cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2598997
title: Various checkpoints prevent the synthesis of <i>Staphylococcus aureus</i> peptidoglycan hydrolase LytM in the stationary growth phase

description: In <i>Staphylococcus aureus</i>, peptidoglycan metabolism plays a role in the host inflammatory response and pathogenesis. Transcription of the peptidoglycan hydrolases is activated by the essential 2-component system WalKR at low cell density. During stationary growth phase, WalKR is not active and transcription of the peptidoglycan hydrolase genes is repressed. In this work, we studied regulation of expression of the glycylglycine endopeptidase LytM. We show that, in addition to the transcriptional regulation mediated by WalKR, the synthesis of LytM is negatively controlled by a unique mechanism at the stationary growth phase. We have identified 2 different mRNAs encoding <i>lytM</i>, which vary in the length of their 5′ untranslated (5′UTR) regions. LytM is predominantly produced from the WalKR-regulated mRNA transcript carrying a short 5′UTR. The <i>lytM</i> mRNA is also transcribed as part of a polycistronic operon with the upstream SA0264 gene and is constitutively expressed. Although SA0264 protein can be synthesized from the longer operon transcript, <i>lytM</i> cannot be translated because its ribosome-binding site is sequestered into a translationally inactive secondary structure. In addition, the effector of the <i>agr</i> system, RNAIII, can inhibit translation of <i>lytM</i> present on the operon without altering the transcript level but does not have an effect on the translation of the upstream gene. We propose that this dual regulation of <i>lytM</i> expression, at the transcriptional and post-transcriptional levels, contributes to prevent cell wall damage during the stationary phase of growth.
DOI: 10.6084/m9.figshare.2951263.v126
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.2597671
title: Misexpression of cyclin D1 in embryonic germ cells promotes testicular teratoma initiation

description: Testicular teratomas result from anomalies in embryonic germ cell development. In the 129 family of inbred mouse strains, teratomas arise during the same developmental period that male germ cells normally enter G1/G0 mitotic arrest and female germ cells initiate meiosis (the mitotic:meiotic switch). Dysregulation of this switch associates with teratoma susceptibility and involves three germ cell developmental abnormalities seemingly critical for tumor initiation: delayed G1/G0 mitotic arrest, retention of pluripotency, and misexpression of genes normally restricted to embryonic female and adult male germ cells. One misexpressed gene, cyclin D1 (<i>Ccnd1</i>), is a known regulator of cell cycle progression and an oncogene in many tissues. Here, we investigated whether <i>Ccnd1</i> misexpression in embryonic germ cells is a determinant of teratoma susceptibility in mice. We found that CCND1 localizes to teratoma-susceptible germ cells that fail to enter G1/G0 arrest during the mitotic:meiotic switch and is the only D-type cyclin misexpressed during this critical developmental time frame. We discovered that <i>Ccnd1</i> deficiency in teratoma-susceptible mice significantly reduced teratoma incidence and suppressed the germ cell proliferation and pluripotency abnormalities associated with tumor initiation. Importantly, <i>Ccnd1</i> expression was dispensable for somatic cell development and male germ cell specification and maturation in tumor-susceptible mice, implying that the mechanisms by which <i>Ccnd1</i> deficiency reduced teratoma incidence were germ cell autonomous and specific to tumorigenesis. We conclude that misexpression of <i>Ccnd1</i> in male germ cells is a key component of a larger pro-proliferative program that disrupts the mitotic:meiotic switch and predisposes 129 inbred mice to testicular teratocarcinogenesis.
DOI: 10.6084/m9.figshare.2597671.v1
title: Misexpression of cyclin D1 in embryonic germ cells promotes testicular teratoma initiation

description: Testicular teratomas result from anomalies in embryonic germ cell development. In the 129 family of inbred mouse strains, teratomas arise during the same developmental period that male germ cells normally enter G1/G0 mitotic arrest and female germ cells initiate meiosis (the mitotic:meiotic switch). Dysregulation of this switch associates with teratoma susceptibility and involves three germ cell developmental abnormalities seemingly critical for tumor initiation: delayed G1/G0 mitotic arrest, retention of pluripotency, and misexpression of genes normally restricted to embryonic female and adult male germ cells. One misexpressed gene, cyclin D1 (<i>Ccnd1</i>), is a known regulator of cell cycle progression and an oncogene in many tissues. Here, we investigated whether <i>Ccnd1</i> misexpression in embryonic germ cells is a determinant of teratoma susceptibility in mice. We found that CCND1 localizes to teratoma-susceptible germ cells that fail to enter G1/G0 arrest during the mitotic:meiotic switch and is the only D-type cyclin misexpressed during this critical developmental time frame. We discovered that <i>Ccnd1</i> deficiency in teratoma-susceptible mice significantly reduced teratoma incidence and suppressed the germ cell proliferation and pluripotency abnormalities associated with tumor initiation. Importantly, <i>Ccnd1</i> expression was dispensable for somatic cell development and male germ cell specification and maturation in tumor-susceptible mice, implying that the mechanisms by which <i>Ccnd1</i> deficiency reduced teratoma incidence were germ cell autonomous and specific to tumorigenesis. We conclude that misexpression of <i>Ccnd1</i> in male germ cells is a key component of a larger pro-proliferative program that disrupts the mitotic:meiotic switch and predisposes 129 inbred mice to testicular teratocarcinogenesis.
DOI: 10.6084/m9.figshare.2598997.v1
title: Various checkpoints prevent the synthesis of <i>Staphylococcus aureus</i> peptidoglycan hydrolase LytM in the stationary growth phase

description: In <i>Staphylococcus aureus</i>, peptidoglycan metabolism plays a role in the host inflammatory response and pathogenesis. Transcription of the peptidoglycan hydrolases is activated by the essential 2-component system WalKR at low cell density. During stationary growth phase, WalKR is not active and transcription of the peptidoglycan hydrolase genes is repressed. In this work, we studied regulation of expression of the glycylglycine endopeptidase LytM. We show that, in addition to the transcriptional regulation mediated by WalKR, the synthesis of LytM is negatively controlled by a unique mechanism at the stationary growth phase. We have identified 2 different mRNAs encoding <i>lytM</i>, which vary in the length of their 5′ untranslated (5′UTR) regions. LytM is predominantly produced from the WalKR-regulated mRNA transcript carrying a short 5′UTR. The <i>lytM</i> mRNA is also transcribed as part of a polycistronic operon with the upstream SA0264 gene and is constitutively expressed. Although SA0264 protein can be synthesized from the longer operon transcript, <i>lytM</i> cannot be translated because its ribosome-binding site is sequestered into a translationally inactive secondary structure. In addition, the effector of the <i>agr</i> system, RNAIII, can inhibit translation of <i>lytM</i> present on the operon without altering the transcript level but does not have an effect on the translation of the upstream gene. We propose that this dual regulation of <i>lytM</i> expression, at the transcriptional and post-transcriptional levels, contributes to prevent cell wall damage during the stationary phase of growth.
DOI: 10.6084/m9.figshare.2885308.v120
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. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v127
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.v121
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. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2885308.v122
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. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v128
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.v129
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.v123
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. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v130
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.v124
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. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2592649
title: Estimating the sensitivity of sagebrush to climate change from muli-year monitoring data

description: Understanding how climate change will affect the abundance of dominant plants is a critical question for conservation in the 21<sup>st</sup> century. We used long-term field observations of sagebrush (<i>Artemisia tridentata</i>) cover and production to estimate sagebrush sensitivity to annual precipitation and temperature across its range. Our analysis draws from 17 published and unpublished datasets and includes 5709 observations of year-to-year change in sagebrush cover or production from 944 monitoring sites located across western North America. We coupled these data with monthly precipitation and temperature data for each site from the PRISM and DAYMET climate datasets. We analyzed the effects of spring through fall temperatures and fall through spring accumulated precipitation on sagebrush abundance observed in each year. Our statistical model allowed these short-term climate effects to vary depending on the long-term average climate of each site. Overall, the sensitivity of sagebrush to annual climate covariates was weak compared to unexplained year-to-year variation. Of the climate covariates tested, average temperature of the preceding three growing seasons had the largest effect: sagebrush responded negatively to warmer years in hotter climates but positively to warmer years in colder climates. Our model predicts that sagebrush cover would show an increase at the coldest sites and a decrease at the warmest sites in response to 2°C of warming. However, 95% confidence intervals around these predicted changes were wide and overlapped zero at most sites, indicating low confidence in these predictions. Our analysis shows how long-term monitoring data can be put to use now to predict the ecological effects of climate change in the near future.
DOI: 10.6084/m9.figshare.2885308.v125
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. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2591968
title: Dimethyl Sulfide is a Chemical Attractant for Reef Fish Larvae

description: Data file used for analysis for each fish larva used in the study. meta_data (i.e., descriptions of the files) included<br>
DOI: 10.6084/m9.figshare.2951263.v131
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.v126
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. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v132
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.2591968.v2
title: Dimethyl Sulfide is a Chemical Attractant for Reef Fish Larvae

description: Data file used for analysis for each fish larva used in the study. meta_data (i.e., descriptions of the files) included<br>
DOI: 10.6084/m9.figshare.2591968.v1
title: Publication Data

description: Data file used for analysis for each fish larva used in the study. meta_data (i.e., descriptions of the files) included<br>
DOI: 10.6084/m9.figshare.2951263.v133
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.v127
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. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v134
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.v128
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. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v135
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.v129
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. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v136
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.2584564
title: Joint Circulation of Viral Diseases in Bat a Population

description: This is a placeholder record for slides to be presented at the 2016 Ecological Society of America Annual Meeting in Ft. Lauderdale.
DOI: 10.6084/m9.figshare.2885308.v130
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. See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v137
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.2592649.v7
title: Estimating the sensitivity of sagebrush to climate change from muli-year monitoring data

description: Understanding how climate change will affect the abundance of dominant plants is a critical question for conservation in the 21<sup>st</sup> century. We used long-term field observations of sagebrush (<i>Artemisia tridentata</i>) cover and production to estimate sagebrush sensitivity to annual precipitation and temperature across its range. Our analysis draws from 17 published and unpublished datasets and includes 5709 observations of year-to-year change in sagebrush cover or production from 944 monitoring sites located across western North America. We coupled these data with monthly precipitation and temperature data for each site from the PRISM and DAYMET climate datasets. We analyzed the effects of spring through fall temperatures and fall through spring accumulated precipitation on sagebrush abundance observed in each year. Our statistical model allowed these short-term climate effects to vary depending on the long-term average climate of each site. Overall, the sensitivity of sagebrush to annual climate covariates was weak compared to unexplained year-to-year variation. Of the climate covariates tested, average temperature of the preceding three growing seasons had the largest effect: sagebrush responded negatively to warmer years in hotter climates but positively to warmer years in colder climates. Our model predicts that sagebrush cover would show an increase at the coldest sites and a decrease at the warmest sites in response to 2°C of warming. However, 95% confidence intervals around these predicted changes were wide and overlapped zero at most sites, indicating low confidence in these predictions. Our analysis shows how long-term monitoring data can be put to use now to predict the ecological effects of climate change in the near future.
DOI: 10.6084/m9.figshare.2582119
title: Gaussian Job Archive for CO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.2592649.v6
title: Estimating the sensitivity of sagebrush to climate change from muli-year monitoring data

description: Understanding how climate change will affect the abundance of dominant plants is a critical question for conservation in the 21<sup>st</sup> century. We used long-term field observations of sagebrush (<i>Artemisia tridentata</i>) cover and production to estimate sagebrush sensitivity to annual precipitation and temperature across its range. Our analysis draws from 17 published and unpublished datasets and includes 5709 observations of year-to-year change in sagebrush cover or production from 944 monitoring sites located across western North America. We coupled these data with monthly precipitation and temperature data for each site from the PRISM and DAYMET climate datasets. We analyzed the effects of spring through fall temperatures and fall through spring accumulated precipitation on sagebrush abundance observed in each year. Our statistical model allowed these short-term climate effects to vary depending on the long-term average climate of each site. Overall, the sensitivity of sagebrush to annual climate covariates was weak compared to unexplained year-to-year variation. Of the climate covariates tested, average temperature of the preceding three growing seasons had the largest effect: sagebrush responded negatively to warmer years in hotter climates but positively to warmer years in colder climates. Our model predicts that sagebrush cover would show an increase at the coldest sites and a decrease at the warmest sites in response to 2°C of warming. However, 95% confidence intervals around these predicted changes were wide and overlapped zero at most sites, indicating low confidence in these predictions. Our analysis shows how long-term monitoring data can be put to use now to predict the ecological effects of climate change in the near future.
DOI: 10.6084/m9.figshare.2582119.v1
title: Gaussian Job Archive for CO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.2951263.v138
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.2582110
title: Stable isotopes - Raw data

description: Raw Data - stable isotopes (moths):Stable isotope fractions (<sup>13</sup>C and <sup>15</sup>N) and C/N ratios for 47 species of moth (Lepidoptera) caught by light trapping in the Danube floodplain forest near Vienna, Austria. specimens fall into eight larval dietary guilds (i.e. aquatic plants, grasses, herbaceous plants, lichens, decaying foliage of (mostly) woody plants, mosses, reeds, and roots).<br>Raw Data - stable isotopes (substrate):Stable isotope fractions (<sup>13</sup>C and <sup>15</sup>N) and C/N ratios for 27 types of substrate corresponding to the eight dietary groups outlined above. Samples were likewise taken from the Danube floodplain forest near Vienna, Austria.