cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5817195
title: Supplementary Material for: Clinical Course of Histologically Proven Multifocal Micronodular Pneumocyte Hyperplasia in Tuberous Sclerosis Complex: A Case Series and Comparison with Lymphangiomyomatosis

description: <b><i>Background:</i></b> Multifocal micronodular pneumocyte hyperplasia (MMPH) is a rare pulmonary manifestation of tuberous sclerosis complex (TSC). Because of its rarity, no previous study has described the detailed clinical course of this disease. <b><i>Objectives:</i></b> This study aimed to clarify the longitudinal clinical characteristics of subjects with MMPH. <b><i>Methods:</i></b> Nine patients with MMPH diagnosed at Hokkaido University Hospital were retrospectively analyzed. Changes in computed tomography findings and pulmonary function were compared during the follow-up period. Serum levels of KL-6, surfactant protein (SP)-A, and SP-D were measured to clarify their potentials as blood biomarkers of the disease. Fourteen cases of lymphangiomyomatosis (LAM) were also included to compare their clinical characteristics with those of subjects with MMPH. <b><i>Results:</i></b> Of the 9 patients, 7 were female and 2 were male. The median age at diagnosis was 43 years (range, 19–56), and all cases were diagnosed following incidental abnormal radiographic findings. During the follow-up, 1 patient died of lung cancer, but others were radiographically stable and had stable pulmonary function. Serum levels of SP-A in 5 patients (mean, 146.4 ng/mL) and SP-D in 6 patients (mean, 337.3 ng/mL) were elevated in subjects with MMPH, whereas KL-6 levels were within the reference range (mean, 230 U/mL) in all patients. Levels of SP-A and SP-D were significantly higher in subjects with MMPH than those with LAM (<i>p</i> &lt; 0.05). <b><i>Conclusions:</i></b> Radiographic findings and pulmonary function were stable in all cases of MMPH. Serum SP-A and SP-D, but not KL-6, may be useful markers for suspicion of the presence of MMPH in patients with TSC.
DOI: 10.6084/m9.figshare.5817168
title: Banded and non-banded daily rainfall in APHRODITE (1951-2007)

description: APHRODITE annual rainfall decomposed into banded and non-banded components based on the FREDA algorithm.
DOI: 10.6084/m9.figshare.5817168.v1
title: Banded and non-banded daily rainfall in APHRODITE (1951-2007)

description: APHRODITE annual rainfall decomposed into banded and non-banded components based on the FREDA algorithm.
DOI: 10.6084/m9.figshare.5817147
title: MOESM3 of Outcomes of children aged 6â 59Â months with severe acute malnutrition at the GADO Outpatient Therapeutic Center in Cameroon

description: Additional file 3. DATASET SAM. Raw Data Set.
DOI: 10.6084/m9.figshare.5817147.v1
title: MOESM3 of Outcomes of children aged 6â 59Â months with severe acute malnutrition at the GADO Outpatient Therapeutic Center in Cameroon

description: Additional file 3. DATASET SAM. Raw Data Set.
DOI: 10.6084/m9.figshare.5817129
title: Additional file 8: Table S4. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Mapping of differentially methylated genes for the mCHH sequence context onto metabolic pathways based on annotated coding enzymes. (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.5817129.v1
title: Additional file 8: Table S4. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Mapping of differentially methylated genes for the mCHH sequence context onto metabolic pathways based on annotated coding enzymes. (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.5817123
title: Additional file 7: Table S3. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Mapping of differentially methylated genes for the mCHG sequence context onto metabolic pathways based on annotated coding enzymes. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.5817123.v1
title: Additional file 7: Table S3. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Mapping of differentially methylated genes for the mCHG sequence context onto metabolic pathways based on annotated coding enzymes. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.5817111
title: Additional file 6: Table S2. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Mapping of differentially methylated genes for the mCG sequence context on the metabolic pathways based on annotated coding enzymes. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.5817111.v1
title: Additional file 6: Table S2. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Mapping of differentially methylated genes for the mCG sequence context on the metabolic pathways based on annotated coding enzymes. (XLSX 40Â kb)
DOI: 10.6084/m9.figshare.5817069
title: Additional file 7: Table S6. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: The table presents the sequences of primer sets used for ChIP-PCR. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.5817069.v1
title: Additional file 7: Table S6. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: The table presents the sequences of primer sets used for ChIP-PCR. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.5817048
title: Additional file 6: Table S5. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: This Excel spreadsheet provides fold change, p values, and adjusted p values for the RNAseq data described in the text. Fold change and statistical significance are given for the comparisons within dietary groups across bacterial transfer. (XLSX 2254 kb)
DOI: 10.6084/m9.figshare.5817048.v1
title: Additional file 6: Table S5. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: This Excel spreadsheet provides fold change, p values, and adjusted p values for the RNAseq data described in the text. Fold change and statistical significance are given for the comparisons within dietary groups across bacterial transfer. (XLSX 2254 kb)
DOI: 10.6084/m9.figshare.5817045
title: Additional file 1: Table S1. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Oligonucleotides used in the qPCR and the methylation status of the corresponding gene on different component. Promoters were indicated as (P), exon (E) and intron (I). (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5817045.v1
title: Additional file 1: Table S1. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Oligonucleotides used in the qPCR and the methylation status of the corresponding gene on different component. Promoters were indicated as (P), exon (E) and intron (I). (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5817033
title: Additional file 5: Table S4. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: This Excel table provides the relative abundance of microbiota in donor mice and in recipient mice after bacterial transfer across the time points, diets, and transfer strategies outlined in the text. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.5817033.v1
title: Additional file 5: Table S4. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: This Excel table provides the relative abundance of microbiota in donor mice and in recipient mice after bacterial transfer across the time points, diets, and transfer strategies outlined in the text. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.5817030
title: Additional file 12: Table S7. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Functional annotation and gene ontology of differentially methylated genes for the mCHH sequence context based on coding sequences. (XLSX 417Â kb)
DOI: 10.6084/m9.figshare.5817030.v1
title: Additional file 12: Table S7. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Functional annotation and gene ontology of differentially methylated genes for the mCHH sequence context based on coding sequences. (XLSX 417Â kb)
DOI: 10.6084/m9.figshare.5817015
title: Additional file 11: Table S6. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Functional annotation and gene ontology of differentially methylated genes for the mCHG sequence context based on coding sequences. (XLSX 463Â kb)
DOI: 10.6084/m9.figshare.5817015.v1
title: Additional file 11: Table S6. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Functional annotation and gene ontology of differentially methylated genes for the mCHG sequence context based on coding sequences. (XLSX 463Â kb)
DOI: 10.6084/m9.figshare.5817009
title: Additional file 4: Table S3. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: This file contains a table providing the p value and fold change for the Affymetrix gene expression microarray experiment performed on animals at 20 weeks of dietary treatment. (XLSX 4268 kb)
DOI: 10.6084/m9.figshare.5817009.v1
title: Additional file 4: Table S3. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: This file contains a table providing the p value and fold change for the Affymetrix gene expression microarray experiment performed on animals at 20 weeks of dietary treatment. (XLSX 4268 kb)
DOI: 10.6084/m9.figshare.5816997
title: Additional file 10: Table S5. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Functional annotation and gene ontology of differentially methylated genes for the mCG sequence context based on coding sequences. (XLSX 425Â kb)
DOI: 10.6084/m9.figshare.5816997.v1
title: Additional file 10: Table S5. of Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

description: Functional annotation and gene ontology of differentially methylated genes for the mCG sequence context based on coding sequences. (XLSX 425Â kb)
DOI: 10.6084/m9.figshare.5816994
title: Additional file 3: Table S2. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: This file contains tables providing bacterial abundance for male and female mice across the time points and diets utilized in the study. (XLSX 94 kb)
DOI: 10.6084/m9.figshare.5816994.v1
title: Additional file 3: Table S2. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: This file contains tables providing bacterial abundance for male and female mice across the time points and diets utilized in the study. (XLSX 94 kb)
DOI: 10.6084/m9.figshare.5816970
title: Additional file 1: Table S1. of Spherical: an iterative workflow for assembling metagenomic datasets

description: Effect of kmer size on assembly. For each dataset (column 1) the alignment rate (%) (column 3) of raw data aligning back to assembly produced using different kmers (column 2) was assessed. Table S2. Effect of kmer size across iterations of assembly using the simulated dataset. The percentage of raw data aligning to each iterations assembly was identified and iterations stopped once the alignment rate was under 0.1%. Table S3. Analysis of the quality of contigs produced in each iteration of assembling the simulated dataset using contig scores. The contig score identifies the percentage accuracy of a contig compared to the genomes used to create the simulated metagenome. We present the percentage of contigs from each iterations assembly with contig scores gereater than 95 or less than 50. Table S4. Percentage of reads assigned to each of the 400 genomes within the simulated dataset, base assembly and Spherical assembly of the simulated dataset. Table S5. Assembly statistics comparing dataset assemblies for each method. The first column indicates the dataset utilized whilst the second column identified the assembly methodology. Due to Spherical having a sub-sampling option the size of the sample utilized by Spherical was stated for each assembly in column 5. The final 6 columns provide information on the computational needs for each assembly (RAM usage) as well as statistics about the produced assemblies e.g. number of contigs and alignment (%). Table S6. The number of reads aligning to genes within the Spherical iterations assembling each dataset. Figure S1. The taxonomic variations at the phylum level between each experimental assembly method for each dataset. Each bar represents the number of reads that could be assigned to a taxonomic Phyla within each assembly method for the datasets. The legend identifies which Phyla is represented by each colour. (ZIP 562 kb)
DOI: 10.6084/m9.figshare.5816970.v1
title: Additional file 1: Table S1. of Spherical: an iterative workflow for assembling metagenomic datasets

description: Effect of kmer size on assembly. For each dataset (column 1) the alignment rate (%) (column 3) of raw data aligning back to assembly produced using different kmers (column 2) was assessed. Table S2. Effect of kmer size across iterations of assembly using the simulated dataset. The percentage of raw data aligning to each iterations assembly was identified and iterations stopped once the alignment rate was under 0.1%. Table S3. Analysis of the quality of contigs produced in each iteration of assembling the simulated dataset using contig scores. The contig score identifies the percentage accuracy of a contig compared to the genomes used to create the simulated metagenome. We present the percentage of contigs from each iterations assembly with contig scores gereater than 95 or less than 50. Table S4. Percentage of reads assigned to each of the 400 genomes within the simulated dataset, base assembly and Spherical assembly of the simulated dataset. Table S5. Assembly statistics comparing dataset assemblies for each method. The first column indicates the dataset utilized whilst the second column identified the assembly methodology. Due to Spherical having a sub-sampling option the size of the sample utilized by Spherical was stated for each assembly in column 5. The final 6 columns provide information on the computational needs for each assembly (RAM usage) as well as statistics about the produced assemblies e.g. number of contigs and alignment (%). Table S6. The number of reads aligning to genes within the Spherical iterations assembling each dataset. Figure S1. The taxonomic variations at the phylum level between each experimental assembly method for each dataset. Each bar represents the number of reads that could be assigned to a taxonomic Phyla within each assembly method for the datasets. The legend identifies which Phyla is represented by each colour. (ZIP 562 kb)
DOI: 10.6084/m9.figshare.5816958
title: Additional file 1: Table S1. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: This file contains Table S1 which provides detailed descriptions of the components of the diets used in this study. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5816958.v1
title: Additional file 1: Table S1. of An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression

description: This file contains Table S1 which provides detailed descriptions of the components of the diets used in this study. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5816892
title: Additional file 5: Table S3. of Genetical genomics of growth in a chicken model

description: Most common Gene Ontology Biological process terms among eQTL. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.5816892.v1
title: Additional file 5: Table S3. of Genetical genomics of growth in a chicken model

description: Most common Gene Ontology Biological process terms among eQTL. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.5816874
title: Additional file 6: Table S6. of Genetical genomics of quality related traits in potato tubers using proteomics

description: Proteomics data from 2002 and 2003 and phenotypic data sets. (XLSX 409 kb)
DOI: 10.6084/m9.figshare.5816874.v1
title: Additional file 6: Table S6. of Genetical genomics of quality related traits in potato tubers using proteomics

description: Proteomics data from 2002 and 2003 and phenotypic data sets. (XLSX 409 kb)
DOI: 10.6084/m9.figshare.5816865
title: Additional file 3: Table S2. of Genetical genomics of growth in a chicken model

description: All eQTL. (CSV 124Â kb)
DOI: 10.6084/m9.figshare.5816865.v1
title: Additional file 3: Table S2. of Genetical genomics of growth in a chicken model

description: All eQTL. (CSV 124Â kb)
DOI: 10.6084/m9.figshare.5816862
title: Additional file 4: of Diversity of plant defense elicitor peptides within the Rosaceae

description: Primers used in this work, with their use and optimal reaction conditions. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.5816862.v1
title: Additional file 4: of Diversity of plant defense elicitor peptides within the Rosaceae

description: Primers used in this work, with their use and optimal reaction conditions. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.5816841
title: Additional file 1: Table S1. of Genetical genomics of growth in a chicken model

description: Number of overlaps between quantitative trait locus regions and selective sweep regions from [50]. (CSV 426 bytes)
DOI: 10.6084/m9.figshare.5816841.v1
title: Additional file 1: Table S1. of Genetical genomics of growth in a chicken model

description: Number of overlaps between quantitative trait locus regions and selective sweep regions from [50]. (CSV 426 bytes)
DOI: 10.6084/m9.figshare.5816823
title: Additional file 2: of Diversity of plant defense elicitor peptides within the Rosaceae

description: DNA and protein sequences of the identified Pyreae Pep and, in many examples, PROPEP sequences. Intron sequences are shown in lower case. In specific cases a given variety contained two sequences: the different nucleotide and amino acid positions are indicated with a bar. (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.5816823.v1
title: Additional file 2: of Diversity of plant defense elicitor peptides within the Rosaceae

description: DNA and protein sequences of the identified Pyreae Pep and, in many examples, PROPEP sequences. Intron sequences are shown in lower case. In specific cases a given variety contained two sequences: the different nucleotide and amino acid positions are indicated with a bar. (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.5816814
title: Additional file 14: of Genetical genomics of growth in a chicken model

description: Genotype and phenotype data underlying expression quantitative trait locus mapping analysis in R/qtl format. (CSV 39860Â kb)
DOI: 10.6084/m9.figshare.5816814.v1
title: Additional file 14: of Genetical genomics of growth in a chicken model

description: Genotype and phenotype data underlying expression quantitative trait locus mapping analysis in R/qtl format. (CSV 39860Â kb)
DOI: 10.6084/m9.figshare.5816805
title: Additional file 1: of Diversity of plant defense elicitor peptides within the Rosaceae

description: DNA and protein sequences of the identified Amygdaleae Pep and, in many examples, PROPEP sequences. Intron sequences are shown in lower case. In specific cases a given variety contained two sequences: the different nucleotide and amino acid positions are indicated with a bar. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.5816805.v1
title: Additional file 1: of Diversity of plant defense elicitor peptides within the Rosaceae

description: DNA and protein sequences of the identified Amygdaleae Pep and, in many examples, PROPEP sequences. Intron sequences are shown in lower case. In specific cases a given variety contained two sequences: the different nucleotide and amino acid positions are indicated with a bar. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.5816793
title: Additional file 13: of Genetical genomics of growth in a chicken model

description: Genotype and phenotype data underlying quantitative trait locus mapping analysis in R/qtl format. (CSV 1191Â kb)
DOI: 10.6084/m9.figshare.5816793.v1
title: Additional file 13: of Genetical genomics of growth in a chicken model

description: Genotype and phenotype data underlying quantitative trait locus mapping analysis in R/qtl format. (CSV 1191Â kb)
DOI: 10.6084/m9.figshare.5816775
title: Additional file 12: Table S4. of Genetical genomics of growth in a chicken model

description: Genes with expression levels associated with growth traits. (CSV 2Â kb)
DOI: 10.6084/m9.figshare.5816775.v1
title: Additional file 12: Table S4. of Genetical genomics of growth in a chicken model

description: Genes with expression levels associated with growth traits. (CSV 2Â kb)
DOI: 10.6084/m9.figshare.5816751
title: Additional file 3: of Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia

description: Mutagenesis data and RTEL1-mapping for Fan et al. and Kuper et al. XPD variants. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.5816751.v1
title: Additional file 3: of Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia

description: Mutagenesis data and RTEL1-mapping for Fan et al. and Kuper et al. XPD variants. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.5816739
title: Additional file 10: Table S5. of Genetical genomics of growth in a chicken model

description: Trans-expression quantitative trait locus hotspots. (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.5816739.v1
title: Additional file 10: Table S5. of Genetical genomics of growth in a chicken model

description: Trans-expression quantitative trait locus hotspots. (XLSX 35Â kb)
DOI: 10.6084/m9.figshare.5816733
title: Additional file 2: of Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia

description: Computational homology model of the protein structure of RTEL1. (PDB 1274Â kb)
DOI: 10.6084/m9.figshare.5816733.v1
title: Additional file 2: of Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia

description: Computational homology model of the protein structure of RTEL1. (PDB 1274Â kb)
DOI: 10.6084/m9.figshare.5816730
title: MOESM2 of Use of DAVID algorithms for clustering custom annotated gene lists in a non-model organism, rainbow trout

description: Additional file 2: Table S1. Changes in the number of genes harbored in each module with kappa score. Table S2. The enrichment score for the largest module estimated by using three GO categories. Table S3. Changes in the enrichment score for the largest module with kappa score, estimated for each GO category.
DOI: 10.6084/m9.figshare.5816730.v1
title: MOESM2 of Use of DAVID algorithms for clustering custom annotated gene lists in a non-model organism, rainbow trout

description: Additional file 2: Table S1. Changes in the number of genes harbored in each module with kappa score. Table S2. The enrichment score for the largest module estimated by using three GO categories. Table S3. Changes in the enrichment score for the largest module with kappa score, estimated for each GO category.