cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1004600
title: Data from Higuera et al. 2011. Variability of tundra fire regimes in Arctic Alaska: millennial scale patterns and ecological implications. Ecological Applications, 21: 3211-3226.

description: Charcoal, pollen, and chronological data from: Higuera, P.E., Chipman, M.L., Barnes, J.L., Urban, M.A., and F.S. Hu. 2011. Variability of tundra fire regimes in Arctic Alaska: millennial scale patterns and ecological implications. Ecological Applications, 21: 3211-3226. As in Ecological Archives A021-144
DOI: 10.6084/m9.figshare.1004557.v1
title: Gaussian Job Archive for C6H8O13P2(4-)

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1004600.v1
title: Data from Higuera et al. 2011. Ecological Application

description: Charcoal, pollen, and chronological data from: Higuera, P.E., Chipman, M.L., Barnes, J.L., Urban, M.A., and F.S. Hu. 2011. Variability of tundra fire regimes in Arctic Alaska: millennial scale patterns and ecological implications. Ecological Applications, 21: 3211-3226. As in Ecological Archives A021-144
DOI: 10.6084/m9.figshare.1004600.v2
title: Data from Higuera et al. 2011. Ecological Applications

description: Charcoal, pollen, and chronological data from: Higuera, P.E., Chipman, M.L., Barnes, J.L., Urban, M.A., and F.S. Hu. 2011. Variability of tundra fire regimes in Arctic Alaska: millennial scale patterns and ecological implications. Ecological Applications, 21: 3211-3226. As in Ecological Archives A021-144
DOI: 10.6084/m9.figshare.1004473
title: Assembly of synthetic community members from simulated reads (depth = 100x)

description: Please see also "Supplementary Table 1. SOAPdenovo assembly results." of Beitel et al., (2014)
DOI: 10.6084/m9.figshare.1004471
title: Assembly of synthetic community members from simulated reads (depth = 50x)

description: Please see also "Supplementary Table 1. SOAPdenovo assembly results." of Beitel et al., (2014)
DOI: 10.6084/m9.figshare.1004472
title: Assembly of synthetic community members from simulated reads (depth = 5x)

description: Please see also "Supplementary Table 1. SOAPdenovo assembly results." of Beitel et al., (2014)
DOI: 10.6084/m9.figshare.1004473.v1
title: Assembly of synthetic community members from simulated reads (depth = 100x)

description: Please see also "Supplementary Table 1. SOAPdenovo assembly results." of Beitel et al., (2014)
DOI: 10.6084/m9.figshare.1004464
title: Crassostrea gigas male gonad transcriptome data comparison

description: This fileset represents a comparison of RNA-seq data from a Pacific oyster (<em>Crassostrea gigas</em>) male gamete library to microarray data from Dheilly et al. 2012 "Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes". Specifically sequence reads were mapped to full-length transcripts represented on the array platformed used by Dheilly et al 2012. Data was joined using SQLShare. File Descriptions: <em>Fastafile_Microarray</em> - fasta file corresponding to targets on microarray. Used for RNA-seq analysis. <em>Rcode_OlsonandRoberts.R - </em>The R code used to visualize expression levels of RNA-Seq data relative to clusters of gene expression patterns during oyster gonad development identified by Dheilly et al. 2012. <em>SupplFig_OlsonandRoberts.pdf -</em> Boxplots of expression levels (RPKM) from RNA-Seq data relative to the 10 clusters of similar gene expression patterns during oyster gonad development identified by Dheilly et al. 2012. The number of genes represented are 511 (Cluster 1), 222 (Cluster 2), 312 (Cluster 3), 197 (Cluster 4), 226 (Cluster 5), 146 (Cluster 6), 200 (Cluster 7), 295 (Cluster 8), 332 (Cluster 9), and 41 (Cluster 10). <em>Dheilly_SexSpecific_S1_GonadRNAseq.txt - </em>Tab-delimited file that includes Dheilly et al table S1 and corresponding RNA-seq data from single male gamete library. <em>Dheilly_DiffGametogenesis_S2_GonadRNAseq.txt - </em>Tab-delimited file that includes Dheilly et al table S2 and corresponding RNA-seq data from single male gamete library. References: Dheilly, N. M., Lelong, C., Huvet, A., Kellner, K., Dubos, M., Riviere, G., Boudry, P., and Favrel, Pascal. (2012). Gametogenesis in the Pacific Oyster <em>Crassostrea gigas</em>: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes. PLoS ONE. 7:e36353-e36353. doi: 10.1371/journal.pone.0036353
DOI: 10.6084/m9.figshare.1004471.v1
title: Assembly of synthetic community members from simulated reads (depth = 10x)

description: Please see also "Supplementary Table 1. SOAPdenovo assembly results." of Beitel et al., (2014)
DOI: 10.6084/m9.figshare.1004422
title: Files from: The Ethidium-UA/AU Intercalation Site: Effect of Model Fragmentation and Backbone Charge State

description: Atomic coordinates for the molecular systems studied in The ethidium-UA/AU intercalation site: effect of model fragmentation and backbone charge state, <em>J. Chem. Theory Comp.</em>, <strong>2011</strong>, 7, pp 2600-2609.
DOI: 10.6084/m9.figshare.1004418
title: ATAM 9

description: ATAM 9
DOI: 10.6084/m9.figshare.1004422.v1
title: Files from: The Ethidium-UA/AU Intercalation Site: Effect of Model Fragmentation and Backbone Charge State

description: Atomic coordinates for the molecular systems studied in The ethidium-UA/AU intercalation site: effect of model fragmentation and backbone charge state, <em>J. Chem. Theory Comp.</em>, <strong>2011</strong>, 7, pp 2600-2609.
DOI: 10.6084/m9.figshare.1004464.v1
title: Crassostrea gigas male gonad transcriptional data comparison

description: This fileset contains transcriptomic data for the Pacific oyster (<em>Crassostrea gigas)</em> male gonad tissue in comparison in relation with that previously studied by Dheilly et al. 2012.
DOI: 10.6084/m9.figshare.1004415
title: ATAM 7

description: ATAM 7
DOI: 10.6084/m9.figshare.1004417
title: ATAM 8

description: ATAM 8
DOI: 10.6084/m9.figshare.1004471.v2
title: Assembly of synthetic community members from simulated reads (depth = 50x)

description: Please see also "Supplementary Table 1. SOAPdenovo assembly results." of Beitel et al., (2014)
DOI: 10.6084/m9.figshare.1004416
title: ATAM 6

description: ATAM 6
DOI: 10.6084/m9.figshare.1004417.v1
title: ATAM 8

description: ATAM 8
DOI: 10.6084/m9.figshare.1004464.v2
title: Crassostrea gigas male gonad transcriptional data comparison

description: This fileset contains transcriptomic data results for the Pacific oyster (<em>Crassostrea gigas) </em>male gonad tissue in relation with that previously described by Dheilly et al. 2012. File Descriptions: <em>SupplFig_OlsonandRoberts.pdf -</em> Boxplots of expression levels (RPKM) from RNA-Seq data relative to the 10 clusters of similar gene expression patterns during oyster gonad development identified by Dheilly et al. 2012. The number of genes represented are 511 (Cluster 1), 222 (Cluster 2), 312 (Cluster 3), 197 (Cluster 4), 226 (Cluster 5), 146 (Cluster 6), 200 (Cluster 7), 295 (Cluster 8), 332 (Cluster 9), and 41 (Cluster 10). <em>Dheilly_SexSpecific_S1_GonadRNAseq.txt - </em>The expression values we obtained for sex specific genes are represented in this file. <em>Dheilly_DiffGametogenesis_S2_GonadRNAseq.txt - </em>The expression values we obtained within each of the 10 clusters of distinct expression patterns are represented in this file. Overall expression levels were higher in clusters 5 and 6 (average RPKM 156.1 and 174.5, standard deviation 211.8 and 944.9), corresponding to genes exhibiting a change in expression patterns as the oyster gonad is maturing from stage 2 to stage 3 of development during spermatogenesis. Furthermore, clusters 1-4 exhibited very low expression levels, as these clusters correspond to genes differentially expressed during female oogenesis. We observed high expression among genes from cluster 5, corresponding to genes distinct among mature stage 3 spermatozoids/gametes. and therefore conclude that our sample was indeed a mature stage 3 male gonad. References: Dheilly, N. M., Lelong, C., Huvet, A., Kellner, K., Dubos, M., Riviere, G., Boudry, P., and Favrel, Pascal. (2012). Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes. PLoS ONE. 7:e36353-e36353. doi: 10.1371/journal.pone.0036353 Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998). Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment. Genome Research. 8: 175-185. doi: 10.1101/gr.8.3.175 Ewing, Brent; Green, P. (1998). Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities. Genome Research. 8:186-194. doi: 10.1101/gr.8.3.175 Fang, X., Li, L., Luo, R., Xu, F., Wang, X., Zhu, Y., Yang, L., Huang, Z. (2012). Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. doi: http://dx.doi.org/10.5524/100030 Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5:621-628. doi: 10.1038/nmeth.1226
DOI: 10.6084/m9.figshare.1004414
title: ATAM 4

description: ATAM 4
DOI: 10.6084/m9.figshare.1004414.v1
title: ATAM 4

description: ATAM 4
DOI: 10.6084/m9.figshare.1004416.v1
title: ATAM 6

description: ATAM 6
DOI: 10.6084/m9.figshare.1004413
title: ATAM README

description: ATAM README
DOI: 10.6084/m9.figshare.1004411
title: ATAM 2

description: ATAM 2
DOI: 10.6084/m9.figshare.1004412
title: ATAM 5

description: ATAM 5
DOI: 10.6084/m9.figshare.1004412.v1
title: ATAM 5

description: ATAM 5
DOI: 10.6084/m9.figshare.1004410
title: ATAM 3

description: ATAM 3
DOI: 10.6084/m9.figshare.1004464.v3
title: Crassostrea gigas male gonad transcriptomic data comparison

description: This fileset represents a comparison of RNA-seq data from a Pacific oyster (Crassostrea gigas) male gamete library to microarray data from Dheilly et al. 2012. Specifically sequence reads were mapped to full-length transcripts represented on the array platformed used by Dheilly et al 2012. Data was joined using SQLShare. File Descriptions: <em>Fastafile</em> - fasta file corresponding to targets on microarray. Used for RNA-seq analysis. <em>R code - </em>The R code used to visualize expression levels of RNA-Seq data relative to clusters of gene expression patterns during oyster gonad development identified by Dheilly et al. 2012. <em>SupplFig_OlsonandRoberts.pdf -</em> Boxplots of expression levels (RPKM) from RNA-Seq data relative to the 10 clusters of similar gene expression patterns during oyster gonad development identified by Dheilly et al. 2012. The number of genes represented are 511 (Cluster 1), 222 (Cluster 2), 312 (Cluster 3), 197 (Cluster 4), 226 (Cluster 5), 146 (Cluster 6), 200 (Cluster 7), 295 (Cluster 8), 332 (Cluster 9), and 41 (Cluster 10). <em>Dheilly_SexSpecific_S1_GonadRNAseq.txt - </em>Tab-delimited file that includes Dheilly et al table S1 and corresponding RNA-seq data from single male gamete library. <em>Dheilly_DiffGametogenesis_S2_GonadRNAseq.txt - </em>Tab-delimited file that includes Dheilly et al table S2 and corresponding RNA-seq data from single male gamete library. References: Dheilly, N. M., Lelong, C., Huvet, A., Kellner, K., Dubos, M., Riviere, G., Boudry, P., and Favrel, Pascal. (2012). Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes. PLoS ONE. 7:e36353-e36353. doi: 10.1371/journal.pone.0036353 Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998). Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment. Genome Research. 8: 175-185. doi: 10.1101/gr.8.3.175 Ewing, Brent; Green, P. (1998). Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities. Genome Research. 8:186-194. doi: 10.1101/gr.8.3.175 Fang, X., Li, L., Luo, R., Xu, F., Wang, X., Zhu, Y., Yang, L., Huang, Z. (2012). Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. doi: http://dx.doi.org/10.5524/100030 Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5:621-628. doi: 10.1038/nmeth.1226
DOI: 10.6084/m9.figshare.1004408
title: ATAM 0

description: ATAM 0
DOI: 10.6084/m9.figshare.1004410.v1
title: ATAM 3

description: ATAM 3
DOI: 10.6084/m9.figshare.1004407
title: ATAM Top Words

description: ATAM Top Words
DOI: 10.6084/m9.figshare.1004409
title: ATAM 1

description: ATAM 1
DOI: 10.6084/m9.figshare.1004464.v4
title: Crassostrea gigas male gonad transcriptomic data comparison

description: This fileset represents a comparison of RNA-seq data from a Pacific oyster (Crassostrea gigas) male gamete library to microarray data from Dheilly et al. 2012. Specifically sequence reads were mapped to full-length transcripts represented on the array platformed used by Dheilly et al 2012. "Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes". Data was joined using SQLShare. File Descriptions: <em>Fastafile</em> - fasta file corresponding to targets on microarray. Used for RNA-seq analysis. <em>Rcode_OlsonandRoberts.R - </em>The R code used to visualize expression levels of RNA-Seq data relative to clusters of gene expression patterns during oyster gonad development identified by Dheilly et al. 2012. <em>SupplFig_OlsonandRoberts.pdf -</em> Boxplots of expression levels (RPKM) from RNA-Seq data relative to the 10 clusters of similar gene expression patterns during oyster gonad development identified by Dheilly et al. 2012. The number of genes represented are 511 (Cluster 1), 222 (Cluster 2), 312 (Cluster 3), 197 (Cluster 4), 226 (Cluster 5), 146 (Cluster 6), 200 (Cluster 7), 295 (Cluster 8), 332 (Cluster 9), and 41 (Cluster 10). <em>Dheilly_SexSpecific_S1_GonadRNAseq.txt - </em>Tab-delimited file that includes Dheilly et al table S1 and corresponding RNA-seq data from single male gamete library. <em>Dheilly_DiffGametogenesis_S2_GonadRNAseq.txt - </em>Tab-delimited file that includes Dheilly et al table S2 and corresponding RNA-seq data from single male gamete library. References: Dheilly, N. M., Lelong, C., Huvet, A., Kellner, K., Dubos, M., Riviere, G., Boudry, P., and Favrel, Pascal. (2012). Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes. PLoS ONE. 7:e36353-e36353. doi: 10.1371/journal.pone.0036353 Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998). Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment. Genome Research. 8: 175-185. doi: 10.1101/gr.8.3.175 Ewing, Brent; Green, P. (1998). Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities. Genome Research. 8:186-194. doi: 10.1101/gr.8.3.175 Fang, X., Li, L., Luo, R., Xu, F., Wang, X., Zhu, Y., Yang, L., Huang, Z. (2012). Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. doi: http://dx.doi.org/10.5524/100030 Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5:621-628. doi: 10.1038/nmeth.1226
DOI: 10.6084/m9.figshare.1004407.v1
title: ATAM Top Words

description: ATAM Top Words
DOI: 10.6084/m9.figshare.1004408.v1
title: ATAM 0

description: ATAM 0
DOI: 10.6084/m9.figshare.1004409.v1
title: ATAM 1

description: ATAM 1
DOI: 10.6084/m9.figshare.1004171
title: Identified plant remains from Ballinglanna North 1, Cork, Ireland (open dataset)

description: .csv file with identified charred plant remains from archaeobotanical samples taken during excavation of a multi-period site (Bronze Age, early medieval and post-medieval) at Ballinglanna North 1, Cork, Ireland.
DOI: 10.6084/m9.figshare.1004413.v1
title: ATAM README

description: ATAM README
DOI: 10.6084/m9.figshare.1004464.v5
title: Crassostrea gigas male gonad transcriptomic data comparison

description: This fileset represents a comparison of RNA-seq data from a Pacific oyster (<em>Crassostrea gigas</em>) male gamete library to microarray data from Dheilly et al. 2012 "Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes". Specifically sequence reads were mapped to full-length transcripts represented on the array platformed used by Dheilly et al 2012. Data was joined using SQLShare. File Descriptions: <em>Fastafile_Microarray</em> - fasta file corresponding to targets on microarray. Used for RNA-seq analysis. <em>Rcode_OlsonandRoberts.R - </em>The R code used to visualize expression levels of RNA-Seq data relative to clusters of gene expression patterns during oyster gonad development identified by Dheilly et al. 2012. <em>SupplFig_OlsonandRoberts.pdf -</em> Boxplots of expression levels (RPKM) from RNA-Seq data relative to the 10 clusters of similar gene expression patterns during oyster gonad development identified by Dheilly et al. 2012. The number of genes represented are 511 (Cluster 1), 222 (Cluster 2), 312 (Cluster 3), 197 (Cluster 4), 226 (Cluster 5), 146 (Cluster 6), 200 (Cluster 7), 295 (Cluster 8), 332 (Cluster 9), and 41 (Cluster 10). <em>Dheilly_SexSpecific_S1_GonadRNAseq.txt - </em>Tab-delimited file that includes Dheilly et al table S1 and corresponding RNA-seq data from single male gamete library. <em>Dheilly_DiffGametogenesis_S2_GonadRNAseq.txt - </em>Tab-delimited file that includes Dheilly et al table S2 and corresponding RNA-seq data from single male gamete library. References: Dheilly, N. M., Lelong, C., Huvet, A., Kellner, K., Dubos, M., Riviere, G., Boudry, P., and Favrel, Pascal. (2012). Gametogenesis in the Pacific Oyster <em>Crassostrea gigas</em>: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes. PLoS ONE. 7:e36353-e36353. doi: 10.1371/journal.pone.0036353
DOI: 10.6084/m9.figshare.1004170
title: Gaussian Job Archive for C50H68N4O11Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1004170.v1
title: Gaussian Job Archive for C50H68N4O11Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1004413.v2
title: ATAM README

description: ATAM README
DOI: 10.6084/m9.figshare.1004171.v1
title: Identified plant remains from Ballinglanna North 1, Cork, Ireland (open dataset)

description: .csv file with identified charred plant remains from archaeobotanical samples taken during excavation of a multi-period site (Bronze Age, early medieval and post-medieval) at Ballinglanna North 1, Cork, Ireland.
DOI: 10.6084/m9.figshare.1004184.v1
title: Bioética Complexa: modelo explicativo

description: Elementos básicos do modelo explicativo de Bioética Complexa.
DOI: 10.6084/m9.figshare.1004171.v2
title: Identified plant remains from Ballinglanna North 1, Cork, Ireland (open dataset)

description: .csv file with identified charred plant remains from archaeobotanical samples taken during excavation of a multi-period site (Bronze Age, early medieval and post-medieval) at Ballinglanna North 1, Cork, Ireland.
DOI: 10.6084/m9.figshare.1004184.v2
title: Bioética Complexa: modelo explicativo

description: Elementos básicos do modelo explicativo de Bioética Complexa.
DOI: 10.6084/m9.figshare.1004171.v3
title: Identified plant remains from Ballinglanna North 1, Cork, Ireland (open dataset)

description: .csv file with identified charred plant remains from archaeobotanical samples taken during excavation of a multi-period site (Bronze Age, early medieval and post-medieval) at Ballinglanna North 1, Cork, Ireland.
DOI: 10.6084/m9.figshare.1004184.v3
title: biocomplex

description: Elementos básicos do modelo explicativo de Bioética Complexa.
DOI: 10.6084/m9.figshare.1004142
title: Heart Signal Recordings - Invitro and Invivo

description: A collection of sound wave files of heart signal recordings acquired with a hydrophone and a mechanical heart valve (invitro) or an electronic stethoscope using live humans (invivo).
DOI: 10.6084/m9.figshare.1004142.v1
title: Heart Signal Recordings - Invitro and Invivo

description: A collection of sound wave files of heart signal recordings acquired with a hydrophone and a mechanical heart valve (invitro) or an electronic stethoscope using live humans (invivo).
DOI: 10.6084/m9.figshare.1004138
title: Annual temperature trends for &gt;6000 weather station records.

description: Graphical plots of annual temperature trends for all GHCN stations not in the USHCN dataset (unadjusted, adjusted and adjustments) Stations are labelled as "rural", "inter" or "urban" depending on how urbanized the station is in terms of associated population <em>and</em> night brightness Data used for generating plots was the GHCN monthly dataset, downloaded from NOAA NCDC website in January 2013. Plots were generated by Ronan Connolly as preliminary analysis for the following article: R. Connolly, and M. Connolly (2014). <em>Urbanization bias III. Estimating the extent of bias in the Historical Climatology Network datasets</em> Open Peer Rev. J., 34 (Clim. Sci.),, ver. 0.1 (non peer reviewed draft)
DOI: 10.6084/m9.figshare.1004138.v1
title: output_station_plots.zip

description: Annual temperature trends for all GHCN stations not in the USHCN dataset.
DOI: 10.6084/m9.figshare.1004138.v3
title: Annual temperature trends for &gt;6000 weather station records.

description: Graphical plots of annual temperature trends for all GHCN stations not in the USHCN dataset (unadjusted, adjusted and adjustments) Stations are labelled as "rural", "inter" or "urban" depending on how urbanized the station is in terms of associated population <em>and</em> night brightness Data used for generating plots was the GHCN monthly dataset, downloaded from NOAA NCDC website in January 2013. Plots were generated by Ronan Connolly as preliminary analysis for the following article: R. Connolly, and M. Connolly (2014). <em>Urbanization bias III. Estimating the extent of bias in the Historical Climatology Network datasets</em> Open Peer Rev. J., 34 (Clim. Sci.),, ver. 0.1 (non peer reviewed draft)
DOI: 10.6084/m9.figshare.1004138.v2
title: Annual temperature trends for 6000 weather station records.

description: Annual temperature trends for all GHCN stations not in the USHCN dataset. Stations are labelled as "rural", "inter" or "urban" depending on how urbanized the station is in terms of associated population <em>and</em> night brightness Details