cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9777059
title: Additional file 2: of Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds

description: Differential gene expression according to the respective reference genomes of E. coli O157:H− strain 3072/96, E. coli O104:H4 strain C227–11φcu and E. coli O157:H7 strain Sakai. For each differentially expressed gene, the gene ID, the log2 fold change between both treatment groups (log2FoldChange), and the Benjamini-Hochberg adjusted p-value (padj.) are indicated. (XLSX 183 kb)
DOI: 10.6084/m9.figshare.9777065
title: Additional file 3: of Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds

description: Table of the shared genome of E. coli O157:H− strain 3072/96, E. coli O104:H4 strain C227–11φcu, E. coli O157:H7 strain Sakai and E. coli strain K-12 substrain MG1655. For every homologous gene group (rows with unique identifier) the genes of the respective strains (columns) are listed. Names of homologous gene group are based on gene names of E. coli MG1655, if a respective homolog of this strain is present in the group. For homologous relationships between genes, a minimal nucleotide identity of 90% and length-coverage of 75% was assumed. The calculation of the shared genome was performed on the basis of a whole genome alignment of the four strains and a subsequent refinement by a RBH BLAST approach. (XLSX 476 kb)
DOI: 10.6084/m9.figshare.9777068
title: Additional file 4: of A randomized controlled trial to examine the effect of two teaching methods on preschool children’s language and communication, executive functions, socioemotional comprehension, and early math skills

description: Supplementary ERP data. Supplementary ERP grand average plots for all head electrodes, HEOG and VEOG. 1. All pre intervention 2. All post intervention 3. Control pre 4. Control post 5. DIL pre 6. DIL post 7. SEMLA pre 8. SEMLA post. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.9777059.v1
title: Additional file 2: of Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds

description: Differential gene expression according to the respective reference genomes of E. coli O157:H− strain 3072/96, E. coli O104:H4 strain C227–11φcu and E. coli O157:H7 strain Sakai. For each differentially expressed gene, the gene ID, the log2 fold change between both treatment groups (log2FoldChange), and the Benjamini-Hochberg adjusted p-value (padj.) are indicated. (XLSX 183 kb)
DOI: 10.6084/m9.figshare.9777065.v1
title: Additional file 3: of Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds

description: Table of the shared genome of E. coli O157:H− strain 3072/96, E. coli O104:H4 strain C227–11φcu, E. coli O157:H7 strain Sakai and E. coli strain K-12 substrain MG1655. For every homologous gene group (rows with unique identifier) the genes of the respective strains (columns) are listed. Names of homologous gene group are based on gene names of E. coli MG1655, if a respective homolog of this strain is present in the group. For homologous relationships between genes, a minimal nucleotide identity of 90% and length-coverage of 75% was assumed. The calculation of the shared genome was performed on the basis of a whole genome alignment of the four strains and a subsequent refinement by a RBH BLAST approach. (XLSX 476 kb)
DOI: 10.6084/m9.figshare.9777068.v1
title: Additional file 4: of A randomized controlled trial to examine the effect of two teaching methods on preschool children’s language and communication, executive functions, socioemotional comprehension, and early math skills

description: Supplementary ERP data. Supplementary ERP grand average plots for all head electrodes, HEOG and VEOG. 1. All pre intervention 2. All post intervention 3. Control pre 4. Control post 5. DIL pre 6. DIL post 7. SEMLA pre 8. SEMLA post. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.9777050
title: Additional file 1: of Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds

description: Differential gene expression in the shared genome of E. coli O157:H− strain 3072/96, E. coli O104:H4 strain C227–11φcu and E. coli O157:H7 strain Sakai. For each differentially expressed gene, the gene ID, the log2 fold change between both treatment groups (log2FoldChange), and the Benjamini-Hochberg adjusted p-value (padj.) are indicated. (XLSX 120 kb)
DOI: 10.6084/m9.figshare.9777044
title: Additional file 1 of Interval-cohort designs and bias in the estimation of per-protocol effects: a simulation study

description: R code to implement the simulation and IP weighted estimation procedures. (R 23 kb)
DOI: 10.6084/m9.figshare.9777044.v1
title: Additional file 1 of Interval-cohort designs and bias in the estimation of per-protocol effects: a simulation study

description: R code to implement the simulation and IP weighted estimation procedures. (R 23 kb)
DOI: 10.6084/m9.figshare.9777050.v1
title: Additional file 1: of Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds

description: Differential gene expression in the shared genome of E. coli O157:H− strain 3072/96, E. coli O104:H4 strain C227–11φcu and E. coli O157:H7 strain Sakai. For each differentially expressed gene, the gene ID, the log2 fold change between both treatment groups (log2FoldChange), and the Benjamini-Hochberg adjusted p-value (padj.) are indicated. (XLSX 120 kb)
DOI: 10.6084/m9.figshare.9776981
title: Additional file 1: of Challenges in the construction of knowledge bases for human microbiome-disease associations

description: Supplementary tables. (XLSX 39 kb)
DOI: 10.5281/zenodo.4002414
title: Last Interglacial Sea Levels within the Gulf of Mexico and northwestern Caribbean Sea

description: This file provides a summary of the ages and elevations of previously published relative sea-level constraints during the Last Interglacial (LIG; also known as marine isotope stage 5e, MIS5e) across the Gulf of Mexico and northwestern Caribbean Sea including the Yucatan Peninsula. I used a standardized database template to compile 32 sea-level indicators including the insertion of 16 U-series ages on corals, 1 electron spin resonance age, 2 amino acid racemization ages and 26 luminescence ages.
DOI: 10.6084/m9.figshare.9776981.v1
title: Additional file 1: of Challenges in the construction of knowledge bases for human microbiome-disease associations

description: Supplementary tables. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.9776939
title: Additional file 8: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: CCD8 alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 84 kb)
DOI: 10.6084/m9.figshare.9776939.v1
title: Additional file 8: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: CCD8 alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 84 kb)
DOI: 10.6084/m9.figshare.9776915
title: Additional file 5: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: CCD alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 115 kb)
DOI: 10.6084/m9.figshare.9776906
title: Additional file 4: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: CCD7 alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 54 kb)
DOI: 10.6084/m9.figshare.9776915.v1
title: Additional file 5: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: CCD alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 115 kb)
DOI: 10.6084/m9.figshare.9776906.v1
title: Additional file 4: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: CCD7 alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 54 kb)
DOI: 10.6084/m9.figshare.9776894
title: Additional file 2: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: D27 alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 33 kb)
DOI: 10.6084/m9.figshare.9776894.v1
title: Additional file 2: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: D27 alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 33 kb)
DOI: 10.6084/m9.figshare.9776888
title: Additional file 1: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: List of sequences used in this study. Sequences listed in red were not used for phylogenetic analyses on account of incompleteness. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.9776888.v1
title: Additional file 1: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: List of sequences used in this study. Sequences listed in red were not used for phylogenetic analyses on account of incompleteness. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.9776861
title: Additional file 14: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: SMXL alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 335 kb)
DOI: 10.6084/m9.figshare.9776861.v1
title: Additional file 14: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: SMXL alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 335 kb)
DOI: 10.6084/m9.figshare.9776840
title: Additional file 12: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: LBO alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 46 kb)
DOI: 10.6084/m9.figshare.9776828
title: Additional file 10: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: MAX1 alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 47 kb)
DOI: 10.6084/m9.figshare.9776840.v1
title: Additional file 12: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: LBO alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 46 kb)
DOI: 10.6084/m9.figshare.9776828.v1
title: Additional file 10: of Strigolactone synthesis is ancestral in land plants, but canonical strigolactone signalling is a flowering plant innovation

description: MAX1 alignment. Trimmed alignment showing all conserved parts of the gene, not only those residues used for phylogenetic reconstruction. (FAS 47 kb)
DOI: 10.6084/m9.figshare.9776804
title: Additional file 3: of Microbial population dynamics under microdoses of the essential oil arborvitae

description: Table S1. Instructions for making the broth-oil solution and various assigned doses that were created and tested in this experiment. Broth indicated as MH in the table represents Mueller-Hinton broth for bacterial tests and GPP in the table indicates Glucose Phosphate Proline broth for fungal tests. Plate numbers correspond to which run and include the doses that correspond to the percentage of the solutions that were tested in each particular plate. A two-step dilution process was done to create the desired dose percentages. See methods section for a description of the percentages that corresponds to the doses that were created and used. Table S2. Results from ANOVA and t-tests. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.9776795
title: Additional file 1: of Microbial population dynamics under microdoses of the essential oil arborvitae

description: The raw data used for the analyses described in the manuscript. (XLSX 370 kb)
DOI: 10.6084/m9.figshare.9776804.v1
title: Additional file 3: of Microbial population dynamics under microdoses of the essential oil arborvitae

description: Table S1. Instructions for making the broth-oil solution and various assigned doses that were created and tested in this experiment. Broth indicated as MH in the table represents Mueller-Hinton broth for bacterial tests and GPP in the table indicates Glucose Phosphate Proline broth for fungal tests. Plate numbers correspond to which run and include the doses that correspond to the percentage of the solutions that were tested in each particular plate. A two-step dilution process was done to create the desired dose percentages. See methods section for a description of the percentages that corresponds to the doses that were created and used. Table S2. Results from ANOVA and t-tests. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.9776795.v1
title: Additional file 1: of Microbial population dynamics under microdoses of the essential oil arborvitae

description: The raw data used for the analyses described in the manuscript. (XLSX 370 kb)
DOI: 10.6084/m9.figshare.9776636
title: Additional file 1: of RhoC regulates radioresistance via crosstalk of ROCK2 with the DNA repair machinery in cervical cancer

description: Supplementary figures. (ZIP 9690 kb)
DOI: 10.6084/m9.figshare.9776636.v1
title: Additional file 1: of RhoC regulates radioresistance via crosstalk of ROCK2 with the DNA repair machinery in cervical cancer

description: Supplementary figures. (ZIP 9690 kb)
DOI: 10.6084/m9.figshare.9776615
title: MOESM1 of Applying fuzzy logic to assess the biogeographical risk of dengue in South America

description: Additional file 1: Table S1. Dengue cases, Aedes aegypti and Ae. albopictus occurrences (presences as 1, and absences as 0 in each South America grid), values of the significant variables in the models by South America grid, and favorability values for each model by grid (F-dengue; F-Ae. aegypti and F-Ae. albopictus). Variable abbreviations are given in Table 1.
DOI: 10.6084/m9.figshare.9776615.v1
title: MOESM1 of Applying fuzzy logic to assess the biogeographical risk of dengue in South America

description: Additional file 1: Table S1. Dengue cases, Aedes aegypti and Ae. albopictus occurrences (presences as 1, and absences as 0 in each South America grid), values of the significant variables in the models by South America grid, and favorability values for each model by grid (F-dengue; F-Ae. aegypti and F-Ae. albopictus). Variable abbreviations are given in Table 1.
DOI: 10.6084/m9.figshare.9776603
title: Additional file 9: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Benchmarking the accuracy of acn.sh against PICRUSt, CopyRighter, and PAPRICA: summary statistics. Table showing the Medians, Means and Standard Deviations of the Average Percentage Error (i.e., MdAPE, MAPE, and SDAPE, respectively), and Pearsonâ s r correlation coefficients obtained in the analysis benchmarking the accuracy of acn.sh against PICRUSt, CopyRighter, and PAPRICA. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.9776600
title: Additional file 9: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S5. Differentially expressed genes in male and female cardiac precursors (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9776603.v1
title: Additional file 9: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Benchmarking the accuracy of acn.sh against PICRUSt, CopyRighter, and PAPRICA: summary statistics. Table showing the Medians, Means and Standard Deviations of the Average Percentage Error (i.e., MdAPE, MAPE, and SDAPE, respectively), and Pearsonâ s r correlation coefficients obtained in the analysis benchmarking the accuracy of acn.sh against PICRUSt, CopyRighter, and PAPRICA. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.9776600.v1
title: Additional file 9: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S5. Differentially expressed genes in male and female cardiac precursors (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9776582
title: Additional file 7: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S4. Gene ontology for protein-protein interaction networks (XLSX 15 kb)
DOI: 10.6084/m9.figshare.9776588
title: Additional file 7: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Evaluating the running time of acn.sh. Table showing the mean running time of acn.sh, and ags.sh plus acn.sh, using 4, 8, and 16 threads, for the estimation of the ACN in five TARA Oceans metagenomes subsampled to two million paired-end reads. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.9776579
title: Additional file 6: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Benchmarking the accuracy of ags.sh against MicrobeCensus: summary statistics. Table showing the Medians, Means and Standard Deviations of the Average Percentage Error (i.e., MdAPE, MAPE, and SDAPE, respectively), and Pearsonâ s r correlation coefficients obtained in the analysis benchmarking the accuracy of ags.sh against MicrobeCensus. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.9776579.v1
title: Additional file 6: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Benchmarking the accuracy of ags.sh against MicrobeCensus: summary statistics. Table showing the Medians, Means and Standard Deviations of the Average Percentage Error (i.e., MdAPE, MAPE, and SDAPE, respectively), and Pearsonâ s r correlation coefficients obtained in the analysis benchmarking the accuracy of ags.sh against MicrobeCensus. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.9776588.v1
title: Additional file 7: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Evaluating the running time of acn.sh. Table showing the mean running time of acn.sh, and ags.sh plus acn.sh, using 4, 8, and 16 threads, for the estimation of the ACN in five TARA Oceans metagenomes subsampled to two million paired-end reads. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.9776582.v1
title: Additional file 7: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S4. Gene ontology for protein-protein interaction networks (XLSX 15 kb)
DOI: 10.6084/m9.figshare.9776561
title: Additional file 4: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Benchmarking the running time of ags.sh against MicrobeCensus. Table showing the mean running time of ags.sh and MicrobeCensus using 4, 8, and 16 threads, for the estimation of the AGS in five TARA Oceans metagenomes subsampled to two million paired-end reads. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.9776555
title: Additional file 3: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Simulated metagenomic datasets. Table showing main characteristics describing the simulated metagenomic datasets. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9776561.v1
title: Additional file 4: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Benchmarking the running time of ags.sh against MicrobeCensus. Table showing the mean running time of ags.sh and MicrobeCensus using 4, 8, and 16 threads, for the estimation of the AGS in five TARA Oceans metagenomes subsampled to two million paired-end reads. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.9776564
title: Additional file 5: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S3. Topology analysis for protein-protein interaction networks (XLSX 141 kb)
DOI: 10.6084/m9.figshare.9776558
title: Additional file 4: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S2. Ingenuity Pathway Analysis Upstream Regulators (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9776552
title: Additional file 3: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S1. Genes in blue/violet module eigengene (XLSX 29 kb)
DOI: 10.6084/m9.figshare.9776564.v1
title: Additional file 5: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S3. Topology analysis for protein-protein interaction networks (XLSX 141 kb)
DOI: 10.6084/m9.figshare.9776549
title: Additional file 2: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Reference genome datasets. Excel sheets with the accession, taxid, organism name, and FTP URL of the genomes used to generate the simulated metagenomic datasets. (XLSX 105 kb)
DOI: 10.6084/m9.figshare.9776555.v1
title: Additional file 3: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Simulated metagenomic datasets. Table showing main characteristics describing the simulated metagenomic datasets. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9776549.v1
title: Additional file 2: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Reference genome datasets. Excel sheets with the accession, taxid, organism name, and FTP URL of the genomes used to generate the simulated metagenomic datasets. (XLSX 105 kb)
DOI: 10.6084/m9.figshare.9776552.v1
title: Additional file 3: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S1. Genes in blue/violet module eigengene (XLSX 29 kb)
DOI: 10.6084/m9.figshare.9776558.v1
title: Additional file 4: of The developmental origins of sex-biased expression in cardiac development

description: Dataset S2. Ingenuity Pathway Analysis Upstream Regulators (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9776534
title: Additional file 1: of The developmental origins of sex-biased expression in cardiac development

description: Table S1. List of antibodies used for ChIP-seq (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9776540
title: Additional file 1: of Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

description: Single-copy genes universally present in prokaryotes. Table showing the COG number of the 35 single-copy genes identified by Raes et al. (2007), and the number of sequences included in each COG. (XLSX 42 kb)