cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12580558
title: Single-cell proteo-transcriptomic profiling reveals altered characteristics of stem and progenitor cells in patients receiving cytoreductive hydroxyurea in early-phase chronic myeloid leukemia

description: This repository contains CITE-seq data generated from CML stem and progenitor cells before and after hydroxyurea treatment using the BD Rhapsody Single-Cell Analysis System. 

File descriptions:

1. RSEC-adjusted UMI count files generated using the BD Rhapsody Targeted Analysis Pipeline (v. 1.10.1):



CartridgeS1_RSEC_MolsPerCell.csv


2. RSEC-adjusted UMI counts for cells remaining after cell quality filtering using SeqGeq software (genes expressed vs library size):



CartridgeS1_RSEC_MolsPerCell_postQC.csv


3. Sample tag (sample of origin) calls for each putative cell, outputted by the BD Rhapsody Targeted Analysis Pipeline (v. 1.10.1). 



CartridgeS1_Sample_Tag_Calls.csv
DOI: 10.5281/zenodo.12580559
title: Single-cell proteo-transcriptomic profiling reveals altered characteristics of stem and progenitor cells in patients receiving cytoreductive hydroxyurea in early-phase chronic myeloid leukemia

description: This repository contains CITE-seq data generated from CML stem and progenitor cells before and after hydroxyurea treatment using the BD Rhapsody Single-Cell Analysis System. 

File descriptions:

1. RSEC-adjusted UMI count files generated using the BD Rhapsody Targeted Analysis Pipeline (v. 1.10.1):



CartridgeS1_RSEC_MolsPerCell.csv


2. RSEC-adjusted UMI counts for cells remaining after cell quality filtering using SeqGeq software (genes expressed vs library size):



CartridgeS1_RSEC_MolsPerCell_postQC.csv


3. Sample tag (sample of origin) calls for each putative cell, outputted by the BD Rhapsody Targeted Analysis Pipeline (v. 1.10.1). 



CartridgeS1_Sample_Tag_Calls.csv
DOI: 10.6084/m9.figshare.c.3792151_d1.v1
title: Additional file 1: Table S1. of Transoral endoscopic head and neck surgery (eHNS) for minor salivary gland tumors of the oropharynx

description: Original data on patients included in report. (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.c.3792151_d1
title: Additional file 1: Table S1. of Transoral endoscopic head and neck surgery (eHNS) for minor salivary gland tumors of the oropharynx

description: Original data on patients included in report. (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.c.3792154_d1
title: Additional file 1: of Benchmarking computational fluid dynamics models of lava flow simulation for hazard assessment, forecasting, and risk management

description: Excel spreadsheet containing all benchmark parameters and data, model setup information, and model results. (XLSX 180 kb)
DOI: 10.15468/dl.w92qu5
title: Occurrence Download

description: A dataset containing 1659 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carcharhinus falciformis (Müller & Henle, 1839)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 1659 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039212-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3793378_d2
title: Additional file 2: Table S2. of Comparison of molecular serotyping approaches of Streptococcus agalactiae from genomic sequences

description: Metadata for all clinical isolates used in this study (nÂ =Â 790). (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.c.3793378_d3
title: Additional file 3: Table S3. of Comparison of molecular serotyping approaches of Streptococcus agalactiae from genomic sequences

description: Investigation of the previously published SNPs using the 10 reference strains. SNPs highlighted in yellow do not correlate with the respective reference and are removed from subsequent analysis. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3793378_d4.v1
title: Additional file 4: Table S4. of Comparison of molecular serotyping approaches of Streptococcus agalactiae from genomic sequences

description: Investigation of the SNPs (previously published and novel) identified using multiple alignment of the reference cps loci using a small a small dataset of clinical samples (nÂ =Â 28). SNP positions highlighted in grey represent SNPs not found in all isolates of a particular serotype. These positions were removed and the remaining SNPs represent the final set used in this study. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.c.3793378_d5.v1
title: Additional file 5: Table S5. of Comparison of molecular serotyping approaches of Streptococcus agalactiae from genomic sequences

description: Sequence analysis for the serotype pairs identified using the full cps locus approach. Hit coverage corresponds to the mapping coverage observed during analysis whereas the BLAST coverage corresponds to the percent coverage seen during pairwise alignment using BLAST. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.c.3793378_d4
title: Additional file 4: Table S4. of Comparison of molecular serotyping approaches of Streptococcus agalactiae from genomic sequences

description: Investigation of the SNPs (previously published and novel) identified using multiple alignment of the reference cps loci using a small a small dataset of clinical samples (nÂ =Â 28). SNP positions highlighted in grey represent SNPs not found in all isolates of a particular serotype. These positions were removed and the remaining SNPs represent the final set used in this study. (XLSX 23Â kb)
DOI: 10.6084/m9.figshare.c.3793378_d5
title: Additional file 5: Table S5. of Comparison of molecular serotyping approaches of Streptococcus agalactiae from genomic sequences

description: Sequence analysis for the serotype pairs identified using the full cps locus approach. Hit coverage corresponds to the mapping coverage observed during analysis whereas the BLAST coverage corresponds to the percent coverage seen during pairwise alignment using BLAST. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.c.3793378_d6.v1
title: Additional file 6: Table S6. of Comparison of molecular serotyping approaches of Streptococcus agalactiae from genomic sequences

description: Investigation of the not-typeable (â  Serotype undeterminedâ  ) isolates from the SNP-based approach. The pileup file created during the analysis was investigated in detail to determine the aetiology behind the incomplete SNP profiles. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3793396_d4.v1
title: MOESM4 of Effect of user preferences on ITN use: a review of literature and data

description: Additional file 4. Excel tool for cost and utility function calculation. This file provides instructions for calculating mean users per net from DHS and MIS datasets, and an excel-based tool to calculate increases or decreases in ITN users, depending on the cost differentials of different nets and the differentials in mean users per nets of different attributes.
DOI: 10.6084/m9.figshare.c.3793378_d6
title: Additional file 6: Table S6. of Comparison of molecular serotyping approaches of Streptococcus agalactiae from genomic sequences

description: Investigation of the not-typeable (â  Serotype undeterminedâ  ) isolates from the SNP-based approach. The pileup file created during the analysis was investigated in detail to determine the aetiology behind the incomplete SNP profiles. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3793402_d2.v1
title: Additional file 2: of 
			                  Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol

description: SBML format of iCbu641Genome Scale Metabolic Model. (XML 2250 kb)
DOI: 10.6084/m9.figshare.c.3793402_d1
title: Additional file 1: of 
			                  Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol

description: Excel format of iCbu641Genome Scale Metabolic Model. (XLSX 203 kb)
DOI: 10.6084/m9.figshare.c.3793402_d1.v1
title: Additional file 1: of 
			                  Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol

description: Excel format of iCbu641Genome Scale Metabolic Model. (XLSX 203 kb)
DOI: 10.3886/e186241
title: Data and code for "Digital Information Provision and Behavior Change: Lessons from Six Experiments in East Africa"

description: While some studies suggest mobile phone-based information programs change behavior, others  find no effect. We evaluate six text-message agricultural extension programs, collectively covering 128,000 farmers. A meta-analysis  finds a 1.22-fold increase in the odds of adoption of recommended practices (95% CI: 1.16,1.29). We cannot reject similar impacts across experiments. Impacts are increased by message repetition, but not by providing more granular information, using behavioral framings, or complementing texts with phone calls. There is little evidence of message fatigue or crowd-out. Despite modest absolute impacts detectable only with large samples or a meta-analysis, texts are inexpensive enough to be cost-effective. The accompanying files provide guidance, data, and code to replicate the analysis.
description: Response Rates: The response rate varied by each experiment and type of data. See the journal article for details.
description: We combine six different experiments with smallholder farmers in Kenya and Rwanda. Sampling strategies varied by each experiment. See the journal article for details.
description: Smallholder farmers in Kenya and Rwanda. .
DOI: 10.3886/e186241v1
title: Data and code for "Digital Information Provision and Behavior Change: Lessons from Six Experiments in East Africa"

description: While some studies suggest mobile phone-based information programs change behavior, others  find no effect. We evaluate six text-message agricultural extension programs, collectively covering 128,000 farmers. A meta-analysis  finds a 1.22-fold increase in the odds of adoption of recommended practices (95% CI: 1.16,1.29). We cannot reject similar impacts across experiments. Impacts are increased by message repetition, but not by providing more granular information, using behavioral framings, or complementing texts with phone calls. There is little evidence of message fatigue or crowd-out. Despite modest absolute impacts detectable only with large samples or a meta-analysis, texts are inexpensive enough to be cost-effective. The accompanying files provide guidance, data, and code to replicate the analysis.
description: Response Rates: The response rate varied by each experiment and type of data. See the journal article for details.
description: We combine six different experiments with smallholder farmers in Kenya and Rwanda. Sampling strategies varied by each experiment. See the journal article for details.
description: Smallholder farmers in Kenya and Rwanda. .
DOI: 10.6084/m9.figshare.c.3794686_d1
title: MOESM1 of Meristem culture and subsequent micropropagation of Chilean strawberry (Fragaria chiloensis (L.) Duch.)

description: Additional file 1. Raw data.
DOI: 10.6084/m9.figshare.c.3794674_d2.v1
title: Additional file 2: Table S3. of Identification of sympatric cryptic species of Aedes albopictus subgroup in Vietnam: new perspectives in phylosymbiosis of insect vector

description: b-ARISA dataset. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.c.3794674_d2
title: Additional file 2: Table S3. of Identification of sympatric cryptic species of Aedes albopictus subgroup in Vietnam: new perspectives in phylosymbiosis of insect vector

description: b-ARISA dataset. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.c.3794761_d1.v1
title: Additional file 1: of Development and evaluation of adsorption sheet (HD safe sheet-U) using active carbon for the purpose of the preventing the contamination diffusion of urinary excreted anticancer drug

description: Appendix 1 and 2. Adsorption properties of the activated carbon to the urinary anticancer drug. (ZIP 103 kb)
DOI: 10.15468/dl.hrk964
title: Occurrence Download

description: A dataset containing 217 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chilo partellus Swinhoe, 1885"
 ]
}

 The dataset includes 217 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039214-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3794761_d1
title: Additional file 1: of Development and evaluation of adsorption sheet (HD safe sheet-U) using active carbon for the purpose of the preventing the contamination diffusion of urinary excreted anticancer drug

description: Appendix 1 and 2. Adsorption properties of the activated carbon to the urinary anticancer drug. (ZIP 103 kb)
DOI: 10.15468/dl.cv5wfs
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carcharhinus isodon (Müller & Henle, 1839)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 86 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039215-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3795871_d2.v1
title: Additional file 2: of The skeletal proteome of the sea star Patiria miniata and evolution of biomineralization in echinoderms

description: Proteins identified from MS/MS analysis. Scaffold (version Scaffold_4.6.1, Proteome Software Inc., Portland, OR) was used to validate MS/MS based peptide and protein identifications. Peptide identifications were accepted if they could be established at greater than 50.0% probability by the Peptide Prophet algorithm with Scaffold delta-mass correction. Protein identifications were accepted if they could be established at greater than 90.0% probability and contained at least 2 identified peptides. Protein probabilities were assigned by the Protein Prophet algorithm. Proteins that contained similar peptides and could not be differentiated based on MS/MS analysis alone were grouped to satisfy the principles of parsimony. (TXT 80Â kb)
DOI: 10.6084/m9.figshare.c.3795874_d2.v1
title: MOESM1 of Second generation multiple reaction monitoring assays for enhanced detection of ultra-low abundance Mycobacterium tuberculosis peptides in human serum

description: Additional file 1. Table of native and isotope-labeled peptide multiple reaction monitoring parameters including parent and transition m/z, retention time and collision energy.
DOI: 10.15468/dl.2uvaxu
title: Occurrence Download

description: A dataset containing 41068 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Kenya",
 "DatasetKey is Observation.org, Nature data from around the World"
 ]
}

 The dataset includes 41068 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039213-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3795871_d2
title: Additional file 2: of The skeletal proteome of the sea star Patiria miniata and evolution of biomineralization in echinoderms

description: Proteins identified from MS/MS analysis. Scaffold (version Scaffold_4.6.1, Proteome Software Inc., Portland, OR) was used to validate MS/MS based peptide and protein identifications. Peptide identifications were accepted if they could be established at greater than 50.0% probability by the Peptide Prophet algorithm with Scaffold delta-mass correction. Protein identifications were accepted if they could be established at greater than 90.0% probability and contained at least 2 identified peptides. Protein probabilities were assigned by the Protein Prophet algorithm. Proteins that contained similar peptides and could not be differentiated based on MS/MS analysis alone were grouped to satisfy the principles of parsimony. (TXT 80Â kb)
DOI: 10.6084/m9.figshare.c.3795874_d2
title: MOESM1 of Second generation multiple reaction monitoring assays for enhanced detection of ultra-low abundance Mycobacterium tuberculosis peptides in human serum

description: Additional file 1. Table of native and isotope-labeled peptide multiple reaction monitoring parameters including parent and transition m/z, retention time and collision energy.
DOI: 10.6084/m9.figshare.c.3795889_d1.v1
title: Additional file 10: of Molecular characterization of breast cancer cell lines through multiple omic approaches

description: Table S6. Complete kinome data for all peptide substrates and all breast cell lines evaluated. Fold change is given for the phosphorylation of each peptide substrate, relative to the mean of four non-tumorigenic breast cell lines (184B5, MCF10A, MCF10F, MCF12A). Site refers to the amino acid residue in the human protein. (XLSX 443 kb)
DOI: 10.6084/m9.figshare.c.3795874_d3.v1
title: MOESM2 of Second generation multiple reaction monitoring assays for enhanced detection of ultra-low abundance Mycobacterium tuberculosis peptides in human serum

description: Additional file 2. Limit of Detection/Quantitation (LOD/LOQ) summary for transitions in each peptide in mixed exosome matrix. Values are in fmol/Îźl.
DOI: 10.6084/m9.figshare.c.3795889_d1
title: Additional file 10: of Molecular characterization of breast cancer cell lines through multiple omic approaches

description: Table S6. Complete kinome data for all peptide substrates and all breast cell lines evaluated. Fold change is given for the phosphorylation of each peptide substrate, relative to the mean of four non-tumorigenic breast cell lines (184B5, MCF10A, MCF10F, MCF12A). Site refers to the amino acid residue in the human protein. (XLSX 443 kb)
DOI: 10.6084/m9.figshare.c.3795892_d1.v1
title: Additional file 1 of Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies

description: Detailed phenotypic data. Phenotypic data per year, cross and trait, comprising descriptive statistics. (CSV 3 kb)
DOI: 10.6084/m9.figshare.c.3795874_d3
title: MOESM2 of Second generation multiple reaction monitoring assays for enhanced detection of ultra-low abundance Mycobacterium tuberculosis peptides in human serum

description: Additional file 2. Limit of Detection/Quantitation (LOD/LOQ) summary for transitions in each peptide in mixed exosome matrix. Values are in fmol/Îźl.
DOI: 10.6084/m9.figshare.c.3795892_d1
title: Additional file 1 of Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies

description: Detailed phenotypic data. Phenotypic data per year, cross and trait, comprising descriptive statistics. (CSV 3 kb)
DOI: 10.6084/m9.figshare.c.3795889_d2.v1
title: Additional file 11: of Molecular characterization of breast cancer cell lines through multiple omic approaches

description: Table S7. Kinome peptides in array, grouped according to the major biological pathways to which they contribute. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3795874_d4.v1
title: MOESM3 of Second generation multiple reaction monitoring assays for enhanced detection of ultra-low abundance Mycobacterium tuberculosis peptides in human serum

description: Additional file 3. Table of normalized TPA cut-off values determined by the healthy donor group. False discovery rates (FDR) are calculated as the false positives (healthy controls with nTPA above the cut-off)/total number of healthy controls.
DOI: 10.6084/m9.figshare.c.3796027_d1
title: Additional file 1:Table S1. of The effect of body size evolution and ecology on encephalization in cave bears and extant relatives

description: Basicranial length, body mass estimates, brain volumes and brain mass for all examined bear skulls. (XLSX 33Â kb)
DOI: 10.6084/m9.figshare.c.3796027_d4.v1
title: Additional file 4: Table S3. of The effect of body size evolution and ecology on encephalization in cave bears and extant relatives

description: Additional results for slope and intercept pairwise comparisons. (XLSX 31Â kb)
DOI: 10.6084/m9.figshare.c.3796027_d4
title: Additional file 4: Table S3. of The effect of body size evolution and ecology on encephalization in cave bears and extant relatives

description: Additional results for slope and intercept pairwise comparisons. (XLSX 31Â kb)
DOI: 10.6084/m9.figshare.c.3796027_d2
title: Additional file 2: Table S2. of The effect of body size evolution and ecology on encephalization in cave bears and extant relatives

description: Data subset of brain volume estimates based on external measurements by Finarelli [74] and glass bead method. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3796036_d1.v1
title: Additional file 1 of Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene

description: ID correspondence table and information on the SRA Runs. The correspondences among Entrez Gene ID, Kegg Gene ID, and Ensemble Gene ID are shown in Table 1. Information (Run ID, Experiment ID, Study ID, sample tissue and cultivar) on the SRA Runs used to construct the gene expression matrix is shown in Table 2. (XLSX 1015 kb)
DOI: 10.6084/m9.figshare.c.3796027_d5.v1
title: Additional file 5: Table S4. of The effect of body size evolution and ecology on encephalization in cave bears and extant relatives

description: Node values for ancestral stage reconstructions. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3796027_d5
title: Additional file 5: Table S4. of The effect of body size evolution and ecology on encephalization in cave bears and extant relatives

description: Node values for ancestral stage reconstructions. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3796036_d1
title: Additional file 1 of Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene

description: ID correspondence table and information on the SRA Runs. The correspondences among Entrez Gene ID, Kegg Gene ID, and Ensemble Gene ID are shown in Table 1. Information (Run ID, Experiment ID, Study ID, sample tissue and cultivar) on the SRA Runs used to construct the gene expression matrix is shown in Table 2. (XLSX 1015 kb)
DOI: 10.6084/m9.figshare.c.3796936_d8
title: Additional file 7: of Symbionts in waiting: the dynamics of incipient endosymbiont complementation and replacement in minimal bacterial communities of psyllids

description: OTU table for 191 samples. Original dataset was rarefied to 970 reads (the lowest number of reads in a sample) (XLSX 718 kb).
DOI: 10.6084/m9.figshare.c.3796915_d14.v1
title: Additional file 8: Table S7. of Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts

description: Estimates of proportions of explained variance by explanatory variables for OTUs (DNA). Estimates for random components (cage and residual) and fixed terms (gender and age) are calculated for each of the CMM OTUs log10-relative abundances and alpha diversity indices as profiled based on DNA in G15 (n = 270). When taxa are redundant, only the lowest rank is shown. Un: unclassified. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3796954_d7.v1
title: Additional file 7: of Analysis of the lipid body proteome of the oleaginous alga Lobosphaera incisa

description: Quantification of total fatty acids in complemented A. thaliana lines. GC measurements of seeds and seedlings for Fig. 8c are shown. (XLSX 127Â kb)