cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3716182_d3.v1
title: Additional file 3 of Bicodon bias can determine the role of synonymous SNPs in human diseases

description: Table S1. Genetic diseases and sSNPs. The first column corresponds to the disease or genetic trait. The second and third columns correspond to the associated gene and SNP (where both can be more than one), respectively. Each SNP affects only one codon (third SNP row), but two bicodons, when the mutation is in the P-site (first SNP row), and when the mutation is in the A-site (second SNP row). Fourth, fifth, sixth and seventh columns, refer to the starting bicodon, list the bicodon sequence, the p-value, the residual score ( χ 2 = χ L 2 + χ H 2 $\chi ^{2}=\chi _{L}^{2}+ \chi _{H}^{2}$ ) and π value, respectively. The following four columns, refer to the resulting bicodon, list the bicodon sequence, the log-transformed p-value, the residual score and π value, respectively. The following three columns enumerate the relative p-value, the pause propensity variation, Δ π, and the corresponding Z-score due to the synonymous bicodon variant. The last two columns contain a summarized result of our analysis for each disease and the related references. (XLS 41 kb)
DOI: 10.6084/m9.figshare.c.3718318_d2.v1
title: Additional file 2: of Delineating functional principles of the bow tie structure of a kinase-phosphatase network in the budding yeast

description: KP-Net phosphorylation and dephosphorylation interactions: Phosphorylation and dephosphorylation interactions (PDI) that were included in the KP-Net and the experimental methods that validated them with the Pubmed references of the articles in which PDIs were reported. The KID database pipeline was used to score and annotate these interactions (Additional file 1: Supplementary Methods). (XLSX 280Â kb)
DOI: 10.5281/zenodo.14510896
title: Gel and plate images - Burmann et al "Mechanism of DNA capture by the MukBEF SMC complex and its inhibition by a viral DNA mimic"
DOI: 10.5281/zenodo.14510897
title: Gel and plate images - Burmann et al "Mechanism of DNA capture by the MukBEF SMC complex and its inhibition by a viral DNA mimic"
DOI: 10.15468/dl.v552jr
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calamus proridens Jordan & Gilbert, 1884",
 "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 41 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039170-241126133413365/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.3721483_d1.v1
title: Additional file 1: Table S1. of Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status

description: Levels of inflammatory cytokines in serum of control subjects and SLE patients. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3721465_d3.v1
title: Additional file 12: Table S5. of Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

description: Significantly enriched Gene Ontology terms for sequences in the “Core” transcriptome after orthogroup classification. Terms are enriched if they have FDR-corrected p-values &lt; 0.05 (Fisher’s Exact Test). Those terms that are overrepresented when all species are analyzed together (“Combined” column) are in bold. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3721483_d1
title: Additional file 1: Table S1. of Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status

description: Levels of inflammatory cytokines in serum of control subjects and SLE patients. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3721465_d3
title: Additional file 12: Table S5. of Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

description: Significantly enriched Gene Ontology terms for sequences in the “Core” transcriptome after orthogroup classification. Terms are enriched if they have FDR-corrected p-values &lt; 0.05 (Fisher’s Exact Test). Those terms that are overrepresented when all species are analyzed together (“Combined” column) are in bold. (XLSX 16 kb)
DOI: 10.60893/figshare.jap.27950535
title: Supplementary material

description: Supplementary text
DOI: 10.60893/figshare.jap.27950535.v1
title: Supplementary material

description: Supplementary text
DOI: 10.6084/m9.figshare.c.3721465_d4.v1
title: Additional file 13: Table S6. of Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

description: Significantly enriched Gene Ontology terms for sequences in the “Shared Achimenes” clusters after orthogroup classification. Terms are enriched if they have FDR-corrected p-values &lt; 0.05 (Fisher’s Exact Test). Those terms that are overrepresented when all species are analyzed together (“Combined” column) are in bold. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.c.3721483_d2.v1
title: Additional file 2: Table S2. of Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status

description: OTU table. (TXT 278 kb)
DOI: 10.48597/46gk-q2js
title: Measurement of Ozone at Longmont Union Reservoir

description: Measurement of Ozone at Longmont Union Reservoir
DOI: 10.6084/m9.figshare.c.3721642_d4.v1
title: Additional file 4: of Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding

description: PCR and sequencing primers used in this study. (XLS 80Â kb)
DOI: 10.6084/m9.figshare.c.3721642_d4
title: Additional file 4: of Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding

description: PCR and sequencing primers used in this study. (XLS 80Â kb)
DOI: 10.6084/m9.figshare.c.3721684_d2.v1
title: Additional file 2: Figure S2. of Human and feline adipose-derived mesenchymal stem cells have comparable phenotype, immunomodulatory functions, and transcriptome

description: Transcriptome analysis of ASCs. Full dataset of ASC gene expression profile. RNA-Seq analysis was performed on total mRNA prepared from three separate feline noninduced ASC culture preparations (passage 3), followed by data analysis with a standard HISAT-Cufflinks pipeline to yield gene expression values expressed as FPKM. (XLSX 1420 kb)
DOI: 10.6084/m9.figshare.c.3721684_d2
title: Additional file 2: Figure S2. of Human and feline adipose-derived mesenchymal stem cells have comparable phenotype, immunomodulatory functions, and transcriptome

description: Transcriptome analysis of ASCs. Full dataset of ASC gene expression profile. RNA-Seq analysis was performed on total mRNA prepared from three separate feline noninduced ASC culture preparations (passage 3), followed by data analysis with a standard HISAT-Cufflinks pipeline to yield gene expression values expressed as FPKM. (XLSX 1420 kb)
DOI: 10.6084/m9.figshare.c.3721672_d8.v1
title: Additional file 8: Table S3. of EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples

description: Result of the K fold cross validation (nâ  =â  10) for the optimization of bound, Spec and the global scoring using fraction 5 training dataset (True vs. False dataset). (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.c.3721672_d8
title: Additional file 8: Table S3. of EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples

description: Result of the K fold cross validation (nâ  =â  10) for the optimization of bound, Spec and the global scoring using fraction 5 training dataset (True vs. False dataset). (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.c.3714217_d2.v1
title: Additional file 2: of Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms

description: Supplementary Information - Table S2. (XLSX 30Â kb)
DOI: 10.6084/m9.figshare.c.3723097_d1
title: Additional file 1: Figure S1. of Differential cytokine profiling in Chagasic patients according to their arrhythmogenic-status

description: One phase association fit curves for pattern curve data. Axes represent association between mean fluorescence (MFI) values obtained for different know cytokine with results expressed in pg/ml (y axis). Y=Y0 + (Plateau-Y0)*(1-exp.(-K*x)) equation was used for calculating cytokine concentration for patient samples. Figure S2. High producer frequencies for Lown stratified Chagasic patients. Bar graph shows the percentage of high producers for the different cytokines studied for Lown clinical scoring. Control high producer’s percentages is showed as dotted line and Chagasic frequencies (high & low SD risk) as bars. Threshold to determining high producers was calculated on ROC curve values for patients included in this group. Figure S3. High producer frequencies for blood pressure stratified Chagasic patients. Bar graph shows the percentage of high producers for the different cytokines studied for blood pressure clinical scoring. Control high producer’s percentages is showed as dotted line and Chagasic frequencies (normotensive & hypertensive) as bars. Threshold to determining high producers was calculated on ROC curve values for patients included in this group. Figure S3. High producer frequencies for amiodarone treatment stratified Chagasic patients. Bar graph shows the percentage of high producers for the different cytokines studied for blood pressure clinical scoring. Control high producer’s percentages is showed as dotted line and Chagasic frequencies (untreated & treated) as bars. Threshold to determining high producers was calculated on ROC curve values for patients included in this group. (XLSX 980 kb)
DOI: 10.15468/dl.pv5ftu
title: Occurrence Download

description: A dataset containing 350 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Scolytus scolytus (J.C.Fabricius, 1775)",
 "Year 2000-2024"
 ]
}

 The dataset includes 350 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039171-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5519/qd.7n7qi55o
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (256 records)
DOI: 10.15468/dl.9m94sf
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Callanthias ruber (Rafinesque, 1810)",
 "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 62 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039172-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60893/figshare.jcp.27905022
title: Supplementary Material

description: Additional tables with fundamental vibrational frequencies for all 30 dimers calculated with various methods as well as DFT-SAPT interaction energies.
DOI: 10.60893/figshare.jcp.27905022.v1
title: Supplementary Material

description: Additional tables with fundamental vibrational frequencies for all 30 dimers calculated with various methods as well as DFT-SAPT interaction energies.
DOI: 10.6084/m9.figshare.c.3723766_d32.v1
title: Additional file 9: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

description: Table of Risbano dataset pathophenotype associations with WGCNA co-expression modules. (TXT 772 bytes)
DOI: 10.6084/m9.figshare.c.3723847_d1
title: Additional file 1: of Competitive and cooperative arm rehabilitation games played by a patient and unimpaired person: effects on motivation and exercise intensity

description: Raw data (questionnaire results and hand velocity) for all participants. (XLSX 24 kb)
DOI: 10.48597/nwny-prp4
title: Measurement of Nitrogen oxides at Broomfield Soaring Eagle Park

description: Measurement of Nitrogen oxides at Broomfield Soaring Eagle Park
DOI: 10.6084/m9.figshare.c.3723820_d9
title: Additional file 18 of Proteobacteria explain significant functional variability in the human gut microbiome

description: Module and pathway enrichments for gene families variable in each phylum-specific test (Fisherâ  s exact test, qâ ¤0.25). (CSV 2 kb)
DOI: 10.48597/mfr2-bzf7
title: Measurement of Ozone at Longmont Union Reservoir

description: Measurement of Ozone at Longmont Union Reservoir
DOI: 10.6084/m9.figshare.c.3723820_d12.v1
title: Additional file 20 of Proteobacteria explain significant functional variability in the human gut microbiome

description: SRA IDs and characteristics (read length, average genome size from MicrobeCensus) for samples used in this study. (CSV 5 kb)
DOI: 10.48597/9ban-2ka5
title: Nitrogen oxides at Broomfield Soaring Eagle Park

description: Measurement of Nitrogen oxides at Broomfield Soaring Eagle Park
DOI: 10.48597/pnmt-c88h
title: Measurement of Nitrogen oxides at Broomfield Soaring Eagle Park

description: Measurement of Nitrogen oxides at Broomfield Soaring Eagle Park
DOI: 10.48597/8746-kx8m
title: Measurement of Nitrogen oxides at Broomfield Soaring Eagle Park

description: Measurement of Nitrogen oxides at Broomfield Soaring Eagle Park
DOI: 10.6084/m9.figshare.c.3723820_d15.v1
title: Additional file 23 of Proteobacteria explain significant functional variability in the human gut microbiome

description: Predicted tree densities. (CSV 314 kb)
DOI: 10.48597/4kqq-kakb
title: Measurement of Ozone at Longmont Union Reservoir

description: Measurement of Ozone at Longmont Union Reservoir
DOI: 10.48597/ktab-kq4p
title: Ozone at Longmont Union Reservoir

description: Measurement of Ozone at Longmont Union Reservoir
DOI: 10.48597/2y5u-2pku
title: Measurement of Ozone at Longmont Union Reservoir

description: Measurement of Ozone at Longmont Union Reservoir
DOI: 10.6084/m9.figshare.c.3723820_d16.v1
title: Additional file 24 of Proteobacteria explain significant functional variability in the human gut microbiome

description: Source data for figures. Figure 1, source data 1: matrix of read counts (after rarefaction) for every gene family in each sample included in the present study. Figure 1, source data 2: matrix of average family lengths for every gene family in each sample included in the present study. Figure 1, source data 3: log-RPKG abundances for every gene family mapped in the present study. Figure 2, source data 1: residual log-RPKG abundances (i.e., after fitting the linear model) for every gene family mapped in the present study. Figure 3, source data 1: counts of invariable, non-significant, and variable gene families per pathway. “Strong,” “medium,” and “weak” refer to FDR cutoffs of 0.05, 0.10, and 0.25, respectively. Figure 3, source data 2: counts of invariable, non-significant, and variable gene families for ribosomes in each domain of life. Figure 4, source data 1: residual log-RPKG scaled by the expected variance under the null model (see the “Methods” section). Figure 6, source data 1: log10 phylogenetic distribution (PD), log10 residual variance statistics (residvar), significance at 5% FDR (invariable coded as “dn”, variable coded as “up”, non-significant coded as “ns”), presence in at least one bacterial/archaeal genome in KEGG, and annotations for all measured gene families. Figure 6, source data 2: counts of significant associations of invariable, non-significant, and variable gene families with taxonomic summary statistics. Figure 7, source data 1: counts of significant associations of invariable, non-significant, and variable gene families with phylum-level abundances. Figure 8, source data 1: q values for gene families in the overall test. Figure 8, source data 2: q values for gene families in phylum-specific tests. Figure 8, source data 3: JSON-formatted lists of significantly (in)variable or non-significant gene families at 5% (“strong”), 10% (“med”), and 25% FDR (“weak”); overall test. Figure 8, source data 4: JSON-formatted lists of significantly (in)variable or non-significant gene families at 5% (“strong”), 10% (“med”), and 25% FDR (“weak”); phylum-specific tests. (BZ 51464 kb)
DOI: 10.6084/m9.figshare.c.3723820_d12
title: Additional file 20 of Proteobacteria explain significant functional variability in the human gut microbiome

description: SRA IDs and characteristics (read length, average genome size from MicrobeCensus) for samples used in this study. (CSV 5 kb)
DOI: 10.6084/m9.figshare.c.3723820_d15
title: Additional file 23 of Proteobacteria explain significant functional variability in the human gut microbiome

description: Predicted tree densities. (CSV 314 kb)
DOI: 10.6084/m9.figshare.c.3723820_d16
title: Additional file 24 of Proteobacteria explain significant functional variability in the human gut microbiome

description: Source data for figures. Figure 1, source data 1: matrix of read counts (after rarefaction) for every gene family in each sample included in the present study. Figure 1, source data 2: matrix of average family lengths for every gene family in each sample included in the present study. Figure 1, source data 3: log-RPKG abundances for every gene family mapped in the present study. Figure 2, source data 1: residual log-RPKG abundances (i.e., after fitting the linear model) for every gene family mapped in the present study. Figure 3, source data 1: counts of invariable, non-significant, and variable gene families per pathway. “Strong,” “medium,” and “weak” refer to FDR cutoffs of 0.05, 0.10, and 0.25, respectively. Figure 3, source data 2: counts of invariable, non-significant, and variable gene families for ribosomes in each domain of life. Figure 4, source data 1: residual log-RPKG scaled by the expected variance under the null model (see the “Methods” section). Figure 6, source data 1: log10 phylogenetic distribution (PD), log10 residual variance statistics (residvar), significance at 5% FDR (invariable coded as “dn”, variable coded as “up”, non-significant coded as “ns”), presence in at least one bacterial/archaeal genome in KEGG, and annotations for all measured gene families. Figure 6, source data 2: counts of significant associations of invariable, non-significant, and variable gene families with taxonomic summary statistics. Figure 7, source data 1: counts of significant associations of invariable, non-significant, and variable gene families with phylum-level abundances. Figure 8, source data 1: q values for gene families in the overall test. Figure 8, source data 2: q values for gene families in phylum-specific tests. Figure 8, source data 3: JSON-formatted lists of significantly (in)variable or non-significant gene families at 5% (“strong”), 10% (“med”), and 25% FDR (“weak”); overall test. Figure 8, source data 4: JSON-formatted lists of significantly (in)variable or non-significant gene families at 5% (“strong”), 10% (“med”), and 25% FDR (“weak”); phylum-specific tests. (BZ 51464 kb)
DOI: 10.6084/m9.figshare.c.3725200_d2.v1
title: Additional file 2: of Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor

description: Excel table of the results of MFAP1 and Spp381 ortholog searches with InParanoid 8. UniProt IDs of orthologs identified by BLAST searches against the 273 species covered by the InParanoid 8 program [37] and by searching the InParanoid 8 ortholog database [37] that are indicated in Fig.Â 1. Orthologs identified by both methods are highlighted in green; orthologs identified by one method alone are highlighted in yellow; red indicates that no ortholog was identified. (XLSX 45Â kb)
DOI: 10.15468/dl.dkkepj
title: Occurrence Download

description: A dataset containing 4146 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tomicus piniperda (C.Linnaeus, 1758)",
 "Year 2000-2024"
 ]
}

 The dataset includes 4146 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039173-241126133413365/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.3725200_d3.v1
title: Additional file 3: of Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor

description: Excel table of the results of MFAP1 ortholog searches focused on the fungal kingdom. Data generated by BLAST searches against 103 fungi species (Fig. 2). UniProt IDs of potential orthologs are highlighted in green if the BLAST score (calculated with the BLOSUM45 scoring matrix) was ≥ 30 with an E-value ≤ 0.01 and query coverage was ≥ 20%, or highlighted in orange if the BLAST score (BLOSUM45 matrix) was ≥ 30 with an E-value ≤ 0.01 and query coverage ≥ 10%. Score - BLAST scores, calculated with the BLOSUM45 scoring matrix; Coverage - percentage of query sequence covered by alignment to the database sequence; E-value - Expect-value: number of hits expected to be seen by chance when searching a database of particular size; Identity - percentage of identical residues of query sequence and BLAST hit within the covered region. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.c.3725200_d2
title: Additional file 2: of Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor

description: Excel table of the results of MFAP1 and Spp381 ortholog searches with InParanoid 8. UniProt IDs of orthologs identified by BLAST searches against the 273 species covered by the InParanoid 8 program [37] and by searching the InParanoid 8 ortholog database [37] that are indicated in Fig.Â 1. Orthologs identified by both methods are highlighted in green; orthologs identified by one method alone are highlighted in yellow; red indicates that no ortholog was identified. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.c.3725200_d3
title: Additional file 3: of Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor

description: Excel table of the results of MFAP1 ortholog searches focused on the fungal kingdom. Data generated by BLAST searches against 103 fungi species (Fig. 2). UniProt IDs of potential orthologs are highlighted in green if the BLAST score (calculated with the BLOSUM45 scoring matrix) was ≥ 30 with an E-value ≤ 0.01 and query coverage was ≥ 20%, or highlighted in orange if the BLAST score (BLOSUM45 matrix) was ≥ 30 with an E-value ≤ 0.01 and query coverage ≥ 10%. Score - BLAST scores, calculated with the BLOSUM45 scoring matrix; Coverage - percentage of query sequence covered by alignment to the database sequence; E-value - Expect-value: number of hits expected to be seen by chance when searching a database of particular size; Identity - percentage of identical residues of query sequence and BLAST hit within the covered region. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.c.3725200_d5
title: Additional file 5: of Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor

description: Excel table of the results of pairwise sequence identity/similarity analyses. The table presents sequence identity and sequence similarity values for pairs of selected MFAP1 orthologs identified in this study. The sequence identity and similarity values were obtained by the EMBOSS Needle tool [55] using a BLOSUM62 scoring matrix. (XLSX 43Â kb)