cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2083105.v1
title: Provenance shifts in an evolving Eurekan foreland basin: the Tertiary Central Basin, Spitsbergen

description: Supplemental Data File: U207/235 and U206/238 ages for all zircons
DOI: 10.6084/m9.figshare.2087719.v5
title: Experimental Evolution Datasets (C. elegans wildtype and mutant genotypes)

description: 20 generations of experimental evolution data for 14 genetic mutant strains of C elegans and 1 wildtype strain. 15 generations of experimental evolution data for 3 genetic mutant strains. <br>Includes four pieces of data: 1) POPSIZE, which are measurements of population size over 3d intervals for 15-20 generations<br>2) RCO (Reproductive Carry-Over), which is a derivative of the population size measure<br>3) POP BY DAY, which is a control condition that measures fecundity day-by-day over a 4d period across replicates.<br>4) POP OVER 4d, which is a control condition that measures cumulative fecundity over a 4d period across replicates.
DOI: 10.6084/m9.figshare.2951263.v365
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2087719.v6
title: Experimental Evolution Datasets (C. elegans wildtype and mutant genotypes)

description: 20 generations of experimental evolution data for 11 genetic mutant strains of C elegans and 1 wildtype strain. 15 generations of experimental evolution data for 3 genetic mutant strains. <br>Includes four pieces of data: 1) POPSIZE, which are measurements of population size over 3d intervals for 15-20 generations<br>2) RCO (Reproductive Carry-Over), which is a derivative of the population size measure<br>3) POP BY DAY, which is a control condition that measures fecundity day-by-day over a 4d period across replicates.<br>4) POP OVER 4d, which is a control condition that measures cumulative fecundity over a 4d period across replicates.
DOI: 10.6084/m9.figshare.2885308.v364
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2083309.v1
title: Appendices

description: Appendices from the thesis entitled:<br>Analysis of <i>Staphylococcus aureus</i> Virulence Determinants. <br>By John Connolly
DOI: 10.6084/m9.figshare.2083309.v2
title: Appendices

description: Appendices from the thesis entitled:<br>Analysis of <i>Staphylococcus aureus</i> Virulence Determinants. <br>By John Connolly
DOI: 10.6084/m9.figshare.2951263.v366
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2885308.v365
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2087719.v7
title: Experimental Evolution Datasets (C. elegans wildtype and mutant genotypes)

description: 20 generations of experimental evolution data for 11 genetic mutant strains of C elegans and 1 wildtype strain. 15 generations of experimental evolution data for 3 genetic mutant strains. <br>Includes four pieces of data: 1) POPSIZE, which are measurements of population size over 3d intervals for 15-20 generations<br>2) RCO (Reproductive Carry-Over), which is a derivative of the population size measure<br>3) POP BY DAY, which is a control condition that measures fecundity day-by-day over a 4d period across replicates.<br>4) POP OVER 4d, which is a control condition that measures cumulative fecundity over a 4d period across replicates.
DOI: 10.6084/m9.figshare.2083309.v3
title: Appendices

description: Appendices from the thesis entitled:<br>Analysis of <i>Staphylococcus aureus</i> Virulence Determinants. <br>By John Connolly
DOI: 10.6084/m9.figshare.2083309.v5
title: Appendices

description: Appendices from the thesis entitled:<br>Analysis of <i>Staphylococcus aureus</i> Virulence Determinants. <br>By John Connolly<br>The University of Sheffield
DOI: 10.6084/m9.figshare.2087719.v8
title: Experimental Evolution Datasets (C. elegans wildtype and mutant genotypes)

description: 20 generations of experimental evolution data for 11 genetic mutant strains of C elegans and 1 wildtype strain. 15 generations of experimental evolution data for 3 genetic mutant strains. <br>Includes four pieces of data: 1) POPSIZE, which are measurements of population size over 3d intervals for 15-20 generations<br>2) RCO (Reproductive Carry-Over), which is a derivative of the population size measure<br>3) POP BY DAY, which is a control condition that measures fecundity day-by-day over a 4d period across replicates.<br>4) POP OVER 4d, which is a control condition that measures cumulative fecundity over a 4d period across replicates.
DOI: 10.6084/m9.figshare.2951263.v367
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2083309.v4
title: Appendices

description: Appendices from the thesis entitled:<br>Analysis of <i>Staphylococcus aureus</i> Virulence Determinants. <br>By John Connolly
DOI: 10.6084/m9.figshare.2885308.v366
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2082805
title: New draft item

description: Libraries, IT, research administration, and grant support will have to collaborate to find the expertise necessary to provide data management support through the research process. Analyzing the data needs of researchers across institutional domains may require the library to identify and connect researchers across formal and informal functional units for sharing, analyzing, and reusing data.
DOI: 10.6084/m9.figshare.2087719.v9
title: Experimental Evolution Datasets (C. elegans wildtype and mutant genotypes)

description: 20 generations of experimental evolution data for 11 genetic mutant strains of C elegans and 1 wildtype strain. 15 generations of experimental evolution data for 3 genetic mutant strains. <br>Includes four pieces of data: 1) POPSIZE, which are measurements of population size over 3d intervals for 15-20 generations<br>2) RCO (Reproductive Carry-Over), which is a derivative of the population size measure<br>3) POP BY DAY, which is a control condition that measures fecundity day-by-day over a 4d period across replicates.<br>4) POP OVER 4d, which is a control condition that measures cumulative fecundity over a 4d period across replicates.
DOI: 10.6084/m9.figshare.2885308.v367
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v368
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2082769
title: The ALSFRS as an outcome measure in therapeutic trials and its relationship to symptom onset

description: The reduction in ALS Functional Rating Score (ALSFRS) from reported symptom onset to diagnosis is used to estimate rate of disease progression. ALSFRS decline may be non-linear or distorted by drop-outs in therapeutic trials, reducing the reliability of change in slope as an outcome measure. The PRO-ACT database uniquely allows such measures to be explored using historical data from negative therapeutic trials. The decline of functional scores was analysed in 18 pooled trials, comparing rates of decline based on symptom onset with rates calculated between interval assessments. Strategies to mitigate the effects of trial drop-out were considered. Results showed that progression rate calculated by symptom onset underestimated the subsequent rate of disability accumulation, although it predicted survival more accurately than four-month interval estimates of δALSFRS or δFVC. Individual ALSFRS and FVC progression within a typical trial duration were linear. No simple solution to correct for trial drop-out was identified, but imputation using δALSFRS appeared least disruptive. In conclusion, there is a trade-off between the drive to recruit trial participants soon after symptom onset, and reduced reliability of the ALSFRS-derived progression rate at enrolment. The need for objective markers of disease activity as an alternative to survival-based end-points is clear and pressing.
DOI: 10.6084/m9.figshare.2082805.v1
title: New draft item

description: Libraries, IT, research administration, and grant support will have to collaborate to find the expertise necessary to provide data management support through the research process. Analyzing the data needs of researchers across institutional domains may require the library to identify and connect researchers across formal and informal functional units for sharing, analyzing, and reusing data.
DOI: 10.6084/m9.figshare.2885308.v368
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2082769.v1
title: The ALSFRS as an outcome measure in therapeutic trials and its relationship to symptom onset

description: The reduction in ALS Functional Rating Score (ALSFRS) from reported symptom onset to diagnosis is used to estimate rate of disease progression. ALSFRS decline may be non-linear or distorted by drop-outs in therapeutic trials, reducing the reliability of change in slope as an outcome measure. The PRO-ACT database uniquely allows such measures to be explored using historical data from negative therapeutic trials. The decline of functional scores was analysed in 18 pooled trials, comparing rates of decline based on symptom onset with rates calculated between interval assessments. Strategies to mitigate the effects of trial drop-out were considered. Results showed that progression rate calculated by symptom onset underestimated the subsequent rate of disability accumulation, although it predicted survival more accurately than four-month interval estimates of δALSFRS or δFVC. Individual ALSFRS and FVC progression within a typical trial duration were linear. No simple solution to correct for trial drop-out was identified, but imputation using δALSFRS appeared least disruptive. In conclusion, there is a trade-off between the drive to recruit trial participants soon after symptom onset, and reduced reliability of the ALSFRS-derived progression rate at enrolment. The need for objective markers of disease activity as an alternative to survival-based end-points is clear and pressing.
DOI: 10.6084/m9.figshare.2087719.v10
title: Experimental Evolution Datasets (C. elegans wildtype and mutant genotypes)

description: 20 generations of experimental evolution data for 11 genetic mutant strains of C elegans and 1 wildtype strain. 15 generations of experimental evolution data for 3 genetic mutant strains. <br>Includes four pieces of data: 1) POPSIZE, which are measurements of population size over 3d intervals for 15-20 generations<br>2) RCO (Reproductive Carry-Over), which is a derivative of the population size measure<br>3) POP BY DAY, which is a control condition that measures fecundity day-by-day over a 4d period across replicates.<br>4) POP OVER 4d, which is a control condition that measures cumulative fecundity over a 4d period across replicates.
DOI: 10.6084/m9.figshare.2951263.v369
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2885308.v369
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2087719.v12
title: Experimental Evolution Datasets (C. elegans wildtype and mutant genotypes)

description: 20 generations of experimental evolution data for 14 genetic mutant strains of C elegans and 1 wildtype strain. 15 generations of experimental evolution data for 3 genetic mutant strains. <br>Includes four pieces of data: 1) POPSIZE, which are measurements of population size over 3d intervals for 15-20 generations<br>2) RCO (Reproductive Carry-Over), which is a derivative of the population size measure<br>3) POP BY DAY, which is a control condition that measures fecundity day-by-day over a 4d period across replicates.<br>4) POP OVER 4d, which is a control condition that measures cumulative fecundity over a 4d period across replicates.
DOI: 10.6084/m9.figshare.2951263.v370
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2885308.v370
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2087719.v11
title: Experimental Evolution Datasets (C. elegans wildtype and mutant genotypes)

description: 20 generations of experimental evolution data for 14 genetic mutant strains of C elegans and 1 wildtype strain. 15 generations of experimental evolution data for 3 genetic mutant strains. <br>Includes four pieces of data: 1) POPSIZE, which are measurements of population size over 3d intervals for 15-20 generations<br>2) RCO (Reproductive Carry-Over), which is a derivative of the population size measure<br>3) POP BY DAY, which is a control condition that measures fecundity day-by-day over a 4d period across replicates.<br>4) POP OVER 4d, which is a control condition that measures cumulative fecundity over a 4d period across replicates.
DOI: 10.6084/m9.figshare.2885308.v371
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v371
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2082748.v2
title: Estimation of Directed Acyclic Graphs Through Two-Stage Adaptive Lasso for Gene Network Inference

description: Graphical models are a popular approach to find dependence and conditional independence relationships between gene expressions. Directed acyclic graphs (DAGs) are a special class of directed graphical models, where all the edges are directed edges and contain no directed cycles. <i>The DAGs are well known models for discovering causal relationships between genes in gene regulatory networks.</i> However, estimating DAGs without assuming known ordering is challenging due to high dimensionality, the acyclic constraints, and the presence of equivalence class from observational data. To overcome these challenges, we propose a two-stage adaptive Lasso approach, called NS-DIST, which performs neighborhood selection (NS) in stage 1, and then estimates DAGs by the discrete improving search with Tabu (DIST) algorithm within the selected neighborhood. Simulation studies are presented to demonstrate the effectiveness of the method and its computational efficiency. Two real data examples are used to demonstrate the practical usage of our method for gene regulatory network inference. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.2082748.v1
title: Estimation of Directed Acyclic Graphs Through Two-stage Adaptive Lasso for Gene Network Inference

description: Graphical models are a popular approach to find dependence and conditional independence relationships between gene expressions. Directed acyclic graphs (DAGs) are a special class of directed graphical models, where all the edges are directed edges and contain no directed cycles. <b>The DAGs are well known models for discovering causal relationships between genes in gene regulatory networks.</b> However, estimating DAGs without assuming known ordering is challenging due to high dimensionality, the acyclic constraints, and the presence of equivalence class from observational data. To overcome these challenges, we propose a two-stage adaptive Lasso approach, called NS-DIST, which performs neighborhood selection (NS) in stage 1, and then estimates DAGs by the Discrete Improving Search with Tabu (DIST) algorithm within the selected neighborhood. Simulation studies are presented to demonstrate the effectiveness of the method and its computational efficiency. Two real data examples are used to demonstrate the practical usage of our method for gene regulatory network inference.
DOI: 10.6084/m9.figshare.2951263.v372
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2885308.v372
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2082733
title: A Multiresolution Stochastic Process Model for Predicting Basketball Possession Outcomes

description: Basketball games evolve continuously in space and time as players constantly interact with their teammates, the opposing team, and the ball. However, current analyses of basketball outcomes rely on discretized summaries of the game that reduce such interactions to tallies of points, assists, and similar events. In this article, we propose a framework for using optical player tracking data to estimate, in real time, the expected number of points obtained by the end of a possession. This quantity, called <i>expected possession value</i> (EPV), derives from a stochastic process model for the evolution of a basketball possession. We model this process at multiple levels of resolution, differentiating between continuous, infinitesimal movements of players, and discrete events such as shot attempts and turnovers. Transition kernels are estimated using hierarchical spatiotemporal models that share information across players while remaining computationally tractable on very large data sets. In addition to estimating EPV, these models reveal novel insights on players’ decision-making tendencies as a function of their spatial strategy. In the supplementary material, we provide a data sample and R code for further exploration of our model and its results.
DOI: 10.6084/m9.figshare.2951263.v373
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2885308.v373
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v374
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2082733.v2
title: A Multiresolution Stochastic Process Model for Predicting Basketball Possession Outcomes

description: Basketball games evolve continuously in space and time as players constantly interact with their teammates, the opposing team, and the ball. However, current analyses of basketball outcomes rely on discretized summaries of the game that reduce such interactions to tallies of points, assists, and similar events. In this article, we propose a framework for using optical player tracking data to estimate, in real time, the expected number of points obtained by the end of a possession. This quantity, called <i>expected possession value</i> (EPV), derives from a stochastic process model for the evolution of a basketball possession. We model this process at multiple levels of resolution, differentiating between continuous, infinitesimal movements of players, and discrete events such as shot attempts and turnovers. Transition kernels are estimated using hierarchical spatiotemporal models that share information across players while remaining computationally tractable on very large data sets. In addition to estimating EPV, these models reveal novel insights on players’ decision-making tendencies as a function of their spatial strategy. In the supplementary material, we provide a data sample and R code for further exploration of our model and its results.
DOI: 10.6084/m9.figshare.2885308.v374
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.