cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16569845
title: Additional file 1 of A spatial analysis of parliamentary elections in Sweden 1985–2018

description: Additional file 1: Microsoft Excel file containing the results of the ten parliamentary elections held in Sweden between 1985 and 2018 at the municipality level.
DOI: 10.6084/m9.figshare.16569845.v1
title: Additional file 1 of A spatial analysis of parliamentary elections in Sweden 1985–2018

description: Additional file 1: Microsoft Excel file containing the results of the ten parliamentary elections held in Sweden between 1985 and 2018 at the municipality level.
DOI: 10.6084/m9.figshare.16569848
title: Additional file 2 of A spatial analysis of parliamentary elections in Sweden 1985–2018

description: Additional file 2: Microsoft Excel file containing the distance matrix between Swedish municipalities.
DOI: 10.6084/m9.figshare.16569848.v1
title: Additional file 2 of A spatial analysis of parliamentary elections in Sweden 1985–2018

description: Additional file 2: Microsoft Excel file containing the distance matrix between Swedish municipalities.
DOI: 10.6084/m9.figshare.16569883
title: Additional file 5 of Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development

description: Additional file 5. Processed lists of all genes expressed in either genotype, in body and BRGCs, respectively. F-values, P-values and FDR were derived using the Exact test within the EdgeR package.
DOI: 10.6084/m9.figshare.16569886
title: Additional file 6 of Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development

description: Additional file 6. Significantly enriched GO-terms from GORILLA and REVIGO online tools.
DOI: 10.6084/m9.figshare.16569889
title: Additional file 7 of Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development

description: Additional file 7. Expression levels, in Dfr14 relative to control, of genes involved in either ecdysteroid biosynthesis or the response to ecdysone.
DOI: 10.6084/m9.figshare.16569883.v1
title: Additional file 5 of Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development

description: Additional file 5. Processed lists of all genes expressed in either genotype, in body and BRGCs, respectively. F-values, P-values and FDR were derived using the Exact test within the EdgeR package.
DOI: 10.6084/m9.figshare.16569886.v1
title: Additional file 6 of Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development

description: Additional file 6. Significantly enriched GO-terms from GORILLA and REVIGO online tools.
DOI: 10.6084/m9.figshare.16569889.v1
title: Additional file 7 of Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development

description: Additional file 7. Expression levels, in Dfr14 relative to control, of genes involved in either ecdysteroid biosynthesis or the response to ecdysone.
DOI: 10.6084/m9.figshare.16569928
title: Additional file 1 of Local plant knowledge and its variation among farmer’s families in the Napf region, Switzerland

description: Additional file 1. List oft the species and reported uses.
DOI: 10.6084/m9.figshare.16569928.v1
title: Additional file 1 of Local plant knowledge and its variation among farmer’s families in the Napf region, Switzerland

description: Additional file 1. List oft the species and reported uses.
DOI: 10.6084/m9.figshare.16569934
title: Additional file 1 of Insights into 6S RNA in lactic acid bacteria (LAB)

description: Additional file 1 List of genomes and 6S RNAs (xls). List of LAB genomes used in this study including tax annotation, assembly status, location of the predicted 6S RNA.
DOI: 10.6084/m9.figshare.16569934.v1
title: Additional file 1 of Insights into 6S RNA in lactic acid bacteria (LAB)

description: Additional file 1 List of genomes and 6S RNAs (xls). List of LAB genomes used in this study including tax annotation, assembly status, location of the predicted 6S RNA.
DOI: 10.6084/m9.figshare.16569952
title: Additional file 7 of Insights into 6S RNA in lactic acid bacteria (LAB)

description: Additional file 7 Predicted cre site motifs (xls). Predicted cre sites sequences and positions relative to the 6S RNA start site.
DOI: 10.6084/m9.figshare.16569952.v1
title: Additional file 7 of Insights into 6S RNA in lactic acid bacteria (LAB)

description: Additional file 7 Predicted cre site motifs (xls). Predicted cre sites sequences and positions relative to the 6S RNA start site.
DOI: 10.6084/m9.figshare.15139412
title: Additional file 2 of Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

description: Additional file 2: Table S3: CAUSES exome sequence data summary. Table S4: Commands and parameters used for the implementation of lobSTR, RepeatSeq, HipSTR, TREDPARSE, ExpansionHunter, STRetch, exSTRa, and GangSTR. Table S5: Summary of repeat loci in catalogs used by short tandem repeat analysis methods. Table S6: Short tandem repeat calls of ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, RepeatSeq, STRetch, and exSTRa in the Isaac-aligned European Genome-phenome Archive and simulated genomes. Table S7: Short tandem repeat calls of ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, RepeatSeq, STRetch, and exSTRa in the BWA-aligned European Genome-phenome Archive and simulated genomes. Table S8: Known normal alleles characterised by ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, and RepeatSeq in the European Genome-phenome Archive and simulated genomes. Table S9: Known FMR1 intermediate and premutation alleles characterised by ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, and RepeatSeq in the European Genome-phenome Archive and simulated genomes. Table S10: Full-mutation alleles characterised by ExpansionHunter, GangSTR, and TREDPARSE in the European Genome-phenome Archive and simulated genomes. Table S11: Performance of short tandem repeat callers on simulated and real genomes with FMR1 CGG-repeat expansions in normal, premutation, and full-mutation size ranges. Table S12: Analysis and detection of DMPK, FMR1, and FXN full-mutation alleles using ExpansionHunter version 2 and GangSTR with and without off-target sites. Table S13: ExpansionHunter, STRetch, and exSTRa calls and molecular validation results of the short tandem repeat candidates identified in the CAUSES and IMAGINE genomes and exomes. Table S14: Repeat length distributions of the genotyped AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, ATXN8/ATXN8OS, ATXN10, C9orf72, CACNA1A, CBL, CNBP, CSTB, DMPK, FMR1, FMR2, FXN, HTT, JPH3, NOP56, PHOX2B, PPP2R2B, and TBP alleles in the CAUSES and IMAGINE genomes. Table S15: Summary of performance metrics of the best model and individual STR tools in BWA modified analysis. Table S16: Run-time and peak memory requirements of short tandem repeat callers and aligners on a 40x human genome.
DOI: 10.6084/m9.figshare.15139412.v1
title: Additional file 2 of Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

description: Additional file 2: Table S3: CAUSES exome sequence data summary. Table S4: Commands and parameters used for the implementation of lobSTR, RepeatSeq, HipSTR, TREDPARSE, ExpansionHunter, STRetch, exSTRa, and GangSTR. Table S5: Summary of repeat loci in catalogs used by short tandem repeat analysis methods. Table S6: Short tandem repeat calls of ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, RepeatSeq, STRetch, and exSTRa in the Isaac-aligned European Genome-phenome Archive and simulated genomes. Table S7: Short tandem repeat calls of ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, RepeatSeq, STRetch, and exSTRa in the BWA-aligned European Genome-phenome Archive and simulated genomes. Table S8: Known normal alleles characterised by ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, and RepeatSeq in the European Genome-phenome Archive and simulated genomes. Table S9: Known FMR1 intermediate and premutation alleles characterised by ExpansionHunter, GangSTR, TREDPARSE, lobSTR, HipSTR, and RepeatSeq in the European Genome-phenome Archive and simulated genomes. Table S10: Full-mutation alleles characterised by ExpansionHunter, GangSTR, and TREDPARSE in the European Genome-phenome Archive and simulated genomes. Table S11: Performance of short tandem repeat callers on simulated and real genomes with FMR1 CGG-repeat expansions in normal, premutation, and full-mutation size ranges. Table S12: Analysis and detection of DMPK, FMR1, and FXN full-mutation alleles using ExpansionHunter version 2 and GangSTR with and without off-target sites. Table S13: ExpansionHunter, STRetch, and exSTRa calls and molecular validation results of the short tandem repeat candidates identified in the CAUSES and IMAGINE genomes and exomes. Table S14: Repeat length distributions of the genotyped AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, ATXN8/ATXN8OS, ATXN10, C9orf72, CACNA1A, CBL, CNBP, CSTB, DMPK, FMR1, FMR2, FXN, HTT, JPH3, NOP56, PHOX2B, PPP2R2B, and TBP alleles in the CAUSES and IMAGINE genomes. Table S15: Summary of performance metrics of the best model and individual STR tools in BWA modified analysis. Table S16: Run-time and peak memory requirements of short tandem repeat callers and aligners on a 40x human genome.
DOI: 10.6084/m9.figshare.16570028
title: Additional file 1 of Pilot investigation of circulating angiogenic and inflammatory biomarkers associated with vascular malformations

description: Additional file 1: Table S1. Linear regression of biomarker levels between vascular malformation diseases. CI = confidence interval; PI = proportional increase; Bold values indicate markers with a q-value less than 0.05. Sample sizes vary from 45 to 59 for HHT vs. CCM, 38 to 52 for HHT vs. Sporadic BAVM, and 17 to 27 for CCM vs. Sporadic BAVM.
DOI: 10.6084/m9.figshare.16570028.v1
title: Additional file 1 of Pilot investigation of circulating angiogenic and inflammatory biomarkers associated with vascular malformations

description: Additional file 1: Table S1. Linear regression of biomarker levels between vascular malformation diseases. CI = confidence interval; PI = proportional increase; Bold values indicate markers with a q-value less than 0.05. Sample sizes vary from 45 to 59 for HHT vs. CCM, 38 to 52 for HHT vs. Sporadic BAVM, and 17 to 27 for CCM vs. Sporadic BAVM.
DOI: 10.6084/m9.figshare.16570009
title: Additional file 10 of Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots

description: Additional file 10: Supplementary Table S8. Predicted functional PFAM domains encoded by transcripts differentially expressed by Diabrioca virgifera virgifera exposed to Metarhizium anisopliae compared to controls. Counts provided for instances when ≥3 transcripts received an annotation within at least one of the treatments. InterPro identification (InterPro_ID) are also given, with NA indicating corresponding InterPro_ID not available.
DOI: 10.6084/m9.figshare.16570009.v1
title: Additional file 10 of Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots

description: Additional file 10: Supplementary Table S8. Predicted functional PFAM domains encoded by transcripts differentially expressed by Diabrioca virgifera virgifera exposed to Metarhizium anisopliae compared to controls. Counts provided for instances when ≥3 transcripts received an annotation within at least one of the treatments. InterPro identification (InterPro_ID) are also given, with NA indicating corresponding InterPro_ID not available.
DOI: 10.6084/m9.figshare.16570015
title: Additional file 12 of Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots

description: Additional file 12: Supplementary Table S9. Transcripts with significant differences in read counts (expression) between Diabrotica virgifera virgifera larvae feeding on transgenic maize expressing the insecticidal B. thuringiensis (Bt) Cry3Bb1 toxin (T8; Table 2) and Gpp34/Tpp35Ab1 (T5) compared to control non-Bt maize (T7). For each transcript, indication of differential expression also predicted when larvae were exposed to Heterorhabditis bacteriophora (Hb) and Metarhizium anisopliae (Ma) is indicated with a “1”. Standard output are shown for DeSeq2 (baseMean = the average of the normalized counts taken over all samples; log2FC = log2 fold change between the groups; lfcSE = standard error of the log2FoldChange; stat = Wald statistic; pvalue = Wald test P-value; BH_padj = Benjamini-Hochberg adjusted P-value) and EdgeR (logFC = log2 fold change between the groups; logCPM = the average log2-counts-per-million; PValue = the two-sided P-value; BF_FDR = Bonferroni adjusted P-value). Lack of significance for any given transcript in DESeq2 or EdgeR results shown as “-”. Mean log2FC among DESeq2 and EdgeR estimates are provided for each transcript. Transcript annotations include presence (Y) or absence (N) of signal_peptide probability (signalp_prob) threshold of &gt; 0.700 shown only for “complete” proteins (match length = 1.0 to Drosophila melanogaster (Dm) or Trobiolium castaneum (Tc) protein models). PFAMSCAN_PfamA search results (format transcript query start, transcript query end: frame, strand (+ or -), range of hit to PFAM domain/PFAM domain name/ E-value/percent identity). Predicted protein information given (transcript start: transcript end: frame: strand (+ or -): amino acid sequence). BLASTx query results to indicated databases shown in standard output format with “/” indicating no values for queries receiving of hits.
DOI: 10.6084/m9.figshare.16570015.v1
title: Additional file 12 of Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots

description: Additional file 12: Supplementary Table S9. Transcripts with significant differences in read counts (expression) between Diabrotica virgifera virgifera larvae feeding on transgenic maize expressing the insecticidal B. thuringiensis (Bt) Cry3Bb1 toxin (T8; Table 2) and Gpp34/Tpp35Ab1 (T5) compared to control non-Bt maize (T7). For each transcript, indication of differential expression also predicted when larvae were exposed to Heterorhabditis bacteriophora (Hb) and Metarhizium anisopliae (Ma) is indicated with a “1”. Standard output are shown for DeSeq2 (baseMean = the average of the normalized counts taken over all samples; log2FC = log2 fold change between the groups; lfcSE = standard error of the log2FoldChange; stat = Wald statistic; pvalue = Wald test P-value; BH_padj = Benjamini-Hochberg adjusted P-value) and EdgeR (logFC = log2 fold change between the groups; logCPM = the average log2-counts-per-million; PValue = the two-sided P-value; BF_FDR = Bonferroni adjusted P-value). Lack of significance for any given transcript in DESeq2 or EdgeR results shown as “-”. Mean log2FC among DESeq2 and EdgeR estimates are provided for each transcript. Transcript annotations include presence (Y) or absence (N) of signal_peptide probability (signalp_prob) threshold of &gt; 0.700 shown only for “complete” proteins (match length = 1.0 to Drosophila melanogaster (Dm) or Trobiolium castaneum (Tc) protein models). PFAMSCAN_PfamA search results (format transcript query start, transcript query end: frame, strand (+ or -), range of hit to PFAM domain/PFAM domain name/ E-value/percent identity). Predicted protein information given (transcript start: transcript end: frame: strand (+ or -): amino acid sequence). BLASTx query results to indicated databases shown in standard output format with “/” indicating no values for queries receiving of hits.
DOI: 10.6084/m9.figshare.16570039.v1
title: Additional file 4 of Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots

description: Additional file 4: Supplementary Table S3. Transcripts with significant differences in read counts (expression) between Diabrotica virgifera virgifera larvae feeding on transgenic maize expressing the insecticidal B. thuringiensis (Bt) Cry3Bb1 toxin (T8; Table 2) compared to control non-Bt maize (T7). For each transcript, indication of differential expression also being shared when larvae were exposed to Heterorhabditis bacteriophora (Hb) and Metarhizium anisopliae (Ma) is indicated with a “1”. Standard output are shown for DESeq2 (baseMean = the average of the normalized counts taken over all samples; log2FoldChange = log2 fold change between the groups; lfcSE = standard error of the log2FoldChange; stat = Wald statistic; pvalue = Wald test P-value; BH_padj = Benjamini-Hochberg adjusted p-value) and EdgeR (logFC = log2 fold change between the groups; logCPM = the average log2-counts-per-million; PValue = the two-sided P-value; BF_FDR = Bonferroni adjusted P-value). Lack of significance for any given transcript in DESeq2 or EdgeR results shown as “-”. The 1055 transcripts differentially expressed in both DESeq2 and EdgeR estimates are shown above the horizonal line. Transcript annotations include presence (Y) or absence (N) of signal_peptide probability (signalp_prob) threshold of &gt; 0.700 shown only for “complete” proteins (match length = 1.0 to Drosophila melanogaster (Dm) or Trobiolium castaneum (Tc) protein models). PFAMSCAN_PfamA search results (format transcript query start, transcript query end: frame, strand (+ or -), range of hit to PFAM domain/PFAM domain name/ E-value/percent identity). Predicted protein information given (transcript start: transcript end: frame: strand (+ or -): amino acid sequence). BLASTx query results to indicated databases shown in standard output format with “/” indicating no values for queries receiving of hits. The 9 transcripts in blue italicized text are putatively derived from Hb or Ma.
DOI: 10.6084/m9.figshare.16570042
title: Additional file 5 of Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots

description: Additional file 5: Supplementary Table S4. Transcripts with significant differences in read counts (expression) between Diabrotica virgifera virgifera larvae feeding on transgenic maize expressing the insecticidal B. thuringiensis (Bt) Gpp34/Tpp35Ab1 toxin (T5; Table 2) compared to control non-Bt maize (T7). For each transcript, indication of differential expression also being shared when larvae were exposed to Heterorhabditis bacteriophora (Hb) and Metarhizium anisopliae (MA) is indicated with a “1”. Standard output are shown for DESeq2 (baseMean = the average of the normalized counts taken over all samples; log2FoldChange = log2 fold change between the groups; lfcSE = standard error of the log2FoldChange; stat = Wald statistic; pvalue = Wald test P-value; BH_padj = Benjamini-Hochberg adjusted P-value) and EdgeR (logFC = log2 fold change between the groups; logCPM = the average log2-counts-per-million; PValue = the two-sided P-value; BF_FDR = Bonferroni adjusted P-value). Lack of significance for any given transcript in DESeq2 or EdgeR results shown as “-”. The 1374 transcripts differentially expressed in both DESeq2 and EdgeR estimates are shown above the horizonal line. Transcript annotations include presence (Y) or absence (N) of signal_peptide probability (signalp_prob) threshold of &gt; 0.700 shown only for “complete” proteins (match length = 1.0 to Drosophila melanogaster (Dm) or Trobiolium castaneum (Tc) protein models). PFAMSCAN_PfamA search results (format transcript query start, transcript query end: frame, strand (+ or -), range of hit to PFAM domain/PFAM domain name/ E-value/percent identity). Predicted protein information given (transcript start: transcript end: frame: strand (+ or -): amino acid sequence). BLASTx query results to indicated databases shown in standard output format with “/” indicating no values for queries receiving of hits. The 13 transcripts in blue italicized text are putatively derived from Hb or Ma.
DOI: 10.6084/m9.figshare.16570039
title: Additional file 4 of Up-regulation of apoptotic- and cell survival-related gene pathways following exposures of western corn rootworm to B. thuringiensis crystalline pesticidal proteins in transgenic maize roots

description: Additional file 4: Supplementary Table S3. Transcripts with significant differences in read counts (expression) between Diabrotica virgifera virgifera larvae feeding on transgenic maize expressing the insecticidal B. thuringiensis (Bt) Cry3Bb1 toxin (T8; Table 2) compared to control non-Bt maize (T7). For each transcript, indication of differential expression also being shared when larvae were exposed to Heterorhabditis bacteriophora (Hb) and Metarhizium anisopliae (Ma) is indicated with a “1”. Standard output are shown for DESeq2 (baseMean = the average of the normalized counts taken over all samples; log2FoldChange = log2 fold change between the groups; lfcSE = standard error of the log2FoldChange; stat = Wald statistic; pvalue = Wald test P-value; BH_padj = Benjamini-Hochberg adjusted p-value) and EdgeR (logFC = log2 fold change between the groups; logCPM = the average log2-counts-per-million; PValue = the two-sided P-value; BF_FDR = Bonferroni adjusted P-value). Lack of significance for any given transcript in DESeq2 or EdgeR results shown as “-”. The 1055 transcripts differentially expressed in both DESeq2 and EdgeR estimates are shown above the horizonal line. Transcript annotations include presence (Y) or absence (N) of signal_peptide probability (signalp_prob) threshold of &gt; 0.700 shown only for “complete” proteins (match length = 1.0 to Drosophila melanogaster (Dm) or Trobiolium castaneum (Tc) protein models). PFAMSCAN_PfamA search results (format transcript query start, transcript query end: frame, strand (+ or -), range of hit to PFAM domain/PFAM domain name/ E-value/percent identity). Predicted protein information given (transcript start: transcript end: frame: strand (+ or -): amino acid sequence). BLASTx query results to indicated databases shown in standard output format with “/” indicating no values for queries receiving of hits. The 9 transcripts in blue italicized text are putatively derived from Hb or Ma.