cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13467037
title: Additional file 3 of annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

description: Additional file 3: Table S2. Domain retention conditions for annotation. Listed are conditions for domain retention status for Gene1A (5` gene) and Gene1B (3` gene). Domain retention status for Gene1A depends on the direction of the left breakpoint with respect to the domain and the gene body and domain retention status for Gene1B depends on the direction of the right breakpoint with respect to domain and gene body.
DOI: 10.6084/m9.figshare.13467089.v1
title: Additional file 6 of Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic

description: Additional file 6 : Table S1. Reported / simulated total number of Zika cases / ZIKV infections imported in each susceptible spatial unit during 2015–2016, together with the estimated reporting index.
DOI: 10.6084/m9.figshare.13467083.v1
title: Additional file 3 of Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic

description: Additional file 3. : R Code.
DOI: 10.6084/m9.figshare.13467083
title: Additional file 3 of Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic

description: Additional file 3. : R Code.
DOI: 10.6084/m9.figshare.13467091
title: Additional file 7 of Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic

description: Additional file 7 : Table S2. Estimated probability that no onward spread of ZIKV occurred following importation during 2015–2016 for each susceptible spatial unit.
DOI: 10.6084/m9.figshare.13467089
title: Additional file 6 of Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic

description: Additional file 6 : Table S1. Reported / simulated total number of Zika cases / ZIKV infections imported in each susceptible spatial unit during 2015–2016, together with the estimated reporting index.
DOI: 10.6084/m9.figshare.13467081
title: Additional file 2 of Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic

description: Additional file 2 : Data S1. Weekly number of reported autochthonous Zika cases by each country or subdivision during 2015–2016.
DOI: 10.6084/m9.figshare.13467091.v1
title: Additional file 7 of Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic

description: Additional file 7 : Table S2. Estimated probability that no onward spread of ZIKV occurred following importation during 2015–2016 for each susceptible spatial unit.
DOI: 10.6084/m9.figshare.13467081.v1
title: Additional file 2 of Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic

description: Additional file 2 : Data S1. Weekly number of reported autochthonous Zika cases by each country or subdivision during 2015–2016.
DOI: 10.6084/m9.figshare.13467093
title: Additional file 8 of Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic

description: Additional file 8 : Table S3. List of first-level country subdivisions belonging to each susceptible spatial unit.
DOI: 10.6084/m9.figshare.13467093.v1
title: Additional file 8 of Mapping the cryptic spread of the 2015–2016 global Zika virus epidemic

description: Additional file 8 : Table S3. List of first-level country subdivisions belonging to each susceptible spatial unit.
DOI: 10.6084/m9.figshare.13467101.v1
title: Additional file 11 of In Xenopus ependymal cilia drive embryonic CSF circulation and brain development independently of cardiac pulsatile forces

description: Additional file 11: Movie S9. Video shows a stage 49 tadpole mid-sagittal plane focused on the hypothalamic region following NiCl2 injection. Pulsatile flow pointed with the white arrow.
DOI: 10.6084/m9.figshare.13467121
title: Additional file 5 of In Xenopus ependymal cilia drive embryonic CSF circulation and brain development independently of cardiac pulsatile forces

description: Additional file 5: Movie S4. Video is focused at the lateral and 3rd ventricle of the stage 49 tadpole. Intercompartmental CSF movement is bidirectional. Dorsal—rostral CSF flow from the third ventricle is opposite to the dorsal- caudal flow generated from the lateral ventricle. Similarly, ventral flow is also polarized in the opposite direction, 3rd ventricle flow is now caudal, whereas the lateral ventricle flow is directed rostrally (30fps).
DOI: 10.6084/m9.figshare.13467121.v1
title: Additional file 5 of In Xenopus ependymal cilia drive embryonic CSF circulation and brain development independently of cardiac pulsatile forces

description: Additional file 5: Movie S4. Video is focused at the lateral and 3rd ventricle of the stage 49 tadpole. Intercompartmental CSF movement is bidirectional. Dorsal—rostral CSF flow from the third ventricle is opposite to the dorsal- caudal flow generated from the lateral ventricle. Similarly, ventral flow is also polarized in the opposite direction, 3rd ventricle flow is now caudal, whereas the lateral ventricle flow is directed rostrally (30fps).
DOI: 10.6084/m9.figshare.13467101
title: Additional file 11 of In Xenopus ependymal cilia drive embryonic CSF circulation and brain development independently of cardiac pulsatile forces

description: Additional file 11: Movie S9. Video shows a stage 49 tadpole mid-sagittal plane focused on the hypothalamic region following NiCl2 injection. Pulsatile flow pointed with the white arrow.
DOI: 10.6084/m9.figshare.13467163
title: Additional file 2 of Quantitative assessment of the impact of cryopreservation on human bone marrow-derived mesenchymal stem cells: up to 24 h post-thaw and beyond

description: Additional file 2: Figures S9-S15. fresh and cryopreserved cells stained positive for Oil Red O staining and Alizarin Red staining after incubation with adipogenic and osteogenic differentiation media. Figure S9. Oil Red O staining of fresh and cryopreserved M4 cells following 19 days of incubation in adipogenic differentiation media: Light microscopy representative images: (A) M4 fresh control well, (B) M4 fresh differentiation well, (C) M4 cryopreserved control well, (D) M4 cryopreserved differentiation well. Scale bars represent 100μm. Figure S10. Oil Red O staining of fresh and cryopreserved M6 cells following 19 days of incubation in adipogenic differentiation media: Light microscopy representative images: (A) M6 fresh control well, (B) M6 fresh differentiation well, (C) M6 cryopreserved control well, (D) M6 cryopreserved differentiation well. Scale bars represent 100μm. Figure S11. Oil Red O staining of fresh and cryopreserved M7 cells following 19 days of incubation in adipoegnic differentiation media: Light microscopy representative images: (A) M7 fresh control well, (B) M7 fresh differentiation well, (C) M7 cryopreserved control well, (D) M7 cryopreserved differentiation well. Scale bars represent 100μm. Figure S12. Alizarin Red staining of fresh and cryopreserved M4 cells following 16 days of incubation in osteogenic differentiation media: Light microscopy representative images: (A) M4 fresh control well, (B) M4 fresh differentiation well, (C) M4 cryopreserved control well, (D) M4 cryopreserved differentiation well. Scale bars represent 100μm. Figure S13. Alizarin Red staining of fresh and cryopreserved M6 cells following 16 days of incubation with osteogenic differentiation media: Light microscopy representative images: (A) M6 fresh control well, (B) M6 fresh differentiation well, (C) M6 cryopreserved control well, (D) M6 cryopreserved differentiation well. Scale bars represent 100μm. Figure S14. Alizarin Red staining of fresh and cryopreserved M7 cells following 16 days of incubation in osteogenic differentiation media: Light microscopy representative images: (A) M7 fresh control well, (B) M7 fresh differentiation well, (C) M7 cryopreserved control well, (D) M7 cryopreserved differentiation well. Scale bars represent 100μm.Figure S15. (A) Adipogenic differentiation: Representative zoomed image to clearly show the formation of lipid droplets and (B) Osteogenic differentiation: Representative zoomed image to clearly show the formation of a mineralized nodule.
DOI: 10.6084/m9.figshare.13467163.v1
title: Additional file 2 of Quantitative assessment of the impact of cryopreservation on human bone marrow-derived mesenchymal stem cells: up to 24 h post-thaw and beyond

description: Additional file 2: Figures S9-S15. fresh and cryopreserved cells stained positive for Oil Red O staining and Alizarin Red staining after incubation with adipogenic and osteogenic differentiation media. Figure S9. Oil Red O staining of fresh and cryopreserved M4 cells following 19 days of incubation in adipogenic differentiation media: Light microscopy representative images: (A) M4 fresh control well, (B) M4 fresh differentiation well, (C) M4 cryopreserved control well, (D) M4 cryopreserved differentiation well. Scale bars represent 100μm. Figure S10. Oil Red O staining of fresh and cryopreserved M6 cells following 19 days of incubation in adipogenic differentiation media: Light microscopy representative images: (A) M6 fresh control well, (B) M6 fresh differentiation well, (C) M6 cryopreserved control well, (D) M6 cryopreserved differentiation well. Scale bars represent 100μm. Figure S11. Oil Red O staining of fresh and cryopreserved M7 cells following 19 days of incubation in adipoegnic differentiation media: Light microscopy representative images: (A) M7 fresh control well, (B) M7 fresh differentiation well, (C) M7 cryopreserved control well, (D) M7 cryopreserved differentiation well. Scale bars represent 100μm. Figure S12. Alizarin Red staining of fresh and cryopreserved M4 cells following 16 days of incubation in osteogenic differentiation media: Light microscopy representative images: (A) M4 fresh control well, (B) M4 fresh differentiation well, (C) M4 cryopreserved control well, (D) M4 cryopreserved differentiation well. Scale bars represent 100μm. Figure S13. Alizarin Red staining of fresh and cryopreserved M6 cells following 16 days of incubation with osteogenic differentiation media: Light microscopy representative images: (A) M6 fresh control well, (B) M6 fresh differentiation well, (C) M6 cryopreserved control well, (D) M6 cryopreserved differentiation well. Scale bars represent 100μm. Figure S14. Alizarin Red staining of fresh and cryopreserved M7 cells following 16 days of incubation in osteogenic differentiation media: Light microscopy representative images: (A) M7 fresh control well, (B) M7 fresh differentiation well, (C) M7 cryopreserved control well, (D) M7 cryopreserved differentiation well. Scale bars represent 100μm.Figure S15. (A) Adipogenic differentiation: Representative zoomed image to clearly show the formation of lipid droplets and (B) Osteogenic differentiation: Representative zoomed image to clearly show the formation of a mineralized nodule.
DOI: 10.6084/m9.figshare.13467257.v1
title: Additional file 1 of Inter-protein residue covariation information unravels physically interacting protein dimers

description: Additional file 1. Norm values of whole inter-protein residue interactions in specific ASA thresholds.
DOI: 10.6084/m9.figshare.13467261.v1
title: Additional file 3 of Inter-protein residue covariation information unravels physically interacting protein dimers

description: Additional file 3. Prediction evaluation results for SVM models developed by single norm features for separate ASA thresholds in comparison with all norm features for all ASA thresholds on CCMpred and MI-based methods. Accuracy, sensitivity, specificity, precision, NPV, FPR, FNR and Informedness results of CCMpred, MI, MIp and CLR methods are compared in groups of tables for single norm features in separate ASA thresholds and all norm features in all ASA groups.
DOI: 10.6084/m9.figshare.13467263
title: Additional file 4 of Inter-protein residue covariation information unravels physically interacting protein dimers

description: Additional file 4. SVM prediction evaluation results for multiple feature sets in groups of ASA thresholds. Accuracy, sensitivity, specificity, precision, NPV, FPR, FNR and Informedness results of CCMpred, MI, MIp and CLR methods are compared in groups of tables..
DOI: 10.6084/m9.figshare.13467257
title: Additional file 1 of Inter-protein residue covariation information unravels physically interacting protein dimers

description: Additional file 1. Norm values of whole inter-protein residue interactions in specific ASA thresholds.
DOI: 10.6084/m9.figshare.13467261
title: Additional file 3 of Inter-protein residue covariation information unravels physically interacting protein dimers

description: Additional file 3. Prediction evaluation results for SVM models developed by single norm features for separate ASA thresholds in comparison with all norm features for all ASA thresholds on CCMpred and MI-based methods. Accuracy, sensitivity, specificity, precision, NPV, FPR, FNR and Informedness results of CCMpred, MI, MIp and CLR methods are compared in groups of tables for single norm features in separate ASA thresholds and all norm features in all ASA groups.
DOI: 10.6084/m9.figshare.13467265.v1
title: Additional file 5 of Inter-protein residue covariation information unravels physically interacting protein dimers

description: Additional file 5. Final ER-MSAs at different ASA thresholds. Available on Mendeley data (http://dx.doi.org/10.17632/9bk2r55286.1).
DOI: 10.6084/m9.figshare.13467263.v1
title: Additional file 4 of Inter-protein residue covariation information unravels physically interacting protein dimers

description: Additional file 4. SVM prediction evaluation results for multiple feature sets in groups of ASA thresholds. Accuracy, sensitivity, specificity, precision, NPV, FPR, FNR and Informedness results of CCMpred, MI, MIp and CLR methods are compared in groups of tables..
DOI: 10.6084/m9.figshare.13467265
title: Additional file 5 of Inter-protein residue covariation information unravels physically interacting protein dimers

description: Additional file 5. Final ER-MSAs at different ASA thresholds. Available on Mendeley data (http://dx.doi.org/10.17632/9bk2r55286.1).
DOI: 10.6084/m9.figshare.13467277
title: Additional file 10 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 10: Table S8. The TM7 pangenome and the functional enrichment analysis. (a) Extended summary information for each of the 40,505 genes that were analyzed in the TM7 pangenomic analysis, including gene cluster (GC) affiliation, functional annotations, contig name, start and stop positions, and functional enrichment information. (b) GC frequencies. (c) Manually selected bins of GCs. (d) COG functions associated with each GC bin. (e) TM7 genes associated with type IV pilus. (f) Functional enrichment output. (g) Summary of prophage predictions using Virsorter, the inovirus detector or manual approaches. (h) Information on contigs that are associated with prophages. (i) Start and stop nucleotide positions for prophages. (j) Genomic information on phage integrases. (k) Genomic information on phage terminases. (l) Output of CRISPRCasFinder. (m) Results of sequence search (using blastn) for CRISPR spacers. (n) Information on terminases identified in TM7 genomes. (o) Blast results of terminases against the NCBI protein database. (p) Blast results for CAS9 sequences. (q) Functional occurrence table for the TM7 pangenome. (r) Functions that are associated with the ‘Extended Core 2’ GC bin and occur in the clade P4 genome (ORAL_P_C_M_MAG_00010).
DOI: 10.6084/m9.figshare.13467279
title: Additional file 11 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 11: Table S9. The SR1 and GN02 metapangenomes. (a) Reference information on GN02 genomes used for analysis. (b) Reference information on SR1 genomes used for analysis. (c) Summary information of GN02 pangenome. (d) Summary information of SR1 pangenome. (e) Average nucleotide identity (ANI) pairwise coverage values for the 25 GN02 genomes. (f) ANI percent identity values for the GN02 genomes. (g) ANI pairwise coverage values for the 14 SR1 genomes. (h) ANI percent identity values for the SR1 genomes. (i) Occurrence summary for the GN02 genomes in the HMP oral metagenomes. (j) Non-outlier mean coverage of the GN02 genomes in the HMP samples as computed by anvi-mcg-classifier. (k) The portion of reads that mapped to each GN02 genome from each of the HMP samples. (l) Occurrence summary for the SR1 genomes in the HMP oral metagenomes. (m) Non-outlier mean coverage of the SR1 genomes in the HMP samples as computed by anvi-mcg-classifier. (n) The portion of reads that mapped to each GN02 genome from each of the HMP samples.
DOI: 10.6084/m9.figshare.13467293
title: Additional file 1 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 1: Table S1. Details of collected samples, including statistics and accession numbers for metagenomes and 16S rRNA amplicon data. (a) Summary of all 71 samples along with summary of QC and assembly statistics for metagenomic short reads. (b) Summary of statistics of contigs resulting from assemblies of metagenomes. (c) Number of reads before and after QC for 16S rRNA gene amplicons. (d) Description of human subjects and sample collection dates.
DOI: 10.6084/m9.figshare.13467283
title: Additional file 12 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 12: Table S10. Novel MAGs. (a) Group affiliations for the novel MAGs. (b) Blast results for ribosomal proteins of novel MAGs. (c) Summary of the blast results of ribosomal proteins of novel MAGs. (d) Summary information on the groups of novel MAGs. (e) Occurrence summary for the novel MAGs in the HMP oral metagenomes. (f) Detection and (g) non-outlier mean coverage of the novel MAGs in the HMP samples as computerd by anvi-mcg-classifier. (h) The portion of reads that mapped to each novel MAG from each of the HMP samples. (i) ANI pairwise coverage values for 41 Flavobacteriaceae (our 5 f__Flavobacteriaceae MAGs and 36 representatives of Flavobacteriaceae species). (j) ANI pairwise identity values for the 41 Flavobacteriaceae genomes.
DOI: 10.6084/m9.figshare.13467293.v1
title: Additional file 1 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 1: Table S1. Details of collected samples, including statistics and accession numbers for metagenomes and 16S rRNA amplicon data. (a) Summary of all 71 samples along with summary of QC and assembly statistics for metagenomic short reads. (b) Summary of statistics of contigs resulting from assemblies of metagenomes. (c) Number of reads before and after QC for 16S rRNA gene amplicons. (d) Description of human subjects and sample collection dates.
DOI: 10.6084/m9.figshare.13467277.v1
title: Additional file 10 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 10: Table S8. The TM7 pangenome and the functional enrichment analysis. (a) Extended summary information for each of the 40,505 genes that were analyzed in the TM7 pangenomic analysis, including gene cluster (GC) affiliation, functional annotations, contig name, start and stop positions, and functional enrichment information. (b) GC frequencies. (c) Manually selected bins of GCs. (d) COG functions associated with each GC bin. (e) TM7 genes associated with type IV pilus. (f) Functional enrichment output. (g) Summary of prophage predictions using Virsorter, the inovirus detector or manual approaches. (h) Information on contigs that are associated with prophages. (i) Start and stop nucleotide positions for prophages. (j) Genomic information on phage integrases. (k) Genomic information on phage terminases. (l) Output of CRISPRCasFinder. (m) Results of sequence search (using blastn) for CRISPR spacers. (n) Information on terminases identified in TM7 genomes. (o) Blast results of terminases against the NCBI protein database. (p) Blast results for CAS9 sequences. (q) Functional occurrence table for the TM7 pangenome. (r) Functions that are associated with the ‘Extended Core 2’ GC bin and occur in the clade P4 genome (ORAL_P_C_M_MAG_00010).
DOI: 10.6084/m9.figshare.13467295.v1
title: Additional file 2 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 2: Table S2. Details for MAGs. (a) Summary of sequence statistics, taxonomy, and redundancy status for all 857 MAGs. (b) Summary of sequence statistics, taxonomy, and redundancy status for the 790 non-redundant MAGs. (c) Mean coverage; (d) Detection values; (e) Relative abundance estimations across our collection of 71 metagenomes for the 790 non-redundant MAGs. (f) Relative abundance estimations for the 16 most abundant genera in our metagenomes based on our MAGs, in addition to relative abundance estimations for TM7 and the collection of contigs not assigned to any genomic bin (the ‘UNKNOWN’ bin). (g) Summary of sequence statistics for all 2463 genomic bins.
DOI: 10.6084/m9.figshare.13467295
title: Additional file 2 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 2: Table S2. Details for MAGs. (a) Summary of sequence statistics, taxonomy, and redundancy status for all 857 MAGs. (b) Summary of sequence statistics, taxonomy, and redundancy status for the 790 non-redundant MAGs. (c) Mean coverage; (d) Detection values; (e) Relative abundance estimations across our collection of 71 metagenomes for the 790 non-redundant MAGs. (f) Relative abundance estimations for the 16 most abundant genera in our metagenomes based on our MAGs, in addition to relative abundance estimations for TM7 and the collection of contigs not assigned to any genomic bin (the ‘UNKNOWN’ bin). (g) Summary of sequence statistics for all 2463 genomic bins.
DOI: 10.6084/m9.figshare.13467313
title: Additional file 6 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 6: Table S5. 16S ribosomal RNA amplicon sequencing results. Taxonomic annotations of amplicons in each of the 71 samples using GAST for each taxonomic level: (a) Phylum. (b) Class. (c) Order. (d) Family. (e) Genus. (f) Species. (g) Counts of amplicon sequence variants (ASVs) generated by the MED pipeline in each of the 71 samples. (h) Percent of counts of ASVs in the 71 samples. (i) Taxonomic affiliation of ASVs. (j) Relative abundance estimations for the 16 most abundant genera in our metagenomes based on MED/GAST results, in addition to relative abundance estimations for TM7 and the collection of ASVs not assigned any genus affiliation.
DOI: 10.6084/m9.figshare.13467309.v1
title: Additional file 5 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

description: Additional file 5. Table S4. Taxonomic annotation of metagenomes. Taxonomic annotation of short reads using KrakenUniq for each taxonomic level: (a) Domain. (b) Phylum. (c) Class. (d) Order. (e) Family. (f) Genus. (g) Species. (h) Relative abundance estimations for the 16 most abundant genera in our metagenomes based on KrakenUniq counts, in addition to relative abundance estimations for TM7 and the collection of reads not assigned any genus affiliation.