cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7393133
title: Partition Weighted Approach For Estimating the Marginal Posterior Density With Applications

description: The computation of marginal posterior density in Bayesian analysis is essential in that it can provide complete information about parameters of interest. Furthermore, the marginal posterior density can be used for computing Bayes factors, posterior model probabilities, and diagnostic measures. The conditional marginal density estimator (CMDE) is theoretically the best for marginal density estimation but requires the closed-form expression of the conditional posterior density, which is often not available in many applications. We develop the partition weighted marginal density estimator (PWMDE) to realize the CMDE. This unbiased estimator requires only a single Markov chain Monte Carlo output from the joint posterior distribution and the known unnormalized posterior density. The theoretical properties and various applications of the PWMDE are examined in detail. The PWMDE method is also extended to the estimation of conditional posterior densities. We carry out simulation studies to investigate the empirical performance of the PWMDE and further demonstrate the desirable features of the proposed method with two real data sets from a study of dissociative identity disorder patients and a prostate cancer study, respectively. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7393142.v2
title: Robust and Accurate Inference via a Mixture of Gaussian and Student’s <i>t</i> Errors

description: A Gaussian measurement error assumption, that is, an assumption that the data are observed up to Gaussian noise, can bias any parameter estimation in the presence of outliers. A heavy tailed error assumption based on Student’s <i>t</i> distribution helps reduce the bias. However, it may be less efficient in estimating parameters if the heavy tailed assumption is uniformly applied to all of the data when most of them are normally observed. We propose a mixture error assumption that selectively converts Gaussian errors into Student’s <i>t</i> errors according to latent outlier indicators, leveraging the best of the Gaussian and Student’s <i>t</i> errors; a parameter estimation can be not only robust but also accurate. Using simulated hospital profiling data and astronomical time series of brightness data, we demonstrate the potential for the proposed mixture error assumption to estimate parameters accurately in the presence of outliers. Supplemental materials for this article are available online.
DOI: 10.7284/120126
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise OC1409C using a Sea-Bird SBE-911+ instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120129
title: Fluorometer data collected during research cruise OC1409C using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7393133.v1
title: Partition Weighted Approach for Estimating the Marginal Posterior Density with Applications

description: The computation of marginal posterior density in Bayesian analysis is essential in that it can provide complete information about parameters of interest. Furthermore, the marginal posterior density can be used for computing Bayes factors, posterior model probabilities, and diagnostic measures. The conditional marginal density estimator (CMDE) is theoretically the best for marginal density estimation but requires the closed-form expression of the conditional posterior density, which is often not available in many applications. We develop the partition weighted marginal density estimator (PWMDE) to realize the CMDE. This unbiased estimator requires only a single MCMC output from the joint posterior distribution and the known unnormalized posterior density. The theoretical properties and various applications of the PWMDE are examined in detail. The PWMDE method is also extended to the estimation of conditional posterior densities. We carry out simulation studies to investigate the empirical performance of the PWMDE and further demonstrate the desirable features of the proposed method with two real data sets from a study of dissociative identity disorder patients and a prostate cancer study, respectively.
DOI: 10.6084/m9.figshare.7393139.v3
title: Accelerating Bayesian Synthetic Likelihood With the Graphical Lasso

description: Simulation-based Bayesian inference methods are useful when the statistical model of interest does not possess a computationally tractable likelihood function. One such likelihood-free method is approximate Bayesian computation (ABC), which approximates the likelihood of a carefully chosen summary statistic via model simulation and nonparametric density estimation. ABC is known to suffer a curse of dimensionality with respect to the size of the summary statistic. When the model summary statistic is roughly normally distributed in regions of the parameter space of interest, Bayesian synthetic likelihood (BSL), which uses a normal likelihood approximation for a summary statistic, is a useful method that can be more computationally efficient than ABC. However, BSL requires estimation of the covariance matrix of the summary statistic for each proposed parameter, which requires a large number of simulations to estimate precisely using the sample covariance matrix when the summary statistic is high dimensional. In this article, we propose to use the graphical lasso to provide a sparse estimate of the precision matrix. This approach can estimate the covariance matrix accurately with significantly fewer model simulations. We discuss the nontrivial issue of tuning parameter choice in the context of BSL and demonstrate on several complex applications that our method, which we call BSLasso, provides significant improvements in computational efficiency whilst maintaining the ability to produce similar posterior distributions to BSL. The BSL and BSLasso methods applied to the examples of this article are implemented in the BSL package in R, which is available on the Comprehensive R Archive Network. Supplemental materials for this article are available online.
DOI: 10.6084/m9.figshare.7393037
title: Pigeon microbiome responses to probiotics

description: Sequences and metadata from a longitudinal study on birmingham roller pigeons microbiomes that were fed different probiotics.
DOI: 10.6084/m9.figshare.7393133.v2
title: Partition Weighted Approach For Estimating the Marginal Posterior Density With Applications

description: The computation of marginal posterior density in Bayesian analysis is essential in that it can provide complete information about parameters of interest. Furthermore, the marginal posterior density can be used for computing Bayes factors, posterior model probabilities, and diagnostic measures. The conditional marginal density estimator (CMDE) is theoretically the best for marginal density estimation but requires the closed-form expression of the conditional posterior density, which is often not available in many applications. We develop the partition weighted marginal density estimator (PWMDE) to realize the CMDE. This unbiased estimator requires only a single Markov chain Monte Carlo output from the joint posterior distribution and the known unnormalized posterior density. The theoretical properties and various applications of the PWMDE are examined in detail. The PWMDE method is also extended to the estimation of conditional posterior densities. We carry out simulation studies to investigate the empirical performance of the PWMDE and further demonstrate the desirable features of the proposed method with two real data sets from a study of dissociative identity disorder patients and a prostate cancer study, respectively. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7393133.v3
title: Partition Weighted Approach For Estimating the Marginal Posterior Density With Applications

description: The computation of marginal posterior density in Bayesian analysis is essential in that it can provide complete information about parameters of interest. Furthermore, the marginal posterior density can be used for computing Bayes factors, posterior model probabilities, and diagnostic measures. The conditional marginal density estimator (CMDE) is theoretically the best for marginal density estimation but requires the closed-form expression of the conditional posterior density, which is often not available in many applications. We develop the partition weighted marginal density estimator (PWMDE) to realize the CMDE. This unbiased estimator requires only a single Markov chain Monte Carlo output from the joint posterior distribution and the known unnormalized posterior density. The theoretical properties and various applications of the PWMDE are examined in detail. The PWMDE method is also extended to the estimation of conditional posterior densities. We carry out simulation studies to investigate the empirical performance of the PWMDE and further demonstrate the desirable features of the proposed method with two real data sets from a study of dissociative identity disorder patients and a prostate cancer study, respectively. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7393037.v1
title: Pigeon microbiome responses to probiotics

description: Sequences and metadata from a longitudinal study on birmingham roller pigeons microbiomes that were fed different probiotics.
DOI: 10.7284/120130
title: Gyrocompass data collected during research cruise OC1409C using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7392887
title: Supplementary Material for: microRNA-29a-3p, Up-Regulated in Human Gastric Cells and Tissues with <b><i>H.Pylori</i></b> Infection, Promotes the Migration of GES-1 Cells via A20-Mediated EMT Pathway

description: <b><i>Background/Aims:</i></b> <i>Helicobacter pylori</i> (<i>H. pylori</i>) infection is closely related to human gastric mucosa-associated diseases. Several recent studies on miRNAs have expanded our insights on <i>H.pylori</i> pathogenesis. This study aimed to investigate the biological roles and underlying molecular mechanisms of miR-29a-3p in human gastric cells and tissues with <i>H.pylori</i> infection. <b><i>Methods:</i></b> miR-29a-3p expression was quantified by quantitative RT-PCR (qRT-PCR). A miR-29a-3p target gene was validated by bioinformatics analysis, western blotting and dual luciferase reporter gene assays. Western blotting and immunohistochemistry (IHC) assay were performed to detect the protein expression. Transwell assay was used to determine the cell migration ability. <b><i>Results:</i></b> MiR-29a-3p was up-regulated in <i>H.pylori</i>-positive gastric mucosa tissues and <i>H.pylori</i>-infected gastric cells. The up-regulation of miR-29a-3p was dose-dependent in BGC-823 and GES-1 cells infected with <i>H.pylori</i>. Using gain- and loss-of-function experiments <i>in vitro</i>, we demonstrated that miR-29a-3p promoted the migration of gastric epithelial cells. We further characterized A20 as a direct target of miR-29a-3p. The expression of A20 was decreased in <i>H.pylori</i>-positive gastric mucosa tissues compared with <i>H.pylori</i>-negative gastric mucosa tissues. A20 downregulation was time- and dose-dependent in GES-1 and BGC-823 cells infected with <i>H.pylori</i>. In GES-1 and BGC-823 cells infected with <i>H.pylori</i>, the miR-29a-3p mimic significantly blocked A20 expression, which suggests that <i>H.pylori</i> decreased A20 expression through up-regulating miR-29a-3p in GES-1 and BGC-823 cells infected with <i>H.pylori</i>. The knockdown of A20 by siRNA enhanced the migration of human gastric epithelial cells and promoted the expression of Snail, Vimentin, and N-cadherin and inhibited the expression of E-cadherin. <b><i>Conclusion:</i></b> The miR-29a-3p may act as a tumor promotive miRNA by regulating cells migration through directly targeting of A20 gene in human gastric epithelial cells infected with <i>H.pylori</i>.
DOI: 10.6084/m9.figshare.7392791
title: Complete catalogue of lncRNA in genome-wide promoters across multiple human cancer cells

description: Promoter associated noncoding transcripts derived from 41 GRO-Seq datasets of human cancer cell lines in different conditions.Only non-overlapping promoters are considered. Sense and antisense transcripts relative to adjacent gene direction are reported.
DOI: 10.7284/120132
title: Hygrometer data collected during research cruise OC1409C using a Vaisala HMT300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7392776
title: Supplementary Material for: L-Carnitine Supplementation Increases Trimethylamine-N-Oxide but not Markers of Atherosclerosis in Healthy Aged Women

description: <b><i>Background:</i></b> L-carnitine can be metabolized to trimethylamine N-oxide (TMAO), a molecule that promotes atherogenesis through its interaction with macrophages and lipid metabolism. <b><i>Objective:</i></b> The aim of the present study was to assess whether L-carnitine supplementation may promote changes in selected serum biomarkers of atherosclerosis. <b><i>Methods:</i></b> Before the start, in the mid-point and after completing the 24-weeks supplementation protocol, fasting blood samples were taken from the antecubital vein. Plasma free L-carnitine and TMAO were determined by the UPLC/MS/MS method. Serum proteins were determined by the enzyme immunoassay method using commercially available kits. Total cholesterol, high-density lipoprotein-cholesterol, low-density lipoprotein-cholesterol, and triglycerides have been determined using standard automatic analyzer. <b><i>Results:</i></b> L-carnitine supplementation elevated fasting plasma carnitine in the mid-point of our study and it remained increased until the end of supplementation period. Moreover, it induced tenfold increase in plasma TMAO concentration but did not affect serum C-reactive protein, interleukin-6, tumour necrosis factor-α, L-selectin, P-selectin, vascular cell adhesion molecule-1, intercellular adhesion molecule-1 or lipid profile markers. <b><i>Conclusion:</i></b> We demonstrated that ­although oral L-carnitine supplementation significantly ­increased plasma TMAO concentration, no lipid profile changes or other markers of adverse cardiovascular events were detected in healthy aged women over the period of 24 weeks.
DOI: 10.6084/m9.figshare.7392731
title: 6TH SENSE COSMETIC DATA SET (Version 0.1)

description: 6TH SENSE COSMETIC DATA SET (VERSION 0.1)<br>Observations: 125 soap details <br>Source: Cosmetics-soap details data collected by 6TH SENSE,Tamil Nadu,INDIA<br>Data set Description:The dossier is a collection of cosmetics from different products wherein featuring soaps as basic consumable product.Herein the soaps are classified into toilet,bathing and medicated soaps.The particulars collected includes types of soaps based on consumption,quality characteristics namely Total Fatty Matter(TFM) and Grades,Ingredients with/without proportion,Classification based on contents-Natural,chemical and semi natural,Technical process and making,Caustic soda dependent-direct/indirect,Price in INR,Weight and the shelf life of the products as expiry date.These contents constituted a general information for soaps.<br>Version : 0.1Year : 2018Month of Publication : November<br>
DOI: 10.7284/120131
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1409C using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7392731.v1
title: 6TH SENSE COSMETIC DATA SET (Version 0.1)

description: 6TH SENSE COSMETIC DATA SET (VERSION 0.1)<br>Observations: 125 soap details <br>Source: Cosmetics-soap details data collected by 6TH SENSE,Tamil Nadu,INDIA<br>Data set Description:The dossier is a collection of cosmetics from different products wherein featuring soaps as basic consumable product.Herein the soaps are classified into toilet,bathing and medicated soaps.The particulars collected includes types of soaps based on consumption,quality characteristics namely Total Fatty Matter(TFM) and Grades,Ingredients with/without proportion,Classification based on contents-Natural,chemical and semi natural,Technical process and making,Caustic soda dependent-direct/indirect,Price in INR,Weight and the shelf life of the products as expiry date.These contents constituted a general information for soaps.<br>Version : 0.1Year : 2018Month of Publication : November<br>
DOI: 10.7284/120133
title: Radiometer data collected during research cruise OC1409C using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7392677
title: A bioprinted human-glioblastoma-on-a-chip reproduces patient-specific responses to chemoradiotherapy

description: The dataset is for the figures in the study published in Nature Biomedical Engineering.
DOI: 10.7284/120134
title: Radiometer data collected during research cruise OC1409C using a Biospherical QSR-2200 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7392593
title: Final AICAR Data

description: Raw data underlying the manuscript entitled "Effects of intravenous AICAR (5'-aminoimidazole-4-carboximide ribosie) administration on insulin signaling and resistance in premature baboons, Papio sp."
DOI: 10.6084/m9.figshare.7392674
title: Original data.zip

description: This zip file contains the all original data used to support the findings of this studyon the Mechanism of Wumei Pill in Treating Pancreatic Neoplasms with the Method of Network Pharmacology
DOI: 10.6084/m9.figshare.7392593.v1
title: Final AICAR Data

description: Raw data underlying the manuscript entitled "Effects of intravenous AICAR (5'-aminoimidazole-4-carboximide ribosie) administration on insulin signaling and resistance in premature baboons, Papio sp."
DOI: 10.6084/m9.figshare.7392674.v1
title: Original data.zip

description: This zip file contains the all original data used to support the findings of this studyon the Mechanism of Wumei Pill in Treating Pancreatic Neoplasms with the Method of Network Pharmacology
DOI: 10.7284/120135
title: Rain Gauge data collected during research cruise OC1409C using a RM Young 50202 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7392677.v1
title: 3D printing of glioblastoma-on-a-chip with human-derived glioblastoma cells for patient-specific drug testing

description: The dataset is cDNA expression profiles of glioblastoma cells derived from a patient before and after receiving the standard treatment of glioblastoma.
DOI: 10.7284/120127
title: Singlebeam Echosounder data collected during research cruise OC1409C using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7392536
title: Supplementary Material for: Different PDGF Receptor Dimers Drive Distinct Migration Modes of the Mouse Skin Fibroblast

description: <b><i>Background/Aims:</i></b> The migration of mesenchymal cells is a fundamental cellular process that has been implicated in many pathophysiological conditions and is induced by chemoattractants such as platelet-derived growth factors (PDGFs). However, the regulatory mechanisms shaping this migration remain to be elucidated. <b><i>Methods:</i></b> Here, we prepared mouse skin fibroblasts inactivated for different PDGF receptor genes and systematically measured their chemotactic responses within a gradient of different chemoattractants. <b><i>Results:</i></b> We found that PDGFRαβ and PDGFRββ dimers were strong inducers of random and directionally-persistent migration, respectively, that was sustained for up to 24 h. MAPK and PI3K were necessary to mediate random and directional migration, respectively. Directional migration was accompanied by abundant ventral stress fiber formation and consistent cell shape with less frequent formation of branch-like processes. <b><i>Conclusion:</i></b> This is the first systematic study that characterized the chemotaxis mediated by three-different types of PDGFR dimers in mesenchymal cell migration. Our data demonstrate that PDGFR dimer formation is the critical step to determine the specific mode of fibroblast chemotaxis, while the accompanying cytoskeletal remodeling might contribute to migration persistence.
DOI: 10.7284/120136
title: Speedlog data collected during research cruise OC1409C using a Furuno DS-50 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120125
title: Water Temperature data collected during research cruise OC1409C using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7392506
title: Supplementary Material for: Characterization of the Transcriptome of Hair Cell Regeneration in the Neonatal Mouse Utricle

description: <b><i>Background/Aims:</i></b> Hearing and balance deficits are mainly caused by loss of sensory inner ear hair cells. The key signals that control hair cell regeneration are of great interest. However, the molecular events by which the cellular signals mediate hair cell regeneration in the mouse utricle are largely unknown. <b><i>Methods:</i></b> In the present study, we investigated gene expression changes and related molecular pathways using RNA-seq and qRT-PCR in the newborn mouse utricle in response to neomycin-induced damage. <b><i>Results:</i></b> There were 302 and 624 genes that were found to be up-regulated and down-regulated in neomycin-treated samples. GO and KEGG pathway analyses of these genes revealed many deregulated cellular components, molecular functions, biological processes and signaling pathways that may be related to hair cell development. More importantly, the differentially expressed genes included 9 transcription factors from the zf-C2H2 family, and eight of them were consistently down-regulated during hair cell damage and subsequent regeneration. <b><i>Conclusion:</i></b> Our results provide a valuable source for future studies and highlighted some promising genes, pathways or processes that may be useful for therapeutic applications.
DOI: 10.7284/120137
title: Water Temperature data collected during research cruise OC1409C using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition