cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6208487
title: Additional file 2: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Table S1. Table of 8289 H. euphorbiae transcripts with BLASTX hits (NCBI nr protein database version 09/2016). (XLSX 1824Â kb)
DOI: 10.6084/m9.figshare.6208487.v1
title: Additional file 2: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Table S1. Table of 8289 H. euphorbiae transcripts with BLASTX hits (NCBI nr protein database version 09/2016). (XLSX 1824Â kb)
DOI: 10.6084/m9.figshare.6208493
title: MOESM2 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 2: Table S1. Plasmid gene annotation and functional analysis.
DOI: 10.6084/m9.figshare.6208493.v1
title: MOESM2 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 2: Table S1. Plasmid gene annotation and functional analysis.
DOI: 10.6084/m9.figshare.6208502
title: Additional file 3: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Figure S2. Distribution of species names among BLAST hits. The 20 most frequent species names affiliated with best BLASTX hits against nr are shown, making up (a) 8626 transcripts among the entire annotated H. euphorbiae assembly, and (b) 8219 (95%) among Lepidoptera matches only. (ZIP 259Â kb)
DOI: 10.6084/m9.figshare.6208502.v1
title: Additional file 3: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Figure S2. Distribution of species names among BLAST hits. The 20 most frequent species names affiliated with best BLASTX hits against nr are shown, making up (a) 8626 transcripts among the entire annotated H. euphorbiae assembly, and (b) 8219 (95%) among Lepidoptera matches only. (ZIP 259Â kb)
DOI: 10.6084/m9.figshare.6208505
title: Additional file 1: of Multi-cellular human bronchial models exposed to diesel exhaust particles: assessment of inflammation, oxidative stress and macrophage polarization

description: Supplement. Table S1. Primer Used for Quantitative Real-Time PCR (qPCR). Figure S1. Positive controls for inflammation, oxidative stress and M1/M2 polarization. Figure S2. Release and mRNA expression of inflammatory biomarkers after exposures to diesel exhaust particulates (DEPs). Figure S3. Cytotoxicity and cell viability assays to assess the effect of diesel exhaust particles (DEP) exposure in air-liquid interface models using lactate dehydrogenase assay (LDH) and apoptotic cell rate. Figure S4. The ratios of primary bronchial epithelial cells (PBEC) and THP-1 cell derived macrophages (MQ) in PBEC-ALI/MQ after exposure to diesel exhaust particulates (DEPs). Figure S5. mRNA expression of M1 macrophage markers after exposure to diesel exhaust particles (DEP). (ZIP 1014ย�kb)
DOI: 10.6084/m9.figshare.6208505.v1
title: Additional file 1: of Multi-cellular human bronchial models exposed to diesel exhaust particles: assessment of inflammation, oxidative stress and macrophage polarization

description: Supplement. Table S1. Primer Used for Quantitative Real-Time PCR (qPCR). Figure S1. Positive controls for inflammation, oxidative stress and M1/M2 polarization. Figure S2. Release and mRNA expression of inflammatory biomarkers after exposures to diesel exhaust particulates (DEPs). Figure S3. Cytotoxicity and cell viability assays to assess the effect of diesel exhaust particles (DEP) exposure in air-liquid interface models using lactate dehydrogenase assay (LDH) and apoptotic cell rate. Figure S4. The ratios of primary bronchial epithelial cells (PBEC) and THP-1 cell derived macrophages (MQ) in PBEC-ALI/MQ after exposure to diesel exhaust particulates (DEPs). Figure S5. mRNA expression of M1 macrophage markers after exposure to diesel exhaust particles (DEP). (ZIP 1014ย�kb)
DOI: 10.6084/m9.figshare.6208523
title: Additional file 4: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Table S2. List of 125 KEGG pathways and 513 different enzyme codes. Enzyme commission numbers (EC) and KEGG pathways are given; to which 2806 BLAST annotated H. euphorbiae transcripts have been mapped. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.6208523.v1
title: Additional file 4: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Table S2. List of 125 KEGG pathways and 513 different enzyme codes. Enzyme commission numbers (EC) and KEGG pathways are given; to which 2806 BLAST annotated H. euphorbiae transcripts have been mapped. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.6208532
title: MOESM4 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 4: Table S3. RNA-Seq metadata.
DOI: 10.6084/m9.figshare.6208532.v1
title: MOESM4 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 4: Table S3. RNA-Seq metadata.
DOI: 10.6084/m9.figshare.6208538
title: Additional file 5: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Figure S3. Distribution among ortholog hit ratio (OHR) classes. This is taken from BLASTX against Lepidoptera databases for (a) all protein annotated H. euphorbiae transcripts, and (b) only transcripts that were best BLASTN hits for differentially expressed DeepSuperSAGE tags in detoxification or cold treatments. (ZIP 33Â kb)
DOI: 10.6084/m9.figshare.6208538.v1
title: Additional file 5: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Figure S3. Distribution among ortholog hit ratio (OHR) classes. This is taken from BLASTX against Lepidoptera databases for (a) all protein annotated H. euphorbiae transcripts, and (b) only transcripts that were best BLASTN hits for differentially expressed DeepSuperSAGE tags in detoxification or cold treatments. (ZIP 33Â kb)
DOI: 10.6084/m9.figshare.6208547
title: MOESM5 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 5: Table S4. Plasmid gene RNA-Seq counts.
DOI: 10.6084/m9.figshare.6208547.v1
title: MOESM5 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 5: Table S4. Plasmid gene RNA-Seq counts.
DOI: 10.6084/m9.figshare.6208550
title: Additional file 6: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Figure S4. Distribution of DeepSuperSAGE tag frequencies and p-value vs. fold change (FC) of tags. Left panel: Normalized tag counts per million tags (tpm) in treatment and control libraries. Right panel: Relationship between tag FC (ratio of tpm counts) and p-value of significance. Up- and down-regulated tags (p &lt; 10− 10, − 1 &gt; Log2FC &gt; 1) are marked in red and green, respectively. Of those, the best BLASTN hits to a transcript, according to bit score and e-value, were used to assess the transcript expression value. (a) cooled (C) vs. uncooled (UC) library. (b) TPA treated (T) vs. untreated (UT) library. (ZIP 946 kb)
DOI: 10.6084/m9.figshare.6208550.v1
title: Additional file 6: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Figure S4. Distribution of DeepSuperSAGE tag frequencies and p-value vs. fold change (FC) of tags. Left panel: Normalized tag counts per million tags (tpm) in treatment and control libraries. Right panel: Relationship between tag FC (ratio of tpm counts) and p-value of significance. Up- and down-regulated tags (p &lt; 10− 10, − 1 &gt; Log2FC &gt; 1) are marked in red and green, respectively. Of those, the best BLASTN hits to a transcript, according to bit score and e-value, were used to assess the transcript expression value. (a) cooled (C) vs. uncooled (UC) library. (b) TPA treated (T) vs. untreated (UT) library. (ZIP 946 kb)
DOI: 10.6084/m9.figshare.6208562
title: Additional file 7: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Table S3. Table of 389 detoxification related differentially expressed H. euphorbiae tags. Assignment with BLASTN transcript hits and annotated protein sequence descriptions (nr protein database version 09/2016). (XLSX 152Â kb)
DOI: 10.6084/m9.figshare.6208562.v1
title: Additional file 7: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Table S3. Table of 389 detoxification related differentially expressed H. euphorbiae tags. Assignment with BLASTN transcript hits and annotated protein sequence descriptions (nr protein database version 09/2016). (XLSX 152Â kb)
DOI: 10.6084/m9.figshare.6208565
title: MOESM6 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 6: Table S5. Comparison of RNA-Seq from 6% and 9% ACSH.
DOI: 10.6084/m9.figshare.6208565.v1
title: MOESM6 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 6: Table S5. Comparison of RNA-Seq from 6% and 9% ACSH.
DOI: 10.6084/m9.figshare.6208580
title: Additional file 8: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Table S4. Table of 605 cold related differentially expressed H. euphorbiae tags. Assignment with BLASTN transcript hits and annotated protein sequence descriptions (nr protein database version 09/2016). (XLSX 169Â kb)
DOI: 10.6084/m9.figshare.6208580.v1
title: Additional file 8: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptomeÂ reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

description: Table S4. Table of 605 cold related differentially expressed H. euphorbiae tags. Assignment with BLASTN transcript hits and annotated protein sequence descriptions (nr protein database version 09/2016). (XLSX 169Â kb)
DOI: 10.6084/m9.figshare.6208583
title: MOESM7 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 7: Table S6. Comparison of RNA-Seq from anaerobic and aerobic conditions.
DOI: 10.6084/m9.figshare.6208583.v1
title: MOESM7 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 7: Table S6. Comparison of RNA-Seq from anaerobic and aerobic conditions.
DOI: 10.6084/m9.figshare.6208595
title: MOESM8 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 8: Table S7. Proteomic data of ZM4 in ethanol shock and sodium acetate stress conditions.
DOI: 10.6084/m9.figshare.6208595.v1
title: MOESM8 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 8: Table S7. Proteomic data of ZM4 in ethanol shock and sodium acetate stress conditions.
DOI: 10.6084/m9.figshare.6208607
title: MOESM9 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 9: Table S8. Proteomic data of ZM4 in anaerobic and aerobic fermentation in rich and minimal media.
DOI: 10.6084/m9.figshare.6208607.v1
title: MOESM9 of Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

description: Additional file 9: Table S8. Proteomic data of ZM4 in anaerobic and aerobic fermentation in rich and minimal media.
DOI: 10.6084/m9.figshare.6208670
title: Additional file 1: of NLRP3 promotes tumor growth and metastasis in human oral squamous cell carcinoma

description: Table S1. IHC Staining score of the expression levels of NLRP3 and IL-1β in 77 OSCC tissues. The positive grade was determined based on the Immuno-Reactive-Score (IRS), which was calculated by multiplying staining proportion score (PS) and staining intensity score (IS). PS was classified as 0 (0%), 1 (1%–25%), 2 (26%–50%), 3 (51%–75%), and 4 (76%–100%). IS was classified as 0 (negative), 1 (weak), 2 (moderate) and 3 (strong). The final staining score was calculated by multiplying IS by PS. According to the final score, patients with different expression were divided into three groups: negative expression group (IRS = 0), weak expression group (IRS = 1–3) and strong positive expression group (IRS = 4–12). (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6208670.v1
title: Additional file 1: of NLRP3 promotes tumor growth and metastasis in human oral squamous cell carcinoma

description: Table S1. IHC Staining score of the expression levels of NLRP3 and IL-1β in 77 OSCC tissues. The positive grade was determined based on the Immuno-Reactive-Score (IRS), which was calculated by multiplying staining proportion score (PS) and staining intensity score (IS). PS was classified as 0 (0%), 1 (1%–25%), 2 (26%–50%), 3 (51%–75%), and 4 (76%–100%). IS was classified as 0 (negative), 1 (weak), 2 (moderate) and 3 (strong). The final staining score was calculated by multiplying IS by PS. According to the final score, patients with different expression were divided into three groups: negative expression group (IRS = 0), weak expression group (IRS = 1–3) and strong positive expression group (IRS = 4–12). (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6208673
title: Additional file 2: of Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

description: Table S1. Primer information for CNV validation. Table S2. Characteristics of CNV and their overlapped genes. Table S3. Gene ontology (GO) of genes that overlap with CNV. Table S4. CNV-based GWAS results for the 10 phenotypes of interest among Holstein cattle. Table S5. qPCR validation of the significant CNV. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.6208673.v1
title: Additional file 2: of Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

description: Table S1. Primer information for CNV validation. Table S2. Characteristics of CNV and their overlapped genes. Table S3. Gene ontology (GO) of genes that overlap with CNV. Table S4. CNV-based GWAS results for the 10 phenotypes of interest among Holstein cattle. Table S5. qPCR validation of the significant CNV. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.6208778
title: MOESM1 of CIPK9 is involved in seed oil regulation in Brassica napus L. and Arabidopsis thaliana (L.) Heynh.

description: Additional file 1: Table S1. Primers used in the present study.
DOI: 10.6084/m9.figshare.6208778.v1
title: MOESM1 of CIPK9 is involved in seed oil regulation in Brassica napus L. and Arabidopsis thaliana (L.) Heynh.

description: Additional file 1: Table S1. Primers used in the present study.
DOI: 10.6084/m9.figshare.6208868
title: Additional file 11: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S6. Identified P. falciparum genes that possibly contribute to cerebral malaria. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6208868.v1
title: Additional file 11: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S6. Identified P. falciparum genes that possibly contribute to cerebral malaria. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6208886
title: Additional file 1: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S1. The corresponding relationships between 33,314 genes and 4605 clusters. (XLSX 605Â kb)
DOI: 10.6084/m9.figshare.6208886.v1
title: Additional file 1: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S1. The corresponding relationships between 33,314 genes and 4605 clusters. (XLSX 605Â kb)
DOI: 10.6084/m9.figshare.6208919
title: Additional file 3: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S2. Enriched values of all clusters in six Plasmodium species. (XLSX 154Â kb)
DOI: 10.6084/m9.figshare.6208919.v1
title: Additional file 3: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S2. Enriched values of all clusters in six Plasmodium species. (XLSX 154Â kb)
DOI: 10.6084/m9.figshare.6208934
title: Additional file 4: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S3. The candidate P. falciparum genes probably responsible for parasitizing human erythrocytes. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.6208934.v1
title: Additional file 4: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S3. The candidate P. falciparum genes probably responsible for parasitizing human erythrocytes. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.6208940
title: Additional file 5: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S4. The P. berghei genes included in rodent malaria parasite-enriched clusters. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.6208940.v1
title: Additional file 5: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S4. The P. berghei genes included in rodent malaria parasite-enriched clusters. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.6208955
title: Additional file 9: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S5. Candidate genes related to virulence of the P. falciparum parasite. (XLSX 31Â kb)
DOI: 10.6084/m9.figshare.6208955.v1
title: Additional file 9: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

description: Table S5. Candidate genes related to virulence of the P. falciparum parasite. (XLSX 31Â kb)
DOI: 10.6084/m9.figshare.6214712
title: Additional file 10: of GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes

description: Table S14. Secondary structure change between cold-water fishes and tropical fishes. Table S15. Secondary structure change between cold-water fishes and tropical fishes when molecular weight is decreased in cold-water fishes. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6214712.v1
title: Additional file 10: of GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes

description: Table S14. Secondary structure change between cold-water fishes and tropical fishes. Table S15. Secondary structure change between cold-water fishes and tropical fishes when molecular weight is decreased in cold-water fishes. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.6214721
title: Additional file 1: of GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes

description: Table S1. numerical indices of physicochemical and biochemical properties of amino acids. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6214721.v1
title: Additional file 1: of GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes

description: Table S1. numerical indices of physicochemical and biochemical properties of amino acids. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6214760
title: MOESM2 of Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa

description: Additional file 2. Amplicon deep sequencing data of 135 P. vivax samples.
DOI: 10.6084/m9.figshare.6214760.v1
title: MOESM2 of Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa

description: Additional file 2. Amplicon deep sequencing data of 135 P. vivax samples.
DOI: 10.6084/m9.figshare.6214766
title: Additional file 3: of GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes

description: Table S3. GC/AT synonymous substitution counts between cold-water and tropical species. Table S4. GC/AT nonsynonymous substitution counts between cold-water and tropical species. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.6214766.v1
title: Additional file 3: of GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes

description: Table S3. GC/AT synonymous substitution counts between cold-water and tropical species. Table S4. GC/AT nonsynonymous substitution counts between cold-water and tropical species. (XLSX 16Â kb)
DOI: 10.6084/m9.figshare.6214778
title: MOESM3 of Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa

description: Additional file 3. Population frequency, sample counts, and GenBank blast results of the 88 haplotypes identified in the 135 P. vivax samples.
DOI: 10.6084/m9.figshare.6214778.v1
title: MOESM3 of Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa

description: Additional file 3. Population frequency, sample counts, and GenBank blast results of the 88 haplotypes identified in the 135 P. vivax samples.