cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5108626
title: Sequential Co-Sparse Factor Regression

description: In multivariate regression models, a sparse singular value decomposition of the regression component matrix is appealing for reducing dimensionality and facilitating interpretation. However, the recovery of such a decomposition remains very challenging, largely due to the simultaneous presence of orthogonality constraints and co-sparsity regularization. By delving into the underlying statistical data generation mechanism, we reformulate the problem as a supervised co-sparse factor analysis, and develop an efficient computational procedure, named sequential factor extraction via co-sparse unit-rank estimation (SeCURE), that completely bypasses the orthogonality requirements. At each step, the problem reduces to a sparse multivariate regression with a unit-rank constraint. Nicely, each sequentially extracted sparse and unit-rank coefficient matrix automatically leads to co-sparsity in its pair of singular vectors. Each latent factor is thus a sparse linear combination of the predictors and may influence only a subset of responses. The proposed algorithm is guaranteed to converge, and it ensures efficient computation even with incomplete data and/or when enforcing exact orthogonality is desired. Our estimators enjoy the oracle properties asymptotically; a non-asymptotic error bound further reveals some interesting finite-sample behaviors of the estimators. The efficacy of SeCURE is demonstrated by simulation studies and two applications in genetics. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5108626.v1
title: Sequential Co-Sparse Factor Regression

description: In multivariate regression models, a sparse singular value decomposition of the regression component matrix is appealing for reducing dimensionality and facilitating interpretation. However, the recovery of such a decomposition remains very challenging, largely due to the simultaneous presence of orthogonality constraints and co-sparsity regularization. By delving into the underlying statistical data generation mechanism, we reformulate the problem as a supervised co-sparse factor analysis, and develop an efficient computational procedure, named sequential factor extraction via co-sparse unit-rank estimation (SeCURE), that completely bypasses the orthogonality requirements. At each step, the problem reduces to a sparse multivariate regression with a unit-rank constraint. Nicely, each sequentially extracted sparse and unit-rank coefficient matrix automatically leads to co-sparsity in its pair of singular vectors. Each latent factor is thus a sparse linear combination of the predictors and may influence only a subset of responses. The proposed algorithm is guaranteed to converge, and it ensures efficient computation even with incomplete data and/or when enforcing exact orthogonality is desired. Our estimators enjoy the oracle properties asymptotically; a non-asymptotic error bound further reveals some interesting finite-sample behaviors of the estimators. The efficacy of SeCURE is demonstrated by simulation studies and two applications in genetics. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5109808
title: Pharmacological Risk Factors Associated with Hospital Readmission Rates in a Psychiatric Cohort Identified using Prescriptome Data Mining

description: <i>Using prescription data mining approach, we identified factors influencing readmission in a cohort of 1,275 patients. </i>
DOI: 10.6084/m9.figshare.5109808.v1
title: Pharmacological Risk Factors Associated with Hospital Readmission Rates in a Psychiatric Cohort Identified using Prescriptome Data Mining

description: <i>Using prescription data mining approach, we identified factors influencing readmission in a cohort of 1,275 patients. </i>
DOI: 10.6084/m9.figshare.5109808.v3
title: Pharmacological Risk Factors Associated with Hospital Readmission Rates in a Psychiatric Cohort Identified using Prescriptome Data Mining

description: <i>Using prescription data mining approach, we identified factors influencing readmission in a cohort of 1,275 patients. </i>
DOI: 10.6084/m9.figshare.5109808.v2
title: Pharmacological Risk Factors Associated with Hospital Readmission Rates in a Psychiatric Cohort Identified using Prescriptome Data Mining

description: <i>Using prescription data mining approach, we identified factors influencing readmission in a cohort of 1,275 patients. </i>
DOI: 10.6084/m9.figshare.5110114
title: Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

description: Sequence matrix for phylogenetic analysis.
DOI: 10.6084/m9.figshare.5110114.v1
title: Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

description: Sequence matrix for phylogenetic analysis.
DOI: 10.6084/m9.figshare.5114050
title: Validation efficiency of coupling of beads and probes, used in high-throughput multiplexed nucleic acid detection of respiratory and reproductive pathogens in swine

description: This file set contains results files from the Bio-Plex integrated biomolecular assay system, each containing the data from a reading, the Protocol parameters used to collect that data and analysis tools for interpreting the data. The .rbx format data files must be opened by the Bio-Plex Manager integrated software. Please see the references link below for .xls format data related to this study.<br><br>Magnetic carboxylic beads were coupled to different virus probes as follows: PRV (no. 26), PRRSV (no. 29), CSFV (no. 34), JEV (no. 36), PCV-2 (no. 46), ASFV (no. 62) and PPV (no. 65). <br>Validation of coupling was performed with different amounts of biotin-modified RCS. The curve was drawn with 0, 5, 10, 20, 50, 100 and 200 fmol RCS, respectively.<br>Article abstract:<br>Background: The aim of this study was to develop a multiple PCR assay based on the suspension array system for the simultaneous detection of respiratory and reproductive pathogens in swine. Pseudorabies virus (PRV), Japanese encephalitis virus (JEV), classic swine fever virus (CFSV), African swine fever virus (ASFV), porcine circovirus type 2 (PCV-2), porcine reproductive and respiratory syndrome virus (PRRSV) and porcine parvovirus (PPV) are the major respiratory and reproductive viral pathogens in pig farms.<br>Results: Seven pairs of specific primers and probes were designed, and multiple PCR was performed, with the PCR products hybridized to beads coupled to probes, which were then detected by Bio-Plex suspension array system. The limit of detection, specificity and repeatability of this method was determined. The assay was further tested using 137 clinical samples, and the results were compared with conventional PCR to evaluate the ability of the method to diagnose porcine viruses. The results showed that the assay had a high degree of specificity and repeatability, and the simultaneous detection limit for the seven viruses reached 103 copies/μL. The detection of viruses in clinical samples using the Bio-Plex method was high and comparable to conventional PCR (&gt; 90%).
DOI: 10.6084/m9.figshare.5114050.v1
title: Validation efficiency of coupling of beads and probes, used in high-throughput multiplexed nucleic acid detection of respiratory and reproductive pathogens in swine

description: This file set contains results files from the Bio-Plex integrated biomolecular assay system, each containing the data from a reading, the Protocol parameters used to collect that data and analysis tools for interpreting the data. The .rbx format data files must be opened by the Bio-Plex Manager integrated software. Please see the references link below for .xls format data related to this study.<br><br>Magnetic carboxylic beads were coupled to different virus probes as follows: PRV (no. 26), PRRSV (no. 29), CSFV (no. 34), JEV (no. 36), PCV-2 (no. 46), ASFV (no. 62) and PPV (no. 65). <br>Validation of coupling was performed with different amounts of biotin-modified RCS. The curve was drawn with 0, 5, 10, 20, 50, 100 and 200 fmol RCS, respectively.<br>Article abstract:<br>Background: The aim of this study was to develop a multiple PCR assay based on the suspension array system for the simultaneous detection of respiratory and reproductive pathogens in swine. Pseudorabies virus (PRV), Japanese encephalitis virus (JEV), classic swine fever virus (CFSV), African swine fever virus (ASFV), porcine circovirus type 2 (PCV-2), porcine reproductive and respiratory syndrome virus (PRRSV) and porcine parvovirus (PPV) are the major respiratory and reproductive viral pathogens in pig farms.<br>Results: Seven pairs of specific primers and probes were designed, and multiple PCR was performed, with the PCR products hybridized to beads coupled to probes, which were then detected by Bio-Plex suspension array system. The limit of detection, specificity and repeatability of this method was determined. The assay was further tested using 137 clinical samples, and the results were compared with conventional PCR to evaluate the ability of the method to diagnose porcine viruses. The results showed that the assay had a high degree of specificity and repeatability, and the simultaneous detection limit for the seven viruses reached 103 copies/μL. The detection of viruses in clinical samples using the Bio-Plex method was high and comparable to conventional PCR (&gt; 90%).
DOI: 10.6084/m9.figshare.5114242
title: Placental imprinting variation associated with assisted reproductive technologies and subfertility

description: Infertility affects one in 6 couples in developed nations, resulting in an increasing use of assisted reproductive technologies (ART). Both ART and subfertility appear to be linked to lower birth weight outcomes, setting infants up for poor long-term health. Prenatal growth is, in part, regulated via epigenetically-controlled imprinted genes in the placenta. Although differences in DNA methylation between ART and control infants have been found, it remains unclear whether these differences are due to the ART procedures or to the underlying parental subfertility and how these methylation differences affect imprinted gene expression. In this study, we examined the expression of 108 imprinted genes in placental tissues from infants born to subfertile parents (n = 79), matched naturally-conceived controls (n = 158), and infants conceived using <i>in vitro</i> fertilization (IVF, n = 18). Forty-five genes were identified as having significantly different expression between the subfertile infants and controls, whereas no significant differences were identified between the IVF and control groups. The expression of 4 genes—<i>IGF2, NAPIL5, PAX8-AS1</i>, and <i>TUBGCP5</i>—was significantly downregulated in the IVF compared with the subfertile group. Three of the 45 genes significantly dysregulated between subfertile and control placentae—<i>GRB10, NDN</i>, and <i>CD44</i> —were found to have a significant positive correlation between expression and birth weight. Methylation levels for these 3 genes and 4 others—<i>MKRN3, WRB, DHCR24</i>, and <i>CYR61</i>—were significantly correlated with expression. Our findings indicate that epigenetic differences in placentas resulting from IVF pregnancies may be related to the underlying subfertility in parents using IVF rather than the IVF procedure itself.
DOI: 10.6084/m9.figshare.5114242.v2
title: Placental imprinting variation associated with assisted reproductive technologies and subfertility

description: Infertility affects one in 6 couples in developed nations, resulting in an increasing use of assisted reproductive technologies (ART). Both ART and subfertility appear to be linked to lower birth weight outcomes, setting infants up for poor long-term health. Prenatal growth is, in part, regulated via epigenetically-controlled imprinted genes in the placenta. Although differences in DNA methylation between ART and control infants have been found, it remains unclear whether these differences are due to the ART procedures or to the underlying parental subfertility and how these methylation differences affect imprinted gene expression. In this study, we examined the expression of 108 imprinted genes in placental tissues from infants born to subfertile parents (n = 79), matched naturally-conceived controls (n = 158), and infants conceived using <i>in vitro</i> fertilization (IVF, n = 18). Forty-five genes were identified as having significantly different expression between the subfertile infants and controls, whereas no significant differences were identified between the IVF and control groups. The expression of 4 genes—<i>IGF2, NAPIL5, PAX8-AS1</i>, and <i>TUBGCP5</i>—was significantly downregulated in the IVF compared with the subfertile group. Three of the 45 genes significantly dysregulated between subfertile and control placentae—<i>GRB10, NDN</i>, and <i>CD44</i> —were found to have a significant positive correlation between expression and birth weight. Methylation levels for these 3 genes and 4 others—<i>MKRN3, WRB, DHCR24</i>, and <i>CYR61</i>—were significantly correlated with expression. Our findings indicate that epigenetic differences in placentas resulting from IVF pregnancies may be related to the underlying subfertility in parents using IVF rather than the IVF procedure itself.
DOI: 10.6084/m9.figshare.5114242.v1
title: Placental Imprinting Variation Associated with Assisted Reproductive Technologies and Subfertility

description: Infertility affects one in six couples in developed nations, resulting in an increasing use of assisted reproductive technologies (ART). Both ART and subfertility appear to be linked to lower birth weight outcomes, setting infants up for poor long-term health. Prenatal growth is, in part, regulated via epigenetically controlled imprinted genes in the placenta. Although differences in DNA methylation between ART and control infants have been found, it remains unclear whether these differences are due to the ART procedures or to the underlying parental subfertility and how these methylation differences affect imprinted gene expression. In this study, we examined the expression of 108 imprinted genes in placental tissues from infants born to subfertile parents (n = 79), matched naturally conceived controls (n = 158), and infants conceived using <i>in vitro</i> fertilization (IVF, n = 18). Forty-five genes were identified as having significantly different expression between the subfertile infants and controls, whereas no significant differences were identified between the IVF and control groups. The expression of four genes—<i>IGF2, NAPIL5, PAX8-AS1</i>, and <i>TUBGCP5</i>—was significantly downregulated in the IVF compared to the subfertile group. Three of the 45 genes significantly dysregulated between subfertile and control placentae—<i>GRB10, NDN</i>, and <i>CD44</i> —were found to have a significant positive correlation between expression and birth weight. Methylation levels for these three genes and four others—<i>MKRN3, WRB, DHCR24</i>, and <i>CYR61</i>—were significantly correlated with expression. Our findings indicate that epigenetic differences in placentas resulting from IVF pregnancies may be related to the underlying subfertility in parents utilizing IVF rather than the IVF procedure itself.
DOI: 10.6084/m9.figshare.5117914
title: Analysis of Field Return Data With Failed-But-Not-Reported Events

description: Warranty data contain valuable information on product field reliability and customer behaviors. Most previous studies on analysis of warranty data implicitly assume that all failures within the warranty period are reported and recorded. However, the failed-but-not-reported (FBNR) phenomenon is quite common for a product whose price is not very high. Ignorance of the FBNR phenomenon leads to an overestimate of product reliability based on field return data or an overestimate of warranty cost based on lab data or tracking data. Being an indicator of customer satisfaction, the FBNR proportion provides valuable managerial insights. In this study, statistical inference for the FBNR phenomenon as well as field lifetime distribution is described. We first propose a flexible FBNR function to model the time-dependent FBNR behavior. Then, a framework for data analysis is developed. In the framework, both semiparametric and parametric approaches are used to jointly analyze warranty claim data and supplementary tracking data from a follow-up of selected customers. The FBNR problem in the tracking data is minimal and thus the data can be used to effectively decouple the FBNR information from the warranty claim data. The proposed methods are illustrated with an example. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5117914.v1
title: Analysis of Field Return Data With Failed-But-Not-Reported Events

description: Warranty data contain valuable information on product field reliability and customer behaviors. Most previous studies on analysis of warranty data implicitly assume that all failures within the warranty period are reported and recorded. However, the failed-but-not-reported (FBNR) phenomenon is quite common for a product whose price is not very high. Ignorance of the FBNR phenomenon leads to an overestimate of product reliability based on field return data or an overestimate of warranty cost based on lab data or tracking data. Being an indicator of customer satisfaction, the FBNR proportion provides valuable managerial insights. In this study, statistical inference for the FBNR phenomenon as well as field lifetime distribution is described. We first propose a flexible FBNR function to model the time-dependent FBNR behavior. Then, a framework for data analysis is developed. In the framework, both semiparametric and parametric approaches are used to jointly analyze warranty claim data and supplementary tracking data from a follow-up of selected customers. The FBNR problem in the tracking data is minimal and thus the data can be used to effectively decouple the FBNR information from the warranty claim data. The proposed methods are illustrated with an example. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5139232
title: Association of the lipoprotein lipase gene Ser447Ter polymorphism with hypertension and blood pressure variation: evidence from an updated meta-analysis

description: The polymorphism of lipoprotein lipase (LPL) gene Ser447Ter (S447X) has long been linked to hypertension and blood pressure variation, but the established data remained controversial. To better elucidate this inconsistency, a meta-analysis was conducted. We comprehensively searched electronic databases, including Pubmed, EMBASE, China National Knowledge Infrastructure (CNKI), Web of Science, for all literatures with the last update on February 2016. The strength of association was calculated by using odds ratios (ORs) and weighted mean differences (WMDs) with corresponding 95% confidence intervals (CIs). Further stratified analyses, cumulative meta-analysis analysis, and sensitivity analyses were performed. A total of 14 studies (3592 cases and 4643 controls) for hypertension and 14 studies (<i>n</i> = 9254) for blood pressure were included. Overall, significant associations were revealed between S447X polymorphism and hypertension risk using allelic comparison (OR = 0.86, 95%CI 0.77 to 0.96), heterozygote comparison (OR = 0.85, 95%CI 0.75 to 0.96), and the dominant model (OR = 0.85, 95%CI 0.75 to 0.96), especially in Asians. Furthermore, in subgroup analyses restricted to the population-based controls studies, the high-quality studies, and the large sample size studies, these significant associations were still observed. As for blood pressure association, significant reductions of systolic blood pressure (WMD = −1.25 mmHg, 95%CI −2.25 to −0.25 mmHg) and diastolic blood pressure (WMD = −1.91 mmHg, 95%CI −3.25 to −0.56 mmHg) levels were found using dominant model. No publication bias was observed in any comparison model. Therefore, current meta-analysis suggested that the LPL S447X polymorphism is likely to be a protective factor in the development of hypertension.
DOI: 10.6084/m9.figshare.5139232.v1
title: Association of the lipoprotein lipase gene Ser447Ter polymorphism with hypertension and blood pressure variation: evidence from an updated meta-analysis

description: The polymorphism of lipoprotein lipase (LPL) gene Ser447Ter (S447X) has long been linked to hypertension and blood pressure variation, but the established data remained controversial. To better elucidate this inconsistency, a meta-analysis was conducted. We comprehensively searched electronic databases, including Pubmed, EMBASE, China National Knowledge Infrastructure (CNKI), Web of Science, for all literatures with the last update on February 2016. The strength of association was calculated by using odds ratios (ORs) and weighted mean differences (WMDs) with corresponding 95% confidence intervals (CIs). Further stratified analyses, cumulative meta-analysis analysis, and sensitivity analyses were performed. A total of 14 studies (3592 cases and 4643 controls) for hypertension and 14 studies (<i>n</i> = 9254) for blood pressure were included. Overall, significant associations were revealed between S447X polymorphism and hypertension risk using allelic comparison (OR = 0.86, 95%CI 0.77 to 0.96), heterozygote comparison (OR = 0.85, 95%CI 0.75 to 0.96), and the dominant model (OR = 0.85, 95%CI 0.75 to 0.96), especially in Asians. Furthermore, in subgroup analyses restricted to the population-based controls studies, the high-quality studies, and the large sample size studies, these significant associations were still observed. As for blood pressure association, significant reductions of systolic blood pressure (WMD = −1.25 mmHg, 95%CI −2.25 to −0.25 mmHg) and diastolic blood pressure (WMD = −1.91 mmHg, 95%CI −3.25 to −0.56 mmHg) levels were found using dominant model. No publication bias was observed in any comparison model. Therefore, current meta-analysis suggested that the LPL S447X polymorphism is likely to be a protective factor in the development of hypertension.
DOI: 10.6084/m9.figshare.25467679
title: Capstone Course Survey Data

description: Data from an experiential capstone course for fourth year medical students. This included various assessments of entrustable professional activities for entering residency.
DOI: 10.6084/m9.figshare.25467679.v1
title: Capstone Course Survey Data

description: Data from an experiential capstone course for fourth year medical students. This included various assessments of entrustable professional activities for entering residency.
DOI: 10.17909/a2k0-tf62
title: JWST observation of Star-Forming Clusters in the Extreme Outer Galaxy
DOI: 10.6084/m9.figshare.5146888
title: Analytical solution for solute concentration in the inner and outer domains of the eroding vascular graft. from Degradation and erosion mechanisms of bioresorbable porous acellular vascular grafts: an <i>in</i> <i>vitro</i> investigation.

description: This supplemental material provide details of the derivation of the analytical solution for solute (eroded PGS) concentration as a function of time and radial position resulting from diffusion of eroding PGS from the inner and outer surfaces of the graft.
DOI: 10.6084/m9.figshare.5146888.v1
title: Analytical solution for solute concentration in the inner and outer domains of the eroding vascular graft. from Degradation and erosion mechanisms of bioresorbable porous acellular vascular grafts: an <i>in</i> <i>vitro</i> investigation

description: This supplemental material provide details of the derivation of the analytical solution for solute (eroded PGS) concentration as a function of time and radial position resulting from diffusion of eroding PGS from the inner and outer surfaces of the graft.