cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13467283.v1
title: Additional file 12 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 12: Table S10. Novel MAGs. (a) Group affiliations for the novel MAGs. (b) Blast results for ribosomal proteins of novel MAGs. (c) Summary of the blast results of ribosomal proteins of novel MAGs. (d) Summary information on the groups of novel MAGs. (e) Occurrence summary for the novel MAGs in the HMP oral metagenomes. (f) Detection and (g) non-outlier mean coverage of the novel MAGs in the HMP samples as computerd by anvi-mcg-classifier. (h) The portion of reads that mapped to each novel MAG from each of the HMP samples. (i) ANI pairwise coverage values for 41 Flavobacteriaceae (our 5 f__Flavobacteriaceae MAGs and 36 representatives of Flavobacteriaceae species). (j) ANI pairwise identity values for the 41 Flavobacteriaceae genomes.
DOI: 10.6084/m9.figshare.13467299
title: Additional file 3 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 3: Table S3. Dereplication statistics of metagenome-assembled genomes. (a) Phylum affiliation for all 857 MAGs. (b) Length and completion/redundancy of SCGs for the 857 MAGs. (c) Average nucleotide identity results for each pair of MAGs (only between pairs of MAGs that were classified to the same phylum). (d) Pairwise data for MAGs; this was used as the input for the redundancy analysis. (e) Affiliations for the 123 redundant MAGs to one of 59 redundant groups.
DOI: 10.6084/m9.figshare.13467299.v1
title: Additional file 3 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 3: Table S3. Dereplication statistics of metagenome-assembled genomes. (a) Phylum affiliation for all 857 MAGs. (b) Length and completion/redundancy of SCGs for the 857 MAGs. (c) Average nucleotide identity results for each pair of MAGs (only between pairs of MAGs that were classified to the same phylum). (d) Pairwise data for MAGs; this was used as the input for the redundancy analysis. (e) Affiliations for the 123 redundant MAGs to one of 59 redundant groups.
DOI: 10.6084/m9.figshare.13467321
title: Additional file 9 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 9: Table S7. Metagenomic analysis of the TM7 genomes. (a) Detection of our 43 non-redundant TM7 MAGs in our 71 samples as computed by anvi-mcg-classifier. (b) Non-outlier mean coverage of our 43 non-redundant TM7 MAGs in our 71 samples as computed by anvi-mcg-classifier. (c) Occurrence statistics for our 43 non-redundant TM7 MAGs in our 71 samples as computed by anvi-mcg-classifier including normalized coverage. (d) Accession and reference information for the 12 previously published TM7 genomes used in the pangenomic and metagenomic analyses. (e) Metadata, including accession numbers, for the 150 TM7 genomes from NCBI used for the phylogenomic analysis in Fig. 3. (f) Average nucleotide identity (ANI) pairwise coverage values for the 55 TM7 genomes (our 43 in addition to the previously published 12). (g) ANI percent identity values. (h) ANI summary information for pairs of TM7 genomes with alignment coverage greater than 0.25. (i) Clade affiliation (as defined in this study) and group affiliation (as defined by Camanocha & Dewhirst [34]) for the 52 oral TM7 genomes. (j) Summary of mapping results of short reads from 481 oral metagenomes from the Human Microbiome Projects (HMP) to the 55 TM7 genomes, including the total number of reads that mapped from each sample, the total number of reads in each sample, and the percentage of reads that mapped, as well as the oral site affiliation of each metagenomic sample. (k) Metadata for HMP samples used in this study, including accession numbers. (l) Detection and (m) non-outlier mean coverage of the 55 TM7 genomes in the HMP samples as computed by anvi-mcg-classifier. (n) Summary of occurrence of the 55 TM7 genomes in the HMP samples including the mean value of the non-outlier mean coverage for each genome, number of samples in which a genome was detected above threshold of 0.5 with breakdown for plaque and tongue samples, the percent of HMP samples in which the genome was above detection threshold, and the results from a chi-squared test to compare occurrence of each genome between tongue and plaque samples. (o) Percent detection (above 0.5 threshold) for each TM7 genome broken down by the 9 HMP sample types. (p) Detection values as computed by anvi-mcg-classifier in subgingival plaque metagenomes from the HMP and from [84]. (q) Non-outlier mean coverage and (r) detection summary statistics for TM7 genomes in subgingival plaque metagenomes. (s) Percent of reads from each subgingival plaque sample that mapped to each TM7 genome. (t) Variability information as computed by anvi-gen-variability-profile for the “cosmopolitan” TM7 MAG (T_C_M_Bin_00022).
DOI: 10.6084/m9.figshare.13467317
title: Additional file 7 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 7: Table S6. Description of Human Oral Microbiome Database (HOMD) genomes used in this study. (a) Summary statistics for contigs for each of 1334 HOMD genomes used in this study, including total length, number of contigs, and count of SCGs. (b) accession number information for each of the 1334 HOMD genomes.
DOI: 10.6084/m9.figshare.13467321.v1
title: Additional file 9 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 9: Table S7. Metagenomic analysis of the TM7 genomes. (a) Detection of our 43 non-redundant TM7 MAGs in our 71 samples as computed by anvi-mcg-classifier. (b) Non-outlier mean coverage of our 43 non-redundant TM7 MAGs in our 71 samples as computed by anvi-mcg-classifier. (c) Occurrence statistics for our 43 non-redundant TM7 MAGs in our 71 samples as computed by anvi-mcg-classifier including normalized coverage. (d) Accession and reference information for the 12 previously published TM7 genomes used in the pangenomic and metagenomic analyses. (e) Metadata, including accession numbers, for the 150 TM7 genomes from NCBI used for the phylogenomic analysis in Fig. 3. (f) Average nucleotide identity (ANI) pairwise coverage values for the 55 TM7 genomes (our 43 in addition to the previously published 12). (g) ANI percent identity values. (h) ANI summary information for pairs of TM7 genomes with alignment coverage greater than 0.25. (i) Clade affiliation (as defined in this study) and group affiliation (as defined by Camanocha & Dewhirst [34]) for the 52 oral TM7 genomes. (j) Summary of mapping results of short reads from 481 oral metagenomes from the Human Microbiome Projects (HMP) to the 55 TM7 genomes, including the total number of reads that mapped from each sample, the total number of reads in each sample, and the percentage of reads that mapped, as well as the oral site affiliation of each metagenomic sample. (k) Metadata for HMP samples used in this study, including accession numbers. (l) Detection and (m) non-outlier mean coverage of the 55 TM7 genomes in the HMP samples as computed by anvi-mcg-classifier. (n) Summary of occurrence of the 55 TM7 genomes in the HMP samples including the mean value of the non-outlier mean coverage for each genome, number of samples in which a genome was detected above threshold of 0.5 with breakdown for plaque and tongue samples, the percent of HMP samples in which the genome was above detection threshold, and the results from a chi-squared test to compare occurrence of each genome between tongue and plaque samples. (o) Percent detection (above 0.5 threshold) for each TM7 genome broken down by the 9 HMP sample types. (p) Detection values as computed by anvi-mcg-classifier in subgingival plaque metagenomes from the HMP and from [84]. (q) Non-outlier mean coverage and (r) detection summary statistics for TM7 genomes in subgingival plaque metagenomes. (s) Percent of reads from each subgingival plaque sample that mapped to each TM7 genome. (t) Variability information as computed by anvi-gen-variability-profile for the “cosmopolitan” TM7 MAG (T_C_M_Bin_00022).
DOI: 10.6084/m9.figshare.13467313.v1
title: Additional file 6 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 6: Table S5. 16S ribosomal RNA amplicon sequencing results. Taxonomic annotations of amplicons in each of the 71 samples using GAST for each taxonomic level: (a) Phylum. (b) Class. (c) Order. (d) Family. (e) Genus. (f) Species. (g) Counts of amplicon sequence variants (ASVs) generated by the MED pipeline in each of the 71 samples. (h) Percent of counts of ASVs in the 71 samples. (i) Taxonomic affiliation of ASVs. (j) Relative abundance estimations for the 16 most abundant genera in our metagenomes based on MED/GAST results, in addition to relative abundance estimations for TM7 and the collection of ASVs not assigned any genus affiliation.
DOI: 10.6084/m9.figshare.13467279.v1
title: Additional file 11 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 11: Table S9. The SR1 and GN02 metapangenomes. (a) Reference information on GN02 genomes used for analysis. (b) Reference information on SR1 genomes used for analysis. (c) Summary information of GN02 pangenome. (d) Summary information of SR1 pangenome. (e) Average nucleotide identity (ANI) pairwise coverage values for the 25 GN02 genomes. (f) ANI percent identity values for the GN02 genomes. (g) ANI pairwise coverage values for the 14 SR1 genomes. (h) ANI percent identity values for the SR1 genomes. (i) Occurrence summary for the GN02 genomes in the HMP oral metagenomes. (j) Non-outlier mean coverage of the GN02 genomes in the HMP samples as computed by anvi-mcg-classifier. (k) The portion of reads that mapped to each GN02 genome from each of the HMP samples. (l) Occurrence summary for the SR1 genomes in the HMP oral metagenomes. (m) Non-outlier mean coverage of the SR1 genomes in the HMP samples as computed by anvi-mcg-classifier. (n) The portion of reads that mapped to each GN02 genome from each of the HMP samples.
DOI: 10.6084/m9.figshare.13467309
title: Additional file 5 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 5. Table S4. Taxonomic annotation of metagenomes. Taxonomic annotation of short reads using KrakenUniq for each taxonomic level: (a) Domain. (b) Phylum. (c) Class. (d) Order. (e) Family. (f) Genus. (g) Species. (h) Relative abundance estimations for the 16 most abundant genera in our metagenomes based on KrakenUniq counts, in addition to relative abundance estimations for TM7 and the collection of reads not assigned any genus affiliation.
DOI: 10.6084/m9.figshare.13467317.v1
title: Additional file 7 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 7: Table S6. Description of Human Oral Microbiome Database (HOMD) genomes used in this study. (a) Summary statistics for contigs for each of 1334 HOMD genomes used in this study, including total length, number of contigs, and count of SCGs. (b) accession number information for each of the 1334 HOMD genomes.
DOI: 10.6084/m9.figshare.13467439.v1
title: Additional file 2 of T cell phenotypes associated with insulin resistance: results from the Berlin Aging Study II

description: Additional file 2: Supplementary Figure 1. Gating strategy for CD4+ T cells. Supplementary Figure 2 Gating strategy for CD8+ T cells.
DOI: 10.6084/m9.figshare.13467439
title: Additional file 2 of T cell phenotypes associated with insulin resistance: results from the Berlin Aging Study II

description: Additional file 2: Supplementary Figure 1. Gating strategy for CD4+ T cells. Supplementary Figure 2 Gating strategy for CD8+ T cells.
DOI: 10.6084/m9.figshare.13467453
title: Additional file 1 of What evidence exists on conservation actions to conserve insects? A protocol for a systematic map of literature reviews

description: Additional file 1. ROSES form for systematic map protocols. This file holds the completed ROSES form for the systematic map protocol.
DOI: 10.6084/m9.figshare.13467453.v1
title: Additional file 1 of What evidence exists on conservation actions to conserve insects? A protocol for a systematic map of literature reviews

description: Additional file 1. ROSES form for systematic map protocols. This file holds the completed ROSES form for the systematic map protocol.
DOI: 10.6084/m9.figshare.13467493
title: Additional file 1 of Climate stress resistance in male Queensland fruit fly varies among populations of diverse geographic origins and changes during domestication

description: Additional file 1: Table S1. Climatic variables from the Qfly collection sites. Table S2. Individual populations for which the wild (G2/G3) and domesticated (G10–15) bioassays results differed significantly. Contrast is calculated for the estimated mean response variable for each population by looking at the differences of the domesticated over the wild populations. The estimated mean of the contrast is calculated on the log-transformed data for the response variables. Table S3. Methodological differences between the standard desiccation resistance and that used for the resampled 2017/2018 collection. Table S4. Euclidean distance between site’s geographical coordinates. Fig. S1. Correlation among 11 climatic variables. Correlation values are presented together with asterisks indicating significance values for each correlation. ‘*’ P
DOI: 10.6084/m9.figshare.13467493.v1
title: Additional file 1 of Climate stress resistance in male Queensland fruit fly varies among populations of diverse geographic origins and changes during domestication

description: Additional file 1: Table S1. Climatic variables from the Qfly collection sites. Table S2. Individual populations for which the wild (G2/G3) and domesticated (G10–15) bioassays results differed significantly. Contrast is calculated for the estimated mean response variable for each population by looking at the differences of the domesticated over the wild populations. The estimated mean of the contrast is calculated on the log-transformed data for the response variables. Table S3. Methodological differences between the standard desiccation resistance and that used for the resampled 2017/2018 collection. Table S4. Euclidean distance between site’s geographical coordinates. Fig. S1. Correlation among 11 climatic variables. Correlation values are presented together with asterisks indicating significance values for each correlation. ‘*’ P
DOI: 10.6084/m9.figshare.13467495
title: Additional file 1 of A randomized controlled trial on the comparative effectiveness of mindfulness-based cognitive therapy and health qigong-based cognitive therapy among Chinese people with depression and anxiety disorders

description: Additional file 1.
DOI: 10.6084/m9.figshare.13467495.v1
title: Additional file 1 of A randomized controlled trial on the comparative effectiveness of mindfulness-based cognitive therapy and health qigong-based cognitive therapy among Chinese people with depression and anxiety disorders

description: Additional file 1.
DOI: 10.6084/m9.figshare.13467507
title: Additional file 2 of Consolidated bioprocessing of cellulose to itaconic acid by a co-culture of Trichoderma reesei and Ustilago maydis

description: Additional file 2. Numerical data.
DOI: 10.6084/m9.figshare.13467507.v1
title: Additional file 2 of Consolidated bioprocessing of cellulose to itaconic acid by a co-culture of Trichoderma reesei and Ustilago maydis

description: Additional file 2. Numerical data.
DOI: 10.6084/m9.figshare.13467517
title: Additional file 10 of Transcriptome analysis of Anastrepha fraterculus sp. 1 males, females, and embryos: insights into development, courtship, and reproduction

description: Additional file 10. List of transcripts containing microsatellite motif and primers designed available to be tested.
DOI: 10.6084/m9.figshare.13467527.v1
title: Additional file 5 of Transcriptome analysis of Anastrepha fraterculus sp. 1 males, females, and embryos: insights into development, courtship, and reproduction

description: Additional file 5. EdgeR results. Each Excel sheet shows the paired-comparison between libraries (72 h embryo vs male; female vs male; and female vs 72 h embryo). LogFC: logarithm of the fold change for each contrast performed; LogCPM: logarithm of the counts per million for each transcript; P value: statistical P value for the individual test performed; FDR: false discovery rate (adjusted P value considering multiple testing).
DOI: 10.6084/m9.figshare.13467535
title: Additional file 9 of Transcriptome analysis of Anastrepha fraterculus sp. 1 males, females, and embryos: insights into development, courtship, and reproduction

description: Additional file 9. List of transcripts containing microsatellite motifs and description by repeat type classes and number of repeating motif.
DOI: 10.6084/m9.figshare.13467517.v1
title: Additional file 10 of Transcriptome analysis of Anastrepha fraterculus sp. 1 males, females, and embryos: insights into development, courtship, and reproduction

description: Additional file 10. List of transcripts containing microsatellite motif and primers designed available to be tested.
DOI: 10.6084/m9.figshare.13467527
title: Additional file 5 of Transcriptome analysis of Anastrepha fraterculus sp. 1 males, females, and embryos: insights into development, courtship, and reproduction

description: Additional file 5. EdgeR results. Each Excel sheet shows the paired-comparison between libraries (72 h embryo vs male; female vs male; and female vs 72 h embryo). LogFC: logarithm of the fold change for each contrast performed; LogCPM: logarithm of the counts per million for each transcript; P value: statistical P value for the individual test performed; FDR: false discovery rate (adjusted P value considering multiple testing).
DOI: 10.6084/m9.figshare.13467531
title: Additional file 7 of Transcriptome analysis of Anastrepha fraterculus sp. 1 males, females, and embryos: insights into development, courtship, and reproduction

description: Additional file 7. Selection of putative transcripts associated with function of interest. A. Transcripts selected according to their differential expression among libraries and predicted function (GO or BLAST hit). B. Transcript selected according to the literature associated to early development, sex determination, and communication.
DOI: 10.6084/m9.figshare.13467531.v1
title: Additional file 7 of Transcriptome analysis of Anastrepha fraterculus sp. 1 males, females, and embryos: insights into development, courtship, and reproduction

description: Additional file 7. Selection of putative transcripts associated with function of interest. A. Transcripts selected according to their differential expression among libraries and predicted function (GO or BLAST hit). B. Transcript selected according to the literature associated to early development, sex determination, and communication.
DOI: 10.6084/m9.figshare.13467535.v1
title: Additional file 9 of Transcriptome analysis of Anastrepha fraterculus sp. 1 males, females, and embryos: insights into development, courtship, and reproduction

description: Additional file 9. List of transcripts containing microsatellite motifs and description by repeat type classes and number of repeating motif.
DOI: 10.6084/m9.figshare.13467551.v1
title: Additional file 4 of BRAFV600E mutation impinges on gut microbial markers defining novel biomarkers for serrated colorectal cancer effective therapies

description: Additional file 4: Supplementary Table S3. Relative abundance of predicted function for specific KEGG modules (level 1–3) in fecal microbiota of mice at 43 DPT.
DOI: 10.6084/m9.figshare.13467545
title: Additional file 3 of BRAFV600E mutation impinges on gut microbial markers defining novel biomarkers for serrated colorectal cancer effective therapies

description: Additional file 3: Supplementary Table S2. Relative bacterial abundance at the phylum, genus and species level in fecal microbiota of mice at 43 DPT.
DOI: 10.6084/m9.figshare.13467545.v1
title: Additional file 3 of BRAFV600E mutation impinges on gut microbial markers defining novel biomarkers for serrated colorectal cancer effective therapies

description: Additional file 3: Supplementary Table S2. Relative bacterial abundance at the phylum, genus and species level in fecal microbiota of mice at 43 DPT.
DOI: 10.6084/m9.figshare.13467553.v1
title: Additional file 5 of BRAFV600E mutation impinges on gut microbial markers defining novel biomarkers for serrated colorectal cancer effective therapies

description: Additional file 5: Supplementary Table S4. Relative bacterial abundance at the phylum, genus and species level in fecal microbiota of human subjects.
DOI: 10.6084/m9.figshare.13467555.v1
title: Additional file 6 of BRAFV600E mutation impinges on gut microbial markers defining novel biomarkers for serrated colorectal cancer effective therapies

description: Additional file 6: Supplementary Table S5. Relative abundance of predicted function for specific KEGG modules (level 1–3) in fecal microbiota of human subjects.
DOI: 10.6084/m9.figshare.13467541
title: Additional file 2 of BRAFV600E mutation impinges on gut microbial markers defining novel biomarkers for serrated colorectal cancer effective therapies

description: Additional file 2: Supplementary Table S1. Relative bacterial abundance at the phylum, genus and species level in fecal microbiota of mice at 7 DPT.
DOI: 10.6084/m9.figshare.13467541.v1
title: Additional file 2 of BRAFV600E mutation impinges on gut microbial markers defining novel biomarkers for serrated colorectal cancer effective therapies

description: Additional file 2: Supplementary Table S1. Relative bacterial abundance at the phylum, genus and species level in fecal microbiota of mice at 7 DPT.
DOI: 10.6084/m9.figshare.13467551
title: Additional file 4 of BRAFV600E mutation impinges on gut microbial markers defining novel biomarkers for serrated colorectal cancer effective therapies

description: Additional file 4: Supplementary Table S3. Relative abundance of predicted function for specific KEGG modules (level 1–3) in fecal microbiota of mice at 43 DPT.
DOI: 10.6084/m9.figshare.13467553
title: Additional file 5 of BRAFV600E mutation impinges on gut microbial markers defining novel biomarkers for serrated colorectal cancer effective therapies

description: Additional file 5: Supplementary Table S4. Relative bacterial abundance at the phylum, genus and species level in fecal microbiota of human subjects.
DOI: 10.6084/m9.figshare.13467555
title: Additional file 6 of BRAFV600E mutation impinges on gut microbial markers defining novel biomarkers for serrated colorectal cancer effective therapies

description: Additional file 6: Supplementary Table S5. Relative abundance of predicted function for specific KEGG modules (level 1–3) in fecal microbiota of human subjects.
DOI: 10.6084/m9.figshare.13467577
title: Additional file 1 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

description: Additional file 1. NGS metrics. The table shows the sequencing metrics detected from the three NGS platform for each sample. Each column reported the number of read per amplicon of each sample. Coverage lower than 200x is indicated in bold.
DOI: 10.6084/m9.figshare.13467577.v1
title: Additional file 1 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

description: Additional file 1. NGS metrics. The table shows the sequencing metrics detected from the three NGS platform for each sample. Each column reported the number of read per amplicon of each sample. Coverage lower than 200x is indicated in bold.