cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3491345.v1
title: Robust multivariate mixture regression models with incomplete data

description: Multivariate mixture regression models can be used to investigate the relationships between two or more response variables and a set of predictor variables by taking into consideration unobserved population heterogeneity. It is common to take multivariate normal distributions as mixing components, but this mixing model is sensitive to heavy-tailed errors and outliers. Although normal mixture models can approximate any distribution in principle, the number of components needed to account for heavy-tailed distributions can be very large. Mixture regression models based on the multivariate <i>t</i> distributions can be considered as a robust alternative approach. Missing data are inevitable in many situations and parameter estimates could be biased if the missing values are not handled properly. In this paper, we propose a multivariate <i>t</i> mixture regression model with missing information to model heterogeneity in regression function in the presence of outliers and missing values. Along with the robust parameter estimation, our proposed method can be used for (i) visualization of the partial correlation between response variables across latent classes and heterogeneous regressions, and (ii) outlier detection and robust clustering even under the presence of missing values. We also propose a multivariate <i>t</i> mixture regression model using MM-estimation with missing information that is robust to high-leverage outliers. The proposed methodologies are illustrated through simulation studies and real data analysis.
DOI: 10.6084/m9.figshare.3491198.v2
title: ENSAYOS SOBRE TEMAS VETERINARIOS

description: LIBRO DE ENSAYOS QUE ABORDA TEMAS DE MEDICINA VETERINARIA
DOI: 10.6084/m9.figshare.3491057
title: Raw proteomic data for analysis of peptide vocabulary usage

description: Whole sets of proteins downloaded from NCBI (without filtration)
DOI: 10.6084/m9.figshare.3491057.v1
title: Raw proteomic data for analysis of peptide vocabulary usage

description: Whole sets of proteins downloaded from NCBI (without filtration)
DOI: 10.6084/m9.figshare.3490955
title: The exact behaviour of the Reimann Zeta conjugate pair ratio function

description: Graphical examination of the Riemann Zeta conjugate pair ratio function ζ(s)/ζ(1−s) reveals a simple AM-FM lineshape for the real and imaginary components with (i) the FM terms present in the exact terms of the Riemann Siegel θ ( t ) function and Γ(0 . 5 + it ) and (ii) only the AM term is dependent on the distance of the real value of s from 0.5. The envelope function abs (ζ(s)/ζ(1−s) ) is smooth and increases (decreases) with increasing distance from the critical line for Re ( s ) &lt; 0 . 5 ( Re ( s ) &gt; 0 . 5) indicating no zeroes away from the critical line in agreement with the Riemann Hypothesis.
DOI: 10.6084/m9.figshare.3490955.v3
title: The exact behaviour of the Reimann Zeta conjugate pair ratio function

description: Graphical examination of the Riemann Zeta conjugate pair ratio function ζ(s)/ζ(1−s) reveals a simple AM-FM lineshape for the real and imaginary components with (i) the FM terms present in the exact terms of the Riemann Siegel θ ( t ) function and Γ(0 . 5 + it ) and (ii) only the AM term is dependent on the distance of the real value of s from 0.5. The envelope function abs (ζ(s)/ζ(1−s) ) is smooth and increases (decreases) with increasing distance from the critical line for Re ( s ) &lt; 0 . 5 ( Re ( s ) &gt; 0 . 5) indicating no zeroes away from the critical line in agreement with the Riemann Hypothesis.
DOI: 10.6084/m9.figshare.3490955.v2
title: The exact behaviour of the Reimann Zeta conjugate pair ratio function

description: Graphical examination of the Reimann Zeta conjugate pair ratio function ζ(s)/ζ(1−s) reveals a simple AM-FM lineshape for the real and imaginary components with (i) the FM terms present in the exact terms of the Reimann Seigal θ ( t ) function and Γ(0 . 5 + it ) and (ii) only the AM term is dependent on the distance of the real value of s from 0.5. The envelope function abs (ζ(s)/ζ(1−s) ) is smooth and increases (decreases) with increasing distance from the critical line for Re ( s ) &lt; 0 . 5 ( Re ( s ) &gt; 0 . 5) indicating no zeroes away from the critical line in agreement with the Reimann Hypothesis.
DOI: 10.6084/m9.figshare.3490808
title: Davis-Stober, Park, Brown & Regenwetter (PNAS, 2016) Materials

description: A ZIP file containing all necessary Matlab code, data and guide for recreating the figures and analyses from Davis-Stober, Park, Brown and Regenwetter's (2016) PNAS comment on Tsetsos et al. (2016).
DOI: 10.6084/m9.figshare.3490808.v1
title: Davis-Stober, Park, Brown & Regenwetter (PNAS, 2016) Materials

description: A ZIP file containing all necessary Matlab code, data and guide for recreating the figures and analyses from Davis-Stober, Park, Brown and Regenwetter's (2016) PNAS comment on Tsetsos et al. (2016).
DOI: 10.6084/m9.figshare.3490754
title: Tests on Thin Reinforced Concrete Walls Subjected to In-plane and Out-of-plane Cyclic Loading - Overview, General folders and TW1 (1/3)

description: The present dataset describes an experimental campaign on five thin T-shaped reinforced concrete walls. The tests aimed at assessing the influence of wall thickness on member stability, the role of lap splices on damage distribution and displacement ductility, and the effects of the simultaneous application of out-of-plane loading on the member response. This link contains the principal data for all five tests. Further data can be downloaded from the links below.<br> If you use the data, please cite: Almeida, J. P., O. Prodan, A. Rosso, and K. Beyer. 2016. Tests on Thin Reinforced Concrete Walls Subjected to in-Plane and out-of-Plane Cyclic Loading. <i>Earthquake Spectra</i>.
DOI: 10.6084/m9.figshare.3490754.v1
title: Tests on Thin Reinforced Concrete Walls Subjected to In-plane and Out-of-plane Cyclic Loading - Overview, General folders and TW1 (1/3)

description: The present dataset describes an experimental campaign on five thin T-shaped reinforced concrete walls. The tests aimed at assessing the influence of wall thickness on member stability, the role of lap splices on damage distribution and displacement ductility, and the effects of the simultaneous application of out-of-plane loading on the member response. This link contains the principal data for all five tests. Further data can be downloaded from the links below.<br> If you use the data, please cite: Almeida, J. P., O. Prodan, A. Rosso, and K. Beyer. 2016. Tests on Thin Reinforced Concrete Walls Subjected to in-Plane and out-of-Plane Cyclic Loading. <i>Earthquake Spectra</i>.
DOI: 10.6084/m9.figshare.3490667
title: Phosphorylation of Tyr188 in the WW domain of YAP1 plays an essential role in YAP1-induced cellular transformation

description: The Hippo signaling pathway regulates cellular proliferation and survival, thus exerting profound effects on normal cell fate and tumorigenesis. The pivotal effector of this pathway is YAP1, a transcriptional co-activator amplified in mouse and human cancers where it promotes epithelial-to-mesenchymal transition (EMT) and malignant transformation. The Hippo tumor suppressor pathway has been suggested to inhibit the YAP1 function through serine phosphorylation-induced cytoplasmic retention and degradation. Here we report that the tyrosine188 (Y188) site of YAP1 isoform with 2 WW domains (known as YAP1-2) plays an important role in YAP1-induced cellular transformation. IP-Mass Spectrometry analysis of YAP1 identified the phosphorylation of Y188 but not other tyrosine residues. In contrast to the aberrant 3D acinus formation observed in YAP1-WT transduced cells, overexpression of YAP1-Y188F (non-phosphorylated mimic) displayed normal 3D structures. In addition, knockdown of the endogenous YAP1 in MDA-MB231 breast cancer cells inhibited cell proliferation and migration, which were then successfully rescued by the exogenous YAP1-WT and YAP1-Y188E but not Y188F. Mechanistically, we also demonstrated that YAP1-Y188F had a higher affinity to the upstream negative regulator PTPN14 and was extensively localized in the cytoplasm. Since the Y188 is located in the conserved aromatic core of the WW domain of YAP1, our finding has a wide implication for WW domain signaling in general, where Y phosphorylation may act as a common positive regulator of the complex formation via WW domains. In summary, our results indicate that tyrosine 188 plays an important role in the YAP1-induced cellular transformation and its phosphorylation may intriguingly serve as a positive indicator of YAP1 activation.
DOI: 10.6084/m9.figshare.3490667.v1
title: Phosphorylation of Tyr188 in the WW domain of YAP1 plays an essential role in YAP1-induced cellular transformation

description: The Hippo signaling pathway regulates cellular proliferation and survival, thus exerting profound effects on normal cell fate and tumorigenesis. The pivotal effector of this pathway is YAP1, a transcriptional co-activator amplified in mouse and human cancers where it promotes epithelial-to-mesenchymal transition (EMT) and malignant transformation. The Hippo tumor suppressor pathway has been suggested to inhibit the YAP1 function through serine phosphorylation-induced cytoplasmic retention and degradation. Here we report that the tyrosine188 (Y188) site of YAP1 isoform with 2 WW domains (known as YAP1-2) plays an important role in YAP1-induced cellular transformation. IP-Mass Spectrometry analysis of YAP1 identified the phosphorylation of Y188 but not other tyrosine residues. In contrast to the aberrant 3D acinus formation observed in YAP1-WT transduced cells, overexpression of YAP1-Y188F (non-phosphorylated mimic) displayed normal 3D structures. In addition, knockdown of the endogenous YAP1 in MDA-MB231 breast cancer cells inhibited cell proliferation and migration, which were then successfully rescued by the exogenous YAP1-WT and YAP1-Y188E but not Y188F. Mechanistically, we also demonstrated that YAP1-Y188F had a higher affinity to the upstream negative regulator PTPN14 and was extensively localized in the cytoplasm. Since the Y188 is located in the conserved aromatic core of the WW domain of YAP1, our finding has a wide implication for WW domain signaling in general, where Y phosphorylation may act as a common positive regulator of the complex formation via WW domains. In summary, our results indicate that tyrosine 188 plays an important role in the YAP1-induced cellular transformation and its phosphorylation may intriguingly serve as a positive indicator of YAP1 activation.
DOI: 10.6084/m9.figshare.3490661
title: N3_price.pdf

description: <br>Product page of N3 as sold by Sigma Aldrich.<br>Available on-line at the following URL: http://www.sigmaaldrich.com/catalog/product/aldrich/703206?lang=en®ion=GB<br><br>As accessed Monday 18 Jul 2016<br>
DOI: 10.6084/m9.figshare.3490661.v1
title: N3_price.pdf

description: <br>Product page of N3 as sold by Sigma Aldrich.<br>Available on-line at the following URL: http://www.sigmaaldrich.com/catalog/product/aldrich/703206?lang=en®ion=GB<br><br>As accessed Monday 18 Jul 2016<br>
DOI: 10.6084/m9.figshare.3490658
title: Early-age-dependent selective decrease of differentiation potential of hair-follicle-associated pluripotent (HAP) stem cells to beating cardiac-muscle cells

description: We have previously discovered nestin-expressing hair-follicle-associated pluripotent (HAP) stem cells and have shown that they can differentiate to neurons, glia, and many other cell types. HAP stem cells can be used for nerve and spinal cord repair. We have recently shown the HAP stem cells can differentiate to beating heart-muscle cells and tissue sheets of beating heart-muscle cells. In the present study, we determined the efficiency of HAP stem cells from mouse vibrissa hair follicles of various ages to differentiate to beating heart-muscle cells. We observed that the whiskers located near the ear were more efficient to differentiate to cardiac-muscle cells compared to whiskers located near the nose. Differentiation to cardiac-muscle cells from HAP stem cells in cultured whiskers in 4-week-old mice was significantly greater than in 10-, 20-, and 40-week-old mice. There was a strong decrease in differentiation potential of HAP stem cells to cardiac-muscle cells by 10 weeks of age. In contrast, the differentiation potential of HAP stem cells to other cell types did not decrease with age. The possibility of rejuvenation of HAP stem cells to differentiate at high efficiency to cardiac-muscle cells is discussed.
DOI: 10.6084/m9.figshare.3490658.v2
title: Early-age-dependent selective decrease of differentiation potential of hair-follicle-associated pluripotent (HAP) stem cells to beating cardiac-muscle cells

description: We have previously discovered nestin-expressing hair-follicle-associated pluripotent (HAP) stem cells and have shown that they can differentiate to neurons, glia, and many other cell types. HAP stem cells can be used for nerve and spinal cord repair. We have recently shown the HAP stem cells can differentiate to beating heart-muscle cells and tissue sheets of beating heart-muscle cells. In the present study, we determined the efficiency of HAP stem cells from mouse vibrissa hair follicles of various ages to differentiate to beating heart-muscle cells. We observed that the whiskers located near the ear were more efficient to differentiate to cardiac-muscle cells compared to whiskers located near the nose. Differentiation to cardiac-muscle cells from HAP stem cells in cultured whiskers in 4-week-old mice was significantly greater than in 10-, 20-, and 40-week-old mice. There was a strong decrease in differentiation potential of HAP stem cells to cardiac-muscle cells by 10 weeks of age. In contrast, the differentiation potential of HAP stem cells to other cell types did not decrease with age. The possibility of rejuvenation of HAP stem cells to differentiate at high efficiency to cardiac-muscle cells is discussed.
DOI: 10.6084/m9.figshare.3490658.v1
title: Early-age-dependent selective decrease of differentiation potential of hair-follicle-associated pluripotent (HAP) stem cells to beating cardiac muscle cells

description: We have previously discovered nestin-expressing hair-follicle-associated pluripotent (HAP) stem cells and have shown that they can differentiate to neurons, glia, and many other cell types. HAP stem cells can be used for nerve and spinal cord repair. We have recently shown the HAP stem cells can differentiate to beating heart muscle cells and tissue sheets of beating heart muscle cells. In the present study, we determined the efficiency of HAP stem cells from mouse vibrissa hair follicles of various ages to differentiate to beating heart muscle cells. We observed that the whiskers located near the ear were more efficient to differentiate to cardiac muscle cells compared to whiskers located near the nose. Differentiation to cardiac muscle cells from HAP stem cells in cultured whiskers in 4-week-old mice was significantly greater than in 10-, 20-, and 40-week-old mice. There was a strong decrease in differentiation potential of HAP stem cells to cardiac muscle cells by 10 weeks of age. In contrast, the differentiation potential of HAP stem cells to other cell types did not decrease with age. The possibility of rejuvenation of HAP stem cells to differentiate at high efficiency to cardiac muscle cells is discussed.
DOI: 10.6084/m9.figshare.3490619
title: Mutation screening of the <i>LRIT3, CABP4</i>, and <i>GPR179</i> genes in Chinese patients with Schubert-Bornschein congenital stationary night blindness

description: <i>Background</i>: Schubert-Bornschein congenital stationary night blindness (CSNB) is a rare retinal disorder that may lead to severe visual impairment in patients. The aim of this study was to detect mutations in the <i>LRIT3, CABP4</i>, and <i>GPR179</i> genes in Chinese patients with Schubert-Bornschein CSNB. <i>Materials and methods</i>: A cohort of eight unrelated Chinese probands with Schubert-Bornschein CSNB was recruited for this study. Six of these probands were assessed in our previous study, in which we screened the <i>NYX, CACNA1F, GRM6</i>, and <i>TRPM1</i> genes for mutations but identified none. The other two patients were newly recruited and had not been screened for mutations in these genes. Genomic DNA and clinical data were collected from the eight recruited families. Variants of the <i>LRIT3, CABP4</i>, and <i>GPR179</i> genes were identified by Sanger sequencing. All of the identified variants were also assessed in 192 control individuals. <i>Results</i>: In this study, a novel compound heterozygous mutation, c.[1A&gt;G]; [608G&gt;T] (p.[0?]; p.[W203L]), was identified in the <i>LRIT3</i> gene of a proband. These two mutations were not present in any of the 192 normal control individuals or in the other patients, and the missense mutation c.608G&gt;T was predicted to be pathogenic. No mutations were identified in the <i>CABP4</i> or <i>GPR179</i> gene. <i>Conclusions</i>: These results expand the mutational spectrum of <i>LRIT3</i>, thus potentially enriching our understanding of the molecular basis of complete CSNB. Additional genes that potentially contribute to incomplete CSNB remain to be identified in future studies.
DOI: 10.6084/m9.figshare.3490619.v1
title: Mutation screening of the <i>LRIT3, CABP4</i>, and <i>GPR179</i> genes in Chinese patients with Schubert-Bornschein congenital stationary night blindness

description: <i>Background</i>: Schubert-Bornschein congenital stationary night blindness (CSNB) is a rare retinal disorder that may lead to severe visual impairment in patients. The aim of this study was to detect mutations in the <i>LRIT3, CABP4</i>, and <i>GPR179</i> genes in Chinese patients with Schubert-Bornschein CSNB. <i>Materials and methods</i>: A cohort of eight unrelated Chinese probands with Schubert-Bornschein CSNB was recruited for this study. Six of these probands were assessed in our previous study, in which we screened the <i>NYX, CACNA1F, GRM6</i>, and <i>TRPM1</i> genes for mutations but identified none. The other two patients were newly recruited and had not been screened for mutations in these genes. Genomic DNA and clinical data were collected from the eight recruited families. Variants of the <i>LRIT3, CABP4</i>, and <i>GPR179</i> genes were identified by Sanger sequencing. All of the identified variants were also assessed in 192 control individuals. <i>Results</i>: In this study, a novel compound heterozygous mutation, c.[1A&gt;G]; [608G&gt;T] (p.[0?]; p.[W203L]), was identified in the <i>LRIT3</i> gene of a proband. These two mutations were not present in any of the 192 normal control individuals or in the other patients, and the missense mutation c.608G&gt;T was predicted to be pathogenic. No mutations were identified in the <i>CABP4</i> or <i>GPR179</i> gene. <i>Conclusions</i>: These results expand the mutational spectrum of <i>LRIT3</i>, thus potentially enriching our understanding of the molecular basis of complete CSNB. Additional genes that potentially contribute to incomplete CSNB remain to be identified in future studies.
DOI: 10.6084/m9.figshare.3490613
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: scripts]

description: This repository contains the shell, R and python scripts used to generate 4 different analyses:<br>Pre-processing: scripts responsible for generating of alignment files for downstream analyses, merging of said alignment files, generating of bigWig files for data visualisation and various Quality Control (QC)<br>Differential histone post-translational modifications (DHPTMs): scripts which estimate shift sizes and peaks from ChIP-seq data, and identify DHPTMs in peaks, transcription start site (TSS) regions and gene bodies<br>Differentially methylated regions (DMRs): scripts which identify DMRs within MeDIP-seq data<br>Differentially expressed genes (DEGs) and exons (DEEs): scripts responsible for counting number of reads in genes and exons, and determining DEGs and DEEs<br><br>The complete details on how to run the various scripts are included in the file run_scientific_data_analysis.pdf, which shows how to run all analyses with the aid of reference files (https://dx.doi.org/10.6084/m9.figshare.3487679) and demo samples (https://dx.doi.org/10.6084/m9.figshare.3487391)<br>
DOI: 10.6084/m9.figshare.3490613.v1
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: scripts]

description: This repository contains the various shell, R and python scripts used to generate the data for the Nature Neuroscience paper by Halder et. al.<br>
DOI: 10.6084/m9.figshare.3490613.v2
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: scripts]

description: This repository contains the various shell, R and python scripts used to generate the data for the Nature Neuroscience paper by Halder et. al.<br>
DOI: 10.6084/m9.figshare.3490613.v3
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: scripts]

description: This repository contains the shell, R and python scripts used to generate 4 different analyses:<br>Pre-processing: scripts responsible for generating of alignment files for downstream analyses, merging of said alignment files, generating of bigWig files for data visualisation and various Quality Control (QC)<br>Differential histone post-translational modifications (DHPTMs): scripts which estimate shift sizes and peaks from ChIP-seq data, and identify DHPTMs in peaks, transcription start site (TSS) regions and gene bodies<br>Differentially methylated regions (DMRs): scripts which identify DMRs within MeDIP-seq data<br>Differentially expressed genes (DEGs) and exons (DEEs): scripts responsible for counting number of reads in genes and exons, and determining DEGs and DEEs<br><br>The complete details on how to run the various scripts are included in the file run_scientific_data_analysis.pdf, which shows how to run all analyses with the aid of reference files (https://dx.doi.org/10.6084/m9.figshare.3487679) and demo samples (https://dx.doi.org/10.6084/m9.figshare.3487391)<br>
DOI: 10.6084/m9.figshare.3490613.v4
title: Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: scripts]

description: This repository contains the shell, R and python scripts used to generate 4 different analyses:<br>Pre-processing: scripts responsible for generating of alignment files for downstream analyses, merging of said alignment files, generating of bigWig files for data visualisation and various Quality Control (QC)<br>Differential histone post-translational modifications (DHPTMs): scripts which estimate shift sizes and peaks from ChIP-seq data, and identify DHPTMs in peaks, transcription start site (TSS) regions and gene bodies<br>Differentially methylated regions (DMRs): scripts which identify DMRs within MeDIP-seq data<br>Differentially expressed genes (DEGs) and exons (DEEs): scripts responsible for counting number of reads in genes and exons, and determining DEGs and DEEs<br><br>The complete details on how to run the various scripts are included in the file run_scientific_data_analysis.pdf, which shows how to run all analyses with the aid of reference files (https://dx.doi.org/10.6084/m9.figshare.3487679) and demo samples (https://dx.doi.org/10.6084/m9.figshare.3487391)<br>