cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29079004.v1
title: Additional file 2 of Supercritical methanolysis of leather tanning waste biomass: experimental investigation, process simulation, and sustainable biodiesel production

description: Supplementary material 2
DOI: 10.15468/dl.p4t2vt
title: Occurrence Download

description: A dataset containing 5568 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (South America, North America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is NT",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera onca (Linnaeus, 1758)",
 "Year 1000-2025"
 ]
}

 The dataset includes 5568 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000550-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29078989
title: Additional file 6 of Genome-wide identification and expression analysis of TCP transcription factors in Chrysanthemum indicum reveals their critical role in the response to various abiotic stresses

description: Additional file 6. The GO enrichment analysis of TCP genes in C. indicum.
DOI: 10.6084/m9.figshare.29078980
title: Additional file 3 of Genome-wide identification and expression analysis of TCP transcription factors in Chrysanthemum indicum reveals their critical role in the response to various abiotic stresses

description: Additional file 3. Synteny blocks of TCP genes between C. indicum and Arabidopsis, rice, soybean, populus and grape genome.
DOI: 10.6084/m9.figshare.29078980.v1
title: Additional file 3 of Genome-wide identification and expression analysis of TCP transcription factors in Chrysanthemum indicum reveals their critical role in the response to various abiotic stresses

description: Additional file 3. Synteny blocks of TCP genes between C. indicum and Arabidopsis, rice, soybean, populus and grape genome.
DOI: 10.6084/m9.figshare.29078986
title: Additional file 5 of Genome-wide identification and expression analysis of TCP transcription factors in Chrysanthemum indicum reveals their critical role in the response to various abiotic stresses

description: Additional file 5. Details of the cis-acting elements identified in this study.
DOI: 10.6084/m9.figshare.29078983
title: Additional file 4 of Genome-wide identification and expression analysis of TCP transcription factors in Chrysanthemum indicum reveals their critical role in the response to various abiotic stresses

description: Additional file 4. Ten predicted conserved motifs of the 26 CiTCP proteins.
DOI: 10.6084/m9.figshare.29078995
title: Additional file 8 of Genome-wide identification and expression analysis of TCP transcription factors in Chrysanthemum indicum reveals their critical role in the response to various abiotic stresses

description: Additional file 8. Primers used in quantitative RT-PCR of CiTCP genes.
DOI: 10.6084/m9.figshare.29078992.v1
title: Additional file 7 of Genome-wide identification and expression analysis of TCP transcription factors in Chrysanthemum indicum reveals their critical role in the response to various abiotic stresses

description: Additional file 7. RNA-seq data of the CiTCP genes in different tissues and treatments.
DOI: 10.6084/m9.figshare.29079151.v1
title: Additional file 2 of Exploring barriers and facilitators to integrating health equity into health and climate change policies in Nepal – a qualitative study among federal level stakeholders

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.29079169.v1
title: Additional file 1 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 1.
DOI: 10.6084/m9.figshare.29079178
title: Additional file 4 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 4.
DOI: 10.6084/m9.figshare.29079070
title: Additional file 1 of Inverted U-shaped relationship between HbA1c and diabetic retinopathy in diabetic patients: a cross-sectional study

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.29079070.v1
title: Additional file 1 of Inverted U-shaped relationship between HbA1c and diabetic retinopathy in diabetic patients: a cross-sectional study

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.29079178.v1
title: Additional file 4 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 4.
DOI: 10.6084/m9.figshare.29079187
title: Additional file 7 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 7.
DOI: 10.6084/m9.figshare.29079187.v1
title: Additional file 7 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 7.
DOI: 10.6084/m9.figshare.29079151
title: Additional file 2 of Exploring barriers and facilitators to integrating health equity into health and climate change policies in Nepal – a qualitative study among federal level stakeholders

description: Supplementary Material 2.
DOI: 10.6084/m9.figshare.29079169
title: Additional file 1 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 1.
DOI: 10.6084/m9.figshare.29079175
title: Additional file 3 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 3.
DOI: 10.6084/m9.figshare.29079088
title: Additional file 1 of Investigation of the mechanism by which miR-223-3p inhibits reflux esophagitis through targeting the NLRP3 inflammasome

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.29079088.v1
title: Additional file 1 of Investigation of the mechanism by which miR-223-3p inhibits reflux esophagitis through targeting the NLRP3 inflammasome

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.29079277.v1
title: Additional file 20 of Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

description: Additional file 21: Table S5 – Primer sequences used for small RNA library preparation. Adapters and primers used in library preparation. Samples were indexed on the 3’ end during PCR amplification. Indexed primers are indicated with their associated samples. Control and Dcr2R172fsX mosquitoes were sequenced on two separate flow cells and thus share the same indexes for tissues and replicates.
DOI: 10.6084/m9.figshare.29079175.v1
title: Additional file 3 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 3.
DOI: 10.6084/m9.figshare.29079184
title: Additional file 6 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 6.
DOI: 10.6084/m9.figshare.29079118
title: Additional file 1 of Exome sequencing revealed a novel homozygous variant in TRMT61 A in a multiplex family with atypical Cornelia de Lange Syndrome from Rwanda

description: Supplementary Material 1: Supplementary Figure 1: Superimposed three-dimensionalstructures of TRMT61 A.Greenand light blueshowing no significant structural changes. Supplementary Figure S2: TRMT61 A_orignal Western blots
DOI: 10.6084/m9.figshare.29079118.v1
title: Additional file 1 of Exome sequencing revealed a novel homozygous variant in TRMT61 A in a multiplex family with atypical Cornelia de Lange Syndrome from Rwanda

description: Supplementary Material 1: Supplementary Figure 1: Superimposed three-dimensionalstructures of TRMT61 A.Greenand light blueshowing no significant structural changes. Supplementary Figure S2: TRMT61 A_orignal Western blots
DOI: 10.6084/m9.figshare.29078899
title: Additional file 1 of Comparative transcriptome analysis of differentially expressed genes of Medicago falcata L. breeding lines response to saline-alkaline stress

description: Additional file 1: Table S1. qRT-PCR primer of genes selected for RNA-seq data confirmation.
DOI: 10.6084/m9.figshare.29079193.v1
title: Additional file 9 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 9.
DOI: 10.6084/m9.figshare.29079367.v1
title: Additional file 7 of Comprehensive single-cell transcriptomic reveals different destinies of melanocytes and dynamic changes of immune microenvironment in a psychological stress-induced leukoderma and leukotrichia mouse model

description: Supplementary Material 7
DOI: 10.5281/zenodo.15426470
title: Phylogenomics reveal widespread ancient hybridization in the evolution of Lychnophorinae (Vernonieae, Asteraceae)

description: Data, scripts and figures from "Phylogenomics reveal widespread ancient hybridization in the evolution of Lychnophorinae (Vernonieae, Asteraceae)", under revision in TAXON. This is a copy of the GitHub repository made in 5/15/2025, when it was publicly released.  



Repository structure:




alignments: contains all the aligments used for analyses, separated into phyluce and HybPiper assemblies.

assembly_comparisons: this folder contains the R script used to plot figures in the Appendix, with the necessary data files to run it. PDF of the figures are provided.

PhyloNetworks: this folder has all the inputs and outputs of all the seven PhyloNetworks analyses. Files are named similarly in each folder, except for the input trees. The scripts folder has a general script that can be used to replicate analysis. The loglik_plot folder has the input and script to produce the plot in Fig 4I. TICR_results has the p-values of all seven tests.

QuartetSampling: contains the species tree and concatenated alignment needed to run the QS analysis, plus all the output files. The figtree file was used as basis for Fig 3.

tree_comparisons: contains script and data files used to generate the overlayed trees from Fig 2, plus some of the Supplemental Figures. PDFs are provided.

trees: contains all trees generated, divided by assembly method.
DOI: 10.5281/zenodo.15426471
title: Phylogenomics reveal widespread ancient hybridization in the evolution of Lychnophorinae (Vernonieae, Asteraceae)

description: Data, scripts and figures from "Phylogenomics reveal widespread ancient hybridization in the evolution of Lychnophorinae (Vernonieae, Asteraceae)", under revision in TAXON. This is a copy of the GitHub repository made in 5/15/2025, when it was publicly released.  



Repository structure:




alignments: contains all the aligments used for analyses, separated into phyluce and HybPiper assemblies.

assembly_comparisons: this folder contains the R script used to plot figures in the Appendix, with the necessary data files to run it. PDF of the figures are provided.

PhyloNetworks: this folder has all the inputs and outputs of all the seven PhyloNetworks analyses. Files are named similarly in each folder, except for the input trees. The scripts folder has a general script that can be used to replicate analysis. The loglik_plot folder has the input and script to produce the plot in Fig 4I. TICR_results has the p-values of all seven tests.

QuartetSampling: contains the species tree and concatenated alignment needed to run the QS analysis, plus all the output files. The figtree file was used as basis for Fig 3.

tree_comparisons: contains script and data files used to generate the overlayed trees from Fig 2, plus some of the Supplemental Figures. PDFs are provided.

trees: contains all trees generated, divided by assembly method.
DOI: 10.6084/m9.figshare.29079181
title: Additional file 5 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 5.
DOI: 10.6084/m9.figshare.29079181.v1
title: Additional file 5 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 5.
DOI: 10.6084/m9.figshare.29079190
title: Additional file 8 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 8.
DOI: 10.6084/m9.figshare.29079190.v1
title: Additional file 8 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 8.
DOI: 10.6084/m9.figshare.29079184.v1
title: Additional file 6 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 6.
DOI: 10.6084/m9.figshare.29079193
title: Additional file 9 of Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cancer: retrospective review of multi-institutional datasets

description: Additional file 9.
DOI: 10.6084/m9.figshare.29079289.v1
title: Additional file 2 of Guanine quadruplexes mediate mitochondrial RNA polymerase pausing

description: Additional file 2: Table S1 465 pause locations. Table S2 G4Hunter Predicted G4. Table S3 QGRS predicted G4. Table S4 List of mutations near pause sites. Table S5 Oligonucleotide list. Table S6 Key Resources table.
DOI: 10.6084/m9.figshare.29079289
title: Additional file 2 of Guanine quadruplexes mediate mitochondrial RNA polymerase pausing

description: Additional file 2: Table S1 465 pause locations. Table S2 G4Hunter Predicted G4. Table S3 QGRS predicted G4. Table S4 List of mutations near pause sites. Table S5 Oligonucleotide list. Table S6 Key Resources table.
DOI: 10.6084/m9.figshare.29078935.v1
title: Additional file 13 of Comparative transcriptome analysis of differentially expressed genes of Medicago falcata L. breeding lines response to saline-alkaline stress

description: Additional file 13: Table S11. Co-DEGs involved in major metabolic pathways.
DOI: 10.6084/m9.figshare.29078941.v1
title: Additional file 15 of Comparative transcriptome analysis of differentially expressed genes of Medicago falcata L. breeding lines response to saline-alkaline stress

description: Additional file 15: Table S13. Expression profiles of hub genes in the MEturquoise module.
DOI: 10.6084/m9.figshare.29078992
title: Additional file 7 of Genome-wide identification and expression analysis of TCP transcription factors in Chrysanthemum indicum reveals their critical role in the response to various abiotic stresses

description: Additional file 7. RNA-seq data of the CiTCP genes in different tissues and treatments.
DOI: 10.6084/m9.figshare.29078917.v1
title: Additional file 7 of Comparative transcriptome analysis of differentially expressed genes of Medicago falcata L. breeding lines response to saline-alkaline stress

description: Additional file 7: Table S5. GO functional annotation of HL differentially expressed genes.
DOI: 10.6084/m9.figshare.29079379
title: Additional file 4 of Characterization and purification of Pseudomonas aeruginosa phages for the treatment of canine infections

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.29079379.v1
title: Additional file 4 of Characterization and purification of Pseudomonas aeruginosa phages for the treatment of canine infections

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.29079424
title: Additional file 5 of Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis

description: Additional file 5.
DOI: 10.6084/m9.figshare.29078926
title: Additional file 10 of Comparative transcriptome analysis of differentially expressed genes of Medicago falcata L. breeding lines response to saline-alkaline stress

description: Additional file 10: Table S8. KEGG pathways are significantly enriched in DEGs from HL.
DOI: 10.6084/m9.figshare.29079271.v1
title: Additional file 18 of Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

description: Additional file 19: Table S3 – Gene sets of interest. Groupings of genes into gene sets, as well as the retrieved genes and their Ae. aegypti homologs. Retrieved KEGG pathways and their component genes are also included.
DOI: 10.6084/m9.figshare.29079433
title: Additional file 8 of Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis

description: Additional file 8.
DOI: 10.6084/m9.figshare.29079436
title: Additional file 9 of Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis

description: Additional file 9.
DOI: 10.6084/m9.figshare.29079439
title: Additional file 10 of Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis

description: Additional file 10.
DOI: 10.6084/m9.figshare.29079442
title: Additional file 11 of Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis

description: Additional file 11.
DOI: 10.6084/m9.figshare.29079442.v1
title: Additional file 11 of Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis

description: Additional file 11.
DOI: 10.6084/m9.figshare.29079481.v1
title: Additional file 11 of Lettuce immune responses and apoplastic metabolite profile contribute to reduced internal leaf colonization by human bacterial pathogens

description: Supplementary Material 11: Dataset S6. Relative accumulation of metabolites detected in the apoplastic wash fluid (AWF) from lettuce leaves inoculated with mock or bacterial inoculum at 1 and 7 days post inoculation (DPI) with Escherichia coli O157:H7 or Salmonella enterica serovar Typhimurium 14028s. Raw peak heights were normalized with the Log10 transformation and auto-scaling functions and subjected to Student’s t-test pair-wise comparisons (bacterium vs. mock) to identify differentially accumulated metabolites (DAMs) through the MetaboAnalyst5.0 software. DAMs were determined as those having a p-value &lt; 0.05 and a Log2 fold change (FC) ≤ −1 or ≥ 1. DAMs are highlighted in green. FDR = False Discovery Rate.
DOI: 10.6084/m9.figshare.29079454
title: Additional file 2 of Lettuce immune responses and apoplastic metabolite profile contribute to reduced internal leaf colonization by human bacterial pathogens

description: Supplementary Material 2: Dataset S1. Gene annotation and corresponding protein KEGG assignment, relative gene expression, and pairwise comparisons for each lettuce cultivar. FC = fold change. DPI = days post inoculation. O157:H7 = Escherichia coli O157:H7. STm 14028s = Salmonella enterica serovar Typhimurium 14028s.
DOI: 10.6084/m9.figshare.29079457
title: Additional file 3 of Lettuce immune responses and apoplastic metabolite profile contribute to reduced internal leaf colonization by human bacterial pathogens

description: Supplementary Material 3: Dataset S2. Relative expression of all identified transcripts calculated as Log2 fold change between bacterium vs. mock inoculated samples. These values were used to create Figure S2. RT = Red Tide. GT = Green Tower. LR = Lollo Rossa. DPI = days post inoculation. O157:H7 = Escherichia coli O157:H7. STm 14028s = Salmonella enterica serovar Typhimurium 14028s.
DOI: 10.6084/m9.figshare.29078911.v1
title: Additional file 5 of Comparative transcriptome analysis of differentially expressed genes of Medicago falcata L. breeding lines response to saline-alkaline stress

description: Additional file 5: Table S3. Summary table of the top 10 up-regulated genes in LM18 and HL.
DOI: 10.6084/m9.figshare.29078923.v1
title: Additional file 9 of Comparative transcriptome analysis of differentially expressed genes of Medicago falcata L. breeding lines response to saline-alkaline stress

description: Additional file 9: Table S7. Expression profiles of DEGs enriched in the “Phenylpropanoid biosynthesis” pathway.
DOI: 10.6084/m9.figshare.29079454.v1
title: Additional file 2 of Lettuce immune responses and apoplastic metabolite profile contribute to reduced internal leaf colonization by human bacterial pathogens

description: Supplementary Material 2: Dataset S1. Gene annotation and corresponding protein KEGG assignment, relative gene expression, and pairwise comparisons for each lettuce cultivar. FC = fold change. DPI = days post inoculation. O157:H7 = Escherichia coli O157:H7. STm 14028s = Salmonella enterica serovar Typhimurium 14028s.
DOI: 10.6084/m9.figshare.29079502
title: Additional file 4 of RNA-binding protein gene NOP58 exhibits crucial prognostic and therapeutic value in Ewing sarcoma

description: Supplementary Material 4: Table S2. 179 candidate genes.
DOI: 10.6084/m9.figshare.29079499.v1
title: Additional file 3 of RNA-binding protein gene NOP58 exhibits crucial prognostic and therapeutic value in Ewing sarcoma

description: Supplementary Material 3: Table S1. RBP genes used for candidate genes screening.
DOI: 10.6084/m9.figshare.29079505
title: Additional file 5 of RNA-binding protein gene NOP58 exhibits crucial prognostic and therapeutic value in Ewing sarcoma

description: Supplementary Material 5: Table S3. GO and KEGG enrichment analysis.
DOI: 10.6084/m9.figshare.29079415.v1
title: Additional file 2 of Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis

description: Additional file 2.
DOI: 10.6084/m9.figshare.29079505.v1
title: Additional file 5 of RNA-binding protein gene NOP58 exhibits crucial prognostic and therapeutic value in Ewing sarcoma

description: Supplementary Material 5: Table S3. GO and KEGG enrichment analysis.
DOI: 10.6084/m9.figshare.29078932
title: Additional file 12 of Comparative transcriptome analysis of differentially expressed genes of Medicago falcata L. breeding lines response to saline-alkaline stress

description: Additional file 12: Table S10. Co-DEGs GO function annotation.