cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3605855_d12
title: Additional file 13: of Development and clinical application of an integrative genomic approach to personalized cancer therapy

description: A gzipped tarball (.tgz file) of VCF files containing somatic mutations (i.e. present exclusively in tumor) for the 25 patients (one VCF file per patient) on whom paired normal/tumor WES was carried out and whose consents permitted public release of the full variant call data. For patients where multiple assays were carried out (WGS, WES, targeted panel, PacBio validation for troubleshooting), the VCF file contains the final variant call set where any discordance amongst the assays was resolved. Only mutations altering amino acid sequence (missense, nonsense, canonical splice site, indel) in a canonical isoform of a gene are given. Mutations are included that are not explicitly reported in returned findings due to lack of known relevance to cancer. Mutations rejected during our manual review protocol are not included. Thus, VCFs may contain mutations that were not manually reviewed. Three patients (P0009, P0025, and P0040) have two tumor specimens available, therefore those VCFs are multi-sample and report which mutations are recurrent among tumors and which are not; the rest are single-sample. (ZIP 37 kb)
DOI: 10.6084/m9.figshare.c.3605885_d6
title: Additional file 7: Table S6. of The comprehensive immunomodulation of NeurimmiRs in haemocytes of oyster Crassostrea gigas after acetylcholine and norepinephrine stimulation

description: Differentially expressed miRNAs identified by edgeR software at FDRâ
DOI: 10.15468/dl.hgb92j
title: Occurrence Download

description: A dataset containing 640 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Upeneus japonicus (Houttuyn, 1782)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 640 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032244-241126133413365/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.3605822_d2
title: MOESM2 of Integrated isotope-assisted metabolomics and 13C metabolic flux analysis reveals metabolic flux redistribution for high glucoamylase production by Aspergillus niger

description: Additional file 2 . The best-fit flux distribution and minimal weighted residual from the parameter estimations.
DOI: 10.6084/m9.figshare.c.3605792_d4
title: Additional file 1: Table S1. of The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)

description: Comparison of COG assignments of the genes between M. fulvus 124B02 and M. stipitatus DSM 14675. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3605792_d5
title: Additional file 2: Table S2. of The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)

description: Comparison of COG assignments of the genes between M. fulvus 124B02 and M. fulvus HW-1. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3605792_d3
title: Additional file 4: Table S4. of The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)

description: Strain-specific genes in the family of DNA replication, recombination and repair in M. fulvus 124B02, compared with DSM 14675. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3605792_d2
title: Additional file 5: Table S5. of The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)

description: Homologues of pMF1.19 and pMF1.20 in M. fulvus 124B02. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3605792_d1
title: Additional file 3: Table S3. of The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)

description: Comparison of COG assignments of the genes between M. fulvus 124B02 and M. xanthus DK1622. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3605681_d5
title: Additional file 5: of Development of EMS-induced mutation population for amylose and resistant starch variation in bread wheat (Triticum aestivum) and identification of candidate genes responsible for amylose variation

description: Normalized threshold cycle (ΔCт) of two SBEII isoforms (SBEIIa and SBEIIb) during seed development. The data was taken at three stages of seed development (21, 28, and 35 days after anthesis, DAA) in two mutant lines, ‘TAC 75’(amylose content - 64 %) and ‘TAC 6’(amylose content– 6.8 %), in comparison to the parent variety, ‘C 306’ (amylose content - 26 %). The data was taken in two biological replications, each represented as mean ± SD from three technical replicates. Wheat ADP Ribosylation Factor (ARF) was used as an internal control gene for normalization. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3605681_d2
title: Additional file 1: of Development of EMS-induced mutation population for amylose and resistant starch variation in bread wheat (Triticum aestivum) and identification of candidate genes responsible for amylose variation

description: Evaluation of 1035 (M3) mutant lines for amylose variation using five-time diluted standard Iodine-Potassium Iodide (I2â  KI) solution. Time taken to develop blue color was recorded using a digital electronic stopwatch, while color intensity was scored as zero for no color development, + for light blue color, and ++ for deep blue color. All the data was given as a mean of three seeds. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.c.3605681_d3
title: Additional file 4: of Development of EMS-induced mutation population for amylose and resistant starch variation in bread wheat (Triticum aestivum) and identification of candidate genes responsible for amylose variation

description: Normalized threshold cycle (ΔCт) of chromosome specific alleles of GBSSI (GBSSI–7A, GBSSI–4A, and GBSSI–7D) during seed development. The data was taken at three stages of seed development (21, 28, and 35 days after anthesis, DAA) in two mutant lines, ‘TAC 75’(amylose content - 64 %) and ‘TAC 6’(amylose content– 6.8 %), in comparison to the parent variety, ‘C 306’ (amylose content - 26 %). The data was taken in two biological replications, each represented as mean ± SD from three technical replicates. Wheat ADP Ribosylation Factor (ARF) was used as an internal control gene for normalization. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3605681_d1
title: Additional file 3: of Development of EMS-induced mutation population for amylose and resistant starch variation in bread wheat (Triticum aestivum) and identification of candidate genes responsible for amylose variation

description: Normalized threshold cycle (ΔCт) of 20 starch metabolic genes during seed development. The data was taken at three stages of seed development (21, 28, and 35 days after anthesis, DAA) in two mutant lines, ‘TAC 75’(amylose content - 64 %) and ‘TAC 6’(amylose content– 6.8 %), in comparison to the parent variety, ‘C 306’ (amylose content - 26 %). The data was taken in two biological replications, each represented as mean ± SD from three technical replicates. Wheat ADP Ribosylation Factor (ARF) was used as an internal control gene for normalization. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.c.3605378_d6
title: Additional file 1: Table S1. of Cancer network activity associated with therapeutic response and synergism

description: Drugs classified as “single node” or “multiple node” perturbation. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.c.3605378_d5
title: Additional file 6: Table S3. of Cancer network activity associated with therapeutic response and synergism

description: Drugs with their IC50 negatively correlated with CNA values. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.c.3605378_d3
title: Additional file 2: Table S2. of Cancer network activity associated with therapeutic response and synergism

description: Normalized CNA values for all cancer cell lines. (XLSX 55 kb)
DOI: 10.6084/m9.figshare.c.3605360_d2
title: Additional file 1: of Seroprevalence of avian hepatitis E virus and avian leucosis virus subgroup J in chicken flocks with hepatitis syndrome, China

description: OD450 values of anti-avian HEV IgG antibodies in the serum samples collected from Shandong and Shaanxi provinces. (The cut-off value is 0.368). (XLS 218 kb)
DOI: 10.6084/m9.figshare.c.3605360_d1
title: Additional file 2: of Seroprevalence of avian hepatitis E virus and avian leucosis virus subgroup J in chicken flocks with hepatitis syndrome, China

description: OD650 values of anti-ALV-J IgG antibodies in the serum samples collected from Shandong and Shaanxi provinces. [S/P&lt;=0.6: Negative; S/P&gt;0.6: Positive. S/P= (Average of sample â   Average of negative control)/(Average of positive â   Average of negative)]. (XLS 82 kb)
DOI: 10.6084/m9.figshare.c.3605255_d6
title: Additional file 3: Table S3. of Functional analysis of Orco and odorant receptors in odor recognition in Aedes albopictus

description: List of oligonucleotide primers for qRT-PCR. (XLS 18Â kb)
DOI: 10.6084/m9.figshare.c.3605255_d4
title: Additional file 2: Table S2. of Functional analysis of Orco and odorant receptors in odor recognition in Aedes albopictus

description: List of oligonucleotide primers for RACE. (XLS 18Â kb)
DOI: 10.6084/m9.figshare.c.3605255_d1
title: Additional file 1: Table S1. of Functional analysis of Orco and odorant receptors in odor recognition in Aedes albopictus

description: List of oligonucleotide primers for RT-PCR. (XLS 21Â kb)
DOI: 10.25810/bx1d-gc92
title: FIRED Germany Nov 2000 - July 2024

description: This is event-level polygons for the fire event delineation (FIRED) product for GERMANY from November 2000  to July 2024. It is derived from the MODIS MCD64A1 burned area product (see https://lpdaac.usgs.gov/products/mcd64a1v061/ for more details). The MCD64A1 is a monthly raster grid of estimated burned dates. Firedpy (https://github.com/earthlab/firedpy) is an algorithm that converts these rasters into events by stacking the entire time series into a spatial-temporal data cube, then uses an algorithm to assign event identification numbers to pixels that fit into the same 3-dimensional spatial temporal window. This particular dataset was created using a spatial parameter of 1 pixels and 5 days. Daily polygons are included and the event identification numbers are the same for both files, but the event-level product has only single polygons for each entire event, while the daily product has separate polygons for each date per event. See the associated paper for more details on the methods and more:

Balch, J.K.; St. Denis, L.A.; Mahood, A.L.; Mietkiewicz, N.P.; Williams, T.M.; McGlinchy, J.; Cook, M.C. FIRED (Fire Events Delineation): An Open, Flexible Algorithm and Database of US Fire Events Derived from the MODIS Burned Area Product (2001–2019). Remote Sens. 2020, 12, 3498. https://doi.org/10.3390/rs12213498
DOI: 10.15468/dl.bpykgs
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mullus bensasi Temminck & Schlegel, 1843",
 "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/0032245-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.c.3605084_d3
title: Additional file 13: of Comprehensive characterization of a time-course transcriptional response induced by autotoxins in Panax ginseng using RNA-Seq

description: The differentially expressed genes across all the time points. (XLS 66Â kb)
DOI: 10.6084/m9.figshare.c.3605027_d2
title: Additional file 1: of Members of WRKY Group III transcription factors are important in TYLCV defense signaling pathway in tomato (Solanum lycopersicum)

description: Table S1. WRKY transcription factors name in rice, Arabidopsis, and tomato. Red color in tomato represented the SolyWRKY Group III TFs. Table S2. The orthologous WRKY genes in tomato, Arabidopsis, and rice. Red represented the orthologous genes of Group III genes responded to TYLCV infection in tomato. Table S3. The paralogous WRKY genes in tomato, Arabidopsis, and rice. Red represented the paralogous genes of Group III genes responded to TYLCV infection in tomato. (XLS 48Â kb)
DOI: 10.5281/zenodo.14421919
title: ENVIRONMENTAL LAW
DOI: 10.5281/zenodo.14421920
title: ENVIRONMENTAL LAW
DOI: 10.6084/m9.figshare.c.3604985_d10
title: Additional file 6: Table S5. of Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize

description: Joint linkage analysis summary for days to tasseling trait in CN-NAM and US-NAM, respectively. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3604985_d9
title: Additional file 10: Table S8. of Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize

description: Phenotypic data for days to tasseling in five environments for the US-NAM population. (XLSX 179 kb)
DOI: 10.6084/m9.figshare.c.3604985_d8
title: Additional file 9: Table S7. of Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize

description: Phenotypic data for days to tasseling in six environments for the CN-NAM population. (XLSX 193 kb)
DOI: 10.6084/m9.figshare.c.3604985_d7
title: Additional file 2: Table S2. of Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize

description: Recombination bin map information within the 36 families of the two NAM populations, based on high-quality SNPs obtained from population sequencing. (XLSX 4828 kb)
DOI: 10.6084/m9.figshare.c.3605009_d2
title: Additional file 2: Table S1. of Three-dimensional poly-(ε-caprolactone) nanofibrous scaffolds directly promote the cardiomyocyte differentiation of murine-induced pluripotent stem cells through Wnt/β-catenin signaling

description: Primers and cycling conditions for RT-PCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3604985_d4
title: Additional file 8: Table S6. of Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize

description: Information about joint recombination bin maps for the combined CN-NAM and US-NAM populations. (XLSX 411 kb)
DOI: 10.7274/27927858
title: Hybrid Numerical Methods and Solution Verification for the Neutron Transport Equation

description: The neutron transport equation approximates how neutrons interact with different materials in various systems. This work focuses on applying hybrid numerical methods to improve the current methods used to approximate the neutron flux in addition to further developing a single spatial grid error estimator. One hybrid method employs machine learning and neural networks to predict the matrix-vector multiplication product in k-eigenvalue problems. This alleviates the use of large scattering and fission matrices where these machine learning models require less than 3% of the original memory storage. These models are able to remain accurate to the reference solution and improve convergence times while being used in a plurality of problems not trained on. The training process is also improved by using random forests to initialize neural networks and encoders to limit the model input size. A collision-based hybrid method separates the time-dependent neutron transport equation into uncollided and collided equations. High fidelity angular and energy grids are used with the uncollided equation to increase accuracy while low fidelity grids are used with the collided equation to improve convergence times. This technique is applied to one- and two-dimensional problems which demonstrate better convergence times than similar high fidelity grid coarsening schemes and more accurate results when compared to low fidelity grid coarsening. In certain instances, the hybrid method converges in half the time it takes source iteration. Solution verification is important to ensure an approximate solution is sufficiently close to the true solution of the governing equation. The method of nearby problems is a spatial grid error estimator that can identify locations of high spatial error without requiring multiple spatial grids. This is shown to be effective with one- and two-dimensional problems for fixed source and k-eigenvalue problems using both discrete ordinates and Monte Carlo neutron transport solvers. The method of nearby problems identifies areas of high spatial error with similar accuracy to methods that use multiple spatial grids.
DOI: 10.7274/27927858.v1
title: Hybrid Numerical Methods and Solution Verification for the Neutron Transport Equation

description: The neutron transport equation approximates how neutrons interact with different materials in various systems. This work focuses on applying hybrid numerical methods to improve the current methods used to approximate the neutron flux in addition to further developing a single spatial grid error estimator. One hybrid method employs machine learning and neural networks to predict the matrix-vector multiplication product in k-eigenvalue problems. This alleviates the use of large scattering and fission matrices where these machine learning models require less than 3% of the original memory storage. These models are able to remain accurate to the reference solution and improve convergence times while being used in a plurality of problems not trained on. The training process is also improved by using random forests to initialize neural networks and encoders to limit the model input size. A collision-based hybrid method separates the time-dependent neutron transport equation into uncollided and collided equations. High fidelity angular and energy grids are used with the uncollided equation to increase accuracy while low fidelity grids are used with the collided equation to improve convergence times. This technique is applied to one- and two-dimensional problems which demonstrate better convergence times than similar high fidelity grid coarsening schemes and more accurate results when compared to low fidelity grid coarsening. In certain instances, the hybrid method converges in half the time it takes source iteration. Solution verification is important to ensure an approximate solution is sufficiently close to the true solution of the governing equation. The method of nearby problems is a spatial grid error estimator that can identify locations of high spatial error without requiring multiple spatial grids. This is shown to be effective with one- and two-dimensional problems for fixed source and k-eigenvalue problems using both discrete ordinates and Monte Carlo neutron transport solvers. The method of nearby problems identifies areas of high spatial error with similar accuracy to methods that use multiple spatial grids.
DOI: 10.15468/dl.nyyyx5
title: Occurrence Download

description: A dataset containing 3334 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1019.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pinus elliottii Engelm."
 ]
}

 The dataset includes 3334 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032246-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.65gcat
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Upeneus bensasi (Temminck & Schlegel, 1843)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 23 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032247-241126133413365/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.3604559_d1
title: Additional file 1: of Epigenomic profiling of prostate cancer identifies differentially methylated genes in TMPRSS2:ERG fusion-positive versus fusion-negative tumors

description: List of 3101 top-ranked differentially methylated CpG sites.
DOI: 10.6084/m9.figshare.c.3604532_d2
title: Additional file 2: Tables S1â  S16. of Global histone modification profiling reveals the epigenomic dynamics during malignant transformation in a four-stage breast cancer model

description: Table S1. Differential expression genes between L and P6 cell lines. Table S2. Differential expression genes between LT and P6 cell lines. Table S3. Differential expression genes between LTR and P6 cell lines. Table S4. DEGs between LT and L cell lines. Table S5. DEGs between LTR and LT cell lines. Table S6. DEGs between TCGA breast cancer and normal tissues (â Ľthreefolds). Table S7. Genes overlapped between DEGs of TCGA and transformed cell lines. Table S8. Genes localized in H3K9me3 small LOCKs of HMC-p6. Table S9. Genes localized in decreased H3K9me2 boundaries in HMC-LT. Table S10. Genes localized in decreased H3K9me2 boundaries in HMC-LTR. Table S11. Uniprot cancer-related genes in the boundaries of decreased H3K9me2 LOCKs (compared to HMC-p6). Table S12. Genes overlapped between LT_NC/LT_shKDM3A and LT/P6 DEGs. Table S13. DEGs between LT_NC and LT_shKDM3a cells. Table S14. Genes overlapped between LTR_NC/LTR_siKDM3A and LTR/P6 DEGs. Table S15. DEGs between LTR_NC and LTR_siKDM3a cells. Table S16. Primer and siRNA sequences. (XLS 1135 kb)
DOI: 10.6084/m9.figshare.c.3604520_d1
title: Additional file 3: of Hepatic resection provided long-term survival for patients with intermediate and advanced-stage resectable hepatocellular carcinoma

description: Figure S2. Kaplan-Meier Curve showing DFS of surgery plus TACE and surgery alone. (ZIP 396 KB)
DOI: 10.15468/dl.mxf5pa
title: Occurrence Download

description: A dataset containing 15392 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Datos de monitoreo de la estructura de los manglares de la Ciénaga Grande de Santa Marta (Magdalena)"
 ]
}

 The dataset includes 15392 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032248-241126133413365/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.3604187_d1
title: Additional file 1: of Integrated transcriptional profiling and genomic analyses reveal RPN2 and HMGB1 as promising biomarkers in colorectal cancer

description: Table S1. List of differentially expressed genes with transcriptional regulation. Table S2. Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) of differentially expressed genes based on biological processes, canonical pathways and upstream regulators. a GO biological processes enriched (P&lt;0.01, FDR&lt;5%). b Upstream regulator analysis using Ingenuity Pathway Analysis 2013 (P&lt;0.00001) Table S3. Comparison of differentially expressed genes with published CRC microarray studies
DOI: 10.6084/m9.figshare.c.3604148_d1
title: Additional file 1: of Maternal uniparental disomy 14 and mosaic trisomy 14 in a Chinese boy with moderate to severe intellectual disability

description: SNP array raw data for chromosome 14 of the family trio. (XLS 1028Â kb)
DOI: 10.6084/m9.figshare.c.3604130_d1
title: Additional file 1: of Health system strengthening and hypertension management in China

description: Appendix 1. (XLSX 408 kb)
DOI: 10.6084/m9.figshare.c.3604097_d6
title: MOESM3 of Whole genome sequencing uncovers a novel IND-16 metallo-Î˛-lactamase from an extensively drug-resistant Chryseobacterium indologenes strain J31

description: Additional files 3: Table S3. Insertion sequence, integrase gene and transposase genes analysis.