cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8087765.v1
title: Additional file 2: of Genetic mechanism underlying sexual plasticity and its association with colour patterning in zebrafish (Danio rerio)

description: Table S9. Selected candidate sex determination genes used in this study. Table S10. Selected candidate colour patterning genes used in this study. Table S11. Quantile distribution of colour patterning genes in the caudal fin in the transcriptome profile (Log2CPM per mega base pairs). (XLSX 1847â kb)
DOI: 10.6084/m9.figshare.8087705
title: Additional file 8 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Coordinates of the genomic islands of SP-41 and XCL-2. Coordinates of the 7 genomic islands in the SP-41 genome and of the 9 genomic islands in the XCL-2 genome, as predicted by IslandViewer [26]. (CSV 1 kb)
DOI: 10.6084/m9.figshare.8087708
title: Additional file 9 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Coding sequences of SP-41 overlapping genomic islands. Coordinates and product description of coding sequence (CDS) annotations of the SP-41 genome partially or completely overlapping genomic islands predicted by IslandViewer [26]. (CSV 12 kb)
DOI: 10.6084/m9.figshare.8087702
title: Additional file 7 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Collinear, divergent, exclusive and translocated regions of the alignment of the SP-41 and XCL-2 genomes. Coordinates of the regions of the alignment of the genomes of SP-41 and XCL-2, classified as collinear (same gene order), translocated (same gene order but moved in another genomic context), divergent (two different regions present in the two genomes, with different genes), exclusive (additional region with at least one annotated feature present only in one of the two genome, while in the other genome the region is absent, or a different sequence, with no annotated features is present). (CSV 16 kb)
DOI: 10.6084/m9.figshare.8087705.v1
title: Additional file 8 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Coordinates of the genomic islands of SP-41 and XCL-2. Coordinates of the 7 genomic islands in the SP-41 genome and of the 9 genomic islands in the XCL-2 genome, as predicted by IslandViewer [26]. (CSV 1 kb)
DOI: 10.6084/m9.figshare.8087702.v1
title: Additional file 7 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Collinear, divergent, exclusive and translocated regions of the alignment of the SP-41 and XCL-2 genomes. Coordinates of the regions of the alignment of the genomes of SP-41 and XCL-2, classified as collinear (same gene order), translocated (same gene order but moved in another genomic context), divergent (two different regions present in the two genomes, with different genes), exclusive (additional region with at least one annotated feature present only in one of the two genome, while in the other genome the region is absent, or a different sequence, with no annotated features is present). (CSV 16 kb)
DOI: 10.6084/m9.figshare.8087708.v1
title: Additional file 9 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Coding sequences of SP-41 overlapping genomic islands. Coordinates and product description of coding sequence (CDS) annotations of the SP-41 genome partially or completely overlapping genomic islands predicted by IslandViewer [26]. (CSV 12 kb)
DOI: 10.6084/m9.figshare.8087681
title: Additional file 2 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: KO annotations of SP-41 proteins. KO assignments by Blastkoala [24], using the prokaryotes taxonomy group and the species_prokaryotes database to the proteins encoded by the SP-41 genome. KO annotations were assigned to 64.2% of the SP-41 proteins. (CSV 118 kb)
DOI: 10.6084/m9.figshare.8087690
title: Additional file 4 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Best Blast hit in XCL-2 proteins for each protein of SP-41. Table reporting the results of the alignment of SP-41 proteins to the XCL-2 proteins using BlastP. Only the best hit (if any) for each SP-41 protein is reported. (CSV 314 kb)
DOI: 10.6084/m9.figshare.8087693
title: Additional file 5 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Alignment of the 16S rRNA genes of SP-41 and XCL-2. Multiple sequence alignment of the three 16S rRNA genes of SP-41, XCL-2 (in a single sequence, as its 3 copies are identical) and E. coli K12. The borders of the hypervariable regions in the alignment were annotated, based on their coordinates in the E. coli sequence. (TXT 17 kb)
DOI: 10.6084/m9.figshare.8087684
title: Additional file 3 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Pairwise average nucleotide identity. Pairwise average nucleotide identity (ANI) computed using the ANIb algorithm, of the genome of SP-41 and related genomes. (CSV 1 kb)
DOI: 10.6084/m9.figshare.8087690.v1
title: Additional file 4 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Best Blast hit in XCL-2 proteins for each protein of SP-41. Table reporting the results of the alignment of SP-41 proteins to the XCL-2 proteins using BlastP. Only the best hit (if any) for each SP-41 protein is reported. (CSV 314 kb)
DOI: 10.6084/m9.figshare.8087693.v1
title: Additional file 5 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Alignment of the 16S rRNA genes of SP-41 and XCL-2. Multiple sequence alignment of the three 16S rRNA genes of SP-41, XCL-2 (in a single sequence, as its 3 copies are identical) and E. coli K12. The borders of the hypervariable regions in the alignment were annotated, based on their coordinates in the E. coli sequence. (TXT 17 kb)
DOI: 10.6084/m9.figshare.8087681.v1
title: Additional file 2 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: KO annotations of SP-41 proteins. KO assignments by Blastkoala [24], using the prokaryotes taxonomy group and the species_prokaryotes database to the proteins encoded by the SP-41 genome. KO annotations were assigned to 64.2% of the SP-41 proteins. (CSV 118 kb)
DOI: 10.6084/m9.figshare.8087678
title: Additional file 1 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: COG annotations of SP-41 proteins. COG assignments by CD-search [23] using the COG database [74] to the proteins encoded by the SP-41 genome. COG annotations were assigned to 64.0% of the SP-41 proteins. (CSV 44 kb)
DOI: 10.6084/m9.figshare.8087684.v1
title: Additional file 3 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Pairwise average nucleotide identity. Pairwise average nucleotide identity (ANI) computed using the ANIb algorithm, of the genome of SP-41 and related genomes. (CSV 1 kb)
DOI: 10.6084/m9.figshare.8087678.v1
title: Additional file 1 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: COG annotations of SP-41 proteins. COG assignments by CD-search [23] using the COG database [74] to the proteins encoded by the SP-41 genome. COG annotations were assigned to 64.0% of the SP-41 proteins. (CSV 44 kb)
DOI: 10.6084/m9.figshare.8087663
title: Additional file 14 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: KO annotations of XCL-2 proteins. KO assignments by Blastkoala [24], using the prokaryotes taxonomy group and the species_prokaryotes database to the proteins encoded by the XCL-2 genome. KO annotations were assigned to 63.9% of the XCL-2 proteins. (CSV 115 kb)
DOI: 10.6084/m9.figshare.8087663.v1
title: Additional file 14 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: KO annotations of XCL-2 proteins. KO assignments by Blastkoala [24], using the prokaryotes taxonomy group and the species_prokaryotes database to the proteins encoded by the XCL-2 genome. KO annotations were assigned to 63.9% of the XCL-2 proteins. (CSV 115 kb)
DOI: 10.6084/m9.figshare.8087651
title: MOESM1 of Strong concordance between percent inhibition in oocyst and sporozoite intensities in a Plasmodium falciparum standard membrane-feeding assay

description: Additional file 1: Table S1. Oocyst and sporozoite numbers used for the analysis. Details of each feeding condition and resulting oocyst and sporozoite numbers in each mosquito are shown (XLSX 29 kb).
DOI: 10.6084/m9.figshare.8087654
title: Additional file 13 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: COG annotations of XCL-2 proteins. COG assignments by CD-search [23] using the COG database [74] to the proteins encoded by the XCL-2 genome. COG annotations were assigned to 62.7% of the XCL-2 proteins. (CSV 42 kb)
DOI: 10.6084/m9.figshare.8087648
title: Additional file 12 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Homologs of the Hydrogenase Gene Cluster II proteins. Hits by BlastP in the NCBI Refseq Protein database of the protein encoded by the Hydrogenase Gene Cluster II region of the SP-41 genome. (CSV 1389 kb)
DOI: 10.6084/m9.figshare.8087651.v1
title: MOESM1 of Strong concordance between percent inhibition in oocyst and sporozoite intensities in a Plasmodium falciparum standard membrane-feeding assay

description: Additional file 1: Table S1. Oocyst and sporozoite numbers used for the analysis. Details of each feeding condition and resulting oocyst and sporozoite numbers in each mosquito are shown (XLSX 29 kb).
DOI: 10.6084/m9.figshare.8087654.v1
title: Additional file 13 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: COG annotations of XCL-2 proteins. COG assignments by CD-search [23] using the COG database [74] to the proteins encoded by the XCL-2 genome. COG annotations were assigned to 62.7% of the XCL-2 proteins. (CSV 42 kb)
DOI: 10.6084/m9.figshare.8087636
title: Additional file 10 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Coding sequences of XCL-2 overlapping genomic islands. Coordinates and product description of coding sequence (CDS) annotations of the XCL-2 genome partially or completely overlapping genomic islands predicted by IslandViewer [26]. (CSV 19 kb)
DOI: 10.6084/m9.figshare.8087645
title: Additional file 11 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Presence of CRISPR loci and transposase abundance in genomes of a group of autotroph Proteobacteria. Presence of CRISPRs and transposases belonging to Pfam families previously selected for a similar analysis by [21] in a set of genomes of autotroph proteobacterial strains, described in the same study. The annotation data (number of CRISPRs and Pfam annotations) was obtained from the IMG/M platform [77]. The file also contains a transcript of the R session in which the statistical significance of the differences was assessed.(CSV 7 kb)
DOI: 10.6084/m9.figshare.8087636.v1
title: Additional file 10 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Coding sequences of XCL-2 overlapping genomic islands. Coordinates and product description of coding sequence (CDS) annotations of the XCL-2 genome partially or completely overlapping genomic islands predicted by IslandViewer [26]. (CSV 19 kb)
DOI: 10.6084/m9.figshare.8087645.v1
title: Additional file 11 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Presence of CRISPR loci and transposase abundance in genomes of a group of autotroph Proteobacteria. Presence of CRISPRs and transposases belonging to Pfam families previously selected for a similar analysis by [21] in a set of genomes of autotroph proteobacterial strains, described in the same study. The annotation data (number of CRISPRs and Pfam annotations) was obtained from the IMG/M platform [77]. The file also contains a transcript of the R session in which the statistical significance of the differences was assessed.(CSV 7 kb)
DOI: 10.6084/m9.figshare.8087648.v1
title: Additional file 12 of Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

description: Homologs of the Hydrogenase Gene Cluster II proteins. Hits by BlastP in the NCBI Refseq Protein database of the protein encoded by the Hydrogenase Gene Cluster II region of the SP-41 genome. (CSV 1389 kb)
DOI: 10.6084/m9.figshare.8087603
title: Additional file 2: of Factors that influence transition to advanced roles by RN to BSN nurses, in three selected hospitals of Central-Uganda

description: Data set (XLS). This is the data file where all the survey data collected was entered and used for analysis. (XLS 170 kb)
DOI: 10.6084/m9.figshare.8087603.v1
title: Additional file 2: of Factors that influence transition to advanced roles by RN to BSN nurses, in three selected hospitals of Central-Uganda

description: Data set (XLS). This is the data file where all the survey data collected was entered and used for analysis. (XLS 170 kb)
DOI: 10.6084/m9.figshare.8087570
title: Additional file 1: of Staphylococcus aureus colonization in hemodialysis patients: a prospective 25 months observational study

description: Overview on detected S. aureus isolates and their classification. 1Table is read line by line for each patient ID. Each patient ID is divided into detections in nose and CVC for each sampling month. Same results are framed. 2Loc. – swab location (Nose and if present CVC); negative – no S. aureus found; no – no CVC existing; MRSA in bold. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.8087570.v1
title: Additional file 1: of Staphylococcus aureus colonization in hemodialysis patients: a prospective 25 months observational study

description: Overview on detected S. aureus isolates and their classification. 1Table is read line by line for each patient ID. Each patient ID is divided into detections in nose and CVC for each sampling month. Same results are framed. 2Loc. – swab location (Nose and if present CVC); negative – no S. aureus found; no – no CVC existing; MRSA in bold. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.8087549
title: Additional file 6 of Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

description: Supplementary data table for the Quest for Orthologs benchmark containing the underlying data to Additional fileÂ 4: Figure S4. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8087549.v1
title: Additional file 6 of Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

description: Supplementary data table for the Quest for Orthologs benchmark containing the underlying data to Additional fileÂ 4: Figure S4. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8087522
title: Additional file 3: of The influence of vgll3 genotypes on sea age at maturity is altered in farmed mowi strain Atlantic salmon

description: A table describing the individual fish number (Pit tag), smolt weight, smolt length, family, sex, sea age at maturity and vgll3 genotype. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.8087522.v1
title: Additional file 3: of The influence of vgll3 genotypes on sea age at maturity is altered in farmed mowi strain Atlantic salmon

description: A table describing the individual fish number (Pit tag), smolt weight, smolt length, family, sex, sea age at maturity and vgll3 genotype. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.8087477
title: Additional file 2: of Frequency of pathogenic germline variants in BRCA1, BRCA2, PALB2, CHEK2 and TP53 in ductal carcinoma in situ diagnosed in women under the age of 50â years

description: Coverage data for all pathogenic variants identified. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8087477.v1
title: Additional file 2: of Frequency of pathogenic germline variants in BRCA1, BRCA2, PALB2, CHEK2 and TP53 in ductal carcinoma in situ diagnosed in women under the age of 50â years

description: Coverage data for all pathogenic variants identified. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8087417
title: Additional file 7: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: Mapped candidate single nucleotide polymorphisms (SNPs) identified between mesotrione-resistant and susceptible waterhemp (Amaranthus tuberculatus (GZ 19875 kb)
DOI: 10.6084/m9.figshare.8087405
title: Additional file 5: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: Characterization of waterhemp (Amaranthus tuberculatus) differentially expressed transcripts (DETs) using gene ontology overrepresentation. A Fisher’s Exact Test [42] with a Bonferroni correction [43] was used to identify significantly (P
DOI: 10.6084/m9.figshare.8087411
title: Additional file 6: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: Waterhemp (Amaranthus tuberculatus) differentially expressed transcripts (DETs) cluster relative to Amaranthus hypochondriacus genome. BLASTN (E
DOI: 10.6084/m9.figshare.8087405.v1
title: Additional file 5: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: Characterization of waterhemp (Amaranthus tuberculatus) differentially expressed transcripts (DETs) using gene ontology overrepresentation. A Fisher’s Exact Test [42] with a Bonferroni correction [43] was used to identify significantly (P
DOI: 10.6084/m9.figshare.8087411.v1
title: Additional file 6: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: Waterhemp (Amaranthus tuberculatus) differentially expressed transcripts (DETs) cluster relative to Amaranthus hypochondriacus genome. BLASTN (E
DOI: 10.6084/m9.figshare.8087399
title: Additional file 4: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: dentification of waterhemp (Amaranthus tuberculatus) transcripts significantly (FDR
DOI: 10.6084/m9.figshare.8087417.v1
title: Additional file 7: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: Mapped candidate single nucleotide polymorphisms (SNPs) identified between mesotrione-resistant and susceptible waterhemp (Amaranthus tuberculatus (GZ 19875 kb)
DOI: 10.6084/m9.figshare.8087399.v1
title: Additional file 4: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: dentification of waterhemp (Amaranthus tuberculatus) transcripts significantly (FDR
DOI: 10.6084/m9.figshare.8087393
title: Additional file 3: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: Annotation of the waterhemp (Amaranthus tuberculatus) version 4 transcriptome. BLASTX [26] was used to compare waterhemp transcriptome sequences against the Uniref100 (version 01/22/2016, [31]) nonredundant protein database. (XLSX 919 kb)
DOI: 10.6084/m9.figshare.8087393.v1
title: Additional file 3: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: Annotation of the waterhemp (Amaranthus tuberculatus) version 4 transcriptome. BLASTX [26] was used to compare waterhemp transcriptome sequences against the Uniref100 (version 01/22/2016, [31]) nonredundant protein database. (XLSX 919 kb)
DOI: 10.6084/m9.figshare.8087381
title: Additional file 2: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: Waterhemp (Amaranthus tuberculatus) v4 transcriptome sequences in FASTA format. (XLSX 21386 kb)
DOI: 10.6084/m9.figshare.8087381.v1
title: Additional file 2: of Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

description: Waterhemp (Amaranthus tuberculatus) v4 transcriptome sequences in FASTA format. (XLSX 21386 kb)
DOI: 10.6084/m9.figshare.8087360
title: MOESM4 of Tissue-specific signatures in tick cell line MS profiles

description: Additional file 4: Table S7. List of all proteins identified using 2DE followed by MALDI-TOF/TOF MS/MS.
DOI: 10.6084/m9.figshare.8087354
title: MOESM2 of Tissue-specific signatures in tick cell line MS profiles

description: Additional file 2: Table S2. Lists of all proteins identified in the acidic extracts of IRE11 tick cell line using in solution digestion followed by ESI-Q-TOF-MS/MS. Table S3. Lists of all proteins identified in the acidic extracts of IRE/CTVM19 tick cell line using in solution digestion followed by ESI-Q-TOF-MS/MS. Table S4. Lists of all proteins identified in the acidic extracts of IRE/CTVM20 tick cell line using in solution digestion followed by ESI-Q-TOF-MS/MS. Table S5. Lists of all proteins identified in the acidic extracts of ISE6 tick cell line using in solution digestion followed by ESI-Q-TOF-MS/MS. Table S6. Lists of all proteins identified in the acidic extracts of ISE18 tick cell line using in solution digestion followed by ESI-Q-TOF-MS/MS.