cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7802702.v1
title: Additional file 3: of Patients with idiopathic recurrent miscarriage have abnormally high TGFß+ blood NK, NKT and T cells in the presence of abnormally low TGFß plasma levels

description: Figure S3a + b. Plasma levels of cytokines and chemokines. iRM patients showed the lowest plasma levels of TGFß1, TGFß3, IL10, TNFα, IL1ß, IL6, IL8, IL17 and GM-CSF and the highest plasma levels of G-CSF and CXCL5 of all examined groups (for all p &lt; 0.050). Moreover, they had normal levels of IL2, IL4, IL12, TPO and VEGF that were lower than those in male and female ESRD and transplant recipients early and late post-transplant (for all p &lt; 0.050). IFNy, IL1α and TGFß2 plasma levels were similar in iRM patients, male and female HC and transplant recipients (for all p &gt; 0.050). Thirty-five HC, 34 ESRD, 37 renal transplant recipients late and 10 renal transplant recipients early post-transplant as well as 33 iRM patients were studied. Data are given as median ± interquartile range. (ZIP 2437 kb)
DOI: 10.6084/m9.figshare.11472723
title: MOESM2 of Epidemiological characteristics of bacillary dysentery from 2009 to 2016 and its incidence prediction model based on meteorological factors

description: Additional file 2: Core code and data set of the establishment of predictive model.
DOI: 10.6084/m9.figshare.11472723.v1
title: MOESM2 of Epidemiological characteristics of bacillary dysentery from 2009 to 2016 and its incidence prediction model based on meteorological factors

description: Additional file 2: Core code and data set of the establishment of predictive model.
DOI: 10.6084/m9.figshare.9899861
title: DACT1 Involvement in the Cytoskeletal Arrangement of Cardiomyocytes in Atrial Fibrillation by Regulating Cx43

description: Abstract Objective: To determine the role of the dishevelled binding antagonist of beta catenin 1 (DACT1) in the cytoskeletal arrangement of cardiomyocytes in atrial fibrillation (AF). Methods: The DACT1 expression and its associations with the degree of fibrosis and β-catenin in valvular disease patients were analyzed by immunohistochemistry and Masson’s staining. DACT1 was overexpressed in the atrial myocyte cell line (HL-1) and the cardiac cell line (H9C2) by adenoviral vectors. Alterations in the fibrous actin (F-actin) content and organization and the expression of β-catenin were detected by flow cytometry, immunofluorescence, and Western blotting. Additionally, the association of DACT1 with gap junctions connexin 43 (Cx43) was detected by immunohistochemistry, immunofluorescence, and Western blotting. Results: Decreased cytoplasmic DACT1 expression in the myocardium was associated with AF (P=0.037) and a high degree of fibrosis (weak vs. strong, P=0.028; weak vs. very strong, P=0.029). A positive association was observed between DACT1 and β-catenin expression in clinical samples (P=0.028, Spearman’s rho=0.408). Furthermore, overexpression of DACT1 in HL-1 and H9C2 cells induced an increase in β-catenin and subsequent partial colocalization of DACT1 and β-catenin. In addition, F-actin content and organization were enhanced. Interestingly, DACT1 was positively correlated with the Cx43 expression in clinical samples (P=0.048, Spearman’s rho=0.370) and changed the Cx43 distribution in cardiac cell lines. Conclusion: DACT1 proved to be a novel AF-related gene by regulating Cx43 via cytoskeletal organization induced by β-catenin accumulation in cardiomyocytes. DACT1 could thus serve as a potential therapeutic marker for AF.
DOI: 10.6084/m9.figshare.9899861.v1
title: DACT1 Involvement in the Cytoskeletal Arrangement of Cardiomyocytes in Atrial Fibrillation by Regulating Cx43

description: Abstract Objective: To determine the role of the dishevelled binding antagonist of beta catenin 1 (DACT1) in the cytoskeletal arrangement of cardiomyocytes in atrial fibrillation (AF). Methods: The DACT1 expression and its associations with the degree of fibrosis and β-catenin in valvular disease patients were analyzed by immunohistochemistry and Masson’s staining. DACT1 was overexpressed in the atrial myocyte cell line (HL-1) and the cardiac cell line (H9C2) by adenoviral vectors. Alterations in the fibrous actin (F-actin) content and organization and the expression of β-catenin were detected by flow cytometry, immunofluorescence, and Western blotting. Additionally, the association of DACT1 with gap junctions connexin 43 (Cx43) was detected by immunohistochemistry, immunofluorescence, and Western blotting. Results: Decreased cytoplasmic DACT1 expression in the myocardium was associated with AF (P=0.037) and a high degree of fibrosis (weak vs. strong, P=0.028; weak vs. very strong, P=0.029). A positive association was observed between DACT1 and β-catenin expression in clinical samples (P=0.028, Spearman’s rho=0.408). Furthermore, overexpression of DACT1 in HL-1 and H9C2 cells induced an increase in β-catenin and subsequent partial colocalization of DACT1 and β-catenin. In addition, F-actin content and organization were enhanced. Interestingly, DACT1 was positively correlated with the Cx43 expression in clinical samples (P=0.048, Spearman’s rho=0.370) and changed the Cx43 distribution in cardiac cell lines. Conclusion: DACT1 proved to be a novel AF-related gene by regulating Cx43 via cytoskeletal organization induced by β-catenin accumulation in cardiomyocytes. DACT1 could thus serve as a potential therapeutic marker for AF.
DOI: 10.6084/m9.figshare.11472732
title: MOESM3 of Epidemiological characteristics of bacillary dysentery from 2009 to 2016 and its incidence prediction model based on meteorological factors

description: Additional file 3: Core code and data set of the establishment of predictive model.
DOI: 10.6084/m9.figshare.11472732.v1
title: MOESM3 of Epidemiological characteristics of bacillary dysentery from 2009 to 2016 and its incidence prediction model based on meteorological factors

description: Additional file 3: Core code and data set of the establishment of predictive model.
DOI: 10.6084/m9.figshare.8327036
title: Statistical Inference for Covariate-Adaptive Randomization Procedures

description: Covariate-adaptive randomization (CAR) procedures are frequently used in comparative studies to increase the covariate balance across treatment groups. However, because randomization inevitably uses the covariate information when forming balanced treatment groups, the validity of classical statistical methods after such randomization is often unclear. In this article, we derive the theoretical properties of statistical methods based on general CAR under the linear model framework. More importantly, we explicitly unveil the relationship between covariate-adaptive and inference properties by deriving the asymptotic representations of the corresponding estimators. We apply the proposed general theory to various randomization procedures such as complete randomization, rerandomization, pairwise sequential randomization, and Atkinson’s <i>D</i><sub><i>A</i></sub>-biased coin design and compare their performance analytically. Based on the theoretical results, we then propose a new approach to obtain valid and more powerful tests. These results open a door to understand and analyze experiments based on CAR. Simulation studies provide further evidence of the advantages of the proposed framework and the theoretical results. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.8327036.v1
title: Statistical Inference for Covariate-Adaptive Randomization Procedures

description: Covariate-adaptive randomization (CAR) procedures are frequently used in comparative studies to increase the covariate balance across treatment groups. However, because randomization inevitably uses the covariate information when forming balanced treatment groups, the validity of classical statistical methods after such randomization is often unclear. In this article, we derive the theoretical properties of statistical methods based on general CAR under the linear model framework. More importantly, we explicitly unveil the relationship between covariate-adaptive and inference properties by deriving the asymptotic representations of the corresponding estimators. We apply the proposed general theory to various randomization procedures such as complete randomization, rerandomization, pairwise sequential randomization, and Atkinson’s <i>D</i><sub><i>A</i></sub>-biased coin design and compare their performance analytically. Based on the theoretical results, we then propose a new approach to obtain valid and more powerful tests. These results open a door to understand and analyze experiments based on CAR. Simulation studies provide further evidence of the advantages of the proposed framework and the theoretical results. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.8327036.v2
title: Statistical Inference for Covariate-Adaptive Randomization Procedures

description: Covariate-adaptive randomization (CAR) procedures are frequently used in comparative studies to increase the covariate balance across treatment groups. However, because randomization inevitably uses the covariate information when forming balanced treatment groups, the validity of classical statistical methods after such randomization is often unclear. In this article, we derive the theoretical properties of statistical methods based on general CAR under the linear model framework. More importantly, we explicitly unveil the relationship between covariate-adaptive and inference properties by deriving the asymptotic representations of the corresponding estimators. We apply the proposed general theory to various randomization procedures such as complete randomization, rerandomization, pairwise sequential randomization, and Atkinson’s <i>D</i><sub><i>A</i></sub>-biased coin design and compare their performance analytically. Based on the theoretical results, we then propose a new approach to obtain valid and more powerful tests. These results open a door to understand and analyze experiments based on CAR. Simulation studies provide further evidence of the advantages of the proposed framework and the theoretical results. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3084160
title: Cyclin A1 regulates the interactions between mouse haematopoietic stem and progenitor cells and their niches

description: It remains poorly understood how the haematopoietic stem/progenitor cells (HSPC) are attracted to their niches and the functional consequences of such interaction. In the present study, we show that the cell cycle regulator cyclin A1 in association with vascular endothelial growth factor receptor 1 (VEGFR1), is required for HSPC and their niches to maintain their function and proper interaction. In the absence of cyclin A1, the HSPC in the BM are increased in their frequency and display an increased migratory and homing ability. Concomitantly, the ability of the endosteal and central BM niche zones to attract and home the wild-type HSPC is significantly reduced in cyclin A1-null mice as compared to the wild-type controls. The impaired proliferation and homing of HSPC in the BM of cyclin A1-null mice are attributed to the increased density of microvessels in the endosteal and central BM niche zones, which is associated with the increased VEGFR1 expression. Thus, modulation of cyclin A1 and VEGFR1 in HSPC and their niches may provide new insights into therapeutic approaches.
DOI: 10.6084/m9.figshare.3084160.v1
title: Cyclin A1 regulates the interactions between mouse haematopoietic stem and progenitor cells and their niches

description: It remains poorly understood how the haematopoietic stem/progenitor cells (HSPC) are attracted to their niches and the functional consequences of such interaction. In the present study, we show that the cell cycle regulator cyclin A1 in association with vascular endothelial growth factor receptor 1 (VEGFR1), is required for HSPC and their niches to maintain their function and proper interaction. In the absence of cyclin A1, the HSPC in the BM are increased in their frequency and display an increased migratory and homing ability. Concomitantly, the ability of the endosteal and central BM niche zones to attract and home the wild-type HSPC is significantly reduced in cyclin A1-null mice as compared to the wild-type controls. The impaired proliferation and homing of HSPC in the BM of cyclin A1-null mice are attributed to the increased density of microvessels in the endosteal and central BM niche zones, which is associated with the increased VEGFR1 expression. Thus, modulation of cyclin A1 and VEGFR1 in HSPC and their niches may provide new insights into therapeutic approaches.
DOI: 10.6084/m9.figshare.8327042
title: Detecting Strong Signals in Gene Perturbation Experiments: An Adaptive Approach With Power Guarantee and FDR Control

description: <b>The perturbation of a transcription factor should affect the expression levels of its direct targets. However, not all genes showing changes in expression are direct targets. To increase the chance of detecting direct targets, we propose a modified two-group model where the null group corresponds to genes which are not direct targets, but can have small nonzero effects. We model the behavior of genes from the null set by a Gaussian distribution with unknown variance</b>τ2<b>. To estimate</b>τ2<b>, we focus on a simple estimation approach, the iterated empirical Bayes estimation. We conduct a detailed analysis of the properties of the iterated EB estimate and provide theoretical guarantee of its good performance under mild conditions. We provide simulations comparing the new modeling approach with existing methods, and the new approach shows more stable and better performance under different situations. We also apply it to a real dataset from gene knock-down experiments and obtained better results compared with the original two-group model testing for nonzero effects.</b>
DOI: 10.6084/m9.figshare.8327042.v1
title: Detecting strong signals in gene perturbation experiments: An adaptive approach with power guarantee and FDR control

description: The perturbation of a transcription factor should affect the expression levels of its direct targets. However, not all genes showing changes in expression are direct targets. To increase the chance of detecting direct targets, we propose a modified two-group model where the null group corresponds to genes which are not direct targets, but can have small non-zero effects. We model the behavior of genes from the null set by a Gaussian distribution with unknown variance τ2. To estimate τ2, we focus on a simple estimation approach, the iterated empirical Bayes estimation. We conduct a detailed analysis of the properties of the iterated EB estimate and provide theoretical guarantee of its good performance under mild conditions. We provide simulations comparing the new modeling approach with existing methods, and the new approach shows more stable and better performance under different situations. We also apply it to a real data set from gene knock-down experiments and obtained better results compared with the original two-group model testing for non-zero effects.
DOI: 10.6084/m9.figshare.8327042.v2
title: Detecting Strong Signals in Gene Perturbation Experiments: An Adaptive Approach With Power Guarantee and FDR Control

description: <b>The perturbation of a transcription factor should affect the expression levels of its direct targets. However, not all genes showing changes in expression are direct targets. To increase the chance of detecting direct targets, we propose a modified two-group model where the null group corresponds to genes which are not direct targets, but can have small nonzero effects. We model the behavior of genes from the null set by a Gaussian distribution with unknown variance</b>τ2<b>. To estimate</b>τ2<b>, we focus on a simple estimation approach, the iterated empirical Bayes estimation. We conduct a detailed analysis of the properties of the iterated EB estimate and provide theoretical guarantee of its good performance under mild conditions. We provide simulations comparing the new modeling approach with existing methods, and the new approach shows more stable and better performance under different situations. We also apply it to a real dataset from gene knock-down experiments and obtained better results compared with the original two-group model testing for nonzero effects.</b>
DOI: 10.6084/m9.figshare.8327042.v3
title: Detecting Strong Signals in Gene Perturbation Experiments: An Adaptive Approach With Power Guarantee and FDR Control

description: <b>The perturbation of a transcription factor should affect the expression levels of its direct targets. However, not all genes showing changes in expression are direct targets. To increase the chance of detecting direct targets, we propose a modified two-group model where the null group corresponds to genes which are not direct targets, but can have small nonzero effects. We model the behavior of genes from the null set by a Gaussian distribution with unknown variance</b>τ2<b>. To estimate</b>τ2<b>, we focus on a simple estimation approach, the iterated empirical Bayes estimation. We conduct a detailed analysis of the properties of the iterated EB estimate and provide theoretical guarantee of its good performance under mild conditions. We provide simulations comparing the new modeling approach with existing methods, and the new approach shows more stable and better performance under different situations. We also apply it to a real dataset from gene knock-down experiments and obtained better results compared with the original two-group model testing for nonzero effects.</b>
DOI: 10.6084/m9.figshare.11997084
title: Essential oil from Euphorbia esula inhibits proliferation and induces apoptosis in HepG2 cells via mitochondrial dysfunction

description: Hepatocellular carcinoma is one of the most prevalent malignancies and a leading cause of cancer-related mortality worldwide. However, the therapies to prevent hepatocellular carcinoma are still limited and the emergence of drug resistance leads to the development of new anti-cancer drugs and combinational chemotherapy regimens. Our study was aimed to explore the anticancer effects of the essential oil extract (EEEO) from Euphorbia esula which has been widely used in traditional Chinese folk medicine and possessed potential cytotoxic effects in several human tumor cells. However, the mechanisms of EEEO-induced anti-proliferation and apoptosis have not been completely elucidated. In this study, EEEO was prepared by hydro-distillation and the main chemical component of EEEO was identified by GC-MS. HepG2 cells were treated with EEEO in vitro and then evaluated with respect to proliferation, apoptosis, and levels of reactive oxygen species (ROS) and apoptotic proteins. Our studies showed that EEEO decreased cell viability, elevated ROS levels, and induced apoptosis of HepG2 cells in a concentration- and time-dependent manner. Furthermore, Bcl-2 was down-regulated, while Bax was up-regulated in HepG2 after EEEO treatment. These results suggest that EEEO induced apoptosis of HepG2 cells and indicate that this apoptosis might be mediated by the mitochondrial pathway.
DOI: 10.6084/m9.figshare.11997084.v1
title: Essential oil from Euphorbia esula inhibits proliferation and induces apoptosis in HepG2 cells via mitochondrial dysfunction

description: Hepatocellular carcinoma is one of the most prevalent malignancies and a leading cause of cancer-related mortality worldwide. However, the therapies to prevent hepatocellular carcinoma are still limited and the emergence of drug resistance leads to the development of new anti-cancer drugs and combinational chemotherapy regimens. Our study was aimed to explore the anticancer effects of the essential oil extract (EEEO) from Euphorbia esula which has been widely used in traditional Chinese folk medicine and possessed potential cytotoxic effects in several human tumor cells. However, the mechanisms of EEEO-induced anti-proliferation and apoptosis have not been completely elucidated. In this study, EEEO was prepared by hydro-distillation and the main chemical component of EEEO was identified by GC-MS. HepG2 cells were treated with EEEO in vitro and then evaluated with respect to proliferation, apoptosis, and levels of reactive oxygen species (ROS) and apoptotic proteins. Our studies showed that EEEO decreased cell viability, elevated ROS levels, and induced apoptosis of HepG2 cells in a concentration- and time-dependent manner. Furthermore, Bcl-2 was down-regulated, while Bax was up-regulated in HepG2 after EEEO treatment. These results suggest that EEEO induced apoptosis of HepG2 cells and indicate that this apoptosis might be mediated by the mitochondrial pathway.
DOI: 10.6084/m9.figshare.11472801
title: MOESM1 of Specific enrichment of microbes and increased ruminal propionate production: the potential mechanism underlying the high energy efficiency of Holstein heifers fed steam-flaked corn

description: Additional file 1: Table S1. Summary of the relative abundance of phyla; Table S2. Summary of the relative abundance of genera.
DOI: 10.6084/m9.figshare.11472801.v1
title: MOESM1 of Specific enrichment of microbes and increased ruminal propionate production: the potential mechanism underlying the high energy efficiency of Holstein heifers fed steam-flaked corn

description: Additional file 1: Table S1. Summary of the relative abundance of phyla; Table S2. Summary of the relative abundance of genera.
DOI: 10.6084/m9.figshare.7802789
title: Additional file 1: of Discovery and validation of DNA methylation markers for overall survival prognosis in patients with thymic epithelial tumors

description: Table S2. List of significantly expressed methylation probes. In this table, the “mean_AB” and “mean_C” stands for the average values of beta values in cases with WHO histological type A to B3 and WHO histological type C, respectively. “FC” for fold changes which is calculated as (mean_C- mean_AB)/mean_AB. The “p” for crude probabilities resulting from t test for each probe. (XLSX 1490 kb)
DOI: 10.6084/m9.figshare.7802789.v1
title: Additional file 1: of Discovery and validation of DNA methylation markers for overall survival prognosis in patients with thymic epithelial tumors

description: Table S2. List of significantly expressed methylation probes. In this table, the “mean_AB” and “mean_C” stands for the average values of beta values in cases with WHO histological type A to B3 and WHO histological type C, respectively. “FC” for fold changes which is calculated as (mean_C- mean_AB)/mean_AB. The “p” for crude probabilities resulting from t test for each probe. (XLSX 1490 kb)
DOI: 10.6084/m9.figshare.7802795
title: Additional file 2: of Discovery and validation of DNA methylation markers for overall survival prognosis in patients with thymic epithelial tumors

description: Table S3. Results from KEGG enrichment analysis for genes corresponding to the significantly expressed methylation probes. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7802795.v1
title: Additional file 2: of Discovery and validation of DNA methylation markers for overall survival prognosis in patients with thymic epithelial tumors

description: Table S3. Results from KEGG enrichment analysis for genes corresponding to the significantly expressed methylation probes. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7802804
title: Additional file 3: of Discovery and validation of DNA methylation markers for overall survival prognosis in patients with thymic epithelial tumors

description: Table S4. The list of genes transcriptionally affected by methylation of significantly expressed methylation probes within promotor regions. In this table, meaning of the “mean_AB”, “mean_C”, “FC” and “p” is the same asdescribed in “Additional file 1: Table S2”. (XLSX 119 kb)