cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12117174.v1
title: Supplementary Table S6 from Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in <i>Arabidopsis</i>

description: Changes in the functional state of mitochondria have profound effects on other cellular compartments. Genome-wide expression analysis of <i>Arabidopsis rps10</i> mutants with an RNAi-silenced expression of mitoribosomal S10 protein has revealed extensive transcriptional reprogramming. A meta-analysis comparing expression datasets of 25 mitochondrial perturbations showed a high similarity of the <i>aox1a:rpoTmp</i> mutant<i>,</i> which is defective in the alternative oxidase (AOX1a) and dual-targeted mitochondrial and plastid RNA polymerase (RPOTmp), to <i>rps10</i>. Both <i>rps10</i> and <i>aox1a:rpoTmp</i> showed a significantly decreased electron flux through both the cytochrome and the alternative respiratory pathways, and a markedly decreased the expression of nuclear-encoded components of the chloroplast transcription machinery. In line with this, a decreased level of plastid transcripts was observed in <i>rps10</i> and <i>aox1a:rpoTmp</i>, which was reflected in a reduced rate of chloroplast transcription. Chemical treatment of wild-type seedlings with respiratory inhibitors showed that only simultaneous and direct inhibition of complex IV and AOX activity decreased the level of plastid transcripts. Taken together, both chemical and genetic studies show that the limitation of the activity of two mitochondrial terminal oxidases, complex IV and AOX, negatively impacts chloroplast transcription. Salicylic acid and oxygen are discussed as putative mediators of the signalling pathway between mitochondria, nucleus and chloroplasts.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117183.v1
title: Supplementary Table S3 from Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in <i>Arabidopsis</i>

description: Changes in the functional state of mitochondria have profound effects on other cellular compartments. Genome-wide expression analysis of <i>Arabidopsis rps10</i> mutants with an RNAi-silenced expression of mitoribosomal S10 protein has revealed extensive transcriptional reprogramming. A meta-analysis comparing expression datasets of 25 mitochondrial perturbations showed a high similarity of the <i>aox1a:rpoTmp</i> mutant<i>,</i> which is defective in the alternative oxidase (AOX1a) and dual-targeted mitochondrial and plastid RNA polymerase (RPOTmp), to <i>rps10</i>. Both <i>rps10</i> and <i>aox1a:rpoTmp</i> showed a significantly decreased electron flux through both the cytochrome and the alternative respiratory pathways, and a markedly decreased the expression of nuclear-encoded components of the chloroplast transcription machinery. In line with this, a decreased level of plastid transcripts was observed in <i>rps10</i> and <i>aox1a:rpoTmp</i>, which was reflected in a reduced rate of chloroplast transcription. Chemical treatment of wild-type seedlings with respiratory inhibitors showed that only simultaneous and direct inhibition of complex IV and AOX activity decreased the level of plastid transcripts. Taken together, both chemical and genetic studies show that the limitation of the activity of two mitochondrial terminal oxidases, complex IV and AOX, negatively impacts chloroplast transcription. Salicylic acid and oxygen are discussed as putative mediators of the signalling pathway between mitochondria, nucleus and chloroplasts.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117180.v1
title: Supplementary Table S1 from Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in <i>Arabidopsis</i>

description: Changes in the functional state of mitochondria have profound effects on other cellular compartments. Genome-wide expression analysis of <i>Arabidopsis rps10</i> mutants with an RNAi-silenced expression of mitoribosomal S10 protein has revealed extensive transcriptional reprogramming. A meta-analysis comparing expression datasets of 25 mitochondrial perturbations showed a high similarity of the <i>aox1a:rpoTmp</i> mutant<i>,</i> which is defective in the alternative oxidase (AOX1a) and dual-targeted mitochondrial and plastid RNA polymerase (RPOTmp), to <i>rps10</i>. Both <i>rps10</i> and <i>aox1a:rpoTmp</i> showed a significantly decreased electron flux through both the cytochrome and the alternative respiratory pathways, and a markedly decreased the expression of nuclear-encoded components of the chloroplast transcription machinery. In line with this, a decreased level of plastid transcripts was observed in <i>rps10</i> and <i>aox1a:rpoTmp</i>, which was reflected in a reduced rate of chloroplast transcription. Chemical treatment of wild-type seedlings with respiratory inhibitors showed that only simultaneous and direct inhibition of complex IV and AOX activity decreased the level of plastid transcripts. Taken together, both chemical and genetic studies show that the limitation of the activity of two mitochondrial terminal oxidases, complex IV and AOX, negatively impacts chloroplast transcription. Salicylic acid and oxygen are discussed as putative mediators of the signalling pathway between mitochondria, nucleus and chloroplasts.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117171
title: Supplementary Table S4 from Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in <i>Arabidopsis</i>

description: Changes in the functional state of mitochondria have profound effects on other cellular compartments. Genome-wide expression analysis of <i>Arabidopsis rps10</i> mutants with an RNAi-silenced expression of mitoribosomal S10 protein has revealed extensive transcriptional reprogramming. A meta-analysis comparing expression datasets of 25 mitochondrial perturbations showed a high similarity of the <i>aox1a:rpoTmp</i> mutant<i>,</i> which is defective in the alternative oxidase (AOX1a) and dual-targeted mitochondrial and plastid RNA polymerase (RPOTmp), to <i>rps10</i>. Both <i>rps10</i> and <i>aox1a:rpoTmp</i> showed a significantly decreased electron flux through both the cytochrome and the alternative respiratory pathways, and a markedly decreased the expression of nuclear-encoded components of the chloroplast transcription machinery. In line with this, a decreased level of plastid transcripts was observed in <i>rps10</i> and <i>aox1a:rpoTmp</i>, which was reflected in a reduced rate of chloroplast transcription. Chemical treatment of wild-type seedlings with respiratory inhibitors showed that only simultaneous and direct inhibition of complex IV and AOX activity decreased the level of plastid transcripts. Taken together, both chemical and genetic studies show that the limitation of the activity of two mitochondrial terminal oxidases, complex IV and AOX, negatively impacts chloroplast transcription. Salicylic acid and oxygen are discussed as putative mediators of the signalling pathway between mitochondria, nucleus and chloroplasts.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117171.v1
title: Supplementary Table S4 from Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in <i>Arabidopsis</i>

description: Changes in the functional state of mitochondria have profound effects on other cellular compartments. Genome-wide expression analysis of <i>Arabidopsis rps10</i> mutants with an RNAi-silenced expression of mitoribosomal S10 protein has revealed extensive transcriptional reprogramming. A meta-analysis comparing expression datasets of 25 mitochondrial perturbations showed a high similarity of the <i>aox1a:rpoTmp</i> mutant<i>,</i> which is defective in the alternative oxidase (AOX1a) and dual-targeted mitochondrial and plastid RNA polymerase (RPOTmp), to <i>rps10</i>. Both <i>rps10</i> and <i>aox1a:rpoTmp</i> showed a significantly decreased electron flux through both the cytochrome and the alternative respiratory pathways, and a markedly decreased the expression of nuclear-encoded components of the chloroplast transcription machinery. In line with this, a decreased level of plastid transcripts was observed in <i>rps10</i> and <i>aox1a:rpoTmp</i>, which was reflected in a reduced rate of chloroplast transcription. Chemical treatment of wild-type seedlings with respiratory inhibitors showed that only simultaneous and direct inhibition of complex IV and AOX activity decreased the level of plastid transcripts. Taken together, both chemical and genetic studies show that the limitation of the activity of two mitochondrial terminal oxidases, complex IV and AOX, negatively impacts chloroplast transcription. Salicylic acid and oxygen are discussed as putative mediators of the signalling pathway between mitochondria, nucleus and chloroplasts.This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
DOI: 10.6084/m9.figshare.12117066
title: Household cooking and cardiovascular diseases

description: This database contains all data used for the study of household cooking with biomass fuel and cardiovascular diseases: a cross-sectional study among rural villagers in Phitsanulok, Thailand.<br>
DOI: 10.6084/m9.figshare.12117033
title: repositry.xlsx

description: TERT promoter mutation in bladder cancer.
DOI: 10.6084/m9.figshare.12117033.v1
title: repositry.xlsx

description: TERT promoter mutation in bladder cancer.
DOI: 10.6084/m9.figshare.12117066.v1
title: Household cooking and cardiovascular diseases

description: This database contains all data used for the study of household cooking with biomass fuel and cardiovascular diseases: a cross-sectional study among rural villagers in Phitsanulok, Thailand.<br>
DOI: 10.6084/m9.figshare.12116988
title: Additional file 4 of Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner

description: Additional file 4. : Excel sheet containing supporting data showing: 1) the 16,279 rRF sequences that pass Threshold-seq, 10 RPM, and Length Cutoff thresholds, 2) the normalized abundance (RPM) of the i-, 3´-, and x-rRFs from the 3´-end of 5S, and 3) the 5´-rRFs from the 28S rRFs, for the 293T cells and 293T derived EV.
DOI: 10.6084/m9.figshare.12116988.v1
title: Additional file 4 of Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner

description: Additional file 4. : Excel sheet containing supporting data showing: 1) the 16,279 rRF sequences that pass Threshold-seq, 10 RPM, and Length Cutoff thresholds, 2) the normalized abundance (RPM) of the i-, 3´-, and x-rRFs from the 3´-end of 5S, and 3) the 5´-rRFs from the 28S rRFs, for the 293T cells and 293T derived EV.
DOI: 10.6084/m9.figshare.12116907
title: NCOMMS-19-10044C Source Data

description: Vesicular Transport Mediates the Uptake of Cytoplasmic Proteins into Mitochondria in <i>Drosophila melanogaster</i><br>
DOI: 10.6084/m9.figshare.12116829
title: Data Sharing_raw data for publisher

description: Raw data from the article entitled, "Data sharing policies of journals in life, health, and physical sciences indexed in Journal Citation Reports"
DOI: 10.6084/m9.figshare.12116907.v1
title: NCOMMS-19-10044C Source Data

description: Vesicular Transport Mediates the Uptake of Cytoplasmic Proteins into Mitochondria in <i>Drosophila melanogaster</i><br>
DOI: 10.6084/m9.figshare.12116817
title: Supporting data, "Phylogenomic evidence confirms the topology of sponge interrelationships in Lake Baikal"

description: Supporting data from "Phylogenomic evidence confirms the topology of sponge interrelationships in Lake Baikal". Including a novel Swartschewskia papyracea transcriptome and data used for phylogenetic inference.
DOI: 10.6084/m9.figshare.12116784
title: Molecular dynamics free energy calculations highlighting the role of F357 in the function of the CLC-ec1 Cl-/H+ antiporter

description: Figure 2:•Molecular system snapshots extracted from the PMFs of Figures 2C (X1=-70º) and 2D (X1=-160º), in PDB format.<br>Figure 3:•Molecular system snapshots extracted from the PMFs of Figure 2A and Figure 3 - Figure supplement 1, in PDB format. <br><br>
DOI: 10.6084/m9.figshare.12116817.v2
title: Supporting data, "Phylogenomic evidence confirms the topology of sponge interrelationships in Lake Baikal"

description: Supporting data from "Phylogenomic evidence confirms the topology of sponge interrelationships in Lake Baikal". Including a novel Swartschewskia papyracea transcriptome and data used for phylogenetic inference.
DOI: 10.6084/m9.figshare.12116784.v2
title: Molecular dynamics free energy calculations highlighting the role of F357 in the function of the CLC-ec1 Cl-/H+ antiporter

description: Figure 2:•Molecular system snapshots extracted from the PMFs of Figures 2C (X1=-70º) and 2D (X1=-160º), in PDB format.<br>Figure 3:•Molecular system snapshots extracted from the PMFs of Figure 2A and Figure 3 - Figure supplement 1, in PDB format. <br><br>
DOI: 10.6084/m9.figshare.12116817.v1
title: Supporting data, "Phylogenomic evidence confirms the structure of sponge interrelationships in Lake Baikal"

description: Supporting data from "Phylogenomic evidence confirms the structure of sponge interrelationships in Lake Baikal". Including a novel Swartschewskia papyracea transcriptome and data used for phylogenetic inference.
DOI: 10.6084/m9.figshare.12116715
title: Experimental and Mathematical Characterization of Coronary Polyamide 12 Balloon Catheter Membranes

description: The experimental quantification and modeling of the multiaxial mechanical response of polymer membranes of coronary balloon catheters have not yet been carried out.<br>Due to the lack of knowledge of such a study, it is not known whether isotropic material models can describe the material response of balloon catheter membranes expanded with the nominal or an even higher pressure. Therefore, for the first time, specimens of commercial polyamide 12 balloon catheters membranes were observed by performing uniaxial and biaxial extension tests. The quasi-static and dynamic testing scenarios include rupture, relaxation, and equibixial testing procedures. Novel clamping techniques are described, which allow even to test tiny specimens taken from the balloon membranes. The results of this study reveal the semi-compliant, nonlinear, and viscoelastic character of polyamide 12 balloon catheter membranes.Above nominal pressure, the membranes show a pronounced anisotropic mechanical behavior with a stiffer response in the circumferential direction.The anisotropic feature intensifies with an increasing strain-rate. A modified polynomial model was applied to represent the realistic mechanical response of the balloon catheter membranes during dynamic biaxial extension tests.This study also includes a compact set of constitutive model parameters for the use of the proposed model in future finite element analyses to perform more accurate simulations of expanding balloon catheters.<br>This data set contains experimental data collected in biaxial tensile tests presented in Figs 6, 7, 8, 9, 10, 13, 14, and the Cauchy stress-stretch relation until failure of the median and all single samples as depicted in Fig 12 in the respective publication.<br>See the attached readme file for a description of the data.<br>
DOI: 10.6084/m9.figshare.12116727
title: BJDP data: Textual inaccuracy and children's selective trust in webpages

description: The data link to the in press article:<br>Einav, S., Levey, A., Patel, P. & Westwood, A. (in press). Epistemic vigilance online: Textual inaccuracy and children's selective trust in webpages. British Journal of Developmental Psychology.
DOI: 10.6084/m9.figshare.12116784.v1
title: Molecular dynamics free energy calculations highlighting the role of F357 in the function of the CLC-ec1 Cl-/H+ antiporter

description: Figure 2:•2D PMF calculations describing the permeation of two Cl- ions in the pore of the CLC-ec1 Cl-/H+ antiporter, with F357 side chain restrained to either of two rotamers, or without any restraint.•1D PMF calculations describing the side chain rotameric transition of residue F357 in the CLC-ec1 Cl-/H+ antiporter. The reaction coordinate is the chi1 angle of F357. PMFs are obtained for different ion occupancy states of sites Scen and Sext (without ion, Sext occupied, Scen occupied, both sites occupied). Each calculation is repeated from two different starting states: chi1 = -70º, or chi1 = -160º. Some of the calculations were also repeated in presence of a crosslink. Figure 3:•Molecular system snapshots extracted from the PMFs of Figure 2A and Figure 3 - Figure supplement 1, in PDB format. •1D PMF calculations describing the binding of a single Cl- ion to the permeation pathway of the CLC-ec1 Cl-/H+ antiporter, when E148 is bound to Scen and is either charged or protonated.The PMF calculations imply umbrella sampling simulations using the CHARMM software version 36 and the CHARMM c36 force field (params.zip).<br>
DOI: 10.6084/m9.figshare.12116715.v2
title: Experimental and Mathematical Characterization of Coronary Polyamide 12 Balloon Catheter Membranes

description: The experimental quantification and modeling of the multiaxial mechanical response of polymer membranes of coronary balloon catheters have not yet been carried out.<br>Due to the lack of knowledge of such a study, it is not known whether isotropic material models can describe the material response of balloon catheter membranes expanded with the nominal or an even higher pressure. Therefore, for the first time, specimens of commercial polyamide 12 balloon catheters membranes were observed by performing uniaxial and biaxial extension tests. The quasi-static and dynamic testing scenarios include rupture, relaxation, and equibixial testing procedures. Novel clamping techniques are described, which allow even to test tiny specimens taken from the balloon membranes. The results of this study reveal the semi-compliant, nonlinear, and viscoelastic character of polyamide 12 balloon catheter membranes.Above nominal pressure, the membranes show a pronounced anisotropic mechanical behavior with a stiffer response in the circumferential direction.The anisotropic feature intensifies with an increasing strain-rate. A modified polynomial model was applied to represent the realistic mechanical response of the balloon catheter membranes during dynamic biaxial extension tests.This study also includes a compact set of constitutive model parameters for the use of the proposed model in future finite element analyses to perform more accurate simulations of expanding balloon catheters.<br>This data set contains experimental data collected in biaxial tensile tests presented in Figs 6, 7, 8, 9, 10, 13, 14, and the Cauchy stress-stretch relation until failure of the median and all single samples as depicted in Fig 12 in the respective publication.<br>See the attached readme file for a description of the data.<br>
DOI: 10.6084/m9.figshare.12116727.v1
title: BJDP data: Textual inaccuracy and children's selective trust in webpages

description: The data link to the in press article:<br>Einav, S., Levey, A., Patel, P. & Westwood, A. (in press). Epistemic vigilance online: Textual inaccuracy and children's selective trust in webpages. British Journal of Developmental Psychology.
DOI: 10.6084/m9.figshare.12116688
title: Supplemental File for Developmental Programming: Granulosa and Theca Cell-Specific Transcriptional Regulation by Prenatal Testosterone in Sheep

description: Supporting material for the submission to Endocrinology "Developmental Programming: Granulosa and Theca Cell-Specific Transcriptional Regulation by Prenatal Testosterone in Sheep"
DOI: 10.6084/m9.figshare.12116682
title: Additional Tables

description: Additional Tables included in the Manuscript of this project
DOI: 10.18119/n9dw3m
title: IMEx/IntAct Coronavirus Dataset: SARS-CoV-1 + human context
DOI: 10.6084/m9.figshare.12116616
title: Hypothesis D: Host plant family groups

description: Direction of gene regulation for selected host detection and immune defense genes meeting the criteria of logFC &lt; -2 or &gt; 2 and ΔFPKM &gt; 1, when comparing weevil transcriptomes from citrus, legume, and aster host plant families. Column 1: comparison identification code. Column 2: weevil species. Column 3: Tissue type (abdomen, head, or immature). Column 4: range locality (introduced range, native range, introduced vs. native range, or a mix of both in each comparison group). Column 5: TRINITY transript ID. Column 6: Gene transcript identity assignment. Column 7: Direction of gene regulation.
DOI: 10.6084/m9.figshare.12116619
title: Hypothesis E: Conventional vs. organic host plant cultivation

description: Direction of gene regulation for selected host detection and immune defense genes meeting the criteria of logFC &lt; -2 or &gt; 2 and ΔFPKM &gt; 1, when comparing weevil transcriptomes from the same host species raised using conventional vs. organic cultivation methods.. Column 1: comparison identification code. Column 2: weevil species. Column 3: Tissue type (abdomen, head, or immature). Column 4: range locality (introduced range, native range, introduced vs. native range, or a mix of both in each comparison group). Column 5: TRINITY transript ID. Column 6: Gene transcript identity assignment. Column 7: Direction of gene regulation.
DOI: 10.6084/m9.figshare.12116622
title: Hypothesis F: Host switch vs. non-host switch experiment.

description: Direction of gene regulation for selected host detection and immune defense genes meeting the criteria of logFC &lt; -2 or &gt; 2 and ΔFPKM &gt; 1, when comparing weevil transcriptomes raised and maintained on one host plant, versus raised on that host plant and subsequently switched to another. Column 1: comparison identification code. Column 2: weevil species. Column 3: Tissue type (abdomen, head, or immature). Column 4: range locality (introduced range, native range, introduced vs. native range, or a mix of both in each comparison group). Column 5: TRINITY transript ID. Column 6: Gene transcript identity assignment. Column 7: Direction of gene regulation.
DOI: 10.6084/m9.figshare.12116613
title: Hypothesis C: Legume vs. citrus hosts

description: Direction of gene regulation for selected host detection and immune defense genes meeting the criteria of logFC &lt; -2 or &gt; 2 and ΔFPKM &gt; 1, when comparing weevil transcriptomes from legume hosts versus citrus hosts. Column 1: comparison identification code. Column 2: weevil species. Column 3: Tissue type (abdomen, head, or immature). Column 4: range locality (introduced range, native range, introduced vs. native range, or a mix of both in each comparison group). Column 5: TRINITY transript ID. Column 6: Gene transcript identity assignment. Column 7: Direction of gene regulation.
DOI: 10.6084/m9.figshare.12116688.v1
title: Supplemental File for Developmental Programming: Granulosa and Theca Cell-Specific Transcriptional Regulation by Prenatal Testosterone in Sheep

description: Supporting material for the submission to Endocrinology "Developmental Programming: Granulosa and Theca Cell-Specific Transcriptional Regulation by Prenatal Testosterone in Sheep"