cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1241586.v1
title: What Happens Depends on When It Happens: Copula-based Ordered Event History Analysis of Civil War Duration and Outcome

description: Scholars are interested in not just what event happens but also when the event happens. If there is dependence among events or dependence between time and events, however, the currently common methods (e.g. competing risks approaches) produce biased estimates. To deal with these problems, this article proposes a new method of copula-based ordered event history analysis (COEHA). A merit of working with copulas is that, whatever marginal distributions time and event variables follow (including the Cox model), researchers can derive whatever joint distribution exists between the two. Application of the COEHA model to a dataset of civil war supports two controversial hypotheses. First, as wars become longer, rebel victory becomes more likely but settlement does not (there is dependence between time and events at both tails). Second, stronger rebels make wars longer but do not necessarily tend to win, as experts predict but fail to establish (rebels’ strength lengthens time but has no effect on which events occur).
DOI: 10.6084/m9.figshare.1241583.v2
title: Likelihood Estimation for the INAR(<i>p</i>) Model by Saddlepoint Approximation

description: Saddlepoint techniques have been used successfully in many applications, owing to the high accuracy with which they can approximate intractable densities and tail probabilities. This article concerns their use for the estimation of high-order integer-valued autoregressive, INAR(<i>p</i>), processes. Conditional least squares estimation and maximum likelihood estimation have been proposed for INAR(<i>p</i>) models, but the first is inefficient for estimating parametric models, and the second becomes difficult to implement as the order <i>p</i> increases. We propose a simple saddlepoint approximation to the log-likelihood that performs well even in the tails of the distribution and with complicated INAR models. We consider Poisson and negative binomial innovations, and show empirically that the estimator that maximises the saddlepoint approximation behaves very similarly to the maximum likelihood estimator in realistic settings. The approach is applied to data on meningococcal disease counts. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1241579
title: V-ATPase and osmotic imbalances activate endolysosomal LC3 lipidation

description: Recently a noncanonical activity of autophagy proteins has been discovered that targets lipidation of microtubule-associated protein 1 light chain 3 (LC3) onto macroendocytic vacuoles, including macropinosomes, phagosomes, and entotic vacuoles. While this pathway is distinct from canonical autophagy, the mechanism of how these nonautophagic membranes are targeted for LC3 lipidation remains unclear. Here we present evidence that this pathway requires activity of the vacuolar-type H<sup>+</sup>-ATPase (V-ATPase) and is induced by osmotic imbalances within endolysosomal compartments. LC3 lipidation by this mechanism is induced by treatment of cells with the lysosomotropic agent chloroquine, and through exposure to the <i>Heliobacter pylori</i> pore-forming toxin VacA. These data add novel mechanistic insights into the regulation of noncanonical LC3 lipidation and its associated processes, including LC3-associated phagocytosis (LAP), and demonstrate that the widely and therapeutically used drug chloroquine, which is conventionally used to inhibit autophagy flux, is an inducer of LC3 lipidation.
DOI: 10.6084/m9.figshare.1241583.v1
title: Likelihood estimation for the INAR(<i>p</i>) model by saddlepoint approximation

description: Saddlepoint techniques have been used successfully in many applications, owing to the high accuracy with which they can approximate intractable densities and tail probabilities. This paper concerns their use for the estimation of high-order INteger-valued AutoRegressive, INAR(<i>p</i>), processes. Conditional least squares estimation and maximum likelihood estimation have been proposed for INAR(<i>p</i>) models, but the first is inefficient for estimating parametric models, and the second becomes difficult to implement as the order <i>p</i> increases. We propose a simple saddlepoint approximation to the log-likelihood that performs well even in the tails of the distribution and with complicated INAR models. We consider Poisson and negative binomial innovations, and show empirically that the estimator that maximises the saddlepoint approximation behaves very similarly to the maximum likelihood estimator in realistic settings. The approach is applied to data on meningococcal disease counts. This article has supplementary materials online.
DOI: 10.6084/m9.figshare.1241579.v2
title: V-ATPase and osmotic imbalances activate endolysosomal LC3 lipidation

description: Recently a noncanonical activity of autophagy proteins has been discovered that targets lipidation of microtubule-associated protein 1 light chain 3 (LC3) onto macroendocytic vacuoles, including macropinosomes, phagosomes, and entotic vacuoles. While this pathway is distinct from canonical autophagy, the mechanism of how these nonautophagic membranes are targeted for LC3 lipidation remains unclear. Here we present evidence that this pathway requires activity of the vacuolar-type H<sup>+</sup>-ATPase (V-ATPase) and is induced by osmotic imbalances within endolysosomal compartments. LC3 lipidation by this mechanism is induced by treatment of cells with the lysosomotropic agent chloroquine, and through exposure to the <i>Heliobacter pylori</i> pore-forming toxin VacA. These data add novel mechanistic insights into the regulation of noncanonical LC3 lipidation and its associated processes, including LC3-associated phagocytosis (LAP), and demonstrate that the widely and therapeutically used drug chloroquine, which is conventionally used to inhibit autophagy flux, is an inducer of LC3 lipidation.
DOI: 10.6084/m9.figshare.1241579.v1
title: V-ATPase and osmotic imbalances activate endolysosomal LC3 lipidation

description: Recently a noncanonical activity of autophagy proteins has been discovered that targets lipidation of microtubule-associated protein 1 light chain 3 (LC3) onto macroendocytic vacuoles, including macropinosomes, phagosomes, and entotic vacuoles. While this pathway is distinct from canonical autophagy, the mechanism of how these nonautophagic membranes are targeted for LC3 lipidation remains unclear. Here we present evidence that this pathway requires activity of the vacuolar-type H<sup>+</sup>-ATPase (V-ATPase) and is induced by osmotic imbalances within endolysosomal compartments. LC3 lipidation by this mechanism is induced by treatment of cells with the lysosomotropic agent chloroquine, and through exposure to the <i>Heliobacter pylori</i> pore-forming toxin VacA. These data add novel mechanistic insights into the regulation of noncanonical LC3 lipidation and its associated processes, including LC3-associated phagocytosis (LAP), and demonstrate that the widely and therapeutically used drug chloroquine, which is conventionally used to inhibit autophagy flux, is an inducer of LC3 lipidation.
DOI: 10.6084/m9.figshare.1241577
title: A Cluster-Based Outlier Detection Scheme for Multivariate Data

description: Detection power of the squared Mahalanobis distance statistic is significantly reduced when several outliers exist within a multivariate dataset of interest. To overcome this masking effect, we propose a computer-intensive cluster-based approach that incorporates a reweighted version of Rousseeuw’s minimum covariance determinant method with a multi-step cluster-based algorithm that initially filters out potential masking points. Compared to the most robust procedures, simulation studies show that our new method is better for outlier detection. Additional real data comparisons are given. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1241576
title: High-Dimensional Variable Selection With Reciprocal <i>L</i><sub>1</sub>-Regularization

description: During the past decade, penalized likelihood methods have been widely used in variable selection problems, where the penalty functions are typically symmetric about 0, continuous and nondecreasing in (0, ∞). We propose a new penalized likelihood method, reciprocal Lasso (or in short, rLasso), based on a new class of penalty functions that are decreasing in (0, ∞), discontinuous at 0, and converge to infinity when the coefficients approach zero. The new penalty functions give nearly zero coefficients infinity penalties; in contrast, the conventional penalty functions give nearly zero coefficients nearly zero penalties (e.g., Lasso and smoothly clipped absolute deviation [SCAD]) or constant penalties (e.g., <i>L</i><sub>0</sub> penalty). This distinguishing feature makes rLasso very attractive for variable selection. It can effectively avoid to select overly dense models. We establish the consistency of the rLasso for variable selection and coefficient estimation under both the low- and high-dimensional settings. Since the rLasso penalty functions induce an objective function with multiple local minima, we also propose an efficient Monte Carlo optimization algorithm to solve the involved minimization problem. Our simulation results show that the rLasso outperforms other popular penalized likelihood methods, such as Lasso, SCAD, minimax concave penalty, sure independence screening, interative sure independence screening, and extended Bayesian information criterion. It can produce sparser and more accurate coefficient estimates, and catch the true model with a higher probability. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1241577.v2
title: A Cluster-Based Outlier Detection Scheme for Multivariate Data

description: Detection power of the squared Mahalanobis distance statistic is significantly reduced when several outliers exist within a multivariate dataset of interest. To overcome this masking effect, we propose a computer-intensive cluster-based approach that incorporates a reweighted version of Rousseeuw’s minimum covariance determinant method with a multi-step cluster-based algorithm that initially filters out potential masking points. Compared to the most robust procedures, simulation studies show that our new method is better for outlier detection. Additional real data comparisons are given. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1241576.v2
title: High-Dimensional Variable Selection With Reciprocal <i>L</i><sub>1</sub>-Regularization

description: During the past decade, penalized likelihood methods have been widely used in variable selection problems, where the penalty functions are typically symmetric about 0, continuous and nondecreasing in (0, ∞). We propose a new penalized likelihood method, reciprocal Lasso (or in short, rLasso), based on a new class of penalty functions that are decreasing in (0, ∞), discontinuous at 0, and converge to infinity when the coefficients approach zero. The new penalty functions give nearly zero coefficients infinity penalties; in contrast, the conventional penalty functions give nearly zero coefficients nearly zero penalties (e.g., Lasso and smoothly clipped absolute deviation [SCAD]) or constant penalties (e.g., <i>L</i><sub>0</sub> penalty). This distinguishing feature makes rLasso very attractive for variable selection. It can effectively avoid to select overly dense models. We establish the consistency of the rLasso for variable selection and coefficient estimation under both the low- and high-dimensional settings. Since the rLasso penalty functions induce an objective function with multiple local minima, we also propose an efficient Monte Carlo optimization algorithm to solve the involved minimization problem. Our simulation results show that the rLasso outperforms other popular penalized likelihood methods, such as Lasso, SCAD, minimax concave penalty, sure independence screening, interative sure independence screening, and extended Bayesian information criterion. It can produce sparser and more accurate coefficient estimates, and catch the true model with a higher probability. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1241574
title: Data set used to explore relationship between socio-economic position and HIV status among young rural Zimbabwean women

description: Stata dataset used to explore relationship between socio-economic position and HIV status among young rural Zimbabwean women and whether different socio-economic domains (asset wealth; ability to afford essential items; and food sufficiency) are associated with HIV risk in different ways. See associated questionnaire.
DOI: 10.6084/m9.figshare.1241571
title: Training data set user for training EpiceaUntangler

description: This file contains a dataset of untangled code changes, created with the help of two developers who accurately split their code changes into self contained tasks over a period of four months. The developers worked in Pharo [1], and their code changes were recorded using Epicea [2]. The format of the files is STON [3], which is very similar to JSON. Contact: tinchodias@gmail.com [1]: http://pharo.org/ [2]: http://smalltalkhub.com/#!/~MartinDias/Epicea [3]: https://github.com/svenvc/ston/blob/master/ston-paper.md
DOI: 10.6084/m9.figshare.1241576.v1
title: High Dimensional Variable Selection with Reciprocal <i>L</i><sub>1</sub>-Regularization

description: During the past decade, penalized likelihood methods have been widely used in variable selection problems, where the penalty functions are typically symmetric about 0, continuous and nondecreasing in (0, ∞). We propose a new penalized likelihood method, reciprocal Lasso (or in short, rLasso), based on a new class of penalty functions which are decreasing in (0, ∞), discontinuous at 0, and converge to infinity when the coefficients approach zero. The new penalty functions give nearly zero coefficients infinity penalties; in contrast, the conventional penalty functions give nearly zero coefficients nearly zero penalties (e.g., Lasso and SCAD) or constant penalties (e.g., <i>L</i><sub>0</sub> penalty). This distinguishing feature makes rLasso very attractive for variable selection: It can effectively avoid to select overly dense models. We establish the consistency of the rLasso for variable selection and coefficient estimation under both the low and high dimensional settings. Since the rLasso penalty functions induce an objective function with multiple local minima, we also propose an efficient Monte Carlo optimization algorithm to solve the involved minimization problem. Our simulation results show that the rLasso outperforms other popular penalized likelihood methods, such as Lasso, SCAD, MCP, SIS, ISIS and EBIC: It can produce sparser and more accurate coefficient estimates, and catch the true model with a higher probability.
DOI: 10.6084/m9.figshare.1241558
title: The checkpoint clamp protein Rad9 facilitates DNA-end resection and prevents alternative non-homologous end joining

description: DNA damage activates the cell cycle checkpoint to regulate cell cycle progression. The checkpoint clamp (Rad9-Hus1-Rad1 complex) is recruited to damage sites, and is required for checkpoint activation. While functions of the checkpoint clamp in checkpoint activation have been well studied, its functions in DNA repair regulation remain elusive. Here we show that Rad9 is required for efficient homologous recombination (HR), and facilitates DNA-end resection. The role of Rad9 in homologous recombination is independent of its function in checkpoint activation, and this function is important for preventing alternative non-homologous end joining (altNHEJ). These findings reveal novel function of the checkpoint clamp in HR.
DOI: 10.6084/m9.figshare.1241574.v1
title: Data set used to explore relationship between socio-economic position and HIV status among young rural Zimbabwean women

description: Stata dataset used to explore relationship between socio-economic position and HIV status among young rural Zimbabwean women and whether different socio-economic domains (asset wealth; ability to afford essential items; and food sufficiency) are associated with HIV risk in different ways. See associated questionnaire.
DOI: 10.6084/m9.figshare.1241554
title: The leukemia-associated Rho guanine nucleotide exchange factor LARG is required for efficient replication stress signaling

description: We previously identified and characterized TELO2 as a human protein that facilitates efficient DNA damage response (DDR) signaling. A subsequent yeast 2-hybrid screen identified LARG; Leukemia-Associated Rho Guanine Nucleotide Exchange Factor (also known as Arhgef12), as a potential novel TELO2 interactor. LARG was previously shown to interact with Pericentrin (PCNT), which, like TELO2, is required for efficient replication stress signaling. Here we confirm interactions between LARG, TELO2 and PCNT and show that a sub-set of LARG co-localizes with PCNT at the centrosome. LARG-deficient cells exhibit replication stress signaling defects as evidenced by; supernumerary centrosomes, reduced replication stress-induced γH2AX and RPA nuclear foci formation, and reduced activation of the replication stress signaling effector kinase Chk1 in response to hydroxyurea. As such, LARG-deficient cells are sensitive to replication stress-inducing agents such as hydroxyurea and mitomycin C. Conversely we also show that depletion of TELO2 and the replication stress signaling kinase ATR leads to RhoA signaling defects. These data therefore reveal a level of crosstalk between the RhoA and DDR signaling pathways. Given that mutations in both ATR and PCNT can give rise to the related primordial dwarfism disorders of Seckel Syndrome and Microcephalic osteodysplastic primordial dwarfism type II (MOPDII) respectively, which both exhibit defects in ATR-dependent checkpoint signaling, these data also raise the possibility that mutations in LARG or disruption to RhoA signaling may be contributory factors to the etiology of a sub-set of primordial dwarfism disorders.
DOI: 10.6084/m9.figshare.1241557
title: Cytokinetic abscission is an acute G1 event

description: Animal cell division ends with the cutting of the microtubule and membrane intercellular bridge connecting the 2 daughter cells. This process, known as cytokinetic abscission (abscission), is widely regarded as the last step of cytokinesis, i.e., the last step of the cell cycle. Major breakthroughs have been recently achieved, illuminating mechanistic aspects of abscission; however, the timing of abscission with respect to the mammalian cell cycle remains unclear. In this study, we carefully measured the onset and progression of abscission in dividing cells expressing a G1 reporter. We conclude that abscission commences long after cells enter the G1 phase. Affiliating abscission with G1 is beyond semantics since it essentially postulates that the last step of the cell cycle is regulated in, and probably by, the following cycle.
DOI: 10.6084/m9.figshare.1241554.v2
title: The leukemia-associated Rho guanine nucleotide exchange factor LARG is required for efficient replication stress signaling

description: We previously identified and characterized TELO2 as a human protein that facilitates efficient DNA damage response (DDR) signaling. A subsequent yeast 2-hybrid screen identified LARG; Leukemia-Associated Rho Guanine Nucleotide Exchange Factor (also known as Arhgef12), as a potential novel TELO2 interactor. LARG was previously shown to interact with Pericentrin (PCNT), which, like TELO2, is required for efficient replication stress signaling. Here we confirm interactions between LARG, TELO2 and PCNT and show that a sub-set of LARG co-localizes with PCNT at the centrosome. LARG-deficient cells exhibit replication stress signaling defects as evidenced by; supernumerary centrosomes, reduced replication stress-induced γH2AX and RPA nuclear foci formation, and reduced activation of the replication stress signaling effector kinase Chk1 in response to hydroxyurea. As such, LARG-deficient cells are sensitive to replication stress-inducing agents such as hydroxyurea and mitomycin C. Conversely we also show that depletion of TELO2 and the replication stress signaling kinase ATR leads to RhoA signaling defects. These data therefore reveal a level of crosstalk between the RhoA and DDR signaling pathways. Given that mutations in both ATR and PCNT can give rise to the related primordial dwarfism disorders of Seckel Syndrome and Microcephalic osteodysplastic primordial dwarfism type II (MOPDII) respectively, which both exhibit defects in ATR-dependent checkpoint signaling, these data also raise the possibility that mutations in LARG or disruption to RhoA signaling may be contributory factors to the etiology of a sub-set of primordial dwarfism disorders.
DOI: 10.6084/m9.figshare.1241557.v2
title: Cytokinetic abscission is an acute G1 event

description: Animal cell division ends with the cutting of the microtubule and membrane intercellular bridge connecting the 2 daughter cells. This process, known as cytokinetic abscission (abscission), is widely regarded as the last step of cytokinesis, i.e., the last step of the cell cycle. Major breakthroughs have been recently achieved, illuminating mechanistic aspects of abscission; however, the timing of abscission with respect to the mammalian cell cycle remains unclear. In this study, we carefully measured the onset and progression of abscission in dividing cells expressing a G1 reporter. We conclude that abscission commences long after cells enter the G1 phase. Affiliating abscission with G1 is beyond semantics since it essentially postulates that the last step of the cell cycle is regulated in, and probably by, the following cycle.
DOI: 10.6084/m9.figshare.1241557.v1
title: Cytokinetic abscission is an acute G1 event

description: Animal cell division ends with the cutting of the microtubule and membrane intercellular bridge connecting the 2 daughter cells. This process, known as cytokinetic abscission (abscission), is widely regarded as the last step of cytokinesis, i.e., the last step of the cell cycle. Major breakthroughs have been recently achieved, illuminating mechanistic aspects of abscission; however, the timing of abscission with respect to the mammalian cell cycle remains unclear. In this study, we carefully measured the onset and progression of abscission in dividing cells expressing a G1 reporter. We conclude that abscission commences long after cells enter the G1 phase. Affiliating abscission with G1 is beyond semantics since it essentially postulates that the last step of the cell cycle is regulated in, and probably by, the following cycle.
DOI: 10.6084/m9.figshare.1241558.v1
title: The checkpoint clamp protein Rad9 facilitates DNA-end resection and prevents alternative non-homologous end joining

description: DNA damage activates the cell cycle checkpoint to regulate cell cycle progression. The checkpoint clamp (Rad9-Hus1-Rad1 complex) is recruited to damage sites, and is required for checkpoint activation. While functions of the checkpoint clamp in checkpoint activation have been well studied, its functions in DNA repair regulation remain elusive. Here we show that Rad9 is required for efficient homologous recombination (HR), and facilitates DNA-end resection. The role of Rad9 in homologous recombination is independent of its function in checkpoint activation, and this function is important for preventing alternative non-homologous end joining (altNHEJ). These findings reveal novel function of the checkpoint clamp in HR.