cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5998454
title: 16 Re-Visualisations of The Caledonian Mercury, 15 June 1835, by Source Type and Source Location with legends and associated data

description: This set of sixteen (16) figures (.png) are re-visualisations the pages of the 15 June 1835 issue of the Caledonian Mercury as stored in the British Library 19th-Century Newspapers, Part 1 digital collection (<b>http://gale.cengage.co.uk/british-library-newspapers/19th-century-british-library-newspapers-part-i.aspx</b>). <br><br>They have been shaded to illustrate the purported source type or source location of each article. A horizontal (four page lengths) and vertical (one page height) legend has been included for each set.<br><br>They were created using the data set provided (<b>Data_CaledonianMercury_1835615.tsv</b>) and the Newspaper Dissector v.0.2.1.0 (<b>http://dx.doi.org/ 10.5281/zenodo.1206930</b>).<br><br><b>Data Fields:</b><br><b>Year:</b> The year of the issue in which the snippet (article) appears<br><b>Month: </b>The month of the issue in which the snippet (article) appears<br><b>Day: </b>The day of the issue in which the snippet (article) appears<br><b>Title:</b> The title of the issue in which the snippet (article) appears<br><b>Page: </b>The page on which the snippet (article) appears<br><b>Column: </b>The column in which the snippet (article) appears, numbered left to right on the page<br><b>Snippet:</b> The number of the snippet (article), numbered from top to bottom in the column<br><b>Type: </b>The type of content contained in the snippet <br><b>Topic: </b>An open-ended description of the content of the snippet<br><b>Action Location: </b>The location in which the events mentioned in the snippet take place, recorded as explicitly stated in the snippet<br><b>Source Location: </b>The location, title, or name of the source of the snippet, recorded as explicitly stated in the snippet<br><b>Source Type:</b> The type of source<br><b>Source Location Type: </b>The location of the source<br><b>Word Count: </b>The length of the snippet, as determined by optical character recognised transcription<br>
DOI: 10.6084/m9.figshare.5998448
title: maxi dataset

description: maxi data used for plots and analyses
DOI: 10.6084/m9.figshare.5998448.v1
title: maxi dataset

description: maxi data used for plots and analyses
DOI: 10.6084/m9.figshare.5998241
title: Eddy covariance journals and data sharing policies

description: Data backing Figure 1 in submitted JGR-B commentary on Dat et al. (2018). From figure legend: "Diversity of data availability policies among the 20 journals with the greatest number of highly cited eddy covariance publications (top 1000 cited papers, searched in ISI Web of Knowledge 15 March 2018 using the term “eddy covariance”)."<br>
DOI: 10.6084/m9.figshare.5998241.v1
title: Eddy covariance journals and data sharing policies

description: Data backing Figure 1 in submitted JGR-B commentary on Dat et al. (2018). From figure legend: "Diversity of data availability policies among the 20 journals with the greatest number of highly cited eddy covariance publications (top 1000 cited papers, searched in ISI Web of Knowledge 15 March 2018 using the term “eddy covariance”)."<br>
DOI: 10.6084/m9.figshare.5997656
title: A basic total evidence matrix for basal angiosperms — combining Soltis et al. (2011) with Doyle & Endress (2010)

description: This fileset includes a curated, reduced version of the matrix used by Soltis et al. (2011) that I generated in 2012 for a colleague at the Swedish Museum of Natural History, who was looking for plant matrices that can be used for total-evidence dating. The experiment failed, and the project was abondoned (see Footnote 7 of the linked post).<br><br>The taxon set was reduced to match the set used in Sareela et al. (2007), respectively Doyle & Endress (2010).<br><br>The final matrix combines data from placeholder-genera and well-covered gene regions (nuclear-encoded 18S rDNA, 25S rDNA; mitochondrial <i>atp1</i>, <i>matR, nad5; </i>plastid <i>atpB, matK, ndhF, psbB...psbH, rbcL, rpoC2) </i>and corresponding morphological data as extra partition<i>.<br> <br></i><b>Content<br></b>— An 7z-archive (http://www.7-zip.org/) including the matrices, a fully annotated version generated with and optimised for Mesquite (http://mesquiteproject.wikispaces.com/) and a simple-NEXUS version for MrBayes.<br>— Several draft graphs as PDF: a ML tree inferred from the matrix (bootstrap support annotated) with RAxML (00all.ML...); a Bayesian total evidence generated with MrBayes by my colleague (01b.withFossils....); a neighbour-net based on morphological distance inferred from the morphological partition in the combined matrix.<br>— A tabulation of the checked data, with some curating information, in two formats: CSV (for general compatibility), and xlsx (for further functionality, includes summarising Pivot-table)— Additional figures (v. 2) shown in blogposts using this matrix or subsets of it (see provided links)<br><br>Cited literature (make sure to include as <b>addititional</b> reference when re-using the data provided here)<br>Sareela JM, Rai HS, Doyle JA, ... , Briggs BG, Graham SW. 2007. Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree. Nature 446:312–315. — no data from this study has been used for generating the matrix.<br>Soltis DE, Smith SA, Cellinese N, ..., Donoghue MJ, Soltis PS. 2011. Angiosperm phylogeny: 17 genes, 640 taxa. American Journal of Botany 98:704–730 — this is the main source, but not exclusive source, for the genetic data (some data has been updated, and blanks filled)<br>Doyle JA, Endress PK. 2010. Integrating Early Cretaceous fossils into the phylogeny of living angiosperms: Magnoliidae and eudicots. Journal of Systematics and Evolution 48:1–35. — this is the source of the morphological data<br><b></b><br><br><br><br><br>
DOI: 10.6084/m9.figshare.5997656.v1
title: A basic total evidence matrix for basal angiosperms — combining Soltis et al. (2011) with Doyle & Endress (2010)

description: This fileset includes a curated, reduced version of the matrix used by Soltis et al. (2011) that I generated in 2012 for a colleague at the Swedish Museum of Natural History, who was looking for plant matrices that can be used for total-evidence dating. The experiment failed, and the project was abondoned (see Footnote 7 of the linked post).<br><br>The taxon set was reduced to match the set used in Sareela et al. (2007), respectively Doyle & Endress (2010).<br><br>The final matrix combines data from placeholder-genera and well-covered gene regions (nuclear-encoded 18S rDNA, 25S rDNA; mitochondrial <i>atp1</i>, <i>matR, nad5; </i>plastid <i>atpB, matK, ndhF, psbB...psbH, rbcL, rpoC2) </i>and corresponding morphological data as extra partition<i>.<br> <br></i><b>Content<br></b>— An 7z-archive (http://www.7-zip.org/) including the matrices, a fully annotated version generated with and optimised for Mesquite (http://mesquiteproject.wikispaces.com/) and a simple-NEXUS version for MrBayes.<br>— Several draft graphs as PDF: a ML tree inferred from the matrix (bootstrap support annotated) with RAxML (00all.ML...); a Bayesian total evidence generated with MrBayes by my colleague (01b.withFossils....); a neighbour-net based on morphological distance inferred from the morphological partition in the combined matrix.<br>— A tabulation of the checked data, with some curating information, in two formats: CSV (for general compatibility), and xlsx (for further functionality, includes summarising Pivot-table)<br><br>Cited literature (make sure to include as <b>addititional</b> reference when re-using the data provided here)<br>Sareela JM, Rai HS, Doyle JA, ... , Briggs BG, Graham SW. 2007. Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree. Nature 446:312–315. — no data from this study has been used for generating the matrix.<br>Soltis DE, Smith SA, Cellinese N, ..., Donoghue MJ, Soltis PS. 2011. Angiosperm phylogeny: 17 genes, 640 taxa. American Journal of Botany 98:704–730 — this is the main source, but not exclusive source, for the genetic data (some data has been updated, and blanks filled)<br>Doyle JA, Endress PK. 2010. Integrating Early Cretaceous fossils into the phylogeny of living angiosperms: Magnoliidae and eudicots. Journal of Systematics and Evolution 48:1–35. — this is the source of the morphological data<br><b></b><br><br><br><br><br>
DOI: 10.6084/m9.figshare.5997614
title: gamma = 1.1

description: gamma = 1.1<br>
DOI: 10.6084/m9.figshare.5997614.v1
title: gamma = 1.1

description: gamma = 1.1<br>
DOI: 10.6084/m9.figshare.5996786.v2
title: Infographic - Practical challenges for researchers in data sharing

description: Infographic highlighting some of the key findings and elements of the Springer Nature whitepaper 'Practical challenges for researchers in data sharing'.<br>
DOI: 10.6084/m9.figshare.5996606
title: Additional file 26: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S18. Genes which are significantly differentially expressed uniquely in CORT + DFP and have a greater than 0.75-fold change in expression between saline and CORT + DFP in both frontal cortex and hippocampus. All six show an increase in expression. (CSV 3Â kb)
DOI: 10.6084/m9.figshare.5996606.v1
title: Additional file 26: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S18. Genes which are significantly differentially expressed uniquely in CORT + DFP and have a greater than 0.75-fold change in expression between saline and CORT + DFP in both frontal cortex and hippocampus. All six show an increase in expression. (CSV 3Â kb)
DOI: 10.6084/m9.figshare.5996600
title: Additional file 24: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S7. Comparison of significantly enriched gene ontology biological process annotations in each of our analyses. UpSetR diagram [73] of Gene Ontology (GO) biological process (BP) annotations enriched in genes significant in each of our differential analyses: frontal cortex RRBS (FC RRBS), frontal cortex H3K27ac ChIP-seq (FC ChIP), hippocampus RNA-seq (Hipp RNA), frontal cortex RNA-seq (FC RNA) and hippocampus RRBS (Hipp RRBS). (CSV 79Â kb)
DOI: 10.6084/m9.figshare.5996600.v1
title: Additional file 24: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S7. Comparison of significantly enriched gene ontology biological process annotations in each of our analyses. UpSetR diagram [73] of Gene Ontology (GO) biological process (BP) annotations enriched in genes significant in each of our differential analyses: frontal cortex RRBS (FC RRBS), frontal cortex H3K27ac ChIP-seq (FC ChIP), hippocampus RNA-seq (Hipp RNA), frontal cortex RNA-seq (FC RNA) and hippocampus RRBS (Hipp RRBS). (CSV 79Â kb)
DOI: 10.6084/m9.figshare.5996597
title: Additional file 23: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S17. KEGG pathways found to be enriched in genes identified as uniquely differentially enrichment H3K27ac in by both PePr and diffReps (Additional file 20: Table S15). (CSV 3 kb)
DOI: 10.6084/m9.figshare.5996597.v1
title: Additional file 23: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S17. KEGG pathways found to be enriched in genes identified as uniquely differentially enrichment H3K27ac in by both PePr and diffReps (Additional file 20: Table S15). (CSV 3 kb)
DOI: 10.6084/m9.figshare.5996594
title: Additional file 22: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S16. Gene Ontology (GO) Biological Process (BP) annotations found to be enriched in genes identified as uniquely differentially enrichment H3K27ac in by both PePr and diffReps (Additional file 20: Table S15). (CSV 1 kb)
DOI: 10.6084/m9.figshare.5996594.v1
title: Additional file 22: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S16. Gene Ontology (GO) Biological Process (BP) annotations found to be enriched in genes identified as uniquely differentially enrichment H3K27ac in by both PePr and diffReps (Additional file 20: Table S15). (CSV 1 kb)
DOI: 10.6084/m9.figshare.5996588
title: Additional file 20: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S15. Genes identified by both PePr and diffReps as having differential enrichment of H3K27ac in the frontal cortex of CORT + DFP exposed animals. (CSV 26Â kb)
DOI: 10.6084/m9.figshare.5996588.v1
title: Additional file 20: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S15. Genes identified by both PePr and diffReps as having differential enrichment of H3K27ac in the frontal cortex of CORT + DFP exposed animals. (CSV 26Â kb)
DOI: 10.6084/m9.figshare.5996582
title: Additional file 18: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S13. Genes identified by PePr as having differential enrichment of H3K27ac in the frontal cortex of CORT + DFP exposed animals. (CSV 519 bytes)
DOI: 10.6084/m9.figshare.5996582.v1
title: Additional file 18: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S13. Genes identified by PePr as having differential enrichment of H3K27ac in the frontal cortex of CORT + DFP exposed animals. (CSV 519 bytes)
DOI: 10.6084/m9.figshare.5996573
title: Additional file 15: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S10. Gene Ontology (GO) Biological Process (BP) annotations found to be enriched in genes identified as uniquely differentially expressed in both the frontal cortex (Additional file 3: Table S1) and the hippocampus (Additional file 7: Table S4) after CORT + DFP exposure, compared to all other groups. (CSV 12 kb)
DOI: 10.6084/m9.figshare.5996573.v1
title: Additional file 15: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S10. Gene Ontology (GO) Biological Process (BP) annotations found to be enriched in genes identified as uniquely differentially expressed in both the frontal cortex (Additional file 3: Table S1) and the hippocampus (Additional file 7: Table S4) after CORT + DFP exposure, compared to all other groups. (CSV 12 kb)
DOI: 10.6084/m9.figshare.5996570
title: Additional file 14: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S9. KEGG pathways found to be enriched in genes identified as uniquely differentially expressed in both the frontal cortex (Additional file 3: Table S1) and the hippocampus (Additional file 7: Table S4) after CORT + DFP exposure, compared to all other groups. (CSV 67 kb)
DOI: 10.6084/m9.figshare.5996570.v1
title: Additional file 14: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S9. KEGG pathways found to be enriched in genes identified as uniquely differentially expressed in both the frontal cortex (Additional file 3: Table S1) and the hippocampus (Additional file 7: Table S4) after CORT + DFP exposure, compared to all other groups. (CSV 67 kb)
DOI: 10.6084/m9.figshare.5996564
title: Additional file 12: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S5. Overlap of genes significantly differentially expressed with CORT + DFP exposure in the frontal cortex and hippocampus. (CSV 18Â kb)
DOI: 10.6084/m9.figshare.5996564.v1
title: Additional file 12: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S5. Overlap of genes significantly differentially expressed with CORT + DFP exposure in the frontal cortex and hippocampus. (CSV 18Â kb)
DOI: 10.6084/m9.figshare.5996558
title: Additional file 10: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S6. Gene Ontology (GO) Biological Process (BP) annotations enriched in the genes identified as uniquely differentially expressed in the hippocampus after CORT + DFP exposure, compared to all other groups. (CSV 55Â kb)
DOI: 10.6084/m9.figshare.5996558.v1
title: Additional file 10: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S6. Gene Ontology (GO) Biological Process (BP) annotations enriched in the genes identified as uniquely differentially expressed in the hippocampus after CORT + DFP exposure, compared to all other groups. (CSV 55Â kb)
DOI: 10.6084/m9.figshare.5996555
title: Additional file 9: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S5. KEGG pathways enriched in the genes identified as uniquely differentially expressed in the hippocampus after CORT + DFP exposure, compared to all other groups. (CSV 103Â kb)
DOI: 10.6084/m9.figshare.5996555.v1
title: Additional file 9: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S5. KEGG pathways enriched in the genes identified as uniquely differentially expressed in the hippocampus after CORT + DFP exposure, compared to all other groups. (CSV 103Â kb)
DOI: 10.6084/m9.figshare.5996552
title: Additional file 8: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S4. Hippocampus RNA-seq significantly enriched KEGG pathway annotations. KEGG pathways significantly enriched in genes that were differentially expressed in hippocampus of CORT + DFP exposed mice. (CSV 3Â kb)
DOI: 10.6084/m9.figshare.5996552.v1
title: Additional file 8: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S4. Hippocampus RNA-seq significantly enriched KEGG pathway annotations. KEGG pathways significantly enriched in genes that were differentially expressed in hippocampus of CORT + DFP exposed mice. (CSV 3Â kb)
DOI: 10.6084/m9.figshare.5996549
title: Additional file 7: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S4. Genes identified as uniquely differentially expressed in the hippocampus after CORT + DFP exposure, compared to all other groups. (CSV 1Â kb)
DOI: 10.6084/m9.figshare.5996549.v1
title: Additional file 7: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S4. Genes identified as uniquely differentially expressed in the hippocampus after CORT + DFP exposure, compared to all other groups. (CSV 1Â kb)
DOI: 10.6084/m9.figshare.5996546
title: Additional file 6: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S3. Gene Ontology (GO) Biological Process (BP) annotations enriched in the genes identified as uniquely differentially expressed in the frontal cortex after CORT + DFP exposure, compared to all other groups. (CSV 38Â kb)
DOI: 10.6084/m9.figshare.5996546.v1
title: Additional file 6: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S3. Gene Ontology (GO) Biological Process (BP) annotations enriched in the genes identified as uniquely differentially expressed in the frontal cortex after CORT + DFP exposure, compared to all other groups. (CSV 38Â kb)
DOI: 10.6084/m9.figshare.5996543
title: Additional file 5: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S2. KEGG pathways enriched in the genes identified as uniquely differentially expressed in the frontal cortex after CORT + DFP exposure, compared to all other groups. (CSV 4Â kb)
DOI: 10.6084/m9.figshare.5996543.v1
title: Additional file 5: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Table S2. KEGG pathways enriched in the genes identified as uniquely differentially expressed in the frontal cortex after CORT + DFP exposure, compared to all other groups. (CSV 4Â kb)
DOI: 10.6084/m9.figshare.5996540
title: Additional file 4: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S3. Frontal cortex RNA-seq significantly enriched KEGG pathway annotations. KEGG pathways significantly enriched in genes that were differentially expressed in the frontal cortex of CORT + DFP exposed mice. (CSV 6Â kb)
DOI: 10.6084/m9.figshare.5996540.v1
title: Additional file 4: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S3. Frontal cortex RNA-seq significantly enriched KEGG pathway annotations. KEGG pathways significantly enriched in genes that were differentially expressed in the frontal cortex of CORT + DFP exposed mice. (CSV 6Â kb)
DOI: 10.6084/m9.figshare.5996531
title: Additional file 2: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S2. Poisson dissimilarity matrix from frontal cortex RNA-seq. Heatmaps showing the Poisson dissimilarity matrix for our frontal cortex (B) RNA-seq samples. Darker blue indicates more similar samples. (CSV 2Â kb)
DOI: 10.6084/m9.figshare.5996531.v1
title: Additional file 2: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S2. Poisson dissimilarity matrix from frontal cortex RNA-seq. Heatmaps showing the Poisson dissimilarity matrix for our frontal cortex (B) RNA-seq samples. Darker blue indicates more similar samples. (CSV 2Â kb)
DOI: 10.6084/m9.figshare.5996525
title: Additional file 1: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S1. Poisson dissimilarity matrix for hippocampus RNA-seq. Heatmaps showing the Poisson dissimilarity matrix for our hippocampus RNA-seq samples. Darker blue indicates more similar samples. (CSV 52Â kb)
DOI: 10.6084/m9.figshare.5996525.v1
title: Additional file 1: of Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness

description: Figure S1. Poisson dissimilarity matrix for hippocampus RNA-seq. Heatmaps showing the Poisson dissimilarity matrix for our hippocampus RNA-seq samples. Darker blue indicates more similar samples. (CSV 52Â kb)