cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7012427
title: Supplementary File S3 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses.

description: Results for the reaction knockout and host-derived enforcement analyses. Model reactions and model subsystems are listed. The resulting virus optima, for CHIKV, DENV and ZIKV, are shown as a percentage of the original model (without the additional constraints imposed by the analyses). The lower and upper flux bounds used for the host-derived enforcement analysis are listed for the relevant reaction and associated virus optimisation result.
DOI: 10.6084/m9.figshare.7012412.v1
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.7012430
title: Supplementary File S4 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses.

description: A list of model reactions identified from the host-enforcement analysis that are able to reduce one of the three viruses, CHIKV, DENV and ZIKV, to below 80% of the original virus optima in the original model (without additional constraints). Inhibitors are listed for the respective reactions and were identified through the Brenda Enzymatic Database via the Enzyme Commission Number associated with the reaction.
DOI: 10.5281/zenodo.4090905
title: Source Data of "Coherent control of individual electron spins in a 2D quantum dot array"

description: Coherent manipulation of individual quantum objects organized in arrays is a prerequisite to any scalable quantum information platform.<br> The cumulated efforts to control electron spins in quantum dot arrays have permitted the recent realization of quantum simulators and multi-electron spin coherent manipulations.<br> While being a natural path to resolve complex quantum matter problems and to process quantum information, the two-dimensional (2D) scaling with high connectivity of such implementations remains undemonstrated.<br> Here, we demonstrate the 2D coherent control of individual electron spins in a 3x3 array of tunnel coupled quantum dots.<br> We focus on several key quantum functionalities: charge deterministic loading and displacement, local spin readout, and local coherent exchange manipulation between two electron spins trapped in adjacent dots.<br> This work lays some of the foundations for exploiting a 2D array of electron spins for quantum simulation and information processing.
DOI: 10.6084/m9.figshare.7012421.v1
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.
DOI: 10.5281/zenodo.4090904
title: Source Data of "Coherent control of individual electron spins in a 2D quantum dot array"

description: Coherent manipulation of individual quantum objects organized in arrays is a prerequisite to any scalable quantum information platform.<br> The cumulated efforts to control electron spins in quantum dot arrays have permitted the recent realization of quantum simulators and multi-electron spin coherent manipulations.<br> While being a natural path to resolve complex quantum matter problems and to process quantum information, the two-dimensional (2D) scaling with high connectivity of such implementations remains undemonstrated.<br> Here, we demonstrate the 2D coherent control of individual electron spins in a 3x3 array of tunnel coupled quantum dots.<br> We focus on several key quantum functionalities: charge deterministic loading and displacement, local spin readout, and local coherent exchange manipulation between two electron spins trapped in adjacent dots.<br> This work lays some of the foundations for exploiting a 2D array of electron spins for quantum simulation and information processing.
DOI: 10.6084/m9.figshare.7012433
title: Supplementary File S10 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses.

description: Results from the literature analysis of antiviral compounds with metabolic targets (reactions). Compound names and descriptions are provided, as identified from the literature (references column). Targets are described in terms of the metabolic pathway and reaction they target (along with the reaction abbreviation from the metabolic model for the aforementioned reaction). Where identifiable, virus taxonomy is defined (species, genera and family), genomic material type (RNA) and genome sense (positive [+] or negative [-]) are shown.
DOI: 10.6084/m9.figshare.7012427.v1
title: Supplementary File S3 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses

description: Results for the reaction knockout and host-derived enforcement analyses. Model reactions and model subsystems are listed. The resulting virus optima, for CHIKV, DENV and ZIKV, are shown as a percentage of the original model (without the additional constraints imposed by the analyses). The lower and upper flux bounds used for the host-derived enforcement analysis are listed for the relevant reaction and associated virus optimisation result.
DOI: 10.6084/m9.figshare.7012439
title: Supplementary File S7 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses.

description: Results from the mutation-based sensitivity analyses to evaluate the effectiveness of the host-derived enforcement antiviral targets for mutated CHIKV, DENV and ZIKV viruses.
DOI: 10.6084/m9.figshare.7012430.v1
title: Supplementary File S4 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses

description: A list of model reactions identified from the host-enforcement analysis that are able to reduce one of the three viruses, CHIKV, DENV and ZIKV, to below 80% of the original virus optima in the original model (without additional constraints). Inhibitors are listed for the respective reactions and were identified through the Brenda Enzymatic Database via the Enzyme Commission Number associated with the reaction.
DOI: 10.6084/m9.figshare.7012409
title: Supplementary File S8 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses.

description: Results from the one-way ANOVA and tukey HSD tests on the effect of host-derived enforcements across point and randomised mutation conditions for CHIKV, DENV and ZIKV. Chikungunya virus, CHIKV; Dengue virus, DENV; Zika virus, ZIKV.
DOI: 10.6084/m9.figshare.7012433.v1
title: Supplementary File S10 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses

description: Results from the literature analysis of antiviral compounds with metabolic targets (reactions). Compound names and descriptions are provided, as identified from the literature (references column). Targets are described in terms of the metabolic pathway and reaction they target (along with the reaction abbreviation from the metabolic model for the aforementioned reaction). Where identifiable, virus taxonomy is defined (species, genera and family), genomic material type (RNA) and genome sense (positive [+] or negative [-]) are shown.
DOI: 10.6084/m9.figshare.7012436
title: Supplementary File S6 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses.

description: Results from the <i>in-silico</i> media variation sensitivity analyses to evaluate the effectiveness of the host-derived enforcement antiviral targets over a range of varied media compositions for CHIKV, DENV and ZIKV viruses.
DOI: 10.6084/m9.figshare.7012439.v1
title: Supplementary File S7 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses

description: Results from the mutation-based sensitivity analyses to evaluate the effectiveness of the host-derived enforcement antiviral targets for mutated CHIKV, DENV and ZIKV viruses.
DOI: 10.6084/m9.figshare.7012409.v1
title: Supplementary File S8 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses

description: Results from the one-way ANOVA and tukey HSD tests on the effect of host-derived enforcements across point and randomised mutation conditions for CHIKV, DENV and ZIKV. Chikungunya virus, CHIKV; Dengue virus, DENV; Zika virus, ZIKV.
DOI: 10.6084/m9.figshare.7013234
title: Dataset from Epidemic dynamics, interactions and predictability of enteroviruses associated with hand, foot and mouth disease in Japan.

description: Hand, foot, and mouth disease in Japan, 1982-2015
DOI: 10.6084/m9.figshare.7013234.v2
title: Dataset from Epidemic dynamics, interactions and predictability of enteroviruses associated with hand, foot and mouth disease in Japan.

description: Hand, foot, and mouth disease in Japan, 1982-2015
DOI: 10.6084/m9.figshare.7012436.v1
title: Supplementary File S6 from Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses

description: Results from the <i>in-silico</i> media variation sensitivity analyses to evaluate the effectiveness of the host-derived enforcement antiviral targets over a range of varied media compositions for CHIKV, DENV and ZIKV viruses.
DOI: 10.6084/m9.figshare.7013234.v1
title: Dataset from Epidemic dynamics, interactions and predictability of enteroviruses associated with hand, foot and mouth disease in Japan

description: Hand, foot, and mouth disease in Japan, 1982-2015
DOI: 10.6084/m9.figshare.7058108
title: BETA code from Modelling tropical forest responses to drought and El Niño with a stomatal optimization model based on xylem hydraulics.

description: Code of the BETA model described in the manuscript written in R
DOI: 10.6084/m9.figshare.7058111
title: SOX code from Modelling tropical forest responses to drought and El Niño with a stomatal optimization model based on xylem hydraulics.

description: Code of the SOX model described in the manuscript written in R
DOI: 10.6084/m9.figshare.7058108.v2
title: BETA code from Modelling tropical forest responses to drought and El Niño with a stomatal optimization model based on xylem hydraulics.

description: Code of the BETA model described in the manuscript written in R
DOI: 10.6084/m9.figshare.7058108.v1
title: BETA code from Modelling tropical forest responses to drought and El Niño with a stomatal optimization model based on xylem hydraulics

description: Code of the BETA model described in the manuscript written in R
DOI: 10.6084/m9.figshare.7058111.v1
title: SOX code from Modelling tropical forest responses to drought and El Niño with a stomatal optimization model based on xylem hydraulics

description: Code of the SOX model described in the manuscript written in R
DOI: 10.6084/m9.figshare.7072103
title: Lambert & Osvath Supplementary Data from Comparing chimpanzees' preparatory responses to known and unknown future outcomes.

description: Supplementary Data
DOI: 10.6084/m9.figshare.7072103.v2
title: Lambert & Osvath Supplementary Data from Comparing chimpanzees' preparatory responses to known and unknown future outcomes.

description: Supplementary Data
DOI: 10.6084/m9.figshare.7072103.v1
title: Lambert & Osvath Supplementary Data from Comparing chimpanzees' preparatory responses to known and unknown future outcomes

description: Supplementary Data
DOI: 10.6084/m9.figshare.7072115
title: Data of AWD and Knepp Wildland from Risks and opportunities of trophic rewilding for arthropod communities.

description: Table S2: Mean additive trend slopes (± standard error) in the abundance of individual butterfly species on monitoring transects in the coastal dunes of AWD (Amsterdam Water-supply Dunes); A copy of the butterfly monitoring data done at Knepp Wildland.
DOI: 10.6084/m9.figshare.7072115.v2
title: Data of AWD and Knepp Wildland from Risks and opportunities of trophic rewilding for arthropod communities.

description: Table S2: Mean additive trend slopes (± standard error) in the abundance of individual butterfly species on monitoring transects in the coastal dunes of AWD (Amsterdam Water-supply Dunes); A copy of the butterfly monitoring data done at Knepp Wildland.
DOI: 10.6084/m9.figshare.7072115.v1
title: Data of AWD and Knepp Wildland from Evidence, risks and opportunities of trophic rewilding for arthropod communities

description: Table S2: Mean additive trend slopes (± standard error) in the abundance of individual butterfly species on monitoring transects in the coastal dunes of AWD (Amsterdam Water-supply Dunes); A copy of the butterfly monitoring data done at Knepp Wildland.
DOI: 10.6084/m9.figshare.7076828
title: Table s1 from Diversification dynamics of mammalian clades during the K–Pg mass extinction.

description: Dataset of fossil occurrences
DOI: 10.6084/m9.figshare.7076828.v2
title: Table s1 from Diversification dynamics of mammalian clades during the K–Pg mass extinction.

description: Dataset of fossil occurrences
DOI: 10.6084/m9.figshare.7076828.v1
title: Table s1 from Diversification dynamics of mammalian clades during the K–Pg mass extinction

description: Dataset of fossil occurrences
DOI: 10.6084/m9.figshare.7110464
title: Simulation code from A topographic mechanism for arcing of dryland vegetation bands.

description: Matlab scripts and output files for simulation of topographically extended Klausmeier model.
DOI: 10.6084/m9.figshare.7110464.v2
title: Simulation code from A topographic mechanism for arcing of dryland vegetation bands.

description: Matlab scripts and output files for simulation of topographically extended Klausmeier model.
DOI: 10.6084/m9.figshare.7110464.v1
title: Simulation code from A topographic mechanism for arcing of dryland vegetation bands

description: Matlab scripts and output files for simulation of topographically extended Klausmeier model.
DOI: 10.6084/m9.figshare.7133102
title: Table S1 from The evolution of fungal substrate specificity in a widespread group of crustose lichens.

description: A complete list of all used sequence vouchers and character coding information used in this study in Excel format.
DOI: 10.6084/m9.figshare.7133102.v2
title: Table S1 from The evolution of fungal substrate specificity in a widespread group of crustose lichens.

description: A complete list of all used sequence vouchers and character coding information used in this study in Excel format.
DOI: 10.6084/m9.figshare.7133102.v1
title: Table S1 from The evolution of fungal substrate specificity in a widespread group of crustose lichens

description: A complete list of all used sequence vouchers and character coding information used in this study in Excel format.
DOI: 10.6084/m9.figshare.7133207
title: Data S2 from Unintentional rewilding: lessons for trophic rewilding from other forms of species introductions.

description: Code for meta-regression model
DOI: 10.6084/m9.figshare.7133210
title: Data S1 from Unintentional rewilding: lessons for trophic rewilding from other forms of species introductions.

description: Meta-analysis dataset
DOI: 10.6084/m9.figshare.7133207.v2
title: Data S2 from Unintentional rewilding: lessons for trophic rewilding from other forms of species introductions.

description: Code for meta-regression model
DOI: 10.6084/m9.figshare.7133207.v1
title: Data S2 from Unintentional rewilding: lessons for trophic rewilding from other forms of species introductions

description: Code for meta-regression model
DOI: 10.6084/m9.figshare.7133210.v2
title: Data S1 from Unintentional rewilding: lessons for trophic rewilding from other forms of species introductions.

description: Meta-analysis dataset
DOI: 10.6084/m9.figshare.7133210.v1
title: Data S1 from Unintentional rewilding: lessons for trophic rewilding from other forms of species introductions

description: Meta-analysis dataset
DOI: 10.6084/m9.figshare.7145054
title: Calculated Attributes of 25 Ecosystem Networks from Biodiversity, functional redundancy and system stability: subtle connections.

description: Results of calculating and correlating measures of trophic functional redundancies
DOI: 10.6084/m9.figshare.7145057
title: Ecosystem Network Data Used for Correlations from Biodiversity, functional redundancy and system stability: subtle connections.

description: Full data on 25 ecosystem trophic networks for comparison of calculated functional redundancies
DOI: 10.6084/m9.figshare.7145054.v2
title: Calculated Attributes of 25 Ecosystem Networks from Biodiversity, functional redundancy and system stability: subtle connections.

description: Results of calculating and correlating measures of trophic functional redundancies
DOI: 10.6084/m9.figshare.7145054.v1
title: Calculated Attributes of 25 Ecosystem Networks from Biodiversity, functional redundancy and system stability: subtle connections

description: Results of calculating and correlating measures of trophic functional redundancies
DOI: 10.6084/m9.figshare.7145057.v2
title: Ecosystem Network Data Used for Correlations from Biodiversity, functional redundancy and system stability: subtle connections.

description: Full data on 25 ecosystem trophic networks for comparison of calculated functional redundancies
DOI: 10.6084/m9.figshare.7145057.v1
title: Ecosystem Network Data Used for Correlations from Biodiversity, functional redundancy and system stability: subtle connections

description: Full data on 25 ecosystem trophic networks for comparison of calculated functional redundancies
DOI: 10.6084/m9.figshare.7171970
title: List of species from The use and misuse of herbarium specimens in evaluating plant extinction risks.

description: Herbarium specimens provide verifiable and citable evidence of the occurrence of particular plants at particular points in space and time, and are vital resources for assessing extinction risk in the tropics, where plant diversity and threats to plants are greatest. We reviewed approaches to assessing extinction risk in response to the Convention on Biological Diversity's Global Strategy for Plant Conservation Target 2: an assessment of the conservation status of all known plant species by 2020. We tested five alternative approaches, using herbarium-derived data for trees, shrubs and herbs in five different plant groups from temperate and tropical regions. All species were previously fully assessed for the IUCN Red List. We found significant variation in the accuracy with which different approaches classified species as threatened or not threatened. Accuracy was highest for the machine learning model (90%) but the least data-intensive approach also performed well (82%). Despite concerns about spatial, temporal and taxonomic biases and uncertainties in herbarium data, when specimens represent the best available evidence for particular species, their use as a basis for extinction risk assessment is appropriate, necessary and urgent. Resourcing herbaria to maintain, increase and disseminate their specimen data is essential to guide and focus conservation action.This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.
DOI: 10.6084/m9.figshare.7171970.v2
title: List of species from The use and misuse of herbarium specimens in evaluating plant extinction risks.

description: Herbarium specimens provide verifiable and citable evidence of the occurrence of particular plants at particular points in space and time, and are vital resources for assessing extinction risk in the tropics, where plant diversity and threats to plants are greatest. We reviewed approaches to assessing extinction risk in response to the Convention on Biological Diversity's Global Strategy for Plant Conservation Target 2: an assessment of the conservation status of all known plant species by 2020. We tested five alternative approaches, using herbarium-derived data for trees, shrubs and herbs in five different plant groups from temperate and tropical regions. All species were previously fully assessed for the IUCN Red List. We found significant variation in the accuracy with which different approaches classified species as threatened or not threatened. Accuracy was highest for the machine learning model (90%) but the least data-intensive approach also performed well (82%). Despite concerns about spatial, temporal and taxonomic biases and uncertainties in herbarium data, when specimens represent the best available evidence for particular species, their use as a basis for extinction risk assessment is appropriate, necessary and urgent. Resourcing herbaria to maintain, increase and disseminate their specimen data is essential to guide and focus conservation action.This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.
DOI: 10.6084/m9.figshare.7171970.v1
title: List of species from The use and misuse of herbarium specimens in evaluating plant extinction risks

description: Herbarium specimens provide verifiable and citable evidence of the occurrence of particular plants at particular points in space and time, and are vital resources for assessing extinction risk in the tropics, where plant diversity and threats to plants are greatest. We reviewed approaches to assessing extinction risk in response to the Convention on Biological Diversity's Global Strategy for Plant Conservation Target 2: an assessment of the conservation status of all known plant species by 2020. We tested five alternative approaches, using herbarium-derived data for trees, shrubs and herbs in five different plant groups from temperate and tropical regions. All species were previously fully assessed for the IUCN Red List. We found significant variation in the accuracy with which different approaches classified species as threatened or not threatened. Accuracy was highest for the machine learning model (90%) but the least data-intensive approach also performed well (82%). Despite concerns about spatial, temporal and taxonomic biases and uncertainties in herbarium data, when specimens represent the best available evidence for particular species, their use as a basis for extinction risk assessment is appropriate, necessary and urgent. Resourcing herbaria to maintain, increase and disseminate their specimen data is essential to guide and focus conservation action.This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.
DOI: 10.6084/m9.figshare.7190474
title: Supplementary Information from Vertebral morphometrics and lung structure in non-avian dinosaurs.

description: A .zip file containing landmark data, classifier variables and the R code necessary to replicate the main findings of the paper.
DOI: 10.6084/m9.figshare.7190474.v1
title: Supplementary Information from Vertebral morphometrics and lung structure in non-avian dinosaurs

description: A .zip file containing landmark data, classifier variables and the R code necessary to replicate the main findings of the paper.