cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12263105.v1
title: Molecular phylogeny of <i>Cremolobus</i> (Brassicaceae) supports the recognition of the new genus <i>Yunkia</i> and demonstrates the high habitat diversity of tribe Cremolobeae

description: <i>Cremolobus</i> is a genus of seven species distributed along the Andes from northern Argentina and Chile northward into Colombia, and it inhabits a variety of different environments from humid habitats, such as the Yungas in Bolivia and Argentina or the Andean Paramos in Colombia and Ecuador, to the arid regions of the Sechura Desert in Peru. This genus, together with <i>Aimara</i> and <i>Menonvillea</i>, form the South American tribe Cremolobeae, which is morphologically defined by the indehiscent and 1-seeded schizocarpic silicles. To date, phylogenetic analyses in the tribe were mainly focused on <i>Menonvillea</i> and <i>Aimara</i>, but there are no prior studies on <i>Cremolobus</i>. In this paper, we first studied the phylogenetic placement of <i>Cremolobus</i> within Cremolobeae using ribosomal nuclear (ITS) and chloroplast (<i>trnL-F</i>, <i>trnH-psbA</i>, <i>rps16</i> intron) data, including a comprehensive sampling of taxa. We also analysed morphological variation among species, emphasizing habitat adaptation and characterizing main lineages within the genus. Additionally, we studied the biome/habitat preference by the species and main lineages of <i>Cremolobus</i> and other members of the tribe, as well as characterized their climatic niches along the environmental space. Results from our analyses support the monophyly of <i>Cremolobus</i> excluding <i>C. subscandens</i> and <i>C. bolivianus</i>, which are transferred here to the new genus <i>Yunkia</i>. Furthermore, species of Cremolobeae inhabit a wide diversity of habitats along the Andes that are associated with high ecomorphological diversity and, therefore, differing in this aspect from the related tribes Eudemeae and Schizopetaleae. Climatic niche comparison recovered low niche overlap between main lineages of the tribe, but high similarity among species of the same lineage, suggesting the presence of phylogenetic niche conservatism in the tribe. Systematic implications of these results, including a key distinguishing <i>Yunkia</i> from the remaining genera of Cremolobeae and a synopsis of its species, are also provided.
DOI: 10.6084/m9.figshare.12263039
title: Raw data used in the paper from Reversible morphological changes in a juvenile marine fish after exposure to predatory alarm cues

description: Data on body measurements and landmarks for each experiment
DOI: 10.6084/m9.figshare.12263039.v1
title: Raw data used in the paper from Reversible morphological changes in a juvenile marine fish after exposure to predatory alarm cues

description: Data on body measurements and landmarks for each experiment
DOI: 10.6084/m9.figshare.12263009
title: Additional file 7 of Identification of functional mutations associated with environmental variance of litter size in rabbits

description: Additional file 7. Total number of relevant variants identified in the associated genomic regions for the environmental variance of litter size. INDELs and SNVs identified by WGS analysis in a UTR or splicing region or with a missense effect. For each variant, the position is indicated according to the chromosome (OCU) and base pair (bp) location. REF show the allele in the reference genome (Oryctolagus cuniculus v2.0.96) and ALT the alternative variant identified in the rabbit lines. Low and High show the allelic distribution in each line where 0 indicates the reference allele and 1 the alternative allele.
DOI: 10.6084/m9.figshare.12263006
title: Additional file 6 of Identification of functional mutations associated with environmental variance of litter size in rabbits

description: Additional file 6. Candidate genes and their biological function based on the GeneCards and Ensembl databases.
DOI: 10.6084/m9.figshare.12263006.v1
title: Additional file 6 of Identification of functional mutations associated with environmental variance of litter size in rabbits

description: Additional file 6. Candidate genes and their biological function based on the GeneCards and Ensembl databases.
DOI: 10.6084/m9.figshare.12263009.v1
title: Additional file 7 of Identification of functional mutations associated with environmental variance of litter size in rabbits

description: Additional file 7. Total number of relevant variants identified in the associated genomic regions for the environmental variance of litter size. INDELs and SNVs identified by WGS analysis in a UTR or splicing region or with a missense effect. For each variant, the position is indicated according to the chromosome (OCU) and base pair (bp) location. REF show the allele in the reference genome (Oryctolagus cuniculus v2.0.96) and ALT the alternative variant identified in the rabbit lines. Low and High show the allelic distribution in each line where 0 indicates the reference allele and 1 the alternative allele.
DOI: 10.6084/m9.figshare.12262898
title: Additional file 2 of Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome

description: Additional file 2: Table S1. Sequence reads for environmental- and subsistence-related taxa detected. Table S2. Information concerning 14C Accelerator Mass Spectrometry (AMS) dating. Table S3a. Processing protocol and results for isotope analyses. Table S3b. Results for isotope analyses (Merck standard). Table S3c. Results for isotope analyses (DL-Valine standard). Table S4. Abundance of bacterial taxonomic categories in the IM datasets. Table S5. Sequence read-length distribution for taxa identified in this study. Table S6. Significant KEGG pathways in the comparative IM datasets analysed. Table S7. Relative abundance of eighteen significant KEGG pathways in the IM cohorts. Table S8. Enrichment and depletion of KO metabolic gene categories in the comparative IM sample cohorts based on p-value (p=&lt;0.05) designation. Table S9. Enrichment and depletion of KO metabolic gene categories in the comparative IM sample cohorts based on false discovery rate (FDR) corrected p-values (q=&lt;0.05). Table S10. Enrichment and depletion of KO metabolic gene categories in the ancient and modern comparative IM sample cohort as calculated for the twenty-four authenticated ancient IM taxa. Table S11. Comparison of relative abundance of antibiotic resistance genes in the comparative IM cohorts. Table S12. Raw and filtered high-quality sequence read counts as related to the comparative IM datasets. Table S13. Information concerning the comparative NCBI genomes used during this study.
DOI: 10.6084/m9.figshare.12262898.v1
title: Additional file 2 of Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome

description: Additional file 2: Table S1. Sequence reads for environmental- and subsistence-related taxa detected. Table S2. Information concerning 14C Accelerator Mass Spectrometry (AMS) dating. Table S3a. Processing protocol and results for isotope analyses. Table S3b. Results for isotope analyses (Merck standard). Table S3c. Results for isotope analyses (DL-Valine standard). Table S4. Abundance of bacterial taxonomic categories in the IM datasets. Table S5. Sequence read-length distribution for taxa identified in this study. Table S6. Significant KEGG pathways in the comparative IM datasets analysed. Table S7. Relative abundance of eighteen significant KEGG pathways in the IM cohorts. Table S8. Enrichment and depletion of KO metabolic gene categories in the comparative IM sample cohorts based on p-value (p=&lt;0.05) designation. Table S9. Enrichment and depletion of KO metabolic gene categories in the comparative IM sample cohorts based on false discovery rate (FDR) corrected p-values (q=&lt;0.05). Table S10. Enrichment and depletion of KO metabolic gene categories in the ancient and modern comparative IM sample cohort as calculated for the twenty-four authenticated ancient IM taxa. Table S11. Comparison of relative abundance of antibiotic resistance genes in the comparative IM cohorts. Table S12. Raw and filtered high-quality sequence read counts as related to the comparative IM datasets. Table S13. Information concerning the comparative NCBI genomes used during this study.
DOI: 10.6084/m9.figshare.12262850
title: Additional file 8 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 8: Table S8. Genes differentially expressed (DESeq2, Padj &lt; 0.05) at 18 dpi only.
DOI: 10.6084/m9.figshare.12262856
title: Additional file 9 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 9: Table S9. Enriched GO terms for genes shown in the different compartments of the Venn diagrams (Fig. 4).
DOI: 10.6084/m9.figshare.12262850.v1
title: Additional file 8 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 8: Table S8. Genes differentially expressed (DESeq2, Padj &lt; 0.05) at 18 dpi only.
DOI: 10.6084/m9.figshare.12262856.v1
title: Additional file 9 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 9: Table S9. Enriched GO terms for genes shown in the different compartments of the Venn diagrams (Fig. 4).
DOI: 10.6084/m9.figshare.12262844
title: Additional file 7 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 7: Table S7. Genes differentially expressed (DESeq2, Padj &lt; 0.05) in both samplings taken at 10 dpi but not at 18 dpi.
DOI: 10.6084/m9.figshare.12262838
title: Additional file 6 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 6: Table S6. Genes differentially expressed in all 3 samplings (DESeq2, Padj &lt; 0.05) but with different sign in different samplings.
DOI: 10.6084/m9.figshare.12262844.v1
title: Additional file 7 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 7: Table S7. Genes differentially expressed (DESeq2, Padj &lt; 0.05) in both samplings taken at 10 dpi but not at 18 dpi.
DOI: 10.6084/m9.figshare.12262826
title: Additional file 4 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 4: Table S4. Genes differentially expressed in all 3 samplings (DESeq2, Padj &lt; 0.05). Higher expressed in lice sampled from gills.
DOI: 10.6084/m9.figshare.12262832
title: Additional file 5 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 5: Table S5. Genes differentially expressed in all 3 samplings (DESeq2, Padj &lt; 0.05). Higher expressed in lice sampled from skin.
DOI: 10.6084/m9.figshare.12262838.v1
title: Additional file 6 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 6: Table S6. Genes differentially expressed in all 3 samplings (DESeq2, Padj &lt; 0.05) but with different sign in different samplings.
DOI: 10.6084/m9.figshare.12262820
title: Additional file 2 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 2: Table S2. CPM values of all transcripts included in this study for the three different samplings: Experiment 1 (10 dpi), Experiment 2 (10 dpi) and Experiment 2 (18 dpi) (38 samples).
DOI: 10.6084/m9.figshare.12262823
title: Additional file 3 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 3: Table S3. Genes, at least in one of the samplings differentially expressed (DESeq2, Padj &lt; 0.05).
DOI: 10.6084/m9.figshare.12262823.v1
title: Additional file 3 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 3: Table S3. Genes, at least in one of the samplings differentially expressed (DESeq2, Padj &lt; 0.05).
DOI: 10.6084/m9.figshare.12262826.v1
title: Additional file 4 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 4: Table S4. Genes differentially expressed in all 3 samplings (DESeq2, Padj &lt; 0.05). Higher expressed in lice sampled from gills.
DOI: 10.6084/m9.figshare.12262832.v1
title: Additional file 5 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 5: Table S5. Genes differentially expressed in all 3 samplings (DESeq2, Padj &lt; 0.05). Higher expressed in lice sampled from skin.
DOI: 10.6084/m9.figshare.12262814
title: Additional file 1 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 1: Table S1. Results from all DESeq2 analyses for all genes analyzed.
DOI: 10.6084/m9.figshare.12262820.v1
title: Additional file 2 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 2: Table S2. CPM values of all transcripts included in this study for the three different samplings: Experiment 1 (10 dpi), Experiment 2 (10 dpi) and Experiment 2 (18 dpi) (38 samples).
DOI: 10.6084/m9.figshare.12262814.v1
title: Additional file 1 of Host gill attachment causes blood-feeding by the salmon louse (Lepeophtheirus salmonis) chalimus larvae and alters parasite development and transcriptome

description: Additional file 1: Table S1. Results from all DESeq2 analyses for all genes analyzed.
DOI: 10.6084/m9.figshare.12262724
title: Additional file 6 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 6: Table S4. Union and intersection of heterozygous blocks in each chromosome.
DOI: 10.6084/m9.figshare.12262727
title: Additional file 7 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 7: Table S5. Detailed results of the inference of heterozygous SNPs ancestrality for the three groups of C. albicans strains.
DOI: 10.6084/m9.figshare.12262727.v1
title: Additional file 7 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 7: Table S5. Detailed results of the inference of heterozygous SNPs ancestrality for the three groups of C. albicans strains.
DOI: 10.6084/m9.figshare.12262718
title: Additional file 5 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 5: Table S3. Detailed information on the variability observed in heterozygous and LOH blocks for all C. albicans strains when mapped to haplotype A.
DOI: 10.6084/m9.figshare.12262724.v1
title: Additional file 6 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 6: Table S4. Union and intersection of heterozygous blocks in each chromosome.
DOI: 10.6084/m9.figshare.12262718.v1
title: Additional file 5 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 5: Table S3. Detailed information on the variability observed in heterozygous and LOH blocks for all C. albicans strains when mapped to haplotype A.
DOI: 10.6084/m9.figshare.12262697
title: Additional file 2 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 2: Table S1. Detailed information on read coverage, mapping statistics and genomic variability of all C. albicans strains when aligned to the haplotype A.
DOI: 10.6084/m9.figshare.12262703
title: Additional file 3 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 3: Table S2. Detailed information on genomic variability of all analyzed non-albicans strains when aligned to the respective genome assemblies.
DOI: 10.6084/m9.figshare.12262697.v1
title: Additional file 2 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 2: Table S1. Detailed information on read coverage, mapping statistics and genomic variability of all C. albicans strains when aligned to the haplotype A.
DOI: 10.6084/m9.figshare.12262703.v1
title: Additional file 3 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 3: Table S2. Detailed information on genomic variability of all analyzed non-albicans strains when aligned to the respective genome assemblies.
DOI: 10.6084/m9.figshare.12262685
title: Additional file 13 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 13: Table S9. Level of heterozygosity of SC5314 considering a sliding-window approach.
DOI: 10.6084/m9.figshare.12262685.v1
title: Additional file 13 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 13: Table S9. Level of heterozygosity of SC5314 considering a sliding-window approach.
DOI: 10.6084/m9.figshare.12262673
title: Additional file 4 of Selecting and tailoring implementation interventions: a concept mapping approach

description: Additional file 4. Prioritized implementation strategies, associated barriers and mechanisms of action.
DOI: 10.6084/m9.figshare.12262679
title: Additional file 12 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 12: Table S8. Comparison of the variant calling results obtained with trimming quality thresholds of 15 and 28.
DOI: 10.6084/m9.figshare.12262679.v1
title: Additional file 12 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 12: Table S8. Comparison of the variant calling results obtained with trimming quality thresholds of 15 and 28.
DOI: 10.6084/m9.figshare.12262670
title: Additional file 11 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 11: Table S7. Detailed results of the inference of heterozygous SNPs ancestrality in comparison to C. africana for the three groups of C. albicans strains.
DOI: 10.6084/m9.figshare.12262664
title: Additional file 10 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 10: Table S6. Detailed information on read coverage, mapping statistics and genomic variability of all C. africana strains when aligned to the haplotype A of C. albicans.
DOI: 10.6084/m9.figshare.12262667
title: Additional file 3 of Selecting and tailoring implementation interventions: a concept mapping approach

description: Additional file 3. Statements included in each concept map category.
DOI: 10.6084/m9.figshare.12262667.v1
title: Additional file 3 of Selecting and tailoring implementation interventions: a concept mapping approach

description: Additional file 3. Statements included in each concept map category.
DOI: 10.6084/m9.figshare.12262670.v1
title: Additional file 11 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 11: Table S7. Detailed results of the inference of heterozygous SNPs ancestrality in comparison to C. africana for the three groups of C. albicans strains.
DOI: 10.6084/m9.figshare.12262673.v1
title: Additional file 4 of Selecting and tailoring implementation interventions: a concept mapping approach

description: Additional file 4. Prioritized implementation strategies, associated barriers and mechanisms of action.
DOI: 10.6084/m9.figshare.12262664.v1
title: Additional file 10 of Genomic evidence for a hybrid origin of the yeast opportunistic pathogen Candida albicans

description: Additional file 10: Table S6. Detailed information on read coverage, mapping statistics and genomic variability of all C. africana strains when aligned to the haplotype A of C. albicans.
DOI: 10.6084/m9.figshare.12262640
title: Additional file 8 of Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

description: Additional file 8: Table S8. PFAM domains used in phylogenetic analysis.
DOI: 10.6084/m9.figshare.12262643
title: Additional file 9 of Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

description: Additional file 9: Table S9. Raw output of Hmmsearch including RMWs and non-RMPs.
DOI: 10.6084/m9.figshare.12262643.v1
title: Additional file 9 of Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

description: Additional file 9: Table S9. Raw output of Hmmsearch including RMWs and non-RMPs.
DOI: 10.6084/m9.figshare.12262640.v1
title: Additional file 8 of Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

description: Additional file 8: Table S8. PFAM domains used in phylogenetic analysis.
DOI: 10.6084/m9.figshare.12262631
title: Additional file 6 of Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

description: Additional file 6: Table S6. Dysregulation scores of significantly dysregulated RMPs.
DOI: 10.6084/m9.figshare.12262634
title: Additional file 7 of Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

description: Additional file 7: Table S7. Survival p-values of RMPs whose expression is significantly associated with survival.
DOI: 10.6084/m9.figshare.12262625
title: Additional file 5 of Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

description: Additional file 5: Table S5. Number of samples analyzed for each cancer type, both in Normal and Tumor tissues.
DOI: 10.6084/m9.figshare.12262625.v1
title: Additional file 5 of Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

description: Additional file 5: Table S5. Number of samples analyzed for each cancer type, both in Normal and Tumor tissues.
DOI: 10.6084/m9.figshare.12262631.v1
title: Additional file 6 of Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

description: Additional file 6: Table S6. Dysregulation scores of significantly dysregulated RMPs.