cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13010405
title: Image_statistics

description: Tables describing the indices calculated for the quantitative analysis of filters:- MSSIM- PSNR- EC- EPI- ENL<br>
DOI: 10.6084/m9.figshare.13010405.v2
title: Image_statistics

description: Tables describing the indices calculated for the quantitative analysis of filters:- MSSIM- PSNR- EC- EPI- ENL<br>
DOI: 10.6084/m9.figshare.13010405.v1
title: Image_statistics

description: Tables describing the indices calculated for the quantitative analysis of filters:- MSSIM- PSNR- EC- EPI- ENL<br>
DOI: 10.5281/zenodo.4050654
title: Temperature effect on the velocity-porosity relationship in rocks

description: These data are the compressional wave waveform data obtained by Ba et al. (2019) through ultrasonic experimental measurements on carbonates at different temperatures. In the package of data, each folder of 1, 2, 4, 5, 6, 7, 8, 9, 10 and 11 indicates sample number, respectively. For each sample with different pore fluids, waveforms measured at different temperatures are saved as different TXT files. For the title of each TXT file, it includes the sample number, pore fluid and temperature value. For instance, “1_Fullwater_20℃_80 MPa” denotes that sample 1 with the full water saturation is measured at the 20℃ and confining pressure of 80 MPa, while “2_Fulloil_140℃_20 MPa” denotes that sample 2 with the full oil saturation is measured at 140℃ and confining pressure of 20 MPa. The package also contains the TXT files of sample length and system delay time.
DOI: 10.5281/zenodo.3594270
title: Temperature effect on the velocity-porosity relationship in rocks

description: These data are the compressional wave waveform data obtained by Ba et al. (2019) through ultrasonic experimental measurements on carbonates at different temperatures. In the package of data, each folder of 1, 2, 4, 5, 6, 7, 8, 9, 10 and 11 indicates sample number, respectively. For each sample with different pore fluids, waveforms measured at different temperatures are saved as different TXT files. For the title of each TXT file, it includes the sample number, pore fluid and temperature value. For instance, “1_Fullwater_20℃_80 MPa” denotes that sample 1 with the full water saturation is measured at the 20℃ and confining pressure of 80 MPa, while “2_Fulloil_140℃_20 MPa” denotes that sample 2 with the full oil saturation is measured at 140℃ and confining pressure of 20 MPa. The package also contains the TXT files of sample length and system delay time.
DOI: 10.21227/435x-yn69
title: supplementary materials (Table S1 and Table S1)

description: Supplementary materials (Table S2).
DOI: 10.6084/m9.figshare.13010567
title: Data

description: Data used in the analysis.
DOI: 10.6084/m9.figshare.13010567.v2
title: Data

description: Data used in the analysis.
DOI: 10.6084/m9.figshare.13010567.v1
title: Data

description: Data used in the analysis.
DOI: 10.6084/m9.figshare.13010519
title: R0230_20181029a_videos

description: Rat 0230, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13010519.v1
title: R0230_20181029a_videos

description: Rat 0230, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13010643
title: Additional file 1 of Mitochondrial-nuclear coadaptation revealed through mtDNA replacements in Saccharomyces cerevisiae

description: Additional file 1: Table S1. Strain table. Table S2. SNP table for mitochondrial coding sequences for the 15 parental strains. Allzle numbering is arbitrary. Table S3. Mitochondrial coding sequence statistics. Table S4. Mitochondrial × nuclear interactions (mt × n) within single environments. To determine the significance of each term, ANOVAs comparing the full model with a model lacking the indicated term were evaluated. Each factor was treated as a random effect. Full model: n + mt + (mt × n). Table S5. Phenotypic variance analysis to show the amount of variance contributed by mitochondrial, nuclear background, and mitonuclear interactions in all growth conditions. Table S6. Mitochondrial × nuclear × environment interactions (mt × n × e). To determine the significance of each term, ANOVAs comparing the full model with a model lacking the indicated term were evaluated. Each factor was treated as a random effect. Full model: n + mt + e + (mt × n) + (n × e) + (mt × e) + (mt × n × e). Table S7. Phenotypic variance of strains with original, synthetic, and all possible mitonuclear combinations across all growth conditions. Student’s t-test were performed to determine whether the difference among strains with original and synthetic combinations is statistically significant. Table S8. Fixed effect model, two-way ANOVA table showing mt × n interactions for each mtDNA exchange between two strains. The P values for genetic terms (nuclear, mitochondrial, mitonuclear epistasis), type of epistasis, and estimated strength of epistasis were provided for each pairwise mtDNA exchange. Table S9. Numbers of significant mitonuclear tests following mtDNA exchanges within and between clades. Table S10. Mitochondrial genotype-phenotype association tests.
DOI: 10.6084/m9.figshare.13010643.v1
title: Additional file 1 of Mitochondrial-nuclear coadaptation revealed through mtDNA replacements in Saccharomyces cerevisiae

description: Additional file 1: Table S1. Strain table. Table S2. SNP table for mitochondrial coding sequences for the 15 parental strains. Allzle numbering is arbitrary. Table S3. Mitochondrial coding sequence statistics. Table S4. Mitochondrial × nuclear interactions (mt × n) within single environments. To determine the significance of each term, ANOVAs comparing the full model with a model lacking the indicated term were evaluated. Each factor was treated as a random effect. Full model: n + mt + (mt × n). Table S5. Phenotypic variance analysis to show the amount of variance contributed by mitochondrial, nuclear background, and mitonuclear interactions in all growth conditions. Table S6. Mitochondrial × nuclear × environment interactions (mt × n × e). To determine the significance of each term, ANOVAs comparing the full model with a model lacking the indicated term were evaluated. Each factor was treated as a random effect. Full model: n + mt + e + (mt × n) + (n × e) + (mt × e) + (mt × n × e). Table S7. Phenotypic variance of strains with original, synthetic, and all possible mitonuclear combinations across all growth conditions. Student’s t-test were performed to determine whether the difference among strains with original and synthetic combinations is statistically significant. Table S8. Fixed effect model, two-way ANOVA table showing mt × n interactions for each mtDNA exchange between two strains. The P values for genetic terms (nuclear, mitochondrial, mitonuclear epistasis), type of epistasis, and estimated strength of epistasis were provided for each pairwise mtDNA exchange. Table S9. Numbers of significant mitonuclear tests following mtDNA exchanges within and between clades. Table S10. Mitochondrial genotype-phenotype association tests.
DOI: 10.6084/m9.figshare.13010702
title: Additional file 2 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 2. Lists of common DEGs between the P. margaritifera albino phenotype and black wild-type phenotype overlapping the three datasets (Juvenile, Mantle and Pearl Sac).
DOI: 10.6084/m9.figshare.13010699
title: Additional file 1 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 1. Lists of DEGs between the P. margaritifera albino phenotype and black wild-type phenotype, associated statistics and annotation for the three datasets (Juvenile, Mantle and Pearl Sac).
DOI: 10.6084/m9.figshare.13010705
title: Additional file 3 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 3. Lists of enriched GO terms in the P. margaritifera albino phenotype compared with the black wild-type phenotype in the three datasets (Juvenile, Mantle and Pearl Sac).
DOI: 10.6084/m9.figshare.13010702.v1
title: Additional file 2 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 2. Lists of common DEGs between the P. margaritifera albino phenotype and black wild-type phenotype overlapping the three datasets (Juvenile, Mantle and Pearl Sac).
DOI: 10.6084/m9.figshare.13010711.v1
title: Additional file 5 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 5. List of tyrosinase-related transcripts in P. margaritifera reference transcriptome.
DOI: 10.6084/m9.figshare.13010714.v1
title: Additional file 6 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 6. List of 159 candidate SNPs, i.e., common SNPs among outliers detected with PCAdapt and phenotype-associated SNPs detected with lfmm, based on filtered SNPs called with Freebayes in both Juvenile and Mantle datasets.
DOI: 10.6084/m9.figshare.13010717.v1
title: Additional file 7 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 7. List of transcripts showing significant differential splicing (adjusted p value
DOI: 10.6084/m9.figshare.13010705.v1
title: Additional file 3 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 3. Lists of enriched GO terms in the P. margaritifera albino phenotype compared with the black wild-type phenotype in the three datasets (Juvenile, Mantle and Pearl Sac).
DOI: 10.6084/m9.figshare.13010699.v1
title: Additional file 1 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 1. Lists of DEGs between the P. margaritifera albino phenotype and black wild-type phenotype, associated statistics and annotation for the three datasets (Juvenile, Mantle and Pearl Sac).
DOI: 10.6084/m9.figshare.13010703.v1
title: Additional file 10 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 10: Data S3. All manually corrected FASTA sequences of platyhelminth TNF homologs.
DOI: 10.6084/m9.figshare.13010703
title: Additional file 10 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 10: Data S3. All manually corrected FASTA sequences of platyhelminth TNF homologs.
DOI: 10.6084/m9.figshare.13010706
title: Additional file 11 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 11: Table S4. Detailed information of platyhelminth TNF homologs.
DOI: 10.6084/m9.figshare.13010706.v1
title: Additional file 11 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 11: Table S4. Detailed information of platyhelminth TNF homologs.
DOI: 10.6084/m9.figshare.13010711
title: Additional file 5 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 5. List of tyrosinase-related transcripts in P. margaritifera reference transcriptome.
DOI: 10.6084/m9.figshare.13010712.v1
title: Additional file 13 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 13: Table S5. BLASTp results of alignments between human TNF and platyhelminth TNF homologs.
DOI: 10.6084/m9.figshare.13010718.v1
title: Additional file 1 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 1: Table S1. Accession numbers of all sequences used in the phylogenetic analysis.
DOI: 10.6084/m9.figshare.13010724.v1
title: Additional file 3 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 3: Table S2. Detailed information of platyhelminth TNFR homologs.
DOI: 10.6084/m9.figshare.13010712
title: Additional file 13 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 13: Table S5. BLASTp results of alignments between human TNF and platyhelminth TNF homologs.
DOI: 10.6084/m9.figshare.13010727.v1
title: Additional file 4 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 4: Data S1. All manually corrected FASTA sequences of platyhelminth TNFR homologs.
DOI: 10.6084/m9.figshare.13010733.v1
title: Additional file 6 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 6: Table S3. BLASTp results of alignments between human TNFR and platyhelminth TNFR homologs.
DOI: 10.6084/m9.figshare.13010727
title: Additional file 4 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 4: Data S1. All manually corrected FASTA sequences of platyhelminth TNFR homologs.
DOI: 10.6084/m9.figshare.13010714
title: Additional file 6 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 6. List of 159 candidate SNPs, i.e., common SNPs among outliers detected with PCAdapt and phenotype-associated SNPs detected with lfmm, based on filtered SNPs called with Freebayes in both Juvenile and Mantle datasets.
DOI: 10.6084/m9.figshare.13010717
title: Additional file 7 of Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

description: Additional file 7. List of transcripts showing significant differential splicing (adjusted p value
DOI: 10.6084/m9.figshare.13010834
title: Additional file 2 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 2 Table S2. Taxonomy of C-Type Lectin-Like HMM Hits. The consensus sequence of cyanobacterial C-type lectin-like predicted domains was generated via alignment of DGR-associated C-termini (up to 200 amino acids) and confirmed with pHMM scan. The taxonomy is summarized for those genomes that contain orthologs.
DOI: 10.6084/m9.figshare.13010831
title: Additional file 1 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 1 Table S1. RT/Species Table. Summary of all DGR-RTs found in cyanobacterial genomes with taxonomic and known physiological information noted. Domain annotations for all DGR-internal VPs and Remote VPs identified as having VR/TR homology are also summarized. See Table S6 for information regarding taxonomic affiliations.
DOI: 10.6084/m9.figshare.13010837
title: Additional file 3 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 3 Table S3. Clec Variable Protein Paralogs. A subset of 21 high quality genomes were chosen to assess the presence of DGR-VP paralogs. This is a summary of VP paralogs identified and their domains.
DOI: 10.6084/m9.figshare.13010831.v1
title: Additional file 1 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 1 Table S1. RT/Species Table. Summary of all DGR-RTs found in cyanobacterial genomes with taxonomic and known physiological information noted. Domain annotations for all DGR-internal VPs and Remote VPs identified as having VR/TR homology are also summarized. See Table S6 for information regarding taxonomic affiliations.
DOI: 10.6084/m9.figshare.13010849
title: Additional file 7 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 7 Table S6. Updated Cyanobacterial Taxonomy. Taxonomic assignment for each cyanobacterial genome was generated using relative evolutionary divergence and average nucleotide identity with the Genome Taxonomy Database Toolkit (GTDB-Tk) [75] based on the Genome Taxonomy Database (GTDB) [76].
DOI: 10.6084/m9.figshare.13010840
title: Additional file 4 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 4 Table S4. DGR-Proximal Transposable Elements. All transposable elements found in proximity to DGRs are listed, including transposase family and mechanisms of integration.
DOI: 10.6084/m9.figshare.13010843
title: Additional file 5 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 5 Table S5. Genes within DGR Neighborhoods. Genes found proximal to cyanobacterial DGR cassettes are annotated with predicted function and counts for each annotated function displayed.
DOI: 10.6084/m9.figshare.13010837.v1
title: Additional file 3 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 3 Table S3. Clec Variable Protein Paralogs. A subset of 21 high quality genomes were chosen to assess the presence of DGR-VP paralogs. This is a summary of VP paralogs identified and their domains.
DOI: 10.6084/m9.figshare.13010840.v1
title: Additional file 4 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 4 Table S4. DGR-Proximal Transposable Elements. All transposable elements found in proximity to DGRs are listed, including transposase family and mechanisms of integration.
DOI: 10.6084/m9.figshare.13010843.v1
title: Additional file 5 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 5 Table S5. Genes within DGR Neighborhoods. Genes found proximal to cyanobacterial DGR cassettes are annotated with predicted function and counts for each annotated function displayed.
DOI: 10.6084/m9.figshare.13010849.v1
title: Additional file 7 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 7 Table S6. Updated Cyanobacterial Taxonomy. Taxonomic assignment for each cyanobacterial genome was generated using relative evolutionary divergence and average nucleotide identity with the Genome Taxonomy Database Toolkit (GTDB-Tk) [75] based on the Genome Taxonomy Database (GTDB) [76].
DOI: 10.6084/m9.figshare.13010834.v1
title: Additional file 2 of Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

description: Additional file 2 Table S2. Taxonomy of C-Type Lectin-Like HMM Hits. The consensus sequence of cyanobacterial C-type lectin-like predicted domains was generated via alignment of DGR-associated C-termini (up to 200 amino acids) and confirmed with pHMM scan. The taxonomy is summarized for those genomes that contain orthologs.
DOI: 10.6084/m9.figshare.13010862
title: Additional file 1 of Larval ecology and infestation indices of two major arbovirus vectors, Aedes aegypti and Aedes albopictus (Diptera: Culicidae), in Brazzaville, the capital city of the Republic of the Congo

description: Additional file 1: Table S1. Input files used for modelling binary logistic regression and a negative binomial regression model.
DOI: 10.6084/m9.figshare.13010861
title: Additional file 2 of UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells

description: Additional file 2. List of citations supporting UTX-bound genes involved in glial/astrocytic differentiation.
DOI: 10.6084/m9.figshare.13010861.v1
title: Additional file 2 of UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells

description: Additional file 2. List of citations supporting UTX-bound genes involved in glial/astrocytic differentiation.
DOI: 10.6084/m9.figshare.13010862.v1
title: Additional file 1 of Larval ecology and infestation indices of two major arbovirus vectors, Aedes aegypti and Aedes albopictus (Diptera: Culicidae), in Brazzaville, the capital city of the Republic of the Congo

description: Additional file 1: Table S1. Input files used for modelling binary logistic regression and a negative binomial regression model.
DOI: 10.6084/m9.figshare.13010867
title: Additional file 2 of Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells

description: Additional file 2 List of R. conorii coding genes and their expression during infection of HMECs and AAE2 cells, in vitro.
DOI: 10.6084/m9.figshare.13010873.v1
title: Additional file 4 of Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells

description: Additional file 4 List of different categories (Ad, Ai, I, O and IP) of transcription start sites identified by TSSAR in R. conorii genome during the infection of HMECs, in vitro.
DOI: 10.6084/m9.figshare.13010873
title: Additional file 4 of Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells

description: Additional file 4 List of different categories (Ad, Ai, I, O and IP) of transcription start sites identified by TSSAR in R. conorii genome during the infection of HMECs, in vitro.
DOI: 10.6084/m9.figshare.13010876
title: Additional file 5 of Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells

description: Additional file 5 List of different categories (Ad, Ai, I, O and IP) of transcription start sites identified by TSSAR in R. conorii genome during the infection of AAE2 cells, in vitro.
DOI: 10.6084/m9.figshare.13010724
title: Additional file 3 of The evolution of TNF signaling in platyhelminths suggests the cooptation of TNF receptor in the host-parasite interplay

description: Additional file 3: Table S2. Detailed information of platyhelminth TNFR homologs.
DOI: 10.6084/m9.figshare.13010867.v1
title: Additional file 2 of Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells

description: Additional file 2 List of R. conorii coding genes and their expression during infection of HMECs and AAE2 cells, in vitro.
DOI: 10.6084/m9.figshare.13010885.v1
title: Additional file 8 of Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells

description: Additional file 8. List of primers used in this study.