cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1340007
title: University of Salford APCs 2014

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Salford during 2014. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/) and has been released with permission of the University of Salford Library.
DOI: 10.6084/m9.figshare.1340021.v1
title: 2 Police Officers shot during Ferguson protest Co-Retweeted Network

description: The Co-Retweeted network of users tweeting about the two Ferguson police officers who were shot during a protest March 12, 2015.
DOI: 10.6084/m9.figshare.1340007.v1
title: University of Salford APCs 2014

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Salford during 2014. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/) and has been released with permission of the University of Salford Library.
DOI: 10.6084/m9.figshare.1340078.v3
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.1340004
title: ISOMEROS

description: YARLEDIS SUAREZ ERWIN SEQUEDA RUBEN CAMARGO
DOI: 10.6084/m9.figshare.1340005
title: Whittals thesis design guide

description: This is an infographic summarising the design of a standard thesis document at all levels. It is not directive and chapters can be merged, or content spread into each chapter as directed by the supervisor. It is, however, a point of departure and shows the link between theory, methods and analysis as well as between data - informaion - meaning. At the bottom it also summarizes the intention of each chapter as this is what students seem to struggle with. Note that due to space the conclusions are not in the table - see note beneath.
DOI: 10.6084/m9.figshare.1339970
title: Fecal nitrogen concentration as a nutritional quality indicator for European rabbit ecological studies: Datasets

description: Supporting datasets for the accepted article: TITLE: Fecal nitrogen concentration as a nutritional quality indicator for European rabbit ecological studies. AUTHORS: Esperanza Gil-Jiménez, Miriam Villamuelas, Emmanuel Serrano, Miguel Delibes, Néstor Fernández JOURNAL: PLOS ONE YEAR: 2015
DOI: 10.6084/m9.figshare.1340003
title: Emotionally biased cognitive processes

description: Emotional biases in attention, interpretation, and memory are predictive of future depressive symptoms. It remains unknown, however, how these biased cognitive processes interact to predict depressive symptom levels in the long-term. In the present study, we tested the predictive value of two integrative approaches to model relations between multiple biased cognitive processes, namely the additive (i.e., cognitive processes have a cumulative effect) vs. the weakest link (i.e., the dominant pathogenic process is important) model. We also tested whether these integrative models interacted with perceived stress to predict prospective changes in depressive symptom severity. At Time 1, participants completed measures of depressive symptom severity and emotional biases in attention, interpretation, and memory. At Time 2, one year later, participants were reassessed to determine depressive symptom levels and perceived stress. Results revealed that the weakest link model had incremental validity over the additive model in predicting prospective changes in depressive symptoms, though both models explained a significant proportion of variance in the change in depressive symptoms from Time 1 to Time 2. None of the integrative models interacted with perceived stress to predict changes in depressive symptomatology. These findings suggest that the best cognitive marker of the evolution in depressive symptoms is the cognitive process that is dominantly biased toward negative material, which operates independent from experienced stress. This highlights the importance of considering idiographic cognitive profiles with multiple cognitive processes for understanding and modifying effects of cognitive biases in depression.
DOI: 10.6084/m9.figshare.1339970.v1
title: Fecal nitrogen concentration as a nutritional quality indicator for European rabbit ecological studies: Datasets

description: Supporting datasets for the accepted article: TITLE: Fecal nitrogen concentration as a nutritional quality indicator for European rabbit ecological studies. AUTHORS: Esperanza Gil-Jiménez, Miriam Villamuelas, Emmanuel Serrano, Miguel Delibes, Néstor Fernández JOURNAL: PLOS ONE YEAR: 2015
DOI: 10.6084/m9.figshare.1340003.v1
title: Emotionally biased cognitive processes

description: Emotional biases in attention, interpretation, and memory are predictive of future depressive symptoms. It remains unknown, however, how these biased cognitive processes interact to predict depressive symptom levels in the long-term. In the present study, we tested the predictive value of two integrative approaches to model relations between multiple biased cognitive processes, namely the additive (i.e., cognitive processes have a cumulative effect) vs. the weakest link (i.e., the dominant pathogenic process is important) model. We also tested whether these integrative models interacted with perceived stress to predict prospective changes in depressive symptom severity. At Time 1, participants completed measures of depressive symptom severity and emotional biases in attention, interpretation, and memory. At Time 2, one year later, participants were reassessed to determine depressive symptom levels and perceived stress. Results revealed that the weakest link model had incremental validity over the additive model in predicting prospective changes in depressive symptoms, though both models explained a significant proportion of variance in the change in depressive symptoms from Time 1 to Time 2. None of the integrative models interacted with perceived stress to predict changes in depressive symptomatology. These findings suggest that the best cognitive marker of the evolution in depressive symptoms is the cognitive process that is dominantly biased toward negative material, which operates independent from experienced stress. This highlights the importance of considering idiographic cognitive profiles with multiple cognitive processes for understanding and modifying effects of cognitive biases in depression.
DOI: 10.6084/m9.figshare.1340004.v3
title: Isomeros-Jose Jarava

description: JOSE JARAVA JUAN TOVAR YESID CASTILLO
DOI: 10.6084/m9.figshare.1340078.v4
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.1339938
title: An alternative approach to transverse and profile terrain curvature

description: Terrain curvature is one of the most important parameters of land surface topography. Well-established methods used in its measurement compute an index of plan or profile curvature for every single cell of a digital elevation model (DEM). The interpretation of these outputs may be delicate, especially when selected locations have to be analyzed. Furthermore, they involve a high level of simplification, contrasting with the complex and multiscalar nature of the surface curvature itself. In this paper, we present a new method to assess vertical transverse and profile curvature combining real-scale visualization and the possibility to measure these two terrain derivatives over a large range of scales. To this purpose, we implemented a GIS tool that extracts longitudinal and transverse elevation profiles from a high-resolution DEM. The performance of our approach was compared with some of the most commonly used methods (ArcMap, Redlands, CA, USA; ArcSIE, Landserf) by analyzing the terrain curvature around charcoal production sites in southern Switzerland. The different methods produced comparable results. While conventional methods quickly summarize terrain curvature in the form of a matrix of values, they involve a loss of information. The advantage of the new method lies in the possibility to measure and visualize the shape and size of the curvature, and to obtain a realistic representation of the average curvature for different subsets of spatial points. Moreover, the new method makes it possible to control the conditions in which the index of curvature is calculated.
DOI: 10.6084/m9.figshare.1340004.v4
title: ISOMEROS

description: YARLEDIS SUAREZ ERWIN SEQUEDA RUBEN CAMARGO
DOI: 10.6084/m9.figshare.1340078.v5
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.1340004.v6
title: ISOMEROS

description: YARLEDIS SUAREZ ERWIN SEQUEDA RUBEN CAMARGO
DOI: 10.6084/m9.figshare.1339938.v2
title: An alternative approach to transverse and profile terrain curvature

description: Terrain curvature is one of the most important parameters of land surface topography. Well-established methods used in its measurement compute an index of plan or profile curvature for every single cell of a digital elevation model (DEM). The interpretation of these outputs may be delicate, especially when selected locations have to be analyzed. Furthermore, they involve a high level of simplification, contrasting with the complex and multiscalar nature of the surface curvature itself. In this paper, we present a new method to assess vertical transverse and profile curvature combining real-scale visualization and the possibility to measure these two terrain derivatives over a large range of scales. To this purpose, we implemented a GIS tool that extracts longitudinal and transverse elevation profiles from a high-resolution DEM. The performance of our approach was compared with some of the most commonly used methods (ArcMap, Redlands, CA, USA; ArcSIE, Landserf) by analyzing the terrain curvature around charcoal production sites in southern Switzerland. The different methods produced comparable results. While conventional methods quickly summarize terrain curvature in the form of a matrix of values, they involve a loss of information. The advantage of the new method lies in the possibility to measure and visualize the shape and size of the curvature, and to obtain a realistic representation of the average curvature for different subsets of spatial points. Moreover, the new method makes it possible to control the conditions in which the index of curvature is calculated.
DOI: 10.6084/m9.figshare.1340004.v5
title: ISOMEROS

description: YARLEDIS SUAREZ ERWIN SEQUEDA RUBEN CAMARGO
DOI: 10.6084/m9.figshare.1340078.v6
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.1339938.v1
title: An alternative approach to transverse and profile terrain curvature

description: Terrain curvature is one of the most important parameters of land surface topography. Well-established methods used in its measurement compute an index of plan or profile curvature for every single cell of a digital elevation model (DEM). The interpretation of these outputs may be delicate, especially when selected locations have to be analyzed. Furthermore, they involve a high level of simplification, contrasting with the complex and multiscalar nature of the surface curvature itself. In this paper, we present a new method to assess vertical transverse and profile curvature combining real-scale visualization and the possibility to measure these two terrain derivatives over a large range of scales. To this purpose, we implemented a GIS tool that extracts longitudinal and transverse elevation profiles from a high-resolution DEM. The performance of our approach was compared with some of the most commonly used methods (ArcMap, Redlands, CA, USA; ArcSIE, Landserf) by analyzing the terrain curvature around charcoal production sites in southern Switzerland. The different methods produced comparable results. While conventional methods quickly summarize terrain curvature in the form of a matrix of values, they involve a loss of information. The advantage of the new method lies in the possibility to measure and visualize the shape and size of the curvature, and to obtain a realistic representation of the average curvature for different subsets of spatial points. Moreover, the new method makes it possible to control the conditions in which the index of curvature is calculated.
DOI: 10.6084/m9.figshare.1340078.v7
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.