cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19663904.v1
title: Expression of ATP-binding cassette subfamily B member 1 gene in peripheral blood of patients with acute myocardial infarction

description: This study aimed to determine the amount of expression of the <i>ATP-binding cassette subfamily B member 1 (ABCB1)</i> gene chip as a prospective diagnostic marker for acute myocardial infarction (AMI) in a wide population . In the AMI and control groups, 113 patients with AMI and 83 persons with non-coronary artery disease were selected for peripheral venous leukocyte collection. Western blot and real-time polymerase chain reaction (RT-PCR) were employed to detect relative <i>ABCB1</i> expression in both groups. The results showed that the <i>ABCB1</i> transcription and protein levels in the AMI group were higher than in the control. The relative mRNA expression of <i>ABCB1</i> was 0.26 (0.03–0.79) in the AMI group and 0.13 (0.01–0.52) in the control group (P &lt; 0.05). The expression of the <i>ABCB1</i> gene at the protein level in the AMI group was 1.65 times that in the control (P &lt; 0.05). Further, the subjects in the AMI group were older (P &lt; 0.001), had lower levels of high-density lipoprotein cholesterol (P = 0.038), and had higher incidence of type II diabetes mellitus (P = 0.003) compared with the control. Logistic regression analysis showed that the expression of <i>ABCB1</i> in peripheral blood was correlated with the occurrence of AMI (P = 0.003). High <i>ABCB1</i> expression, type II diabetes, and advanced age were found to serve as potential independent risk factors for AMI, with a 4.88-fold, 2.99-fold, and 2.63-fold increased risk of AMI. Overall, the high expression of <i>ABCB1</i> in peripheral blood might be related to the occurrence of AMI.
DOI: 10.6084/m9.figshare.13372313
title: Elevated atherogenic index and higher triglyceride increase risk of kidney function decline: a 7-year cohort study in Chinese adults

description: This study explored whether lipid disorders or an elevated atherogenic index of plasma (AIP, a risk factor for cardiovascular diseases) could predict major kidney function decline. We conducted a retrospective 7-year cohort study of 3712 Chinese adults followed up between 2010 and 2017. Major kidney function decline was defined as <i>a</i> ≥ 30% reduction in the estimated glomerular filtration rate (eGFR) from baseline. Multivariable logistic regression models were used to evaluate the relationship between lipid profiles and major kidney function decline. Smoking habits, waist circumference, and physical activity were not assessed. During the 7-year follow-up, 1.70% (<i>n</i> = 63) of the participants developed major kidney function decline. After adjustment for potential confounders, the odds ratios (ORs) for developing eGFR decline with per standard deviation increase were 1.23 [95% confidence interval (CI): 1.06–1.43] for triglyceride and 2.55 (95% CI: 1.01–6.42) for AIP in all participants. Furthermore, in the stratified analysis, we found sex-related differences; triglyceride and AIP were only independently associated with the risk of eGFR decline in men (OR, 1.27, 95% CI: 1.08–1.48; OR, 3.98, 95% CI: 1.22–12.99, respectively). When the participants were divided into groups according to the baseline lipid status, association was observed only between abnormal AIP and eGFR decline (all <i>p</i> values &lt; 0.05). Our findings suggest that a higher serum triglyceride level or an elevated AIP increases the risk of major kidney function decline in Chinese men with normal kidney function. Thus, assessment of AIP may help identify the risk of eGFR decline.
DOI: 10.6084/m9.figshare.14944954
title: Additional file 4 of Construction of lncRNA-related competing endogenous RNA network and identification of hub genes in recurrent implantation failure

description: Additional file 4: Table S2. Predicted lncRNA-miRNA and mRNA-miRNA pairs for WGCNA modules. WGCNA, weighted gene co‐expression network analysis.
DOI: 10.6084/m9.figshare.14944960.v1
title: Additional file 6 of Construction of lncRNA-related competing endogenous RNA network and identification of hub genes in recurrent implantation failure

description: Additional file 6: Table S4. Topological characteristics of 23 genes overlapped in WGCNA and ceRNA networks. WGCNA, weighted gene co‐expression network analysis; ceRNA, competing endogenous RNA.
DOI: 10.6084/m9.figshare.14944957.v1
title: Additional file 5 of Construction of lncRNA-related competing endogenous RNA network and identification of hub genes in recurrent implantation failure

description: Additional file 5: Table S3. Predicted lncRNA-miRNA and mRNA-miRNA pairs for the seven hub lncRNA-related ceRNA networks. ceRNA, competing endogenous RNA.
DOI: 10.6084/m9.figshare.14944960
title: Additional file 6 of Construction of lncRNA-related competing endogenous RNA network and identification of hub genes in recurrent implantation failure

description: Additional file 6: Table S4. Topological characteristics of 23 genes overlapped in WGCNA and ceRNA networks. WGCNA, weighted gene co‐expression network analysis; ceRNA, competing endogenous RNA.
DOI: 10.6084/m9.figshare.7138730
title: Additional file 5: of Identification, characterization and expression analysis of the VQ motif-containing gene family in tea plant (Camellia sinensis)

description: Table S4. List of predicted novel microRNA target sites of CsVQ transcripts. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8129642.v1
title: Additional file 1: of A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph

description: The results of prediction of known cancer genes for lung, breast and prostate cancer. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.13372313.v1
title: Elevated atherogenic index and higher triglyceride increase risk of kidney function decline: a 7-year cohort study in Chinese adults

description: This study explored whether lipid disorders or an elevated atherogenic index of plasma (AIP, a risk factor for cardiovascular diseases) could predict major kidney function decline. We conducted a retrospective 7-year cohort study of 3712 Chinese adults followed up between 2010 and 2017. Major kidney function decline was defined as <i>a</i> ≥ 30% reduction in the estimated glomerular filtration rate (eGFR) from baseline. Multivariable logistic regression models were used to evaluate the relationship between lipid profiles and major kidney function decline. Smoking habits, waist circumference, and physical activity were not assessed. During the 7-year follow-up, 1.70% (<i>n</i> = 63) of the participants developed major kidney function decline. After adjustment for potential confounders, the odds ratios (ORs) for developing eGFR decline with per standard deviation increase were 1.23 [95% confidence interval (CI): 1.06–1.43] for triglyceride and 2.55 (95% CI: 1.01–6.42) for AIP in all participants. Furthermore, in the stratified analysis, we found sex-related differences; triglyceride and AIP were only independently associated with the risk of eGFR decline in men (OR, 1.27, 95% CI: 1.08–1.48; OR, 3.98, 95% CI: 1.22–12.99, respectively). When the participants were divided into groups according to the baseline lipid status, association was observed only between abnormal AIP and eGFR decline (all <i>p</i> values &lt; 0.05). Our findings suggest that a higher serum triglyceride level or an elevated AIP increases the risk of major kidney function decline in Chinese men with normal kidney function. Thus, assessment of AIP may help identify the risk of eGFR decline.
DOI: 10.6084/m9.figshare.7080968.v1
title: Convex Bidirectional Large Margin Classifiers

description: Classification problems are commonly seen in practice. In this article, we aim to develop classifiers that can enjoy great interpretability as linear classifiers, and at the same time have model flexibility as nonlinear classifiers. We propose convex bidirectional large margin classifiers to fill the gap between linear and general nonlinear classifiers for high-dimensional data. Our method provides a new data visualization tool for classification of high-dimensional data. The obtained bilinear projection structure makes the proposed classifier very interpretable. Additional shrinkage to approximate variable selection is also considered. Through analysis of simulated and real data in high-dimensional settings, our method is shown to have superior prediction performance and interpretability when there are potential subpopulations in the data. The computer code of the proposed method is available as supplemental materials.
DOI: 10.6084/m9.figshare.8129522
title: Additional file 2: of Biological and RNA regulatory function of MOV10 in mammalian germ cells

description: Table S2. Transcript IDs with different 3â ˛-UTR length corresponding to 13,210 mRNA targets. (XLS 1387 kb)
DOI: 10.6084/m9.figshare.8129648
title: Additional file 2: of A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph

description: The results of GO and KEGG enrichment analysis in lung cancer. (XLSX 114 kb)
DOI: 10.6084/m9.figshare.8129654
title: Additional file 3: of A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph

description: The results of GO and KEGG enrichment analysis in breast cancer. (XLSX 147 kb)
DOI: 10.6084/m9.figshare.8129522.v1
title: Additional file 2: of Biological and RNA regulatory function of MOV10 in mammalian germ cells

description: Table S2. Transcript IDs with different 3â ˛-UTR length corresponding to 13,210 mRNA targets. (XLS 1387 kb)
DOI: 10.6084/m9.figshare.12848090
title: Intracranial collaterals and arterial wall features in severe symptomatic vertebrobasilar stenosis

description: The protective role of intracranial primary collaterals on plaque vulnerability is not well established. We aimed to explore the association of intracranial collateral status with arterial wall features including arterial remodeling and culprit plaque features in severe symptomatic intracranial vertebrobasilar atherosclerosis (sIVBAS). Posterior circulation stroke or TIA patients owing to sIVBAS from a three-dimensional high-resolution MRI (3D HRMRI) prospective observational study was included for current analysis. Participants were dichotomized into poor and good collateral groups according to a modified semiquantitative grading system for primary collateral of posterior circulation. Differences of arterial remodeling, culprit plaque distribution, enhancement, intraplaque hemorrhage (IPH), and calcification on HRMRI were compared between the two groups. Seventy-four eligible patients were included, wherein 39 in poor collateral group and 35 in good collateral group. The average age was 57.0 ± 9.0 years, 65 (87.8%) were male, 62 (83.8%) were diagnosed with ischemic stroke and 12 (16.2%) with TIA. Patients with good collateral had lower occurrence of arterial positive remodeling and plaque diffuse distribution, enhancement (Adjusted OR = 0.17 [0.05–0.54], p &lt; 0.01; adjusted OR = 0.26 [0.06–0.99], p = 0.05; adjusted OR = 0.17 [0.03–0.96], p = 0.04, respectively). No significant differences on IPH and calcification were found between poor and good collateral group (p &gt; 0.05). Intracranial good collateral of posterior circulation may be associated with lower risk of arterial positive remodeling and culprit plaque diffuse distribution, plaque enhancement in patients with severe sIVBAS. clinicaltrials.gov Identifier: NCT02705599.
DOI: 10.6084/m9.figshare.12848090.v1
title: Intracranial collaterals and arterial wall features in severe symptomatic vertebrobasilar stenosis

description: The protective role of intracranial primary collaterals on plaque vulnerability is not well established. We aimed to explore the association of intracranial collateral status with arterial wall features including arterial remodeling and culprit plaque features in severe symptomatic intracranial vertebrobasilar atherosclerosis (sIVBAS). Posterior circulation stroke or TIA patients owing to sIVBAS from a three-dimensional high-resolution MRI (3D HRMRI) prospective observational study was included for current analysis. Participants were dichotomized into poor and good collateral groups according to a modified semiquantitative grading system for primary collateral of posterior circulation. Differences of arterial remodeling, culprit plaque distribution, enhancement, intraplaque hemorrhage (IPH), and calcification on HRMRI were compared between the two groups. Seventy-four eligible patients were included, wherein 39 in poor collateral group and 35 in good collateral group. The average age was 57.0 ± 9.0 years, 65 (87.8%) were male, 62 (83.8%) were diagnosed with ischemic stroke and 12 (16.2%) with TIA. Patients with good collateral had lower occurrence of arterial positive remodeling and plaque diffuse distribution, enhancement (Adjusted OR = 0.17 [0.05–0.54], p &lt; 0.01; adjusted OR = 0.26 [0.06–0.99], p = 0.05; adjusted OR = 0.17 [0.03–0.96], p = 0.04, respectively). No significant differences on IPH and calcification were found between poor and good collateral group (p &gt; 0.05). Intracranial good collateral of posterior circulation may be associated with lower risk of arterial positive remodeling and culprit plaque diffuse distribution, plaque enhancement in patients with severe sIVBAS. clinicaltrials.gov Identifier: NCT02705599.
DOI: 10.6084/m9.figshare.9178235
title: Additional file 6: of Improved the expression level of active transglutaminase by directional increasing copy of mtg gene in Pichia pastoris

description: Table S1, Figure S3. Effect on expression and enzyme activity of mtg gene copies. Table S1. The MTG activity in different copy strains. Figure S6. Detection of protein expression in strains with different mtg copy by Western blotting. The protein (MTG) in 20 μl of culture supernatant were separated by Western blot analysis (anti-MTG). Lane 1–3: mtg-2c, lane 4–6: mtg-3c, lane 7–9: mtg-6c. (ZIP 48 kb)
DOI: 10.6084/m9.figshare.9178235.v1
title: Additional file 6: of Improved the expression level of active transglutaminase by directional increasing copy of mtg gene in Pichia pastoris

description: Table S1, Figure S3. Effect on expression and enzyme activity of mtg gene copies. Table S1. The MTG activity in different copy strains. Figure S6. Detection of protein expression in strains with different mtg copy by Western blotting. The protein (MTG) in 20 μl of culture supernatant were separated by Western blot analysis (anti-MTG). Lane 1–3: mtg-2c, lane 4–6: mtg-3c, lane 7–9: mtg-6c. (ZIP 48 kb)
DOI: 10.6084/m9.figshare.8129642
title: Additional file 1: of A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph

description: The results of prediction of known cancer genes for lung, breast and prostate cancer. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8129546.v1
title: Additional file 5: of Biological and RNA regulatory function of MOV10 in mammalian germ cells

description: Table S6. Mass spectrometry analysis of subcellular MOV10 IP in mice testes. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.12848138.v1
title: Time varying mixed effects model with fused lasso regularization

description: The associations between covariates and the outcomes often vary over time, regardless of whether the covariate is time-varying or time-invariant. For example, we hypothesize that the impact of chronic diseases, such as diabetes and heart disease, on people’s physical functions differ with aging. However, the age-varying effect would be missed if one models the covariate simply as a time-invariant covariate (yes/no) with a time-constant coefficient. We propose a fused lasso-based time-varying linear mixed effect (FTLME) model and an efficient two-stage parameter estimation algorithm to estimate the longitudinal trajectories of fixed-effect coefficients. Simulation studies are presented to demonstrate the efficacy of the method and its computational efficiency in estimating smooth time-varying effects in high dimensional settings. A real data example on the Health and Retirement Study (HRS) analysis is used to demonstrate the practical usage of our method to infer age-varying impact of chronic disease on older people’s physical functions.
DOI: 10.6084/m9.figshare.12848138
title: Time varying mixed effects model with fused lasso regularization

description: The associations between covariates and the outcomes often vary over time, regardless of whether the covariate is time-varying or time-invariant. For example, we hypothesize that the impact of chronic diseases, such as diabetes and heart disease, on people’s physical functions differ with aging. However, the age-varying effect would be missed if one models the covariate simply as a time-invariant covariate (yes/no) with a time-constant coefficient. We propose a fused lasso-based time-varying linear mixed effect (FTLME) model and an efficient two-stage parameter estimation algorithm to estimate the longitudinal trajectories of fixed-effect coefficients. Simulation studies are presented to demonstrate the efficacy of the method and its computational efficiency in estimating smooth time-varying effects in high dimensional settings. A real data example on the Health and Retirement Study (HRS) analysis is used to demonstrate the practical usage of our method to infer age-varying impact of chronic disease on older people’s physical functions.
DOI: 10.6084/m9.figshare.22810102
title: U–Pb geochronology and geochemistry of dikes in the Changbaishan Tianchi volcanic field (NE China) and their relations with the coeval Jingbohu and Longgang monogenetic volcanic fields

description: The plain around the intraplate Changbaishan Tianchi volcano in NE China includes monogenetic cones whose shallowest plumbing system consists of dikes, and three main phases of activity are recognized since 2.8 Ma. The monogenetic volcanism mainly developed in the shield-forming phase (2.8–0.3 Ma), but the age and geochemical features of many of these vents remain poorly known. Here, we present geochemical, Sr‒Nd‒Pb isotopic and zircon trace element data from two dikes feeding monogenetic vents located north and northwest of the Changbaishan Tianchi volcano. Our aim is to constrain the emplacement age, the magma evolution processes, and the mantle source. We compare our results with those from the Jingbohu and Longgang monogenetic vents located north and west of the Changbaishan Tianchi volcano to investigate possible mantle heterogeneities in the recent NE China volcanism. The two Changbaishan dikes have <sup>230</sup>Th disequilibrium-corrected ages of 1.27 and 1.00 Ma and show a basaltic composition with a potassic affinity. The Mg<sup>#</sup> values are 35.48–34.27 and 66.09–65.79. The whole-rock compositions, trace element compositions, and Sr‒Nd variations are consistent with fractional crystallization and minor contamination with lower crustal material, indicating an OIB-like mantle source with an EMI component possibly related to fluids released from the underlying Pacific flat slab. The melting depth determined from Na/Ti and Sm/Yb is between 140 and 180 km, i.e. the asthenospheric mantle. The dikes are characterized by (K<sub>2</sub>O+Na<sub>2</sub>O)/δEu, La/Ba, Ba/Nb, La/Sm, and La/Nb values similar to those of the Jingbohu and Longgang basaltic rocks. We conclude that the NE China volcanism at approximately 1 Ma was related to a single, relatively homogeneous OIB-like mantle source modified by ascending slab-derived fluids. According to the available geophysical data, the ascending magmas stopped at the mantle/lower crust interface and experienced limited crustal contamination.
DOI: 10.6084/m9.figshare.22810102.v1
title: U–Pb geochronology and geochemistry of dikes in the Changbaishan Tianchi volcanic field (NE China) and their relations with the coeval Jingbohu and Longgang monogenetic volcanic fields

description: The plain around the intraplate Changbaishan Tianchi volcano in NE China includes monogenetic cones whose shallowest plumbing system consists of dikes, and three main phases of activity are recognized since 2.8 Ma. The monogenetic volcanism mainly developed in the shield-forming phase (2.8–0.3 Ma), but the age and geochemical features of many of these vents remain poorly known. Here, we present geochemical, Sr‒Nd‒Pb isotopic and zircon trace element data from two dikes feeding monogenetic vents located north and northwest of the Changbaishan Tianchi volcano. Our aim is to constrain the emplacement age, the magma evolution processes, and the mantle source. We compare our results with those from the Jingbohu and Longgang monogenetic vents located north and west of the Changbaishan Tianchi volcano to investigate possible mantle heterogeneities in the recent NE China volcanism. The two Changbaishan dikes have <sup>230</sup>Th disequilibrium-corrected ages of 1.27 and 1.00 Ma and show a basaltic composition with a potassic affinity. The Mg<sup>#</sup> values are 35.48–34.27 and 66.09–65.79. The whole-rock compositions, trace element compositions, and Sr‒Nd variations are consistent with fractional crystallization and minor contamination with lower crustal material, indicating an OIB-like mantle source with an EMI component possibly related to fluids released from the underlying Pacific flat slab. The melting depth determined from Na/Ti and Sm/Yb is between 140 and 180 km, i.e. the asthenospheric mantle. The dikes are characterized by (K<sub>2</sub>O+Na<sub>2</sub>O)/δEu, La/Ba, Ba/Nb, La/Sm, and La/Nb values similar to those of the Jingbohu and Longgang basaltic rocks. We conclude that the NE China volcanism at approximately 1 Ma was related to a single, relatively homogeneous OIB-like mantle source modified by ascending slab-derived fluids. According to the available geophysical data, the ascending magmas stopped at the mantle/lower crust interface and experienced limited crustal contamination.