cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11558004.v1
title: MOESM9 of The transcriptome of Pinus pinaster under Fusarium circinatum challenge

description: Additional file 9. Clustering of Pinus pinaster and Fusarium circinatum differential expressed (DE) genes. For each cluster with gene ontology (GO) enriched terms, number of genes and percentage for genes are indicated.
DOI: 10.6084/m9.figshare.11557995
title: MOESM7 of The transcriptome of Pinus pinaster under Fusarium circinatum challenge

description: Additional file 7. mapped reads for each species. Number of differential expressed (DE) genes for Pinus pinaster and DE genes for Fusarium circinatum at each time point in inoculated samples (FDR 0.5). Ppin: P. pinaster; Fcir: F. circinatum;HC: high confident.
DOI: 10.6084/m9.figshare.11557995.v1
title: MOESM7 of The transcriptome of Pinus pinaster under Fusarium circinatum challenge

description: Additional file 7. mapped reads for each species. Number of differential expressed (DE) genes for Pinus pinaster and DE genes for Fusarium circinatum at each time point in inoculated samples (FDR 0.5). Ppin: P. pinaster; Fcir: F. circinatum;HC: high confident.
DOI: 10.6084/m9.figshare.11557986
title: MOESM6 of The transcriptome of Pinus pinaster under Fusarium circinatum challenge

description: Additional file 6. Pinus pinaster de novo transcriptome annotation by Mercator tool.
DOI: 10.6084/m9.figshare.11557986.v1
title: MOESM6 of The transcriptome of Pinus pinaster under Fusarium circinatum challenge

description: Additional file 6. Pinus pinaster de novo transcriptome annotation by Mercator tool.
DOI: 10.6084/m9.figshare.11557977
title: MOESM5 of The transcriptome of Pinus pinaster under Fusarium circinatum challenge

description: Additional file 5. Pinus pinaster de novo transcriptome annotation.
DOI: 10.6084/m9.figshare.11557977.v1
title: MOESM5 of The transcriptome of Pinus pinaster under Fusarium circinatum challenge

description: Additional file 5. Pinus pinaster de novo transcriptome annotation.
DOI: 10.6084/m9.figshare.11557953
title: MOESM9 of Novel molecular components involved in callose-mediated Arabidopsis defense against Salmonella enterica and Escherichia coli O157:H7

description: Additional file 9. Sequence of primers used to validate the microarray results by RT-qPCR analysis.
DOI: 10.6084/m9.figshare.11557953.v1
title: MOESM9 of Novel molecular components involved in callose-mediated Arabidopsis defense against Salmonella enterica and Escherichia coli O157:H7

description: Additional file 9. Sequence of primers used to validate the microarray results by RT-qPCR analysis.
DOI: 10.6084/m9.figshare.11557941
title: MOESM8 of Novel molecular components involved in callose-mediated Arabidopsis defense against Salmonella enterica and Escherichia coli O157:H7

description: Additional file 8. List of Arabidopsis mutants and primer sequences used to validate the mutation.
DOI: 10.6084/m9.figshare.11557941.v1
title: MOESM8 of Novel molecular components involved in callose-mediated Arabidopsis defense against Salmonella enterica and Escherichia coli O157:H7

description: Additional file 8. List of Arabidopsis mutants and primer sequences used to validate the mutation.
DOI: 10.6084/m9.figshare.11557926
title: MOESM5 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

description: Additional file 5. Outputs of dDDH and ANI analyses comparing strain ES5 and T. flocculiformis. XLSX 22 kb.
DOI: 10.6084/m9.figshare.11557926.v1
title: MOESM5 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

description: Additional file 5. Outputs of dDDH and ANI analyses comparing strain ES5 and T. flocculiformis. XLSX 22 kb.
DOI: 10.6084/m9.figshare.11557911
title: MOESM4 of Novel molecular components involved in callose-mediated Arabidopsis defense against Salmonella enterica and Escherichia coli O157:H7

description: Additional file 4. GO Single Enrichment Analysis (SEA) of genes up-regulated (310 genes) or down-regulated (275 genes) by SL1344, using the online tool AgriGO. Only GO terms that contained more than 5 entries and were significantly over-represented (FDR
DOI: 10.6084/m9.figshare.11557908
title: MOESM12 of The transcriptome of Pinus pinaster under Fusarium circinatum challenge

description: Additional file 12: Pathogenesis related (PR) genes differentially expressed (DE) in Pinus pinaster.
DOI: 10.6084/m9.figshare.11557911.v1
title: MOESM4 of Novel molecular components involved in callose-mediated Arabidopsis defense against Salmonella enterica and Escherichia coli O157:H7

description: Additional file 4. GO Single Enrichment Analysis (SEA) of genes up-regulated (310 genes) or down-regulated (275 genes) by SL1344, using the online tool AgriGO. Only GO terms that contained more than 5 entries and were significantly over-represented (FDR
DOI: 10.6084/m9.figshare.11557905
title: MOESM3 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

description: Additional file 3. Common protein domains in Trichococcus strains. XLSX 28 kb.
DOI: 10.6084/m9.figshare.11557908.v1
title: MOESM12 of The transcriptome of Pinus pinaster under Fusarium circinatum challenge

description: Additional file 12: Pathogenesis related (PR) genes differentially expressed (DE) in Pinus pinaster.
DOI: 10.6084/m9.figshare.11557905.v1
title: MOESM3 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

description: Additional file 3. Common protein domains in Trichococcus strains. XLSX 28 kb.
DOI: 10.6084/m9.figshare.11557896
title: MOESM2 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

description: Additional file 2. SAPP-generated protein domain matrix. XLSX 628 kb.
DOI: 10.6084/m9.figshare.11557899
title: MOESM11 of The transcriptome of Pinus pinaster under Fusarium circinatum challenge

description: Additional file 11: Phytohormone related differentially expressed (DE) genes in Pinus pinaster.
DOI: 10.6084/m9.figshare.11557893
title: MOESM2 of Novel molecular components involved in callose-mediated Arabidopsis defense against Salmonella enterica and Escherichia coli O157:H7

description: Additional file 2. Relative gene expression analysis (mock- versus SL1344-treated leaves) using Log2 Fold Change and Z-ratio methods. Gene expression for each gene was calculated based on an average of three biological replicates. A total of 541 array probes corresponding to 585 genes were identified as differentially expessed based on Z-ratio analysis (the extreme 2% of up or down-regulated). Genes hilightes in bold had their expression evaluated by RT-qPCR.
DOI: 10.6084/m9.figshare.11557896.v1
title: MOESM2 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

description: Additional file 2. SAPP-generated protein domain matrix. XLSX 628 kb.
DOI: 10.6084/m9.figshare.11557899.v1
title: MOESM11 of The transcriptome of Pinus pinaster under Fusarium circinatum challenge

description: Additional file 11: Phytohormone related differentially expressed (DE) genes in Pinus pinaster.
DOI: 10.6084/m9.figshare.11557893.v1
title: MOESM2 of Novel molecular components involved in callose-mediated Arabidopsis defense against Salmonella enterica and Escherichia coli O157:H7

description: Additional file 2. Relative gene expression analysis (mock- versus SL1344-treated leaves) using Log2 Fold Change and Z-ratio methods. Gene expression for each gene was calculated based on an average of three biological replicates. A total of 541 array probes corresponding to 585 genes were identified as differentially expessed based on Z-ratio analysis (the extreme 2% of up or down-regulated). Genes hilightes in bold had their expression evaluated by RT-qPCR.
DOI: 10.6084/m9.figshare.11557827
title: MOESM3 of Enhanced inference of ecological networks by parameterizing ensembles of population dynamics models constrained with prior knowledge

description: Additional file 3. Standardized fish abundance indices for all six observation sites in the Upper Mississippi and Illinois Rivers.
DOI: 10.6084/m9.figshare.11557827.v1
title: MOESM3 of Enhanced inference of ecological networks by parameterizing ensembles of population dynamics models constrained with prior knowledge

description: Additional file 3. Standardized fish abundance indices for all six observation sites in the Upper Mississippi and Illinois Rivers.
DOI: 10.6084/m9.figshare.11557818
title: MOESM2 of Enhanced inference of ecological networks by parameterizing ensembles of population dynamics models constrained with prior knowledge

description: Additional file 2. Additional Tables.
DOI: 10.6084/m9.figshare.11557818.v1
title: MOESM2 of Enhanced inference of ecological networks by parameterizing ensembles of population dynamics models constrained with prior knowledge

description: Additional file 2. Additional Tables.
DOI: 10.6084/m9.figshare.11557800
title: MOESM1 of LOX family and ZFPM2 as novel diagnostic biomarkers for malignant pleural mesothelioma

description: Additional file 1. Gene expression list in pleural mesothelioma compared to lung adenocarcinoma. Note that expression logarithmic score was presented to each gene list by comparing 14 MPM and 32 lung adenocarcinoma cell lines from CCLE database.
DOI: 10.6084/m9.figshare.11557800.v1
title: MOESM1 of LOX family and ZFPM2 as novel diagnostic biomarkers for malignant pleural mesothelioma

description: Additional file 1. Gene expression list in pleural mesothelioma compared to lung adenocarcinoma. Note that expression logarithmic score was presented to each gene list by comparing 14 MPM and 32 lung adenocarcinoma cell lines from CCLE database.
DOI: 10.6084/m9.figshare.11557761
title: MOESM1 of Species-specific differences in Toxoplasma gondii, Neospora caninum and Besnoitia besnoiti seroprevalence in Namibian wildlife

description: Additional file 1: Table S1. Data table of ELISA and IB results containing information on all samples (species, suborder, site, ELISA, IB and final results for T. gondii, N. caninum and B. besnoiti, respectively).
DOI: 10.6084/m9.figshare.11557761.v1
title: MOESM1 of Species-specific differences in Toxoplasma gondii, Neospora caninum and Besnoitia besnoiti seroprevalence in Namibian wildlife

description: Additional file 1: Table S1. Data table of ELISA and IB results containing information on all samples (species, suborder, site, ELISA, IB and final results for T. gondii, N. caninum and B. besnoiti, respectively).
DOI: 10.6084/m9.figshare.11557731
title: MOESM2 of Hypertension and diabetes treatment affordability and government expenditures following changes in patient cost sharing in the “Farmácia popular” program in Brazil: an interrupted time series study

description: Additional file 2. Diabetes and Hypertension interrupted time series models - original, analyzed data and graphs.
DOI: 10.6084/m9.figshare.11557731.v1
title: MOESM2 of Hypertension and diabetes treatment affordability and government expenditures following changes in patient cost sharing in the “Farmácia popular” program in Brazil: an interrupted time series study

description: Additional file 2. Diabetes and Hypertension interrupted time series models - original, analyzed data and graphs.
DOI: 10.6084/m9.figshare.11557719
title: Additional file 5 of DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors

description: Additional file 5. Genes annotated to CGI+ regions that are differentially methylated in T21 neural lines.
DOI: 10.6084/m9.figshare.11557719.v2
title: Additional file 5 of DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors

description: Additional file 5. Genes annotated to CGI+ regions that are differentially methylated in T21 neural lines.
DOI: 10.6084/m9.figshare.11557719.v1
title: MOESM5 of DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors

description: Additional file 5. Genes annotated to CGI+ regions that are differentially methylated in T21 neural lines.
DOI: 10.6084/m9.figshare.11557707
title: Additional file 3 of DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors

description: Additional file 3. List of all 500 DMPs called in T21 neural lines.
DOI: 10.6084/m9.figshare.11557707.v2
title: Additional file 3 of DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors

description: Additional file 3. List of all 500 DMPs called in T21 neural lines.
DOI: 10.6084/m9.figshare.11557707.v1
title: MOESM3 of DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors

description: Additional file 3. List of all 500 DMPs called in T21 neural lines.
DOI: 10.6084/m9.figshare.11557686
title: MOESM9 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 9: Overlap between the top CLR and iHS selection signatures. Overlapped regions and genes between CLR and iHS candidate selection regions.
DOI: 10.6084/m9.figshare.11557683
title: MOESM8 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 8: Candidate selection signatures detected using iHS. Genomic coordinates, |iHS| values, p values and encompassed genes for 162 candidate selection signatures.
DOI: 10.6084/m9.figshare.11557686.v1
title: MOESM9 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 9: Overlap between the top CLR and iHS selection signatures. Overlapped regions and genes between CLR and iHS candidate selection regions.
DOI: 10.6084/m9.figshare.11557677
title: MOESM7 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 7: Candidate selection signatures detected using CLR. Genomic coordinates, CLR values, p values and encompassed genes for 95 candidate selection signatures.
DOI: 10.6084/m9.figshare.11557683.v1
title: MOESM8 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 8: Candidate selection signatures detected using iHS. Genomic coordinates, |iHS| values, p values and encompassed genes for 162 candidate selection signatures.
DOI: 10.6084/m9.figshare.11557677.v1
title: MOESM7 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 7: Candidate selection signatures detected using CLR. Genomic coordinates, CLR values, p values and encompassed genes for 95 candidate selection signatures.
DOI: 10.6084/m9.figshare.11557665
title: MOESM5 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 5: ROH statistics of each animal (high coverage). Number, length, average length and genomic fraction of all ROH in each animal. Also categorized in short, medium and long ROH category.
DOI: 10.6084/m9.figshare.11557665.v1
title: MOESM5 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 5: ROH statistics of each animal (high coverage). Number, length, average length and genomic fraction of all ROH in each animal. Also categorized in short, medium and long ROH category.
DOI: 10.6084/m9.figshare.11557659
title: MOESM4 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 4: OMIA variants detected in OB. Six OMIA variants detected in 49 sequenced OB animals with their respective frequency and information.
DOI: 10.6084/m9.figshare.11557659.v1
title: MOESM4 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 4: OMIA variants detected in OB. Six OMIA variants detected in 49 sequenced OB animals with their respective frequency and information.
DOI: 10.6084/m9.figshare.11557647
title: MOESM14 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 14: Bovine QTL information downloaded from the AnimalQTL database. Number of QTL for each trait. Traits are grouped in six trait categories.
DOI: 10.6084/m9.figshare.11557647.v1
title: MOESM14 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 14: Bovine QTL information downloaded from the AnimalQTL database. Number of QTL for each trait. Traits are grouped in six trait categories.
DOI: 10.6084/m9.figshare.11557641
title: MOESM12 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 12: Frequency of candidate causal variants for a stature QTL on BTA14. Genomic coordinates and allele frequencies of 14 variants nearby bovine PLAG1 that were reported as candidate causal variants for a stature QTL in cattle by Karim et al. [70].
DOI: 10.6084/m9.figshare.11557638
title: MOESM11 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 11: Overlap between QTL and signatures of selection. QTL (from all 6 categories) that overlapped with CLR and iHS selection signatures.
DOI: 10.6084/m9.figshare.11557641.v1
title: MOESM12 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 12: Frequency of candidate causal variants for a stature QTL on BTA14. Genomic coordinates and allele frequencies of 14 variants nearby bovine PLAG1 that were reported as candidate causal variants for a stature QTL in cattle by Karim et al. [70].
DOI: 10.6084/m9.figshare.11557638.v1
title: MOESM11 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 11: Overlap between QTL and signatures of selection. QTL (from all 6 categories) that overlapped with CLR and iHS selection signatures.
DOI: 10.6084/m9.figshare.11557632
title: MOESM10 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 10: Summary of Gene Ontology enrichment analysis. PANTHER and GO-Slim pathways enriched using genes encompassed in signatures of selection from CLR and iHS analyses.
DOI: 10.6084/m9.figshare.11557632.v1
title: MOESM10 of Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

description: Additional file 10: Summary of Gene Ontology enrichment analysis. PANTHER and GO-Slim pathways enriched using genes encompassed in signatures of selection from CLR and iHS analyses.
DOI: 10.6084/m9.figshare.11557479
title: MOESM3 of Time is of the essence when treating necrotizing soft tissue infections: a systematic review and meta-analysis

description: Additional file 3: Extracted data from eligible studies assessing surgical timing related to mortality and amputation due to necrotizing soft tissue infection.
DOI: 10.6084/m9.figshare.11557332
title: MOESM5 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 5. Accessory gene presence-absence matrix.
DOI: 10.6084/m9.figshare.11557335
title: MOESM6 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 6. KO number assignments for amino acid biosynthesis genes.
DOI: 10.6084/m9.figshare.11557335.v1
title: MOESM6 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 6. KO number assignments for amino acid biosynthesis genes.
DOI: 10.6084/m9.figshare.11557332.v1
title: MOESM5 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 5. Accessory gene presence-absence matrix.
DOI: 10.6084/m9.figshare.11557323
title: MOESM4 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 4. Presence-absence table given by Roary.
DOI: 10.6084/m9.figshare.11557320
title: MOESM3 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 3. List of the 129 bifidobacteria strains across all environments included in the analysis.
DOI: 10.6084/m9.figshare.11557323.v1
title: MOESM4 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 4. Presence-absence table given by Roary.
DOI: 10.6084/m9.figshare.11557314
title: MOESM5 of Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes

description: Additional file 5. Statistical analysis of PTM enrichment/depletion within human PrLDs. For each PTM type, statistical enrichment or depletion within PrLDs was evaluated using a two-sided Fisher exact test (see Methods section for detailed description).
DOI: 10.6084/m9.figshare.11557317
title: MOESM2 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 2. List of the 60 bifidobacteria human-derived strains included in the analysis.
DOI: 10.6084/m9.figshare.11557320.v1
title: MOESM3 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 3. List of the 129 bifidobacteria strains across all environments included in the analysis.
DOI: 10.6084/m9.figshare.11557314.v1
title: MOESM5 of Natural and pathogenic protein sequence variation affecting prion-like domains within and across human proteomes

description: Additional file 5. Statistical analysis of PTM enrichment/depletion within human PrLDs. For each PTM type, statistical enrichment or depletion within PrLDs was evaluated using a two-sided Fisher exact test (see Methods section for detailed description).
DOI: 10.6084/m9.figshare.11557317.v1
title: MOESM2 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 2. List of the 60 bifidobacteria human-derived strains included in the analysis.
DOI: 10.6084/m9.figshare.11557308
title: MOESM1 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 1. List of all the 446 bifidobacteria isolates and their isolation sources.
DOI: 10.6084/m9.figshare.11557308.v1
title: MOESM1 of Evolutionary relationships among bifidobacteria and their hosts and environments

description: Additional file 1. List of all the 446 bifidobacteria isolates and their isolation sources.