cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1618841
title: GADD45A Inhibits Autophagy Through Regulating the Interaction Between BECN1 and PIK3C3

description: GADD45A is a TP53-regulated and DNA damage-inducible tumor suppressor protein, which regulates cell cycle arrest, apoptosis, DNA repair, inhibits tumor growth and angiogenesis. However, the function of GADD45A in autophagy remains unknown. In this report, we demonstrate that GADD45A plays an important role in regulating the process of autophagy. GADD45A is able to decrease LC3-II expression and numbers of autophagosomes in mouse tissues and different cancer cell lines. Using bafilomycin A<sub>1</sub> treatment, we have observed that GADD45A regulates autophagosome initiation. Likely, GADD45A inhibition of autophagy is through its influence on the interaction between BECN1 and PIK3C3. Immunoprecipitation and GST affinity isolation assays exhibit that GADD45A directly interacts with BECN1, and in turn dissociates the BECN1-PIK3C3 complex. Furthermore, we have mapped the 71 to 81 amino acids of the GADD45A protein that are necessary for the GADD45A interaction with BECN1. Knockdown of BECN1 can abolish autophagy alterations induced by GADD45A. Taken together, these findings provide the novel evidence that GADD45A inhibits autophagy via impairing the BECN1-PIK3C3 complex formation.
DOI: 10.6084/m9.figshare.1618841.v1
title: GADD45A Inhibits Autophagy Through Regulating the Interaction Between BECN1 and PIK3C3

description: GADD45A is a TP53-regulated and DNA damage-inducible tumor suppressor protein, which regulates cell cycle arrest, apoptosis, DNA repair, inhibits tumor growth and angiogenesis. However, the function of GADD45A in autophagy remains unknown. In this report, we demonstrate that GADD45A plays an important role in regulating the process of autophagy. GADD45A is able to decrease LC3-II expression and numbers of autophagosomes in mouse tissues and different cancer cell lines. Using bafilomycin A<sub>1</sub> treatment, we have observed that GADD45A regulates autophagosome initiation. Likely, GADD45A inhibition of autophagy is through its influence on the interaction between BECN1 and PIK3C3. Immunoprecipitation and GST affinity isolation assays exhibit that GADD45A directly interacts with BECN1, and in turn dissociates the BECN1-PIK3C3 complex. Furthermore, we have mapped the 71 to 81 amino acids of the GADD45A protein that are necessary for the GADD45A interaction with BECN1. Knockdown of BECN1 can abolish autophagy alterations induced by GADD45A. Taken together, these findings provide the novel evidence that GADD45A inhibits autophagy via impairing the BECN1-PIK3C3 complex formation.
DOI: 10.6084/m9.figshare.1618856
title: A Hidden Markov Model for Urban-scale Traffic estimation Using Floating Car Data

description: Urban-scale traffic monitoring plays a vital role in reducing traffic congestion. Owing to its low cost and wide coverage, floating car data (FCD) serves as a novel approach to collecting traffic data. However, sparse probe data represents the vast majority of the data available on arterial roads in most urban environments. In order to overcome the problem of data sparseness, this paper proposes a hidden Markov model (HMM)-based traffic estimation model, in which the traffic condition on a road segment is considered as a hidden state that can be estimated according to the conditions of road segments having similar traffic characteristics. An algorithm based on clustering and pattern mining rather than on adjacency relationships is proposed to find clusters with road segments having similar traffic characteristics. A multi-clustering strategy is adopted to achieve a trade-off between clustering accuracy and coverage. Finally, the proposed model is designed and implemented on the basis of a real-time algorithm. Results of experiments based on real FCD confirm the applicability, accuracy, and efficiency of the model. In addition, the results indicate that the model is practicable for traffic estimation on urban arterials and works well even when more than 70% of the probe data are missing.
DOI: 10.6084/m9.figshare.1618856.v1
title: FCD_DATA

description: Urban-scale traffic monitoring plays a vital role in reducing traffic congestion. Owing to its low cost and wide coverage, floating car data (FCD) serves as a novel approach to collecting traffic data. However, sparse probe data represents the vast majority of the data available on arterial roads in most urban environments. In order to overcome the problem of data sparseness, this paper proposes a hidden Markov model (HMM)-based traffic estimation model, in which the traffic condition on a road segment is considered as a hidden state that can be estimated according to the conditions of road segments having similar traffic characteristics. An algorithm based on clustering and pattern mining rather than on adjacency relationships is proposed to find clusters with road segments having similar traffic characteristics. A multi-clustering strategy is adopted to achieve a trade-off between clustering accuracy and coverage. Finally, the proposed model is designed and implemented on the basis of a real-time algorithm. Results of experiments based on real FCD confirm the applicability, accuracy, and efficiency of the model. In addition, the results indicate that the model is practicable for traffic estimation on urban arterials and works well even when more than 70% of the probe data are missing.
DOI: 10.6084/m9.figshare.1621265
title: Geochronology and geochemistry of Carboniferous metabasalts in eastern Tianshan, Central Asia: evidence of a back-arc basin

description: ABSTRACTCarboniferous volcanic rocks are widely distributed in the Jueluotage belt of eastern Tianshan, located in the southern Central Asian Orogenic belt. The petrogenesis and tectonic history of this region have long been a matter of debate. These volcanic rocks erupted in two episodes, with zircon U–Pb ages of ca. 336 Ma and ca. 320 Ma. The ca. 336 Ma volcanic rocks are dominated by arc-like igneous rocks. They show enrichment of light rare earth elements (LREEs) and large-ion lithophile elements (LILEs), and depletion of high field-strength elements (HFSEs) according to the N-MORB-normalized and chondrite-normalized diagrams. However, the ca. 320 Ma volcanic rocks mainly consist of MORB-like igneous rocks that show nearly flat REE patterns. They are also slightly enriched in LILEs and LREEs according to the N-MORB-normalized and chondrite-normalized diagrams. These Carboniferous volcanic rocks are geochemically similar to the back-arc basin basalt (BABB) from the Mariana and Okinawa troughs. The inherited zircon ages of volcanic rocks from the Jueluotage belt show similar trends and features to those of the Central Tianshan Block, suggesting they shared the same basement, at least before the early Carboniferous. The evolution from arc-like volcanic rocks to MORB-like volcanic rocks reflects the development of the back-arc basin in the northern Central Tianshan Block during the Carboniferous. The Palaeo-Asian oceanic plate subducted beneath the Central Tianshan Block. The position of one of the major sutures of the Palaeo-Asian Ocean should be in the north of the Jueluotage belt. The Jueluotage belt may have the same basement as the Central Tianshan Block. The back-arc basin formed above the Central Tianshan ‘whole’ Block due to the subduction-exhumation of the Palaeo-Asian oceanic plate.
DOI: 10.6084/m9.figshare.1621265.v1
title: Geochronology and geochemistry of Carboniferous metabasalts in eastern Tianshan, Central Asia: evidence of a back-arc basin

description: ABSTRACTCarboniferous volcanic rocks are widely distributed in the Jueluotage belt of eastern Tianshan, located in the southern Central Asian Orogenic belt. The petrogenesis and tectonic history of this region have long been a matter of debate. These volcanic rocks erupted in two episodes, with zircon U–Pb ages of ca. 336 Ma and ca. 320 Ma. The ca. 336 Ma volcanic rocks are dominated by arc-like igneous rocks. They show enrichment of light rare earth elements (LREEs) and large-ion lithophile elements (LILEs), and depletion of high field-strength elements (HFSEs) according to the N-MORB-normalized and chondrite-normalized diagrams. However, the ca. 320 Ma volcanic rocks mainly consist of MORB-like igneous rocks that show nearly flat REE patterns. They are also slightly enriched in LILEs and LREEs according to the N-MORB-normalized and chondrite-normalized diagrams. These Carboniferous volcanic rocks are geochemically similar to the back-arc basin basalt (BABB) from the Mariana and Okinawa troughs. The inherited zircon ages of volcanic rocks from the Jueluotage belt show similar trends and features to those of the Central Tianshan Block, suggesting they shared the same basement, at least before the early Carboniferous. The evolution from arc-like volcanic rocks to MORB-like volcanic rocks reflects the development of the back-arc basin in the northern Central Tianshan Block during the Carboniferous. The Palaeo-Asian oceanic plate subducted beneath the Central Tianshan Block. The position of one of the major sutures of the Palaeo-Asian Ocean should be in the north of the Jueluotage belt. The Jueluotage belt may have the same basement as the Central Tianshan Block. The back-arc basin formed above the Central Tianshan ‘whole’ Block due to the subduction-exhumation of the Palaeo-Asian oceanic plate.
DOI: 10.6084/m9.figshare.1621375
title: High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns in <i>Arabidopsis</i> and rice

description: Histone acetylation and deacetylation are key epigenetic gene regulatory mechanisms that play critical roles in eukaryotes. Acetylation of histone 4 lysine 16 (H4K16ac) is implicated in many cellular processes. However, its biological function and relationship with transcription are largely unexplored in plants. We generated first genome-wide high-resolution maps of H4K16ac in <i>Arabidopsis thaliana</i> and <i>Oryza sativa</i>. We showed that H4K16ac is preferentially enriched around the transcription start sites and positively correlates with gene expression levels. Co-existence of H4K16ac and H3K23ac is correlated with high gene expression levels, suggesting a potentially combinatorial effect of H4K16ac and H3K23ac histone 3 lysine 23 acetylation on gene expression. Our data further revealed that while genes enriched with both H4K16ac and H3K23ac are ubiquitously expressed, genes enriched with only H4K16ac or H3K23ac showed significantly distinct expression patterns in association with particular developmental stages. Unexpectedly, and unlike in <i>Arabidopsis</i>, there are significant levels of both H4K16ac and H3K23ac in the lowly expressed genes in rice. Furthermore, we found that H4K16ac-enriched genes are associated with different biological processes in <i>Arabidopsis</i> and rice, suggesting a potentially species-specific role of H4K16ac in plants. Together, our genome-wide profiling reveals the conserved and unique distribution patterns of H4K16ac and H3K23ac in <i>Arabidopsis</i> and rice and provides a foundation for further understanding their function in plants.
DOI: 10.6084/m9.figshare.1621375.v1
title: High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns in <i>Arabidopsis</i> and rice

description: Histone acetylation and deacetylation are key epigenetic gene regulatory mechanisms that play critical roles in eukaryotes. Acetylation of histone 4 lysine 16 (H4K16ac) is implicated in many cellular processes. However, its biological function and relationship with transcription are largely unexplored in plants. We generated first genome-wide high-resolution maps of H4K16ac in <i>Arabidopsis thaliana</i> and <i>Oryza sativa</i>. We showed that H4K16ac is preferentially enriched around the transcription start sites and positively correlates with gene expression levels. Co-existence of H4K16ac and H3K23ac is correlated with high gene expression levels, suggesting a potentially combinatorial effect of H4K16ac and H3K23ac histone 3 lysine 23 acetylation on gene expression. Our data further revealed that while genes enriched with both H4K16ac and H3K23ac are ubiquitously expressed, genes enriched with only H4K16ac or H3K23ac showed significantly distinct expression patterns in association with particular developmental stages. Unexpectedly, and unlike in <i>Arabidopsis</i>, there are significant levels of both H4K16ac and H3K23ac in the lowly expressed genes in rice. Furthermore, we found that H4K16ac-enriched genes are associated with different biological processes in <i>Arabidopsis</i> and rice, suggesting a potentially species-specific role of H4K16ac in plants. Together, our genome-wide profiling reveals the conserved and unique distribution patterns of H4K16ac and H3K23ac in <i>Arabidopsis</i> and rice and provides a foundation for further understanding their function in plants.
DOI: 10.6084/m9.figshare.1621396
title: Dichotomizing Continuous Data Which Retains Statistical Precision Using a Bayesian Distributional Approach That Reflects the True Uncertainty

description: Although dichotomization is widely criticized by statisticians, it is sometimes useful and necessary in medical research for decision-making or communication purposes. In order to address the issue of dichotomization, a previous literature developed an asymptotic distributional approach from a frequentist perspective assuming that the data are normally distributed and the variances in two groups are equivalent. This approach was further extended to the case of unequal variances. The previous works improve the dichotomization in many ways but assumes that the variance of data is known which does not reflect the realistic situation where both mean and variance are unknown. In this paper, we develop a Bayesian distributional methodology that inherits the advantages of previous attempts but considers all levels of uncertainty. For comparison purposes, we also reframe the original asymptotic approach from a Bayesian perspective. We show through simulation studies that the Bayesian asymptotic method overestimates or underestimates the true variation under certain situations. An example of pain data is also provided to illustrate the performance of the proposed approach. The effects of unequal variances on the asymptotic method are demonstrated in the example as well.
DOI: 10.6084/m9.figshare.1621396.v1
title: Dichotomizing Continuous Data Which Retains Statistical Precision Using a Bayesian Distributional Approach That Reflects the True Uncertainty

description: Although dichotomization is widely criticized by statisticians, it is sometimes useful and necessary in medical research for decision-making or communication purposes. In order to address the issue of dichotomization, a previous literature developed an asymptotic distributional approach from a frequentist perspective assuming that the data are normally distributed and the variances in two groups are equivalent. This approach was further extended to the case of unequal variances. The previous works improve the dichotomization in many ways but assumes that the variance of data is known which does not reflect the realistic situation where both mean and variance are unknown. In this paper, we develop a Bayesian distributional methodology that inherits the advantages of previous attempts but considers all levels of uncertainty. For comparison purposes, we also reframe the original asymptotic approach from a Bayesian perspective. We show through simulation studies that the Bayesian asymptotic method overestimates or underestimates the true variation under certain situations. An example of pain data is also provided to illustrate the performance of the proposed approach. The effects of unequal variances on the asymptotic method are demonstrated in the example as well.
DOI: 10.6084/m9.figshare.1621903
title: Tomato HsfA1a plays a critical role in plant drought tolerance by activating <i>ATG</i> genes and inducing autophagy

description: Autophagy plays critical roles in plant responses to stress. In contrast to the wealth of information concerning the core process of plant autophagosome assembly, our understanding of the regulation of autophagy is limited. In this study, we demonstrated that transcription factor HsfA1a played a critical role in tomato tolerance to drought stress, in part through its positive role in induction of autophagy under drought stress. <i>HsfA1a</i> expression was induced by drought stress. Virus-induced <i>HsfA1a</i> gene silencing reduced while its overexpression increased plant drought tolerance based on both symptoms and membrane integrity. <i>HsfA1a</i>-silenced plants were more sensitive to endogenous ABA-mediated stomatal closure, while its overexpression lines were resistant under drought stress, indicating that phytohormone ABA did not play a major role in <i>HsfA1a</i>-induced drought tolerance. On the other hand, <i>HsfA1a</i>-silenced plants increased while its overexpression decreased the levels of insoluble proteins which were highly ubiquitinated under drought stress. Furthermore, drought stress induced numerous <i>ATGs</i> expression and autophagosome formation in wild-type plants. The expression of <i>ATG10</i> and <i>ATG18f</i>, and the formation of autophagosomes were compromised in <i>HsfA1a</i>-silenced plants but were enhanced in <i>HsfA1a</i>-overexpressing plants. Both electrophoretic mobility shift assay and chromatin immunoprecipitation coupled with qPCR analysis revealed that HsfA1a bound to <i>ATG10</i> and <i>ATG18f</i> gene promoters. Silencing of <i>ATG10</i> and <i>ATG18f</i> reduced HsfA1a-induced drought tolerance and autophagosome formation in plants overexpressing <i>HsfA1a</i>. These results demonstrate that HsfA1a induces drought tolerance by activating <i>ATG</i> genes and inducing autophagy, which may promote plant survival by degrading ubiquitinated protein aggregates under drought stress.
DOI: 10.6084/m9.figshare.1621903.v1
title: Tomato HsfA1a plays a critical role in plant drought tolerance by activating <i>ATG</i> genes and inducing autophagy

description: Autophagy plays critical roles in plant responses to stress. In contrast to the wealth of information concerning the core process of plant autophagosome assembly, our understanding of the regulation of autophagy is limited. In this study, we demonstrated that transcription factor HsfA1a played a critical role in tomato tolerance to drought stress, in part through its positive role in induction of autophagy under drought stress. <i>HsfA1a</i> expression was induced by drought stress. Virus-induced <i>HsfA1a</i> gene silencing reduced while its overexpression increased plant drought tolerance based on both symptoms and membrane integrity. <i>HsfA1a</i>-silenced plants were more sensitive to endogenous ABA-mediated stomatal closure, while its overexpression lines were resistant under drought stress, indicating that phytohormone ABA did not play a major role in <i>HsfA1a</i>-induced drought tolerance. On the other hand, <i>HsfA1a</i>-silenced plants increased while its overexpression decreased the levels of insoluble proteins which were highly ubiquitinated under drought stress. Furthermore, drought stress induced numerous <i>ATGs</i> expression and autophagosome formation in wild-type plants. The expression of <i>ATG10</i> and <i>ATG18f</i>, and the formation of autophagosomes were compromised in <i>HsfA1a</i>-silenced plants but were enhanced in <i>HsfA1a</i>-overexpressing plants. Both electrophoretic mobility shift assay and chromatin immunoprecipitation coupled with qPCR analysis revealed that HsfA1a bound to <i>ATG10</i> and <i>ATG18f</i> gene promoters. Silencing of <i>ATG10</i> and <i>ATG18f</i> reduced HsfA1a-induced drought tolerance and autophagosome formation in plants overexpressing <i>HsfA1a</i>. These results demonstrate that HsfA1a induces drought tolerance by activating <i>ATG</i> genes and inducing autophagy, which may promote plant survival by degrading ubiquitinated protein aggregates under drought stress.
DOI: 10.6084/m9.figshare.1621904
title: A pivotal role of FOS-mediated BECN1/Beclin 1 upregulation in dopamine D2 and D3 receptor agonist-induced autophagy activation

description: Autophagy dysfunction is implicated in the pathogenesis of Parkinson disease (PD). BECN1/Beclin 1 acts as a critical regulator of autophagy and other cellular processes; yet, little is known about the function and regulation of BECN1 in PD. In this study, we report that dopamine D2 and D3 receptor (DRD2 and DRD3) activation by pramipexole and quinpirole could enhance <i>BECN1</i> transcription and promote autophagy activation in several cell lines, including PC12, MES23.5 and differentiated SH-SY5Y cells, and also in tyrosine hydroxylase positive primary midbrain neurons. Moreover, we identified a novel FOS (FBJ murine osteosarcoma viral oncogene homolog) binding sequence (5′-TGCCTCA-3′) in the rat and human <i>Becn1</i>/<i>BECN1</i> promoter and uncovered an essential role of FOS binding in the enhancement of <i>Becn1</i> transcription in PC12 cells in response to the dopamine agonist(s). In addition, we demonstrated a critical role of intracellular Ca<sup>2+</sup> elevation, followed by the enhanced phosphorylation of CAMK4 (calcium/calmodulin-dependent protein kinase IV) and CREB (cAMP responsive element binding protein) in the increases of FOS expression and autophagy activity. More importantly, pramipexole treatment ameliorated the SNCA/α-synuclein accumulation in rotenone-treated PC12 cells that overexpress wild-type or A53T mutant SNCA by promoting autophagy flux. This effect was also demonstrated in the substantia nigra and the striatum of <i>SNCA</i><sup>A53T</sup> transgenic mice. The inhibition of SNCA accumulation by pramipexole was attenuated by cotreatment with the DRD2 and DRD3 antagonists and <i>Becn1</i> siRNAs. Thus, our findings suggest that DRD2 and DRD3 agonist(s) may induce autophagy activation via a BECN1-dependent pathway and have the potential to reduce SNCA accumulation in PD.
DOI: 10.6084/m9.figshare.1621904.v1
title: A pivotal role of FOS-mediated BECN1/Beclin 1 upregulation in dopamine D2 and D3 receptor agonist-induced autophagy activation

description: Autophagy dysfunction is implicated in the pathogenesis of Parkinson disease (PD). BECN1/Beclin 1 acts as a critical regulator of autophagy and other cellular processes; yet, little is known about the function and regulation of BECN1 in PD. In this study, we report that dopamine D2 and D3 receptor (DRD2 and DRD3) activation by pramipexole and quinpirole could enhance <i>BECN1</i> transcription and promote autophagy activation in several cell lines, including PC12, MES23.5 and differentiated SH-SY5Y cells, and also in tyrosine hydroxylase positive primary midbrain neurons. Moreover, we identified a novel FOS (FBJ murine osteosarcoma viral oncogene homolog) binding sequence (5′-TGCCTCA-3′) in the rat and human <i>Becn1</i>/<i>BECN1</i> promoter and uncovered an essential role of FOS binding in the enhancement of <i>Becn1</i> transcription in PC12 cells in response to the dopamine agonist(s). In addition, we demonstrated a critical role of intracellular Ca<sup>2+</sup> elevation, followed by the enhanced phosphorylation of CAMK4 (calcium/calmodulin-dependent protein kinase IV) and CREB (cAMP responsive element binding protein) in the increases of FOS expression and autophagy activity. More importantly, pramipexole treatment ameliorated the SNCA/α-synuclein accumulation in rotenone-treated PC12 cells that overexpress wild-type or A53T mutant SNCA by promoting autophagy flux. This effect was also demonstrated in the substantia nigra and the striatum of <i>SNCA</i><sup>A53T</sup> transgenic mice. The inhibition of SNCA accumulation by pramipexole was attenuated by cotreatment with the DRD2 and DRD3 antagonists and <i>Becn1</i> siRNAs. Thus, our findings suggest that DRD2 and DRD3 agonist(s) may induce autophagy activation via a BECN1-dependent pathway and have the potential to reduce SNCA accumulation in PD.
DOI: 10.5281/zenodo.10865994
title: 04 PerformDevelop_F_long_final for LMM