cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8240465.v1
title: Additional file 3: of Airway host-microbiome interactions in chronic obstructive pulmonary disease

description: Cross associations among microbiome (9 microbiome genera and Shannon diversity), host transcriptome (9 tPCs) and proteome (8 pPCs) data both across all samples and within stable samples in the multivariate analysis. FDR P-values are indicated in the table. Significant positive correlations are highlighted in red. Significant negative correlations are highlighted in blue. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8240456.v1
title: Additional file 2: of Airway host-microbiome interactions in chronic obstructive pulmonary disease

description: a. MetaCore pathways significantly enriched for differential expressed genes (DEGs) between stable and exacerbations (FDR P ≤ 0.01). b. Significantly differentially expressed proteins between sputum samples of COPD ex-smokers and current smokers (Wilcoxon, FDR P ≤ 0.05). (XLSX 68 kb)
DOI: 10.6084/m9.figshare.8240444
title: Additional file 4: of A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

description: Sinularia specimen data. Table of specimen data with morphospecies identifications and assigned species delimitations based on MOTUs and RADSeq data. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8240441
title: Additional file 3: of A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

description: ABBA-BABA test results. Results of ABBA-BABA tests for both clades 4 and 5C. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.8240444.v1
title: Additional file 4: of A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

description: Sinularia specimen data. Table of specimen data with morphospecies identifications and assigned species delimitations based on MOTUs and RADSeq data. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8240432
title: Additional file 2: of A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

description: ABBA-BABA tests. List of ABBA-BABA tests performed in ipyRAD. (TXT 13 kb)
DOI: 10.6084/m9.figshare.8240432.v1
title: Additional file 2: of A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

description: ABBA-BABA tests. List of ABBA-BABA tests performed in ipyRAD. (TXT 13 kb)
DOI: 10.6084/m9.figshare.8240441.v1
title: Additional file 3: of A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

description: ABBA-BABA test results. Results of ABBA-BABA tests for both clades 4 and 5C. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.8240420
title: Additional file 1: of A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

description: Figure S1. ML trees of barcode data. ML phylogenies generated using mtMutS and 28S rDNA barcode data. Figure S2. ML tree of combined barcode data. ML phylogeny generated using a mtMutS + 28S rDNA dataset. Figure S3. BIC plots. Bayesian Information Criteria indicating optimal number of K clusters. Figure S4. Probability of membership plot for Clade 4. Individual reassignments based on discriminant functions. Figure S5. Probability of membership plot for Clade 5C. Individual reassignments based on discriminant functions. Figure S6. Character based barcodes. Species-diagnostic nucleotide characters. Figure S7. Optimal a-scores. A-scores indicate the optimal number of principal components to retain. Figure S8. Discriminant analysis eigenvalues. Total number of discriminant eigenvalues retained. Figure S9. Clade 4 species models and RAxML phylogeny. Species models used in BFD* analysis with phylogeny constructed using RAxML on RADSeq data. Figure S10. Clade 5C species models and RAxML phylogeny. Species models used in BFD* analysis with phylogeny constructed using RAxML on RADSeq data. (ZIP 22000 kb)
DOI: 10.6084/m9.figshare.8240420.v1
title: Additional file 1: of A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals

description: Figure S1. ML trees of barcode data. ML phylogenies generated using mtMutS and 28S rDNA barcode data. Figure S2. ML tree of combined barcode data. ML phylogeny generated using a mtMutS + 28S rDNA dataset. Figure S3. BIC plots. Bayesian Information Criteria indicating optimal number of K clusters. Figure S4. Probability of membership plot for Clade 4. Individual reassignments based on discriminant functions. Figure S5. Probability of membership plot for Clade 5C. Individual reassignments based on discriminant functions. Figure S6. Character based barcodes. Species-diagnostic nucleotide characters. Figure S7. Optimal a-scores. A-scores indicate the optimal number of principal components to retain. Figure S8. Discriminant analysis eigenvalues. Total number of discriminant eigenvalues retained. Figure S9. Clade 4 species models and RAxML phylogeny. Species models used in BFD* analysis with phylogeny constructed using RAxML on RADSeq data. Figure S10. Clade 5C species models and RAxML phylogeny. Species models used in BFD* analysis with phylogeny constructed using RAxML on RADSeq data. (ZIP 22000 kb)
DOI: 10.6084/m9.figshare.8240405
title: Additional file 9: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S9. Genes targeted by selected 8 miRNAs along with the list of targeting miRNAs. Experimentally validated and predicted targets have been summarized in this table showing results of in silico analysis. (XLSX 164 kb)
DOI: 10.6084/m9.figshare.8240402
title: Additional file 8: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S8. Genes targeted by selected 8 miRNAs along with the list of targeting miRNAs. Only experimentally validated targets have been summarized in this table showing results of in silico analysis. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8240402.v1
title: Additional file 8: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S8. Genes targeted by selected 8 miRNAs along with the list of targeting miRNAs. Only experimentally validated targets have been summarized in this table showing results of in silico analysis. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8240405.v1
title: Additional file 9: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S9. Genes targeted by selected 8 miRNAs along with the list of targeting miRNAs. Experimentally validated and predicted targets have been summarized in this table showing results of in silico analysis. (XLSX 164 kb)
DOI: 10.6084/m9.figshare.8240396
title: Additional file 7: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S7. Results of pairwise comparisons between the three groups in qPCR validation. AVG average, DNET dysembryoplastic neuroepithelial tumor, FC fold change, FDR false discovery rate, GG ganglioglioma, PA pilocytic astrocytoma, SD standard deviation. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8240396.v1
title: Additional file 7: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S7. Results of pairwise comparisons between the three groups in qPCR validation. AVG average, DNET dysembryoplastic neuroepithelial tumor, FC fold change, FDR false discovery rate, GG ganglioglioma, PA pilocytic astrocytoma, SD standard deviation. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8240387
title: Additional file 6: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S6. Transformed delta Ct (2^-dCt) values of miRNAs expression obtained in validation stage. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8240378
title: Additional file 5: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S5. List of miRNAs differentially expressed in BRAFV600E mutated and wild type cases (GG12, GG25, GG28, GG33, GG55). Negative fold change indicates downregulation in mutated cases. miRNAs selected for validation has been appended to the Table. FC fold change, FDR false detection rate. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8240387.v1
title: Additional file 6: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S6. Transformed delta Ct (2^-dCt) values of miRNAs expression obtained in validation stage. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8240372
title: Additional file 4: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S4. Results of microarray data pairwise comparisons between the three groups. AVG average, DNET dysembryoplastic neuroepithelial tumor, FC fold change, FDR false discovery rate, GG ganglioglioma, PA pilocytic astrocytoma, SD standard deviation. (XLSX 182 kb)
DOI: 10.6084/m9.figshare.8240378.v1
title: Additional file 5: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S5. List of miRNAs differentially expressed in BRAFV600E mutated and wild type cases (GG12, GG25, GG28, GG33, GG55). Negative fold change indicates downregulation in mutated cases. miRNAs selected for validation has been appended to the Table. FC fold change, FDR false detection rate. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8240369
title: Additional file 3: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S3. Log2-transformed expression data of samples assessed using microarrays in profiling stage. DNET dysembryoplastic neuroepithelial tumor, GG ganglioglioma, PA pilocytic astrocytoma. (XLSX 1599 kb)
DOI: 10.6084/m9.figshare.8240372.v1
title: Additional file 4: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S4. Results of microarray data pairwise comparisons between the three groups. AVG average, DNET dysembryoplastic neuroepithelial tumor, FC fold change, FDR false discovery rate, GG ganglioglioma, PA pilocytic astrocytoma, SD standard deviation. (XLSX 182 kb)
DOI: 10.6084/m9.figshare.8240363
title: Additional file 2: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S2. Configuration of hyperparameters set a priori for modelling in WEKA software. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8240366
title: MOESM3 of Human monocyte-to-macrophage differentiation involves highly localized gain and loss of DNA methylation at transcription factor binding sites

description: Additional file 3: Table S3 Chromatin states in monocytes and macrophages. Chromatin states in both monocytes and macrophages defined using a hidden Markov model based on H3K4me1, H3K4me3, H3K27ac and H3K27me3 histone marks available from public BLUEPRINT data.
DOI: 10.6084/m9.figshare.8240363.v1
title: Additional file 2: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S2. Configuration of hyperparameters set a priori for modelling in WEKA software. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8240369.v1
title: Additional file 3: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S3. Log2-transformed expression data of samples assessed using microarrays in profiling stage. DNET dysembryoplastic neuroepithelial tumor, GG ganglioglioma, PA pilocytic astrocytoma. (XLSX 1599 kb)
DOI: 10.6084/m9.figshare.8240366.v1
title: MOESM3 of Human monocyte-to-macrophage differentiation involves highly localized gain and loss of DNA methylation at transcription factor binding sites

description: Additional file 3: Table S3 Chromatin states in monocytes and macrophages. Chromatin states in both monocytes and macrophages defined using a hidden Markov model based on H3K4me1, H3K4me3, H3K27ac and H3K27me3 histone marks available from public BLUEPRINT data.
DOI: 10.6084/m9.figshare.8240357
title: MOESM2 of Human monocyte-to-macrophage differentiation involves highly localized gain and loss of DNA methylation at transcription factor binding sites

description: Additional file 2: Table S2 Differentially methylated CpGs (DMCs). The table includes all 5870 DMCs with the characteristics for each position. Column 1: CpG identifier, Column 2-4: Effect size (mean squares), F-statistic and P-value of the overall effect, Column 5-10: Partial t-statistics for monocytes, macrophages and activated macrophages (LPS/IFNÎł, IL-4, oxLDL and acLDL), Column 11: Cell type contributing most to the overall effect based on partial t-statistics, Column 12: Gain or loss of methylation during monocyte-to-macrophage differentiation or during subsequent macrophage activation, Column 13: Nearest gene, Column 14-15: Transcription levels of nearest gene in monocytes and macrophages (logTPM), Column 16-17: Chromatin states in monocytes and macrophages based on histone modifications, Column 18-20: Number, length (bp) and mean methylation (%) of differentially methylated CpGs in region (DMR), Column 21-22: Overlap with DNAseI hypersensitive sites in monocytes and macrophages.
DOI: 10.6084/m9.figshare.8240354
title: Additional file 1: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S1. Tumor detailed characteristics. * indicates samples used in profiling experiment, *^ indicates samples included both in profiling and validation cohort. DNET dysembryoplastic neuroepithelial tumor, GG ganglioglioma, PA pilocytic astrocytoma. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8240357.v1
title: MOESM2 of Human monocyte-to-macrophage differentiation involves highly localized gain and loss of DNA methylation at transcription factor binding sites

description: Additional file 2: Table S2 Differentially methylated CpGs (DMCs). The table includes all 5870 DMCs with the characteristics for each position. Column 1: CpG identifier, Column 2-4: Effect size (mean squares), F-statistic and P-value of the overall effect, Column 5-10: Partial t-statistics for monocytes, macrophages and activated macrophages (LPS/IFNÎł, IL-4, oxLDL and acLDL), Column 11: Cell type contributing most to the overall effect based on partial t-statistics, Column 12: Gain or loss of methylation during monocyte-to-macrophage differentiation or during subsequent macrophage activation, Column 13: Nearest gene, Column 14-15: Transcription levels of nearest gene in monocytes and macrophages (logTPM), Column 16-17: Chromatin states in monocytes and macrophages based on histone modifications, Column 18-20: Number, length (bp) and mean methylation (%) of differentially methylated CpGs in region (DMR), Column 21-22: Overlap with DNAseI hypersensitive sites in monocytes and macrophages.
DOI: 10.6084/m9.figshare.8240354.v1
title: Additional file 1: of Expression-based decision tree model reveals distinct microRNA expression pattern in pediatric neuronal and mixed neuronal-glial tumors

description: Table S1. Tumor detailed characteristics. * indicates samples used in profiling experiment, *^ indicates samples included both in profiling and validation cohort. DNET dysembryoplastic neuroepithelial tumor, GG ganglioglioma, PA pilocytic astrocytoma. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8240342
title: Additional file 4: of A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency

description: Table S4. Common differentially expressed genes in liver & muscle. This table lists the genes that were differentially expressed in both liver and muscle. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8240336
title: Additional file 3. of A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency

description: Table S3. Differentially expressed genes in liver. This table lists the genes that were differentially expressed in liver. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.8240342.v1
title: Additional file 4: of A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency

description: Table S4. Common differentially expressed genes in liver & muscle. This table lists the genes that were differentially expressed in both liver and muscle. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8240330
title: Additional file 2: of A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency

description: Table S2. Differentially expressed genes in muscle. This table lists the genes that were differentially expressed in muscle. (XLSX 705 kb)
DOI: 10.6084/m9.figshare.8240336.v1
title: Additional file 3. of A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency

description: Table S3. Differentially expressed genes in liver. This table lists the genes that were differentially expressed in liver. (XLSX 118 kb)
DOI: 10.6084/m9.figshare.8240324
title: Additional file 1: of A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency

description: Table S1. Sequencing information. This file contains raw sequence, read alignment and gene annotation information. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8240330.v1
title: Additional file 2: of A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency

description: Table S2. Differentially expressed genes in muscle. This table lists the genes that were differentially expressed in muscle. (XLSX 705 kb)
DOI: 10.6084/m9.figshare.8240324.v1
title: Additional file 1: of A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency

description: Table S1. Sequencing information. This file contains raw sequence, read alignment and gene annotation information. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8240285
title: Additional file 5: of The USA lags behind other agricultural nations in banning harmful pesticides

description: Total use of pesticides in the USA in 2016 that are banned, being phased out or not approved in other agricultural nations. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.8240279
title: Additional file 4: of The USA lags behind other agricultural nations in banning harmful pesticides

description: Total pesticide use in the USA in 2016 itemized by active ingredient. (XLSX 14860 kb)
DOI: 10.6084/m9.figshare.8240285.v1
title: Additional file 5: of The USA lags behind other agricultural nations in banning harmful pesticides

description: Total use of pesticides in the USA in 2016 that are banned, being phased out or not approved in other agricultural nations. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.8240270
title: Additional file 2: of The USA lags behind other agricultural nations in banning harmful pesticides

description: Sources used to compile the final list of agricultural pesticides. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.8240273
title: Additional file 3: of The USA lags behind other agricultural nations in banning harmful pesticides

description: Approval status of agricultural pesticides in the USA, EU, China and Brazil. (XLSX 133 kb)
DOI: 10.6084/m9.figshare.8240279.v1
title: Additional file 4: of The USA lags behind other agricultural nations in banning harmful pesticides

description: Total pesticide use in the USA in 2016 itemized by active ingredient. (XLSX 14860 kb)
DOI: 10.6084/m9.figshare.8240270.v1
title: Additional file 2: of The USA lags behind other agricultural nations in banning harmful pesticides

description: Sources used to compile the final list of agricultural pesticides. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.8240273.v1
title: Additional file 3: of The USA lags behind other agricultural nations in banning harmful pesticides

description: Approval status of agricultural pesticides in the USA, EU, China and Brazil. (XLSX 133 kb)
DOI: 10.6084/m9.figshare.8240258
title: Additional file 2: of Coding algorithms for defining Charlson and Elixhauser co-morbidities in Read-coded databases

description: Read codes for Elixhauser co-morbidities. (CSV 513 kb)
DOI: 10.6084/m9.figshare.8240249
title: Additional file 1: of Coding algorithms for defining Charlson and Elixhauser co-morbidities in Read-coded databases

description: Read codes for Charlson co-morbidities. (CSV 417 kb)
DOI: 10.6084/m9.figshare.8240258.v1
title: Additional file 2: of Coding algorithms for defining Charlson and Elixhauser co-morbidities in Read-coded databases

description: Read codes for Elixhauser co-morbidities. (CSV 513 kb)
DOI: 10.6084/m9.figshare.8240249.v1
title: Additional file 1: of Coding algorithms for defining Charlson and Elixhauser co-morbidities in Read-coded databases

description: Read codes for Charlson co-morbidities. (CSV 417 kb)
DOI: 10.6084/m9.figshare.8240120
title: Additional file 3: of What determines host specificity in hyperspecialized plant parasitic nematodes?

description: Table S2. Homozygous non-synonymous predicted variants in non-PCN populations that were located on a loci under selection; * mark known effector genes. SeqID and Gene description corresponds to sequences ID and annotation of G. rostochiensis reference transcriptome (nGr.v1.1). (XLSX 53 kb)
DOI: 10.6084/m9.figshare.8240120.v1
title: Additional file 3: of What determines host specificity in hyperspecialized plant parasitic nematodes?

description: Table S2. Homozygous non-synonymous predicted variants in non-PCN populations that were located on a loci under selection; * mark known effector genes. SeqID and Gene description corresponds to sequences ID and annotation of G. rostochiensis reference transcriptome (nGr.v1.1). (XLSX 53 kb)
DOI: 10.6084/m9.figshare.8240111
title: Additional file 2: of What determines host specificity in hyperspecialized plant parasitic nematodes?

description: Table S1. Differentially expressed genes (DEG, PÂ
DOI: 10.6084/m9.figshare.8240111.v1
title: Additional file 2: of What determines host specificity in hyperspecialized plant parasitic nematodes?

description: Table S1. Differentially expressed genes (DEG, PÂ
DOI: 10.6084/m9.figshare.8240063
title: Additional file 2: of Identification and evaluation of a core microsatellite panel for use in white-tailed deer (Odocoileus virginianus)

description: Table S2. Summary of microsatellite loci used in previous studies of white-tailed deer genetics. Studies are arranged by date. Study area(s) are also indicated and grouped by state (if in North America) and Country. Loci included in the final microsatellite panel are highlighted in blue (XLSX 35 kb)