cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7842641.v1
title: Additional file 5: of Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers

description: Table S4. List of genes differently expressed between normal and tumor METABRIC samples and with concordant results with TCGA breast cancer analyses. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.7842644.v1
title: Additional file 6: of Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers

description: Table S5. Results of OncoScore analyses for the 164 differentially-methylated and differentially-expressed genes. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.7842620
title: Additional file 2: of Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers

description: Table S2. Results of DAVID clustering Gene Ontology analyses. (XLSX 95 kb)
DOI: 10.6084/m9.figshare.7842632.v1
title: Additional file 4: of Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers

description: Table S3. List of CpGs located in genes that are differentially expressed between breast cancer and matched-normal TCGA samples and whose methylation levels are correlated with cognate gene expression. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.7842620.v1
title: Additional file 2: of Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers

description: Table S2. Results of DAVID clustering Gene Ontology analyses. (XLSX 95 kb)
DOI: 10.6084/m9.figshare.7842611
title: Additional file 1: of Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers

description: Table S1. List of CpGs differently methylated between breast cancer and matched-normal samples. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.7842611.v1
title: Additional file 1: of Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers

description: Table S1. List of CpGs differently methylated between breast cancer and matched-normal samples. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.7842467
title: Additional file 8: of Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica

description: Motifs in Eh. (XLSX 748 kb)
DOI: 10.6084/m9.figshare.7842467.v1
title: Additional file 8: of Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica

description: Motifs in Eh. (XLSX 748 kb)
DOI: 10.6084/m9.figshare.7842452
title: Additional file 5: of Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica

description: GO analysis of genes with different motifs and expression class. (XLSX 88 kb)
DOI: 10.6084/m9.figshare.7842452.v1
title: Additional file 5: of Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica

description: GO analysis of genes with different motifs and expression class. (XLSX 88 kb)
DOI: 10.6084/m9.figshare.7842416
title: Additional file 5: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

description: Selection analyses data for UPOs. (XLSX 119 kb)
DOI: 10.6084/m9.figshare.7842422
title: Additional file 6: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

description: Selection analyses data for CPOs. (XLSX 109 kb)
DOI: 10.6084/m9.figshare.7842416.v1
title: Additional file 5: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

description: Selection analyses data for UPOs. (XLSX 119 kb)
DOI: 10.6084/m9.figshare.7842422.v1
title: Additional file 6: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

description: Selection analyses data for CPOs. (XLSX 109 kb)
DOI: 10.6084/m9.figshare.7842392
title: Additional file 14: of Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica

description: Core promoter sequence in Eh genes. (XLSX 75 kb)
DOI: 10.6084/m9.figshare.7842392.v1
title: Additional file 14: of Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica

description: Core promoter sequence in Eh genes. (XLSX 75 kb)
DOI: 10.6084/m9.figshare.7842380
title: Additional file 2: of Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes

description: Gene ontology (GO) enrichment analysis based on the number of DE genes per tissue (FDR cutoff 0.05). The Tabs entitled “TISSUE EnrichGO” contain the detailed lists of the enriched GO total, up- and down-regulated sorted by ontology (Biological process (BP), Cellular compartment (CC) and Molecular function (MF)). (XLSX 49 kb)
DOI: 10.6084/m9.figshare.7842380.v1
title: Additional file 2: of Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes

description: Gene ontology (GO) enrichment analysis based on the number of DE genes per tissue (FDR cutoff 0.05). The Tabs entitled “TISSUE EnrichGO” contain the detailed lists of the enriched GO total, up- and down-regulated sorted by ontology (Biological process (BP), Cellular compartment (CC) and Molecular function (MF)). (XLSX 49 kb)
DOI: 10.6084/m9.figshare.7842362
title: Additional file 16: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

description: Table S3 Information of all the fungal genome sequences used in this study. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7842350
title: Additional file 14: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

description: Functional divergence analysis data for UPOs and CPOs. (XLSX 77 kb)
DOI: 10.6084/m9.figshare.7842362.v1
title: Additional file 16: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

description: Table S3 Information of all the fungal genome sequences used in this study. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7842350.v1
title: Additional file 14: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

description: Functional divergence analysis data for UPOs and CPOs. (XLSX 77 kb)
DOI: 10.6084/m9.figshare.7842332
title: Additional file 7 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 7. List of excluded articles at full text screening.
DOI: 10.6084/m9.figshare.7842323
title: Additional file 6 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 6. List of unobtainable articles.
DOI: 10.6084/m9.figshare.7842311
title: Additional file 4 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 4. Studies excluded due to low validity.
DOI: 10.6084/m9.figshare.7842314
title: Additional file 5 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 5. Data extraction with statistical analysis.
DOI: 10.6084/m9.figshare.7842332.v2
title: Additional file 7 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 7. List of excluded articles at full text screening.
DOI: 10.6084/m9.figshare.7842323.v2
title: Additional file 6 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 6. List of unobtainable articles.
DOI: 10.6084/m9.figshare.7842332.v1
title: MOESM7 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 7. List of excluded articles at full text screening.
DOI: 10.6084/m9.figshare.7842305
title: Additional file 3 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 3. Narrative table.
DOI: 10.6084/m9.figshare.7842323.v1
title: MOESM6 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 6. List of unobtainable articles.
DOI: 10.6084/m9.figshare.7842302
title: Additional file 2 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 2. Search strategy.
DOI: 10.6084/m9.figshare.7842311.v2
title: Additional file 4 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 4. Studies excluded due to low validity.
DOI: 10.6084/m9.figshare.7842314.v2
title: Additional file 5 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 5. Data extraction with statistical analysis.
DOI: 10.6084/m9.figshare.7842299
title: Additional file 1 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 1. ROSES form for systematic reviews.
DOI: 10.6084/m9.figshare.7842305.v2
title: Additional file 3 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 3. Narrative table.
DOI: 10.6084/m9.figshare.7842311.v1
title: MOESM4 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 4. Studies excluded due to low validity.
DOI: 10.6084/m9.figshare.7842314.v1
title: MOESM5 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 5. Data extraction with statistical analysis.
DOI: 10.6084/m9.figshare.7842302.v2
title: Additional file 2 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 2. Search strategy.
DOI: 10.6084/m9.figshare.7842299.v2
title: Additional file 1 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 1. ROSES form for systematic reviews.
DOI: 10.6084/m9.figshare.7842302.v1
title: MOESM2 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 2. Search strategy.
DOI: 10.6084/m9.figshare.7842305.v1
title: MOESM3 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 3. Narrative table.
DOI: 10.6084/m9.figshare.7842284
title: MOESM1 of Prevalence of G6PD Viangchan variant in malaria endemic areas in Lao PDR: an implication for malaria elimination by 2030

description: Additional file 1: Appendix S1. Villagersâ information.
DOI: 10.6084/m9.figshare.7842299.v1
title: MOESM1 of Impact of structural habitat modifications in coastal temperate systems on fish recruitment: a systematic review

description: Additional file 1. ROSES form for systematic reviews.
DOI: 10.6084/m9.figshare.7842272
title: Additional file 5: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S5. The list of differentially expressed genes with statistical significance (FDR
DOI: 10.6084/m9.figshare.7842275
title: Additional file 6: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S6. The list of differentially expressed and differentially methylated genes associated with the ROS signaling genes identified by Willems et al. 2016 [77]. The ROS genes with at least 2-fold expression change in response to at least one stress category were selected. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.7842275.v1
title: Additional file 6: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S6. The list of differentially expressed and differentially methylated genes associated with the ROS signaling genes identified by Willems et al. 2016 [77]. The ROS genes with at least 2-fold expression change in response to at least one stress category were selected. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.7842272.v1
title: Additional file 5: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S5. The list of differentially expressed genes with statistical significance (FDR
DOI: 10.6084/m9.figshare.7842263
title: Additional file 4: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S4. The list of 800 genes that were differentially expressed with statistical significance (FDR
DOI: 10.6084/m9.figshare.7842257
title: Additional file 3: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S3. The list of genes mapped with differentially methylated cytosines (DmCs) with statistical significance (FDRâ
DOI: 10.6084/m9.figshare.7842257.v1
title: Additional file 3: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S3. The list of genes mapped with differentially methylated cytosines (DmCs) with statistical significance (FDRâ
DOI: 10.6084/m9.figshare.7842263.v1
title: Additional file 4: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S4. The list of 800 genes that were differentially expressed with statistical significance (FDR
DOI: 10.6084/m9.figshare.7842245
title: Additional file 1: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S1. The bisulfite conversion efficiency based on conversion ratio of cytosines in chloroplast reference genome. The ratio of converted cytosines in CG, CHG and CHH contexts were calculated using reads mapped to chloroplast reference genome. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7842248
title: Additional file 2: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S2. The list of differentially methylated cytosines (DmCs) with statistical significance FDRâ
DOI: 10.6084/m9.figshare.7842221
title: Negative gene correlates for APOE4+ males Parietal cortex

description: Negative gene correlates for APOE4+ males, Parietal cortex
DOI: 10.6084/m9.figshare.7842245.v1
title: Additional file 1: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S1. The bisulfite conversion efficiency based on conversion ratio of cytosines in chloroplast reference genome. The ratio of converted cytosines in CG, CHG and CHH contexts were calculated using reads mapped to chloroplast reference genome. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7842248.v1
title: Additional file 2: of Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

description: Table S2. The list of differentially methylated cytosines (DmCs) with statistical significance FDRâ
DOI: 10.6084/m9.figshare.7842218
title: Negative gene correlates for APOE4+ males Hippocampus

description: Negative gene correlates for APOE4+ males, Hippocampus
DOI: 10.6084/m9.figshare.7842188
title: Positive gene correlates for APOE4+ males Temporal cortex

description: Positive gene correlates for APOE4+ males, Temporal cortex
DOI: 10.6084/m9.figshare.7842191
title: Positive gene correlates for APOE4+ males Parietal cortex

description: Positive gene correlates for APOE4+ males, Parietal cortex
DOI: 10.6084/m9.figshare.7842215
title: Negative gene correlates for APOE4+ males Frontal white matter

description: Negative gene correlates for APOE4+ males, Frontal white matter
DOI: 10.6084/m9.figshare.7842221.v1
title: Negative gene correlates for APOE4+ males Parietal cortex

description: Negative gene correlates for APOE4+ males, Parietal cortex
DOI: 10.6084/m9.figshare.7842191.v1
title: Positive gene correlates for APOE4+ males Parietal cortex

description: Positive gene correlates for APOE4+ males, Parietal cortex
DOI: 10.6084/m9.figshare.7842218.v1
title: Negative gene correlates for APOE4+ males Hippocampus

description: Negative gene correlates for APOE4+ males, Hippocampus
DOI: 10.6084/m9.figshare.7842182
title: Positive gene correlates for APOE4+ males Frontal white matter

description: Positive gene correlates for APOE4+ males, Frontal white matter
DOI: 10.6084/m9.figshare.7842185
title: Positive gene correlates for APOE4+ males Hippocampus

description: Positive gene correlates for APOE4+ males, Hippocampus
DOI: 10.6084/m9.figshare.7842215.v1
title: Negative gene correlates for APOE4+ males Frontal white matter

description: Negative gene correlates for APOE4+ males, Frontal white matter
DOI: 10.6084/m9.figshare.7842143
title: Supplementary Material for: The Impact of Norms on the Outcome of Children Born Very-Preterm when Using the Bayley-III: Differences between US and German Norms

description: <b><i>Background:</i></b> The Bayley Scales of Infant and Toddler Development, third edition (Bayley-III) are widely used to assess the development of children born preterm. However, it is still unclear whether US norms are adequate for use in other populations. In 2014, the German version of the Bayley-III with German norms was published. <b><i>Objectives:</i></b> We aimed to compare the performance of very-preterm infants at one, two, and three years of age using the German versus US norms of the Bayley-III. <b><i>Methods:</i></b> All children born prior to 32 weeks of gestational age during 2012 and 2015 and taking part in the follow-up program of the Medical University of Vienna were assessed and scored according to both German and US norms by two expert clinical psychologists at the age of one, two, and three years of age. <b><i>Results:</i></b> In total, 843 tests were obtained from 450 children. When looking at scaled scores for cognitive, language, and motor outcomes, preterm children achieved significantly lower scores in nearly all subtests with the German as compared to the US norms. In addition, the proportion of impaired children scoring &lt; 1 standard deviation (SD) and &lt; 2 SD below the norm was significantly higher in nearly all subtests when using the German compared to the US norms (<i>p</i> &lt; 0.05). <b><i>Conclusions:</i></b> Applying German and US norms of the Bayley-III leads to different outcomes in very-preterm children, and these differences are statistically significant and clinically relevant. Thus, comparisons of outcomes of very-preterm children using culturally specific norms are problematic, and these findings have to be considered.
DOI: 10.6084/m9.figshare.7842182.v1
title: Positive gene correlates for APOE4+ males Frontal white matter

description: Positive gene correlates for APOE4+ males, Frontal white matter
DOI: 10.6084/m9.figshare.7842149.v1
title: SAMPLE 2 - BRAZILIAN JOURNAL QUALIS.pdf

description: Table of sample 2.
DOI: 10.6084/m9.figshare.7842071
title: metadata associated with the study

description: Site information and physiochemical properties of the soils used in this study<br> <br>
DOI: 10.6084/m9.figshare.7842029
title: Sequence files associated with the project study

description: NGS data generated after pyrosequencing an amplicon library generated after PCR amplification (18S rRNA gene) of DNA extracted from soil samples. These soil samples were taken from native forests and adjacent monoculture rubber plantations in Yunnan, China.
DOI: 10.6084/m9.figshare.7842071.v1
title: metadata associated with the study

description: Site information and physiochemical properties of the soils used in this study<br> <br>
DOI: 10.6084/m9.figshare.7842026
title: The impact of the Green Revolution on the population structure of rice pathogens

description: Xanthomonas oryzae pv. oryzae genomes in genbank format
DOI: 10.6084/m9.figshare.7842029.v1
title: Sequence files associated with the project study

description: NGS data generated after pyrosequencing an amplicon library generated after PCR amplification (18S rRNA gene) of DNA extracted from soil samples. These soil samples were taken from native forests and adjacent monoculture rubber plantations in Yunnan, China.
DOI: 10.6084/m9.figshare.7842026.v1
title: The impact of the Green Revolution on the population structure of rice pathogens

description: Xanthomonas oryzae pv. oryzae genomes in genbank format
DOI: 10.6084/m9.figshare.7841432
title: Dataset for: Prioritized Concordance Index for Hierarchical Survival Outcomes

description: We propose an extension of Harrell's concordance (C) index to evaluate the prognostic utility of biomarkers for diseases with multiple measurable outcomes that can be prioritized. Our prioritized concordance index measures the probability that, given a random subject pair, the subject with the worst disease status as of a time $\tau$ has the higher predicted risk. Our prioritized concordance index uses the same approach as the win-ratio, by basing generalized pairwise comparisons on the most severe or clinically important comparable outcome. We use an inverse probability weighting technique to correct for study-specific censoring. Asymptotic properties are derived using U-statistic properties. We apply the prioritized concordance index to two types of disease processes with a rare primary outcome and a more common secondary outcome. Our simulation studies show that when a predictor is predictive of both outcomes, the new concordance index can gain efficiency and power in identifying true prognostic variables compared to using the primary outcome alone. Using the prioritized concordance index, we examine whether novel clinical measures can be useful in predicting risk of type II diabetes in patients with impaired glucose resistance whose disease status can also regress to normal glucose resistance. We also examine the discrimination ability of four published risk models among ever-smokers at risk of lung-cancer incidence and subsequent death.
DOI: 10.6084/m9.figshare.7841426.v2
title: Supplemental material for Androga et al. 2019 Anaerobe

description: Supplemental material for Androga et al. 2019 Anaerobe Manuscript: annotated assemblies for 53 Clostridium difficile strains
DOI: 10.6084/m9.figshare.7841411
title: gVCF_HG00097

description: 1000 Genomes gVCF mapped to hs37d5 for HG00097.
DOI: 10.6084/m9.figshare.7841411.v1
title: gVCF_HG00097

description: 1000 Genomes gVCF mapped to hs37d5 for HG00097.