cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6600455.v1
title: Additional file 2: of Extensive exchange of transposable elements in the Drosophila pseudoobscura group

description: Table S1. D. pseudoobscura species group lines used in this study. Table S2. TEs found in D. obscura group. Sorted by if they are previously discovered or novel, then by Order and super family. Transmission states if the TE family is found to transfer between species. Table S3. Diagonal table showing the total number of TE families found in each species for comparison. In brackets, the number of novel TE families found shared between species. Table S4. Comparisons of dN/dS between TEs and nuclear genes. The dS values presented here are compared to the dS values of nuclear genes between the given species calculated previously. We considered a transfer event between two species to have occurred if the TE dS value is less than the 2.5th percentile for nuclear genes. For instances where no dS for nuclear comparisons are available, we used the dS between D. pseudoobscura and the species of interest. Table S5. Number of unique and shared polymorphic sites for each species comparison, for each TE family, used in the boxplots in Fig. 2e. (XLSX 153 kb)
DOI: 10.5281/zenodo.4007382
title: Results for the Implementation of EP-All and SPP-All heuristic.

description: The results for the EP-All<sup>1</sup> heuristic (as implemented by the authors) and SPP-All heuristic have been summarized in the table. Routes, solution time, and quality have been reported. The instances<sup>2</sup> used were the same as used by Agatz et al. 1. Agatz, N., Bouman, P., & Schmidt, M. (2018). Optimization Approaches for the Traveling Salesman Problem with Drone. Transportation Science, 52. doi:10.1287/trsc.2017.0791 2. Bouman, P. (2018). pcbouman-eur/Drones-TSP: Traveling Salesman with Drone (Java code) v1.0.0 (Publication no. 10.5281/zenodo.1204697). from Zenodo https://doi.org/10.5281/zenodo.1204697
DOI: 10.5281/zenodo.4007381
title: Results for the Implementation of EP-All and SPP-All heuristic.

description: The results for the EP-All<sup>1</sup> heuristic (as implemented by the authors) and SPP-All heuristic have been summarized in the table. Routes, solution time, and quality have been reported. The instances<sup>2</sup> used were the same as used by Agatz et al. 1. Agatz, N., Bouman, P., & Schmidt, M. (2018). Optimization Approaches for the Traveling Salesman Problem with Drone. Transportation Science, 52. doi:10.1287/trsc.2017.0791 2. Bouman, P. (2018). pcbouman-eur/Drones-TSP: Traveling Salesman with Drone (Java code) v1.0.0 (Publication no. 10.5281/zenodo.1204697). from Zenodo https://doi.org/10.5281/zenodo.1204697
DOI: 10.6084/m9.figshare.6600437
title: Additional file 1 of Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

description: Supplemental methods for the analysis of the olfactory epithelium data and supplemental figures 1-20. (ZIP 34910 kb)
DOI: 10.6084/m9.figshare.6600437.v1
title: Additional file 1 of Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

description: Supplemental methods for the analysis of the olfactory epithelium data and supplemental figures 1-20. (ZIP 34910 kb)
DOI: 10.6084/m9.figshare.6600095
title: Additional file 9: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S9. Queen Pearsons correlations by carbonyl. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6600095.v1
title: Additional file 9: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S9. Queen Pearsons correlations by carbonyl. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6600083
title: Additional file 1: of In vitro mineral nutrition of Curcuma longa L. affects production of volatile compounds in rhizomes after transfer to the greenhouse

description: Turmeric volatile constituents data. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.6600083.v1
title: Additional file 1: of In vitro mineral nutrition of Curcuma longa L. affects production of volatile compounds in rhizomes after transfer to the greenhouse

description: Turmeric volatile constituents data. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.6600074
title: Additional file 8: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S8. MANCOVA by queen age and source and carbonyl. (XLSX 145 kb)
DOI: 10.6084/m9.figshare.6600074.v1
title: Additional file 8: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S8. MANCOVA by queen age and source and carbonyl. (XLSX 145 kb)
DOI: 10.6084/m9.figshare.6600056
title: Additional file 7: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S7. ANOVA of carbonyl by queen age and source. (XLSX 102 kb)
DOI: 10.6084/m9.figshare.6600056.v1
title: Additional file 7: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S7. ANOVA of carbonyl by queen age and source. (XLSX 102 kb)
DOI: 10.6084/m9.figshare.6600053
title: Additional file 9: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: It contains five “HTML” files with the following names: HERV15_meme-chip.html; LTR13_PANCREAS_meme-chip.html; SVA_ADIPOSE_NUCLEI_meme-chip.html; SVA_LIVER_meme-chip.html; X7C_CHarlie15a_BREAST_ACTIVE.html. The HTML files represent the outputs of the “MEME-ChIP” analyses (i.e. motif analyses) for: HERV15 regions in the liver; LTR13C_ in the pancreas; SVAs in adipose nuclei and liver; X7C_Charlie_15a in Breast. (ZIP 399 kb)
DOI: 10.6084/m9.figshare.6600053.v1
title: Additional file 9: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: It contains five “HTML” files with the following names: HERV15_meme-chip.html; LTR13_PANCREAS_meme-chip.html; SVA_ADIPOSE_NUCLEI_meme-chip.html; SVA_LIVER_meme-chip.html; X7C_CHarlie15a_BREAST_ACTIVE.html. The HTML files represent the outputs of the “MEME-ChIP” analyses (i.e. motif analyses) for: HERV15 regions in the liver; LTR13C_ in the pancreas; SVAs in adipose nuclei and liver; X7C_Charlie_15a in Breast. (ZIP 399 kb)
DOI: 10.6084/m9.figshare.6600044
title: Additional file 8: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S5. Analysis of tissue specific enrichment in active regions. For each TE enriched in active regions (FDR
DOI: 10.6084/m9.figshare.6600044.v1
title: Additional file 8: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S5. Analysis of tissue specific enrichment in active regions. For each TE enriched in active regions (FDR
DOI: 10.6084/m9.figshare.6600035
title: Additional file 6: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S6. MANOVA of worker gut microbiota by age. (XLSX 206 kb)
DOI: 10.6084/m9.figshare.6600035.v1
title: Additional file 6: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S6. MANOVA of worker gut microbiota by age. (XLSX 206 kb)
DOI: 10.6084/m9.figshare.6600032
title: Additional file 3 of How accurate is automated gap filling of metabolic models?

description: Results of executing the curated B. longum metabolic model with Pathway Tools version 22.0. (TXT 67 kb)
DOI: 10.6084/m9.figshare.6600032.v1
title: Additional file 3 of How accurate is automated gap filling of metabolic models?

description: Results of executing the curated B. longum metabolic model with Pathway Tools version 22.0. (TXT 67 kb)
DOI: 10.6084/m9.figshare.6600029
title: Additional file 7: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S7. Analysis of correlation between TE insertion and gene expression variance. Normalized GTEx variance for the four gene categories (see Fig. 3), with gene densities and lengths. (TXT 3233 kb)
DOI: 10.6084/m9.figshare.6600029.v1
title: Additional file 7: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S7. Analysis of correlation between TE insertion and gene expression variance. Normalized GTEx variance for the four gene categories (see Fig. 3), with gene densities and lengths. (TXT 3233 kb)
DOI: 10.6084/m9.figshare.6600017
title: Additional file 5: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S5. Wilcoxon rank sum test of queen age. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6600017.v1
title: Additional file 5: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S5. Wilcoxon rank sum test of queen age. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6600008
title: Additional file 6: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S6. Analysis of age classes across tissues. FDR values for TE age enrichment/depletion across tissues are presented for the active regions. FDR values for repressed regions are found in the second sheet of the table. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.6600008.v1
title: Additional file 6: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S6. Analysis of age classes across tissues. FDR values for TE age enrichment/depletion across tissues are presented for the active regions. FDR values for repressed regions are found in the second sheet of the table. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.6599999
title: Additional file 2 of How accurate is automated gap filling of metabolic models?

description: FBA definition file for curated B. longum metabolic model suitable for execution by Pathway Tools version 22.0. This file defines the nutrients, secretions, and biomass metabolites for execution of the model in conjunction with the B. longum PGDB. (TXT 69 kb)
DOI: 10.6084/m9.figshare.6599999.v1
title: Additional file 2 of How accurate is automated gap filling of metabolic models?

description: FBA definition file for curated B. longum metabolic model suitable for execution by Pathway Tools version 22.0. This file defines the nutrients, secretions, and biomass metabolites for execution of the model in conjunction with the B. longum PGDB. (TXT 69 kb)
DOI: 10.6084/m9.figshare.6599981
title: Additional file 4: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S4. MANOVA of queen age and source by niche. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.6599981.v1
title: Additional file 4: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S4. MANOVA of queen age and source by niche. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.6599975
title: Additional file 5: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S4. Analysis of histone marks in repressed regions. For each tissue, the numbers of repressed regions overlapping H3K9me3 and H3K27me3 are presented. (CSV 2 kb)
DOI: 10.6084/m9.figshare.6599975.v1
title: Additional file 5: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S4. Analysis of histone marks in repressed regions. For each tissue, the numbers of repressed regions overlapping H3K9me3 and H3K27me3 are presented. (CSV 2 kb)
DOI: 10.6084/m9.figshare.6599966
title: Additional file 1 of How accurate is automated gap filling of metabolic models?

description: Curated B. longum PGDB suitable for loading into Pathway Tools version 22.0 for browsing and exploration. This archived directory tree will expand to a set of files readable by Pathway Tools version 22.0. (ZIP 2472 kb)
DOI: 10.6084/m9.figshare.6599966.v1
title: Additional file 1 of How accurate is automated gap filling of metabolic models?

description: Curated B. longum PGDB suitable for loading into Pathway Tools version 22.0 for browsing and exploration. This archived directory tree will expand to a set of files readable by Pathway Tools version 22.0. (ZIP 2472 kb)
DOI: 10.6084/m9.figshare.6599957
title: Additional file 3: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S3 Queen relative and normalized abundance. (XLSX 462 kb)
DOI: 10.6084/m9.figshare.6599957.v1
title: Additional file 3: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S3 Queen relative and normalized abundance. (XLSX 462 kb)
DOI: 10.6084/m9.figshare.6599945
title: Additional file 4: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S3. p-values and corrected p-values from TE-Analysis pipeline for repressed regions (permutation test), For each TE family, uncorrected p-values from permutation analysis for REPRESSED regions are reported. Corrected p-values (FDR) for the ENRICHED TEs are found in the second sheet. (XLSX 188 kb)
DOI: 10.6084/m9.figshare.6599945.v1
title: Additional file 4: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S3. p-values and corrected p-values from TE-Analysis pipeline for repressed regions (permutation test), For each TE family, uncorrected p-values from permutation analysis for REPRESSED regions are reported. Corrected p-values (FDR) for the ENRICHED TEs are found in the second sheet. (XLSX 188 kb)
DOI: 10.6084/m9.figshare.6599942
title: Additional file 1: of Pharmacokinetics of rectal levetiracetam as add-on treatment in dogs affected by cluster seizures or status epilepticus

description: Signalment and history information of patients included. Information on signalment, seizure frequency, diagnosis (if achieved) of patients included in the study. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.6599942.v1
title: Additional file 1: of Pharmacokinetics of rectal levetiracetam as add-on treatment in dogs affected by cluster seizures or status epilepticus

description: Signalment and history information of patients included. Information on signalment, seizure frequency, diagnosis (if achieved) of patients included in the study. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.6599936
title: Additional file 2: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S2. Queen diversity, abundance, qPCR. (XLSX 484 kb)
DOI: 10.6084/m9.figshare.6599936.v1
title: Additional file 2: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S2. Queen diversity, abundance, qPCR. (XLSX 484 kb)
DOI: 10.6084/m9.figshare.6599927
title: Additional file 3: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S2. p-values and corrected p-values from TE-Analysis pipeline for active regions (permutation test). For each TE family, uncorrected p-values from permutation analysis for ACTIVE regions are reported. Corrected p-values (FDR) for the ENRICHED TEs are found in the second sheet. (XLSX 121 kb)
DOI: 10.6084/m9.figshare.6599915
title: Additional file 1: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S1. Queen 16S gene read count, taxonomy and coding. (XLSX 427 kb)
DOI: 10.6084/m9.figshare.6599915.v1
title: Additional file 1: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S1. Queen 16S gene read count, taxonomy and coding. (XLSX 427 kb)
DOI: 10.6084/m9.figshare.6599909
title: Additional file 2: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: It contains two folders “TE_PIPELINE_SUMMARY_STATISTICS_ACTIVE” “TE_PIPELINE_SUMMARY_STATISTICS_REPRESSED”. In each of the two folders are included multiple spreadsheets (txt format) with the summary statistics of the TE analysis pipeline for ACTIVE and REPRESSED regions respectively. (ZIP 3922 kb)
DOI: 10.6084/m9.figshare.6599909.v1
title: Additional file 2: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: It contains two folders “TE_PIPELINE_SUMMARY_STATISTICS_ACTIVE” “TE_PIPELINE_SUMMARY_STATISTICS_REPRESSED”. In each of the two folders are included multiple spreadsheets (txt format) with the summary statistics of the TE analysis pipeline for ACTIVE and REPRESSED regions respectively. (ZIP 3922 kb)
DOI: 10.6084/m9.figshare.6599894
title: Additional file 12: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S12. Queen microbiota correlations. (XLSX 3421 kb)
DOI: 10.6084/m9.figshare.6599894.v1
title: Additional file 12: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S12. Queen microbiota correlations. (XLSX 3421 kb)
DOI: 10.6084/m9.figshare.6599891
title: Additional file 1: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S1. Tissues analyzed in the paper, with Roadmap ID codes. List of the 24 tissues analyzed in the paper, with Roadmap ID codes. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6599891.v1
title: Additional file 1: of Transposable elements generate regulatory novelty in a tissue-specific fashion

description: Table S1. Tissues analyzed in the paper, with Roadmap ID codes. List of the 24 tissues analyzed in the paper, with Roadmap ID codes. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6599882
title: Additional file 2: of Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases

description: Table S1. REP manually identified in REPtrons. (XLSX 66 kb)
DOI: 10.6084/m9.figshare.6599882.v1
title: Additional file 2: of Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases

description: Table S1. REP manually identified in REPtrons. (XLSX 66 kb)
DOI: 10.6084/m9.figshare.6599870
title: Additional file 11: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S11. Anosim by queen age and source. (XLSX 94 kb)
DOI: 10.6084/m9.figshare.6599870.v1
title: Additional file 11: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S11. Anosim by queen age and source. (XLSX 94 kb)
DOI: 10.6084/m9.figshare.6599852
title: Additional file 5 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

description: : Table S4. The presence of notable KEGG metabolic enzymes in 20 fungal species assessed by GhostKOALA. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6599852.v1
title: Additional file 5 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

description: : Table S4. The presence of notable KEGG metabolic enzymes in 20 fungal species assessed by GhostKOALA. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6599849
title: Additional file 2: of A new TaqMan method for the reliable diagnosis of Ehrlichia spp. in canine whole blood

description: Table S1. Comparison of PCRunÂŽ canine Ehrlichia positivity data to the E. canis gltA TaqMan PCR. Both PCRunÂŽ and TaqMan PCR assays assessed 33 genomic DNA extracts isolated from whole canine blood samples at Langford House at the University of Bristol. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.6599849.v1
title: Additional file 2: of A new TaqMan method for the reliable diagnosis of Ehrlichia spp. in canine whole blood

description: Table S1. Comparison of PCRunÂŽ canine Ehrlichia positivity data to the E. canis gltA TaqMan PCR. Both PCRunÂŽ and TaqMan PCR assays assessed 33 genomic DNA extracts isolated from whole canine blood samples at Langford House at the University of Bristol. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.6599846
title: Additional file 1: of Occurrence of health-compromising protozoan and helminth infections in tortoises kept as pet animals in Germany

description: Table S1. Data obtained from necropsies and faecal samples such as date of receive, post code and information collected from pet owners such as age, husbandry conditions, gender, length, weight, species and diagnosed parasites. (XLSX 394 kb)
DOI: 10.6084/m9.figshare.6599846.v1
title: Additional file 1: of Occurrence of health-compromising protozoan and helminth infections in tortoises kept as pet animals in Germany

description: Table S1. Data obtained from necropsies and faecal samples such as date of receive, post code and information collected from pet owners such as age, husbandry conditions, gender, length, weight, species and diagnosed parasites. (XLSX 394 kb)
DOI: 10.6084/m9.figshare.6599843
title: Additional file 10: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S10. PCA of queen microbial communities. (XLSX 222 kb)
DOI: 10.6084/m9.figshare.6599843.v1
title: Additional file 10: of The queenâ s gut refines with age: longevity phenotypes in a social insect model

description: Table S10. PCA of queen microbial communities. (XLSX 222 kb)
DOI: 10.6084/m9.figshare.6599837
title: Additional file 4 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

description: : Table S3. KEGG pathways affected by genes missing in R. clarus and R. irregularis but present in other fungi. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6599837.v1
title: Additional file 4 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

description: : Table S3. KEGG pathways affected by genes missing in R. clarus and R. irregularis but present in other fungi. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6599810
title: Additional file 3 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

description: : Table S2. MGCGs in R. clarus compared with other AM fungi. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.6599810.v1
title: Additional file 3 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

description: : Table S2. MGCGs in R. clarus compared with other AM fungi. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.6599807
title: Additional file 1: of A new TaqMan method for the reliable diagnosis of Ehrlichia spp. in canine whole blood

description: Available Ehrlichia sp. genome accessions. A list of the Genbank accession numbers used to generate the cladogram in Fig.Â 1. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6599807.v1
title: Additional file 1: of A new TaqMan method for the reliable diagnosis of Ehrlichia spp. in canine whole blood

description: Available Ehrlichia sp. genome accessions. A list of the Genbank accession numbers used to generate the cladogram in Fig.Â 1. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6599789
title: Additional file 2 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

description: : Table S1. Homology search results for FAS genes. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.6599789.v1
title: Additional file 2 of The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

description: : Table S1. Homology search results for FAS genes. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.6599780
title: Additional file 1: of The patient experience in community mental health services for older people: a concept mapping approach to support the development of a new quality measure

description: Stata Do File. Contains a STATA do file for multidimensional scaling, including the similarity matrix (raw data) used to construct the analysis presented within the manuscript. (TXT 46 kb)