cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6010706
title: Morphology and composition of the internal axis in two morphologically contrasting deep-water sea pens (Cnidaria: Octocorallia)

description: <i>Umbellula encrinus</i> Linnaeus, 1758 and <i>Anthoptilum grandiflorum</i> (Verrill, 1879) are two species of deep-water sea pens (Cnidaria: Octocorallia) commonly found in the Northwest Atlantic. These sea pens are frequently caught as fishing bycatch, but little is known about their biology. Here we characterise the internal skeleton (axis) of these two morphologically contrasting species, in terms of axis carbonate composition and proportion, morphology and metrics (i.e. cross-sectional area and weight) through gradients along their lengths. Using the conspicuous growth rings present in the axis of <i>U. encrinus</i> we also estimated intra-colonial variation in radial growth rates for this species. X-ray diffraction (XRD) analyses revealed that the carbonate portion of the axis is composed of magnesian calcite (Ca, Mg)CO<sub>3</sub> in both species. On average, the axis is composed of 71% carbonate material in <i>U. encrinus</i>, and 65% carbonate in <i>A. grandiflorum</i>. The carbonate proportion was greatly reduced from base (71%) to tip (33%) in the axis of <i>U. encrinus</i>, while in <i>A. grandiflorum</i> changes were less abrupt (~6% difference from base to tip). In <i>U. encrinus</i>, the axis is quadrangular in shape through its whole length, twisting longitudinally. Twisting can occur in both clockwise and anti-clockwise directions. The axis of <i>A. grandiflorum</i> varied from elliptical near the base to cylindrical through most of the remaining length, with no twisting observed. Axes’ cross-sectional areas also decreased with distance from the base in both species, being the largest near the base. Estimated radial growth rates in <i>U. encrinus</i> were variable within a single colony, ranging between 0.04 and 0.08 mm.yr<sup>−1</sup>. This is the first study to describe changes along the axes of sea pens, and to characterise the axes in the studied species. It provides a baseline for studies considering sea pens’ skeletons (e.g. ocean acidification and palaeoceanography).
DOI: 10.6084/m9.figshare.6010706.v1
title: Morphology and composition of the internal axis in two morphologically contrasting deep-water sea pens (Cnidaria: Octocorallia)

description: <i>Umbellula encrinus</i> Linnaeus, 1758 and <i>Anthoptilum grandiflorum</i> (Verrill, 1879) are two species of deep-water sea pens (Cnidaria: Octocorallia) commonly found in the Northwest Atlantic. These sea pens are frequently caught as fishing bycatch, but little is known about their biology. Here we characterise the internal skeleton (axis) of these two morphologically contrasting species, in terms of axis carbonate composition and proportion, morphology and metrics (i.e. cross-sectional area and weight) through gradients along their lengths. Using the conspicuous growth rings present in the axis of <i>U. encrinus</i> we also estimated intra-colonial variation in radial growth rates for this species. X-ray diffraction (XRD) analyses revealed that the carbonate portion of the axis is composed of magnesian calcite (Ca, Mg)CO<sub>3</sub> in both species. On average, the axis is composed of 71% carbonate material in <i>U. encrinus</i>, and 65% carbonate in <i>A. grandiflorum</i>. The carbonate proportion was greatly reduced from base (71%) to tip (33%) in the axis of <i>U. encrinus</i>, while in <i>A. grandiflorum</i> changes were less abrupt (~6% difference from base to tip). In <i>U. encrinus</i>, the axis is quadrangular in shape through its whole length, twisting longitudinally. Twisting can occur in both clockwise and anti-clockwise directions. The axis of <i>A. grandiflorum</i> varied from elliptical near the base to cylindrical through most of the remaining length, with no twisting observed. Axes’ cross-sectional areas also decreased with distance from the base in both species, being the largest near the base. Estimated radial growth rates in <i>U. encrinus</i> were variable within a single colony, ranging between 0.04 and 0.08 mm.yr<sup>−1</sup>. This is the first study to describe changes along the axes of sea pens, and to characterise the axes in the studied species. It provides a baseline for studies considering sea pens’ skeletons (e.g. ocean acidification and palaeoceanography).
DOI: 10.6084/m9.figshare.6010646
title: Conditional survival of patients with hepatocellular carcinoma: results from the Surveillance, Epidemiology, and End Results registry

description: <b>Background</b>: Compared with overall survival, conditional survival is a more relevant measure of prognosis in surviving patients over time. The aim of this study was to describe the conditional survival of patients with hepatocellular carcinoma according to different prognostic variables through an analysis of a national population-based cancer registry. <b>Methods</b>: We analyzed data from 3,082 hepatocellular carcinoma patients who were diagnosed between 2004 and 2014. <b>Results</b>: The conditional overall and cause-specific survival improved from 37.6% to 68.9% and 45% to 79.1%, respectively, in the entire study population. The conditional overall and cause-specific survival improved from 32.6% to 69.3% and 40.1% to 74.8%, respectively, in patients aged 65 to 74 years. The conditional overall and cause-specific survival improved from 8.4% to 44.1% and 12.1% to 66.1%, respectively, in the stage IVB group. The conditional overall and cause-specific survival improved from 32.8% to 71.4% and 40.3% to 78.4%, respectively, in the positive/elevated AFP group. <b>Conclusions</b>: Conditional survival exhibited an improved prognosis over time. For hepatocellular carcinoma patients who survived for a specific period of time after diagnosis, more dramatic improvements occurred in patients aged 65–74 years, patients with AJCC stage IVB, and patients with a positive/elevated AFP value.
DOI: 10.6084/m9.figshare.6010646.v1
title: Conditional survival of patients with hepatocellular carcinoma: results from the Surveillance, Epidemiology, and End Results registry

description: <b>Background</b>: Compared with overall survival, conditional survival is a more relevant measure of prognosis in surviving patients over time. The aim of this study was to describe the conditional survival of patients with hepatocellular carcinoma according to different prognostic variables through an analysis of a national population-based cancer registry. <b>Methods</b>: We analyzed data from 3,082 hepatocellular carcinoma patients who were diagnosed between 2004 and 2014. <b>Results</b>: The conditional overall and cause-specific survival improved from 37.6% to 68.9% and 45% to 79.1%, respectively, in the entire study population. The conditional overall and cause-specific survival improved from 32.6% to 69.3% and 40.1% to 74.8%, respectively, in patients aged 65 to 74 years. The conditional overall and cause-specific survival improved from 8.4% to 44.1% and 12.1% to 66.1%, respectively, in the stage IVB group. The conditional overall and cause-specific survival improved from 32.8% to 71.4% and 40.3% to 78.4%, respectively, in the positive/elevated AFP group. <b>Conclusions</b>: Conditional survival exhibited an improved prognosis over time. For hepatocellular carcinoma patients who survived for a specific period of time after diagnosis, more dramatic improvements occurred in patients aged 65–74 years, patients with AJCC stage IVB, and patients with a positive/elevated AFP value.
DOI: 10.6084/m9.figshare.6010583
title: LISS Panel Data Archive

description: The data in use is combined for the period between 2008 and 2013. The LISS panel data have received the international Data Seal of Approval (DSA) so there is no data available on this web. After signing a statement, the data would be freely available at https://www.lissdata.nl.<br>The LISS panel is a representative sample of Dutch individuals who participate in monthly Internet surveys. The panel is based on a true probability sample of households drawn from the population register. Households that could not otherwise participate are provided with a computer and Internet connection. A longitudinal survey is fielded in the panel every year, covering a large variety of domains:<br>1. Background variables (single wave study);3. Religion and ethnicity (LISS Core studies);4. Social integration and leisure (LISS Core studies);5. Family and households (LISS Core studies);6. Work and schooling (LISS Core studies); 8. Politics and value (LISS Core studies);10. Economic situation-income (LISS Core studies);34. Time use and consumption (Assembled studies).<br>Reference: Scherpenzeel, A.C., and Das, M. (2010).
DOI: 10.6084/m9.figshare.6010022
title: The hitchhikers' guide to writing health research

description: Research methods paper<br>
DOI: 10.6084/m9.figshare.6010022.v1
title: The hitchhikers' guide to writing health research

description: Research methods paper<br>
DOI: 10.6084/m9.figshare.6009143
title: Data_and_Scripts_for_Takasuka_etal_JAMES

description: A part of data and scripts for creating figures in Takasuka et al. (JAMES)
DOI: 10.6084/m9.figshare.6009143.v1
title: Data_and_Scripts_for_Takasuka_etal_JAMES

description: A part of data and scripts for creating figures in Takasuka et al. (JAMES)
DOI: 10.6084/m9.figshare.6009143.v2
title: Data_and_Scripts_for_Takasuka_etal_JAMES

description: A part of data and scripts for creating figures in Takasuka et al. (JAMES)
DOI: 10.6084/m9.figshare.6009143.v3
title: Data_and_Scripts_for_Takasuka_etal_JAMES

description: A part of data and scripts for creating figures in Takasuka et al. (JAMES)
DOI: 10.6084/m9.figshare.6009143.v4
title: Data_and_Scripts_for_Takasuka_etal_JAMES

description: A part of data and scripts for creating figures in Takasuka et al. (JAMES)
DOI: 10.6084/m9.figshare.6009107
title: Additional file 7: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S19. ATAC-seq peaks significantly differentially enriched (DESeq2 nominal p &lt; 0.2) in Other Cells (non-PMCs) compared to PMCs. Column definitions as in Additional file 6: Table S5. (XLSX 207 kb)
DOI: 10.6084/m9.figshare.6009107.v1
title: Additional file 7: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S19. ATAC-seq peaks significantly differentially enriched (DESeq2 nominal p &lt; 0.2) in Other Cells (non-PMCs) compared to PMCs. Column definitions as in Additional file 6: Table S5. (XLSX 207 kb)
DOI: 10.6084/m9.figshare.6009104
title: Additional file 6: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S5.ATAC-seq peaks significantly differentially enriched (DESSeq2 nominal p &lt; 0.2) in isolated PMCs compared to non-PMC cells. Column 1: ATAC-seq Peak Name: Peak number, obtained from ATAC-seq RPS peak names. Column 2: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 3: Start: Start coordinate of the peak. Column 4: End: End coordinate of the peak. Column 5: baseMean: DESeq2 mean of normalized counts for all samples. Column 6: log2FoldChange: the DESeq log2 fold change of the treatment mean over the control mean. Column 7: lfcSE: log 2 fold change standard error. Column 8: stat: Wald statistic comparing treatment condition to control. Column 9: pvalue: Wald test p value. (XLSX 216 kb)
DOI: 10.6084/m9.figshare.6009104.v1
title: Additional file 6: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S5.ATAC-seq peaks significantly differentially enriched (DESSeq2 nominal p &lt; 0.2) in isolated PMCs compared to non-PMC cells. Column 1: ATAC-seq Peak Name: Peak number, obtained from ATAC-seq RPS peak names. Column 2: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 3: Start: Start coordinate of the peak. Column 4: End: End coordinate of the peak. Column 5: baseMean: DESeq2 mean of normalized counts for all samples. Column 6: log2FoldChange: the DESeq log2 fold change of the treatment mean over the control mean. Column 7: lfcSE: log 2 fold change standard error. Column 8: stat: Wald statistic comparing treatment condition to control. Column 9: pvalue: Wald test p value. (XLSX 216 kb)
DOI: 10.6084/m9.figshare.6009101
title: Additional file 5: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S4. All peaks identified in Other Cells (non-PMCs) at 24 hpf (mesenchyme blastula stage). Column definitions as in Additional file 3: Table S2. (XLSX 5816Â kb)
DOI: 10.6084/m9.figshare.6009101.v1
title: Additional file 5: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S4. All peaks identified in Other Cells (non-PMCs) at 24 hpf (mesenchyme blastula stage). Column definitions as in Additional file 3: Table S2. (XLSX 5816Â kb)
DOI: 10.6084/m9.figshare.6009098
title: Additional file 4: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S3. All peaks identified in PMCs at 24 hpf (mesenchyme blastula stage). Column definitions as in Additional file 3: Table S2. (XLSX 6052Â kb)
DOI: 10.6084/m9.figshare.6009098.v1
title: Additional file 4: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S3. All peaks identified in PMCs at 24 hpf (mesenchyme blastula stage). Column definitions as in Additional file 3: Table S2. (XLSX 6052Â kb)
DOI: 10.6084/m9.figshare.6009095
title: Additional file 3: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S2. All peaks identified in both PMCs and Other Cells (non-PMCs) at 24 hpf (mesenchyme blastula stage). Column 1: Scaffold: S. purpuratus genome version 3.1 Scaffold containing the peak. Column 2: Peak Start: Start coordinate of the peak. Column 3: Peak End: End coordinate of the peak. Column 4: Peak Name. (XLSX 8779Â kb)
DOI: 10.6084/m9.figshare.6009095.v1
title: Additional file 3: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S2. All peaks identified in both PMCs and Other Cells (non-PMCs) at 24 hpf (mesenchyme blastula stage). Column 1: Scaffold: S. purpuratus genome version 3.1 Scaffold containing the peak. Column 2: Peak Start: Start coordinate of the peak. Column 3: Peak End: End coordinate of the peak. Column 4: Peak Name. (XLSX 8779Â kb)
DOI: 10.6084/m9.figshare.6009083
title: Additional file 1: of The burden of tooth loss in Italian elderly population living in nursing homes

description: Where you list the following information for each additional/supplementary file in the file inventory: File name raw data.xlsx, The file includes all the raw data of the survey, The data are in a excel file. (XLSX 326 kb)
DOI: 10.6084/m9.figshare.6009083.v1
title: Additional file 1: of The burden of tooth loss in Italian elderly population living in nursing homes

description: Where you list the following information for each additional/supplementary file in the file inventory: File name raw data.xlsx, The file includes all the raw data of the survey, The data are in a excel file. (XLSX 326 kb)
DOI: 10.6084/m9.figshare.6009074
title: Additional file 23: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S17. Transcripts within 10 kb of DNase-seq differential peaks. Column 1: Peak name: Peak number, obtained from DNase-seq RPS peak names. Columns 2-8: as described for Additional file 22: Table S16. (XLSX 178 kb)
DOI: 10.6084/m9.figshare.6009074.v1
title: Additional file 23: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S17. Transcripts within 10 kb of DNase-seq differential peaks. Column 1: Peak name: Peak number, obtained from DNase-seq RPS peak names. Columns 2-8: as described for Additional file 22: Table S16. (XLSX 178 kb)
DOI: 10.6084/m9.figshare.6009050
title: Additional file 22: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S16. Transcripts within 10 kb of ATAC-seq differential peaks. Column 1: Peak name: Peak number, obtained from ATAC-seq RPS peak names. Column 2: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 3: Start: Start coordinate of the peak. Column 4: End: End coordinate of the peak. Column 5: Transcript: Transcript within 10 kb of the peak. Column 6: Location of peak wrt transcript: Location definitions as described in the Methods. Column 7: Distance in bp: Distance of the peak from the transcript in base pairs. Column 8: Name of PMC DE gene: Name of the PMC DE gene withing 10 kb of the peak, if applicable. (XLSX 157 kb)
DOI: 10.6084/m9.figshare.6009050.v1
title: Additional file 22: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S16. Transcripts within 10 kb of ATAC-seq differential peaks. Column 1: Peak name: Peak number, obtained from ATAC-seq RPS peak names. Column 2: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 3: Start: Start coordinate of the peak. Column 4: End: End coordinate of the peak. Column 5: Transcript: Transcript within 10 kb of the peak. Column 6: Location of peak wrt transcript: Location definitions as described in the Methods. Column 7: Distance in bp: Distance of the peak from the transcript in base pairs. Column 8: Name of PMC DE gene: Name of the PMC DE gene withing 10 kb of the peak, if applicable. (XLSX 157 kb)
DOI: 10.6084/m9.figshare.6009038
title: Additional file 21: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S15. Coordinates of overlapping, differential peaks that are also open at the 128-cell stage. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.6009038.v1
title: Additional file 21: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S15. Coordinates of overlapping, differential peaks that are also open at the 128-cell stage. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.6009020
title: Additional file 20: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S14. Coordinates of all differential peaks found using ATAC-seq or DNase-seq that are also open at the 128-cell stage. (XLSX 75 kb)
DOI: 10.6084/m9.figshare.6009020.v1
title: Additional file 20: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S14. Coordinates of all differential peaks found using ATAC-seq or DNase-seq that are also open at the 128-cell stage. (XLSX 75 kb)
DOI: 10.6084/m9.figshare.6008996
title: Additional file 7: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Sequences from nested RT-PCR. The Ig chains obtained from Sanger sequencing of nested RT-PCR. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.6008996.v1
title: Additional file 7: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Sequences from nested RT-PCR. The Ig chains obtained from Sanger sequencing of nested RT-PCR. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.6008984
title: Additional file 19: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S13. All ATAC-seq peaks identified at the 128-cell stage. Column 1: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 2: Peak Start: Start coordinate of the peak. Column 3: Peak End: End coordinate of the peak. Column 4: Peak Name as assigned by F-seq. Column 5: Peak Score as assigned by F-seq. (XLSX 16076 kb)
DOI: 10.6084/m9.figshare.6008984.v1
title: Additional file 19: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S13. All ATAC-seq peaks identified at the 128-cell stage. Column 1: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 2: Peak Start: Start coordinate of the peak. Column 3: Peak End: End coordinate of the peak. Column 4: Peak Name as assigned by F-seq. Column 5: Peak Score as assigned by F-seq. (XLSX 16076 kb)
DOI: 10.6084/m9.figshare.6008981
title: Additional file 6: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Percentage of immunoglobulin reads in human plasmablasts and CD19+ Linâ B cells. The percentage of Ig reads is calculated by dividing the number of reads mapping to the top model to the total number of reads for AW2-AW3 plasmablast dataset and VH CD19+ Linâ B cell dataset. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.6008981.v1
title: Additional file 6: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Percentage of immunoglobulin reads in human plasmablasts and CD19+ Linâ B cells. The percentage of Ig reads is calculated by dividing the number of reads mapping to the top model to the total number of reads for AW2-AW3 plasmablast dataset and VH CD19+ Linâ B cell dataset. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.6008954
title: Additional file 5: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Somatic hypermutations in human single-cell datasets. The number of somatic hypermutations for AW2_AW3 plasmablast and VH CD19+ Linâ single cells compared to the IMGT germline sequences. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.6008954.v1
title: Additional file 5: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Somatic hypermutations in human single-cell datasets. The number of somatic hypermutations for AW2_AW3 plasmablast and VH CD19+ Linâ single cells compared to the IMGT germline sequences. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.6008930
title: Additional file 4: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Discordant reconstructions for AW2_AW3 dataset IgH chains. The V, D, J genes, CDR3 sequences, and complete reconstructed sequence are shown for discordant IgH reconstructions along with annotations for Ig reconstruction with Unfiltered methods and the PCR sequence. Also included are models that were filtered in the BALDR pipeline, as they were not predicted to be productive. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6008930.v1
title: Additional file 4: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Discordant reconstructions for AW2_AW3 dataset IgH chains. The V, D, J genes, CDR3 sequences, and complete reconstructed sequence are shown for discordant IgH reconstructions along with annotations for Ig reconstruction with Unfiltered methods and the PCR sequence. Also included are models that were filtered in the BALDR pipeline, as they were not predicted to be productive. (XLSX 18 kb)