cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3642692_d3
title: Additional file 1: Table S1. of Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate

description: Summary of clinical features and disease/candidate variants identified. The major clinical features and the disease/candidate variantsÂ as well as the prediction scores and classifications for damaging effect of the variants are listed. For Polyphen2 (Pph2), D for probably damaging, P for possibly damaging, and B for benign. For LRT, D for deleterious, N for neutral, and U for unknown. For MutationTaster (MT), A for disease causing automatic, D for disease causing, N for polymorphism, and P for polymorphism automatic. Moreover, this table includes the ranking and ACMG criteria for each gene, the supporting evidence and the discussion of other variants, as well as the frequency/number of the variants in our internal CMG database, Atherosclerosis Risk in Communities Study (ARIC), ExAC database, Thousand Genome project, and NHLBI GO Exome Sequencing Project (ESP). pLI: probability of loss-of-function (LoF) intolerance. Table S2. Categorization of families based on major clinical features. Y: the family has this clinical feature; N: the family does not have this clinical feature. Families with brain malformations were not counted in the ID/DD groups, even if this feature was present. Percentages of families with each feature are shown at the bottom of the table. Table S3. Categorization of disease genes/candidates by major clinical features. Table S4. AOH metrics for the probands carrying known or candidate disease genes. Table S5. Raw data of ddPCR in RPS6KC1 in family 025. Table S6. Homologs of disease genes/candidates between human and fruit fly. The HCOP website ( http://www.genenames.org/cgi-bin/hcop ) was used to identify the fly homologs of the identified disease/candidate genes, listed in the upper panel. These fly homologs are then used to search for additional human homologs to find paralogs of the original human genes, as shown in the bottom part of the list. (XLS 165Â kb)
DOI: 10.6084/m9.figshare.c.3642692_d1
title: Additional file 2: Figure S1. of Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate

description: Thirty one Arab family pedigrees in this study. Family numbers are given as numeric series and individual IDs as BAB series. They are arranged into: known variant in known gene (green), novel variant in known gene (light red), phenotypic expansion (blue), novel disease candidates (light orange), and unsolved cases (gray). Gray shading indicates a minor phenotype. Figure S2. Workflow of WES analysis. The SNVs predicted to have (probably) damaging effects are filtered with the allele frequency data from Atherosclerosis Risk in Communities Study (ARIC) ( http://drupal.cscc.unc.edu/aric/ ), NHLBI GO Exome Sequencing Project (ESP), Seattle, WA ( http://evs.gs.washington.edu/EVS/ ), 1000 Genomes Project ( http://www.1000genomes.org ), and Exome Aggregation Consortium (ExAC) Cambridge, MA ( http://exac.broadinstitute.org ) [Oct 2014] and Baylor-Hopkins Center for Mendelian Genomics (BHCMG) database with more than 5,000 exomes. WES data are also used to predict CNVs. The information of the paralogs of candidate genes provides supporting evidence for the findings. Moreover, cross-database gene mining identifies additional cases. Figure S3. CNV prediction identifies a homozygous deletion in GRID2 in BAB6883. a HMZDelFinder reveals a homozygous deletion in GRID2 (chr4:g.94006145_94032105del). The lower threshold for RPKM is 0.5 and upper threshold is 1. b This deletion is confirmed by clinical array (chr4:g.93,985,826_94,074,965del) and segregates with phenotypes in the family. c Breakpoint junction maps to chr4:g.93,978,239_94,078,203del. Figure S4. Network analysis of known and candidate genes. a Temporal RNA expression in brain. b The protein-protein interaction network: Interaction STRING scores are displayed in an upper triangular heatmap. Low and high values are represented in blue and red, respectively. Figure S5. Protein interaction network of the candidate genes. a KDM2B and MLLT1 are in the chromatin remodeling sub-network. b FOXP4 and its paralogs. c KIF5B and its paralogs. d GRM7 and its related members. (ZIP 4859 kb)
DOI: 10.6084/m9.figshare.c.3642668_d10
title: Additional file 1: Table S1. of MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development

description: Sample Skyline-derived response curve experiment input to MRMPlus. (TXT 128Â kb)
DOI: 10.6084/m9.figshare.c.3642668_d9
title: Additional file 4: Table S4. of MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development

description: Sample Skyline-derived repeatability experiment input to MRMPlus. (TXT 199Â kb)
DOI: 10.6084/m9.figshare.c.3642668_d8
title: Additional file 9: Table S7. of MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development

description: Comparing and contrasting â  Repeatabilityâ   measures between MRMPlus and PanoramaWeb. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3642668_d6
title: Additional file 6: Table S6. of MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development

description: Sample MRMPlus computed assay performance metrics for assay repeatability experiments. (TXT 13Â kb)
DOI: 10.6084/m9.figshare.c.3642668_d3
title: Additional file 5: Table S5. of MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development

description: Sample MRMPlus computed assay performance metrics for the response curve experiments. (TXT 28Â kb)
DOI: 10.6084/m9.figshare.c.3642668_d4
title: Additional file 3: Table S3. of MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development

description: Sample user-defined dilution file. (TXT 130 bytes)
DOI: 10.6084/m9.figshare.c.3642668_d2
title: Additional file 10: Table S8. of MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development

description: Comparing and contrasting â  Responseâ   measures between MRMPlus and PanoramaWeb. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3642668_d1
title: Additional file 2: Table S2. of MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development

description: Sample user-defined response experiment metadata file. (TXT 1Â kb)
DOI: 10.6084/m9.figshare.c.3642650_d4
title: MOESM4 of Identification of potential biomarkers to differentially diagnose solid pseudopapillary tumors and pancreatic malignancies via a gene regulatory network

description: Additional file 4: Differentially expressed genes between SPN and non-neoplastic samples. Table S4 posts differentially expressed TFs with fold change and t-test p-value for each TF. Table S5 posts differentially expressed miRNAs with fold change and t-test p-value too for each miRNA.
DOI: 10.6084/m9.figshare.c.3642650_d5
title: MOESM3 of Identification of potential biomarkers to differentially diagnose solid pseudopapillary tumors and pancreatic malignancies via a gene regulatory network

description: Additional file 3: Previously reported SPN-relevant genes and shortest paths among path genes. Table S1 lists the 26 genes which have been reported to be related with SPN. Table S2 shows in detail the shortest paths for each pair of 26 SPN-related genes listed in table S1. Table S3 lists 43 new candidate genes on the shortest path, together with the corresponding gene type.
DOI: 10.6084/m9.figshare.c.3642650_d3
title: MOESM5 of Identification of potential biomarkers to differentially diagnose solid pseudopapillary tumors and pancreatic malignancies via a gene regulatory network

description: Additional file 5: Biomarkers for differential diagnosis of SPN and two malignant pancreatic. Table S6 lists fold change of 14 biomarkers for SPN, PanNET and PDAC versus normal pancreatic tissues as well as SPN versus PanNET and PDAC. Table S7 lists fold change of 17 biomarkers for SPN and PanNET versus normal pancreatic tissues as well as SPN versus PanNET. Table S8 lists fold change of 17 biomarkers for SPN and PDAC versus normal pancreatic tissues as well as SPN versus PDAC.
DOI: 10.6084/m9.figshare.c.3642650_d2
title: MOESM2 of Identification of potential biomarkers to differentially diagnose solid pseudopapillary tumors and pancreatic malignancies via a gene regulatory network

description: Additional file 2: Gene regulatory network of SPN. The first column represents regulators, while the second column represents corresponding targets.
DOI: 10.6084/m9.figshare.c.3642587_d3
title: Additional file 2 of A map of mobile DNA insertions in the NCI-60 human cancer cell panel

description: A map of Alu insertion site positions in the NCI-60 cell panel. Genomic coordinates of TIP-chip peaks are provided. Reference insertions are indicated in column D (hg19), and known polymorphic variants are indicated by a ‘Y’ in column E (Y/N, yes/no). For each cell line in columns G-BN, a ‘1’ indicates that the insertion is present, while ‘0’ indicates that the insertion is not found. (XLSX 380 kb)
DOI: 10.6084/m9.figshare.c.3642587_d2
title: Additional file 1 of A map of mobile DNA insertions in the NCI-60 human cancer cell panel

description: A map of LINE-1 (L1) insertion site positions in the NCI-60 cell panel. Genomic coordinates of TIP-chip peaks are provided. Reference insertions are indicated in column D (hg19), and known polymorphic variants are indicated by a ‘Y’ in column E (Y/N, yes/no). For each cell line in columns G-BN, a ‘1’ indicates that the insertion is present, while ‘0’ indicates that the insertion is not found. (XLSX 85 kb)
DOI: 10.6084/m9.figshare.c.3642587_d1
title: Additional file 3 of A map of mobile DNA insertions in the NCI-60 human cancer cell panel

description: COMPARE analysis associating insertions with other cell characteristics. Different tabs are used for different datasets. Activity, enzyme activity measures; Decreased / Increased methylation, DNA methylation measures; Metabolome, metabolic intermediates; Drug Effect GI50, concentration for 50 % growth inhibition; Drug Effect TGI, concentration for total growth inhibition; miRNA, microRNA expression levels; RNA, mRNA expression levels; Mutations, somatically-acquired DNA mutations; Protein, protein expression. (XLSX 4049Â kb)
DOI: 10.15468/h6m947
title: EMBRAPA FLORESTAS | Soil macrofauna communities in native Atlantic Forest fragments and agroforestry systems of different ages the Ribeira River Valley, Brazil

description: Soil macrofauna communities were evaluated in a three Atlantic Forest fragments at different stages of regeneration, and in three organic agroforestry systems of different ages in the Ribeira River Valley, Brazil. Sampling was performed in March and August of 2008 in six sites, five of which were located in Barra do Turvo county in São Paulo state, and one in Adrianópolis county in Paraná state. The sites in Barra do Turvo were: a 5, 20 and &gt;30-year-old Atlantic Forest regeneration fragment, and a 4- and 16-year-old organic agroforestry system. In Adrianópolis, only an 8-year-old organic agroforestry system was sampled. Each land use was replicated three times and two samples were taken per plot. Samples were taken using the standard methodology of the Tropical Soil Biology and Fertility Programme (TSBF), where soil (down to 20 cm depth) and litter fauna were hand-sorted from monoliths of 25x25 cm, and the abundance of a total of 42 taxa was assessed.
DOI: 10.6084/m9.figshare.c.3642332_d7
title: Additional file 2: Table S2. of Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta)

description: The genotypes of 6731 LP markers. (XLSX 2652 kb)
DOI: 10.6084/m9.figshare.27173979.v2
title: Simulation data: Crossed evaluation of surgical patient scheduling and admission policies with bed management

description: Directory contentComplete simulation results exported as SQL (txt) database: 'simresults161b10y.sql'SQL table definition of simulation results: 'simresultstab.sql' (see the comments in the file for a description of the table columns)Row simulation output, 161 beds, OB (open block) policy, 10 years: 'kpis_161ob10y.csv'Row simulation output, 161 beds, MSS (master surgery schedule) policy, 10 years: 'kpis_161mss10y.csv'<br>
DOI: 10.6084/m9.figshare.c.3642332_d6
title: Additional file 1: Table S1. of Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta)

description: The genotypes of 4550 LP markers that were mapped onto the genetic map. (XLSX 1645 kb)
DOI: 10.15468/dl.mufjy8
title: Occurrence Download

description: A dataset containing 108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eumetopias jubatus (Schreber, 1776)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 108 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032101-241126133413365/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.3642332_d5
title: Additional file 6: of Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta)

description: Heatmap of the five linkage groups. (RAR 151 kb)
DOI: 10.6084/m9.figshare.c.3642332_d3
title: Additional file 5: of Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta)

description: Haplotype maps of the five linkage groups. (RAR 143 kb)
DOI: 10.6084/m9.figshare.c.3642332_d4
title: Additional file 7: Table S5. of Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta)

description: Phenotypic traits of the 100 DH lines and their parents. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3642332_d2
title: Additional file 4: Table S4. of Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta)

description: The bin markers located on the five linkage groups and their genetic distances. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.c.3642332_d1
title: Additional file 3: Table S3. of Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta)

description: The markers located on the five linkage groups and their genetic distances. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.c.3642323_d1
title: Additional file 6: of Identification and characterization of microRNAs from in vitro-grown pear shoots infected with Apple stem grooving virus in response to high temperature using small RNA sequencing

description: Detailed information about the loci, the corresponding precursor sequences and structures, and the alignments of all reads for each hairpin of the 32 potentially novel miRNAs and 109 candidate miRNAs. (TXT 762 kb)
DOI: 10.6084/m9.figshare.c.3642296_d3
title: Additional file 5: Table S4. of Genome-wide Association Study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice

description: Annotation of candidate genes anchored by associated SNPs. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3642035_d3
title: Additional file 1: of Evaluation of the population structure and genetic diversity of Plasmodium falciparum in southern China

description: The full genotype data for all isolates. Individual genotypes with one row per isolate and one column per locus.
DOI: 10.15468/dl.2sz2wy
title: Occurrence Download

description: A dataset containing 241 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pithecia hirsuta Spix, 1823"
 ]
}

 The dataset includes 241 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032102-241126133413365/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.3642014_d4
title: MOESM2 of Distinct functional enrichment of transcriptional signatures in pigs with high and low IFN-gamma responses after vaccination with a porcine reproductive and respiratory syndrome virus (PRRSV)

description: Additional file 2. Validation of the microarray data using real time qPCR. A subset of 9 regulated transcripts was reassessed using real-time qPCR. Data were used to run a regression analysis between the microarray and the real time qPCR experiment and generate the correlation coefficients R2.
DOI: 10.6084/m9.figshare.c.3642014_d3
title: MOESM3 of Distinct functional enrichment of transcriptional signatures in pigs with high and low IFN-gamma responses after vaccination with a porcine reproductive and respiratory syndrome virus (PRRSV)

description: Additional file 3. Gene ontology analysis of the data using DAVID bioinformatics resources [39]. Analysis was run to generate the most likely gene ontology term for the biological processes, cellular components and molecular functions for each group of regulated transcripts in HR and LR vaccinated pigs based on P-value, number of gene component and fold enrichment. Only data with FDRÂ &lt;5% are shown.
DOI: 10.6084/m9.figshare.c.3642014_d1
title: MOESM4 of Distinct functional enrichment of transcriptional signatures in pigs with high and low IFN-gamma responses after vaccination with a porcine reproductive and respiratory syndrome virus (PRRSV)

description: Additional file 4. Upstream regulators analysis using Ingenuity Pathway Analysis for the HR and LR vaccinated pigs. As described in material and methods section the expression dataset for HR and LR pigs were analysed independently with Fisher’s exact test. To create this dataset, activation z-score| ≥2 for HR and LR pigs were generated and ranked from the highest to the lowest. Data were considered significant with P value
DOI: 10.6084/m9.figshare.c.3642014_d2
title: MOESM1 of Distinct functional enrichment of transcriptional signatures in pigs with high and low IFN-gamma responses after vaccination with a porcine reproductive and respiratory syndrome virus (PRRSV)

description: Additional file 1. List of regulated transcripts with P value
DOI: 10.7278/s5d-hpjr-ckh0
title: Cloud Edge Energy in Radiative Convective Equilibrium
DOI: 10.6084/m9.figshare.c.3641960_d2
title: MOESM1 of Multi-breed genome-wide association study reveals novel loci associated with the weight of internal organs

description: Additional file 1: Table S1. Results of the correlation analysis for traits studied in five populations. This table contains the estimated correlations and 95 % confidence intervals between traits for F2 pigs (Table S1A), Sutai pigs (Table S1B), Laiwu pigs (Table S1C), Erhualian pigs (Table S1D) and DLY pigs (Table S1E).
DOI: 10.6084/m9.figshare.c.3641960_d1
title: MOESM2 of Multi-breed genome-wide association study reveals novel loci associated with the weight of internal organs

description: Additional file 2: Table S2. Suggestive significant SNPs for the weights of four internal organs and carcass in five populations. A total of 248 suggestive significant SNPs were identified in our study, including 91 for heart weight, 125 for liver weight, 6 for spleen weight, 12 for kidney weight and 14 for carcass weight.
DOI: 10.6084/m9.figshare.c.3641927_d5
title: Additional file 3: Table S3. of Identification and characterization of novel and conserved microRNAs in several tissues of the Chinese rare minnow (Gobiocypris rarus) based on illumina deep sequencing technology

description: Putative novel microRNAs with sizes between 18 and 30Â nt. (XLSX 1321 kb)
DOI: 10.6084/m9.figshare.c.3641927_d4
title: Additional file 2: Table S2. of Identification and characterization of novel and conserved microRNAs in several tissues of the Chinese rare minnow (Gobiocypris rarus) based on illumina deep sequencing technology

description: Conserved miRNAs and miRNA*s in rare minnow. (XLSX 26 kb)
DOI: 10.15468/dl.6kfd89
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phoca jubata Schreber, 1776",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032104-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.c.3641927_d3
title: Additional file 4: Table S4. of Identification and characterization of novel and conserved microRNAs in several tissues of the Chinese rare minnow (Gobiocypris rarus) based on illumina deep sequencing technology

description: The location of putative novel microRNAs on the zebrafish whole-genome shotgun (WGS). (XLSX 30 kb)
DOI: 10.6084/m9.figshare.c.3641927_d1
title: Additional file 5: Table S5. of Identification and characterization of novel and conserved microRNAs in several tissues of the Chinese rare minnow (Gobiocypris rarus) based on illumina deep sequencing technology

description: Novel miRNA target prediction using miRanda, TargetScan, RNA22 and PITA (local version). (XLSX 515 kb)
DOI: 10.6084/m9.figshare.c.3641927_d2
title: Additional file 1: Table S1. of Identification and characterization of novel and conserved microRNAs in several tissues of the Chinese rare minnow (Gobiocypris rarus) based on illumina deep sequencing technology

description: Primer sequences used in the qPCR assays. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3641885_d12
title: Additional file 8: of Achieving high-sensitivity for clinical applications using augmented exome sequencing

description: daSNVs in ACMG genes where inadequate coverage was observed among at least one platform, using WES/ACE data normalized to both 12 Gb and 100Ă  mean coverage. (XLSX 312Â kb)
DOI: 10.6084/m9.figshare.c.3641885_d11
title: Additional file 2: of Achieving high-sensitivity for clinical applications using augmented exome sequencing

description: ACE target file, defining regions of the genome targeted by the ACE assay used in this study. Chromosomal position information is based on mapping to GRCh37. (XLSX 5275Â kb)
DOI: 10.6084/m9.figshare.c.3641885_d7
title: Additional file 9: of Achieving high-sensitivity for clinical applications using augmented exome sequencing

description: Common Target File representing regions common in ACE, SS, SSCR, NX, NG (that is, the intersection of platform specific target files), mapped to GRCh37. (XLSX 2666Â kb)
DOI: 10.15468/dl.9th7bx
title: Occurrence Download

description: A dataset containing 17348 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Oryctolagus cuniculus (Linnaeus, 1758)",
 "Year 2014-2024"
 ]
}

 The dataset includes 17348 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032105-241126133413365/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.3641741_d2
title: Additional file 7: of A transcriptomic analysis of bermudagrass (Cynodon dactylon) provides novel insights into the basis of low temperature tolerance

description: The enriched pathways by DEGs and rich factor in comparisons. (xls 15.0 KB)