cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3636716_d16
title: Additional file 12: Table S10. of Transcriptional analysis of phloem-associated cells of potato

description: Abundant transcripts significantly up-regulated under long days. (XLSX 77 kb)
DOI: 10.6084/m9.figshare.c.3636776_d1
title: Additional file 2: of Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

description: Detailed spearman correlation coefficient results for all normalization methods. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3636818_d1
title: Additional file 4: Table S1. of Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells

description: HP1β interacting partners in ESCs and MEFs by co-immunoprecipitation followed by LC-MS/MS analysis. Only proteins that were not identified in the corresponding control co-immunoprecipitation samples were regarded as specific. Hits found in both biological duplicates are in bold and underlined and are shown at the top. The eight proteins that were identified in both cell types are in bold and underlined and are shown at the bottom. Hits found also in negative control experiments similar to our experimental settings in the Contaminant Repository for Affinity Purification through its web interface [91] are most probably false negative interacting partners, and thus were excluded from the final list (Fig. 4a). Those few additional excluded hits are marked by an asterisk in the lists and are in gray and italics. (Control sets: CC76 CC78 CC79 CC80 CC81 CC82 with the following filters: Cell type-HEK293, Affitnity Support-Agaraose beads, Instrument Type for Mass Spectometry- LTQ-FT.) The HP1β interacting partners in MEFs were classified according to their functional annotation and biological process using Gene Ontology (GO). Only the different categories found to be statistically significant are indicated by colors and found in the legend of the pie chart on the right side of the excel sheet “HP1beta interactors MEF”. (XLSX 27.1 kb)
DOI: 10.6084/m9.figshare.c.3636884_d1
title: Additional file 1: of MetICA: independent component analysis for high-resolution mass-spectrometry based non-targeted metabolomics

description: Source code and raw datasets used for MetICA evaluation. Source code, raw datasets and user manual were also available at https://github.com/daniellyz/MetICA. (ZIP 4725 kb)
DOI: 10.6084/m9.figshare.c.3636935_d1
title: Additional file 1: of Prospective study of 158 adult scoliosis treated by a bivalve polyethylene overlapping brace and reviewed at least 5Â years after brace fitting

description: Excel spreadsheet with results of 158 patients. Data from the prospective database (age, Cobb, balance, follow up at the Beginning and last follow-up). (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3636941_d1
title: Additional file 3: of NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

description: Allele-specific length preference for 24 MHC molecules characterized by 20 or more ligand data points for the allmer and 9mer prediction methods compared to the length preference in the SYFPEITHI data. Length profiles for the allmer and 9mer methods were estimated as described in the text. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.c.3636941_d2
title: Additional file 1: of NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

description: Predictive performance on different alleles and peptide lengths for the allmer and 9mer predictive methods. The two methods were trained as described in the text. The predictive performance was measured in terms of Pearsonâ  s correlation coefficient (PCC) and area under the ROC curve (AUC), the latter using a binding threshold of 500 nM. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.c.3636941_d3
title: Additional file 2: of NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

description: Predictive performance on different alleles and peptide lengths for the allmer and allmer-allele predictive methods. The two methods were trained as described in the text. The predictive performance was measured in terms of Pearsonâ  s correlation coefficient (PCC) and area under the ROC curve (AUC), the latter using a binding threshold of 500 nM. (XLSX 66 kb)
DOI: 10.15468/dl.5qckgb
title: Occurrence Download

description: A dataset containing 6690 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panthera tigris (Linnaeus, 1758)"
 ]
}

 The dataset includes 6690 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033860-241126133413365/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.c.3637088_d3
title: Additional file 3: of Gene changes may minimize masculinizing and defeminizing influences of exposure to male cotwins in female callitrichine primates

description: Summary of amino acid residue substitutions and predicted change in structure/function (PROVEAN, SIFT, and PolyPhen) for the six candidate genes for human, Saimiri, and four callitrichine primates. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3637103_d2
title: MOESM2 of Could patents interfere with the development of a cardiovascular polypill?

description: Additional file 2. Cardiovascular drug patent database.
DOI: 10.5281/zenodo.14029814
title: Artifacts for the paper "Automated and Complete Generation of Traffic Scenarios at Road Junctions Using a Multi-level Danger Definition"

description: This deposit contains measurement data and additional artifacts pertaining to the "Automated and Complete Generation of Traffic Scenarios at Road Junctions Using a Multi-level Danger Definition" paper.

 

Specifically, the artifacts are divided into 3 directories:

 



0-generated-scenarios/ contains (1) the generated abstract scenario specifications (i.e. maneuver instance and path region assignments) and (2) concrete scenarios represented in an `xml` format that are executable through the CARLA Scenario Runner framework.

1-simulation-results/ contains the simulation results for our measurement runs. We include simulation traces, which show the exact position of each actor at each frame, in a human-readable, textual format. We also include result analysis (i.e. pertaining to simulation runtime, outcome, preventive maneuvers, etc.) within `measurements.json` files.

2-generated-figures/ contains figures derived from the contents of 1-simulation-results/ (including additional figures not included in the publication).


All the code of the proposed scenario generation approach is implemented as extensions to the Scenic tool (for scenario generation and analysis), and to the Transfuser repository (for simulation). Scenic is available under the 3-Clause BSD License, while Transfuser is available under the MIT License.
DOI: 10.6084/m9.figshare.c.3637148_d1
title: Additional file 2: of Context-specific functional module based drug efficacy prediction

description: Comparison concordance index between our model and elastic net. It contains concordance index of our model and elastic net in each drug. It contains p-value of concordance index of our model and elastic net in each drug. It contains drug target information. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3637148_d4
title: Additional file 3: of Context-specific functional module based drug efficacy prediction

description: Comparison Pearson correlation coefficient between our model and elastic net. It contains correlation coefficient of our model and elastic net in each drug. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3637157_d1
title: Additional file 3:  of Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance

description: Curated ordered gene lists from microarray experiments performed with skin-associated cell types. We aggregated 2178 gene lists generated from microarray experiments included in Gene Expression Omnibus (GEO). Gene lists were derived from one of 11 types of experiments: a KCs stimulated with cytokines (59 lists; *HaCaT; **reconstituted epidermis); b KC gene perturbations (65 lists; *HaCaT; **reconstituted epidermis; “ + ” denotes overexpression of a gene rather than interfering RNA knockdown); c non-cytokine treatments applied to KCs (169 lists; *HaCaT; **reconstituted epidermis); d fibroblast treatments (182 lists; *non-primary cells); e psoriasis treatment responses (26 lists; *comparison to lesions prior to treatment rather than lesions from placebo-treated patients); f laboratory mouse phenotypes (35 lists); g Peripheral blood mononuclear cell (PBMC) treatments (461 lists); h T-cell treatments (358 lists; *transformed cell line rather than primary T cells); i dendritic cell treatments (360 lists); j macrophage treatments (337 lists), and (K) human skin diseases (123 lists; *comparison to uninvolved skin from patients rather than normal skin from independent controls). All lists except (f) were generated from experiments using human cells or tissues. For (f), lists of mouse genes were converted to human genes based upon a mapping of human-mouse orthologues. This additional file includes a description of each list along with GEO series accessions, GEO platform identifiers, and Pubmed IDs (PMIDs) of any associated publications. (XLSX 113 kb)
DOI: 10.6084/m9.figshare.c.3637172_d6
title: Additional file 1: Table S1. of Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies

description: Compiled comparison of RNAseq with new and previously published qPCR data. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3637172_d7
title: Additional file 2: Table S2. of Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies

description: Compiled list of read number for each library. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.c.3637172_d8
title: Additional file 19: Table S5. of Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies

description: List of primers used for qRT-PCR completed for this manuscript. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.c.3637172_d19
title: Additional file 4: Figure S2. of Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies

description: P10 (a) and P21 (b) browser shots of reads per million (RPM) normalized mapped read count for selected genes for each biological replicate show reproducibility of sequencing results between samples. (ZIP 312 kb)
DOI: 10.15468/dl.cezhzn
title: Occurrence Download

description: A dataset containing 399671 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepidoptera",
 "Continent is South America",
 "Year 2014-2023",
 "OccurrenceStatus is Present",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 399671 records from 329 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033837-241126133413365/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.c.3637193_d1
title: Additional file 6: Table S5. of Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum

description: Domain architecture, genetic organization and subcellular localization of A. brasilense CBG497 TCS components. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.c.3637193_d3
title: Additional file 1: Table S1. of Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum

description: Complete list of genomes surveyed during this study. (XLSX 153 kb)
DOI: 10.6084/m9.figshare.c.3637193_d4
title: Additional file 5: Table S4. of Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum

description: Domain architecture, genetic organization and subcellular localization of A. brasilense Sp245 TCS components. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.c.3637193_d5
title: Additional file 4: Table S3. of Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum

description: Domain architecture, genetic organization and subcellular localization of Azospirillum sp. B510 TCS components. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.c.3637244_d4
title: Additional file 2: Table S1. of Natural variation in expression of genes associated with carotenoid biosynthesis and accumulation in cassava (Manihot esculenta Crantz) storage root

description: Compiled information on germplasm documentation of the 23 collected and studied landraces. Compiled information for the 23 cassava landraces used in this document: origin, genetic background, geographical location of origin, color classes, and local utilization of cassava landraces in a center of origin and domestication of cassava in the Brazilian Amazon. W = White, IY = intense yellow, Y = yellow, PY = pale yellow, and P = Pink. (XLS 12090 kb)
DOI: 10.6084/m9.figshare.c.3637244_d8
title: Additional file 9: Table S3. of Natural variation in expression of genes associated with carotenoid biosynthesis and accumulation in cassava (Manihot esculenta Crantz) storage root

description: Information on primers used for qRT-PCR. Abbreviations are phytoene synthase (CasPSY), carotene isomerase (CasCRTISO), phytoene desaturase (CasPDS), lycopene cyclase Î˛ (CasLCYb), carotene hydroxylase Î˛ CasBCHb) and neoxanthin synthase (CasNXS) for cassava cDNA from storage root. (XLS 12142 kb)
DOI: 10.6084/m9.figshare.c.3637244_d9
title: Additional file 8: Table S2. of Natural variation in expression of genes associated with carotenoid biosynthesis and accumulation in cassava (Manihot esculenta Crantz) storage root

description: Cassava genome annotation. Compiled information on annotation of genes coding for enzymes related to carotenoids biosynthesis and plastid division and gene sequences used for gene expression analysis with three biological replications. Proteins sequences, related to carotenoid biosynthesis, generated in this study, were registered in NCBI data baseÂ  http://www.ncbi.nlm.nih.gov/protein/?term=carvalho+cassava . Protein sequences derived from cDNA sequence for microarray elements, related to plastid division, were obtained at NCBI http://www.ncbi.nlm.nih.gov/protein/?term=carvalho+cassava . Both protein sequences were annotated to cassava proteome data base Â  http://www.ncbi.nlm.nih.gov/protein/?term=carvalho+cassava
DOI: 10.6084/m9.figshare.c.3637256_d1
title: Additional file 5: of The prognostic potential of alternative transcript isoforms across human tumors

description: Transcript signatures of tumor stage (XLS 189 kb)
DOI: 10.6084/m9.figshare.c.3637256_d2
title: Additional file 4: of The prognostic potential of alternative transcript isoforms across human tumors

description: Enriched cancer hallmarks. (XLS 66 kb)
DOI: 10.6084/m9.figshare.c.3637256_d3
title: Additional file 6: of The prognostic potential of alternative transcript isoforms across human tumors

description: Correlation of predictive isoforms with stromal and immune scores. (XLS 173 kb)
DOI: 10.6084/m9.figshare.c.3637256_d4
title: Additional file 1: of The prognostic potential of alternative transcript isoforms across human tumors

description: Patient data, blind predictions, and gene-isoform annotations. (XLS 4554 kb)
DOI: 10.6084/m9.figshare.c.3637256_d5
title: Additional file 9: of The prognostic potential of alternative transcript isoforms across human tumors

description: Models in ER+/ER– breast and MITF+/MITF– melanoma tumors. (XLS 177 kb)
DOI: 10.6084/m9.figshare.c.3637256_d7
title: Additional file 8: of The prognostic potential of alternative transcript isoforms across human tumors

description: Predictive signatures based on gene expression and splicing events. (XLS 278 kb)
DOI: 10.6084/m9.figshare.c.3637256_d8
title: Additional file 7: of The prognostic potential of alternative transcript isoforms across human tumors

description: Transcript signatures in pooled tumor types. (XLS 34 kb)
DOI: 10.6084/m9.figshare.c.3637256_d9
title: Additional file 3: of The prognostic potential of alternative transcript isoforms across human tumors

description: Discriminant transcript isoforms between stages and patient groups. (XLS 4562 kb)
DOI: 10.6084/m9.figshare.c.3637289_d5
title: Additional file 9: Table S7. of 
                     De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

description: GO term enrichment analysis of the transcripts of the PERNI data set with FPKM valuesâ  &gt;â  100. (XLS 44Â kb)
DOI: 10.6084/m9.figshare.c.3637289_d8
title: Additional file 17: Table S12. of 
                     De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

description: Pair-wise Ka/Ks calculation between P. perniciosus and P. papatasi and P. perniciosus and L. longipalpis set of orthologs. (XLS 2344Â kb)
DOI: 10.6084/m9.figshare.c.3637289_d10
title: Additional file 7: Table S5. of 
                     De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

description: Putative long non-coding and novel protein coding genes of the PERNI data set. (XLS 340Â kb)
DOI: 10.6084/m9.figshare.c.3637289_d12
title: Additional file 12: Table S9. of 
                     De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

description: Annotation table of the sex-biased PERNI transcripts. (XLS 8646Â kb)
DOI: 10.6084/m9.figshare.c.3637289_d14
title: Additional file 4: Table S2. of 
                     De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

description: GO terms of the annotated transcripts of the PERNI data set. (XLS 594Â kb)
DOI: 10.6084/m9.figshare.c.3637289_d13
title: Additional file 15: Table S11. of 
                     De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

description: Selected PERNI transcripts for semi-quantitative PCR validation of the sex-biased expression. (XLS 51Â kb)
DOI: 10.6084/m9.figshare.c.3637289_d15
title: Additional file 1: Table S1. of 
                     De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

description: Ortholog hit ratio calculation of the transcriptome of P. perniciosus respect to D. melanogaster and P. papatasi. (XLS 876Â kb)
DOI: 10.6084/m9.figshare.c.3637289_d16
title: Additional file 6: Table S4. of 
                     De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

description: Summary of the RepeatMasker search for TEs in the sand flies transcriptomes. (XLS 42Â kb)
DOI: 10.6084/m9.figshare.c.3637289_d17
title: Additional file 8: Table S6. of 
                     De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

description: FPKM values of the PERNI data set. (XLS 2310Â kb)
DOI: 10.6084/m9.figshare.c.3637289_d18
title: Additional file 5: Table S3. of 
                     De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum

description: GO term enrichment analysis of the transcriptomes of P. perniciosus, P. papatasi and L. longipalpis. (XLS 59Â kb)
DOI: 10.6084/m9.figshare.c.3637301_d1
title: Additional file 4: of Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas

description: eP ST outliers for male and females oysters. 53 and 69 outliers ePST mRNAs for male and female oysters respectively, Genbank accession number, putative annotations, E-values, fold changes and GO associated terms. (XLS 160 KB)
DOI: 10.6084/m9.figshare.c.3637301_d2
title: Additional file 3: of Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas

description: ANOVA sex significant transcripts. 80 mRNA differentially expressed in the two-way ANOVA between French and Danish progeny, Genbank accession number, putative annotations E values and GO associated terms. (XLS 132 kb)
DOI: 10.6084/m9.figshare.c.3637301_d3
title: Additional file 2: of Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas

description: GO terms of RDA sex significant transcripts. GO associated terms for transcripts whose contribution accounted for the 0.1 and 99.9 percentile of the RDA2 axis distribution scores. (XLS 179 kb)
DOI: 10.6084/m9.figshare.c.3637301_d4
title: Additional file 1: of Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas

description: Script used for RDA, ANOVA and eP ST calculations. (R 10 kb)
DOI: 10.6084/m9.figshare.c.3637328_d2
title: Additional file 9: of Geminin prevents DNA damage in vagal neural crest cells to ensure normal enteric neurogenesis

description: Figure S8. ENS progenitors established in the gut are resistant to γ-irradiation in the first 2 hours following exposure. Cryosections at the level of the foregut of Wnt1Cre|EYFP control E10.5 embryos (A, B) or Wnt1Cre|EYFP embryos 2 hours (C, D) or 5 hours (E, F) following exposure to irradiation, immunostained for GFP (green) and processed for TUNEL (red). (G), Quantification of GFP+ ENCCs that are undergoing apoptosis (TUNEL+). One-way ANOVA followed by Fisher’s LSD multiple comparison test, ****P value
DOI: 10.6084/m9.figshare.c.3637346_d1
title: Additional file 1: Table S1. of Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors

description: Clinicopathological data for MOTs. Table S2. Summary of whole exome sequencing statistics. Table S3. List of all somatic coding mutations identified by whole exome sequencing and targeted Sanger sequencing. Table S4. Primers used for the validation screens of ELF3, GNAS, KLF5 and ERBB3. Table S5. Mean mutation rates. Table S6. Somatic mutations identified in the validation cohort. (XLSX 208 kb)