cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14404067.v1
title: Additional file 2 of New Indomalayan Nebularmis species (Heterotardigrada: Echiniscidae) provoke a discussion on its intrageneric diversity

description: Additional file 2. 18S rRNA alignment.
DOI: 10.6084/m9.figshare.14404073
title: Additional file 4 of New Indomalayan Nebularmis species (Heterotardigrada: Echiniscidae) provoke a discussion on its intrageneric diversity

description: Additional file 4. ITS-1 alignment.
DOI: 10.6084/m9.figshare.14404073.v1
title: Additional file 4 of New Indomalayan Nebularmis species (Heterotardigrada: Echiniscidae) provoke a discussion on its intrageneric diversity

description: Additional file 4. ITS-1 alignment.
DOI: 10.6084/m9.figshare.14404076.v1
title: Additional file 5 of New Indomalayan Nebularmis species (Heterotardigrada: Echiniscidae) provoke a discussion on its intrageneric diversity

description: Additional file 5. ITS-2 alignment.
DOI: 10.6084/m9.figshare.14404079
title: Additional file 6 of New Indomalayan Nebularmis species (Heterotardigrada: Echiniscidae) provoke a discussion on its intrageneric diversity

description: Additional file 6. COI alignment.
DOI: 10.6084/m9.figshare.14404082
title: Additional file 7 of New Indomalayan Nebularmis species (Heterotardigrada: Echiniscidae) provoke a discussion on its intrageneric diversity

description: Additional file 7. Concatenated 18S + 28S + ITS alignment used for the biogeography reconstructions.
DOI: 10.6084/m9.figshare.14404079.v1
title: Additional file 6 of New Indomalayan Nebularmis species (Heterotardigrada: Echiniscidae) provoke a discussion on its intrageneric diversity

description: Additional file 6. COI alignment.
DOI: 10.6084/m9.figshare.14404070.v1
title: Additional file 3 of New Indomalayan Nebularmis species (Heterotardigrada: Echiniscidae) provoke a discussion on its intrageneric diversity

description: Additional file 3. 28S rRNA alignment.
DOI: 10.6084/m9.figshare.14404076
title: Additional file 5 of New Indomalayan Nebularmis species (Heterotardigrada: Echiniscidae) provoke a discussion on its intrageneric diversity

description: Additional file 5. ITS-2 alignment.
DOI: 10.6084/m9.figshare.14404082.v1
title: Additional file 7 of New Indomalayan Nebularmis species (Heterotardigrada: Echiniscidae) provoke a discussion on its intrageneric diversity

description: Additional file 7. Concatenated 18S + 28S + ITS alignment used for the biogeography reconstructions.
DOI: 10.6084/m9.figshare.14404129
title: Additional file 1 of Reference-free transcriptome signatures for prostate cancer prognosis

description: Additional file 1 Contig sequences and mapping locations in the risk and relapse signatures.
DOI: 10.6084/m9.figshare.14404129.v1
title: Additional file 1 of Reference-free transcriptome signatures for prostate cancer prognosis

description: Additional file 1 Contig sequences and mapping locations in the risk and relapse signatures.
DOI: 10.6084/m9.figshare.14404132
title: Additional file 2 of Reference-free transcriptome signatures for prostate cancer prognosis

description: Additional file 2 Published PCa risk and relapse signatures. Genes in common between published and this publication’s signatures.
DOI: 10.6084/m9.figshare.14404132.v1
title: Additional file 2 of Reference-free transcriptome signatures for prostate cancer prognosis

description: Additional file 2 Published PCa risk and relapse signatures. Genes in common between published and this publication’s signatures.
DOI: 10.6084/m9.figshare.14404135
title: Additional file 3 of Reference-free transcriptome signatures for prostate cancer prognosis

description: Additional file 3 Contents and expression characteristics of all signatures in the discovery and validation datasets.
DOI: 10.6084/m9.figshare.14404135.v1
title: Additional file 3 of Reference-free transcriptome signatures for prostate cancer prognosis

description: Additional file 3 Contents and expression characteristics of all signatures in the discovery and validation datasets.
DOI: 10.6084/m9.figshare.14404139
title: Additional file 1 of Proteomic response of Escherichia coli to a membrane lytic and iron chelating truncated Amaranthus tricolor defensin

description: Additional file 1: Tables S1 and S2. Tables detailing global proteomic identifications (Table S1) and Panther Gene Ontology enrichment analysis (Table S2).
DOI: 10.6084/m9.figshare.14404139.v1
title: Additional file 1 of Proteomic response of Escherichia coli to a membrane lytic and iron chelating truncated Amaranthus tricolor defensin

description: Additional file 1: Tables S1 and S2. Tables detailing global proteomic identifications (Table S1) and Panther Gene Ontology enrichment analysis (Table S2).
DOI: 10.6084/m9.figshare.14404153
title: Additional file 1 of Applicability of somatic monitoring instructions in clinical practice guidelines on antipsychotic drug use

description: Additional file 1: Supplementary Table 1. Clinical Practice Guidelines.
DOI: 10.6084/m9.figshare.14404153.v1
title: Additional file 1 of Applicability of somatic monitoring instructions in clinical practice guidelines on antipsychotic drug use

description: Additional file 1: Supplementary Table 1. Clinical Practice Guidelines.
DOI: 10.6084/m9.figshare.14404156
title: Additional file 2 of Applicability of somatic monitoring instructions in clinical practice guidelines on antipsychotic drug use

description: Additional file 2: Supplementary Table 2. Clinical Practice Guidelines.
DOI: 10.6084/m9.figshare.14404156.v1
title: Additional file 2 of Applicability of somatic monitoring instructions in clinical practice guidelines on antipsychotic drug use

description: Additional file 2: Supplementary Table 2. Clinical Practice Guidelines.
DOI: 10.18112/openneuro.ds003611.v1.0.0
title: MPRAGE Hypersense test data 2
DOI: 10.6084/m9.figshare.14404159
title: Additional file 3 of Applicability of somatic monitoring instructions in clinical practice guidelines on antipsychotic drug use

description: Additional file 3: Supplementary Table 3. Clinical Practice Guidelines.
DOI: 10.6084/m9.figshare.14404159.v1
title: Additional file 3 of Applicability of somatic monitoring instructions in clinical practice guidelines on antipsychotic drug use

description: Additional file 3: Supplementary Table 3. Clinical Practice Guidelines.
DOI: 10.6084/m9.figshare.14404219
title: Additional file 10 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 10. BLASTx results of the 2022 candidate structured RNAs to the nr database. We display the BLASTx [15] results in output format 6 to show with which genes these candidate structures may overlap.
DOI: 10.6084/m9.figshare.14404219.v1
title: Additional file 10 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 10. BLASTx results of the 2022 candidate structured RNAs to the nr database. We display the BLASTx [15] results in output format 6 to show with which genes these candidate structures may overlap.
DOI: 10.6084/m9.figshare.14404225
title: Additional file 1 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 1: Table S1. Overview of candidate structured RNAs. We show information the 3161 candidate structured RNAs, including the p score from RNAphylo [2], number of significant covarying bases from R-scape [11], length of structure, number of instances of structure in HMP2 [9], taxonomic breakdown of contigs in which the structure is found (including domain, phylum, class, order, family, genus, and species) from One Codex [16], average percent of k-mers mapped for classification, and protein domains found within 5 kb of the structures. In a separate tab, we also include the same analyses for the 2022 candidate structured RNAs that overlapped the nr database. Additionally, we indicate which structures in Rfam [13] were predicted using this pipeline and consequently discarded because they were known structures.
DOI: 10.6084/m9.figshare.14404225.v1
title: Additional file 1 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 1: Table S1. Overview of candidate structured RNAs. We show information the 3161 candidate structured RNAs, including the p score from RNAphylo [2], number of significant covarying bases from R-scape [11], length of structure, number of instances of structure in HMP2 [9], taxonomic breakdown of contigs in which the structure is found (including domain, phylum, class, order, family, genus, and species) from One Codex [16], average percent of k-mers mapped for classification, and protein domains found within 5 kb of the structures. In a separate tab, we also include the same analyses for the 2022 candidate structured RNAs that overlapped the nr database. Additionally, we indicate which structures in Rfam [13] were predicted using this pipeline and consequently discarded because they were known structures.
DOI: 10.6084/m9.figshare.14404228
title: Additional file 2 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 2: Table S2. Candidate structured RNAs that may overlap with small proteins. We provide a table of candidate structured RNAs that overlap small protein families predicted using SmORFinder [19] and the sequence of the small proteins.
DOI: 10.6084/m9.figshare.14404228.v1
title: Additional file 2 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 2: Table S2. Candidate structured RNAs that may overlap with small proteins. We provide a table of candidate structured RNAs that overlap small protein families predicted using SmORFinder [19] and the sequence of the small proteins.
DOI: 10.6084/m9.figshare.14404231
title: Additional file 3 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 3: Table S3. Candidate structured RNAs that overlap or are palindromic. We list which candidate structured RNAs are found on the opposing strand of a different candidate structured RNA. All pairwise overlaps are provided both for the 3161 and 2022 (those that overlap the nr database) candidate structured RNAs as separate tabs. Additionally, we list which structures are palindromic, or those in which cmsearch [14] predicts the same structure overlapping the same region in opposing orientations for the 3161 and 2022 candidate structured RNAs as separate tabs.
DOI: 10.6084/m9.figshare.14404231.v1
title: Additional file 3 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 3: Table S3. Candidate structured RNAs that overlap or are palindromic. We list which candidate structured RNAs are found on the opposing strand of a different candidate structured RNA. All pairwise overlaps are provided both for the 3161 and 2022 (those that overlap the nr database) candidate structured RNAs as separate tabs. Additionally, we list which structures are palindromic, or those in which cmsearch [14] predicts the same structure overlapping the same region in opposing orientations for the 3161 and 2022 candidate structured RNAs as separate tabs.
DOI: 10.6084/m9.figshare.14404234.v1
title: Additional file 4 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 4: Table S4. Candidate structured RNAs that may be cis-regulatory based on genomic location. We determined which candidate structured RNAs were found directly upstream of genes, specifically within 25 bp of the 5′ of genes. For those genes only, we determined which protein domains were present. These candidate structured RNAs potentially represent those found in potential 5′ UTRs or at the least may be cis-acting.
DOI: 10.6084/m9.figshare.14404237
title: Additional file 5 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 5: Table S5. RPKM quantifications of structured RNAs. For all candidate structured RNAs in the genomic assemblies from our previous study [29], we provided the RNA-Seq RPKM values of those expressed as well as their genomic position on the assemblies.
DOI: 10.6084/m9.figshare.14404237.v1
title: Additional file 5 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 5: Table S5. RPKM quantifications of structured RNAs. For all candidate structured RNAs in the genomic assemblies from our previous study [29], we provided the RNA-Seq RPKM values of those expressed as well as their genomic position on the assemblies.
DOI: 10.6084/m9.figshare.14404234
title: Additional file 4 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 4: Table S4. Candidate structured RNAs that may be cis-regulatory based on genomic location. We determined which candidate structured RNAs were found directly upstream of genes, specifically within 25 bp of the 5′ of genes. For those genes only, we determined which protein domains were present. These candidate structured RNAs potentially represent those found in potential 5′ UTRs or at the least may be cis-acting.
DOI: 10.6084/m9.figshare.14404249.v1
title: Additional file 9 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 9. Alignment files of the 2022 candidate structured RNAs that overlap the nr database. We provide alignment files for each of the 2022 candidate structured RNAs as well as the calibrated cm file that can be used to search for them.
DOI: 10.6084/m9.figshare.14404246.v1
title: Additional file 8 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 8. Alignment files of the 3161 candidate structured RNAs. We provide alignment files for each of the 3161 candidate structured RNAs as well as the calibrated cm file that can be used to search for them.
DOI: 10.6084/m9.figshare.14404249
title: Additional file 9 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 9. Alignment files of the 2022 candidate structured RNAs that overlap the nr database. We provide alignment files for each of the 2022 candidate structured RNAs as well as the calibrated cm file that can be used to search for them.
DOI: 10.6084/m9.figshare.14404246
title: Additional file 8 of Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

description: Additional file 8. Alignment files of the 3161 candidate structured RNAs. We provide alignment files for each of the 3161 candidate structured RNAs as well as the calibrated cm file that can be used to search for them.
DOI: 10.6084/m9.figshare.14404258.v1
title: Additional file 12 of Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria

description: Additional file 11. Table containing the names of all genes found per MAG using KEGG and COG annotation
DOI: 10.6084/m9.figshare.14404258
title: Additional file 12 of Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria

description: Additional file 11. Table containing the names of all genes found per MAG using KEGG and COG annotation
DOI: 10.6084/m9.figshare.14404285
title: Additional file 6 of Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria

description: Additional file 5. DESeq2 results table with baseMean, Log2FoldChange, lfcSE, stat, pvalue and padj for each of the 49 studied MAGs
DOI: 10.6084/m9.figshare.14404285.v1
title: Additional file 6 of Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria

description: Additional file 5. DESeq2 results table with baseMean, Log2FoldChange, lfcSE, stat, pvalue and padj for each of the 49 studied MAGs
DOI: 10.6084/m9.figshare.14404370
title: Additional file 5 of Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus)

description: Additional file 5: Table S1. Primers sequences used in the study. AP4 (1 and 2) are for the detection of Pir-VP genes. Vpir A is for the detection of Pir-A gene while Vpir B is for the amplification of Pir-B gene. Length represents the length of the amplicon generated by each pair of primers. Table S2. ILI’s genome protein annotation using Prokka against the NCBI’s database. Table S3. ILI’s large plasmid proteins predicted by Prokka against the NCBI’s database with their corresponding functions and ID. The number of ASVs detected per sample is plotted on the axis of Observed OTUs. Function is assigned when hits with an e-value &lt; 1e- 06 were obtained. Table S4. Genomes used to for genomic similarity analysis. The genomic identity between ILI and the selected genome is shown in the last column of the table. Table S5. GenBank accession numbers and genomic characteristics of genomes used for the phylogenetic reconstruction of the ILI strain. Table S6. DDH, ANIb and TETRA values. In silico DNA-DNA hybridization (DDH) was calculated only between the ILI strain and the other evaluated strains. ANIb and TETRA were calculated for all possible comparisons. A heatmap representation of the values can be observed on Figure 3. Table S7. Virulence factors identified in the secretion systems of the strain V. diabolicus ILI. They were compared with the genomes of the V. parahaemolyticus RIMD 2210633 strain, the V. parahaemolyticus NCKU TN S02 strain, the V. parahaemolyticus BA94C2 strain and the V. diabolicus FDA 105 strain. The table includes the respective name of the genes for each genome, the gene product, the percent identity, and the percent coverage. Comparisons based on percentage of identity and coverage included are shown in key color.
DOI: 10.6084/m9.figshare.14404390.v1
title: Additional file 2 of Loss of Calretinin in L5a impairs the formation of the barrel cortex leading to abnormal whisker-mediated behaviors

description: Additional file 2: Statistical results of raw data.
DOI: 10.6084/m9.figshare.14404390
title: Additional file 2 of Loss of Calretinin in L5a impairs the formation of the barrel cortex leading to abnormal whisker-mediated behaviors

description: Additional file 2: Statistical results of raw data.
DOI: 10.6084/m9.figshare.14404391
title: Additional file 11 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 11. Details about target genes and primers used for qPCR validation analyses. Listed are specific details about the qPCR genes and primers, BLASTn results of amplicon sequences, and primer properties for 41 target genes and two normalizer genes.
DOI: 10.5281/zenodo.4682353
title: Galaxy history for the ToolFactory in Planemo.

description: Import this history into the planemo tool_factory Galaxy It contains a variety of simple demonstrations of ToolFactory generated tools
DOI: 10.6084/m9.figshare.14404394
title: Additional file 1 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 1 Results of Significance Analysis of Microarrays (SAM, FDR
DOI: 10.6084/m9.figshare.14404391.v1
title: Additional file 11 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 11. Details about target genes and primers used for qPCR validation analyses. Listed are specific details about the qPCR genes and primers, BLASTn results of amplicon sequences, and primer properties for 41 target genes and two normalizer genes.
DOI: 10.6084/m9.figshare.14404406.v1
title: Additional file 5 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 5 Results of GO/pathway term network analysis (ClueGO) associated with down-regulated differentially expressed genes (DEGs) of the Warm & Normoxic (WN) treatment group. Listed are the significantly enriched Gene Ontology (GO) terms, and KEGG or Reactome pathways (hypergeometric test p
DOI: 10.6084/m9.figshare.14404400
title: Additional file 3 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 3 Results of GO/pathway term network analysis (ClueGO) associated with up-regulated differentially expressed genes (DEGs) of the Warm & Normoxic (WN) treatment group. Listed are the significantly enriched Gene Ontology (GO) terms, and KEGG or Reactome pathways (hypergeometric test p
DOI: 10.6084/m9.figshare.14404403.v1
title: Additional file 4 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 4 Results of GO/pathway term network analysis (ClueGO) associated with up-regulated differentially expressed genes (DEGs) of the Warm & Hypoxic (WH) treatment group. Listed are the significantly enriched Gene Ontology (GO) terms, and KEGG or Reactome pathways (hypergeometric test p
DOI: 10.6084/m9.figshare.14404409
title: Additional file 6 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 6 Results of GO/pathway term network analysis (ClueGO) associated with down-regulated differentially expressed genes (DEGs) of the Warm & Hypoxic (WH) treatment group. Listed are the significantly enriched Gene Ontology (GO) terms, and KEGG or Reactome pathways (hypergeometric test p
DOI: 10.6084/m9.figshare.14404409.v1
title: Additional file 6 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 6 Results of GO/pathway term network analysis (ClueGO) associated with down-regulated differentially expressed genes (DEGs) of the Warm & Hypoxic (WH) treatment group. Listed are the significantly enriched Gene Ontology (GO) terms, and KEGG or Reactome pathways (hypergeometric test p
DOI: 10.6084/m9.figshare.14404394.v1
title: Additional file 1 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 1 Results of Significance Analysis of Microarrays (SAM, FDR
DOI: 10.6084/m9.figshare.14404403
title: Additional file 4 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 4 Results of GO/pathway term network analysis (ClueGO) associated with up-regulated differentially expressed genes (DEGs) of the Warm & Hypoxic (WH) treatment group. Listed are the significantly enriched Gene Ontology (GO) terms, and KEGG or Reactome pathways (hypergeometric test p
DOI: 10.5281/zenodo.4682368
title: On the Discoverability of npm Package Vulnerabilities in Node.js Projects

description: This package contains the scripts used for our approach in the manuscript "On the Discoverability of npm Package Vulnerabilities in Node.js Projects." For more information on how to understand the folder structure, please read the README.md.