cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3637367_d1
title: Additional file 1: Figure S1. of Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancer

description: Analysis of 120 clinically annotated plasma samples from the Komen Tissue Bank, representing 40 samples from Healthy (H) individuals, 40 from disease-free survivors (DFS), and 40 from patients with metastatic breast cancer (MBC). A) Pie chart shows distribution of involved sites of distant metastases in the MBC group. B) Vertical plot shows the number of years disease free in the DFS group. Two clusters are evident. C) Plot shows cfDNA concentrations from three independent extractions obtained after samples were pooled into three groups. D) Vertical plot showing distribution of age at diagnosis for DFS and MBC patients. Age of accrual is represented for H individuals. E) Bar graph depicting the number of samples by race, for H, DFS, and MBC. (ZIP 1052 kb)
DOI: 10.6084/m9.figshare.c.3637418_d2
title: Additional file 3: of Spread and establishment of Aedes albopictus in southern Switzerland between 2003 and 2014: an analysis of oviposition data and weather conditions

description: Aedes albopictus presence in Canton Ticino (southern Switzerland) over the years. The file contains a series of maps for each year from 2003 to 2014. Each map shows for a particular year where ovitraps were positive or negative for Ae. albopictus eggs. A dot represents an ovitrap and is colour-coded according to its status; green indicates the trap was always negative, red shows that eggs were found at least once, purple indicates seasonal establishment (i.e. the trap was repeatedly positive over at least 3Â months), and blue indicates the overwintering (i.e. the trap was positive the last control round of a year and the first control round of the following one). Map layers were purchased from the Swiss Federal Office of Topography. (ZIP 20813Â kb)
DOI: 10.6084/m9.figshare.c.3637433_d1
title: Additional file 1: of 
                     Mycobacterium tuberculosis causing tuberculous lymphadenitis in Maputo, Mozambique

description: Full description of MIRU-VNTR and spoligotyping analysis in this study. *Newly created 12, 15, or 24-MIRU International Types (MIT) were followed by an asterisk. Letters x, y, and z represent respectively MIRU-VNTR double alleles values of loci MIRU26, Mtub21, and Mtub30 (i.e. 7(+5), 5(+1), and 4(+2)). Letters A, B, C, and D, represent respectively MIRU-VNTR loci number of copies 10, 11, 12, and 13. **Mixed infection, Manu 2 isolate. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3637442_d1
title: Additional file 1: Table S1. of Targeted high-throughput sequencing for genetic diagnostics of hemophagocytic lymphohistiocytosis

description: Coverage information for each amplicon. (XLSX 73 kb)
DOI: 10.6084/m9.figshare.c.3637442_d5
title: Additional file 7: Table S5. of Targeted high-throughput sequencing for genetic diagnostics of hemophagocytic lymphohistiocytosis

description: Monoallelic rare variants with in silico pathogenic predictions identified in the 1000 Genomes cohort. (XLSX 100 kb)
DOI: 10.6084/m9.figshare.c.3637442_d8
title: Additional file 6: Table S4. of Targeted high-throughput sequencing for genetic diagnostics of hemophagocytic lymphohistiocytosis

description: Monoallelic rare variants with in silico pathogenic predictions identified in the patients without a definitive diagnosis. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3637445_d4
title: Additional file 7: Table S2. of Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae

description: Sheet 1 shows the transcript names of Aethionema arabicum, Tarenaya hassleriana and Arabidopsis thaliana and whether or not they are conserved by position or only by sequence across the different lineages. Sheet 2 shows the distances of the positionally conserved LncRNAs to the nearest end of A. thaliana chromosomes. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.c.3637445_d3
title: Additional file 3: of Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae

description: Long non-coding RNAs specific for the Brassicaceae, genomic. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3637490_d1
title: Additional file 2 of Boosting the discriminatory power of sparse survival models via optimization of the concordance index and stability selection

description: R Code. This R-file provides the underlying functions to reproduce the results of the simulation and the breast cancer analysis. (R 21 kb)
DOI: 10.6084/m9.figshare.c.3637499_d2
title: Additional file 2: Table S1. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: Output of Binning in E16CE – P0CE and P0CE –P0NE comparisons. Custom bioinformatics pipeline and binning of E16CE - P0CE and P0CE-P0NE comparisons at the gene level (S1.1, S1.3) and isoform level (S1.2, S1.4) as discussed in the strategy in Fig. 1c. (XLSX 10709 kb)
DOI: 10.6084/m9.figshare.c.3637499_d1
title: Additional file 4: Table S3. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: Microarray analysis results. Clusters generated through K-means clustering in Genesis for the microarray. (XLSX 330 kb)
DOI: 10.6084/m9.figshare.c.3637499_d3
title: Additional file 6: Table S5. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: DE based analysis results for static and temporal comparisons. DE based analyses for static (P21WT vs. P21KO) (S5.1) and temporal (P0 vs. P21WT and P0 vs. P21KO) comparisons (S5.2, S5.3). (XLSX 4196 kb)
DOI: 10.6084/m9.figshare.c.3637499_d5
title: Additional file 7: Table S6. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: DAVID analysis output of DE based analyses for static and temporal comparisons. Results of DAVID analysis based on DE genes for P0 vs. P21WT (S6.1), P0 vs. P21KO (S6.2), and P21WT vs. P21KO (S6.3) comparisons. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3637499_d6
title: Additional file 3: Table S2. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: DAVID analysis output for static and temporal comparisons. DAVID output for genes belonging to bins in E16CE-P0CE comparison (S2.1), P0CE-P0NE comparison (S2.2), P0 vs. P21-Nrl-WT comparison (S2.3),P0 vs. P21-Nrl-KO comparison (S2.4) and P21-Nrl-WT vs. P21-Nrl-KO comparison (S2.5). (XLSX 140 kb)
DOI: 10.15468/dl.j9epfq
title: Occurrence Download

description: A dataset containing 4566 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Panthera tigris (Linnaeus, 1758)"
 ]
}

 The dataset includes 4566 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033863-241126133413365/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.3637499_d7
title: Additional file 5: Table S4. of Network-based bioinformatics analysis of spatio-temporal RNA-Seq data reveals transcriptional programs underpinning normal and aberrant retinal development

description: Binning results in P21-Nrl-WT vs. P21-Nrl-KO, P0 vs. P21-Nrl-WT and P0 vs. P21-Nrl-KO comparisons. Custom bioinformatics pipeline and binning of P21-Nrl-WT vs. P21-Nrl-KO (S4.1), P0 (P0CE + P0NE) vs. P21WTcomparison (S4.2) and P0 (P0CE + P0NE) vs. P21KO comparison (S4.3). (XLSX 4018 kb)
DOI: 10.6084/m9.figshare.c.3637502_d4
title: Additional file 1: of 
                     Wolbachia pseudogenes and low prevalence infections in tropical but not temperate Australian tephritid fruit flies: manifestations of lateral gene transfer and endosymbiont spillover?

description: Collection data for field-caught fruit flies from this study. Information for collection location, climate group and year, specimen specific ID number, sex, result for wsp and 16S rDNA screening and GenBank accession number of COI partial gene are included. (CSV 61Â kb)
DOI: 10.15468/dl.92wcjx
title: Occurrence Download

description: A dataset containing 98310 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is China",
 "Year is 1978"
 ]
}

 The dataset includes 98310 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033862-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v2hm6e
title: Occurrence Download

description: A dataset listing the 104 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-70.82773 -33.50324,-70.80917 -33.48581,-70.82877 -33.47129,-70.84247 -33.49867,-70.82773 -33.50324))",
 "TaxonKey is Aves"
 ]
}

 The dataset's 104 records were derived from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033857-241126133413365/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.3637583_d2
title: Additional file 1: Table S1. of Context dependent regulatory patterns of the androgen receptor and androgen receptor target genes

description: Supernatant PSA assay. Various cell lines were stimulated with different combinations of growth factors and in several co-cultures. Represented here is a selection of these samples. Concentrations: R1881 (10 nm), FGF7 (10 ng/ml), PD98059 MAPKK inhibitor (30 mM), EGF (5 ng/ml) and co-culture with 50-75 % EPT1B8 cells. + denotes added growth factor. Mesenchymal EPT1 cells with p63KD (p63 knockdown), CDH1 or ΔNp63α are described in [14]. (XLS 46 kb)
DOI: 10.15468/dl.k7qwye
title: Occurrence Download

description: A dataset containing 20685 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is one of (Spain, Portugal)",
 "OccurrenceStatus is Present",
 "TaxonKey is Salamandra salamandra (Linnaeus, 1758)"
 ]
}

 The dataset includes 20685 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033864-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b8ecqf
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Eufriesea violascens (Mocsáry, 1898), Euglossa violascens Mocsáry, 1898)"
 ]
}

 The dataset includes 36 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033865-241126133413365/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.3637616_d1
title: Additional file 1: of Gross and histopathological evaluation of human inflicted bruises in Danish slaughter pigs

description: Histological evaluation of bruises. Presence/absence (1/0) of: hyper-leukocytosis, leukocytes and hemorrhage in the dermis; neutrophils, hyper-leukocytosis, macrophages and hemorrhage in the subcutis; necrosis, neutrophils, macrophages, leukocytes in the interstitial space, leukocytes present intramuscularly, hyper-leukocytosis and hemorrhage in the muscle tissue. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3637622_d1
title: Additional file 3: of The cell surface mucin podocalyxin regulates collective breast tumor budding

description: Is Movie S3 showing collective invasion of control 4T1 cells that express considerable endogenous podocalyxin in 3-D culture, and Movie S4 showing decreased collective invasion of 4T1 cells in 3-D culture when endogenous podocalyxin is stably knocked down. (ZIP 1243 kb)
DOI: 10.6084/m9.figshare.c.3637622_d2
title: Additional file 1: of The cell surface mucin podocalyxin regulates collective breast tumor budding

description: Is Figure S1 showing podocalyxin has little effect on subcutaneous tumor size a or proliferation in monolayer culture b, Figure S2 showing podocalyxin overexpression promotes local invasion of MCF-7 tumor cell xenografts,. Figure S3 showing that the ezrin inhibitor NSC668394 disrupts apical podocalyxin localization in monolayer culture, Figure S4 showing normal mammary epithelial cells continue to form spheres and form single, polarized lumens in 3-D culture, and Figure S5 showing podocalyxin expression increases EGF-mediated signaling. (ZIP 1056 kb)
DOI: 10.6084/m9.figshare.c.3637622_d3
title: Additional file 2: of The cell surface mucin podocalyxin regulates collective breast tumor budding

description: Is Movie S1 showing control MCF-7 cells present little collective invasion 3-D culture, and Movie S2 showing podo-overexpressing cells send out very dynamic processes and show considerable collective invasion in 3-D culture. (ZIP 2262 kb)
DOI: 10.6084/m9.figshare.c.3637640_d1
title: Additional file 1: of Comparison of clinical outcomes between luminal invasive ductal carcinoma and luminal invasive lobular carcinoma

description: Dataset supporting the conclusions of this article. (XLSX 94Â kb)
DOI: 10.15468/dl.xzrenb
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-141.34125 67.21983,-137.89164 59.36975,-129.28972 59.81201,-132.09806 65.25178,-138.55502 70.75789,-141.34125 67.21983))",
 "OccurrenceStatus is Present",
 "TaxonKey is Limnephilus picturatus McLachlan, 1875"
 ]
}

 The dataset includes 28 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033866-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nezt9h
title: Occurrence Download

description: A dataset containing 18601 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is China",
 "Year is 1979"
 ]
}

 The dataset includes 18601 records from 130 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033867-241126133413365/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.3637685_d2
title: Additional file 1: of The influence of corticosteroid treatment on the outcome of influenza A(H1N1pdm09)-related critical illness

description: Appendix A (Table 5A. Unadjusted Clinical Outcomes among Critically Ill Patients with H1N1pdm09, Table 6A. Baseline Characteristics of Patients Matched by Propensity to Receive Corticosteroids among Critically Ill Patients with H1N1pdm09, Table 6B. Cointerventions Matched by Propensity to Receive Corticosteroids among Critically Ill Patients with H1N1pdm09, Table 6C. Outcome of Patients, Matched by Propensity to Receive Corticosteroids Among Critically Ill Patients with H1N1pdm09, Table 7A: Predictors of In-Hospital Mortality Using Adjustment for Baseline and Time-Dependent Between-Group Differences over the 4 Days of ICU Admission and Until Discharge From ICU Among Critically Ill Patients with H1N1pdm09) and Appendix B (Predictors of In-Hospital Mortality Among Critically Ill Patients with H1N1pdm09 Using Adjustment for Baseline and Time-Dependent Between-Group Differences) and Appendix C (Participating Hospitals) and Appendix D (Case Report Form). (ZIP 94 kb)
DOI: 10.6084/m9.figshare.c.3637691_d1
title: Additional file 1: of Spontaneous phenotypic suppression of GacA-defective Vibrio fischeri is achieved via mutation of csrA and ihfA

description: The predicted mutations in VCW2E2 when Aligned to ES114 reference strain. Predicted mutation of strain VCW2E2 compared to the reference identified as genomic position by sequence ID and nucleotide position, followed by the nucleotide change, annotation of allele variation and gene and gene description of gene affected. Evidence of ancestral allele, if applicable, is provided by a list of the top Basic Local Alignment Search Tool results [49] to the allele variant. If no evidence exists, a description of whether the allele was confirmed as mutated or not confirmed is provided. Primers along with annealing temperatures and elongation times for Sanger re-sequencing of the alleles are listed. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.c.3637697_d1
title: Additional file 3: of Expression profiling of in vivo ductal carcinoma in situ progression models identified B cell lymphoma-9 as a molecular driver of breast cancer invasion

description: Differentially expressed genes in DCIS.COM and SUM225 mouse intraductal xenograft model (MIND) xenografts during transition from 2 to 6 weeks. Significance analysis for microarrays (SAM) software was utilized to determine differentially expressed genes between the 2- to 6-week time point in both DCIS.COM and SUM225 cell lines. The cutoff for significance was determined by &lt;5 % false discovery rate. Two-class unpaired SAM analysis generated a list of significant genes and fold-change values between 2 and 6 weeks in DCIS.COM (18,590 downregulated; 10,227 upregulated) and SUM225 (19,953 downregulated and 14,691 upregulated). (XLSX 3297 kb)
DOI: 10.6084/m9.figshare.c.3637697_d4
title: Additional file 4: of Expression profiling of in vivo ductal carcinoma in situ progression models identified B cell lymphoma-9 as a molecular driver of breast cancer invasion

description: Wnt-pathway-specific genes differentially expressed in ductal carcinoma in situ DCIS.COM and SUM225 mouse intraductal xenograft model (MIND) xenografts during transition from 2 to 6 weeks. Genes significantly differentially expressed between the 2- to 6-week time point in both DCIS.COM and SUM225 cell lines were further analyzed using Ingenuity Pathway AnalysisÂŽ (IPA). The Wnt/Î˛-catenin canonical pathway was identified as a significantly upregulated pathway in both cell line MIND xenografts during transition from 2 to 6 weeks. (XLS 48 kb)
DOI: 10.6084/m9.figshare.c.3637697_d10
title: Additional file 11: of Expression profiling of in vivo ductal carcinoma in situ progression models identified B cell lymphoma-9 as a molecular driver of breast cancer invasion

description: Analysis of the The Cancer Genome Atlas (TCGA) data showed differentially expressed genes in BCL9-high versus BCl9-low tumors. Differential gene expression was performed between TCGA breast cancer samples with a normal range of BCL9 and samples with upregulated BCL9. A list of significant genes (1,756 down regulated 980 upregulated) was obtained with a threshold of a false discovery rate â Ľ0.05 and log fold change 0.26. (XLSX 1492 kb)
DOI: 10.6084/m9.figshare.c.3637697_d9
title: Additional file 10: of Expression profiling of in vivo ductal carcinoma in situ progression models identified B cell lymphoma-9 as a molecular driver of breast cancer invasion

description: Analysis of The Cancer Genome Atlas (TCGA) data showing canonical Wnt pathways genes expressed in BCL9-high versus BCL9-low tumors. TCGA breast cancer samples with BCL9 levels above the range defined by normal samples were labeled upregulated in cancer (414 samples). The significant differentially expressed genes from TCGA analysis of BCL9-high versus BCL9-low tumors were analyzed in Ingenuity Pathway Analysis (IPA) and the canonical pathways with a p value â ¤0.05 were obtained. (XLS 124 kb)
DOI: 10.6084/m9.figshare.c.3637700_d5
title: Additional file 8: of Comparative transcriptome analysis of lufenuron-resistant and susceptible strains of Spodoptera frugiperda (Lepidoptera: Noctuidae)

description: Differentially expressed transcripts between resistant and susceptible strains of S. frugiperda to lufenuron. (XLS 95Â kb)
DOI: 10.15468/dl.ztvmsk
title: Occurrence Download

description: A dataset containing 17767 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is The New York Botanical Garden Herbarium (NY)",
 "Geometry POLYGON((-91.32112 57.67674,-96.97484 54.34548,-97.28464 48.66687,-92.09561 46.31242,-79.549 44.24181,-79.78134 51.83474,-80.32348 55.41473,-91.32112 57.67674))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 17767 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033868-241126133413365/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.3637712_d3
title: Additional file 5: of Inferring microbial interaction network from microbiome data using RMN algorithm

description: List of the reliable OTU-triplets ranking by I ( O m , O c , O t ) values in the ascending order. These OTU-triplets were selected when the threshold was set at 0≦L d(O m, O c, O t) ≦3.8 and D(O m, O c, O t)
DOI: 10.6084/m9.figshare.c.3637712_d5
title: Additional file 3: of Inferring microbial interaction network from microbiome data using RMN algorithm

description: The table of OTUs for all the samples at the genus level with data standardization. (XLS 26 kb)
DOI: 10.6084/m9.figshare.c.3637712_d6
title: Additional file 4: of Inferring microbial interaction network from microbiome data using RMN algorithm

description: List of top 100 possible OTU-triplets ranking by I ( O m , O c , O t ) values in the ascending order. These OTU-triplets were selected without using the threshold set at 0≦L d(O m, O c, O t) ≦3.8 and D(O m, O c, O t)
DOI: 10.6084/m9.figshare.c.3637736_d2
title: MOESM4 of Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus

description: Additional file 4. Proteomics complementary information. For each condition (Maltose, Pine and Aspen), data are given regarding identified proteins (e.g. number of identified spectra, number of unique peptides, number of specific peptides) and data regarding each identified peptide (e.g. sequence, e value, charge).
DOI: 10.6084/m9.figshare.c.3637745_d1
title: Additional file 1: of A proficient cost reduction framework for de-duplication of records in data integration

description: Dataset-A with one duplicate against an original record and one modification per duplicate record. (CSV 92 kb)
DOI: 10.6084/m9.figshare.c.3637745_d2
title: Additional file 2: of A proficient cost reduction framework for de-duplication of records in data integration

description: Dataset-C with up to 9 duplicates against an original record. (CSV 90 kb)
DOI: 10.15468/dl.n5ghhz
title: Occurrence Download

description: A dataset containing 1836 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is United States of America",
 "TaxonKey is Bombus fraternus (Smith, 1854)"
 ]
}

 The dataset includes 1836 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033869-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.