cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1332498.v5
title: Deciphering the dual effect of lipopolysaccharides from plant pathogenic <i>Pectobacterium</i>

description: Lipopolysaccharides (LPS) are a component of the outer cell surface of almost all Gram-negative bacteria and play an essential role for bacterial growth and survival. Lipopolysaccharides represent typical microbe-associated molecular pattern (MAMP) molecules and have been reported to induce defense-related responses, including the expression of defense genes and the suppression of the hypersensitive response in plants. However, depending on their origin and the challenged plant, LPS were shown to have complex and different roles. In this study we showed that LPS from plant pathogens <i>Pectobacterium atrosepticum</i> and <i>Pectobacterium carotovorum subsp. carotovorum</i> induce common and different responses in <i>A. thaliana</i> cells when compared to those induced by LPS from non-phytopathogens <i>Escherichia coli</i> and <i>Pseudomonas aeruginosa</i>. Among common responses to both types of LPS are the transcription of defense genes and their ability to limit of cell death induced by <i>Pectobacterium carotovorum subsp carotovorum</i>. However, the differential kinetics and amplitude in reactive oxygen species (ROS) generation seemed to regulate defense gene transcription and be determinant to induce programmed cell death in response to LPS from the plant pathogenic <i>Pectobacterium</i>. These data suggest that different signaling pathways could be activated by LPS in <i>A. thaliana</i> cells.
DOI: 10.6084/m9.figshare.1332487.v1
title: Data for "Signatures of value comparison in ventral striatum neurons"

description: Data for the PLoS Biology article, "Signatures of value comparison in ventral striatum neurons," by Caleb E. Strait, Brianna J. Sleezer, and Benjamin Y. Hayden.
DOI: 10.6084/m9.figshare.1332498.v4
title: Deciphering the dual effect of lipopolysaccharides from plant pathogenic <i>Pectobacterium</i>

description: Lipopolysaccharides (LPS) are a component of the outer cell surface of almost all Gram-negative bacteria and play an essential role for bacterial growth and survival. Lipopolysaccharides represent typical microbe-associated molecular pattern (MAMP) molecules and have been reported to induce defense-related responses, including the expression of defense genes and the suppression of the hypersensitive response in plants. However, depending on their origin and the challenged plant, LPS were shown to have complex and different roles. In this study we showed that LPS from plant pathogens <i>Pectobacterium atrosepticum</i> and <i>Pectobacterium carotovorum subsp. carotovorum</i> induce common and different responses in <i>A. thaliana</i> cells when compared to those induced by LPS from non-phytopathogens <i>Escherichia coli</i> and <i>Pseudomonas aeruginosa</i>. Among common responses to both types of LPS are the transcription of defense genes and their ability to limit of cell death induced by <i>Pectobacterium carotovorum subsp carotovorum</i>. However, the differential kinetics and amplitude in reactive oxygen species (ROS) generation seemed to regulate defense gene transcription and be determinant to induce programmed cell death in response to LPS from the plant pathogenic <i>Pectobacterium</i>. These data suggest that different signaling pathways could be activated by LPS in <i>A. thaliana</i> cells.
DOI: 10.6084/m9.figshare.1332487.v2
title: Data for "Signatures of value comparison in ventral striatum neurons"

description: Data for the PLoS Biology article, "Signatures of value comparison in ventral striatum neurons," by Caleb E. Strait, Brianna J. Sleezer, and Benjamin Y. Hayden.
DOI: 10.6084/m9.figshare.1332472
title: Matonhodze reuse of participants

description: Cochrane comment and criticism
DOI: 10.6084/m9.figshare.1332472.v1
title: Matonhodze reuse of participants

description: Cochrane comment and criticism
DOI: 10.6084/m9.figshare.1332487.v3
title: Data for "Signatures of value comparison in ventral striatum neurons"

description: Data for the PLoS Biology article, "Signatures of value comparison in ventral striatum neurons," by Caleb E. Strait, Brianna J. Sleezer, and Benjamin Y. Hayden. S1 Data: VS dataset. S2 Data: VM dataset.
DOI: 10.6084/m9.figshare.1332469
title: Time lag and communication in changing unpopular norms

description: Experimental data from CREED lab, Amsterdam, Netherlands, by Klarita Gerxhani and Jeroen Bruggeman.
DOI: 10.6084/m9.figshare.1332487.v5
title: Data for "Signatures of value comparison in ventral striatum neurons"

description: Data for the PLoS Biology article, "Signatures of value comparison in ventral striatum neurons," by Caleb E. Strait, Brianna J. Sleezer, and Benjamin Y. Hayden. S1 Data: VS dataset. S2 Data: VM dataset.
DOI: 10.6084/m9.figshare.1332487.v4
title: Data for "Signatures of value comparison in ventral striatum neurons"

description: Data for the PLoS Biology article, "Signatures of value comparison in ventral striatum neurons," by Caleb E. Strait, Brianna J. Sleezer, and Benjamin Y. Hayden. S1 Data: VS dataset. S2 Data: VM dataset.
DOI: 10.6084/m9.figshare.1332469.v1
title: Time lag and communication in changing unpopular norms

description: Experimental data from CREED lab, Amsterdam, Netherlands, by Klarita Gerxhani and Jeroen Bruggeman.
DOI: 10.6084/m9.figshare.1332459
title: Blocking Schemes for Definitive Screening Designs

description: Jones and Nachtsheim (2011) proposed a new class of screening designs called definitive screening designs. As originally presented, these designs are three-level designs for quantitative factors that provide estimates of main effects that are unbiased by any second-order effect and require only one more than twice as many runs as there are factors. Definitive screening designs avoid direct confounding of any pair of second-order effects, and, for designs that have more than five factors, project to efficient response surface designs for any two or three factors. Recently, Jones and Nachtsheim (2013) expanded the applicability of these designs by showing how to include any number of two-level categorical factors. However, methods for blocking definitive screening designs have not been addressed. In this paper we develop orthogonal blocking schemes for definitive screening designs. We separately consider the cases where all of the factors are quantitative and where there is a mix of quantitative and two-level qualitative factors. The schemes are quite flexible in that the numbers of blocks may vary from two to the number of factors, and block sizes need not be equal. We provide blocking schemes for both fixed and random blocks.
DOI: 10.6084/m9.figshare.1332458
title: Bayesian Inference for a New Class of Distributions on Equivalence Classes of 3-D Orientations With Applications to Materials Science

description: Experiments in materials science investigating cubic crystalline structures often collect data which are in truth <i>equivalence classes</i> of crystallographically symmetric orientations. These intend to represent how lattice structures of particles are orientated relative to a reference coordinate system. Motivated by a materials science application, we formulate parametric probability models for “unlabeled orientation data.” This amounts to developing models on equivalence classes of 3-D rotations. We use a flexible existing model class for random rotations (called uniform-axis-random-spin models) to induce probability distributions on the equivalence classes of rotations. We develop one-sample Bayesian inference for the parameters in these models, and compare this methodology to some likelihood-based approaches. We also contrast the new parametric analysis of unlabeled orientation data with other analyses that proceed as if the data have been preprocessed into honest orientation data. On-line supplementary materials are also available, providing additional computational materials.
DOI: 10.6084/m9.figshare.1332458.v1
title: Bayesian Inference for a New Class of Distributions on Equivalence Classes of 3-D Orientations With Applications to Materials Science

description: Experiments in materials science investigating cubic crystalline structures often collect data which are in truth <i>equivalence classes</i> of crystallographically symmetric orientations. These intend to represent how lattice structures of particles are orientated relative to a reference coordinate system. Motivated by a materials science application, we formulate parametric probability models for “unlabeled orientation data.” This amounts to developing models on equivalence classes of 3-D rotations. We use a flexible existing model class for random rotations (called uniform-axis-random-spin models) to induce probability distributions on the equivalence classes of rotations. We develop one-sample Bayesian inference for the parameters in these models, and compare this methodology to some likelihood-based approaches. We also contrast the new parametric analysis of unlabeled orientation data with other analyses that proceed as if the data have been preprocessed into honest orientation data. On-line supplementary materials are also available, providing additional computational materials.
DOI: 10.6084/m9.figshare.1332459.v1
title: Blocking Schemes for Definitive Screening Designs

description: Jones and Nachtsheim (2011) proposed a new class of screening designs called definitive screening designs. As originally presented, these designs are three-level designs for quantitative factors that provide estimates of main effects that are unbiased by any second-order effect and require only one more than twice as many runs as there are factors. Definitive screening designs avoid direct confounding of any pair of second-order effects, and, for designs that have more than five factors, project to efficient response surface designs for any two or three factors. Recently, Jones and Nachtsheim (2013) expanded the applicability of these designs by showing how to include any number of two-level categorical factors. However, methods for blocking definitive screening designs have not been addressed. In this paper we develop orthogonal blocking schemes for definitive screening designs. We separately consider the cases where all of the factors are quantitative and where there is a mix of quantitative and two-level qualitative factors. The schemes are quite flexible in that the numbers of blocks may vary from two to the number of factors, and block sizes need not be equal. We provide blocking schemes for both fixed and random blocks.
DOI: 10.6084/m9.figshare.1332456
title: Short-Term GDP Forecasting With a Mixed-Frequency Dynamic Factor Model With Stochastic Volatility

description: In this article, we develop a mixed frequency dynamic factor model in which the disturbances of both the latent common factor and of the idiosyncratic components have time-varying stochastic volatilities. We use the model to investigate business cycle dynamics in the euro area and present three sets of empirical results. First, we evaluate the impact of macroeconomic releases on point and density forecast accuracy and on the width of forecast intervals. Second, we show how our setup allows to make a probabilistic assessment of the contribution of releases to forecast revisions. Third, we examine point and density out of sample forecast accuracy. We find that introducing stochastic volatility in the model contributes to an improvement in both point and density forecast accuracy. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1332454
title: Belvedere M., and Farlow J. 2016. A numerical scale for quantifying the quality of preservation of vertebrate tracks. Supplementary Files

description: Belvedere, M. and Farlow, J. 2016. A numerical scale for quantifying the quality of preservation of vertebrate tracks. Supplementary Files For Biped Grade 2 follow the link.
DOI: 10.6084/m9.figshare.1332456.v2
title: Short-Term GDP Forecasting With a Mixed-Frequency Dynamic Factor Model With Stochastic Volatility

description: In this article, we develop a mixed frequency dynamic factor model in which the disturbances of both the latent common factor and of the idiosyncratic components have time-varying stochastic volatilities. We use the model to investigate business cycle dynamics in the euro area and present three sets of empirical results. First, we evaluate the impact of macroeconomic releases on point and density forecast accuracy and on the width of forecast intervals. Second, we show how our setup allows to make a probabilistic assessment of the contribution of releases to forecast revisions. Third, we examine point and density out of sample forecast accuracy. We find that introducing stochastic volatility in the model contributes to an improvement in both point and density forecast accuracy. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1332456.v1
title: Short-term GDP forecasting with a mixed frequency dynamic factor model with stochastic volatility

description: In this paper we develop a mixed frequency dynamic factor model in which the disturbances of both the latent common factor and of the idiosyncratic components have time varying stochastic volatilities. We use the model to investigate business cycle dynamics in the euro area and present three sets of empirical results. First, we evaluate the impact of macroeconomic releases on point and density forecast accuracy and on the width of forecast intervals. Second, we show how our setup allows to make a probabilistic assessment of the contribution of releases to forecast revisions. Third, we examine point and density out of sample forecast accuracy. We find that introducing stochastic volatility in the model contributes to an improvement in both point and density forecast accuracy.
DOI: 10.6084/m9.figshare.1332446
title: diabetes

description: diabetes data
DOI: 10.6084/m9.figshare.1332454.v1
title: Belvedere M., and Farlow J. 2015. A numerical scale for quantifying the quality of preservation of vertebrate tracks. Supplementary Files

description: Belvedere, M. and Farlow, J. 2015. A numerical scale for quantifying the quality of preservation of vertebrate tracks. Supplementary Files For Biped Grade 2 follow the link.
DOI: 10.6084/m9.figshare.1332443
title: An early Pliocene (5.1 Ma) fossil frog community from Langebaanweg, south-western Cape, South Africa

description: The 5.1 million year old fossil site of Langebaanweg (LBW) has provided a wealth of information on the evolution of west coast ecosystems along the southern west coast of South Africa and numerous taxa, including small and large mammals, and birds, make a first appearance in the fossil record at the site. Langebaanweg also contains a rich and diverse anuran fauna which derives from the two main fossil-bearing members at the site. This study identified six families, including Hyperoliidae, Brevicipitidae, Pxyicephalidae, Pipidae, Heleophrynidae and Bufonidae, and some 19 taxa have been differentiated. The majority of frog families identified from the LBW fossil material currently contain a high number of species endemic to the southwestern Cape or South Africa. LBW provides an insight into how current patterns of endemism and distribution may have evolved, and illustrates that the frog community in a region may change substantially over time. The progressive aridification of the west coast subsequent to 5.1 Ma has left very little trace of the rich and diverse frog community which existed during the early Pliocene, and diversity and endemnicity are low today. This challenges the generally held assumption that centres of origin may have a bearing on current-day frog distributions.
DOI: 10.6084/m9.figshare.1332443.v2
title: An early Pliocene (5.1 Ma) fossil frog community from Langebaanweg, south-western Cape, South Africa

description: The 5.1 million year old fossil site of Langebaanweg (LBW) has provided a wealth of information on the evolution of west coast ecosystems along the southern west coast of South Africa and numerous taxa, including small and large mammals, and birds, make a first appearance in the fossil record at the site. Langebaanweg also contains a rich and diverse anuran fauna which derives from the two main fossil-bearing members at the site. This study identified six families, including Hyperoliidae, Brevicipitidae, Pxyicephalidae, Pipidae, Heleophrynidae and Bufonidae, and some 19 taxa have been differentiated. The majority of frog families identified from the LBW fossil material currently contain a high number of species endemic to the southwestern Cape or South Africa. LBW provides an insight into how current patterns of endemism and distribution may have evolved, and illustrates that the frog community in a region may change substantially over time. The progressive aridification of the west coast subsequent to 5.1 Ma has left very little trace of the rich and diverse frog community which existed during the early Pliocene, and diversity and endemnicity are low today. This challenges the generally held assumption that centres of origin may have a bearing on current-day frog distributions.
DOI: 10.6084/m9.figshare.1332446.v2
title: cv

description: CV of Masta Sestelo
DOI: 10.6084/m9.figshare.1332443.v1
title: An early Pliocene (5.1 Ma) fossil frog community from Langebaanweg, south-western Cape, South Africa

description: The 5.1 million year old fossil site of Langebaanweg (LBW) has provided a wealth of information on the evolution of west coast ecosystems along the southern west coast of South Africa and numerous taxa, including small and large mammals, and birds, make a first appearance in the fossil record at the site. Langebaanweg also contains a rich and diverse anuran fauna which derives from the two main fossil-bearing members at the site. This study identified six families, including Hyperoliidae, Brevicipitidae, Pxyicephalidae, Pipidae, Heleophrynidae and Bufonidae, and some 19 taxa have been differentiated. The majority of frog families identified from the LBW fossil material currently contain a high number of species endemic to the southwestern Cape or South Africa. LBW provides an insight into how current patterns of endemism and distribution may have evolved, and illustrates that the frog community in a region may change substantially over time. The progressive aridification of the west coast subsequent to 5.1 Ma has left very little trace of the rich and diverse frog community which existed during the early Pliocene, and diversity and endemnicity are low today. This challenges the generally held assumption that centres of origin may have a bearing on current-day frog distributions.
DOI: 10.6084/m9.figshare.1332438
title: Screening of variable importance for optimizing electrodialytic remediation of heavy metals from polluted harbour sediments

description: Using multivariate design and modelling, the optimal conditions for electrodialytic remediation (EDR) of heavy metals were determined for polluted harbour sediments from Hammerfest harbour located in the geographic Arctic region of Norway. The comparative importance of the variables, current density, remediation time, light/no light, the liquid–solid ratio and stirring rate of the sediment suspension, was determined in 15 laboratory-scale EDR experiments by projection to latent structures (PLS). The relation between the X matrix (experimental variables) and the Y matrix (removal efficiencies) was computed and variable importance in the projection was used to assess the influence of the experimental variables. Current density and remediation time proved to have the highest influence on the remediation of the heavy metals Cr, Cu, Ni, Pb and Zn in the studied experimental domain. In addition, it was shown that excluding the acidification time improved the PLS model, indicating the importance of applying a limited experimental domain that covers the removal phases of each heavy metal in the specific sediment. Based on PLS modelling, the optimal conditions for remediating the Hammerfest sediment were determined; operating in the experimental domain of 0.5–0.8 mA/cm<sup>2</sup> and a remediation time after acidification of 450–570 h met acceptable levels according to Norwegian sediment quality guidelines.
DOI: 10.6084/m9.figshare.1332438.v1
title: Screening of Variable Importance for Optimsing Electrodialytic Remediation of Heavy Metals from Polluted Harbour Sediments

description: Using multivariate design and modelling, optimal conditions for electrodialytic remediation (EDR) of heavy metals were determined for polluted harbour sediments from Hammerfest harbour located in the geographic Arctic region of Norway. The comparative importance of the variables; current density, remediation time, light/no light, the liquid-solid ratio and stirring rate of the sediment suspension were determined in 15 laboratory scale EDR experiments by projection to latent structures (PLS). The relation between the X matrix (experimental variables) and the Y matrix (removal efficiencies) was computed and variable importance in the projection was used to assess the influence of the experimental variables. Current density and remediation time proved to have the highest influence on the remediation of the heavy metals Cr, Cu, Ni, Pb and Zn in the studied experimental domain. In addition it was shown that excluding the acidification time improved the PLS model, indicating the importance of applying a limited experimental domain that covers the removal phases of each heavy metal in the specific sediment. Based on PLS modelling the optimal conditions for remediating the Hammerfest sediment was determined; operating in the experimental domain of 0.5-0.8 mA/cm<sup>2</sup> and a remediation time after acidification of 450-570 hours met acceptable levels according to Norwegian sediment quality guidelines.TENT_1028470_Supplementary_File.zip
DOI: 10.6084/m9.figshare.1332438.v3
title: Screening of variable importance for optimizing electrodialytic remediation of heavy metals from polluted harbour sediments

description: Using multivariate design and modelling, the optimal conditions for electrodialytic remediation (EDR) of heavy metals were determined for polluted harbour sediments from Hammerfest harbour located in the geographic Arctic region of Norway. The comparative importance of the variables, current density, remediation time, light/no light, the liquid–solid ratio and stirring rate of the sediment suspension, was determined in 15 laboratory-scale EDR experiments by projection to latent structures (PLS). The relation between the X matrix (experimental variables) and the Y matrix (removal efficiencies) was computed and variable importance in the projection was used to assess the influence of the experimental variables. Current density and remediation time proved to have the highest influence on the remediation of the heavy metals Cr, Cu, Ni, Pb and Zn in the studied experimental domain. In addition, it was shown that excluding the acidification time improved the PLS model, indicating the importance of applying a limited experimental domain that covers the removal phases of each heavy metal in the specific sediment. Based on PLS modelling, the optimal conditions for remediating the Hammerfest sediment were determined; operating in the experimental domain of 0.5–0.8 mA/cm<sup>2</sup> and a remediation time after acidification of 450–570 h met acceptable levels according to Norwegian sediment quality guidelines.