cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2304085
title: New carnivoraforms from the latest Paleocene of Europe and their bearing on the origin and radiation of Carnivoraformes (Carnivoramorpha, Mammalia)

description: We report the discovery of the earliest European carnivoraforms, based on two new taxa from the latest Paleocene of France and Romania. A new species of <i>Vassacyon, V. prieuri</i>, from the locality of Rivecourt (MP6b; Oise, France) (MP = Mammalian Paleogene reference levels) is described based on a dentary fragment and isolated teeth. This species displays several primitive features compared with species of <i>Vassacyon</i> known from the early Eocene of North America and Europe. A second Paleocene carnivoraform, cf. <i>Gracilocyon</i> sp., is described based on fragmentary specimens from the locality of Jibou (MP6b; Transylvania, Romania). Carnivoraformes were previously unknown in Europe before the Eocene, and <i>Vassacyon prieuri</i> and cf. <i>Gracilocyon</i> sp. are their oldest records in Europe. These discoveries favor the hypothesis of a dispersal of these two genera from Europe to North America during the Paleocene-Eocene Thermal Maximum. <i>Vassacyon prieuri</i> and cf. <i>Gracilocyon</i> sp. strengthen support for the level MP6b and its correlation with the Clarkforkian. The geographic origin of the Carnivoraformes remains unknown. However, based on the observed biochronological and geographic distributions of the carnivoraforms, we infer a possible Asian origin for this group. In this scenario, <i>Gracilocyon</i> and <i>Vassacyon</i> dispersed to Europe during the Clarkforkian MP6b time, probably together with rodent taxa, whereas <i>Uintacyon</i> dispersed from Asia to North America shortly after rodents and tillodonts. http://zoobank.org/urn:lsid:zoobank.org:pub:FC885E7F-877A-4454-9902-DF118B8C8693 SUPPLEMENTAL DATA—Supplemental materials are available forthis article for free at www.tandfonline.com/UJVP Citation for this article: Solé, F., T. Smith, E. de Bast, V. Codrea, and E. Gheerbrant. 2016. New carnivoraforms from the latest Paleocene of Europe and their bearing on the origin and radiation of Carnivoraformes (Carnivoramorpha, Mammalia). Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1082480.
DOI: 10.6084/m9.figshare.2304085.v1
title: New carnivoraforms from the latest Paleocene of Europe and their bearing on the origin and radiation of Carnivoraformes (Carnivoramorpha, Mammalia)

description: We report the discovery of the earliest European carnivoraforms, based on two new taxa from the latest Paleocene of France and Romania. A new species of <i>Vassacyon, V. prieuri</i>, from the locality of Rivecourt (MP6b; Oise, France) (MP = Mammalian Paleogene reference levels) is described based on a dentary fragment and isolated teeth. This species displays several primitive features compared with species of <i>Vassacyon</i> known from the early Eocene of North America and Europe. A second Paleocene carnivoraform, cf. <i>Gracilocyon</i> sp., is described based on fragmentary specimens from the locality of Jibou (MP6b; Transylvania, Romania). Carnivoraformes were previously unknown in Europe before the Eocene, and <i>Vassacyon prieuri</i> and cf. <i>Gracilocyon</i> sp. are their oldest records in Europe. These discoveries favor the hypothesis of a dispersal of these two genera from Europe to North America during the Paleocene-Eocene Thermal Maximum. <i>Vassacyon prieuri</i> and cf. <i>Gracilocyon</i> sp. strengthen support for the level MP6b and its correlation with the Clarkforkian. The geographic origin of the Carnivoraformes remains unknown. However, based on the observed biochronological and geographic distributions of the carnivoraforms, we infer a possible Asian origin for this group. In this scenario, <i>Gracilocyon</i> and <i>Vassacyon</i> dispersed to Europe during the Clarkforkian MP6b time, probably together with rodent taxa, whereas <i>Uintacyon</i> dispersed from Asia to North America shortly after rodents and tillodonts. http://zoobank.org/urn:lsid:zoobank.org:pub:FC885E7F-877A-4454-9902-DF118B8C8693 SUPPLEMENTAL DATA—Supplemental materials are available forthis article for free at www.tandfonline.com/UJVP Citation for this article: Solé, F., T. Smith, E. de Bast, V. Codrea, and E. Gheerbrant. 2016. New carnivoraforms from the latest Paleocene of Europe and their bearing on the origin and radiation of Carnivoraformes (Carnivoramorpha, Mammalia). Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1082480.
DOI: 10.6084/m9.figshare.2885308.v249
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.v258
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.2951263.v259
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.v250
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.2303449
title: Mapping intermolecular interactions and active site conformations: from human MMP-1 crystal structure to molecular dynamics free energy calculations

description: The zinc-dependent Matrix Metalloproteinases (MMPs) found within the extracellular matrix (ECM) of vertebrates are linked to pathological processes such as arthritis, skin ulceration and cancer. Although a general backbone proteolytic mechanism is understood, crystallographic data continue to suggest an active site that is too narrow to encompass the respective substrate. We present a fully parameterised Molecular Dynamics (MD) study of the structural properties of an MMP-1-collagen crystallographic structure (Protein Data Bank – 4AUO), followed by an exploration of the free energy surface of a collagen polypeptide chain entering the active site, using a combined meta-dynamics and umbrella sampling (MDUS) approach. We conclude that the interactions between MMP-1 and the collagen substrate are in good agreement with a number of experimental studies. As such, our unrestrained MD simulations and our MDUS results, which indicate an energetic barrier for a local uncoiling and insertion event, can inform future investigations of the collagen-peptide non-bonded association steps with the active site prior to proteolytic mechanisms. The elucidation of such free energy barriers provides a better understanding of the role of the enzyme in the ECM and is important in the design of future MMP inhibitors.
DOI: 10.6084/m9.figshare.2303449.v1
title: Mapping intermolecular interactions and active site conformations: from human MMP-1 crystal structure to molecular dynamics free energy calculations

description: The zinc-dependent Matrix Metalloproteinases (MMPs) found within the extracellular matrix (ECM) of vertebrates are linked to pathological processes such as arthritis, skin ulceration and cancer. Although a general backbone proteolytic mechanism is understood, crystallographic data continue to suggest an active site that is too narrow to encompass the respective substrate. We present a fully parameterised Molecular Dynamics (MD) study of the structural properties of an MMP-1-collagen crystallographic structure (Protein Data Bank – 4AUO), followed by an exploration of the free energy surface of a collagen polypeptide chain entering the active site, using a combined meta-dynamics and umbrella sampling (MDUS) approach. We conclude that the interactions between MMP-1 and the collagen substrate are in good agreement with a number of experimental studies. As such, our unrestrained MD simulations and our MDUS results, which indicate an energetic barrier for a local uncoiling and insertion event, can inform future investigations of the collagen-peptide non-bonded association steps with the active site prior to proteolytic mechanisms. The elucidation of such free energy barriers provides a better understanding of the role of the enzyme in the ECM and is important in the design of future MMP inhibitors.
DOI: 10.6084/m9.figshare.2303917.v1
title: cset.zip

description: A MATLAB library for compressed sensing (CS) reconstruction of electron tomogram (ET) volumes.<br>See https://github.com/norbert-wiener-center/cset for updated versions of the software.
DOI: 10.6084/m9.figshare.2951263.v260
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.v251
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.2303059
title: A decade of pharmacogenomics research on tyrosine kinase inhibitors in metastatic renal cell cancer: a systematic review

description: <b>Objective</b>: The individual response to targeted tyrosine kinase inhibitors (TKIs) in the treatment of metastatic renal cell cancer (mRCC) is highly variable. Outlined in this article are findings on potential biomarkers for TKI treatment outcome in mRCC and an evaluation of the status of clinical implementation. <b>Methods</b>: Articles were selected by two independent reviewers using a systematic search in five medical databases on renal cell carcinoma, TKIs, and pharmacogenetics. <b>Results</b>: Many researchers have focused on predictive biomarkers for treatment outcome of targeted therapies in mRCC patients. Attempts to explain differences in efficacy and toxicity of TKIs by use of genetic variants in genes related to the pharmacokinetics and pharmacodynamics of the drug have been successful. <b>Conclusion</b>: Most findings on potential biomarkers have not been validated and therefore biomarker testing to guide choice of therapy and dose in mRCC is not yet feasible.
DOI: 10.6084/m9.figshare.2303059.v1
title: A decade of pharmacogenomics research on tyrosine kinase inhibitors in metastatic renal cell cancer: a systematic review

description: <b>Objective</b>: The individual response to targeted tyrosine kinase inhibitors (TKIs) in the treatment of metastatic renal cell cancer (mRCC) is highly variable. Outlined in this article are findings on potential biomarkers for TKI treatment outcome in mRCC and an evaluation of the status of clinical implementation. <b>Methods</b>: Articles were selected by two independent reviewers using a systematic search in five medical databases on renal cell carcinoma, TKIs, and pharmacogenetics. <b>Results</b>: Many researchers have focused on predictive biomarkers for treatment outcome of targeted therapies in mRCC patients. Attempts to explain differences in efficacy and toxicity of TKIs by use of genetic variants in genes related to the pharmacokinetics and pharmacodynamics of the drug have been successful. <b>Conclusion</b>: Most findings on potential biomarkers have not been validated and therefore biomarker testing to guide choice of therapy and dose in mRCC is not yet feasible.
DOI: 10.6084/m9.figshare.2885308.v252
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.v261
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.2302900
title: A robot sets a table: a case for hybrid reasoning with different types of knowledge

description: An important contribution of AI to Robotics is the model-centred approach, whereby competent robot behaviour stems from automated reasoning in models of the world which can be changed to suit different environments, physical capabilities and tasks. However models need to capture diverse (and often application-dependent) aspects of the robot’s environment and capabilities. They must also have good computational properties, as robots need to reason while they act in response to perceived context. In this article, we investigate the use of a meta-CSP-based technique to interleave reasoning in diverse knowledge types. We reify the approach through a robotic waiter case study, for which a particular selection of spatial, temporal, resource and action KR formalisms is made. Using this case study, we discuss general principles pertaining to the selection of appropriate KR formalisms and jointly reasoning about them. The resulting integration is evaluated both formally and experimentally on real and simulated robotic platforms.
DOI: 10.6084/m9.figshare.2885308.v253
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.v262
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.2302774
title: TAFRO syndrome successfully treated with tocilizumab: A case report and systematic review

description: Thrombocytopenia, anasarca, fever, reticulin fibrosis, and organomegaly (TAFRO) syndrome is considered as a unique clinicopathologic variant of multicentric Castleman’s disease and is recently reported in Japan. This entity represents a severe inflammatory state leading to organ failures such as severe liver dysfunction seen in our case, and can be treated by immunosuppressive agents, steroids, and cyclosporine shown in several case reports. A systematic review and our case suggest the potential utility of tocilizumab as a treatment for TAFRO syndrome.
DOI: 10.6084/m9.figshare.2302774.v1
title: TAFRO syndrome successfully treated with tocilizumab: A case report and systematic review

description: Thrombocytopenia, anasarca, fever, reticulin fibrosis, and organomegaly (TAFRO) syndrome is considered as a unique clinicopathologic variant of multicentric Castleman’s disease and is recently reported in Japan. This entity represents a severe inflammatory state leading to organ failures such as severe liver dysfunction seen in our case, and can be treated by immunosuppressive agents, steroids, and cyclosporine shown in several case reports. A systematic review and our case suggest the potential utility of tocilizumab as a treatment for TAFRO syndrome.
DOI: 10.6084/m9.figshare.2302900.v1
title: A robot sets a table: a case for hybrid reasoning with different types of knowledge

description: An important contribution of AI to Robotics is the model-centred approach, whereby competent robot behaviour stems from automated reasoning in models of the world which can be changed to suit different environments, physical capabilities and tasks. However models need to capture diverse (and often application-dependent) aspects of the robot’s environment and capabilities. They must also have good computational properties, as robots need to reason while they act in response to perceived context. In this article, we investigate the use of a meta-CSP-based technique to interleave reasoning in diverse knowledge types. We reify the approach through a robotic waiter case study, for which a particular selection of spatial, temporal, resource and action KR formalisms is made. Using this case study, we discuss general principles pertaining to the selection of appropriate KR formalisms and jointly reasoning about them. The resulting integration is evaluated both formally and experimentally on real and simulated robotic platforms.
DOI: 10.6084/m9.figshare.2885308.v254
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.v263
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.2301364
title: Connecting Users, Data & Data Repositories

description: Presentation for the Rebecca J Holz Seminar Series in Research Data Management - February 17, 2016.
DOI: 10.6084/m9.figshare.2885308.v255
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.2301364.v1
title: Connecting Users, Data & Data Repositories

description: Presentation for the Rebecca J Holz Seminar Series in Research Data Management - February 17, 2016.
DOI: 10.6084/m9.figshare.2300251
title: Validation of assembled contigs of Hypsibius dujardini genome of Boothby et al. using ultra low input sequencing

description: Extent of microbial contamination in assembled contigs of Hypsibius dujardini genome of Boothby et al. is confirmed by mapping sequence reads obtained from a single individual of H. dujardini Z151 (same strain) using ultra low input sequencing protocol using Thruplex kit (Rubicon Genomics). Mapping was performed using BWA, and mapping statistics are calculated using Qualimap software. <br>As shown in the report, nearly 7000 contigs show coverage &lt; 1, including 11 longest contigs.
DOI: 10.6084/m9.figshare.2951263.v264
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.v256
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.2885308.v257
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.v265
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.2951263.v266
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.2290366
title: Devonian magmatism in the accretionary complex of southern Chile.

description: Table S3. Metasedimentary Rocks
DOI: 10.6084/m9.figshare.2885308.v258
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.2290363
title: Devonian magmatism in the accretionary complex of southern Chile.

description: Table S1. U-Pb SHRIMP data for Devonian rocks
DOI: 10.6084/m9.figshare.2290369
title: Devonian magmatism in the accretionary complex of southern Chile.

description: Table S4. Hf and O isotope data for selected zircons
DOI: 10.6084/m9.figshare.2885308.v259
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.2290360
title: Devonian magmatism in the accretionary complex of southern Chile.

description: Table S2. Post-Devonian Igneous Rocks
DOI: 10.6084/m9.figshare.2951263.v267
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.