cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7818464
title: Data: unsupervised gene expression

description: These files contain gene expression data, which can be used to train unsupervised models. Each file is a separate gene set and normalization.<br>A README with some additional details is also provided.
DOI: 10.6084/m9.figshare.7818557.v1
title: Additional file 1: of RhoTermPredict: an algorithm for predicting Rho-dependent transcription terminators based on Escherichia coli, Bacillus subtilis and Salmonella enterica databases

description: Coordinates of the Rho-dependent terminators predicted by RhoTermPredict in E. coli K-12 whole genome. (XLSX 621 kb)
DOI: 10.6084/m9.figshare.7818386
title: Supplementary files for JCEM manuscript under review

description: Supplementary files for JCEM manuscript-jc.2018-02686 under review
DOI: 10.6084/m9.figshare.7818386.v1
title: Supplementary files for JCEM manuscript under review

description: Supplementary files for JCEM manuscript-jc.2018-02686 under review
DOI: 10.26180/5c87495d1c376
title: Figure2

description: Raw data and statistics files to accompany figure 2 of the manuscript <b>Metformin rescues muscle function in BAG3 myofibrillar myopathy</b><b> models</b>
DOI: 10.6084/m9.figshare.7818008
title: Clemente et al JEB Northern Quoll climbing data set

description: Moving in complex environments: a biomechanical analysis of locomotion on inclined and narrow substrates<br>Journal of Experimental Biology (2019) 222, jeb189654. doi:10.1242/jeb.189654<br><br>Data used in the analysis of quolls climbing up narrow and wide substrates.
DOI: 10.6084/m9.figshare.7818008.v1
title: Clemente et al JEB Northern Quoll climbing data set

description: Moving in complex environments: a biomechanical analysis of locomotion on inclined and narrow substrates<br>Journal of Experimental Biology (2019) 222, jeb189654. doi:10.1242/jeb.189654<br><br>Data used in the analysis of quolls climbing up narrow and wide substrates.
DOI: 10.6084/m9.figshare.7817939
title: CCDB_1051.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817942
title: CCDB_1052.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817936
title: CCDB_1050.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817939.v1
title: CCDB_1051.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817942.v1
title: CCDB_1052.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817912
title: CCDB_1047.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817921
title: CCDB_1048.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817930
title: CCDB_1049.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817921.v1
title: CCDB_1048.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817930.v1
title: CCDB_1049.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817936.v1
title: CCDB_1050.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817888
title: CCDB_1044.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817900
title: CCDB_1045.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817906
title: CCDB_1046.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817912.v1
title: CCDB_1047.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817885
title: CCDB_1043.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817888.v1
title: CCDB_1044.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817906.v1
title: CCDB_1046.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817882
title: CCDB_1042.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817885.v1
title: CCDB_1043.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817900.v1
title: CCDB_1045.jpg

description: Optical section series through adjacent protoplasmic astrocytes in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow (green) and Alexa 568 (red) respectively, imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817867
title: CCDB_1040.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817870
title: CCDB_1041.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817870.v1
title: CCDB_1041.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817882.v1
title: CCDB_1042.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817855
title: CCDB_1038.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817861
title: CCDB_1039.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817852
title: CCDB_1037.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscop
DOI: 10.6084/m9.figshare.7817855.v1
title: CCDB_1038.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817867.v1
title: CCDB_1040.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817852.v1
title: CCDB_1037.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscop
DOI: 10.6084/m9.figshare.7817861.v1
title: CCDB_1039.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817849
title: CCDB_1036.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817840
title: Data: supervised tasks

description: These zipped directories contain data for each supervised task, for all gene sets and normalizations. The directories are divided by gene set and normalization, and each file contains the expression data and labels for the specific supervised task.<br>A README with some additional details is also provided.
DOI: 10.6084/m9.figshare.7817849.v1
title: CCDB_1036.jpg

description: Optical section series through a protoplasmic astrocyte in rat hippocampal area CA1 intracellulaly injected Lucifer Yellow and imaged with confocal microscopy
DOI: 10.6084/m9.figshare.7817816
title: Metadata for 'Motility drives bacterial encounter with marine particles responsible for carbon export throughout the ocean'

description: Particle size distributions from published sources. The columns include the slope of the particle size spectrum (lowercase greek letter beta), Coefficient of the particle size spectrum power law (N0), and the reference radius of the power law fit (r0). Also included are references for each particle size distribution used in this study.
DOI: 10.6084/m9.figshare.7817840.v1
title: Data: supervised tasks

description: These zipped directories contain data for each supervised task, for all gene sets and normalizations. The directories are divided by gene set and normalization, and each file contains the expression data and labels for the specific supervised task.<br>A README with some additional details is also provided.
DOI: 10.15131/shef.data.7817690
title: Data for 'Non-invasive measurement of lubricating oil viscosity using an ultrasonic continuously repeated chirp shear wave'

description: Signals for reference and measurement data for Cannon Standard oils. Files are uploaded in CSV format. <br>Each contains 3-4 columns of amplitude data taken using the CRC method in the time domain, this is raw data. To plot amplitude against time use dt=32ns. (or time=[32:32:10000000]*1E-9;) <br>Viscosity values for measurmeent oils (error +/- 10% - as stated in Cannon Instrument Company Data sheet)S3 3.57 mPa.sS20 28.03 mPa.sS60 103.23 mPa.sS200 348.67 mPa.sS600 1058.3 mPa.s
DOI: 10.15131/shef.data.7817690.v1
title: Data for 'Non-invasive measurement of lubricating oil viscosity using an ultrasonic continuously repeated chirp shear wave'

description: Signals for reference and measurement data for Cannon Standard oils. Files are uploaded in CSV format. <br>Each contains 3-4 columns of amplitude data taken using the CRC method in the time domain, this is raw data. To plot amplitude against time use dt=32ns. (or time=[32:32:10000000]*1E-9;) <br>Viscosity values for measurmeent oils (error +/- 10% - as stated in Cannon Instrument Company Data sheet)S3 3.57 mPa.sS20 28.03 mPa.sS60 103.23 mPa.sS200 348.67 mPa.sS600 1058.3 mPa.s
DOI: 10.6084/m9.figshare.7817816.v1
title: Metadata for 'Motility drives bacterial encounter with marine particles responsible for carbon export throughout the ocean'

description: Particle size distributions from published sources. The columns include the slope of the particle size spectrum (lowercase greek letter beta), Coefficient of the particle size spectrum power law (N0), and the reference radius of the power law fit (r0). Also included are references for each particle size distribution used in this study.
DOI: 10.6084/m9.figshare.7817624
title: Global urban area projection under five SSPs

description: This dataset presents the country-level urban area projection (2020 to 2100) under the five SSPs (Unit: km2).
DOI: 10.6084/m9.figshare.7817678
title: Copy Number Data

description: Intermediate CN files
DOI: 10.6084/m9.figshare.7817816.v3
title: Metadata for 'Motility drives bacterial encounter with marine particles responsible for carbon export throughout the ocean'

description: Particle size distributions from published sources. The columns include the slope of the particle size spectrum (lowercase greek letter beta), Coefficient of the particle size spectrum power law (N0), and the reference radius of the power law fit (r0). Also included are references for each particle size distribution used in this study.
DOI: 10.6084/m9.figshare.7817570
title: Supervised results table

description: This is a CSV-formatted table of results from the paper "Deep learning of representations for transcriptomics-based phenotype prediction" by Aaron M. Smith, et. al.<br>The results listed in this file are all supervised evaluation results. Each row contains a nested cross validation score of a model on a single supervised task, as well as metadata describing which model was used and which task was evaluated.
DOI: 10.6084/m9.figshare.7817816.v2
title: Metadata for 'Motility drives bacterial encounter with marine particles responsible for carbon export throughout the ocean'

description: Particle size distributions from published sources. The columns include the slope of the particle size spectrum (lowercase greek letter beta), Coefficient of the particle size spectrum power law (N0), and the reference radius of the power law fit (r0). Also included are references for each particle size distribution used in this study.
DOI: 10.6084/m9.figshare.7817540
title: Data from Sphingosine kinase and sphingosine-1-phosphate regulate epithelial cell architecture by the modulation of de novo sphingolipid synthesis

description: Sphingolipids regulate several aspects of cell behavior and it has been demonstrated that cells adjust their sphingolipid metabolism in response to metabolic needs. Particularly, sphingosine-1-phosphate (S1P), a final product of sphingolipid metabolism, is a potent bioactive lipid involved in the regulation of various cellular processes, including cell proliferation, cell migration, actin cytoskeletal reorganization and cell adhesion. In previous work in rat renal papillae, we showed that sphingosine kinase (SK) expression and S1P levels are developmentally regulated and control de novo sphingolipid synthesis. The aim of the present study was to evaluate the participation of SK/S1P pathway in the triggering of cell differentiation by external hypertonicity. We found that hypertonicity evoked a sharp decrease in SK expression, thus activating the de novo sphingolipid synthesis pathway. Furthermore, the inhibition of SK activity evoked a relaxation of cell-cell adherens junction (AJ) with accumulation of the AJ complex (E-cadherin/β-catenin/α-catenin) in the Golgi complex, preventing the acquisition of the differentiated cell phenotype. This phenotype alteration was a consequence of a sphingolipid misbalance with an increase in ceramide levels. Moreover, we found that SNAI1 and SNAI2 were located in the cell nucleus with impairment of cell differentiation induced by SK inhibition, a fact that is considered a biochemical marker of epithelial to mesenchymal transition. So, we suggest that the expression and activity of SK1, but not SK2, act as a control system, allowing epithelial cells to synchronize the various branches of sphingolipid metabolism for an adequate cell differentiation program.
DOI: 10.6084/m9.figshare.7817564
title: README

description: This is a README file explaining the data in more detail.<br>The CC-BY-4.0 license included here accompanies the processed recount2 released with this data.
DOI: 10.6084/m9.figshare.7817570.v1
title: Supervised results table

description: This is a CSV-formatted table of results from the paper "Deep learning of representations for transcriptomics-based phenotype prediction" by Aaron M. Smith, et. al.<br>The results listed in this file are all supervised evaluation results. Each row contains a nested cross validation score of a model on a single supervised task, as well as metadata describing which model was used and which task was evaluated.
DOI: 10.6084/m9.figshare.7817570.v2
title: Supervised results table

description: This is a CSV-formatted table of results from the paper "Deep learning of representations for transcriptomics-based phenotype prediction" by Aaron M. Smith, et. al.<br>The results listed in this file are all supervised evaluation results. Each row contains a nested cross validation score of a model on a single supervised task, as well as metadata describing which model was used and which task was evaluated.
DOI: 10.6084/m9.figshare.7814960
title: Data from Sphingosine kinase and sphingosine-1-phosphate regulate epithelial cell architecture by the modulation of de novo sphingolipid synthesis

description: Sphingolipids regulate several aspects of cell behavior and it has been demonstrated that cells adjust their sphingolipid metabolism in response to metabolic needs. Particularly, sphingosine-1-phosphate (S1P), a final product of sphingolipid metabolism, is a potent bioactive lipid involved in the regulation of various cellular processes, including cell proliferation, cell migration, actin cytoskeletal reorganization and cell adhesion. In previous work in rat renal papillae, we showed that sphingosine kinase (SK) expression and S1P levels are developmentally regulated and control de novo sphingolipid synthesis. The aim of the present study was to evaluate the participation of SK/S1P pathway in the triggering of cell differentiation by external hypertonicity. We found that hypertonicity evoked a sharp decrease in SK expression, thus activating the de novo sphingolipid synthesis pathway. Furthermore, the inhibition of SK activity evoked a relaxation of cell-cell adherens junction (AJ) with accumulation of the AJ complex (E-cadherin/β-catenin/α-catenin) in the Golgi complex, preventing the acquisition of the differentiated cell phenotype. This phenotype alteration was a consequence of a sphingolipid misbalance with an increase in ceramide levels. Moreover, we found that SNAI1 and SNAI2 were located in the cell nucleus with impairment of cell differentiation induced by SK inhibition, a fact that is considered a biochemical marker of epithelial to mesenchymal transition. So, we suggest that the expression and activity of SK1, but not SK2, act as a control system, allowing epithelial cells to synchronize the various branches of sphingolipid metabolism for an adequate cell differentiation program.
DOI: 10.6084/m9.figshare.7817678.v1
title: Copy Number Data

description: Intermediate CN files
DOI: 10.6084/m9.figshare.7814429
title: Table S1. Rotosphaerida sequencing metadata and statistics

description: Sequencing metadata and statistics of the newly generated molecular data in our study. <br>
DOI: 10.6084/m9.figshare.7814411
title: Rotosphaerida datasets and trees

description: Trees and datasets used to reconstruct the phylogeny of Rotosphaerida
DOI: 10.6084/m9.figshare.7814429.v1
title: Table S1. Rotosphaerida sequencing metadata and statistics

description: Sequencing metadata and statistics of the newly generated molecular data in our study. <br>
DOI: 10.6084/m9.figshare.7814405
title: Data from Sphingosine kinase and sphingosine-1-phosphate regulate epithelial cell architecture by the modulation of de novo sphingolipid synthesis

description: Sphingolipids regulate several aspects of cell behavior and it has been demonstrated that cells adjust their sphingolipid metabolism in response to metabolic needs. Particularly, sphingosine-1-phosphate (S1P), a final product of sphingolipid metabolism, is a potent bioactive lipid involved in the regulation of various cellular processes, including cell proliferation, cell migration, actin cytoskeletal reorganization and cell adhesion. In previous work in rat renal papillae, we showed that sphingosine kinase (SK) expression and S1P levels are developmentally regulated and control de novo sphingolipid synthesis. The aim of the present study was to evaluate the participation of SK/S1P pathway in the triggering of cell differentiation by external hypertonicity. We found that hypertonicity evoked a sharp decrease in SK expression, thus activating the de novo sphingolipid synthesis pathway. Furthermore, the inhibition of SK activity evoked a relaxation of cell-cell adherens junction (AJ) with accumulation of the AJ complex (E-cadherin/β-catenin/α-catenin) in the Golgi complex, preventing the acquisition of the differentiated cell phenotype. This phenotype alteration was a consequence of a sphingolipid misbalance with an increase in ceramide levels. Moreover, we found that SNAI1 and SNAI2 were located in the cell nucleus with impairment of cell differentiation induced by SK inhibition, a fact that is considered a biochemical marker of epithelial to mesenchymal transition. So, we suggest that the expression and activity of SK1, but not SK2, act as a control system, allowing epithelial cells to synchronize the various branches of sphingolipid metabolism for an adequate cell differentiation program.
DOI: 10.6084/m9.figshare.7817678.v3
title: Copy Number Data

description: Intermediate CN files
DOI: 10.6084/m9.figshare.7814396
title: Stokes flow solutions (vertex values), sec. 3.3 https://arxiv.org/abs/1902.03968

description: Stokes flow through random porous media, solution
DOI: 10.6084/m9.figshare.7817678.v5
title: Copy Number Data

description: Intermediate CN files
DOI: 10.6084/m9.figshare.7817678.v4
title: Copy Number Data

description: Intermediate CN files