = maximum estimated exponential of Shannon’s Entropy Index based upon rarefaction; q2_obs = observed value for the inverse of Simpson's Concentration Index; q2_est = maximum estimated value for the inverse of Simpson’s Concentration Index based upon rarefaction.
DOI: 10.6084/m9.figshare.6989276.v1
title: Table S7 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs

description: Metabolic rates for fossil assemblages based upon fossil occurrence data from Supplementary Table 4 and calculated using Equation 2. B_assemblage = mean per capita BMR for relevant formation calculated using mean temperature values; Ba_min_temp = mean per capita BMR for relevant formation calculated using minimum temperature values; Ba_max_temp = mean per capita BMR for relevant formation calculated using maximum temperature values; Ba_no_temp = mean per capita BMR for relevant formation excluding temperature from calculation of BMR; Ba_no_constant = mean per capita BMR for relevant formation excluding the scaling constant from calculation of BMR; q0_obs = observed value for species richness; q0_est = maximum estimated species richness based upon rarefaction; q1_Obs = observed value for exponential of Shannon’s Entropy Index; q1_est = maximum estimated exponential of Shannon’s Entropy Index based upon rarefaction; q2_obs = observed value for the inverse of Simpson's Concentration Index; q2_est = maximum estimated value for the inverse of Simpson’s Concentration Index based upon rarefaction.
DOI: 10.6084/m9.figshare.6989267.v2
title: Table S2 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Data used to convert length to ash-free dry mass (AFDM) for gastropods. Entries represent the minimum and maximum length values for each species in Eklöf et al. [46]. The scaling coefficient and exponent used in our analysis was determined via ordinary least squares linear regression on a log10-transformed version of this data, similar to the method used by Payne et al. [14]. min_length = smallest specimen of the relevant species; max_length = largest specimen of the relevant species; AFDW_min = ash-free dry mass for the smallest specimen of the relevant species; AFDM_max = ash-free dry mass for the largest specimen of the relevant species
DOI: 10.6084/m9.figshare.6989261
title: Table S4 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Fossil occurrence data for early Pliocene to late Pleistocene bivalve and gastropod taxa from the Western Atlantic.
DOI: 10.6084/m9.figshare.6989267.v1
title: Table S2 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs

description: Data used to convert length to ash-free dry mass (AFDM) for gastropods. Entries represent the minimum and maximum length values for each species in Eklöf et al. [46]. The scaling coefficient and exponent used in our analysis was determined via ordinary least squares linear regression on a log10-transformed version of this data, similar to the method used by Payne et al. [14]. min_length = smallest specimen of the relevant species; max_length = largest specimen of the relevant species; AFDW_min = ash-free dry mass for the smallest specimen of the relevant species; AFDM_max = ash-free dry mass for the largest specimen of the relevant species
DOI: 10.6084/m9.figshare.6989246
title: Table S3 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Body size measurements, basal metabolic rate and other pertinent data for Neogene Western Atlantic mollusc specimens. Width, length and max length all in millimetres. Temperature values are all in Kelvin. max_size = maximum of either width or length for the relevant specimen; biomass = biomass (in grams) for individuals calculated using approach listed in Data and Methods Part B (body size); palaeo_lat and palaeo_long = reconstructed palaeo-geographic coordinates, accounting for shifts in geographic position associated with continental drift that has occurred since the Pliocene (this was only performed for mPWP specimens, all younger specimens are listed as NA); and age = geological age of specimen. Abbreviations as per Data and Methods Part C (palaeoclimate); B0 = clade specific scaling constant used in Equation 1; B_ind_avg = BMR for individual specimens determined based upon Equation 1; B_ind_min = mean BMR for individual specimens calculated using minimum temperature values; B_ind_max = BMR for individual specimens calculated using maximum temperature values; B_ind_no_constant = BMR for individual specimens with the scaling constant excluded from Equation 1; B_ind_no_temp = BMR for individual specimens with temperature excluded from Equation 1.
DOI: 10.6084/m9.figshare.6989261.v2
title: Table S4 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Fossil occurrence data for early Pliocene to late Pleistocene bivalve and gastropod taxa from the Western Atlantic.
DOI: 10.6084/m9.figshare.6989261.v1
title: Table S4 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs

description: Fossil occurrence data for early Pliocene to late Pleistocene bivalve and gastropod taxa from the Western Atlantic.
DOI: 10.6084/m9.figshare.6989273
title: Table S6 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Pairwise comparisons of mean B<sub>species</sub> values for Neogene Western Atlantic mollusc families using Dunn’s test. * = adjusted P-values where P &lt; 0.05.
DOI: 10.6084/m9.figshare.6989246.v1
title: Table S3 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs

description: Body size measurements, basal metabolic rate and other pertinent data for Neogene Western Atlantic mollusc specimens. Width, length and max length all in millimetres. Temperature values are all in Kelvin. max_size = maximum of either width or length for the relevant specimen; biomass = biomass (in grams) for individuals calculated using approach listed in Data and Methods Part B (body size); palaeo_lat and palaeo_long = reconstructed palaeo-geographic coordinates, accounting for shifts in geographic position associated with continental drift that has occurred since the Pliocene (this was only performed for mPWP specimens, all younger specimens are listed as NA); and age = geological age of specimen. Abbreviations as per Data and Methods Part C (palaeoclimate); B0 = clade specific scaling constant used in Equation 1; B_ind_avg = BMR for individual specimens determined based upon Equation 1; B_ind_min = mean BMR for individual specimens calculated using minimum temperature values; B_ind_max = BMR for individual specimens calculated using maximum temperature values; B_ind_no_constant = BMR for individual specimens with the scaling constant excluded from Equation 1; B_ind_no_temp = BMR for individual specimens with temperature excluded from Equation 1.
DOI: 10.6084/m9.figshare.6989273.v2
title: Table S6 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Pairwise comparisons of mean B<sub>species</sub> values for Neogene Western Atlantic mollusc families using Dunn’s test. * = adjusted P-values where P &lt; 0.05.
DOI: 10.6084/m9.figshare.6989252.v2
title: Table S1 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Basal metabolic rate and other pertinent data for 299 Neogene mollusc species from the Western Atlantic. Status = extinct or extant; distribution = broad or narrow as per Saupe et al. [33] and references therein; max_length = mean of maximum length for all measured individuals of the relevant species (in millimetres); B_species = mean BMR for species determined based upon Equation 1 and using mean temperature values; Bs_min_temp = mean BMR for species calculated using minimum temperature values; Bs_max_temp = mean BMR for species calculated using maximum temperature values; Bs_no_constant = mean BMR for species with the scaling constant excluded from Equation 1; and Bs_no_temp = mean BMR for species with temperature excluded from Equation 1.
DOI: 10.6084/m9.figshare.6989270
title: Table S5 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Results of all analyses. Definitions for names of rows follows definitions supplied for Supplementary Table 1 with the addition of Bs_size = results where specimens in the top 10% of body size or with body size ≤10mm were omitted. Effect sizes reported as absolute values.
DOI: 10.6084/m9.figshare.6989252.v1
title: Table S1 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs

description: Basal metabolic rate and other pertinent data for 299 Neogene mollusc species from the Western Atlantic. Status = extinct or extant; distribution = broad or narrow as per Saupe et al. [33] and references therein; max_length = mean of maximum length for all measured individuals of the relevant species (in millimetres); B_species = mean BMR for species determined based upon Equation 1 and using mean temperature values; Bs_min_temp = mean BMR for species calculated using minimum temperature values; Bs_max_temp = mean BMR for species calculated using maximum temperature values; Bs_no_constant = mean BMR for species with the scaling constant excluded from Equation 1; and Bs_no_temp = mean BMR for species with temperature excluded from Equation 1.
DOI: 10.6084/m9.figshare.6989273.v1
title: Table S6 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs

description: Pairwise comparisons of mean B<sub>species</sub> values for Neogene Western Atlantic mollusc families using Dunn’s test. * = adjusted P-values where P &lt; 0.05.
DOI: 10.6084/m9.figshare.7001417
title: Species in quadrat data from Regional climate and local-scale biotic acceptance explain native–exotic richness relationships in Australian annual plant communities.

description: Dataframe including the identity and abundance of each species occurring in each quadrat. Used to calculate metrics including the richness of native and exotic species at each scale.
DOI: 10.6084/m9.figshare.7001423
title: Quadrat scale environmental data from Regional climate and local-scale biotic acceptance explain native–exotic richness relationships in Australian annual plant communities.

description: Dataframe corresponding to the neighbourhood scale including information regarding the hierarchical structure of the study design and environmental parameters
DOI: 10.6084/m9.figshare.7001417.v2
title: Species in quadrat data from Regional climate and local-scale biotic acceptance explain native–exotic richness relationships in Australian annual plant communities.

description: Dataframe including the identity and abundance of each species occurring in each quadrat. Used to calculate metrics including the richness of native and exotic species at each scale.
DOI: 10.6084/m9.figshare.7001420
title: R code script from Regional climate and local-scale biotic acceptance explain native–exotic richness relationships in Australian annual plant communities.

description: This script reads in two dataframes of observed data, calculates richness for both native and exotic richness at multiple scales and runs the major analyses presented in this publication
DOI: 10.6084/m9.figshare.6989270.v2
title: Table S5 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs.

description: Results of all analyses. Definitions for names of rows follows definitions supplied for Supplementary Table 1 with the addition of Bs_size = results where specimens in the top 10% of body size or with body size ≤10mm were omitted. Effect sizes reported as absolute values.
DOI: 10.6084/m9.figshare.13073051
title: CANOPUS evaluation data

description: We evaluated CANOPUS on two MS/MS reference datasets: The SVM training dataset, which was also used for training CSI:FingerID (in 10-fold cross-validation), and the Agilent MassHunter library, used as indepenent dataset.<br>The SVM training dataset contains spectra from GNPS, MassBank, and NIST17. As NIST17 is a commercial library, we can only provide the spectra from GNPS and MassBank. Here, we provide the public part of the SVM training dataset (svm_training_data.zip).<br><br>For training the deep neural network we used a subset of PubChem with 1,106,938 structures for which we downloaded ClassyFire annotations (Feunang et al 2016) and another set of 2,997,933 compounds from the ClassyFire database. The PubChem structures, together with ClassyFire annotations for the evaluation data are available as "structures.csv.gz".<br>With CANOPUS, we analyzed data from two biological studies; the mzML and mzXML files are available at MassIVE (https://massive.ucsd.edu/) with the accession numbers MSV000079949 (mice data, Quinn et al 2020) and MSV000081082 (Euphorbia plant data, Ernst et al 2019).The network visualization of the mice data was done using Cytoscape (Shannon et al 2003). Here, we provide the Cytoscape file (mice_multiple_classes.cys).The source code of CANOPUS is part of the SIRIUS GitHub repository (https://github.com/boecker-lab/sirius-libs). The scripts we used for analyzing and visualizing the data are available at the GitHub repository (https://github.com/kaibioinfo/canopus_treemap).<br><br>See the LICENSE.txt for further licensing information on Classyfire annotations and mass spectra.
DOI: 10.6084/m9.figshare.7001417.v1
title: Species in quadrat data from Regional climate and local-scale biotic acceptance explain native–exotic diversity relationships in Australian annual plant communities

description: Dataframe including the identity and abundance of each species occurring in each quadrat. Used to calculate metrics including the richness of native and exotic species at each scale.
DOI: 10.6084/m9.figshare.6989270.v1
title: Table S5 from Metabolic rates, climate and macroevolution: a case study using Neogene molluscs

description: Results of all analyses. Definitions for names of rows follows definitions supplied for Supplementary Table 1 with the addition of Bs_size = results where specimens in the top 10% of body size or with body size ≤10mm were omitted. Effect sizes reported as absolute values.
DOI: 10.6084/m9.figshare.7001420.v2
title: R code script from Regional climate and local-scale biotic acceptance explain native–exotic richness relationships in Australian annual plant communities.

description: This script reads in two dataframes of observed data, calculates richness for both native and exotic richness at multiple scales and runs the major analyses presented in this publication
DOI: 10.6084/m9.figshare.7001423.v2
title: Quadrat scale environmental data from Regional climate and local-scale biotic acceptance explain native–exotic richness relationships in Australian annual plant communities.

description: Dataframe corresponding to the neighbourhood scale including information regarding the hierarchical structure of the study design and environmental parameters
DOI: 10.6084/m9.figshare.7001420.v1
title: R code script from Regional climate and local-scale biotic acceptance explain native–exotic diversity relationships in Australian annual plant communities

description: This script reads in two dataframes of observed data, calculates richness for both native and exotic richness at multiple scales and runs the major analyses presented in this publication
DOI: 10.6084/m9.figshare.7001423.v1
title: Quadrat scale environmental data from Regional climate and local-scale biotic acceptance explain native–exotic diversity relationships in Australian annual plant communities

description: Dataframe corresponding to the neighbourhood scale including information regarding the hierarchical structure of the study design and environmental parameters
DOI: 10.6084/m9.figshare.7007519
title: SIDATA_nonlinear.xlsx from The dynamic role of the ilio-sacral joint in jumping frogs.

description: Inverse dynamics and kinematics time-series data output from 16 simulations using a sigmoidally increasing IS angle.
DOI: 10.6084/m9.figshare.7007516
title: SIDATA_linear.xlsx from The dynamic role of the ilio-sacral joint in jumping frogs.

description: Inverse dynamics and kinematics time-series data output from 16 simulations using a linearly increasing IS angle.
DOI: 10.6084/m9.figshare.7007519.v2
title: SIDATA_nonlinear.xlsx from The dynamic role of the ilio-sacral joint in jumping frogs.

description: Inverse dynamics and kinematics time-series data output from 16 simulations using a sigmoidally increasing IS angle.
DOI: 10.6084/m9.figshare.7007516.v2
title: SIDATA_linear.xlsx from The dynamic role of the ilio-sacral joint in jumping frogs.

description: Inverse dynamics and kinematics time-series data output from 16 simulations using a linearly increasing IS angle.
DOI: 10.6084/m9.figshare.7007519.v1
title: SIDATA_nonlinear.xlsx from The dynamic role of the ilio-sacral joint in jumping frogs

description: Inverse dynamics and kinematics time-series data output from 16 simulations using a sigmoidally increasing IS angle.
DOI: 10.6084/m9.figshare.7007516.v1
title: SIDATA_linear.xlsx from The dynamic role of the ilio-sacral joint in jumping frogs

description: Inverse dynamics and kinematics time-series data output from 16 simulations using a linearly increasing IS angle.
DOI: 10.6084/m9.figshare.7007510
title: invivoDATA.xlsx from The dynamic role of the ilio-sacral joint in jumping frogs.

description: Performance data recorded from in vivo jumps
DOI: 10.6084/m9.figshare.7007510.v2
title: invivoDATA.xlsx from The dynamic role of the ilio-sacral joint in jumping frogs.

description: Performance data recorded from in vivo jumps
DOI: 10.6084/m9.figshare.7012418
title: Supplementary File S1 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses.

description: Biomass objective function stoichiometric coefficients and associated metabolites for the [host] macrophage (iAB-AMØ-1410) biomass maintenance objective function and the Chikungunya (CHIKV), Dengue (DENV) and Zika (ZIKV) virus biomass objective functions.
DOI: 10.6084/m9.figshare.7007510.v1
title: invivoDATA.xlsx from The dynamic role of the ilio-sacral joint in jumping frogs

description: Performance data recorded from in vivo jumps
DOI: 10.6084/m9.figshare.7012415
title: Supplementary File S2 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses.

description: Flux variability analysis results for the host-virus integrated models for CHIKV, DENV and ZIKV. Both the host- and virus-optimal state results are shown. Model reactions, model subsystems and the associated aggregated subsystems are also detailed.
DOI: 10.6084/m9.figshare.7012418.v1
title: Supplementary File S1 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses

description: Biomass objective function stoichiometric coefficients and associated metabolites for the [host] macrophage (iAB-AMØ-1410) biomass maintenance objective function and the Chikungunya (CHIKV), Dengue (DENV) and Zika (ZIKV) virus biomass objective functions.
DOI: 10.6084/m9.figshare.7012412
title: Supplementary File S5 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses.

description: Summary of results for the host-derived enforcement analysis for different conditions: altered media conditions; virus genome point mutations; virus biomass objective function randomised stoichiometric coefficients. Reactions are selected when they are able to reduce virus optima to below 95% of the original virus optima in the original model (without additional constraints).
DOI: 10.6084/m9.figshare.7012415.v1
title: Supplementary File S2 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses

description: Flux variability analysis results for the host-virus integrated models for CHIKV, DENV and ZIKV. Both the host- and virus-optimal state results are shown. Model reactions, model subsystems and the associated aggregated subsystems are also detailed.
DOI: 10.6084/m9.figshare.7012421
title: Supplementary File S9 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses.

description: Results from the comparison of gene expression data and the <i>in silico</i> model predictions, for CHIKV, DENV and ZIKV viral infections. Chikungunya virus, CHIKV; Dengue virus, DENV; Zika virus, ZIKV.