cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5223583
title: Indian Zoroastrian and Indian Hindu genotype data from Lopez et al. 17

description: Indian Zoroastrian and Indian Hindu genotype data in plink binary format from Lopez et al. 2017: The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection.<br><br>Not for commercial purposes.<br>
DOI: 10.6084/m9.figshare.5221963
title: Additive Function-on-Function Regression

description: We study additive function-on-function regression where the mean response at a particular time point depends on the time point itself, as well as the entire covariate trajectory. We develop a computationally efficient estimation methodology based on a novel combination of spline bases with an eigenbasis to represent the trivariate kernel function. We discuss prediction of a new response trajectory, propose an inference procedure that accounts for total variability in the predicted response curves, and construct pointwise prediction intervals. The estimation/inferential procedure accommodates realistic scenarios, such as correlated error structure as well as sparse and/or irregular designs. We investigate our methodology in finite sample size through simulations and two real data applications. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5221963.v1
title: Additive Function-on-Function Regression

description: We study additive function-on-function regression where the mean response at a particular time point depends on the time point itself, as well as the entire covariate trajectory. We develop a computationally efficient estimation methodology based on a novel combination of spline bases with an eigenbasis to represent the trivariate kernel function. We discuss prediction of a new response trajectory, propose an inference procedure that accounts for total variability in the predicted response curves, and construct pointwise prediction intervals. The estimation/inferential procedure accommodates realistic scenarios, such as correlated error structure as well as sparse and/or irregular designs. We investigate our methodology in finite sample size through simulations and two real data applications. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5221603
title: Mechanism for G2 phase-specific nuclear export of the kinetochore protein CENP-F

description: Centromere protein F (CENP-F) is a component of the kinetochore and a regulator of cell cycle progression. CENP-F recruits the dynein transport machinery and orchestrates several cell cycle-specific transport events, including transport of the nucleus, mitochondria and chromosomes. A key regulatory step for several of these functions is likely the G2 phase-specific export of CENP-F from the nucleus to the cytosol, where the cytoplasmic dynein transport machinery resides; however, the molecular mechanism of this process is elusive. Here, we have identified 3 phosphorylation sites within the bipartite classical nuclear localization signal (cNLS) of CENP-F. These sites are specific for cyclin-dependent kinase 1 (Cdk1), which is active in G2 phase. Phosphomimetic mutations of these residues strongly diminish the interaction of the CENP-F cNLS with its nuclear transport receptor karyopherin α. These mutations also diminish nuclear localization of the CENP-F cNLS in cells. Notably, the cNLS is phosphorylated in the −1 position, which is important to orient the adjacent major motif for binding into its pocket on karyopherin α. We propose that localization of CENP-F is regulated by a cNLS, and a nuclear export pathway, resulting in nuclear localization during most of interphase. In G2 phase, the cNLS is weakened by phosphorylation through Cdk1, likely resulting in nuclear export of CENP-F via the still active nuclear export pathway. Once CENP-F resides in the cytosol, it can engage in pathways that are important for cell cycle progression, kinetochore assembly and the faithful segregation of chromosomes into daughter cells.
DOI: 10.6084/m9.figshare.5221321
title: Creative Foraging Game Data (1.0)

description: Raw-data and data description for the following paper:<b><br></b><b>Creative Foraging: an Experimental Paradigm for Studying Exploration and </b><b>Discovery</b>Yuval Hart, Avraham E Mayo, Ruth Mayo, Liron Rozenkrantz, Avichai Tendler, Uri Alon*, and Lior Noy*PLOS ONE, 2017 (in press)-------Version 1.0, with 100 games corresponding to the paper<br>
DOI: 10.6084/m9.figshare.5221351
title: Aggregated Synthesis Parameters for Oxide Materials

description: Text-mined and aggregated synthesis parameters for a collection of inorganic oxides. Provided as a single JSON document.<br>
DOI: 10.6084/m9.figshare.5221306
title: Metal content of commodities

description: This is a dataset of the approximate contentation of the materials steel, plastics, paper, and cement and of the metals Fe, Cu, Al, Cr, Mn, Mo, and V of ca. 4000 Commodity groups in the Eurostat ProdCom database. (NACE v2)<br>The dataset was developed for the following work:<br>"Quantifying Impacts of Consumption Based Charge for Carbon Intensive Materials on Products " Stefan Pauliuk, Karsten Neuhoff, Anne Owen, Richard Wood DIW Discussion paper 1570, German Institute for Economic Research, Berlin.
DOI: 10.6084/m9.figshare.5221321.v1
title: Creative Foraging Game Data (1.0)

description: Raw-data and data description for the following paper:<b><br></b><b>Creative Foraging: an Experimental Paradigm for Studying Exploration and </b><b>Discovery</b>Yuval Hart, Avraham E Mayo, Ruth Mayo, Liron Rozenkrantz, Avichai Tendler, Uri Alon*, and Lior Noy*PLOS ONE, 2017 (in press)-------Version 1.0, with 100 games corresponding to the paper<br>
DOI: 10.6084/m9.figshare.5221285
title: Diffusion-weighted magnetic resonance imaging of parotid glands before and after abatacept therapy in patients with Sjögren’s syndrome associated with rheumatoid arthritis: Utility to evaluate and predict response to treatment

description: <b>Objective:</b> To compare parotid diffusion-weighted images (DWIs) taken before and after abatacept therapy in patients with Sjögren’s syndrome (SS) associated with rheumatoid arthritis (RA) and to examine the utility in evaluation and prediction of response to therapy. <b>Methods:</b> DWIs of the parotid glands taken at baseline and 52 weeks after initiation of abatacept were analyzed in nine SS patients with RA using relative standard deviation (RSD) of the entire glands and signal intensity ratio (SIR) within the residual parenchyma. The correlation between changes in RSD and SIR and changes in salivary secretion based on Saxon’s test was examined. Furthermore, baseline characteristics were compared in patients with increased and decreased salivary secretion after treatment. The predictive power of the parameter at baseline was examined using receiver operating characteristic (ROC) analysis. <b>Results:</b> Abatacept improved salivary secretion from 2076 ± 1535 at baseline to 2857 ± 1431 mg/2 min at 52 weeks (<i>n</i> = 9, <i>p</i> = .05). Increase of salivary secretion was significantly higher in patients with decreased RSD (<i>n</i> = 6) than increased RSD (<i>n</i> = 3) (1241 ± 713, –137 ± 142 mg/2 min, <i>p</i> = .02). The increase and decrease in RSD completely accorded with those of salivary secretion. Furthermore, SIR was the only parameter that was significantly different between patients with posttreatment increase and decrease in salivary secretion (<i>p</i> = .04). ROC analysis showed the sensitivity and specificity of SIR at baseline of ≥13.0 × 10<sup>−2</sup> for the prediction of the response to abatacept were 75.0% and 83.3%, respectively. <b>Conclusions:</b> Parotid DWI seems to be useful for evaluating and predicting the response in salivary secretion to abatacept in SS patients with RA.
DOI: 10.6084/m9.figshare.5221285.v1
title: Diffusion-weighted magnetic resonance imaging of parotid glands before and after abatacept therapy in patients with Sjögren’s syndrome associated with rheumatoid arthritis: Utility to evaluate and predict response to treatment

description: <b>Objective:</b> To compare parotid diffusion-weighted images (DWIs) taken before and after abatacept therapy in patients with Sjögren’s syndrome (SS) associated with rheumatoid arthritis (RA) and to examine the utility in evaluation and prediction of response to therapy. <b>Methods:</b> DWIs of the parotid glands taken at baseline and 52 weeks after initiation of abatacept were analyzed in nine SS patients with RA using relative standard deviation (RSD) of the entire glands and signal intensity ratio (SIR) within the residual parenchyma. The correlation between changes in RSD and SIR and changes in salivary secretion based on Saxon’s test was examined. Furthermore, baseline characteristics were compared in patients with increased and decreased salivary secretion after treatment. The predictive power of the parameter at baseline was examined using receiver operating characteristic (ROC) analysis. <b>Results:</b> Abatacept improved salivary secretion from 2076 ± 1535 at baseline to 2857 ± 1431 mg/2 min at 52 weeks (<i>n</i> = 9, <i>p</i> = .05). Increase of salivary secretion was significantly higher in patients with decreased RSD (<i>n</i> = 6) than increased RSD (<i>n</i> = 3) (1241 ± 713, –137 ± 142 mg/2 min, <i>p</i> = .02). The increase and decrease in RSD completely accorded with those of salivary secretion. Furthermore, SIR was the only parameter that was significantly different between patients with posttreatment increase and decrease in salivary secretion (<i>p</i> = .04). ROC analysis showed the sensitivity and specificity of SIR at baseline of ≥13.0 × 10<sup>−2</sup> for the prediction of the response to abatacept were 75.0% and 83.3%, respectively. <b>Conclusions:</b> Parotid DWI seems to be useful for evaluating and predicting the response in salivary secretion to abatacept in SS patients with RA.
DOI: 10.6084/m9.figshare.5221258
title: The greatwall kinase is dominant over PKA in controlling the antagonistic function of ARPP19 in <i>Xenopus</i> oocytes

description: The small protein ARPP19 plays a dual role during oocyte meiosis resumption. In <i>Xenopus</i>, ARPP19 phosphorylation at S109 by PKA is necessary for maintaining oocytes arrested in prophase of the first meiotic division. Progesterone downregulates PKA, leading to the dephosphorylation of ARPP19 at S109. This initiates a transduction pathway ending with the activation of the universal inducer of M-phase, the kinase Cdk1. This last step depends on ARPP19 phosphorylation at S67 by the kinase Greatwall. Hence, phosphorylated by PKA at S109, ARPP19 restrains Cdk1 activation while when phosphorylated by Greatwall at S67, ARPP19 becomes an inducer of Cdk1 activation. Here, we investigate the functional interplay between S109 and S67-phosphorylations of ARPP19. We show that both PKA and Gwl phosphorylate ARPP19 independently of each other and that Cdk1 is not directly involved in regulating the biological activity of ARPP19. We also show that the phosphorylation of ARPP19 at S67 that activates Cdk1, is dominant over the inhibitory S109 phosphorylation. Therefore our results highlight the importance of timely synchronizing ARPP19 phosphorylations at S109 and S67 to fully activate Cdk1.
DOI: 10.6084/m9.figshare.5221258.v2
title: The greatwall kinase is dominant over PKA in controlling the antagonistic function of ARPP19 in <i>Xenopus</i> oocytes

description: The small protein ARPP19 plays a dual role during oocyte meiosis resumption. In <i>Xenopus</i>, ARPP19 phosphorylation at S109 by PKA is necessary for maintaining oocytes arrested in prophase of the first meiotic division. Progesterone downregulates PKA, leading to the dephosphorylation of ARPP19 at S109. This initiates a transduction pathway ending with the activation of the universal inducer of M-phase, the kinase Cdk1. This last step depends on ARPP19 phosphorylation at S67 by the kinase Greatwall. Hence, phosphorylated by PKA at S109, ARPP19 restrains Cdk1 activation while when phosphorylated by Greatwall at S67, ARPP19 becomes an inducer of Cdk1 activation. Here, we investigate the functional interplay between S109 and S67-phosphorylations of ARPP19. We show that both PKA and Gwl phosphorylate ARPP19 independently of each other and that Cdk1 is not directly involved in regulating the biological activity of ARPP19. We also show that the phosphorylation of ARPP19 at S67 that activates Cdk1, is dominant over the inhibitory S109 phosphorylation. Therefore our results highlight the importance of timely synchronizing ARPP19 phosphorylations at S109 and S67 to fully activate Cdk1.
DOI: 10.6084/m9.figshare.5221258.v1
title: The Greatwall kinase is dominant over PKA in controlling the antagonistic function of ARPP19 in <i>Xenopus</i> oocytes

description: The small protein ARPP19 plays a dual role during oocyte meiosis resumption. In <i>Xenopus</i>, ARPP19 phosphorylation at S109 by PKA is necessary for maintaining oocytes arrested in prophase of the first meiotic division. Progesterone downregulates PKA, leading to the dephosphorylation of ARPP19 at S109. This initiates a transduction pathway ending with the activation of the universal inducer of M-phase, the kinase Cdk1. This last step depends on ARPP19 phosphorylation at S67 by the kinase Greatwall. Hence, phosphorylated by PKA at S109, ARPP19 restrains Cdk1 activation while when phosphorylated by Greatwall at S67, ARPP19 becomes an inducer of Cdk1 activation. Here, we investigate the functional interplay between S109 and S67-phosphorylations of ARPP19. We show that both PKA and Gwl phosphorylate ARPP19 independently of each other and that Cdk1 is not directly involved in regulating the biological activity of ARPP19. We also show that the phosphorylation of ARPP19 at S67 that activates Cdk1, is dominant over the inhibitory S109 phosphorylation. Therefore our results highlight the importance of timely synchronizing ARPP19 phosphorylations at S109 and S67 to fully activate Cdk1.
DOI: 10.6084/m9.figshare.5221252
title: An autophagy-driven pathway of ATP secretion supports the aggressive phenotype of BRAF<sup>V600E</sup> inhibitor-resistant metastatic melanoma cells

description: The ingrained capacity of melanoma cells to rapidly evolve toward an aggressive phenotype is manifested by their increased ability to develop drug-resistance, evident in the case of vemurafenib, a therapeutic-agent targeting BRAF<sup>V600E</sup>. Previous studies indicated a tight correlation between heightened melanoma-associated macroautophagy/autophagy and acquired Vemurafenib resistance. However, how this vesicular trafficking pathway supports Vemurafenib resistance remains unclear. Here, using isogenic human and murine melanoma cell lines of Vemurafenib-resistant and patient-derived melanoma cells with primary resistance to the BRAF<sup>V600E</sup> inhibitor, we found that the enhanced migration and invasion of the resistant melanoma cells correlated with an enhanced autophagic capacity and autophagosome-mediated secretion of ATP. Extracellular ATP (eATP) was instrumental for the invasive phenotype and the expansion of a subset of Vemurafenib-resistant melanoma cells. Compromising the heightened autophagy in these BRAF<sup>V600E</sup> inhibitor-resistant melanoma cells through the knockdown of different autophagy genes (<i>ATG5, ATG7, ULK1</i>), reduced their invasive and eATP-secreting capacity. Furthermore, eATP promoted the aggressive nature of the BRAF<sup>V600E</sup> inhibitor-resistant melanoma cells by signaling through the purinergic receptor P2RX7. This autophagy-propelled eATP-dependent autocrine-paracrine pathway supported the maintenance and expansion of a drug-resistant melanoma phenotype. In conclusion, we have identified an autophagy-driven response that relies on the secretion of ATP to drive P2RX7-based migration and expansion of the Vemurafenib-resistant phenotype. This emphasizes the potential of targeting autophagy in the treatment and management of metastatic melanoma.
DOI: 10.6084/m9.figshare.5221252.v1
title: An autophagy-driven pathway of ATP secretion supports the aggressive phenotype of BRAF<sup>V600E</sup> inhibitor-resistant metastatic melanoma cells

description: The ingrained capacity of melanoma cells to rapidly evolve toward an aggressive phenotype is manifested by their increased ability to develop drug-resistance, evident in the case of vemurafenib, a therapeutic-agent targeting BRAF<sup>V600E</sup>. Previous studies indicated a tight correlation between heightened melanoma-associated macroautophagy/autophagy and acquired Vemurafenib resistance. However, how this vesicular trafficking pathway supports Vemurafenib resistance remains unclear. Here, using isogenic human and murine melanoma cell lines of Vemurafenib-resistant and patient-derived melanoma cells with primary resistance to the BRAF<sup>V600E</sup> inhibitor, we found that the enhanced migration and invasion of the resistant melanoma cells correlated with an enhanced autophagic capacity and autophagosome-mediated secretion of ATP. Extracellular ATP (eATP) was instrumental for the invasive phenotype and the expansion of a subset of Vemurafenib-resistant melanoma cells. Compromising the heightened autophagy in these BRAF<sup>V600E</sup> inhibitor-resistant melanoma cells through the knockdown of different autophagy genes (<i>ATG5, ATG7, ULK1</i>), reduced their invasive and eATP-secreting capacity. Furthermore, eATP promoted the aggressive nature of the BRAF<sup>V600E</sup> inhibitor-resistant melanoma cells by signaling through the purinergic receptor P2RX7. This autophagy-propelled eATP-dependent autocrine-paracrine pathway supported the maintenance and expansion of a drug-resistant melanoma phenotype. In conclusion, we have identified an autophagy-driven response that relies on the secretion of ATP to drive P2RX7-based migration and expansion of the Vemurafenib-resistant phenotype. This emphasizes the potential of targeting autophagy in the treatment and management of metastatic melanoma.
DOI: 10.6084/m9.figshare.5221255.v1
title: Adaptation of mRNA structure to control protein folding

description: Comparison of mRNA and protein structures shows that highly structured mRNAs typically encode compact protein domains suggesting that mRNA structure controls protein folding. This function is apparently performed by distinct structural elements in the mRNA, which implies ‘fine tuning’ of mRNA structure under selection for optimal protein folding. We find that, during evolution, changes in the mRNA folding energy follow amino acid replacements, reinforcing the notion of an intimate connection between the structures of a mRNA and the protein it encodes, and the double encoding of protein sequence and folding in the mRNA.
DOI: 10.6084/m9.figshare.5221219
title: Understanding the context of alcohol impaired driving for fatal crash–involved drivers: A descriptive case analysis

description: <b>Objective</b>: The objective of this study was to understand the social context and circumstances surrounding alcohol-impaired driving prior to fatal crash involvement for drivers with an illegal blood alcohol concentration (BAC ≥ 0.05 g/100 ml or 0.00 g/100 ml for restricted license holders). <b>Methods</b>: Coroners' case reports investigating fatal crashes in South Australia over a 3-year period (2008–2010) were examined. The personal and crash characteristics of drivers with an illegal BAC were compared with those who had a legal BAC. For each driver with an illegal BAC, information was recorded including characteristics of last trip, location and social context of alcohol consumption, quantity and type of alcohol consumed, BAC level, presence of drugs, perceived alcohol intoxication, and alcohol dependence. Official traffic offense records were also obtained. <b>Results</b>: Of the 284 fatal crashes included in the study, 34% (<i>n</i> = 95) involved a driver or rider with an illegal BAC. Prior to the crash, alcohol was most frequently consumed by drivers in rural areas, within private homes, and was part of normal social activities. Drivers recorded a high level of alcohol impairment, with a mean BAC of 0.173 g/100 ml and a level of alcohol dependence that was above the Australian national average (7.4 vs. 3.9%). In addition, 23% of drivers were known to be experiencing psychological stress at the time of the crash. The results also confirm that drink driving recidivism continues to be a significant problem, with 44% of drivers recording at least one prior alcohol driving offense. <b>Conclusions</b>: Alcohol-impaired driving continues to be a leading cause of fatal crashes. The popularity of drinking at home, particularly in rural areas, has implications for police enforcement strategies and suggests that drink driving interventions that focus on community values and looking after friends might be beneficial. Importantly, the study highlights the need for a broader holistic approach to reduce the high levels of alcohol consumption and alcohol dependence underlying drink driving behavior.
DOI: 10.6084/m9.figshare.5221219.v2
title: Understanding the context of alcohol impaired driving for fatal crash–involved drivers: A descriptive case analysis

description: <b>Objective</b>: The objective of this study was to understand the social context and circumstances surrounding alcohol-impaired driving prior to fatal crash involvement for drivers with an illegal blood alcohol concentration (BAC ≥ 0.05 g/100 ml or 0.00 g/100 ml for restricted license holders). <b>Methods</b>: Coroners' case reports investigating fatal crashes in South Australia over a 3-year period (2008–2010) were examined. The personal and crash characteristics of drivers with an illegal BAC were compared with those who had a legal BAC. For each driver with an illegal BAC, information was recorded including characteristics of last trip, location and social context of alcohol consumption, quantity and type of alcohol consumed, BAC level, presence of drugs, perceived alcohol intoxication, and alcohol dependence. Official traffic offense records were also obtained. <b>Results</b>: Of the 284 fatal crashes included in the study, 34% (<i>n</i> = 95) involved a driver or rider with an illegal BAC. Prior to the crash, alcohol was most frequently consumed by drivers in rural areas, within private homes, and was part of normal social activities. Drivers recorded a high level of alcohol impairment, with a mean BAC of 0.173 g/100 ml and a level of alcohol dependence that was above the Australian national average (7.4 vs. 3.9%). In addition, 23% of drivers were known to be experiencing psychological stress at the time of the crash. The results also confirm that drink driving recidivism continues to be a significant problem, with 44% of drivers recording at least one prior alcohol driving offense. <b>Conclusions</b>: Alcohol-impaired driving continues to be a leading cause of fatal crashes. The popularity of drinking at home, particularly in rural areas, has implications for police enforcement strategies and suggests that drink driving interventions that focus on community values and looking after friends might be beneficial. Importantly, the study highlights the need for a broader holistic approach to reduce the high levels of alcohol consumption and alcohol dependence underlying drink driving behavior.
DOI: 10.6084/m9.figshare.5220964
title: Borehole temperature-depth profile database to constrain recent climatic variations in northern Chile

description: Borehole temperature-depth profiles measured in 2012 and 2015 in northern Chile by DTS and the conventional method.<br>
DOI: 10.6084/m9.figshare.5220844
title: supplemental Tables Burkitt Lymphoma cell line

description: Copy number results from SNP array analysis, chimeric fusion transcripts identification and mutational analyses of Burkitt Lymphoma cell line.<br>
DOI: 10.6084/m9.figshare.5220874
title: De novo-assembled Coccinia grandis flower bud transcriptome

description: De novo transcriptome assembled from flower buds of male, female, gynomonoecious and silver nitrate treated plants of <i>Coccinia grandis.</i><br>