cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11352479
title: MOESM3 of Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection

description: Additional file 3: Table S2. Table of gene regions correlated with symptoms based on principal component analysis for patterns among clusters of variants and symptoms.
DOI: 10.6084/m9.figshare.11352485.v1
title: MOESM2 of Peripheral blood metabolome predicts mood change-related activity in mouse model of bipolar disorder

description: Additional file 2: Table S1. The raw data used for this study.
DOI: 10.6084/m9.figshare.11352479.v1
title: MOESM3 of Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection

description: Additional file 3: Table S2. Table of gene regions correlated with symptoms based on principal component analysis for patterns among clusters of variants and symptoms.
DOI: 10.6084/m9.figshare.11352467
title: MOESM2 of Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection

description: Additional file 2: Table S1. Regions excluded from Fisherâ€™s exact test analysis. A number of samples lacked 15 quality reads in the indicated regions, and therefore were excluded in calculating the frequency distribution of variants from all samples.
DOI: 10.6084/m9.figshare.11352467.v1
title: MOESM2 of Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection

description: Additional file 2: Table S1. Regions excluded from Fisherâ€™s exact test analysis. A number of samples lacked 15 quality reads in the indicated regions, and therefore were excluded in calculating the frequency distribution of variants from all samples.
DOI: 10.6084/m9.figshare.11352443
title: MOESM8 of Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes

description: Additional file 8: Table S1. Abundances and PATRIC accession numbers [32] of different species in the mock metagenomes.
DOI: 10.6084/m9.figshare.11352437
title: MOESM9 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 9: Table S8. Gene clustering analysis for the in silico studied P. aeruginosa strains. Shown are only gene clusters that contain sequences from the studied 52 strains.
DOI: 10.6084/m9.figshare.11352437.v1
title: MOESM9 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 9: Table S8. Gene clustering analysis for the in silico studied P. aeruginosa strains. Shown are only gene clusters that contain sequences from the studied 52 strains.
DOI: 10.6084/m9.figshare.11352443.v1
title: MOESM8 of Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes

description: Additional file 8: Table S1. Abundances and PATRIC accession numbers [32] of different species in the mock metagenomes.
DOI: 10.6084/m9.figshare.11352434
title: MOESM8 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 8: Table S7. Description of in silico studied set of 1448 P. aeruginosa strains.
DOI: 10.6084/m9.figshare.11352425
title: MOESM7 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 7: Table S6. Gene targeted by CRISPR spacers.
DOI: 10.6084/m9.figshare.11352434.v1
title: MOESM8 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 8: Table S7. Description of in silico studied set of 1448 P. aeruginosa strains.
DOI: 10.6084/m9.figshare.11352419
title: MOESM6 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 6: Table S5. Bacterial strains generated in the present study. Strains generated in the present study are described with a strain name (AVPae #) and genotype (in both full and short formats).
DOI: 10.6084/m9.figshare.11352425.v1
title: MOESM7 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 7: Table S6. Gene targeted by CRISPR spacers.
DOI: 10.6084/m9.figshare.11352413
title: MOESM5 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 5: Table S4. Nomenclature for the experimentally studied bacterial genes. A set of genes associated with virulence are termed for the P. aeruginosa strains z8 and PAO1. Genes that constitute a gene block frequently found in multiple tandem copies in various strains are termed teg(G to N), for 'tandem element gene'. The region encompassing from tegG to tegN is referred to as 'teg gene block’. The Refseq gene ‘NT41_RS12090’ is termed ghlO (glycosyl hydrolase like ORF) as it exhibits similarity to domain Cdd:cd06549 (E-value: 0.02, CDD database) . The PAO1 genes: PA2228, vqsM, qsrO, and PA225, constitute a putative operon [33] that is referred to as ‘qsr’ operon.
DOI: 10.6084/m9.figshare.11352419.v1
title: MOESM6 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 6: Table S5. Bacterial strains generated in the present study. Strains generated in the present study are described with a strain name (AVPae #) and genotype (in both full and short formats).
DOI: 10.6084/m9.figshare.11352413.v1
title: MOESM5 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 5: Table S4. Nomenclature for the experimentally studied bacterial genes. A set of genes associated with virulence are termed for the P. aeruginosa strains z8 and PAO1. Genes that constitute a gene block frequently found in multiple tandem copies in various strains are termed teg(G to N), for 'tandem element gene'. The region encompassing from tegG to tegN is referred to as 'teg gene block’. The Refseq gene ‘NT41_RS12090’ is termed ghlO (glycosyl hydrolase like ORF) as it exhibits similarity to domain Cdd:cd06549 (E-value: 0.02, CDD database) . The PAO1 genes: PA2228, vqsM, qsrO, and PA225, constitute a putative operon [33] that is referred to as ‘qsr’ operon.
DOI: 10.6084/m9.figshare.11352401
title: MOESM4 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 4: Table S3. Known virulence genes in the interactions between P. aeruginosa and C. elegans under SK condition.
DOI: 10.6084/m9.figshare.11352401.v1
title: MOESM4 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 4: Table S3. Known virulence genes in the interactions between P. aeruginosa and C. elegans under SK condition.
DOI: 10.6084/m9.figshare.11352395
title: MOESM3 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 3: Table S2. Genes significantly associated with virulence. Description of the 79 genes that comprise the HVA and LVA sets.
DOI: 10.6084/m9.figshare.11352395.v1
title: MOESM3 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 3: Table S2. Genes significantly associated with virulence. Description of the 79 genes that comprise the HVA and LVA sets.
DOI: 10.6084/m9.figshare.11352386
title: MOESM2 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 2: Table S1. Description and features of the experimentally studied collection of 52 P. aeruginosa strains. The 52 strains experimentally studied strains are listed, altogether with all the features derived from this study.
DOI: 10.6084/m9.figshare.11352386.v1
title: MOESM2 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 2: Table S1. Description and features of the experimentally studied collection of 52 P. aeruginosa strains. The 52 strains experimentally studied strains are listed, altogether with all the features derived from this study.
DOI: 10.6084/m9.figshare.11352362
title: MOESM10 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 10: Table S9. Sequence of plasmid pAVR85.
DOI: 10.6084/m9.figshare.11352362.v1
title: MOESM10 of The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans

description: Additional file 10: Table S9. Sequence of plasmid pAVR85.
DOI: 10.6084/m9.figshare.11352305
title: MOESM8 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 8: Table S7. Pairwise t-tests were performed for each protein between consecutive life-cycle stages.
DOI: 10.6084/m9.figshare.11352296
title: MOESM7 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 7: Table S6. Enriched Gene Ontology terms in genes coding for haemolymph-associated differentially expressed proteins during the bumblebee queen life cycle stages.
DOI: 10.6084/m9.figshare.11352305.v1
title: MOESM8 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 8: Table S7. Pairwise t-tests were performed for each protein between consecutive life-cycle stages.
DOI: 10.6084/m9.figshare.11352290
title: MOESM6 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 6: Table S5. Gene expression of the haemolymph-associated proteins in the bumblebee queen fat body.
DOI: 10.6084/m9.figshare.11352296.v1
title: MOESM7 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 7: Table S6. Enriched Gene Ontology terms in genes coding for haemolymph-associated differentially expressed proteins during the bumblebee queen life cycle stages.
DOI: 10.6084/m9.figshare.11352290.v1
title: MOESM6 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 6: Table S5. Gene expression of the haemolymph-associated proteins in the bumblebee queen fat body.
DOI: 10.6084/m9.figshare.11352278
title: MOESM1 of Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans

description: Additional file 1: Table S1. Overview of microarray samples used in this study. Includes detailed information on the treatment conditions, previous publications, ArrayExpress accession numbers, and whether they were used for deriving the different axes (H, GH, D, GD). Table S2. Top 5% of genes contributing to the different axes. Table S3. Full output of the enrichment analysis using the webtool DAVID 6.8. Enrichment categories (using standard settings) include: Functional Categories (COG_Ontology, UP_keywords, Up_seq_feature), Gene_ontology (goterm_bp_direct, goterm_cc_direct, goterm_mf_direct), Pathways (KEGG_pathway), Protein_domains (Interpro, Pir_superfamiy, smart). Table S4. Additional enrichment output. The following resources were used: WormBase (https://wormbase.org/) version WS258 gene class names, anatomy terms, phenotypes, RNAi phenotypes, developmental stage expression, and disease-related genes, and the ModERN resource transcription-factor binding sites (http://epic.gs.washington.edu/modERN/). Table S5. Lifespan data. Columns X1-X51 gives the accumulative number of dead worms on day 1-51 post age-synchronization. Each row represents a different genotype. Control conditions are continuous 20°C; heat-stress animals were exposed to 35°C for 4h starting 46h after age-synchronization, after which they were returned to 20°C. Table S6. Lifespan statistics. Output of logrank test comparing lifespan in control conditions and after heat-stress. Tests were performed using the R package “survival” (vs. 2.42-6). The table also includes the FDR-adjusted p-values.
DOI: 10.6084/m9.figshare.11352281
title: MOESM5 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 5: Table S4. Genomic coordinates for members of a novel haemolymph-associated gene family.
DOI: 10.6084/m9.figshare.11352278.v1
title: MOESM1 of Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans

description: Additional file 1: Table S1. Overview of microarray samples used in this study. Includes detailed information on the treatment conditions, previous publications, ArrayExpress accession numbers, and whether they were used for deriving the different axes (H, GH, D, GD). Table S2. Top 5% of genes contributing to the different axes. Table S3. Full output of the enrichment analysis using the webtool DAVID 6.8. Enrichment categories (using standard settings) include: Functional Categories (COG_Ontology, UP_keywords, Up_seq_feature), Gene_ontology (goterm_bp_direct, goterm_cc_direct, goterm_mf_direct), Pathways (KEGG_pathway), Protein_domains (Interpro, Pir_superfamiy, smart). Table S4. Additional enrichment output. The following resources were used: WormBase (https://wormbase.org/) version WS258 gene class names, anatomy terms, phenotypes, RNAi phenotypes, developmental stage expression, and disease-related genes, and the ModERN resource transcription-factor binding sites (http://epic.gs.washington.edu/modERN/). Table S5. Lifespan data. Columns X1-X51 gives the accumulative number of dead worms on day 1-51 post age-synchronization. Each row represents a different genotype. Control conditions are continuous 20°C; heat-stress animals were exposed to 35°C for 4h starting 46h after age-synchronization, after which they were returned to 20°C. Table S6. Lifespan statistics. Output of logrank test comparing lifespan in control conditions and after heat-stress. Tests were performed using the R package “survival” (vs. 2.42-6). The table also includes the FDR-adjusted p-values.
DOI: 10.6084/m9.figshare.11352266
title: MOESM2 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 2: Table S2. Multivariate analysis (ANOVA FDR 5%) of all identified proteins from the haemolymph of unmated and mated queens prior to, during and after diapause.
DOI: 10.6084/m9.figshare.11352272
title: MOESM3 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 3: Table S3. All ANOVA statistically significant proteins (FDR
DOI: 10.6084/m9.figshare.11352281.v1
title: MOESM5 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 5: Table S4. Genomic coordinates for members of a novel haemolymph-associated gene family.
DOI: 10.6084/m9.figshare.11352269
title: MOESM5 of IL-1β-driven amyloid plaque clearance is associated with an expansion of transcriptionally reprogrammed microglia

description: Additional file 5. RNAseq data.
DOI: 10.6084/m9.figshare.11352272.v1
title: MOESM3 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 3: Table S3. All ANOVA statistically significant proteins (FDR
DOI: 10.6084/m9.figshare.11352257
title: MOESM1 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 1: Table S1. The 129 proteins identified from the haemolymph of unmated and mated queens prior to, during and after diapause.
DOI: 10.6084/m9.figshare.11352266.v1
title: MOESM2 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 2: Table S2. Multivariate analysis (ANOVA FDR 5%) of all identified proteins from the haemolymph of unmated and mated queens prior to, during and after diapause.
DOI: 10.6084/m9.figshare.11352269.v1
title: MOESM5 of IL-1β-driven amyloid plaque clearance is associated with an expansion of transcriptionally reprogrammed microglia

description: Additional file 5. RNAseq data.
DOI: 10.6084/m9.figshare.11352257.v1
title: MOESM1 of Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause

description: Additional file 1: Table S1. The 129 proteins identified from the haemolymph of unmated and mated queens prior to, during and after diapause.
DOI: 10.6084/m9.figshare.11352218
title: Dentofacial Esthetics

description: This is the dataset of the manuscript titled <i>Dentofacial Mini- and Microesthetics as Perceived by Dental Students: A Cross-Sectional Multi-Site Study </i>
DOI: 10.6084/m9.figshare.11352179
title: Supplementary Material for: Defining Blood Group Gene Reference Alleles by Long-Read Sequencing: Proof of Concept in the <b><i>ACKR1</i></b> Gene Encoding the Duffy Antigens

description: <b><i>Background:</i></b> In the novel era of blood group genomics, (re-)defining reference gene/allele sequences of blood group genes has become an important goal to achieve, both for diagnostic and research purposes. As novel potent sequencing technologies are available, we thought to investigate the variability encountered in the three most common alleles of <i>ACKR1</i>, the gene encoding the clinically relevant Duffy antigens, at the haplotype level by a long-read sequencing approach. <b><i>Materials and Methods:</i></b> After long-range PCR amplification spanning the whole <i>ACKR1</i> gene locus (∼2.5 kilobases), amplicons generated from 81 samples with known genotypes were sequenced in a single read by using the Pacific Biosciences (PacBio) single molecule, real-time (SMRT) sequencing technology. <b><i>Results:</i></b> High-quality sequencing reads were obtained for the 162 alleles (accuracy &gt;0.999). Twenty-two nucleotide variations reported in databases were identified, defining 19 haplotypes: four, eight, and seven haplotypes in 46 <i>ACKR1</i>*<i>01</i>, 63 <i>ACKR1</i>*<i>02</i>, and 53 <i>ACKR1</i>*<i>02N.01</i> alleles, respectively. <b><i>Discussion:</i></b> Overall, we have defined a subset of reference alleles by third-generation (long-read) sequencing. This technology, which provides a “longitudinal” overview of the loci of interest (several thousand base pairs) and is complementary to the second-generation (short-read) next-generation sequencing technology, is of critical interest for resolving novel, rare, and null alleles.
DOI: 10.6084/m9.figshare.11352179.v1
title: Supplementary Material for: Defining Blood Group Gene Reference Alleles by Long-Read Sequencing: Proof of Concept in the <b><i>ACKR1</i></b> Gene Encoding the Duffy Antigens

description: <b><i>Background:</i></b> In the novel era of blood group genomics, (re-)defining reference gene/allele sequences of blood group genes has become an important goal to achieve, both for diagnostic and research purposes. As novel potent sequencing technologies are available, we thought to investigate the variability encountered in the three most common alleles of <i>ACKR1</i>, the gene encoding the clinically relevant Duffy antigens, at the haplotype level by a long-read sequencing approach. <b><i>Materials and Methods:</i></b> After long-range PCR amplification spanning the whole <i>ACKR1</i> gene locus (∼2.5 kilobases), amplicons generated from 81 samples with known genotypes were sequenced in a single read by using the Pacific Biosciences (PacBio) single molecule, real-time (SMRT) sequencing technology. <b><i>Results:</i></b> High-quality sequencing reads were obtained for the 162 alleles (accuracy &gt;0.999). Twenty-two nucleotide variations reported in databases were identified, defining 19 haplotypes: four, eight, and seven haplotypes in 46 <i>ACKR1</i>*<i>01</i>, 63 <i>ACKR1</i>*<i>02</i>, and 53 <i>ACKR1</i>*<i>02N.01</i> alleles, respectively. <b><i>Discussion:</i></b> Overall, we have defined a subset of reference alleles by third-generation (long-read) sequencing. This technology, which provides a “longitudinal” overview of the loci of interest (several thousand base pairs) and is complementary to the second-generation (short-read) next-generation sequencing technology, is of critical interest for resolving novel, rare, and null alleles.
DOI: 10.6084/m9.figshare.11352218.v1
title: Dentofacial Esthetics

description: This is the dataset of the manuscript titled <i>Dentofacial Mini- and Microesthetics as Perceived by Dental Students: A Cross-Sectional Multi-Site Study </i>
DOI: 10.6084/m9.figshare.11352146
title: test_tweet.csv

description: Haiyan related tweet data (test data, not complete data). Used in the program "btm_model_window.py".CSV format, including "ID", "translate", "time".ID: the unique identifier for a tweetTranslate: tweets translated into English.Time: when the tweet was published
DOI: 10.6084/m9.figshare.11352146.v1
title: test_tweet.csv

description: Haiyan related tweet data (test data, not complete data). Used in the program "btm_model_window.py".CSV format, including "ID", "translate", "time".ID: the unique identifier for a tweetTranslate: tweets translated into English.Time: when the tweet was published
DOI: 10.6084/m9.figshare.11352131
title: Unigene set of the antennal transcriptome of Trialeurodes vaporariorum

description: <b>Analysis of the antennal transcriptome and olfaction-related genes of <i>Trialeurodes vaporariorum</i></b>
DOI: 10.6084/m9.figshare.11352140
title: (OLD) Protein clusters and trees, ALE results

description: small_clusters_eurNOG.tar.gz unaligned sequence files for clusters with less than 4 member sequences<br>ufboot_eurNOG.tar.gz ultrafast bootstrap samples inferred for clusters with at least 4 members<br>events.txt.gz ALE inferred evolutionary events per node and cluster as a table<br>
DOI: 10.6084/m9.figshare.11352131.v1
title: Unigene set of the antennal transcriptome of Trialeurodes vaporariorum

description: <b>Analysis of the antennal transcriptome and olfaction-related genes of <i>Trialeurodes vaporariorum</i></b>