cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7435124
title: Additional file 16: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S14. Relative abundance values of metagenomics and metatranscriptomics reads calculated by using the Metagenomic Intra-Species Diversity Analysis System (MIDAS) pipeline. Bacterial taxa that contributed with 0.5% or more to the total DNA or mRNA read abundance at any time point were included in the analysis. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.7435127
title: Additional file 17: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S15. Gene expression data of putative biosynthetic gene clusters (BSCs) identified in the 31 most active bacterial genomes in the in vitro biofilm community by antiSMASH v. 3.0. A total of 130 biosynthetic BSCs were identified, however only nine were transcriptionally active in the biofilm community. Genomes with no BGC are presented at the end of the table. (XLSX 52 kb)
DOI: 10.7284/135237
title: Singlebeam Echosounder data collected during research cruise NA091 using a Knudsen 3260 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435124.v1
title: Additional file 16: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S14. Relative abundance values of metagenomics and metatranscriptomics reads calculated by using the Metagenomic Intra-Species Diversity Analysis System (MIDAS) pipeline. Bacterial taxa that contributed with 0.5% or more to the total DNA or mRNA read abundance at any time point were included in the analysis. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.7435127.v1
title: Additional file 17: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S15. Gene expression data of putative biosynthetic gene clusters (BSCs) identified in the 31 most active bacterial genomes in the in vitro biofilm community by antiSMASH v. 3.0. A total of 130 biosynthetic BSCs were identified, however only nine were transcriptionally active in the biofilm community. Genomes with no BGC are presented at the end of the table. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.7435115
title: Additional file 14: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S12. DESeq normalized RNASeq data representing specific functions associated with virulence in the in vitro biofilm community. Gene expression of seven groups of virulence functions were analyzed across pH stages (i.e. LPXTG-motifs, feoB genes, capsular polysaccharide genes, Cpl protease encoding genes, lemA genes, oxygen radical associated genes, methionine-R-sulfoxide reductase genes). (XLSX 129 kb)
DOI: 10.6084/m9.figshare.7435121.v1
title: Additional file 15: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S13. DESeq normalized RNASeq data representing expressed genes associated with ammonia production and pH neutralization. (XLSX 123 kb)
DOI: 10.6084/m9.figshare.7435112
title: Additional file 13: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S11. Ratio estimates of metatranscriptome (MT) and metagenome (MG) read mapping results for individual genomes. Values are based on relative abundance estimates from mRNA or DNA read mapping. MT abundance values were divided with MG abundance values. High ratios suggest that genomes are highly active in the community. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.7435115.v1
title: Additional file 14: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S12. DESeq normalized RNASeq data representing specific functions associated with virulence in the in vitro biofilm community. Gene expression of seven groups of virulence functions were analyzed across pH stages (i.e. LPXTG-motifs, feoB genes, capsular polysaccharide genes, Cpl protease encoding genes, lemA genes, oxygen radical associated genes, methionine-R-sulfoxide reductase genes). (XLSX 129 kb)
DOI: 10.7284/135235
title: SSV (Sound Speed Velocimeter) data collected during research cruise NA091 using a AML SV Xchange instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435112.v1
title: Additional file 13: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S11. Ratio estimates of metatranscriptome (MT) and metagenome (MG) read mapping results for individual genomes. Values are based on relative abundance estimates from mRNA or DNA read mapping. MT abundance values were divided with MG abundance values. High ratios suggest that genomes are highly active in the community. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.7435106
title: Additional file 12: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S10. Linear regression analysis between cell division genes (ftsA, ftsZ) and single copy genes (Amphora set of 42 single copy genes). Analyses were conducted for Lactobacillus fermentum IFO3956 (Lf) and S. parasangunis ATCC15912 (Spa) from normalized metagenomic read mapping data. (XLSX 62 kb)
DOI: 10.7284/135350
title: Expendable Probe data collected during research cruise NA092 using a Sippican MK21 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435106.v1
title: Additional file 12: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S10. Linear regression analysis between cell division genes (ftsA, ftsZ) and single copy genes (Amphora set of 42 single copy genes). Analyses were conducted for Lactobacillus fermentum IFO3956 (Lf) and S. parasangunis ATCC15912 (Spa) from normalized metagenomic read mapping data. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.7435097
title: Additional file 11: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S9. Relative abundance (RA) and fold changes values representing mRNA reads mapping to bacterial genomes, and that changes (increased or decreased) 1.5-fold at 9â h of biofilm maturation, when pH dropped below 5.5. RA for each genome was calculated from DESeq normalized metatranscriptomics reads. (XLSX 44 kb)
DOI: 10.7284/135349
title: INS (Inertial Navigation System) data collected during research cruise NA092 using a Kongsberg Seatex MRU-5 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435097.v1
title: Additional file 11: of Uncovering complex microbiome activities via metatranscriptomics during 24â hours of oral biofilm assembly and maturation

description: Table S9. Relative abundance (RA) and fold changes values representing mRNA reads mapping to bacterial genomes, and that changes (increased or decreased) 1.5-fold at 9â h of biofilm maturation, when pH dropped below 5.5. RA for each genome was calculated from DESeq normalized metatranscriptomics reads. (XLSX 44 kb)
DOI: 10.7284/135351
title: INS (Inertial Navigation System) data collected during research cruise NA092 using a Kongsberg Seapath 330+ instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435088
title: Additional file 10: of Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation

description: Table S8. Read mapping results showing DNA and mRNA read mapping reproducibility between replicate libraries. Read mapping was performed using reference genomes representative of oral bacteria (see Methods section). A separate spreadsheet is provided for relative abundance values of mRNA reads mapping to oral reference genomes. Fold change calculations are included in this sheet showing differences between: 9 h and 6 h of growth; 11 h and 9 h of growth; and 24 h and 6 h of growth. (XLSX 161 kb)
DOI: 10.7284/135352
title: Meteorological Station data collected during research cruise NA092 using a Coastal Weatherpak-2000 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435088.v1
title: Additional file 10: of Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation

description: Table S8. Read mapping results showing DNA and mRNA read mapping reproducibility between replicate libraries. Read mapping was performed using reference genomes representative of oral bacteria (see Methods section). A separate spreadsheet is provided for relative abundance values of mRNA reads mapping to oral reference genomes. Fold change calculations are included in this sheet showing differences between: 9 h and 6 h of growth; 11 h and 9 h of growth; and 24 h and 6 h of growth. (XLSX 161 kb)
DOI: 10.7284/136028
title: Multibeam Echosounder data collected during research cruise NA092 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435064
title: Additional file 2: of How is the evolution of tumour resistance at organ-scale impacted by the importance of the organ for fitness?

description: Supplementary results. This file contains a description of the effect of tumour emergence variability on the tumour resistance mechanisms selected at organ-scale. It also contains a test to determine the influence of using Gompertz function to model the trade-off between tumour initiation rate and fecundity rate in the outcomes. (ODT 1764 kb)
DOI: 10.6084/m9.figshare.7435064.v1
title: Additional file 2: of How is the evolution of tumour resistance at organ-scale impacted by the importance of the organ for fitness?

description: Supplementary results. This file contains a description of the effect of tumour emergence variability on the tumour resistance mechanisms selected at organ-scale. It also contains a test to determine the influence of using Gompertz function to model the trade-off between tumour initiation rate and fecundity rate in the outcomes. (ODT 1764 kb)
DOI: 10.7284/136029
title: Multibeam Echosounder data collected during research cruise NA092 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435058
title: Additional file 1: of How is the evolution of tumour resistance at organ-scale impacted by the importance of the organ for fitness?

description: Supplementary methods. This file contains the description of 1) the extended model for different tumour resistance strategies, 2) the mutation function, 3) the fecundity function, 4) the mortality function and a summary of all the functions used in the article (Table S1). (ODT 198 kb)
DOI: 10.6084/m9.figshare.7435058.v1
title: Additional file 1: of How is the evolution of tumour resistance at organ-scale impacted by the importance of the organ for fitness?

description: Supplementary methods. This file contains the description of 1) the extended model for different tumour resistance strategies, 2) the mutation function, 3) the fecundity function, 4) the mortality function and a summary of all the functions used in the article (Table S1). (ODT 198 kb)
DOI: 10.7284/135201
title: Singlebeam Echosounder data collected during research cruise NA092 using a Knudsen 3260 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435043
title: Additional file 4: of How do macro-level structural determinants affect inequalities in mental health? â a systematic review of the literature

description: Quality Assessment Scores. (XLSX 19 kb)
DOI: 10.7284/135348
title: SSV (Sound Speed Velocimeter) data collected during research cruise NA092 using a AML SV Xchange instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435043.v1
title: Additional file 4: of How do macro-level structural determinants affect inequalities in mental health? â a systematic review of the literature

description: Quality Assessment Scores. (XLSX 19 kb)
DOI: 10.7284/129778
title: Expendable Probe data collected during research cruise NA093 using a Sippican MK21 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7435025
title: MOESM1 of What is the impact of continuous cover forestry compared to clearcut forestry on stand-level biodiversity in boreal and temperate forests? A systematic review protocol

description: Additional file 1. ROSES form.
DOI: 10.6084/m9.figshare.7435025.v1
title: MOESM1 of What is the impact of continuous cover forestry compared to clearcut forestry on stand-level biodiversity in boreal and temperate forests? A systematic review protocol

description: Additional file 1. ROSES form.
DOI: 10.7284/129775
title: INS (Inertial Navigation System) data collected during research cruise NA093 using a Kongsberg Seatex MRU-5 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129776
title: INS (Inertial Navigation System) data collected during research cruise NA093 using a Kongsberg Seapath 330+ instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132192
title: Multibeam Echosounder data collected during research cruise NA093 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/129777
title: SSV (Sound Speed Velocimeter) data collected during research cruise NA093 using a AML SVXchange instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132194
title: INS (Inertial Navigation System) data collected during research cruise NA094 using a Kongsberg Seatex MRU-5 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7434989
title: Additional file 2: of Molecular epidemiology and clinical features of hand, foot and mouth disease in northern Thailand in 2016: a prospective cohort study

description: HFMD_Data t is the coded data of the HFMD project which was conducted in northern Thailand. (XLSX 233 kb)
DOI: 10.6084/m9.figshare.7434989.v1
title: Additional file 2: of Molecular epidemiology and clinical features of hand, foot and mouth disease in northern Thailand in 2016: a prospective cohort study

description: HFMD_Data t is the coded data of the HFMD project which was conducted in northern Thailand. (XLSX 233 kb)
DOI: 10.7284/132198
title: INS (Inertial Navigation System) data collected during research cruise NA094 using a Kongsberg Seapath 330+ instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132195
title: Multibeam Echosounder data collected during research cruise NA094 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132196
title: Multibeam Echosounder data collected during research cruise NA094 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132197
title: Singlebeam Echosounder data collected during research cruise NA094 using a Knudsen 3260 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132193
title: SSV (Sound Speed Velocimeter) data collected during research cruise NA094 using a AML SVXchange instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132204
title: Expendable Probe data collected during research cruise NA095 using a Sippican MK21 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132200
title: INS (Inertial Navigation System) data collected during research cruise NA095 using a Kongsberg Seatex MRU-5 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132205
title: INS (Inertial Navigation System) data collected during research cruise NA095 using a Kongsberg Seapath 330+ instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132201
title: Multibeam Echosounder data collected during research cruise NA095 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132202
title: Multibeam Echosounder data collected during research cruise NA095 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132203
title: Singlebeam Echosounder data collected during research cruise NA095 using a Knudsen 3260 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7434887
title: Additional file 4: of Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities

description: SNPs occurring in the CODH-NiFe group 4a locus genes of the compared P. thermoglucosidasius strains. The number of SNPs occurring in the individual CODH-NiFe group 4a genes of particular strains are indicated. The number in brackets indicates the number of non-synonymous amino acid substitutions observed in the amino acid sequence alignments for each individual gene. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7434887.v1
title: Additional file 4: of Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities

description: SNPs occurring in the CODH-NiFe group 4a locus genes of the compared P. thermoglucosidasius strains. The number of SNPs occurring in the individual CODH-NiFe group 4a genes of particular strains are indicated. The number in brackets indicates the number of non-synonymous amino acid substitutions observed in the amino acid sequence alignments for each individual gene. (XLSX 9 kb)
DOI: 10.7284/132199
title: SSV (Sound Speed Velocimeter) data collected during research cruise NA095 using a AML SVXchange instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132209
title: Expendable Probe data collected during research cruise NA096 using a Sippican MK21 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7434869
title: Additional file 3: of Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities

description: Annotations of the protein families shared and unique among the compared P. thermoglucosidasius strains. The protein family datasets which are shared between different combinations of the four compared strains or unique to a particular strain were functionally annotated by RAST [36], comparison against the Conserved Domain Database [37] and classification according to their COG function using EggNOG mapper [36]. The proportions (%) of proteins (unique to strains or shared among different combinations of strains) belonging to each COG are graphically presented. (XLSX 484 kb)
DOI: 10.7284/132211
title: INS (Inertial Navigation System) data collected during research cruise NA096 using a Kongsberg Seatex MRU-5 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7434869.v1
title: Additional file 3: of Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities

description: Annotations of the protein families shared and unique among the compared P. thermoglucosidasius strains. The protein family datasets which are shared between different combinations of the four compared strains or unique to a particular strain were functionally annotated by RAST [36], comparison against the Conserved Domain Database [37] and classification according to their COG function using EggNOG mapper [36]. The proportions (%) of proteins (unique to strains or shared among different combinations of strains) belonging to each COG are graphically presented. (XLSX 484 kb)
DOI: 10.7284/132212
title: INS (Inertial Navigation System) data collected during research cruise NA096 using a Kongsberg Seapath 330+ instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132206
title: Multibeam Echosounder data collected during research cruise NA096 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132207
title: Multibeam Echosounder data collected during research cruise NA096 using a Kongsberg EM302 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132208
title: Singlebeam Echosounder data collected during research cruise NA096 using a Knudsen 3260 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132210
title: SSV (Sound Speed Velocimeter) data collected during research cruise NA096 using a AML SVXchange instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133253
title: Expendable Probe data collected during research cruise NA097 using a Sippican MK21 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133249
title: INS (Inertial Navigation System) data collected during research cruise NA097 using a Kongsberg Seatex MRU-5 instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133254
title: INS (Inertial Navigation System) data collected during research cruise NA097 using a Kongsberg Seapath 330+ instrument system onboard the platform EV Nautilus

description: Original (unprocessed) data collected during a Field_expedition