cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6119486
title: Additional file 8: of Reproducible protocols for metagenomic analysis of human faecal phageomes

description: Table S4. Details on Adonis (PERMANOVA) test output. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6119486.v1
title: Additional file 8: of Reproducible protocols for metagenomic analysis of human faecal phageomes

description: Table S4. Details on Adonis (PERMANOVA) test output. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6119456
title: Additional file 7 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: Consensus gene regulatory network. Rows of the matrix represent 5113 response variables (signature genes); columns represent 1007 predictors (transcription factors + gene-specific copy number). A cellâ s value shows how many times the link from the respective predictor gene to the respective response gene was present across the 100 cross-validation iterations. Negative values indicate repressing links and positive values indicate activating links. (TXT 10209 kb)
DOI: 10.6084/m9.figshare.6119456.v1
title: Additional file 7 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: Consensus gene regulatory network. Rows of the matrix represent 5113 response variables (signature genes); columns represent 1007 predictors (transcription factors + gene-specific copy number). A cellâ s value shows how many times the link from the respective predictor gene to the respective response gene was present across the 100 cross-validation iterations. Negative values indicate repressing links and positive values indicate activating links. (TXT 10209 kb)
DOI: 10.6084/m9.figshare.6119441
title: MOESM5 of Stromal TRIM28-associated signaling pathway modulation within the colorectal cancer microenvironment

description: Additional file 5: Table S4. Significant Spearman’s Rho correlations from RPPA measurements of epithelial cells.
DOI: 10.6084/m9.figshare.6119441.v1
title: MOESM5 of Stromal TRIM28-associated signaling pathway modulation within the colorectal cancer microenvironment

description: Additional file 5: Table S4. Significant Spearman’s Rho correlations from RPPA measurements of epithelial cells.
DOI: 10.6084/m9.figshare.6119438
title: Additional file 6 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: 1006 transcription factors of the gene signature. (XLSX 92.4 kb)
DOI: 10.6084/m9.figshare.6119438.v1
title: Additional file 6 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: 1006 transcription factors of the gene signature. (XLSX 92.4 kb)
DOI: 10.6084/m9.figshare.6119435
title: Additional file 5: of Reproducible protocols for metagenomic analysis of human faecal phageomes

description: Table S3. DESeq2 test results for differential abundance of putative phage contigs in six faecal samples processed three different operators (O1, O2 and O3). (XLSX 730 kb)
DOI: 10.6084/m9.figshare.6119435.v1
title: Additional file 5: of Reproducible protocols for metagenomic analysis of human faecal phageomes

description: Table S3. DESeq2 test results for differential abundance of putative phage contigs in six faecal samples processed three different operators (O1, O2 and O3). (XLSX 730 kb)
DOI: 10.6084/m9.figshare.6119420
title: MOESM4 of Stromal TRIM28-associated signaling pathway modulation within the colorectal cancer microenvironment

description: Additional file 4: Table S3. Significant Spearman’s Rho correlations from RPPA measurements of stromal cells.
DOI: 10.6084/m9.figshare.6119420.v1
title: MOESM4 of Stromal TRIM28-associated signaling pathway modulation within the colorectal cancer microenvironment

description: Additional file 4: Table S3. Significant Spearman’s Rho correlations from RPPA measurements of stromal cells.
DOI: 10.6084/m9.figshare.6119414
title: Additional file 5 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: 104 signature genes differentially expressed between tumor grades II and III. (XLSX 13.7 kb)
DOI: 10.6084/m9.figshare.6119414.v1
title: Additional file 5 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: 104 signature genes differentially expressed between tumor grades II and III. (XLSX 13.7 kb)
DOI: 10.6084/m9.figshare.6119408
title: Additional file 2: of Epidemiology of Sanfilippo syndrome: results of a systematic literature review

description: STROBE Checklist for observational studies. (XLSX 82ย�kb)
DOI: 10.6084/m9.figshare.6119408.v1
title: Additional file 2: of Epidemiology of Sanfilippo syndrome: results of a systematic literature review

description: STROBE Checklist for observational studies. (XLSX 82ย�kb)
DOI: 10.6084/m9.figshare.6119390
title: Additional file 4 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: Normalized expression values of 5113 signature genes. (TXT 6266 kb)
DOI: 10.6084/m9.figshare.6119390.v1
title: Additional file 4 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: Normalized expression values of 5113 signature genes. (TXT 6266 kb)
DOI: 10.6084/m9.figshare.6119372
title: Additional file 2: of Reproducible protocols for metagenomic analysis of human faecal phageomes

description: Table S2. Description of faecal samples used in the study and summary of nucleic acid extraction and sequencing results. (XLSX 161 kb)
DOI: 10.6084/m9.figshare.6119372.v1
title: Additional file 2: of Reproducible protocols for metagenomic analysis of human faecal phageomes

description: Table S2. Description of faecal samples used in the study and summary of nucleic acid extraction and sequencing results. (XLSX 161 kb)
DOI: 10.6084/m9.figshare.6119366
title: MOESM2 of Stromal TRIM28-associated signaling pathway modulation within the colorectal cancer microenvironment

description: Additional file 2: Table S2.
DOI: 10.6084/m9.figshare.6119366.v1
title: MOESM2 of Stromal TRIM28-associated signaling pathway modulation within the colorectal cancer microenvironment

description: Additional file 2: Table S2.
DOI: 10.6084/m9.figshare.6119357
title: Additional file 1: of Reproducible protocols for metagenomic analysis of human faecal phageomes

description: Table S1. Comparison of methods used in published metagenomic studies of viral communities associated with various sites in the human body. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.6119357.v1
title: Additional file 1: of Reproducible protocols for metagenomic analysis of human faecal phageomes

description: Table S1. Comparison of methods used in published metagenomic studies of viral communities associated with various sites in the human body. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.6119351
title: MOESM1 of Stromal TRIM28-associated signaling pathway modulation within the colorectal cancer microenvironment

description: Additional file 1: Table S1.
DOI: 10.6084/m9.figshare.6119351.v1
title: MOESM1 of Stromal TRIM28-associated signaling pathway modulation within the colorectal cancer microenvironment

description: Additional file 1: Table S1.
DOI: 10.6084/m9.figshare.6119342
title: Additional file 2 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: Gene copy number and gene expression data of oligodendrogliomas and gene expression data of normal brain references. (XLSX 35942 kb)
DOI: 10.6084/m9.figshare.6119342.v1
title: Additional file 2 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: Gene copy number and gene expression data of oligodendrogliomas and gene expression data of normal brain references. (XLSX 35942 kb)
DOI: 10.6084/m9.figshare.6119324
title: Additional file 1 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: Oligodendroglioma TCGA identifiers and survival information. (XLSX 14.1 kb)
DOI: 10.6084/m9.figshare.6119324.v1
title: Additional file 1 of Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups

description: Oligodendroglioma TCGA identifiers and survival information. (XLSX 14.1 kb)
DOI: 10.6084/m9.figshare.6119291
title: Additional file 2: of Effect of β-hydroxy-β-methylbutyrate on miRNA expression in differentiating equine satellite cells exposed to hydrogen peroxide

description: Table S2. Biological function of differentially expressed genes (DEG). (XLSX 28 kb)
DOI: 10.6084/m9.figshare.6119291.v1
title: Additional file 2: of Effect of β-hydroxy-β-methylbutyrate on miRNA expression in differentiating equine satellite cells exposed to hydrogen peroxide

description: Table S2. Biological function of differentially expressed genes (DEG). (XLSX 28 kb)
DOI: 10.6084/m9.figshare.6119267
title: Additional file 1: of Effect of β-hydroxy-β-methylbutyrate on miRNA expression in differentiating equine satellite cells exposed to hydrogen peroxide

description: Table S1. Genes differentially expressed in HMB-incubated equine satellite cells exposed to H2O2, compared to control. FDR ≤ 0.05, FC ≥ 1.3, n = 4. (XLSX 550 kb)
DOI: 10.6084/m9.figshare.6119267.v1
title: Additional file 1: of Effect of β-hydroxy-β-methylbutyrate on miRNA expression in differentiating equine satellite cells exposed to hydrogen peroxide

description: Table S1. Genes differentially expressed in HMB-incubated equine satellite cells exposed to H2O2, compared to control. FDR ≤ 0.05, FC ≥ 1.3, n = 4. (XLSX 550 kb)
DOI: 10.6084/m9.figshare.6119255
title: Additional file 9: of Characterizing oral microbial communities across dentition states and colonization niches

description: Table S5. Relative abundances of species level operational taxonomic units (s-OTUs) in the subgingivalÂ microbiome. Values are represented as a percent with standard deviations. (XLSX 73Â kb)
DOI: 10.6084/m9.figshare.6119255.v1
title: Additional file 9: of Characterizing oral microbial communities across dentition states and colonization niches

description: Table S5. Relative abundances of species level operational taxonomic units (s-OTUs) in the subgingivalÂ microbiome. Values are represented as a percent with standard deviations. (XLSX 73Â kb)
DOI: 10.6084/m9.figshare.6119225
title: Additional file 7: of Characterizing oral microbial communities across dentition states and colonization niches

description: Table S3. Predicted functionsÂ in the salivary, supragingival and subgingival microbiomes. Values are represented as a percent abundance. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.6119225.v1
title: Additional file 7: of Characterizing oral microbial communities across dentition states and colonization niches

description: Table S3. Predicted functionsÂ in the salivary, supragingival and subgingival microbiomes. Values are represented as a percent abundance. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.6119198
title: Additional file 5: of Characterizing oral microbial communities across dentition states and colonization niches

description: Table S4. Relative abundances of species level operational taxonomic units (s-OTUs) in the supragingivalÂ microbiome. Values are represented as a percent with standard deviations. (XLSX 62Â kb)
DOI: 10.6084/m9.figshare.6119198.v1
title: Additional file 5: of Characterizing oral microbial communities across dentition states and colonization niches

description: Table S4. Relative abundances of species level operational taxonomic units (s-OTUs) in the supragingivalÂ microbiome. Values are represented as a percent with standard deviations. (XLSX 62Â kb)
DOI: 10.6084/m9.figshare.6119177
title: Additional file 4: of Characterizing oral microbial communities across dentition states and colonization niches

description: Table S2. Relative abundances of species level operational taxonomic units (s-OTUs) in the salivary microbiome. Values are represented as a percent with standard deviations. (XLSX 73Â kb)
DOI: 10.6084/m9.figshare.6119177.v1
title: Additional file 4: of Characterizing oral microbial communities across dentition states and colonization niches

description: Table S2. Relative abundances of species level operational taxonomic units (s-OTUs) in the salivary microbiome. Values are represented as a percent with standard deviations. (XLSX 73Â kb)
DOI: 10.6084/m9.figshare.6119111
title: Additional file 1: of Characterizing oral microbial communities across dentition states and colonization niches

description: Table S1. Demographic and clinicalÂ data of subjects participating in study. (XLSX 59Â kb)
DOI: 10.6084/m9.figshare.6119111.v1
title: Additional file 1: of Characterizing oral microbial communities across dentition states and colonization niches

description: Table S1. Demographic and clinicalÂ data of subjects participating in study. (XLSX 59Â kb)
DOI: 10.6084/m9.figshare.6118967.v3
title: Variasi model bisnis pengelolaan jurnal berdasarkan komponen pendanaan dan modus akses

description: Variasi model bisnis pengelolaan jurnal berdasarkan komponen pendanaan dan modus akses (ID). Variation of journal's business model based on funding and access mode components (EN). <br><br>This image is to explain the variation of funding model and access mode of various existing journals.<br><br>I made with Draw.io (https://draw.io).The repository consists of 3 files: diagram_OA2.png (transparent PNG file), diagram_OA.png (non-transparent PNG), diagram_OA.html (source html file).<br><br>You may reuse, modify, and remix this image using the html source file.<br>
DOI: 10.6084/m9.figshare.6118967.v2
title: Variasi model bisnis pengelolaan jurnal berdasarkan komponen pendanaan dan modus akses

description: Variasi model bisnis pengelolaan jurnal berdasarkan komponen pendanaan dan modus akses (ID). Variation of journal's business model based on funding and access mode components (EN). <br><br>This image is to explain the variation of funding model and access mode of various existing journals.<br><br>I made with Draw.io (https://draw.io).The repository consists of 3 files: diagram_OA2.png (transparent PNG file), diagram_OA.png (non-transparent PNG), diagram_OA.html (source html file).<br><br>You may reuse, modify, and remix this image using the html source file.<br>
DOI: 10.6084/m9.figshare.6118796
title: CT scans accompanying the paper: Fostoria dhimbangunmal gen. et sp. nov., a new iguanodontian (Dinosauria, Ornithopoda) from the mid-Cretaceous of Lightning Ridge, NSW, Australia.

description: .stl and 3D pdf files of skeletal elements (including skull roof, ischium, tibia, dorsal vertebra, metatarsal II, caudal neural arch, rib) and 3D pdf of quadrate of <i>Fostoria dhimbangunmal</i> (Ornithischia, Iguanodontia), from the Cenomanian Griman Creek Formation at Lightning Ridge, New South Wales, Australia.<br>
DOI: 10.6084/m9.figshare.6118676
title: China multi-regional input-output (MRIO) table 2012_V2.xlsx

description: We utilised the latest socioeconomic datasets to compile China MRIO table for 2012 based on the modified gravity model. The MRIO table provides economic flows among China’s 30 regions with 30 economic sectors in each region. For more information, please contact with Dr Zhifu Mi, University College London (Email: z.mi@ucl.ac.uk).
DOI: 10.6084/m9.figshare.6118562
title: Climate-smart sustainable agriculture in low-to-intermediate shade agroforests

description: Results of an extensive field study to understand the balance of the costs and benefits of cocoa agroforests in Ghana. Over a period of two years (2015-2017), including one normal and one exceptionally dry year, we measured cocoa production, losses to disease, soil fertility, temperature, relative humidity, soil moisture, carbon stocks, and biodiversity of multiple taxa in 20 cocoa agroforest plots (30x30 m) selected systematically along a gradient of shade-tree cover (14-76% shade-tree cover) in a globally-significant cocoa growing region in Ghana, West Africa. To isolate the effects of shade trees from confounding factors such as differences in farm management, soil type, and local microclimate, all plots were compared with paired monoculture plots on the same farms. Full methods are published in Blaser et <i>al.</i> 2018 Nature Sustainability.
DOI: 10.6084/m9.figshare.6118562.v2
title: Climate-smart sustainable agriculture in low-to-intermediate shade agroforests

description: Results of an extensive field study to understand the balance of the costs and benefits of cocoa agroforests in Ghana. Over a period of two years (2015-2017), including one normal and one exceptionally dry year, we measured cocoa production, losses to disease, soil fertility, temperature, relative humidity, soil moisture, carbon stocks, and biodiversity of multiple taxa in 20 cocoa agroforest plots (30x30 m) selected systematically along a gradient of shade-tree cover (14-76% shade-tree cover) in a globally-significant cocoa growing region in Ghana, West Africa. To isolate the effects of shade trees from confounding factors such as differences in farm management, soil type, and local microclimate, all plots were compared with paired monoculture plots on the same farms. Full methods are published in Blaser et <i>al.</i> 2018 Nature Sustainability.
DOI: 10.6084/m9.figshare.6118553
title: Simonin et al (2018) Ecological Applications - Raw data.xlsx

description: Dataset from the publication "Engineered nanoparticles interact with nutrients to intensify eutrophication in a wetland ecosystem experiment" by Simonin et al. (2018) published in Ecological Applications
DOI: 10.6084/m9.figshare.6118550
title: Data_Cortex_Mice_77proteins.xlsx

description: Protein Expression Levels of 77 Proteins from Control and Ts65Dn Mice. <br>First column shows mouse id. <br>From each mice, 15 samples, three replicates of a five-point dilution series, were obtained.<br>After first column, subsequent 77 columns represent protein expression data.<br>Last four columns indicate: Genotype (control (c) or trisomy(t)), Treatment (memantine or saline), Behavior (context-shock (C/S) or shock-context (S/C)) and the class of mice according to the three features (c-CS-s, c-CS-m, c-SC-s, c-SC-m, c-SC-s, t-CS-s, t-CS-m, t-SC-s, t-SC-m, t-SC-s ). <br>These data are a subset of those used inAhmed et al. PLoS ONE. 2015;10(3):e0119 491. doi:10.1371/journal.pone.0119491.<br>
DOI: 10.6084/m9.figshare.6118553.v1
title: Simonin et al (2018) Ecological Applications - Raw data.xlsx

description: Dataset from the publication "Engineered nanoparticles interact with nutrients to intensify eutrophication in a wetland ecosystem experiment" by Simonin et al. (2018) published in Ecological Applications
DOI: 10.6084/m9.figshare.6118550.v1
title: Data_Cortex_Mice_77proteins.xlsx

description: Protein Expression Levels of 77 Proteins from Control and Ts65Dn Mice. <br>First column shows mouse id. <br>From each mice, 15 samples, three replicates of a five-point dilution series, were obtained.<br>After first column, subsequent 77 columns represent protein expression data.<br>Last four columns indicate: Genotype (control (c) or trisomy(t)), Treatment (memantine or saline), Behavior (context-shock (C/S) or shock-context (S/C)) and the class of mice according to the three features (c-CS-s, c-CS-m, c-SC-s, c-SC-m, c-SC-s, t-CS-s, t-CS-m, t-SC-s, t-SC-m, t-SC-s ). <br>These data are a subset of those used inAhmed et al. PLoS ONE. 2015;10(3):e0119 491. doi:10.1371/journal.pone.0119491.<br>
DOI: 10.6084/m9.figshare.6118505
title: DBpedia Neural Question Answering (DBNQA) dataset

description: This resource contains a large and comprehensive dataset of 894,499 pairs of questions and SPARQL queries, materialized using the NSpMT.
DOI: 10.6084/m9.figshare.6118505.v1
title: Question-NSpM SPARQL dataset (EN)

description: This resource contains a large and comprehensive dataset of 894,499 pairs of questions and SPARQL queries, materialized using the NSpMT.
DOI: 10.6084/m9.figshare.6118460
title: Supplemental table 1 from Assessment of stem cell differentiation based on genome-wide expression profiles

description: In recent years, protocols have been established to differentiate stem and precursor cells into more mature cell types. However, progress in this field has been hampered by difficulties to assess the differentiation status of stem cell-derived cells in an unbiased manner. Here, we present an analysis pipeline based on published data and methods to quantify the degree of differentiation and to identify transcriptional control factors explaining differences to the intended target cells or tissues. The pipeline requires RNA-seq or gene array data of the stem cell starting population, derived ‘mature’ cells and primary target cells or tissue. It consists of a principle component analysis to represent global expression changes and to identify possible problems of the dataset that require special attention, such as batch effects; clustering techniques to identify gene groups with similar features; over-representation analysis to characterize biological motifs and transcriptional control factors of the identified gene clusters; and metagenes as well as gene regulatory networks for quantitative cell-type assessment and identification of influential transcription factors. Possibilities and limitations of the analysis pipeline are illustrated using the example of human embryonic stem cell and human induced pluripotent cells to generate ‘hepatocyte-like cells'. The pipeline quantifies the degree of incomplete differentiation as well as remaining stemness and identifies unwanted features, such as colon- and fibroblast-associated gene clusters that are absent in real hepatocytes but typically induced by currently available differentiation protocols. Finally, transcription factors responsible for incomplete and unwanted differentiation are identified. The proposed method is widely applicable and allows an unbiased and quantitative assessment of stem cell-derived cells.This article is part of the themed issue ‘Designer human tissue: coming to a lab near you’.