cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7937252.v1
title: Supplementary Material for: Urinary Biomarkers of Tubular Damage Are Associated with Mortality but Not Cardiovascular Risk among Systolic Blood Pressure Intervention Trial Participants with Chronic Kidney Disease

description: <b><i>Background:</i></b> Kidney tubulointerstitial fibrosis on biopsy is a strong predictor of chronic kidney disease (CKD) progression, and CKD is associated with elevated risk of cardiovascular disease (CVD). Tubular health is poorly quantified by traditional kidney function measures, including estimated glomerular filtration rate (eGFR) and albuminuria. We hypothesized that urinary biomarkers of tubular injury, inflammation, and repair would be associated with higher risk of CVD and mortality in persons with CKD. <b><i>Methods:</i></b> We measured urinary concentrations of interleukin-18 (IL-18), kidney injury molecule-1, neutrophil gelatinase-associated lipocalin, monocyte chemoattractant protein-1, and chitinase-3-like protein-1 (YKL-40) at baseline among 2,377 participants of the Systolic Blood Pressure Intervention Trial who had an eGFR &lt; 60 mL/min/1.73 m<sup>2</sup>. We used Cox proportional hazards models to evaluate biomarker associations with CVD events and all-cause mortality. <b><i>Results:</i></b> At baseline, the mean age of participants was 72 ± 9 years, and eGFR was 48 ± 11 mL/min/1.73 m<sup>2</sup>. Over a median follow-up of 3.8 years, 305 CVD events (3.6% per year) and 233 all-cause deaths (2.6% per year) occurred. After multivariable adjustment including eGFR, albuminuria, and urinary creatinine, none of the biomarkers showed statistically significant associations with CVD risk. Urinary IL-18 (hazard ratio [HR] per 2-fold higher value, 1.14; 95% CI 1.01–1.29) and YKL-40 (HR per 2-fold higher value, 1.08; 95% CI 1.02–1.14) concentrations were each incrementally associated with higher mortality risk. Associations were similar when stratified by randomized blood pressure arm. <b><i>Conclusions:</i></b> Among hypertensive trial participants with CKD, higher urinary IL-18 and YKL-40 were associated with higher risk of mortality, but not CVD.
DOI: 10.6084/m9.figshare.7937237
title: Activation of the Mating Pheromone Response Pathway of <i>Lentinula edodes</i> by Synthetic Pheromones

description: Pheromone (PHB)-receptor (RCB) interaction in the mating pheromone response pathway of <i>Lentinula edodes</i> was investigated using synthetic PHBs. Functionality of the C-terminally carboxymethylated synthetic PHBs was demonstrated by concentration-dependent induction of a mating-related gene (<i>znf2</i>) expression and by pseudoclamp formation in a monokaryotic strain S1-11 of <i>L. edodes</i>. Treatment with synthetic PHBs activated the expression of homeodomain genes (<i>HD</i>s) residing in the <i>A</i> mating type locus, and of <i>A</i>-regulated genes, including <i>znf2</i>, <i>clp1</i>, and <i>priA</i>, as well as genes in the <i>B</i> mating type locus, including pheromone (<i>phb</i>) and receptor (<i>rcb</i>) genes. The synthetic PHBs failed to discriminate self from non-self RCBs. PHBs of the <i>B4</i> mating type (<i>B4</i> PHBs) were able to activate the mating pheromone response pathway in both monokaryotic S1-11 and S1-13 strains, whose <i>B</i> mating types were <i>B4</i> (self) and <i>B12</i> (non-self), respectively. The same was true for <i>B12</i> PHBs in the <i>B4</i> (non-self) and <i>B12</i> (self) mating types. The synthetic PHBs also promoted the mating of two monokaryotic strains carrying <i>B4</i>-common incompatible mating types (<i>A5B4</i> ×<i> A1B4</i>). However, the dikaryon generated by this process exhibited abnormally high content of hyphal branching and frequent clamp connections and, more importantly, was found to be genetically unstable due to overexpression of mating-related genes such as <i>clp1</i>. Although synthetic PHBs were unable to discriminate self from non-self RCBs, they showed a higher affinity for non-self RCBs, through which the mating pheromone response pathway in non-self cells may be preferentially activated.
DOI: 10.6084/m9.figshare.7937231
title: Genome-Wide Comparison of Carbohydrate-Active Enzymes (CAZymes) Repertoire of <i>Flammulina ononidis</i>

description: Whole-genome sequencing of <i>Flammulina ononidis</i>, a wood-rotting basidiomycete, was performed to identify genes associated with carbohydrate-active enzymes (CAZymes). A total of 12,586 gene structures with an average length of 2009 bp were predicted by the AUGUSTUS tool from a total 35,524,258 bp length of <i>de novo</i> genome assembly (49.76% GC). Orthologous analysis with other fungal species revealed that 7051 groups contained at least one <i>F. ononidis</i> gene. In addition, 11,252 (89.5%) of 12,586 genes for <i>F. ononidis</i> proteins had orthologs among the Dikarya, and <i>F. ononidis</i> contained 8 species-specific genes, of which 5 genes were paralogous. CAZyme prediction revealed 524 CAZyme genes, including 228 for glycoside hydrolases, 21 for polysaccharide lyases, 87 for glycosyltransferases, 61 for carbohydrate esterases, 87 with auxiliary activities, and 40 for carbohydrate-binding modules in the <i>F. ononidis</i> genome. This genome information including CAZyme repertoire will be useful to understand lignocellulolytic machinery of this white rot fungus <i>F. ononidis</i>.
DOI: 10.6084/m9.figshare.7937237.v1
title: Activation of the Mating Pheromone Response Pathway of <i>Lentinula edodes</i> by Synthetic Pheromones

description: Pheromone (PHB)-receptor (RCB) interaction in the mating pheromone response pathway of <i>Lentinula edodes</i> was investigated using synthetic PHBs. Functionality of the C-terminally carboxymethylated synthetic PHBs was demonstrated by concentration-dependent induction of a mating-related gene (<i>znf2</i>) expression and by pseudoclamp formation in a monokaryotic strain S1-11 of <i>L. edodes</i>. Treatment with synthetic PHBs activated the expression of homeodomain genes (<i>HD</i>s) residing in the <i>A</i> mating type locus, and of <i>A</i>-regulated genes, including <i>znf2</i>, <i>clp1</i>, and <i>priA</i>, as well as genes in the <i>B</i> mating type locus, including pheromone (<i>phb</i>) and receptor (<i>rcb</i>) genes. The synthetic PHBs failed to discriminate self from non-self RCBs. PHBs of the <i>B4</i> mating type (<i>B4</i> PHBs) were able to activate the mating pheromone response pathway in both monokaryotic S1-11 and S1-13 strains, whose <i>B</i> mating types were <i>B4</i> (self) and <i>B12</i> (non-self), respectively. The same was true for <i>B12</i> PHBs in the <i>B4</i> (non-self) and <i>B12</i> (self) mating types. The synthetic PHBs also promoted the mating of two monokaryotic strains carrying <i>B4</i>-common incompatible mating types (<i>A5B4</i> ×<i> A1B4</i>). However, the dikaryon generated by this process exhibited abnormally high content of hyphal branching and frequent clamp connections and, more importantly, was found to be genetically unstable due to overexpression of mating-related genes such as <i>clp1</i>. Although synthetic PHBs were unable to discriminate self from non-self RCBs, they showed a higher affinity for non-self RCBs, through which the mating pheromone response pathway in non-self cells may be preferentially activated.
DOI: 10.6084/m9.figshare.7937225
title: Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic Context

description: The rice blast fungus, <i>Magnaporthe oryzae</i>, is an important pathogen of rice plants. It is well known that genes encoded in the genome have different evolutionary histories that are related to their functions. Phylostratigraphy is a method that correlates the evolutionary origin of genes with evolutionary transitions. Here we applied phylostratigraphy to partition total gene content of <i>M. oryzae</i> into distinct classes (phylostrata), which we designated PS1 to PS7, based on estimation of their emergence time. Genes in individual phylostrata did not show significant biases in their global distribution among seven chromosomes, but at the local level, clustering of genes belonging to the same phylostratum was observed. Our phylostrata-wide analysis of genes revealed that genes in the same phylostratum tend to be similar in many physical and functional characteristics such as gene length and structure, GC contents, codon adaptation index, and level of transcription, which correlates with biological functions in evolutionary context. We also found that a significant proportion of genes in the genome are orphans, for which no orthologs can be detected in the database. Among them, we narrowed down to seven orphan genes having transcriptional and translational evidences, and showed that one of them is implicated in asexual reproduction and virulence, suggesting ongoing evolution in this fungus through lineage-specific genes. Our results provide genomic basis for linking functions of pathogenicity factors and gene emergence time.
DOI: 10.6084/m9.figshare.7937231.v1
title: Genome-Wide Comparison of Carbohydrate-Active Enzymes (CAZymes) Repertoire of <i>Flammulina ononidis</i>

description: Whole-genome sequencing of <i>Flammulina ononidis</i>, a wood-rotting basidiomycete, was performed to identify genes associated with carbohydrate-active enzymes (CAZymes). A total of 12,586 gene structures with an average length of 2009 bp were predicted by the AUGUSTUS tool from a total 35,524,258 bp length of <i>de novo</i> genome assembly (49.76% GC). Orthologous analysis with other fungal species revealed that 7051 groups contained at least one <i>F. ononidis</i> gene. In addition, 11,252 (89.5%) of 12,586 genes for <i>F. ononidis</i> proteins had orthologs among the Dikarya, and <i>F. ononidis</i> contained 8 species-specific genes, of which 5 genes were paralogous. CAZyme prediction revealed 524 CAZyme genes, including 228 for glycoside hydrolases, 21 for polysaccharide lyases, 87 for glycosyltransferases, 61 for carbohydrate esterases, 87 with auxiliary activities, and 40 for carbohydrate-binding modules in the <i>F. ononidis</i> genome. This genome information including CAZyme repertoire will be useful to understand lignocellulolytic machinery of this white rot fungus <i>F. ononidis</i>.
DOI: 10.6084/m9.figshare.7937246.v1
title: Cancer Datasheets

description: Cancer datasheets for classification of cancer samples based on tumor immune phenotype according to expression of the Immunologic Constant of Rejection gene signature.
DOI: 10.6084/m9.figshare.7937225.v1
title: Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic Context

description: The rice blast fungus, <i>Magnaporthe oryzae</i>, is an important pathogen of rice plants. It is well known that genes encoded in the genome have different evolutionary histories that are related to their functions. Phylostratigraphy is a method that correlates the evolutionary origin of genes with evolutionary transitions. Here we applied phylostratigraphy to partition total gene content of <i>M. oryzae</i> into distinct classes (phylostrata), which we designated PS1 to PS7, based on estimation of their emergence time. Genes in individual phylostrata did not show significant biases in their global distribution among seven chromosomes, but at the local level, clustering of genes belonging to the same phylostratum was observed. Our phylostrata-wide analysis of genes revealed that genes in the same phylostratum tend to be similar in many physical and functional characteristics such as gene length and structure, GC contents, codon adaptation index, and level of transcription, which correlates with biological functions in evolutionary context. We also found that a significant proportion of genes in the genome are orphans, for which no orthologs can be detected in the database. Among them, we narrowed down to seven orphan genes having transcriptional and translational evidences, and showed that one of them is implicated in asexual reproduction and virulence, suggesting ongoing evolution in this fungus through lineage-specific genes. Our results provide genomic basis for linking functions of pathogenicity factors and gene emergence time.
DOI: 10.6084/m9.figshare.7937204
title: gVCF_NA11994

description: 1000 Genomes gVCF mapped to hs37d5 for NA11994. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7937201
title: gVCF_NA20359

description: 1000 Genomes gVCF mapped to hs37d5 for NA20359. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7937204.v1
title: gVCF_NA11994

description: 1000 Genomes gVCF mapped to hs37d5 for NA11994. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7937246.v3
title: Cancer Datasheets

description: Cancer datasheets for classification of cancer samples based on tumor immune phenotype according to expression of the Immunologic Constant of Rejection gene signature.
DOI: 10.6084/m9.figshare.7937183
title: Drip irrigation biofouling with treated wastewater: bacterial selection revealed by high-throughput sequencing

description: Clogging of drippers due to the development of biofilms weakens the advantages and impedes the implementation of drip irrigation technology. The objective of this study was to characterise the bacterial community of biofilms that develop in a drip irrigation system supplied with treated wastewater. High-throughput sequencing of 16S rRNA gene amplicons indicated that the bacterial community composition differed between drippers and pipes, mainly due to changes in the abundance of the genus <i>Aquabacterium</i>. Cyanobacteria were found to be involved in the biological fouling of drippers. Moreover, bacterial genera including opportunistic pathogenic bacteria such as <i>Legionella and Pseudomonas</i> were more abundant in dripper and pipe biofilms than in the incoming water. Some genera such as <i>Pseudomonas</i> were mostly recovered from drippers, while others (ie <i>Bacillus</i>, <i>Brevundimonas</i>) mainly occurred in pipes. Variations in the hydraulic conditions and properties of the materials likely explain the shift in bacterial communities observed between pipes and drippers.
DOI: 10.6084/m9.figshare.7937246.v4
title: Cancer Datasheets

description: Cancer datasheets for classification of cancer samples based on tumor immune phenotype according to expression of the Immunologic Constant of Rejection gene signature.
DOI: 10.6084/m9.figshare.7937183.v1
title: Drip irrigation biofouling with treated wastewater: bacterial selection revealed by high-throughput sequencing

description: Clogging of drippers due to the development of biofilms weakens the advantages and impedes the implementation of drip irrigation technology. The objective of this study was to characterise the bacterial community of biofilms that develop in a drip irrigation system supplied with treated wastewater. High-throughput sequencing of 16S rRNA gene amplicons indicated that the bacterial community composition differed between drippers and pipes, mainly due to changes in the abundance of the genus <i>Aquabacterium</i>. Cyanobacteria were found to be involved in the biological fouling of drippers. Moreover, bacterial genera including opportunistic pathogenic bacteria such as <i>Legionella and Pseudomonas</i> were more abundant in dripper and pipe biofilms than in the incoming water. Some genera such as <i>Pseudomonas</i> were mostly recovered from drippers, while others (ie <i>Bacillus</i>, <i>Brevundimonas</i>) mainly occurred in pipes. Variations in the hydraulic conditions and properties of the materials likely explain the shift in bacterial communities observed between pipes and drippers.
DOI: 10.6084/m9.figshare.7937246.v5
title: Cancer Datasheets

description: Cancer datasheets for classification of cancer samples based on tumor immune phenotype according to expression of the Immunologic Constant of Rejection gene signature.
DOI: 10.6084/m9.figshare.12880682.v1
title: Additional file 2 of Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction

description: Additional file 2:Complete results of the strict and relaxed network comparisons. This files contains the complete results of the strict and relaxed network comparisons for pairs of species and three, four, five and six species combinations. The number of OrthoMCL groups, interologs from strict and relaxed definition as well as the total number of CCS and the size of the largest CCS are given. (XLS 40 KB)
DOI: 10.6084/m9.figshare.12880685.v1
title: Additional file 3 of Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction

description: Additional file 3:Complete results of the CCS-based function prediction approach. This file contains the complete results of the combined CCS-based function prediction approach for pairs of species and three, four, five and six species combinations. CCS from strict and relaxed network comparison are used depending on the species combinations. (XLS 52 KB)
DOI: 10.6084/m9.figshare.7936826
title: gVCF_HG02715

description: 1000 Genomes gVCF mapped to hs37d5 for HG02715. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7936826.v1
title: gVCF_HG02715

description: 1000 Genomes gVCF mapped to hs37d5 for HG02715. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7936784
title: gVCF_NA20357

description: 1000 Genomes gVCF mapped to hs37d5 for NA20357. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7936778
title: Genetic Diversity of the Pear Scab Fungus <i>Venturia nashicola</i> in Korea

description: Scab disease caused by <i>Venturia nashicola</i> is of agroeconomic importance in cultivation of Asian pear. However, little is known about the degree of genetic diversity in the populations of this pathogen. In this study, we collected 55 isolates from pear scab lesions in 13 major cultivation areas in Korea and examined the diversity using sequences of internal transcribed spacer (ITS) region, β-tubulin (TUB2), and translation elongation factor-1<i>α</i> (TEF-1<i>α</i>) genes as molecular markers. Despite a low level of overall sequence variation, we found three distinctive subgroups from phylogenetic analysis of combined ITS, TUB2, and TEF-1<i>α</i> sequences. Among the three subgroups, subgroup 1 (60% of isolates collected) was predominant compared to subgroup 2 (23.6%) or subgroup 3 (16.4%) and was distributed throughout Korea. To understand the genetic diversity among the subgroups, RAPD analysis was performed. The isolates yielded highly diverse amplicon patterns and none of the defined subgroups within the dendrogram were supported by bootstrap values greater than 30%. Moreover, there is no significant correlation between the geographical distribution and the subgroups defined by molecular phylogeny. Our data suggest a low level of genetic diversification among the populations of <i>V. nashicola</i> in Korea.
DOI: 10.6084/m9.figshare.7936784.v1
title: gVCF_NA20357

description: 1000 Genomes gVCF mapped to hs37d5 for NA20357. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7936778.v1
title: Genetic Diversity of the Pear Scab Fungus <i>Venturia nashicola</i> in Korea

description: Scab disease caused by <i>Venturia nashicola</i> is of agroeconomic importance in cultivation of Asian pear. However, little is known about the degree of genetic diversity in the populations of this pathogen. In this study, we collected 55 isolates from pear scab lesions in 13 major cultivation areas in Korea and examined the diversity using sequences of internal transcribed spacer (ITS) region, β-tubulin (TUB2), and translation elongation factor-1<i>α</i> (TEF-1<i>α</i>) genes as molecular markers. Despite a low level of overall sequence variation, we found three distinctive subgroups from phylogenetic analysis of combined ITS, TUB2, and TEF-1<i>α</i> sequences. Among the three subgroups, subgroup 1 (60% of isolates collected) was predominant compared to subgroup 2 (23.6%) or subgroup 3 (16.4%) and was distributed throughout Korea. To understand the genetic diversity among the subgroups, RAPD analysis was performed. The isolates yielded highly diverse amplicon patterns and none of the defined subgroups within the dendrogram were supported by bootstrap values greater than 30%. Moreover, there is no significant correlation between the geographical distribution and the subgroups defined by molecular phylogeny. Our data suggest a low level of genetic diversification among the populations of <i>V. nashicola</i> in Korea.
DOI: 10.6084/m9.figshare.7936757
title: gVCF_NA11992

description: 1000 Genomes gVCF mapped to hs37d5 for NA11992. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7936760
title: gVCF_NA20356

description: 1000 Genomes gVCF mapped to hs37d5 for NA20356. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7936760.v1
title: gVCF_NA20356

description: 1000 Genomes gVCF mapped to hs37d5 for NA20356. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7936745
title: gVCF_HG02702

description: 1000 Genomes gVCF mapped to hs37d5 for HG02702. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7936775.v1
title: Isolation of group B <i>Streptococcus</i> with reduced <i>β</i>-lactam susceptibility from pregnant women

description: <i>β</i>-Lactam antibiotics are first-line agents for the treatment and prevention of group B <i>Streptococcus</i> (GBS) infections. We previously reported clinical GBS isolates with reduced <i>β</i>-lactam susceptibility (GBS-RBS) and characterized them as harbouring amino acid substitutions in penicillin-binding proteins (PBPs). However, to our knowledge, GBS-RBS clinical isolates have never previously been isolated from pregnant women worldwide. We obtained 477 clinical GBS isolates from vaginal/rectal swabs of 4530 pregnant women in Japan. We determined the MICs of seven <i>β</i>-lactams for all 477 clinical isolates. Five clinical isolates showed reduced ceftibuten susceptibility. For these isolates, we performed sequencing analysis of <i>pbp</i> genes. None of the 477 isolates were non-susceptible to penicillin G, ampicillin, and meropenem. For five isolates, the MICs of ceftibuten were relatively high (64–128 μg/ml). Each of these isolates possessed a single amino acid substitution in PBP2X, and some of the substitutions had been previously found in GBS with reduced penicillin susceptibility. This is the first report of the isolation of clinical GBS-RBS isolates harbouring amino acid substitutions in PBP2X that confer reduced ceftibuten susceptibility from pregnant women.
DOI: 10.6084/m9.figshare.12880926
title: Additional file 3 of DNA methylation in glioblastoma: impact on gene expression and clinical outcome

description: Additional file 3:CpG sites differentially methylated between GBM and control brain. (XLS 156 KB)
DOI: 10.6084/m9.figshare.12880935.v1
title: Additional file 6 of DNA methylation in glioblastoma: impact on gene expression and clinical outcome

description: Additional file 6:CpG sites significantly associated with overall survival - Log rank analysis. (XLS 58 KB)
DOI: 10.6084/m9.figshare.7936745.v1
title: gVCF_HG02702

description: 1000 Genomes gVCF mapped to hs37d5 for HG02702. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.12880926.v1
title: Additional file 3 of DNA methylation in glioblastoma: impact on gene expression and clinical outcome

description: Additional file 3:CpG sites differentially methylated between GBM and control brain. (XLS 156 KB)