cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8245373
title: Additional file 7: of Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

description: File S3. A summary of the repetitive content estimates from each method. “dnaPipeTE_proportions” are the proportional estimates derived from the dnaPipeTE pipeline applied to read libraries, “dnaPipeTE_Mbp_fromprop” reflects these proportional estimates in Mbp (i.e. for each genome, the proportion of each element * the genome size), “dnaPipeTE_Mbp_RM” is the Mbp of each assembly which was masked by RepeatMasker using the dnaPipeTE repetitive element assemblies as repeat libraries, “RepeatModeler_Mbp_RM” when the RepeatModeler libraries were used for masking the assemblies with RepeatMasker, and “RM_metazoa_Mbp” the Mbp of each assembly which were masked with the “metazoa” library of RepeatMasker. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8245376
title: Additional file 2: of Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes

description: Table S2. DNA repair gene analysis (XLSX 95 kb)
DOI: 10.6084/m9.figshare.8245367
title: Additional file 1: of Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes

description: Table S1.Pathway analysis by PANTHER (XLSX 137 kb)
DOI: 10.6084/m9.figshare.8245367.v1
title: Additional file 1: of Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes

description: Table S1.Pathway analysis by PANTHER (XLSX 137 kb)
DOI: 10.6084/m9.figshare.8245373.v1
title: Additional file 7: of Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

description: File S3. A summary of the repetitive content estimates from each method. “dnaPipeTE_proportions” are the proportional estimates derived from the dnaPipeTE pipeline applied to read libraries, “dnaPipeTE_Mbp_fromprop” reflects these proportional estimates in Mbp (i.e. for each genome, the proportion of each element * the genome size), “dnaPipeTE_Mbp_RM” is the Mbp of each assembly which was masked by RepeatMasker using the dnaPipeTE repetitive element assemblies as repeat libraries, “RepeatModeler_Mbp_RM” when the RepeatModeler libraries were used for masking the assemblies with RepeatMasker, and “RM_metazoa_Mbp” the Mbp of each assembly which were masked with the “metazoa” library of RepeatMasker. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8245376.v1
title: Additional file 2: of Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes

description: Table S2. DNA repair gene analysis (XLSX 95 kb)
DOI: 10.6084/m9.figshare.8245364
title: Additional file 6: of Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

description: File S2. A summary of log-likelihood scores from the nQuire programme, showing the percent of heterozygous sites retained after the denoise step, the score for the free, diploid, triploid, and tetraploid models, and the differences between the diploid, triploid, and tetraploid models and the free model. The “Allreads_nQuire” tab summarises the results for when all decontaminated reads were mapped back to the genome assemblies, “Repfree_selfmaps_nQuire” summarises the results for when repetitive reads were removed from the read libraries (all reads were mapped to the repeats assembled by dnaPipeTE, and read pairs where neither read mapped to the repeats were extracted and considered “repeat free”) and mapped back to the assemblies, and “Repfree_reads_BUSCO_nQuire” summarises the same repeat free mappings, but restricted only to the shared 740 BUSCO genes. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8245355
title: MOESM2 of Prevalence of Helicobacter pylori infection and antibiotic resistance profile in Armenia

description: Additional file 2. Contains all data on macrolide and fluoroquinolone resistance mutation testing in gastric biopsy specimens of 91 patients.
DOI: 10.6084/m9.figshare.8245361
title: Additional file 5: of Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

description: File S1. A table of complete, duplicated, fragmented, and missing BUSCO genes for each of the genomes sequenced here and the average coverage of each of the shared BUSCO genes for each assembly. (XLSX 284 kb)
DOI: 10.6084/m9.figshare.8245364.v1
title: Additional file 6: of Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

description: File S2. A summary of log-likelihood scores from the nQuire programme, showing the percent of heterozygous sites retained after the denoise step, the score for the free, diploid, triploid, and tetraploid models, and the differences between the diploid, triploid, and tetraploid models and the free model. The “Allreads_nQuire” tab summarises the results for when all decontaminated reads were mapped back to the genome assemblies, “Repfree_selfmaps_nQuire” summarises the results for when repetitive reads were removed from the read libraries (all reads were mapped to the repeats assembled by dnaPipeTE, and read pairs where neither read mapped to the repeats were extracted and considered “repeat free”) and mapped back to the assemblies, and “Repfree_reads_BUSCO_nQuire” summarises the same repeat free mappings, but restricted only to the shared 740 BUSCO genes. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8245355.v1
title: MOESM2 of Prevalence of Helicobacter pylori infection and antibiotic resistance profile in Armenia

description: Additional file 2. Contains all data on macrolide and fluoroquinolone resistance mutation testing in gastric biopsy specimens of 91 patients.
DOI: 10.6084/m9.figshare.8245349
title: MOESM1 of Prevalence of Helicobacter pylori infection and antibiotic resistance profile in Armenia

description: Additional file 1. Contains all data on serological study results for H. pylori antibodies in serum of 230 subjects.
DOI: 10.6084/m9.figshare.8245361.v1
title: Additional file 5: of Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

description: File S1. A table of complete, duplicated, fragmented, and missing BUSCO genes for each of the genomes sequenced here and the average coverage of each of the shared BUSCO genes for each assembly. (XLSX 284 kb)
DOI: 10.6084/m9.figshare.8245349.v1
title: MOESM1 of Prevalence of Helicobacter pylori infection and antibiotic resistance profile in Armenia

description: Additional file 1. Contains all data on serological study results for H. pylori antibodies in serum of 230 subjects.
DOI: 10.6084/m9.figshare.8245307
title: Additional file 5: of Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life

description: Gene-wide and individual site tests for positive selection assessed with BUSTED, SLAC and FUBAR. (XLSX 323 kb)
DOI: 10.6084/m9.figshare.8245304
title: Additional file 4: of Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life

description: List of CAZymes identified in the transcriptomes. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.8245307.v1
title: Additional file 5: of Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life

description: Gene-wide and individual site tests for positive selection assessed with BUSTED, SLAC and FUBAR. (XLSX 323 kb)
DOI: 10.6084/m9.figshare.8245295
title: Additional file 3: of Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life

description: Protein sequences of CAZy genes identified in the transcriptomes. (FA 16407 kb)
DOI: 10.6084/m9.figshare.8245304.v1
title: Additional file 4: of Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life

description: List of CAZymes identified in the transcriptomes. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.8245295.v1
title: Additional file 3: of Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life

description: Protein sequences of CAZy genes identified in the transcriptomes. (FA 16407 kb)
DOI: 10.6084/m9.figshare.8245286
title: Additional file 1: of Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life

description: Metrics of samples and associated transcriptomes. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8245280
title: Additional file 7: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: All enriched GO terms in the AM, CA and OR semispecies. List of all GO terms enriched in each condition of the three semispecies. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.8245286.v1
title: Additional file 1: of Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life

description: Metrics of samples and associated transcriptomes. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8245277
title: Additional file 6: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: DE genes in multiple semispecies. List of all DE genes in more than one semispecies. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8245274
title: Additional file 5: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: All DE genes in the AM semispecies. Complete list of all DE genes in the AM semispecies including which condition, sex and tissue it was DE in, fold change, significance value, annotated Flybase gene identities for orthologs in D. willistoni and D. melanogaster, annotated gene name and domain predictions. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.8245280.v1
title: Additional file 7: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: All enriched GO terms in the AM, CA and OR semispecies. List of all GO terms enriched in each condition of the three semispecies. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.8245277.v1
title: Additional file 6: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: DE genes in multiple semispecies. List of all DE genes in more than one semispecies. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8245268
title: Additional file 4: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: All DE genes in the CA semispecies. Complete list of all DE genes in the CA semispecies including which condition, sex and tissue it was DE in, fold change, significance value, annotated Flybase gene identities for orthologs in D. willistoni and D. melanogaster, annotated gene name and domain predictions. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.8245274.v1
title: Additional file 5: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: All DE genes in the AM semispecies. Complete list of all DE genes in the AM semispecies including which condition, sex and tissue it was DE in, fold change, significance value, annotated Flybase gene identities for orthologs in D. willistoni and D. melanogaster, annotated gene name and domain predictions. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.8245262
title: Additional file 3: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: All DE genes in the OR semispecies. Complete list of all DE genes in the OR semispecies including which condition, sex and tissue it was DE in, fold change, significance value, annotated Flybase gene identities for orthologs in D. willistoni and D. melanogaster, annotated gene name and domain predictions. (XLSX 505 kb)
DOI: 10.6084/m9.figshare.8245268.v1
title: Additional file 4: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: All DE genes in the CA semispecies. Complete list of all DE genes in the CA semispecies including which condition, sex and tissue it was DE in, fold change, significance value, annotated Flybase gene identities for orthologs in D. willistoni and D. melanogaster, annotated gene name and domain predictions. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.8245262.v1
title: Additional file 3: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: All DE genes in the OR semispecies. Complete list of all DE genes in the OR semispecies including which condition, sex and tissue it was DE in, fold change, significance value, annotated Flybase gene identities for orthologs in D. willistoni and D. melanogaster, annotated gene name and domain predictions. (XLSX 505 kb)
DOI: 10.6084/m9.figshare.8245247
title: Additional file 1: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: Assembly metrics for the mapping reference transcriptomes of the AM, CA and OR semispecies. Transcriptome assembly metrics, including BUSCO marker recovery, ORF prediction and completeness, and the percentage of reads and ORFs associated with different organisms. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.8245247.v1
title: Additional file 1: of The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

description: Assembly metrics for the mapping reference transcriptomes of the AM, CA and OR semispecies. Transcriptome assembly metrics, including BUSCO marker recovery, ORF prediction and completeness, and the percentage of reads and ORFs associated with different organisms. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.12870059
title: Additional file 1 of Discriminative validity of the Core outcome set functional independence in a population of older adults

description: Additional file 1. Forward, stepwise ordinal regression. Contribution of each of the domains physical capacity, coping, empowerment and health literacy to the model based on the COSFI, determined by forward, stepwise ordinal regression.
DOI: 10.6084/m9.figshare.12870059.v1
title: Additional file 1 of Discriminative validity of the Core outcome set functional independence in a population of older adults

description: Additional file 1. Forward, stepwise ordinal regression. Contribution of each of the domains physical capacity, coping, empowerment and health literacy to the model based on the COSFI, determined by forward, stepwise ordinal regression.
DOI: 10.6084/m9.figshare.12870164
title: Additional file 10 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 10: Number of genes with counts&gt;0 and TPM≥1 and Gene expression in transcripts per million. (TPM) for RNA-Seq libraries from developmental timepoints.
DOI: 10.6084/m9.figshare.12870167
title: Additional file 11 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 11: Gene expression in counts for RNA-Seq libraries from developmental timepoints. Gene counts were extracted with featureCounts.
DOI: 10.6084/m9.figshare.12870167.v1
title: Additional file 11 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 11: Gene expression in counts for RNA-Seq libraries from developmental timepoints. Gene counts were extracted with featureCounts.
DOI: 10.6084/m9.figshare.8245046
title: Additional file 4: of Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation

description: Gene ontology enrichment tables from panther for differentially expressed genes in each comparison of patterned vs. unpatterned or plastic myotubes. (XLSX 41Â kb)
DOI: 10.6084/m9.figshare.12870188.v1
title: Additional file 6 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 6: Database of miRNAs in the Aedes albopictus genome (AalbF2).
DOI: 10.6084/m9.figshare.12870191
title: Additional file 7 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 7: Database of piRNA clusters in the Aedes albopictus genome (AalbF2).
DOI: 10.6084/m9.figshare.12870179
title: Additional file 3 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 3: Metadata including the number of duplication times for 500 bp and 1000 bp flanking regions and the list of the genomic regions with putative artifact duplications.
DOI: 10.6084/m9.figshare.12870182
title: Additional file 4 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 4: Database of viral species used for nrEVEs screening in AalbF2.
DOI: 10.6084/m9.figshare.12870182.v1
title: Additional file 4 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 4: Database of viral species used for nrEVEs screening in AalbF2.
DOI: 10.6084/m9.figshare.8245046.v1
title: Additional file 4: of Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation

description: Gene ontology enrichment tables from panther for differentially expressed genes in each comparison of patterned vs. unpatterned or plastic myotubes. (XLSX 41Â kb)
DOI: 10.6084/m9.figshare.12870185
title: Additional file 5 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 5: Database of nrEVEs in the Aedes albopictus genome (AalbF2).
DOI: 10.6084/m9.figshare.12870194
title: Additional file 8 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 8: Immunity genes annotated in AalbF2.
DOI: 10.6084/m9.figshare.12870188
title: Additional file 6 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 6: Database of miRNAs in the Aedes albopictus genome (AalbF2).
DOI: 10.6084/m9.figshare.8245037
title: Additional file 3: of Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation

description: Differential expression analysis output from sleuth for all patterned vs. unpatterned or plastic myotube comparisons. (XLSX 15029Â kb)
DOI: 10.6084/m9.figshare.12870194.v1
title: Additional file 8 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 8: Immunity genes annotated in AalbF2.
DOI: 10.6084/m9.figshare.12870164.v1
title: Additional file 10 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 10: Number of genes with counts&gt;0 and TPM≥1 and Gene expression in transcripts per million. (TPM) for RNA-Seq libraries from developmental timepoints.
DOI: 10.6084/m9.figshare.12870185.v1
title: Additional file 5 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 5: Database of nrEVEs in the Aedes albopictus genome (AalbF2).
DOI: 10.6084/m9.figshare.12870197
title: Additional file 9 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 9: Metadata of sequenced dataset and read mapping analysis of Ae. albopictus transcripts.
DOI: 10.6084/m9.figshare.12870197.v1
title: Additional file 9 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 9: Metadata of sequenced dataset and read mapping analysis of Ae. albopictus transcripts.
DOI: 10.6084/m9.figshare.12870191.v1
title: Additional file 7 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 7: Database of piRNA clusters in the Aedes albopictus genome (AalbF2).
DOI: 10.6084/m9.figshare.8245031
title: Additional file 2: of Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation

description: Transcripts per million (TPM) for all genes and all analyzed samples. Gene list for the sarcomere GO category and up- and downregulated E18 to P2 in vivo mouse muscle development genes. (XLSX 10615Â kb)
DOI: 10.6084/m9.figshare.8245037.v1
title: Additional file 3: of Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation

description: Differential expression analysis output from sleuth for all patterned vs. unpatterned or plastic myotube comparisons. (XLSX 15029Â kb)
DOI: 10.6084/m9.figshare.12870205.v1
title: Additional file 2 of Knowledge, attitude and practice (KAP) survey of canine rabies in Khyber Pakhtunkhwa and Punjab Province of Pakistan

description: Additional file 2. Datasheet. The excel datasheet used in this study.
DOI: 10.6084/m9.figshare.12870179.v1
title: Additional file 3 of Improved reference genome of the arboviral vector Aedes albopictus

description: Additional file 3: Metadata including the number of duplication times for 500 bp and 1000 bp flanking regions and the list of the genomic regions with putative artifact duplications.
DOI: 10.6084/m9.figshare.12870208
title: Additional file 1 of The importance of vitamin d metabolism as a potential prophylactic, immunoregulatory and neuroprotective treatment for COVID-19

description: Additional file 1: Table S1. Ongoing Clinical Trials as of July 2nd, 2020, of vitamin D in the Prevention and Treatment of COVID-19.
DOI: 10.6084/m9.figshare.8245025
title: Additional file 1: of Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation

description: CAD file for generating silicon wafer. (GDS 318Â kb)
DOI: 10.6084/m9.figshare.8245031.v1
title: Additional file 2: of Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation

description: Transcripts per million (TPM) for all genes and all analyzed samples. Gene list for the sarcomere GO category and up- and downregulated E18 to P2 in vivo mouse muscle development genes. (XLSX 10615Â kb)
DOI: 10.6084/m9.figshare.12870208.v1
title: Additional file 1 of The importance of vitamin d metabolism as a potential prophylactic, immunoregulatory and neuroprotective treatment for COVID-19

description: Additional file 1: Table S1. Ongoing Clinical Trials as of July 2nd, 2020, of vitamin D in the Prevention and Treatment of COVID-19.
DOI: 10.6084/m9.figshare.12870205
title: Additional file 2 of Knowledge, attitude and practice (KAP) survey of canine rabies in Khyber Pakhtunkhwa and Punjab Province of Pakistan

description: Additional file 2. Datasheet. The excel datasheet used in this study.
DOI: 10.6084/m9.figshare.12870212.v1
title: Additional file 1 of Strengthening research capacity through regional partners: the HRP Alliance at the World Health Organization

description: Additional file 1. Version de l'article en français - versão do artigo em português - versión del artículo en español
DOI: 10.6084/m9.figshare.12870212
title: Additional file 1 of Strengthening research capacity through regional partners: the HRP Alliance at the World Health Organization

description: Additional file 1. Version de l'article en français - versão do artigo em português - versión del artículo en español
DOI: 10.6084/m9.figshare.8245025.v1
title: Additional file 1: of Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation

description: CAD file for generating silicon wafer. (GDS 318Â kb)