cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11925324.v2
title: Supplementary Material

description: Supplementary material (Tables and Figures) for Chen <i>et al.</i> – Preterm infants harbour diverse <i>Klebsiella </i>populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors
DOI: 10.6084/m9.figshare.11925324.v1
title: Supplementary Material

description: Supplementary material (Tables and Figures) for Chen <i>et al.</i> – Preterm infants harbour diverse <i>Klebsiella </i>populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors
DOI: 10.6084/m9.figshare.11925138
title: Additional file 1 of Effect of crocin on antioxidant gene expression, fibrinolytic parameters, redox status and blood biochemistry in nicotinamide-streptozotocin-induced diabetic rats

description: Additional file 1. Altogether data for JBR.
DOI: 10.6084/m9.figshare.11925138.v1
title: Additional file 1 of Effect of crocin on antioxidant gene expression, fibrinolytic parameters, redox status and blood biochemistry in nicotinamide-streptozotocin-induced diabetic rats

description: Additional file 1. Altogether data for JBR.
DOI: 10.25386/genetics.12814565
title: Supplemental Material for Touroutine and Tanis, 2020

description: <b>Figure S1.</b> Detailed guidelines for SS primer design.<br><b>Table S1.</b> Primers used in this work.<br>
DOI: 10.25386/genetics.12814565.v1
title: Supplemental Material for Touroutine and Tanis, 2020

description: <b>Figure S1.</b> Detailed guidelines for SS primer design.<br><b>Table S1.</b> Primers used in this work.<br>
DOI: 10.6084/m9.figshare.11925045
title: Additional file 4 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

description: Additional file 4. Taxonomic affiliations of metagenome-assembled genomes (MAGs) of this study originating from HR biofilms.
DOI: 10.6084/m9.figshare.11925048
title: Additional file 1 of Parenting Science Gang: radical co-creation of research projects led by parents of young children

description: Additional file 1. GRIPP2 Long Form PSG. GRIPP2 Long Form Table of Criteria for Parenting Science Gang Project.
DOI: 10.6084/m9.figshare.11925051
title: Additional file 5 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

description: Additional file 5. Analysis of the key enzymes of AD pathways in metagenome-assembled genomes (MAGs). The genetic determinants were categorized according to the four stages of the AD process, namely hydrolysis, acidogenesis, acetogenesis and methanogenesis as described previously [23].
DOI: 10.6084/m9.figshare.11925045.v1
title: Additional file 4 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

description: Additional file 4. Taxonomic affiliations of metagenome-assembled genomes (MAGs) of this study originating from HR biofilms.
DOI: 10.6084/m9.figshare.11925048.v1
title: Additional file 1 of Parenting Science Gang: radical co-creation of research projects led by parents of young children

description: Additional file 1. GRIPP2 Long Form PSG. GRIPP2 Long Form Table of Criteria for Parenting Science Gang Project.
DOI: 10.6084/m9.figshare.11925051.v1
title: Additional file 5 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

description: Additional file 5. Analysis of the key enzymes of AD pathways in metagenome-assembled genomes (MAGs). The genetic determinants were categorized according to the four stages of the AD process, namely hydrolysis, acidogenesis, acetogenesis and methanogenesis as described previously [23].
DOI: 10.6084/m9.figshare.11925039
title: Additional file 3 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

description: Additional file 3. Statistics of the obtained and processed metagenome and metatranscriptome sequences.
DOI: 10.6084/m9.figshare.11925027
title: Additional file 1 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

description: Additional file 1. Statistics of 16S rRNA gene sequence analysis.
DOI: 10.6084/m9.figshare.11925030
title: Additional file 2 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

description: Additional file 2. Relative abundances of most abundant 16S rRNA gene sequences.
DOI: 10.6084/m9.figshare.11925030.v1
title: Additional file 2 of Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

description: Additional file 2. Relative abundances of most abundant 16S rRNA gene sequences.
DOI: 10.6084/m9.figshare.11924772
title: Additional file 6 of The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

description: Additional file 6: Table S4. Analysis of presumptive orthologs in the ‘General Metabolism’ category (G), A. godoyi vs. A. castellanii. Excel file listing 61 A. godoyi proteins predicted to be targeted to mitochondria [Ago(+)] and functioning in various metabolic pathways, compared to their orthologs from A. castellanii [Aca(MS+): direct identification (by MS); Aca(Bio): in silico identification (no supporting MS data); Aca(MS-): no MS data supporting a mitochondrial localization]. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.11924763
title: Additional file 4 of The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

description: Additional file 4: Table S3. Mitochondrial proteins in eukaryotes. Excel file listing selected A. godoyi mitochondrial proteins and their orthologs in other eukaryotes. (A) mitochondrial RecA; (B) mitochondrial SmpB (nucleus-encoded) and tmRNA (specified by mtDNA-encoded ssrA gene); (C) aerobic-type rubrerythrin and associated proteins (DUF3501, RFO). (XLSX 23 kb)
DOI: 10.6084/m9.figshare.11924772.v1
title: Additional file 6 of The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

description: Additional file 6: Table S4. Analysis of presumptive orthologs in the ‘General Metabolism’ category (G), A. godoyi vs. A. castellanii. Excel file listing 61 A. godoyi proteins predicted to be targeted to mitochondria [Ago(+)] and functioning in various metabolic pathways, compared to their orthologs from A. castellanii [Aca(MS+): direct identification (by MS); Aca(Bio): in silico identification (no supporting MS data); Aca(MS-): no MS data supporting a mitochondrial localization]. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.11924763.v1
title: Additional file 4 of The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

description: Additional file 4: Table S3. Mitochondrial proteins in eukaryotes. Excel file listing selected A. godoyi mitochondrial proteins and their orthologs in other eukaryotes. (A) mitochondrial RecA; (B) mitochondrial SmpB (nucleus-encoded) and tmRNA (specified by mtDNA-encoded ssrA gene); (C) aerobic-type rubrerythrin and associated proteins (DUF3501, RFO). (XLSX 23 kb)
DOI: 10.6084/m9.figshare.11924748
title: Additional file 2 of The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

description: Additional file 2: Table S2. Assessment of mitochondrial targeting. Excel file listing predicted mitochondrial targeting probabilities for three classes of mitochondrial matrix proteins assessed with six targeting programs. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.11924748.v1
title: Additional file 2 of The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

description: Additional file 2: Table S2. Assessment of mitochondrial targeting. Excel file listing predicted mitochondrial targeting probabilities for three classes of mitochondrial matrix proteins assessed with six targeting programs. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.11924739
title: Additional file 1 of The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

description: Additional file 1:Table S1. Annotated categories of predicted A. godoyi mitochondrial proteins. Excel file listing candidate mitochondrial proteins from A. godoyi and relevant information about them, including both amino acid and coding sequences. The Key tab defines various aspects of the presentation (calculation of probability of mitochondrial targeting, color coding, etc.). Functional categories as defined in Fig. 1 are organized in subsequent tabs (A) through (J), with relevant statistical data compiled in the final (Statistics) tab. (XLSX 808 kb)
DOI: 10.6084/m9.figshare.11924739.v1
title: Additional file 1 of The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

description: Additional file 1:Table S1. Annotated categories of predicted A. godoyi mitochondrial proteins. Excel file listing candidate mitochondrial proteins from A. godoyi and relevant information about them, including both amino acid and coding sequences. The Key tab defines various aspects of the presentation (calculation of probability of mitochondrial targeting, color coding, etc.). Functional categories as defined in Fig. 1 are organized in subsequent tabs (A) through (J), with relevant statistical data compiled in the final (Statistics) tab. (XLSX 808 kb)
DOI: 10.6084/m9.figshare.11924721
title: Additional file 8 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 8: Table S6. Relationship of single soil variable (OJ/LP) and microbial taxa according to CCA analysis (r2 and p values). ***P
DOI: 10.6084/m9.figshare.11924721.v1
title: Additional file 8 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 8: Table S6. Relationship of single soil variable (OJ/LP) and microbial taxa according to CCA analysis (r2 and p values). ***P
DOI: 10.6084/m9.figshare.11924712
title: Additional file 7 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 7: Table S5. Spearmanâ€™s rank correlation coefficient of soil physicochemical variables and bacterial community composition revealed by Mantel tests (r and p values).
DOI: 10.6084/m9.figshare.11924706
title: Additional file 6 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 6: Table S4. List of the OTUs which comprise the core bacteriome of rhizosphere soil in OJ and LP. Those OTUs which are members of each core bacteriome are indicated in grey. Indicator species analysis was performed using the multipatt function implemented in the indicspecies package in R with 1000 permutations. Significance of each indicator value is represented: *P
DOI: 10.6084/m9.figshare.11924712.v1
title: Additional file 7 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 7: Table S5. Spearmanâ€™s rank correlation coefficient of soil physicochemical variables and bacterial community composition revealed by Mantel tests (r and p values).
DOI: 10.6084/m9.figshare.11924706.v1
title: Additional file 6 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 6: Table S4. List of the OTUs which comprise the core bacteriome of rhizosphere soil in OJ and LP. Those OTUs which are members of each core bacteriome are indicated in grey. Indicator species analysis was performed using the multipatt function implemented in the indicspecies package in R with 1000 permutations. Significance of each indicator value is represented: *P
DOI: 10.6084/m9.figshare.11924679
title: Additional file 3 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 3: Table S3. Two-way ANOVA for plant shade response index in live or sterile soil treatments. Data indicated F values calculated by ANOVA. ***P
DOI: 10.6084/m9.figshare.11924679.v1
title: Additional file 3 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 3: Table S3. Two-way ANOVA for plant shade response index in live or sterile soil treatments. Data indicated F values calculated by ANOVA. ***P
DOI: 10.6084/m9.figshare.11924667
title: Additional file 2 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 2: Table S2. Two-way ANOVA for the effect of shade stress on total plant biomass, shoot biomass, root:shoot ratios, specific root length, specific leaf area, and leaf and root N content in shade-tolerant OJ (Ophiopogon japonicus) and shade-intolerant LP (Lolium perenne) plant. Data indicated F values calculated by ANOVA. ***P
DOI: 10.6084/m9.figshare.11924667.v1
title: Additional file 2 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 2: Table S2. Two-way ANOVA for the effect of shade stress on total plant biomass, shoot biomass, root:shoot ratios, specific root length, specific leaf area, and leaf and root N content in shade-tolerant OJ (Ophiopogon japonicus) and shade-intolerant LP (Lolium perenne) plant. Data indicated F values calculated by ANOVA. ***P
DOI: 10.6084/m9.figshare.11924664
title: Additional file 1 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 1: Table S1. Two-way ANOVA for the effect of shade stress on morphology and photosynthesis in shade-tolerant OJ (Ophiopogon japonicus) and shade-intolerant LP (Lolium perenne) plant. LA, Total leaf area; RL, Total root length; RV, Root volume; RSA, Root surface area; Chl, Chlorophyll. ***P
DOI: 10.6084/m9.figshare.11924664.v1
title: Additional file 1 of Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

description: Additional file 1: Table S1. Two-way ANOVA for the effect of shade stress on morphology and photosynthesis in shade-tolerant OJ (Ophiopogon japonicus) and shade-intolerant LP (Lolium perenne) plant. LA, Total leaf area; RL, Total root length; RV, Root volume; RSA, Root surface area; Chl, Chlorophyll. ***P
DOI: 10.6084/m9.figshare.11924616
title: Additional file 2 of Vaginal, sexual and urinary symptoms following hysterectomy: a multi-centre randomized controlled trial

description: Additional file 2. Datasheet.
DOI: 10.6084/m9.figshare.11924616.v1
title: Additional file 2 of Vaginal, sexual and urinary symptoms following hysterectomy: a multi-centre randomized controlled trial

description: Additional file 2. Datasheet.
DOI: 10.6084/m9.figshare.11924598
title: Additional file 9 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 9: Table S3. Enzymes of essential amino acids biosynthesis. Table S4. Enzymes of methionine recycling. Table S5. Enzymes of amino acids degradation. Table S6. Enzymes of purine biosynthesis and salvage. Table S7. Enzymes of pyrimidine biosynthesis. Table S8. Enzymes involved in fatty acid biosynthesis in Euglenozoa. Table S9. Enzymes involved in the digestion of bacterial cell walls in Euglenozoa. Table S10. Euglenozoan enzymes involved in trypanothione biosynthesis and utulization. Table S11. Protein IDs of the components of the pre-replication complex in Euglenozoa. Table S12. Protein IDs for the elements of conventional and kinetoplastid-specific kinetochore machineries. Table S40. Centromeric and other variants of histone H3 identified in Euglenozoa.
DOI: 10.6084/m9.figshare.11924598.v1
title: Additional file 9 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 9: Table S3. Enzymes of essential amino acids biosynthesis. Table S4. Enzymes of methionine recycling. Table S5. Enzymes of amino acids degradation. Table S6. Enzymes of purine biosynthesis and salvage. Table S7. Enzymes of pyrimidine biosynthesis. Table S8. Enzymes involved in fatty acid biosynthesis in Euglenozoa. Table S9. Enzymes involved in the digestion of bacterial cell walls in Euglenozoa. Table S10. Euglenozoan enzymes involved in trypanothione biosynthesis and utulization. Table S11. Protein IDs of the components of the pre-replication complex in Euglenozoa. Table S12. Protein IDs for the elements of conventional and kinetoplastid-specific kinetochore machineries. Table S40. Centromeric and other variants of histone H3 identified in Euglenozoa.
DOI: 10.6084/m9.figshare.11924556
title: Additional file 20 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 20: File S6. A phylogenetic tree of euglenozoan KKIP7 proteins. (TREEFILE 3 kb)
DOI: 10.6084/m9.figshare.11924556.v1
title: Additional file 20 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 20: File S6. A phylogenetic tree of euglenozoan KKIP7 proteins. (TREEFILE 3 kb)
DOI: 10.6084/m9.figshare.11924538
title: Additional file 18 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 18: File S4. A phylogenetic tree of euglenozoan KKT3 proteins. (TREEFILE 2 kb)
DOI: 10.6084/m9.figshare.11924544
title: Additional file 19 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 19: File S5. A phylogenetic tree of KKT10 and KKT19 proteins. (TREEFILE 2 kb)
DOI: 10.6084/m9.figshare.11924550
title: Additional file 1 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 1: Table S1. Genomes and transcriptomes of diplonemid, euglenid and kinetoplstid species analyzed in this study. Naegleria gruberi was used as an outgroup in phylogenomic analysis. Table S2. Genomes and transcriptomes of free-living and parasitic/symbiotic protists used in this study.
DOI: 10.6084/m9.figshare.11924538.v1
title: Additional file 18 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 18: File S4. A phylogenetic tree of euglenozoan KKT3 proteins. (TREEFILE 2 kb)
DOI: 10.6084/m9.figshare.11924550.v1
title: Additional file 1 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 1: Table S1. Genomes and transcriptomes of diplonemid, euglenid and kinetoplstid species analyzed in this study. Naegleria gruberi was used as an outgroup in phylogenomic analysis. Table S2. Genomes and transcriptomes of free-living and parasitic/symbiotic protists used in this study.
DOI: 10.6084/m9.figshare.11924544.v1
title: Additional file 19 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 19: File S5. A phylogenetic tree of KKT10 and KKT19 proteins. (TREEFILE 2 kb)
DOI: 10.6084/m9.figshare.11924523
title: Additional file 16 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 16: Table S52. Protein IDs and Pfam database Hidden Markov model IDs used for the identification of pre-replication complex subunits. Table S53. Pfam database Hidden Markov model IDs used for identification of the elements of kinetochore machinery.
DOI: 10.6084/m9.figshare.11924529
title: Additional file 17 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 17: File S3. A phylogenetic tree of euglenozoan KKT2 proteins. (TREEFILE 2 kb)
DOI: 10.6084/m9.figshare.11924529.v1
title: Additional file 17 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 17: File S3. A phylogenetic tree of euglenozoan KKT2 proteins. (TREEFILE 2 kb)
DOI: 10.6084/m9.figshare.11924523.v1
title: Additional file 16 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 16: Table S52. Protein IDs and Pfam database Hidden Markov model IDs used for the identification of pre-replication complex subunits. Table S53. Pfam database Hidden Markov model IDs used for identification of the elements of kinetochore machinery.
DOI: 10.6084/m9.figshare.11924514
title: Additional file 15 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 15: File S2. A phylogenetic tree of elongases (euglenozoan sequences along with functionally characterized elongases from several other organisms). (TREEFILE 8 kb)
DOI: 10.6084/m9.figshare.11924514.v1
title: Additional file 15 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 15: File S2. A phylogenetic tree of elongases (euglenozoan sequences along with functionally characterized elongases from several other organisms). (TREEFILE 8 kb)
DOI: 10.6084/m9.figshare.11924496
title: Additional file 13 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 13: Tables S13-S51. Estimates of evolutionary divergence among putative sequences of the following classes: KKTs (Table S13-S31), KKIPs (Tables S32-S38), centromeric histone H3 (Table S39) and enzymes of trypanothione biosynthesis and utilization (Tables S41-S51).
DOI: 10.6084/m9.figshare.11924505
title: Additional file 14 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 14: File S1. A phylogenetic tree of elongases (euglenozoan proteins only). (TREEFILE 7 kb)
DOI: 10.6084/m9.figshare.11924505.v1
title: Additional file 14 of Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids

description: Additional file 14: File S1. A phylogenetic tree of elongases (euglenozoan proteins only). (TREEFILE 7 kb)