cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1339866
title: Comparison of global and mode of action-based models for aquatic toxicity

description: The ability to estimate aquatic toxicity is a critical need for ecological risk assessment and chemical regulation. The consensus in the literature is that mode of action (MOA) based toxicity models yield the most toxicologically meaningful and, theoretically, the most accurate results. In this study, a two-step prediction methodology was developed to estimate acute aquatic toxicity from molecular structure. In the first step, one-against-the-rest linear discriminant analysis (LDA) models were used to predict the MOA. The LDA models were able to predict the MOA with 85.8–88.8% accuracy for broad and specific MOAs, respectively. In the second step, a multiple linear regression (MLR) model corresponding to the predicted MOA was used to predict the acute aquatic toxicity value. The MOA-based approach was found to yield similar external prediction accuracy (<i>r</i><sup>2</sup> = 0.529–0.632) to a single global MLR model (<i>r</i><sup>2</sup> = 0.551–0.562) fit to the entire training set. Overall, the global hierarchical clustering approach yielded a higher combination of accuracy and prediction coverage (<i>r</i><sup>2</sup> = 0.572, coverage = 99.3%) than the other approaches. Utilizing multiple two-dimensional chemical descriptors in MLR models yielded comparable results to using only the octanol–water partition coefficient (log <i>K</i><sub>ow</sub>).
DOI: 10.6084/m9.figshare.1340078.v8
title: Comprehensive analysis of the ubiquitinome during oncogene-induced senescence in human fibroblasts

description: Oncogene-induced senescence (OIS) is an important tumor suppression mechanism preventing uncontrolled proliferation in response to aberrant oncogenic signaling. The profound functional and morphological remodelling of the senescent cell involves extensive changes. In particular, alterations in protein ubiquitination during senescence have not been systematically analyzed previously. Here, we report the first global ubiquitination profile of primary human cells undergoing senescence. We employed a well-characterized <i>in vitro</i> model of OIS, primary human fibroblasts expressing oncogenic RAS. To compare the ubiquitinome of RAS-induced OIS and controls, ubiquitinated peptides were enriched by immune affinity purification and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 4,472 ubiquitination sites, with 397 sites significantly changed (&gt;3 standard deviations) in senescent cells. In addition, we performed mass spectrometry analysis of total proteins in OIS and control cells to account for parallel changes in both protein abundance and ubiquitin levels that did not affect the percentage of ubiquitination of a given protein. Pathway analysis revealed that the OIS-induced ubiquitinome alterations mainly affected 3 signaling networks: eIF2 signaling, eIF4/p70S6K signaling, and mTOR signaling. Interestingly, the majority of the changed ubiquitinated proteins in these pathways belong to the translation machinery. This includes several translation initiation factors (eIF2C2, eIF2B4, eIF3I, eIF3L, eIF4A1) and elongation factors (eEF1G, eEF1A) as well as 40S (RPS4X, RPS7, RPS11 and RPS20) and 60S ribosomal subunits (RPL10, RPL11, RPL18 and RPL35a). In addition, we observed enriched ubiquitination of aminoacyl-tRNA ligases (isoleucyl-, glutamine-, and tyrosine-tRNA ligase), which provide the amino acid-loaded tRNAs for protein synthesis. These results suggest that ubiquitination affects key components of the translation machinery to regulate protein synthesis during OIS. Our results thus point toward ubiquitination as a hitherto unappreciated regulatory mechanism during OIS.
DOI: 10.6084/m9.figshare.1339866.v1
title: Comparison of global and mode of action-based models for aquatic toxicity

description: The ability to estimate aquatic toxicity is a critical need for ecological risk assessment and chemical regulation. The consensus in the literature is that mode of action (MOA) based toxicity models yield the most toxicologically meaningful and, theoretically, the most accurate results. In this study, a two-step prediction methodology was developed to estimate acute aquatic toxicity from molecular structure. In the first step, one-against-the-rest linear discriminant analysis (LDA) models were used to predict the MOA. The LDA models were able to predict the MOA with 85.8–88.8% accuracy for broad and specific MOAs, respectively. In the second step, a multiple linear regression (MLR) model corresponding to the predicted MOA was used to predict the acute aquatic toxicity value. The MOA-based approach was found to yield similar external prediction accuracy (<i>r</i><sup>2</sup> = 0.529–0.632) to a single global MLR model (<i>r</i><sup>2</sup> = 0.551–0.562) fit to the entire training set. Overall, the global hierarchical clustering approach yielded a higher combination of accuracy and prediction coverage (<i>r</i><sup>2</sup> = 0.572, coverage = 99.3%) than the other approaches. Utilizing multiple two-dimensional chemical descriptors in MLR models yielded comparable results to using only the octanol–water partition coefficient (log <i>K</i><sub>ow</sub>).
DOI: 10.6084/m9.figshare.1340078.v9
title: Comprehensive analysis of the ubiquitinome during oncogene-induced senescence in human fibroblasts

description: Oncogene-induced senescence (OIS) is an important tumor suppression mechanism preventing uncontrolled proliferation in response to aberrant oncogenic signaling. The profound functional and morphological remodelling of the senescent cell involves extensive changes. In particular, alterations in protein ubiquitination during senescence have not been systematically analyzed previously. Here, we report the first global ubiquitination profile of primary human cells undergoing senescence. We employed a well-characterized <i>in vitro</i> model of OIS, primary human fibroblasts expressing oncogenic RAS. To compare the ubiquitinome of RAS-induced OIS and controls, ubiquitinated peptides were enriched by immune affinity purification and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 4,472 ubiquitination sites, with 397 sites significantly changed (&gt;3 standard deviations) in senescent cells. In addition, we performed mass spectrometry analysis of total proteins in OIS and control cells to account for parallel changes in both protein abundance and ubiquitin levels that did not affect the percentage of ubiquitination of a given protein. Pathway analysis revealed that the OIS-induced ubiquitinome alterations mainly affected 3 signaling networks: eIF2 signaling, eIF4/p70S6K signaling, and mTOR signaling. Interestingly, the majority of the changed ubiquitinated proteins in these pathways belong to the translation machinery. This includes several translation initiation factors (eIF2C2, eIF2B4, eIF3I, eIF3L, eIF4A1) and elongation factors (eEF1G, eEF1A) as well as 40S (RPS4X, RPS7, RPS11 and RPS20) and 60S ribosomal subunits (RPL10, RPL11, RPL18 and RPL35a). In addition, we observed enriched ubiquitination of aminoacyl-tRNA ligases (isoleucyl-, glutamine-, and tyrosine-tRNA ligase), which provide the amino acid-loaded tRNAs for protein synthesis. These results suggest that ubiquitination affects key components of the translation machinery to regulate protein synthesis during OIS. Our results thus point toward ubiquitination as a hitherto unappreciated regulatory mechanism during OIS.
DOI: 10.6084/m9.figshare.1340078.v10
title: Comprehensive analysis of the ubiquitinome during oncogene-induced senescence in human fibroblasts

description: Oncogene-induced senescence (OIS) is an important tumor suppression mechanism preventing uncontrolled proliferation in response to aberrant oncogenic signaling. The profound functional and morphological remodelling of the senescent cell involves extensive changes. In particular, alterations in protein ubiquitination during senescence have not been systematically analyzed previously. Here, we report the first global ubiquitination profile of primary human cells undergoing senescence. We employed a well-characterized <i>in vitro</i> model of OIS, primary human fibroblasts expressing oncogenic RAS. To compare the ubiquitinome of RAS-induced OIS and controls, ubiquitinated peptides were enriched by immune affinity purification and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 4,472 ubiquitination sites, with 397 sites significantly changed (&gt;3 standard deviations) in senescent cells. In addition, we performed mass spectrometry analysis of total proteins in OIS and control cells to account for parallel changes in both protein abundance and ubiquitin levels that did not affect the percentage of ubiquitination of a given protein. Pathway analysis revealed that the OIS-induced ubiquitinome alterations mainly affected 3 signaling networks: eIF2 signaling, eIF4/p70S6K signaling, and mTOR signaling. Interestingly, the majority of the changed ubiquitinated proteins in these pathways belong to the translation machinery. This includes several translation initiation factors (eIF2C2, eIF2B4, eIF3I, eIF3L, eIF4A1) and elongation factors (eEF1G, eEF1A) as well as 40S (RPS4X, RPS7, RPS11 and RPS20) and 60S ribosomal subunits (RPL10, RPL11, RPL18 and RPL35a). In addition, we observed enriched ubiquitination of aminoacyl-tRNA ligases (isoleucyl-, glutamine-, and tyrosine-tRNA ligase), which provide the amino acid-loaded tRNAs for protein synthesis. These results suggest that ubiquitination affects key components of the translation machinery to regulate protein synthesis during OIS. Our results thus point toward ubiquitination as a hitherto unappreciated regulatory mechanism during OIS.
DOI: 10.6084/m9.figshare.1340078.v11
title: Comprehensive analysis of the ubiquitinome during oncogene-induced senescence in human fibroblasts

description: Oncogene-induced senescence (OIS) is an important tumor suppression mechanism preventing uncontrolled proliferation in response to aberrant oncogenic signaling. The profound functional and morphological remodelling of the senescent cell involves extensive changes. In particular, alterations in protein ubiquitination during senescence have not been systematically analyzed previously. Here, we report the first global ubiquitination profile of primary human cells undergoing senescence. We employed a well-characterized <i>in vitro</i> model of OIS, primary human fibroblasts expressing oncogenic RAS. To compare the ubiquitinome of RAS-induced OIS and controls, ubiquitinated peptides were enriched by immune affinity purification and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 4,472 ubiquitination sites, with 397 sites significantly changed (&gt;3 standard deviations) in senescent cells. In addition, we performed mass spectrometry analysis of total proteins in OIS and control cells to account for parallel changes in both protein abundance and ubiquitin levels that did not affect the percentage of ubiquitination of a given protein. Pathway analysis revealed that the OIS-induced ubiquitinome alterations mainly affected 3 signaling networks: eIF2 signaling, eIF4/p70S6K signaling, and mTOR signaling. Interestingly, the majority of the changed ubiquitinated proteins in these pathways belong to the translation machinery. This includes several translation initiation factors (eIF2C2, eIF2B4, eIF3I, eIF3L, eIF4A1) and elongation factors (eEF1G, eEF1A) as well as 40S (RPS4X, RPS7, RPS11 and RPS20) and 60S ribosomal subunits (RPL10, RPL11, RPL18 and RPL35a). In addition, we observed enriched ubiquitination of aminoacyl-tRNA ligases (isoleucyl-, glutamine-, and tyrosine-tRNA ligase), which provide the amino acid-loaded tRNAs for protein synthesis. These results suggest that ubiquitination affects key components of the translation machinery to regulate protein synthesis during OIS. Our results thus point toward ubiquitination as a hitherto unappreciated regulatory mechanism during OIS.
DOI: 10.6084/m9.figshare.1340078.v12
title: Comprehensive analysis of the ubiquitinome during oncogene-induced senescence in human fibroblasts

description: Oncogene-induced senescence (OIS) is an important tumor suppression mechanism preventing uncontrolled proliferation in response to aberrant oncogenic signaling. The profound functional and morphological remodelling of the senescent cell involves extensive changes. In particular, alterations in protein ubiquitination during senescence have not been systematically analyzed previously. Here, we report the first global ubiquitination profile of primary human cells undergoing senescence. We employed a well-characterized <i>in vitro</i> model of OIS, primary human fibroblasts expressing oncogenic RAS. To compare the ubiquitinome of RAS-induced OIS and controls, ubiquitinated peptides were enriched by immune affinity purification and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 4,472 ubiquitination sites, with 397 sites significantly changed (&gt;3 standard deviations) in senescent cells. In addition, we performed mass spectrometry analysis of total proteins in OIS and control cells to account for parallel changes in both protein abundance and ubiquitin levels that did not affect the percentage of ubiquitination of a given protein. Pathway analysis revealed that the OIS-induced ubiquitinome alterations mainly affected 3 signaling networks: eIF2 signaling, eIF4/p70S6K signaling, and mTOR signaling. Interestingly, the majority of the changed ubiquitinated proteins in these pathways belong to the translation machinery. This includes several translation initiation factors (eIF2C2, eIF2B4, eIF3I, eIF3L, eIF4A1) and elongation factors (eEF1G, eEF1A) as well as 40S (RPS4X, RPS7, RPS11 and RPS20) and 60S ribosomal subunits (RPL10, RPL11, RPL18 and RPL35a). In addition, we observed enriched ubiquitination of aminoacyl-tRNA ligases (isoleucyl-, glutamine-, and tyrosine-tRNA ligase), which provide the amino acid-loaded tRNAs for protein synthesis. These results suggest that ubiquitination affects key components of the translation machinery to regulate protein synthesis during OIS. Our results thus point toward ubiquitination as a hitherto unappreciated regulatory mechanism during OIS.
DOI: 10.6084/m9.figshare.1339843
title: Raw data for the role of acetyl phosphate in bypassing the cell membrane electrical potential sensor LytS

description: Data 1<br>Autophosphorylation of LytS.<br>Quantification of phosphorylated LytS bands by NIH Image J. Average of two trials. Data 2<br>Phosphorylation of LytR by acetyl phosphate.<br>Quantification of phosphorylated LytR bands by NIH ImageJ. Data 3<br>Phosphorylation of LytR-N by acetyl phosphate.<br>Quantification of phosphorylated LytR-N bands by NIH ImageJ. Data 4<br>Quantification of LytR bands in native-PAGEs (Figure 6A and B) by NIH Image J. LytR protein was phosphorylated by acetyl phosphate and its dephosphorylation by LytS was monitored by native-PAGE, whereby the phosphorylated dimer LytR becomes monomer after dephosphorylation. The column “corrected” represents the data after correcting for background signal at 0 min, and considering the band labeled “Monomer”, in the absence of LytS and ATP, as 100% unphosphorylated LytR.
DOI: 10.6084/m9.figshare.1339843.v1
title: Raw data for the role of acetyl phosphate in bypassing the cell membrane electrical potential sensor LytS

description: Data 1<br>Autophosphorylation of LytS.<br>Quantification of phosphorylated LytS bands by NIH Image J. Average of two trials. Data 2<br>Phosphorylation of LytR by acetyl phosphate.<br>Quantification of phosphorylated LytR bands by NIH ImageJ. Data 3<br>Phosphorylation of LytR-N by acetyl phosphate.<br>Quantification of phosphorylated LytR-N bands by NIH ImageJ. Data 4<br>Quantification of LytR bands in native-PAGEs (Figure 6A and B) by NIH Image J. LytR protein was phosphorylated by acetyl phosphate and its dephosphorylation by LytS was monitored by native-PAGE, whereby the phosphorylated dimer LytR becomes monomer after dephosphorylation. The column “corrected” represents the data after correcting for background signal at 0 min, and considering the band labeled “Monomer”, in the absence of LytS and ATP, as 100% unphosphorylated LytR.
DOI: 10.6084/m9.figshare.1339514
title: Renaming Seattle

description: This is a corrected, tabular format of City of Seattle Ordinance 4044, “An ordinance changing the names of certain streets and avenues in the City of Seattle,” which passed on December 23, 1895 and rewrote the landscape of the city.
DOI: 10.6084/m9.figshare.1340078.v13
title: Comprehensive analysis of the ubiquitinome during oncogene-induced senescence in human fibroblasts

description: Oncogene-induced senescence (OIS) is an important tumor suppression mechanism preventing uncontrolled proliferation in response to aberrant oncogenic signaling. The profound functional and morphological remodelling of the senescent cell involves extensive changes. In particular, alterations in protein ubiquitination during senescence have not been systematically analyzed previously. Here, we report the first global ubiquitination profile of primary human cells undergoing senescence. We employed a well-characterized <i>in vitro</i> model of OIS, primary human fibroblasts expressing oncogenic RAS. To compare the ubiquitinome of RAS-induced OIS and controls, ubiquitinated peptides were enriched by immune affinity purification and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 4,472 ubiquitination sites, with 397 sites significantly changed (&gt;3 standard deviations) in senescent cells. In addition, we performed mass spectrometry analysis of total proteins in OIS and control cells to account for parallel changes in both protein abundance and ubiquitin levels that did not affect the percentage of ubiquitination of a given protein. Pathway analysis revealed that the OIS-induced ubiquitinome alterations mainly affected 3 signaling networks: eIF2 signaling, eIF4/p70S6K signaling, and mTOR signaling. Interestingly, the majority of the changed ubiquitinated proteins in these pathways belong to the translation machinery. This includes several translation initiation factors (eIF2C2, eIF2B4, eIF3I, eIF3L, eIF4A1) and elongation factors (eEF1G, eEF1A) as well as 40S (RPS4X, RPS7, RPS11 and RPS20) and 60S ribosomal subunits (RPL10, RPL11, RPL18 and RPL35a). In addition, we observed enriched ubiquitination of aminoacyl-tRNA ligases (isoleucyl-, glutamine-, and tyrosine-tRNA ligase), which provide the amino acid-loaded tRNAs for protein synthesis. These results suggest that ubiquitination affects key components of the translation machinery to regulate protein synthesis during OIS. Our results thus point toward ubiquitination as a hitherto unappreciated regulatory mechanism during OIS.
DOI: 10.6084/m9.figshare.1339031
title: Results of 2015 Amnesty International / Yougov poll on government mass surveillance

description: This archive contains aggregate and raw data associated with the 2015 Amnesty International survey on government mass surveillance.
DOI: 10.6084/m9.figshare.1339514.v1
title: Renaming Seattle's Streets: 1895 Ordinance Number 4044

description: This is a corrected, tabular format of City of Seattle Ordinance 4044, “An ordinance changing the names of certain streets and avenues in the City of Seattle,” which passed on December 23, 1895 and rewrote the landscape of the city.
DOI: 10.6084/m9.figshare.1337937
title: Nucella lapillus transcriptome annotation

description: This directory contains the process and products for a Nucella lapillus transcriptome annotation. This directory was created as part of the Fish 546 course at the University of Washington with Dr. Steven Roberts during Winter 2015.
DOI: 10.6084/m9.figshare.1337938
title: Gaussian Job Archive for C2H5F6NO6S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1337937.v1
title: Nucella lapillus transcriptome annotation

description: This directory contains the process and products for a Nucella lapillus transcriptome annotation. This directory was created as part of the Fish 546 course at the University of Washington with Dr. Steven Roberts during Winter 2015.
DOI: 10.6084/m9.figshare.1337938.v1
title: Gaussian Job Archive for C2H5F6NO6S2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1337912
title: study_level _variables.sav

description: Data for the manuscript: A Cross-Cultural Perspective on the Preference for Potential Effect
DOI: 10.6084/m9.figshare.1337913
title: individual_level_variables.sav

description: Data for the manuscript: A Cross-Cultural Perspective on the Preference for Potential Effect.
DOI: 10.6084/m9.figshare.1337910
title: COS Test files

description: This isn't an actual research. These filesets are for testing purposes only.
DOI: 10.6084/m9.figshare.1337913.v1
title: individual_level_variables.sav

description: Data for the manuscript: A Cross-Cultural Perspective on the Preference for Potential Effect.
DOI: 10.6084/m9.figshare.1337912.v1
title: study_level _variables.sav

description: Data for the manuscript: A Cross-Cultural Perspective on the Preference for Potential Effect
DOI: 10.6084/m9.figshare.1337907
title: Archaeology journal articles from JSTOR DFR

description: Archaeology journal articles from JSTOR DFR for use with https://github.com/benmarwick/textual-macroanalysis-gender-archaeology
DOI: 10.6084/m9.figshare.1337907.v2
title: Archaeology journal articles from JSTOR DFR

description: Archaeology journal articles from JSTOR DFR for use with https://github.com/benmarwick/textual-macroanalysis-gender-archaeology
DOI: 10.6084/m9.figshare.1337898
title: Geochronology and geochemical evidence for a magmatic arc setting for the Ni-Cu mineralised 1.79 Ga Kleva gabbro–diorite intrusive complex, southeast Sweden

description: Magmatic Ni-Cu sulphide deposits are commonly associated with mafic rocks within the marginal areas of Archean or Proterozoic cratons. The Kleva Ni-Cu sulphide deposit in southeast Sweden is hosted by gabbro–diorite rocks and is sandwiched between two Palaeoproterozoic magmatic arcs: the Transscandinavian Igneous Belt (TIB) and the Oskarshamn–Jönköping Belt (OJB). Major and trace element data corroborate an arc origin for the Kleva intrusive complex. The variety of rocks and geochemical signatures suggest that it formed from several magmatic pulses. Despite the occurrence of supracrustal xenoliths, there is a lack of trace element evidence for significant assimilation. Mafic intrusions are abundant in southeast Sweden and are generally inferred to be synchronous with the TIB. Of these, Kleva is the only known Ni-Cu deposit, and it is unclear if it is associated with the OJB or TIB. Here, we present zircon and baddeleyite U-Pb dates of 1788 ± 4 Ma, 1788 ± 5 Ma and 1792 ± 3 Ma. We interpret a 1790 Ma date to be the best estimate of the crystallisation age of the Kleva intrusive complex, indicating that the emplacement of mafic magma is coeval with the voluminous arc-related TIB magmatism in the area.
DOI: 10.6084/m9.figshare.1337907.v1
title: Archaeology journal articles from JSTOR DFR

description: Archaeology journal articles from JSTOR DFR
DOI: 10.6084/m9.figshare.1337910.v2
title: COS Test files

description: This does not include an actual research. These filesets are for testing purposes only.
DOI: 10.6084/m9.figshare.1337897
title: ToPunishOrToLeave_Codebook

description: Codebook for dataset for results published in "To punish or to leave: Distinct cognitive processes underlie partner control and partner choice behaviors"
DOI: 10.6084/m9.figshare.1337897.v1
title: ToPunishOrToLeave_Codebook

description: Codebook for dataset for results published in "To punish or to leave: Distinct cognitive processes underlie partner control and partner choice behaviors"