cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6983225.v1
title: Visual Probe Data

description: Column names are as follows:<br>1) Trial Number <br>The trial number (1-140, repeated 4 times)<br>2) Presentation Condition<br>The condition that stimuli were presented under(Normal/standard, Masking, CFS)<br><br>3) Expression <br>The expression presented (Fear, Neutral, Happy) ('Ghost' indicates that the trial was a noise trial - no faces were presented).<br>4) Inversion (Upright, Inverted, Baseline).<br>This codes the stimulus configuration and trial type<br>Upright = upright facesInverted = control facesBaseline = a 'normal v control/ face bias' trial.<br>5) tloc<br>The target location(1= left, 2= right)<br>6) ploc<br>The probe location(1= left, 2= right)<br>7) Vis<br>Codes whether or not the participant indicated that the trial was a 'signal' trial or a 'noise' trial. Signal =1, Noise = 0. (note that this is a vector of zeros for the standard presentation condition, since they only made this response on masking and CFS trials.)<br>8) RT<br>The latency of the participants response to the probe (ms)<br>9) ps<br><br>The participant number<br>10) correct<br><br>Codes whether or not the response to the probe was correct (0= incorrect, 1 = correct)<br>
DOI: 10.6084/m9.figshare.6983180
title: Full length CLANK BLAST and Trees

description: Phylogenetic Analyses of the top 100 blast hits for each of the 15 Nv-CLANKs analyzed in this paper. CLANK sequences are in red, and bacterial and viral sequences are in green. Clades containing many Trichomonas ankyrin domain encoding genes have been collapsed. Raw tree files and sequence files used to make trees are also provided
DOI: 10.6084/m9.figshare.6983180.v1
title: Full length CLANK BLAST and Trees

description: Phylogenetic Analyses of the top 100 blast hits for each of the 15 Nv-CLANKs analyzed in this paper. CLANK sequences are in red, and bacterial and viral sequences are in green. Clades containing many Trichomonas ankyrin domain encoding genes have been collapsed. Raw tree files and sequence files used to make trees are also provided
DOI: 10.6084/m9.figshare.6983162
title: Additional file 5: of Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates

description: Table S3. This table lists all the candidate upstream kinases identified by NetworKIN analysis, for the upregulated phosphosites. Shown in the table is the substrate (phosphoprotein identified in the SRMS-regulated phosphoproteome), position (corresponding upregulated phosphosite), upstream kinase ID (candidate kinase known to target the corresponding phosphosite), NetworKIN score, kinase group (NetPhorest-annotated kinase group), NetPhorest score, STRING identifier (the corresponding STRING-annotated identifier/ID for the interaction between the kinase and its substrate phosphoprotein), STRING score, Motif sequence (the specific motif corresponding to the phosphosite that is targeted by the candidate kinase) and STRING path. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.6983162.v1
title: Additional file 5: of Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates

description: Table S3. This table lists all the candidate upstream kinases identified by NetworKIN analysis, for the upregulated phosphosites. Shown in the table is the substrate (phosphoprotein identified in the SRMS-regulated phosphoproteome), position (corresponding upregulated phosphosite), upstream kinase ID (candidate kinase known to target the corresponding phosphosite), NetworKIN score, kinase group (NetPhorest-annotated kinase group), NetPhorest score, STRING identifier (the corresponding STRING-annotated identifier/ID for the interaction between the kinase and its substrate phosphoprotein), STRING score, Motif sequence (the specific motif corresponding to the phosphosite that is targeted by the candidate kinase) and STRING path. (XLSX 16 kb)
DOI: 10.7284/119568
title: GNSS (Global Navigation Satellite System) data collected during research cruise PE15-16 using a Trimble SPS351 instrument system onboard the platform RV Pelican
DOI: 10.6084/m9.figshare.6983141
title: Additional file 3: of Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates

description: Table S2. The file is organized into the following spreadsheets: Spreadsheet “Cell. & Biol. processes”: This table shows all the cellular and biological processes identified by IPA analysis ( www.ingenuity.com ) enriched from the upregulated/hyperphosphorylated proteins identified in the SRMS-regulated phosphoproteome. To minimize redundancy, the cellular and biological processes are categorized in specific functional “categories”. Also shown for every cellular and biological process are P-values (Fisher’s exact t-test), activation z-score, predicted activation state (based on a cut-off z-score = +/− 2), protein names and the number of proteins enriched in the corresponding cellular and biological process. Spreadsheet “Upstream regulators”: This table lists all the upstream regulators identified by IPA analysis for the SRMS-dependent upregulated/hyperphosphorylated proteins. Also shown are p-values, activation z-score, predicted activation state (based on a cut-off z-score = +/− 2), protein names and number of proteins for every upstream regulator identified by IPA analyses. Spreadsheet “Signaling pathways”: Shown here are the canonical signaling pathways corresponding to the upregulated/hyperphosphorylated proteins, as identified by IPA analysis. Also shown are the -log p-values, ratio (the ratio estimates the representation of the proteins in each canonical pathway. This is calculated as the ratio of the number of proteins that are enriched in the pathway to the number of proteins in the Ingenuity database reference dataset that make up the pathway) and the protein names corresponding to each canonical pathway. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6983141.v1
title: Additional file 3: of Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates

description: Table S2. The file is organized into the following spreadsheets: Spreadsheet “Cell. & Biol. processes”: This table shows all the cellular and biological processes identified by IPA analysis ( www.ingenuity.com ) enriched from the upregulated/hyperphosphorylated proteins identified in the SRMS-regulated phosphoproteome. To minimize redundancy, the cellular and biological processes are categorized in specific functional “categories”. Also shown for every cellular and biological process are P-values (Fisher’s exact t-test), activation z-score, predicted activation state (based on a cut-off z-score = +/− 2), protein names and the number of proteins enriched in the corresponding cellular and biological process. Spreadsheet “Upstream regulators”: This table lists all the upstream regulators identified by IPA analysis for the SRMS-dependent upregulated/hyperphosphorylated proteins. Also shown are p-values, activation z-score, predicted activation state (based on a cut-off z-score = +/− 2), protein names and number of proteins for every upstream regulator identified by IPA analyses. Spreadsheet “Signaling pathways”: Shown here are the canonical signaling pathways corresponding to the upregulated/hyperphosphorylated proteins, as identified by IPA analysis. Also shown are the -log p-values, ratio (the ratio estimates the representation of the proteins in each canonical pathway. This is calculated as the ratio of the number of proteins that are enriched in the pathway to the number of proteins in the Ingenuity database reference dataset that make up the pathway) and the protein names corresponding to each canonical pathway. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6983129
title: Additional file 2: of Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates

description: Table S1. The table is organized in the following spreadsheets: Spreadsheet “All Phosphopeptides”: This table lists all identified phosphopeptides from three independent replicates, via LC-MS/MS. Additional information corresponding to each phosphopeptide is also shown and includes peptide ID# (numerical ID), fraction (enriched; 1 or flowthrough; 2 fractions), Retention time, m/z, charge, measured mass, mass error, score, peptide sequence, modifications (type of PTM), UniProt accession, Phosphosite(s), sequence window, description of protein, use in quantitation (at least 2 unique tryptic peptides were identified for the corresponding protein), ANOVA p-values corresponding to each phosphopeptide identified across the three independent replicates, normalized abundance (phosphopeptide intensity) of the identified phosphopeptides across each replicate, average phosphopeptide intensities of the peptide in the control cells or cells expressing wild type SRMS, fold-change abundance of phosphopeptide intensities in SRMS-expressing cells (SRMS/Control) and Log2-scaled fold-change of SRMS/control values. Spreadsheet “All unique phosphoproteins”: This table lists all the unique phosphoproteins mapped from the phosphopeptides quantified via LC-MS/MS in the Vector and SRMS-expressing cells. Also shown are all associated phosphosites identified for each protein. Spreadsheet “Phosphopeptides p-value ≤ 0.05”: This table lists all phosphopeptides filtered at an ANOVA p-value threshold of 0.05. Also shown is other relevant information corresponding to each phosphopeptide, as in Spreadsheet “All Phosphopeptides”. Spreadsheet “Hyperphosphorylated proteins”: This table lists all the hyperphosphorylated/upregulated proteins identified in the SRMS-regulated phosphoproteome. These proteins were mapped from the hyperphosphorylated/upregulated peptides (Log2 SRMS/Control ≥1.58 and ANOVA p-value ≤0.05). Therefore, only phosphosites identified at Log2 SRMS/Control ≥1.58 and ANOVA p-value ≤0.05, are shown for every protein. Spreadsheet “Hypophosphorylated proteins”: Shown here is the hypophosphorylated/downregulated protein mapped from the hypophosphorylated/downregulated peptide (Log2 SRMS/Control ≤ − 1 and ANOVA p-value ≤0.05) identified in SRMS-expressing cells. (XLSX 745 kb)
DOI: 10.6084/m9.figshare.6983129.v1
title: Additional file 2: of Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediates

description: Table S1. The table is organized in the following spreadsheets: Spreadsheet “All Phosphopeptides”: This table lists all identified phosphopeptides from three independent replicates, via LC-MS/MS. Additional information corresponding to each phosphopeptide is also shown and includes peptide ID# (numerical ID), fraction (enriched; 1 or flowthrough; 2 fractions), Retention time, m/z, charge, measured mass, mass error, score, peptide sequence, modifications (type of PTM), UniProt accession, Phosphosite(s), sequence window, description of protein, use in quantitation (at least 2 unique tryptic peptides were identified for the corresponding protein), ANOVA p-values corresponding to each phosphopeptide identified across the three independent replicates, normalized abundance (phosphopeptide intensity) of the identified phosphopeptides across each replicate, average phosphopeptide intensities of the peptide in the control cells or cells expressing wild type SRMS, fold-change abundance of phosphopeptide intensities in SRMS-expressing cells (SRMS/Control) and Log2-scaled fold-change of SRMS/control values. Spreadsheet “All unique phosphoproteins”: This table lists all the unique phosphoproteins mapped from the phosphopeptides quantified via LC-MS/MS in the Vector and SRMS-expressing cells. Also shown are all associated phosphosites identified for each protein. Spreadsheet “Phosphopeptides p-value ≤ 0.05”: This table lists all phosphopeptides filtered at an ANOVA p-value threshold of 0.05. Also shown is other relevant information corresponding to each phosphopeptide, as in Spreadsheet “All Phosphopeptides”. Spreadsheet “Hyperphosphorylated proteins”: This table lists all the hyperphosphorylated/upregulated proteins identified in the SRMS-regulated phosphoproteome. These proteins were mapped from the hyperphosphorylated/upregulated peptides (Log2 SRMS/Control ≥1.58 and ANOVA p-value ≤0.05). Therefore, only phosphosites identified at Log2 SRMS/Control ≥1.58 and ANOVA p-value ≤0.05, are shown for every protein. Spreadsheet “Hypophosphorylated proteins”: Shown here is the hypophosphorylated/downregulated protein mapped from the hypophosphorylated/downregulated peptide (Log2 SRMS/Control ≤ − 1 and ANOVA p-value ≤0.05) identified in SRMS-expressing cells. (XLSX 745 kb)
DOI: 10.6084/m9.figshare.6983114
title: Additional file 2: of U–Th isotopic microanalysis of zircon reference materials and KBSI working standards

description: Table S2. U–Th isotopic composition of the zircons. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.6983114.v1
title: Additional file 2: of U–Th isotopic microanalysis of zircon reference materials and KBSI working standards

description: Table S2. U–Th isotopic composition of the zircons. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.6983108
title: Additional file 3: of Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies

description: R script used for all microbiome bioinformatic and statistical analyses. (R 35 kb)
DOI: 10.6084/m9.figshare.6983111
title: Additional file 1: of Uâ Th isotopic microanalysis of zircon reference materials and KBSI working standards

description: Table S1. SHRIMP Pb isotope data with calculated 232Th/238U ratios. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.6983111.v1
title: Additional file 1: of Uâ Th isotopic microanalysis of zircon reference materials and KBSI working standards

description: Table S1. SHRIMP Pb isotope data with calculated 232Th/238U ratios. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.6983108.v1
title: Additional file 3: of Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies

description: R script used for all microbiome bioinformatic and statistical analyses. (R 35 kb)
DOI: 10.6084/m9.figshare.6983099
title: Additional file 2: of Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies

description: Table S3. NCBI GenBank accession numbers for the survey of chloroplast genomes. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.6983099.v1
title: Additional file 2: of Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies

description: Table S3. NCBI GenBank accession numbers for the survey of chloroplast genomes. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.6983072
title: Canonical ankyrin comparison

description: Nasonia DV ankyrin domain proteins were blasted to different insect species to search for orthologs. Results of these are given here, and show that the wasp proteins are lineage restrictedfile descriptions:Additional File 1. (.xlsx) D.melanogaster and A.mellifera BLASTp hits for each Nasonia novel ankyrin-repeat containing transcript. Each of the 15 novel Nasonia transcripts was entered into a BLASTp query to search for homologous proteins in Drosophila and Apis. The top 100 hits were collected (duplicate sequences were removed) for each Nasonia transcript (individual sheets within workbook). Each row represents a distinct BLASTp hit and contains the hit’s description (column A), BLAST e-value (column B), and NCBI accession number (column C). <br>Additional File 2. (.xlsx) Top D.melanogaster and A.mellifera BLASTp novel ankyrin-repeat hits. All sequences from Additional file 1 were pooled (duplicate sequences removed) and entered as a reciprocal BLASTp query to see if they were strongly homologous to the Nasonia novel ankyrin-repeat containing transcripts. Each row represents a distinct BLASTp hit from Additioanl file 1, and again contains the hit’s description (column A, Yellow highlights Apis sequences. Drosophila sequences are left in white), BLAST e-value (column B), and NCBI accession number (column C) as well as the description of the Nasonia protein it reciprocal BLASTs back to (column E), BLAST e-value (column F), and NCBI accession number (column G). <br>
DOI: 10.6084/m9.figshare.6983072.v1
title: Canonical ankyrin comparison

description: Nasonia DV ankyrin domain proteins were blasted to different insect species to search for orthologs. Results of these are given here, and show that the wasp proteins are lineage restrictedfile descriptions:Additional File 1. (.xlsx) D.melanogaster and A.mellifera BLASTp hits for each Nasonia novel ankyrin-repeat containing transcript. Each of the 15 novel Nasonia transcripts was entered into a BLASTp query to search for homologous proteins in Drosophila and Apis. The top 100 hits were collected (duplicate sequences were removed) for each Nasonia transcript (individual sheets within workbook). Each row represents a distinct BLASTp hit and contains the hit’s description (column A), BLAST e-value (column B), and NCBI accession number (column C). <br>Additional File 2. (.xlsx) Top D.melanogaster and A.mellifera BLASTp novel ankyrin-repeat hits. All sequences from Additional file 1 were pooled (duplicate sequences removed) and entered as a reciprocal BLASTp query to see if they were strongly homologous to the Nasonia novel ankyrin-repeat containing transcripts. Each row represents a distinct BLASTp hit from Additioanl file 1, and again contains the hit’s description (column A, Yellow highlights Apis sequences. Drosophila sequences are left in white), BLAST e-value (column B), and NCBI accession number (column C) as well as the description of the Nasonia protein it reciprocal BLASTs back to (column E), BLAST e-value (column F), and NCBI accession number (column G). <br>
DOI: 10.6084/m9.figshare.6983069
title: Model objects

description: Pollimetry v.0.1.2 model objects
DOI: 10.6084/m9.figshare.6983060
title: hov_IT.rdata

description: hoverfly it model
DOI: 10.6084/m9.figshare.6983069.v1
title: Model objects

description: Pollimetry v.0.1.2 model objects
DOI: 10.7284/119572
title: GNSS (Global Navigation Satellite System) data collected during research cruise PE15-21 using a Trimble SPS351 instrument system onboard the platform RV Pelican
DOI: 10.6084/m9.figshare.6983018
title: Faskowitz2018wsbmLifeSpan_data

description: This is the data repository for the paper entitled <em>Weighted Stochastic Block Models of the Human Connectome across the Life Span</em>. See paper and code for how data was preprocessed and analyzed.<br><i><b>A note to help decipher the data:</b></i><br>For the <b>counts</b> and <b>lengths</b> matrices, the rows/columns 1, 2, and 60 should be deleted. After this is done, rows/columns 1:114 will correspond to the ordered strings in the nodeLabels.mat file. Further, the 115:128 will correspond to subcortical structures in this order (in the paper, we do not use these nodes): <br>Left-Thalamus-Proper, Left-Caudate, Left-Putamen, Left-Pallidum, Left-Hippocampus, Left-Amygdala, Left-Accumbens-area, Right-Thalamus-Proper, Right-Caudate, Right-Putamen, Right-Pallidum, Right-Hippocampus, Right-Amygdala, Right-Accumbens-area. <br> Further, rows 1 and 59 should be deleted for the <b>coordinates</b> and <b>volumes</b> files. After this, the rows should be to aligned to the labels described above.<br>For those interested in why these changes need to be made -&gt; In the matrix data that comes out of Dipy, the first row corresponds to streamlines that intersect the label <i>0</i>, which is outside the brain. Labels <i>1</i> and <i>59</i> (which become rows <i>2</i> and <i>60</i> when that Dipy row is present) in the Yeo parcellation correspond to <i>unknown</i> areas in the parcellation, which sometimes get rendered as a few voxels down by the hippocampus + OFC (from what I've observed). <br><sub>Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors(s) and do not necessarily reflect the views of the National Science Foundation.</sub><br>
DOI: 10.6084/m9.figshare.6983012
title: Earth Analytics Bootcamp | DRY Code Teaching Subset

description: This is a teaching data subset that contains data for monthly total precipitation (inches) and average temperature (Fahrenheit) for Boulder, CO. Data included:<br><br>1. Monthly precipitation (inches) for 1988 to 1992 (monthly-precip-1988-to-1992.csv). File is organized with 5 rows/records (one for year from 1988 to 1992) and 12 columns (one for each month from January to December).<br><br>2. Monthly precipitation (inches) for 1993 to 1997 (monthly-precip-1993-to-1997.csv). File is organized with 5 rows/records (one for each year from 1993 to 1997) and 12 columns (one for each month from January to December).<br><br>3. Monthly temperature (Fahrenheit) for 1991 to 1995 (temp-1991-to-1995-months.csv). File contains headers for rows/columns as needed.<br><br>4. Monthly temperature (Fahrenheit) for 1996 to 2000 (temp-1996-to-2000-months.csv). File contains headers for rows/columns as needed.<br><br>Source: NOAA
DOI: 10.6084/m9.figshare.6983012.v1
title: Earth Analytics Bootcamp | DRY Code Teaching Subset

description: This is a teaching data subset that contains data for monthly total precipitation (inches) and average temperature (Fahrenheit) for Boulder, CO. Data included:<br><br>1. Monthly precipitation (inches) for 1988 to 1992 (monthly-precip-1988-to-1992.csv). File is organized with 5 rows/records (one for year from 1988 to 1992) and 12 columns (one for each month from January to December).<br><br>2. Monthly precipitation (inches) for 1993 to 1997 (monthly-precip-1993-to-1997.csv). File is organized with 5 rows/records (one for each year from 1993 to 1997) and 12 columns (one for each month from January to December).<br><br>3. Monthly temperature (Fahrenheit) for 1991 to 1995 (temp-1991-to-1995-months.csv). File contains headers for rows/columns as needed.<br><br>4. Monthly temperature (Fahrenheit) for 1996 to 2000 (temp-1996-to-2000-months.csv). File contains headers for rows/columns as needed.<br><br>Source: NOAA
DOI: 10.6084/m9.figshare.6983006
title: Saudi tweets dataset

description: This dataset was used in the paper entitled "Issues of Dialectal Saudi Twitter Corpus" that will be published by the International Arab Journal of Information Technology.For citation:Alruily, Meshrif, Issues of Dialectal Saudi Twitter Corpus, The International Arab Journal of Information Technology, In press. <br><br>