cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1270351.v1
title: VDR regulation of microRNA differs across prostate cell models suggesting extremely flexible control of transcription

description: The Vitamin D Receptor (VDR) is a member of the nuclear receptor superfamily and is of therapeutic interest in cancer and other settings. Regulation of microRNA (miRNA) by the VDR appears to be important to mediate its actions, for example, to control cell growth. To identify if and to what extent VDR-regulated miRNA patterns change in prostate cancer progression, we undertook miRNA microarray analyses in 7 cell models representing non-malignant and malignant prostate cells (RWPE-1, RWPE-2, HPr1, HPr1AR, LNCaP, LNCaP-C4-2, and PC-3). To focus on primary VDR regulatory events, we undertook expression analyses after 30 minutes treatment with 1α,25(OH)<sub>2</sub>D<sub>3</sub>. Across all models, 111 miRNAs were significantly modulated by 1α,25(OH)<sub>2</sub>D<sub>3</sub> treatment. Of these, only five miRNA were modulated in more than one cell model, and of these, only 3 miRNAs were modulated in the same direction. The patterns of miRNA regulation, and the networks they targeted, significantly distinguished the different cell types. Integration of 1α,25(OH)<sub>2</sub>D<sub>3</sub>-regulated miRNAs with published VDR ChIP-seq data showed significant enrichment of VDR peaks in flanking regions of miRNAs. Furthermore, mRNA and miRNA expression analyses in non-malignant RWPE-1 cells revealed patterns of miRNA and mRNA co-regulation; specifically, 13 significant reciprocal patterns were identified and these patterns were also observed in TCGA prostate cancer data. Lastly, motif search analysis revealed differential motif enrichment within VDR peaks flanking mRNA compared to miRNA genes. Together, this study revealed that miRNA are rapidly regulated in a highly cell-type specific manner, and are significantly co-integrated with mRNA regulation.
DOI: 10.6084/m9.figshare.1270351.v2
title: VDR regulation of microRNA differs across prostate cell models suggesting extremely flexible control of transcription

description: The Vitamin D Receptor (VDR) is a member of the nuclear receptor superfamily and is of therapeutic interest in cancer and other settings. Regulation of microRNA (miRNA) by the VDR appears to be important to mediate its actions, for example, to control cell growth. To identify if and to what extent VDR-regulated miRNA patterns change in prostate cancer progression, we undertook miRNA microarray analyses in 7 cell models representing non-malignant and malignant prostate cells (RWPE-1, RWPE-2, HPr1, HPr1AR, LNCaP, LNCaP-C4–2, and PC-3). To focus on primary VDR regulatory events, we undertook expression analyses after 30 minutes treatment with 1α,25(OH)<sub>2</sub>D<sub>3</sub>. Across all models, 111 miRNAs were significantly modulated by 1α,25(OH)<sub>2</sub>D<sub>3</sub> treatment. Of these, only 5 miRNAs were modulated in more than one cell model, and of these, only 3 miRNAs were modulated in the same direction. The patterns of miRNA regulation, and the networks they targeted, significantly distinguished the different cell types. Integration of 1α,25(OH)<sub>2</sub>D<sub>3</sub>-regulated miRNAs with published VDR ChIP-seq data showed significant enrichment of VDR peaks in flanking regions of miRNAs. Furthermore, mRNA and miRNA expression analyses in non-malignant RWPE-1 cells revealed patterns of miRNA and mRNA co-regulation; specifically, 13 significant reciprocal patterns were identified and these patterns were also observed in TCGA prostate cancer data. Lastly, motif search analysis revealed differential motif enrichment within VDR peaks flanking mRNA compared to miRNA genes. Together, this study revealed that miRNAs are rapidly regulated in a highly cell-type specific manner, and are significantly co-integrated with mRNA regulation.
DOI: 10.6084/m9.figshare.1270351.v4
title: VDR regulation of microRNA differs across prostate cell models suggesting extremely flexible control of transcription

description: The Vitamin D Receptor (VDR) is a member of the nuclear receptor superfamily and is of therapeutic interest in cancer and other settings. Regulation of microRNA (miRNA) by the VDR appears to be important to mediate its actions, for example, to control cell growth. To identify if and to what extent VDR-regulated miRNA patterns change in prostate cancer progression, we undertook miRNA microarray analyses in 7 cell models representing non-malignant and malignant prostate cells (RWPE-1, RWPE-2, HPr1, HPr1AR, LNCaP, LNCaP-C4–2, and PC-3). To focus on primary VDR regulatory events, we undertook expression analyses after 30 minutes treatment with 1α,25(OH)<sub>2</sub>D<sub>3</sub>. Across all models, 111 miRNAs were significantly modulated by 1α,25(OH)<sub>2</sub>D<sub>3</sub> treatment. Of these, only 5 miRNAs were modulated in more than one cell model, and of these, only 3 miRNAs were modulated in the same direction. The patterns of miRNA regulation, and the networks they targeted, significantly distinguished the different cell types. Integration of 1α,25(OH)<sub>2</sub>D<sub>3</sub>-regulated miRNAs with published VDR ChIP-seq data showed significant enrichment of VDR peaks in flanking regions of miRNAs. Furthermore, mRNA and miRNA expression analyses in non-malignant RWPE-1 cells revealed patterns of miRNA and mRNA co-regulation; specifically, 13 significant reciprocal patterns were identified and these patterns were also observed in TCGA prostate cancer data. Lastly, motif search analysis revealed differential motif enrichment within VDR peaks flanking mRNA compared to miRNA genes. Together, this study revealed that miRNAs are rapidly regulated in a highly cell-type specific manner, and are significantly co-integrated with mRNA regulation.
DOI: 10.6084/m9.figshare.1270351.v3
title: VDR regulation of microRNA differs across prostate cell models suggesting extremely flexible control of transcription

description: The Vitamin D Receptor (VDR) is a member of the nuclear receptor superfamily and is of therapeutic interest in cancer and other settings. Regulation of microRNA (miRNA) by the VDR appears to be important to mediate its actions, for example, to control cell growth. To identify if and to what extent VDR-regulated miRNA patterns change in prostate cancer progression, we undertook miRNA microarray analyses in 7 cell models representing non-malignant and malignant prostate cells (RWPE-1, RWPE-2, HPr1, HPr1AR, LNCaP, LNCaP-C4–2, and PC-3). To focus on primary VDR regulatory events, we undertook expression analyses after 30 minutes treatment with 1α,25(OH)<sub>2</sub>D<sub>3</sub>. Across all models, 111 miRNAs were significantly modulated by 1α,25(OH)<sub>2</sub>D<sub>3</sub> treatment. Of these, only 5 miRNAs were modulated in more than one cell model, and of these, only 3 miRNAs were modulated in the same direction. The patterns of miRNA regulation, and the networks they targeted, significantly distinguished the different cell types. Integration of 1α,25(OH)<sub>2</sub>D<sub>3</sub>-regulated miRNAs with published VDR ChIP-seq data showed significant enrichment of VDR peaks in flanking regions of miRNAs. Furthermore, mRNA and miRNA expression analyses in non-malignant RWPE-1 cells revealed patterns of miRNA and mRNA co-regulation; specifically, 13 significant reciprocal patterns were identified and these patterns were also observed in TCGA prostate cancer data. Lastly, motif search analysis revealed differential motif enrichment within VDR peaks flanking mRNA compared to miRNA genes. Together, this study revealed that miRNAs are rapidly regulated in a highly cell-type specific manner, and are significantly co-integrated with mRNA regulation.
DOI: 10.6084/m9.figshare.1270686
title: Elevated serum levels of mannose-binding lectin and diabetic nephropathy in type 2 diabetes

description: PONE-D-14-42071
DOI: 10.6084/m9.figshare.1270686.v1
title: PONE-D-14-42071

description: results
DOI: 10.6084/m9.figshare.1270686.v2
title: Elevated serum levels of mannose-binding lectin and diabetic nephropathy in type 2 diabetes

description: PONE-D-14-42071
DOI: 10.6084/m9.figshare.1272895
title: SUR1-associated mechanisms are not involved in ischemic optic neuropathy 1 day post-injury PLOS One Raw Data

description: The Results of OCT Grading spreadsheet contains the raw data from raters examining OCT images 
of rat optic nerves at the level of the hyaloid artery. The data shows 
no significant change in apparent damage at 1 day post-injury with 
glibenclamide treatment.Optic nerve edema qualitative scoring results with and without PGJ2. Sheet 2 shows raw data for vessel filling calculations.<br>
The other spreadsheet shows real time PCR data.<br>
DOI: 10.6084/m9.figshare.1272895.v1
title: SUR1-associated mechanisms are not involved in ischemic optic neuropathy 1 day post-injury PLOS One Raw Data

description: The Results of OCT Grading spreadsheet contains the raw data from raters examining OCT images 
of rat optic nerves at the level of the hyaloid artery. The data shows 
no significant change in apparent damage at 1 day post-injury with 
glibenclamide treatment.Optic nerve edema qualitative scoring results with and without PGJ2. Sheet 2 shows raw data for vessel filling calculations.<br>
The other spreadsheet shows real time PCR data.<br>
DOI: 10.6084/m9.figshare.25466893
title: Observational data for Soil Carbon Emissions in a Fragmented Subtropical Forest in Eastern China.

description: Soil respiration observations at the fragmented forest site
DOI: 10.6084/m9.figshare.25466893.v2
title: Observational data for Soil Carbon Emissions in a Fragmented Subtropical Forest in Eastern China.

description: Soil respiration observations at the fragmented forest site
DOI: 10.6084/m9.figshare.25466893.v1
title: Wind Speed Decline Amplifies Soil Carbon Emissions in a Fragmented Subtropical Forest: A Study Combining Field and Model Experiments

description: Soil respiration observations at the fragmented forest site
DOI: 10.6084/m9.figshare.1275093
title: Generation and Application of a Novel InsP<sub>3</sub>R<sub>1</sub> Mono-Antibody from Mouse

description: Inositol 1, 4, 5-Trisphosphate Receptor (InsP<sub>3</sub>R) is an intracellular Ca<sup>2+</sup> release channel, which widely participates in cellular processes. Three isoforms of InsP<sub>3</sub>R were identified as InsP<sub>3</sub>R<sub>1</sub>, InsP<sub>3</sub>R<sub>2,</sub> and InsP<sub>3</sub>R<sub>3</sub>. They share 60–0% protein sequence homology and form a channel in a manner of homotetramer or heterotetramer. Several InsP<sub>3</sub>R isoform-specific rabbit antibodies have been generated to distinguish their localization and functions. However, there is no report of such a valid antibody raised from other species. In his article, we prepare a mouse monoclonal antibody against a synthetic peptide with rat InsP<sub>3</sub>R<sub>1</sub>-specific carboxyl terminus sequence. This monoclonal antibody of InsP<sub>3</sub>R<sub>1</sub> (R1-mAb) was purified and characterized as IgG2b, which can recognize InsP<sub>3</sub>R<sub>1</sub> by Western-blot (WB) analysis and immunoprecipitate (IP) InsP<sub>3</sub>R<sub>1</sub> from moue brain lysate tested. Applied in immunofluorescent (IF) and immunohistochemical (IHC) assays, this antibody and rabbit polyclonal antibody could give the consistent results in SH-SY5Y cells, human sperm, and mouse brain paraffin section. In summary, we generate a mouse InsP<sub>3</sub>R<sub>1</sub>-specific IgG 2b antibody identifying InsP<sub>3</sub>R<sub>1</sub> in WB, IF, IHC, and IP analysis, which provides a possible choice for detection of InsP<sub>3</sub>R<sub>1</sub>, especially in application of co-localization analysis with other InsP<sub>3</sub>R isoforms or other proteins.
DOI: 10.6084/m9.figshare.1275093.v2
title: Generation and Application of a Novel InsP<sub>3</sub>R<sub>1</sub> Mono-Antibody from Mouse

description: Inositol 1, 4, 5-Trisphosphate Receptor (InsP<sub>3</sub>R) is an intracellular Ca<sup>2+</sup> release channel, which widely participates in cellular processes. Three isoforms of InsP<sub>3</sub>R were identified as InsP<sub>3</sub>R<sub>1</sub>, InsP<sub>3</sub>R<sub>2,</sub> and InsP<sub>3</sub>R<sub>3</sub>. They share 60–0% protein sequence homology and form a channel in a manner of homotetramer or heterotetramer. Several InsP<sub>3</sub>R isoform-specific rabbit antibodies have been generated to distinguish their localization and functions. However, there is no report of such a valid antibody raised from other species. In his article, we prepare a mouse monoclonal antibody against a synthetic peptide with rat InsP<sub>3</sub>R<sub>1</sub>-specific carboxyl terminus sequence. This monoclonal antibody of InsP<sub>3</sub>R<sub>1</sub> (R1-mAb) was purified and characterized as IgG2b, which can recognize InsP<sub>3</sub>R<sub>1</sub> by Western-blot (WB) analysis and immunoprecipitate (IP) InsP<sub>3</sub>R<sub>1</sub> from moue brain lysate tested. Applied in immunofluorescent (IF) and immunohistochemical (IHC) assays, this antibody and rabbit polyclonal antibody could give the consistent results in SH-SY5Y cells, human sperm, and mouse brain paraffin section. In summary, we generate a mouse InsP<sub>3</sub>R<sub>1</sub>-specific IgG 2b antibody identifying InsP<sub>3</sub>R<sub>1</sub> in WB, IF, IHC, and IP analysis, which provides a possible choice for detection of InsP<sub>3</sub>R<sub>1</sub>, especially in application of co-localization analysis with other InsP<sub>3</sub>R isoforms or other proteins.
DOI: 10.6084/m9.figshare.1275093.v1
title: Generation and application of a novel InsP<sub>3</sub>R<sub>1</sub> mono-antibody from mouse

description: [ABSTRACT]Inositol 1, 4, 5-Trisphosphate Receptor (InsP<sub>3</sub>R) is an intracellular Ca<sup>2+</sup> release channel, which widely participates in cellular processes. Three isoforms of InsP<sub>3</sub>R were identified as InsP<sub>3</sub>R<sub>1</sub>, InsP<sub>3</sub>R<sub>2</sub> and InsP<sub>3</sub>R<sub>3</sub>. They share 60-70% protein sequence homology and form a channel in a manner of homotetramer or heterotetramer. Several InsP<sub>3</sub>R isoform-specific rabbit antibodies have been generated to distinguish their localization and functions. However, there is no report of such a valid antibody raised from other species. In the present report, we prepare a mouse monoclonal antibody against a synthetic peptide with rat InsP<sub>3</sub>R<sub>1</sub>–specific carboxyl terminus sequence. This monoclonal antibody of InsP<sub>3</sub>R<sub>1</sub> (R1-mAb) was purified and characterized as IgG2b, which can recognize InsP<sub>3</sub>R<sub>1</sub> by Western-blot (WB) analysis and immunoprecipitate (IP) InsP<sub>3</sub>R<sub>1</sub> from moue brain lysate tested. Applied in immunofluorescent (IF) and immunohistochemical (IHC) assays, this antibody and rabbit polyclonal antibody could give the consistent results in SH-SY5Y cells, human sperm and mouse brain paraffin section. Summarily, we generate a mouse InsP<sub>3</sub>R<sub>1</sub>–specific IgG 2b antibody identifying InsP<sub>3</sub>R<sub>1</sub> in WB, IF, IHC and IP analysis, which provides a possible choice for detection of InsP<sub>3</sub>R<sub>1</sub>, especially in application of co-localization analysis with other InsP<sub>3</sub>R isoforms or other proteins.
DOI: 10.6084/m9.figshare.1276002
title: A pivotal allocation based algorithm for solving the label switching problem in Bayesian mixture models

description: In Bayesian analysis of mixture models, the label switching problem occurs as a result of the posterior distribution being invariant to any permutation of cluster indices under symmetric priors. To solve this problem, we propose a novel relabeling algorithm and its variants by investigating an approximate posterior distribution of the latent allocation variables instead of dealing with the component parameters directly. We demonstrate that our relabeling algorithm can be formulated in a rigorous framework based on information theory. Under some circumstances, it is shown to resemble the classical Kullback-Leibler relabeling algorithm and include the recently proposed Equivalence Classes Representatives relabeling algorithm as a special case. Using simulation studies and real data examples, we illustrate the efficiency of our algorithm in dealing with various label switching phenomena. Supplemental materials for this article are available online.
DOI: 10.6084/m9.figshare.1276002.v1
title: A pivotal allocation based algorithm for solving the label switching problem in Bayesian mixture models

description: In Bayesian analysis of mixture models, the label switching problem occurs as a result of the posterior distribution being invariant to any permutation of cluster indices under symmetric priors. To solve this problem, we propose a novel relabeling algorithm and its variants by investigating an approximate posterior distribution of the latent allocation variables instead of dealing with the component parameters directly. We demonstrate that our relabeling algorithm can be formulated in a rigorous framework based on information theory. Under some circumstances, it is shown to resemble the classical Kullback-Leibler relabeling algorithm and include the recently proposed Equivalence Classes Representatives relabeling algorithm as a special case. Using simulation studies and real data examples, we illustrate the efficiency of our algorithm in dealing with various label switching phenomena. Supplemental materials for this article are available online.
DOI: 10.6084/m9.figshare.1276276
title: Fluid–structure interaction study on the performance of flexible articulated caudal fin

description: In this paper, the propulsive performance of a flexible articulated caudal fin is investigated by fluid–structure interaction. The caudal fin is composed of two links which are connected by a hinge. One link is driven by pitching motion while the other one moves passively. Five cases of link flexibility are investigated, namely, the rigid–rigid case, the medium flexible–medium flexible case, the flexible–flexible case, the rigid–flexible case and the flexible–rigid case. Their fluid field and structure deformations are analysed and hydrodynamic forces are compared. It is found that the rigid–rigid caudal fin produces larger thrust force than other cases with a low-pitching frequency, while the rigid–flexible case performs better with a higher frequency. The mean thrust force increases with the frequency in our experiments, however, for the medium flexible–medium flexible case, an optimal frequency exists. Besides, the effect of the hinge stiffness is studied. It is seen that the medium flexible–medium flexible case exhibits a striking performance. When the hinge stiffness decreases, its mean thrust force increases and possesses larger amplitude while the forces of other cases decrease. These results can guide the design of flexible propeller with links and will be useful for the development of flexible underwater robots.
DOI: 10.6084/m9.figshare.1276276.v1
title: Fluid–structure interaction study on the performance of flexible articulated caudal fin

description: In this paper, the propulsive performance of a flexible articulated caudal fin is investigated by fluid–structure interaction. The caudal fin is composed of two links which are connected by a hinge. One link is driven by pitching motion while the other one moves passively. Five cases of link flexibility are investigated, namely, the rigid–rigid case, the medium flexible–medium flexible case, the flexible–flexible case, the rigid–flexible case and the flexible–rigid case. Their fluid field and structure deformations are analysed and hydrodynamic forces are compared. It is found that the rigid–rigid caudal fin produces larger thrust force than other cases with a low-pitching frequency, while the rigid–flexible case performs better with a higher frequency. The mean thrust force increases with the frequency in our experiments, however, for the medium flexible–medium flexible case, an optimal frequency exists. Besides, the effect of the hinge stiffness is studied. It is seen that the medium flexible–medium flexible case exhibits a striking performance. When the hinge stiffness decreases, its mean thrust force increases and possesses larger amplitude while the forces of other cases decrease. These results can guide the design of flexible propeller with links and will be useful for the development of flexible underwater robots.
DOI: 10.6084/m9.figshare.1276452
title: Spherical Regression Models Using Projective Linear Transformations

description: This article studies the problem of modeling relationship between two spherical (or directional) random variables in a regression setup. Here the predictor and the response variables are constrained to be on a unit sphere and, due to this nonlinear condition, the standard Euclidean regression models do not apply. Several past papers have studied this problem, termed spherical regression, by modeling the response variable with a von Mises-Fisher (VMF) density with the mean given by a rotation of the predictor variable. The few papers that go beyond rigid rotations are limited to one- or two-dimensional spheres. This article extends the mean transformations to a larger group—the projective linear group of transformations—on unit spheres of arbitrary dimensions, while keeping the VMF density to model the noise. It develops a Newton–Raphson algorithm on the special linear group for estimating the MLE of regression parameter and establishes its asymptotic properties when the sample-size becomes large. Through a variety of experiments, using data taken from projective shape analysis, cloud tracking, etc., and some simulations, this article demonstrates improvements in the prediction and modeling performance of the proposed framework over previously used models. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1276452.v1
title: Spherical Regression Models Using Projective Linear Transformations

description: This article studies the problem of modeling relationship between two spherical (or directional) random variables in a regression setup. Here the predictor and the response variables are constrained to be on a unit sphere and, due to this nonlinear condition, the standard Euclidean regression models do not apply. Several past papers have studied this problem, termed spherical regression, by modeling the response variable with a von Mises-Fisher (VMF) density with the mean given by a rotation of the predictor variable. The few papers that go beyond rigid rotations are limited to one- or two-dimensional spheres. This article extends the mean transformations to a larger group—the projective linear group of transformations—on unit spheres of arbitrary dimensions, while keeping the VMF density to model the noise. It develops a Newton–Raphson algorithm on the special linear group for estimating the MLE of regression parameter and establishes its asymptotic properties when the sample-size becomes large. Through a variety of experiments, using data taken from projective shape analysis, cloud tracking, etc., and some simulations, this article demonstrates improvements in the prediction and modeling performance of the proposed framework over previously used models. Supplementary materials for this article are available online.