cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8082236.v2
title: CellCycle Perez-Posada et al., 2019

description: Supporting information files S1-S19, and Video 1, for the manuscript Perez-Posada et al. 2020 entitled "'Cell cycle transcriptomics of <i>Capsaspora</i> provides insights into the evolution of cyclin-CDK machinery". We characterized the periodic transcriptional program of <i>Capsaspora</i> in two independent cultures (Video 1), retrieving around 800 periodic genes (Supporting files S4 and S5). This dataset was further analyzed by comparative genomics and phylogenies; Supporting file S6 are the significant GeneOntology enrichments of each cluster of periodic genes. Supporting files S12 and S13 are cell cycle regulators in human with known periodic orthologs in <i>Capsaspora</i>; Supporting file S14 is the gene age enrichment/depletion analysis of <i>Capsaspora</i> cell cycle gene clusters. Validation of expression of some genes with qPCR can be found in file S11. Supporting File S8 contains the list of species used in comparative analyses. File S2 contains the human and yeast sequences used as queries to retrieve MTOC orthologs in <i>Capsaspora</i> and other unicellular holozoans, and Figure S3 is the list of BLAST matches in <i>Capsapora</i> and other unicellular holozoans. File S7 contains the fasta sequences of cyclins and CDKS used in the pylogenetic trees, with the updated sequence of the re-annotated <i>Capsaspora</i> CDK1/2/3 also found in File S10. Files S15 describes the procedure used to retrieve gene identifiers for periodic genes of human, yeasts and plant datasets; as well as pipeline parameters to call for periodic genes in our reanalysis. Files S16 and S17 contain the metrics of shared periodic orthogroups between pairs of species. Files 18 and 19 show the GO enriched terms, for each species, of the genes conserved in the core set of periodic orthogroups, as well as the identity of the <i>Capsaspora</i> genes belonging to those orthogroups.
DOI: 10.6084/m9.figshare.8082182
title: Emotion regulation choice: a broad examination of external factors

description: Emotion regulation choices are known to be profoundly consequential across affective, cognitive, and social domains. Prior studies have identified two important external factors of emotion regulation choice: stimulus intensity and reappraisal affordances. However, whether there are other external factors of emotion regulation choice and how these factors contribute to emotion regulation choice when considered simultaneously is not yet clear. The current studies addressed these gaps by examining the relations between emotion regulation choice (distraction vs. reappraisal) and self-reported stimulus intensity, reappraisal affordances, and several other factors including discrete emotions and distraction affordances. Across three studies using different databases of standardised images to enhance generalizability, our results showed that in the context of our experiments, reappraisal affordances were strongly associated with emotion regulation choice (greater reappraisal affordances predicted higher use of reappraisal). Further, stimulus intensity was independently associated with emotion regulation choice in each study. Our results also demonstrated that the discrete emotion of disgust (but not other discrete emotions) is a previously unidentified external factor of emotion regulation choice. We discuss the implications of the current findings.
DOI: 10.6084/m9.figshare.8082236.v1
title: CellCycle Perez-Posada et al., 2019

description: Supporting information files S1-S19, and Video 1, for the manuscript Perez-Posada et al. 2020 entitled "'Cell cycle transcriptomics of <i>Capsaspora</i> provides insights into the evolution of cyclin-CDK machinery". We characterized the periodic transcriptional program of <i>Capsaspora</i> in two independent cultures (Video 1), retrieving around 800 periodic genes (Supporting files S4 and S5). This dataset was further analyzed by comparative genomics and phylogenies; Supporting file S6 are the significant GeneOntology enrichments of each cluster of periodic genes. Supporting files S12 and S13 are cell cycle regulators in human with known periodic orthologs in <i>Capsaspora</i>; Supporting file S14 is the gene age enrichment/depletion analysis of <i>Capsaspora</i> cell cycle gene clusters. Validation of expression of some genes with qPCR can be found in file S11. Supporting File S8 contains the list of species used in comparative analyses. File S2 contains the human and yeast sequences used as queries to retrieve MTOC orthologs in <i>Capsaspora</i> and other unicellular holozoans, and Figure S3 is the list of BLAST matches in <i>Capsapora</i> and other unicellular holozoans. File S7 contains the fasta sequences of cyclins and CDKS used in the pylogenetic trees, with the updated sequence of the re-annotated <i>Capsaspora</i> CDK1/2/3 also found in File S10. Files S15 describes the procedure used to retrieve gene identifiers for periodic genes of human, yeasts and plant datasets; as well as pipeline parameters to call for periodic genes in our reanalysis. Files S16 and S17 contain the metrics of shared periodic orthogroups between pairs of species. Files 18 and 19 show the GO enriched terms, for each species, of the genes conserved in the core set of periodic orthogroups, as well as the identity of the <i>Capsaspora</i> genes belonging to those orthogroups.
DOI: 10.6084/m9.figshare.8082167
title: Of mice and men: Interaction of <i>Corynebacterium diphtheriae</i> strains with murine and human phagocytes

description: Seven non-toxigenic <i>C. diphtheriae</i> strains and one toxigenic strain were analyzed with regard to their interaction with murine macrophages (BMM) and human THP-1 macrophage-like cells. Proliferation assays with BMM and THP-1 revealed similar intracellular CFUs for <i>C. diphtheriae</i> strains independent of the host cell. Strain ISS4060 showed highest intracellular CFUs, while the toxigenic DSM43989 was almost not detectable. This result was confirmed by TLR 9 reporter assays, showing a low signal for DSM43989, indicating that the bacteria are not endocytosed. In contrast, the non-pathogenic <i>C. glutamicum</i> showed almost no intracellular CFUs independent of the host cell, but was recognized by TLR9, indicating that the bacteria were degraded immediately after endocytosis. In terms of G-CSF and IL-6 production, no significant differences between BMM and THP-1 were observed. G-CSF production was considerably higher than IL-6 for all <i>C. diphtheriae</i> strains and the <i>C. glutamicum</i> did not induce high cytokine secretion in general. Furthermore, all corynebacteria investigated in this study were able to induce NFκB signaling but only viable <i>C. diphtheriae</i> strains were able to cause host cell damage, whereas <i>C. glutamicum</i> did not. The absence of Mincle resulted in reduced G-CSF production, while no influence on the uptake of the bacteria was observed. In contrast, when MyD88 was absent, both the uptake of the bacteria and cytokine production were blocked. Consequently, phagocytosis only occurs when the TLR/MyD88 pathway is functional, which was also supported by showing that all corynebacteria used in this study interact with human TLR2.
DOI: 10.6084/m9.figshare.8082182.v1
title: Emotion regulation choice: a broad examination of external factors

description: Emotion regulation choices are known to be profoundly consequential across affective, cognitive, and social domains. Prior studies have identified two important external factors of emotion regulation choice: stimulus intensity and reappraisal affordances. However, whether there are other external factors of emotion regulation choice and how these factors contribute to emotion regulation choice when considered simultaneously is not yet clear. The current studies addressed these gaps by examining the relations between emotion regulation choice (distraction vs. reappraisal) and self-reported stimulus intensity, reappraisal affordances, and several other factors including discrete emotions and distraction affordances. Across three studies using different databases of standardised images to enhance generalizability, our results showed that in the context of our experiments, reappraisal affordances were strongly associated with emotion regulation choice (greater reappraisal affordances predicted higher use of reappraisal). Further, stimulus intensity was independently associated with emotion regulation choice in each study. Our results also demonstrated that the discrete emotion of disgust (but not other discrete emotions) is a previously unidentified external factor of emotion regulation choice. We discuss the implications of the current findings.
DOI: 10.22023/mdx.8082143
title: Zig zag design 9.jpg

description: This project is part of Ceres Artists in Residence at The Museum of Domestic Design & Architecture (MoDA). The aim of the residency was to use objects from MoDA's collection as a starting point for exploration of natural prints and dyes with the aim of raising the awareness of sustainability in design research.<br><br>Design inspired by 'A46 Zig zag design' by Enid Marx for R.D.I London Transport, 1945.<br>I started this design by carving it into a linoleum plate, then transferred it as a repeat pattern onto a film for screen printing, keeping the original mark makings from the linoleum.<br><br>This design was screen printed on hemp silk dyed in buddleia.The colours were produced using plant extracts including indigo and chlorophyll for the main background layer and madder for the zig zag pattern. Weld and chlorophyll for the rectangles and madder and buckhorn for the squares.<br><br>The photo show the final printed repeat pattern design as well as the different printing stages before that. In the final stage, after steaming and washing, the colours revealed brighter.<br>
DOI: 10.6084/m9.figshare.8082146
title: CPS.nc

description: reconstruction NetCDF file.
DOI: 10.6084/m9.figshare.8082167.v1
title: Of mice and men: Interaction of <i>Corynebacterium diphtheriae</i> strains with murine and human phagocytes

description: Seven non-toxigenic <i>C. diphtheriae</i> strains and one toxigenic strain were analyzed with regard to their interaction with murine macrophages (BMM) and human THP-1 macrophage-like cells. Proliferation assays with BMM and THP-1 revealed similar intracellular CFUs for <i>C. diphtheriae</i> strains independent of the host cell. Strain ISS4060 showed highest intracellular CFUs, while the toxigenic DSM43989 was almost not detectable. This result was confirmed by TLR 9 reporter assays, showing a low signal for DSM43989, indicating that the bacteria are not endocytosed. In contrast, the non-pathogenic <i>C. glutamicum</i> showed almost no intracellular CFUs independent of the host cell, but was recognized by TLR9, indicating that the bacteria were degraded immediately after endocytosis. In terms of G-CSF and IL-6 production, no significant differences between BMM and THP-1 were observed. G-CSF production was considerably higher than IL-6 for all <i>C. diphtheriae</i> strains and the <i>C. glutamicum</i> did not induce high cytokine secretion in general. Furthermore, all corynebacteria investigated in this study were able to induce NFκB signaling but only viable <i>C. diphtheriae</i> strains were able to cause host cell damage, whereas <i>C. glutamicum</i> did not. The absence of Mincle resulted in reduced G-CSF production, while no influence on the uptake of the bacteria was observed. In contrast, when MyD88 was absent, both the uptake of the bacteria and cytokine production were blocked. Consequently, phagocytosis only occurs when the TLR/MyD88 pathway is functional, which was also supported by showing that all corynebacteria used in this study interact with human TLR2.
DOI: 10.22023/mdx.8082143.v1
title: Zig zag design 9.jpg

description: This project is part of Ceres Artists in Residence at The Museum of Domestic Design & Architecture (MoDA). The aim of the residency was to use objects from MoDA's collection as a starting point for exploration of natural prints and dyes with the aim of raising the awareness of sustainability in design research.<br><br>Design inspired by 'A46 Zig zag design' by Enid Marx for R.D.I London Transport, 1945.<br>I started this design by carving it into a linoleum plate, then transferred it as a repeat pattern onto a film for screen printing, keeping the original mark makings from the linoleum.<br><br>This design was screen printed on hemp silk dyed in buddleia.The colours were produced using plant extracts including indigo and chlorophyll for the main background layer and madder for the zig zag pattern. Weld and chlorophyll for the rectangles and madder and buckhorn for the squares.<br><br>The photo show the final printed repeat pattern design as well as the different printing stages before that. In the final stage, after steaming and washing, the colours revealed brighter.<br>
DOI: 10.6084/m9.figshare.8082146.v2
title: CPS.nc

description: reconstruction NetCDF file.
DOI: 10.6084/m9.figshare.8082146.v1
title: CPS.nc

description: reconstruction NetCDF file.
DOI: 10.6084/m9.figshare.8082008
title: The annotation for the genus Lasiopodomys genomes

description: The annotation for the two genus Lasiopodomys genomes
DOI: 10.6084/m9.figshare.8082008.v1
title: The annotation for three Lasiopodomys genomes.

description: The annotations for genomes of Lasiopodomys mandarinus, Lasiopodomys brandtii and Lasiopodomys fuscus.
DOI: 10.6084/m9.figshare.8081972
title: Inhibition of neddylation induces mitotic defects and alters MKLP1 accumulation at the midbody during cytokinesis

description: The cullin-RING E3 ubiquitin ligases (CRLs) play crucial roles in modulating the stability of proteins in the cell and are, in turn, regulated by post-translational modification by the ubiquitin-like (Ubl) protein NEDD8. This process, termed neddylation, is reversible through the action of the COP9 signalosome (CSN); a multi-subunit metalloprotease conserved among eukaryotes that plays direct or indirect roles in DNA repair, cell signaling and cell cycle regulation in part through modulating the activity of the CRLs. Previously, inhibition of CRL neddylation by MLN4924, a small molecule inhibitor of the NEDD8-activating enzyme 1 (NAE1), was shown to induce interphase cell cycle arrest and cell death. Using fixed and living cell microscopy, we re-evaluated the cell cycle effects of inhibition of neddylation by MLN4924 in both asynchronous and mitotic cell populations. Consistent with previous studies, treatment of asynchronous cells with MLN4924 increased CDT1 expression levels, induced G2 arrest and increased nuclear size. However, in synchronized cells treated in mitosis, mitotic defects were observed including lagging chromosomes and binucleated daughter cells. Consistent with neddylation and deneddylation playing a role in cytokinesis, NEDD8, as well as subunits of the CSN, could be localized at the midbody and cleavage furrow. Finally, treatment of mitotic cells with MLN4924 induced the premature accumulation of MKLP1 at the cleavage furrow, a key regulator of cytokinesis, which was concomitant with increased abscission delay and failure. Thus, these studies uncover an uncharacterized mitotic effect of MLN4924 on MKLP1 accumulation at the midbody and support a role for neddylation during cytokinesis. <b>Abbreviations</b>: CSN, COP9 Signalosome; MKLP1, mitotic kinesin-like protein 1; NEDD8, Neural precursor cell Expressed, Developmentally Down-regulated 8.
DOI: 10.6084/m9.figshare.8082008.v2
title: Three annotation for the genera Lasiopodomys and Neodon

description: Three annotation for the genera Lasiopodomys and Neodon
DOI: 10.6084/m9.figshare.8082008.v3
title: Three annotation for the genera Lasiopodomys and Neodon

description: Three annotation for the genera Lasiopodomys and Neodon
DOI: 10.6084/m9.figshare.8081972.v3
title: Inhibition of neddylation induces mitotic defects and alters MKLP1 accumulation at the midbody during cytokinesis

description: The cullin-RING E3 ubiquitin ligases (CRLs) play crucial roles in modulating the stability of proteins in the cell and are, in turn, regulated by post-translational modification by the ubiquitin-like (Ubl) protein NEDD8. This process, termed neddylation, is reversible through the action of the COP9 signalosome (CSN); a multi-subunit metalloprotease conserved among eukaryotes that plays direct or indirect roles in DNA repair, cell signaling and cell cycle regulation in part through modulating the activity of the CRLs. Previously, inhibition of CRL neddylation by MLN4924, a small molecule inhibitor of the NEDD8-activating enzyme 1 (NAE1), was shown to induce interphase cell cycle arrest and cell death. Using fixed and living cell microscopy, we re-evaluated the cell cycle effects of inhibition of neddylation by MLN4924 in both asynchronous and mitotic cell populations. Consistent with previous studies, treatment of asynchronous cells with MLN4924 increased CDT1 expression levels, induced G2 arrest and increased nuclear size. However, in synchronized cells treated in mitosis, mitotic defects were observed including lagging chromosomes and binucleated daughter cells. Consistent with neddylation and deneddylation playing a role in cytokinesis, NEDD8, as well as subunits of the CSN, could be localized at the midbody and cleavage furrow. Finally, treatment of mitotic cells with MLN4924 induced the premature accumulation of MKLP1 at the cleavage furrow, a key regulator of cytokinesis, which was concomitant with increased abscission delay and failure. Thus, these studies uncover an uncharacterized mitotic effect of MLN4924 on MKLP1 accumulation at the midbody and support a role for neddylation during cytokinesis. <b>Abbreviations</b>: CSN, COP9 Signalosome; MKLP1, mitotic kinesin-like protein 1; NEDD8, Neural precursor cell Expressed, Developmentally Down-regulated 8.
DOI: 10.6084/m9.figshare.8081972.v2
title: Inhibition of neddylation induces mitotic defects and alters MKLP1 accumulation at the midbody during cytokinesis

description: The cullin-RING E3 ubiquitin ligases (CRLs) play crucial roles in modulating the stability of proteins in the cell and are, in turn, regulated by post-translational modification by the ubiquitin-like (Ubl) protein NEDD8. This process, termed neddylation, is reversible through the action of the COP9 signalosome (CSN); a multi-subunit metalloprotease conserved among eukaryotes that plays direct or indirect roles in DNA repair, cell signaling and cell cycle regulation in part through modulating the activity of the CRLs. Previously, inhibition of CRL neddylation by MLN4924, a small molecule inhibitor of the NEDD8-activating enzyme 1 (NAE1), was shown to induce interphase cell cycle arrest and cell death. Using fixed and living cell microscopy, we re-evaluated the cell cycle effects of inhibition of neddylation by MLN4924 in both asynchronous and mitotic cell populations. Consistent with previous studies, treatment of asynchronous cells with MLN4924 increased CDT1 expression levels, induced G2 arrest and increased nuclear size. However, in synchronized cells treated in mitosis, mitotic defects were observed including lagging chromosomes and binucleated daughter cells. Consistent with neddylation and deneddylation playing a role in cytokinesis, NEDD8, as well as subunits of the CSN, could be localized at the midbody and cleavage furrow. Finally, treatment of mitotic cells with MLN4924 induced the premature accumulation of MKLP1 at the cleavage furrow, a key regulator of cytokinesis, which was concomitant with increased abscission delay and failure. Thus, these studies uncover an uncharacterized mitotic effect of MLN4924 on MKLP1 accumulation at the midbody and support a role for neddylation during cytokinesis. <b>Abbreviations</b>: CSN, COP9 Signalosome; MKLP1, mitotic kinesin-like protein 1; NEDD8, Neural precursor cell Expressed, Developmentally Down-regulated 8.
DOI: 10.6084/m9.figshare.8081936
title: SLRlist

description: The SLR list.
DOI: 10.6084/m9.figshare.8081786
title: Palmer etal 2018_Plant Ecology_data.xlsx

description: Stem and seed bank density after fire, for sites subjected to high and low severity burns. Fire occurred in 2013 in southeastern Australia
DOI: 10.6084/m9.figshare.8081807
title: Germination data for Ma et al 2018 Plant & Soil

description: Germination data for Boronia floribunda using both aerosol smoke and smoke water to test responses: total germination, MGT, differences between seed lots from individual plants
DOI: 10.6084/m9.figshare.8081786.v1
title: Palmer etal 2018_Plant Ecology_data.xlsx

description: Stem and seed bank density after fire, for sites subjected to high and low severity burns. Fire occurred in 2013 in southeastern Australia
DOI: 10.6084/m9.figshare.8081807.v1
title: Germination data for Ma et al 2018 Plant & Soil

description: Germination data for Boronia floribunda using both aerosol smoke and smoke water to test responses: total germination, MGT, differences between seed lots from individual plants
DOI: 10.6084/m9.figshare.8081759
title: Additional file 2: of Towards personalised molecular feedback for weight loss

description: Raw Data. The file includes the raw data collected during the study. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.8081759.v1
title: Additional file 2: of Towards personalised molecular feedback for weight loss

description: Raw Data. The file includes the raw data collected during the study. (XLSX 46 kb)
DOI: 10.26180/5ccfd3e10829a
title: RCDE simulation data

description: Model code and simulation data from Warren et al. (2019): <br>- "crm_code.tar.gz" contains modified code and input data files for the CM1 cloud-resolving model (CRM)<br>- "scm_data.tar.gz" contains processed simulation output from the UM single-column model (SCM)<br><br>Details of the contents of these archives are contained in the files README.RCDE in the top level of each archive.<br><br>Warren, R. A., M. S. Singh, and C. Jakob (2019): Simulations of radiative-convective-dynamical equilibrium. Manuscript submitted to the Journal of Advances in Modeling Earth Systems. <br>
DOI: 10.6084/m9.figshare.8081657
title: hcm data.csv

description: This is a data set that contains CMR features for patients with hypertrophic cardiomyopathy.
DOI: 10.6084/m9.figshare.8081594
title: Alignments used in phylogenetic analyses

description: Alignment for used in phylogenetic analyses for "Molecular phylogenetics of slit-faced bats (Chiroptera: Nycteridae) reveals deeply divergent African lineages"
DOI: 10.6084/m9.figshare.8081582
title: ReN2 experiment#2 3.5 GPa

description: Single-crystal XRD data set for rhenium nitrides collected in a diamond anvil cell at 3.5 GPa at GSECARS (APS, USA)