cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25895984.v1
title: Potential molecular mechanisms of Huangqin Tang for liver cancer treatment by network pharmacology and molecular dynamics simulations

description: This study aims to investigate the mechanism of Huangqin Tang in treating liver cancer. Active ingredients and corresponding targets of Huangqin Tang were obtained from the Traditional Chinese Medicine Systems Pharmacology Database. Differentially expressed genes in liver cancer were identified from mRNA expression data. A protein–protein interaction (PPI) network was constructed using differentially expressed genes and Huangqin Tang targets. Random walk with restart (RWR) analysis was performed on the PPI network. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were conducted. A drug-active ingredient–gene interaction network was established, and molecular docking and molecular dynamics simulations were performed. Finally, the stability of binding between CDK1 and oroxylin was tested according to cellular thermal shift assay (CETSA). 160 active ingredients, 239 targets, and 1093 differentially expressed genes were identified. RWR analysis identified 10 potential targets for liver cancer. Enrichment analysis revealed protein kinase regulator activity and Steroid hormone biosynthesis as significant pathways. Molecular docking suggested a stable complex between oroxylin A and CDK1. CETSA demonstrated that the combination of oroxylin A and CDK1 increased the stability of CDK1, and the combination efficiency was high. Huangqin Tang may treat liver cancer by targeting CDK1 with oroxylin A. Protein kinase regulator activity and Steroid hormone biosynthesis pathways may play a role in liver cancer treatment with Huangqin Tang. This study provides insight into the mechanistic basis of Huangqin Tang for liver cancer treatment.
DOI: 10.6084/m9.figshare.27939030
title: Identification of polyamine metabolism-related prognostic biomarkers for predicting breast cancer prognosis, immune microenvironment, and candidate drugs

description: In this study, polyamine metabolism related genes (PMRGs) were used to establish a breast cancer (BC) prognostic model. Using PMRGs, TCGA BC samples were divided into cluster1 and cluster2. A 13-gene BC prognostic model was constructed by screening differential genes. High-risk BC patients exhibited heightened immunoinfiltration levels, potentially impeding immunotherapy responses. Drug response predicted that BC patients in the low-risk group might benefit more from chemotherapy and targeted therapy. In conclusion, a novel 13-gene BC prognostic risk model based on PMRGs was established to effectively predict prognosis, immune microenvironment, and drug therapy response in patients with BC.
DOI: 10.6084/m9.figshare.27939030.v1
title: Identification of polyamine metabolism-related prognostic biomarkers for predicting breast cancer prognosis, immune microenvironment, and candidate drugs

description: In this study, polyamine metabolism related genes (PMRGs) were used to establish a breast cancer (BC) prognostic model. Using PMRGs, TCGA BC samples were divided into cluster1 and cluster2. A 13-gene BC prognostic model was constructed by screening differential genes. High-risk BC patients exhibited heightened immunoinfiltration levels, potentially impeding immunotherapy responses. Drug response predicted that BC patients in the low-risk group might benefit more from chemotherapy and targeted therapy. In conclusion, a novel 13-gene BC prognostic risk model based on PMRGs was established to effectively predict prognosis, immune microenvironment, and drug therapy response in patients with BC.
DOI: 10.6084/m9.figshare.31108639
title: Soil respiration dataset_try

description: Soil respiration (Rs) is a highly sensitive and consequential process in terrestrial ecosystem carbon (C) cycling under global change scenarios, particularly warming and altered precipitation patterns. However, how warming and delayed rainfall interact to influence Rs and its components remains poorly understood. Here, we combined a field factorial manipulation experiment with δ13C natural abundance partitioning and a complementary meta-analysis to quantify responses of Rs and its components in grassland ecosystems.
DOI: 10.6084/m9.figshare.31108639.v3
title: Soil respiration dataset_try

description: Soil respiration (Rs) is a highly sensitive and consequential process in terrestrial ecosystem carbon (C) cycling under global change scenarios, particularly warming and altered precipitation patterns. However, how warming and delayed rainfall interact to influence Rs and its components remains poorly understood. Here, we combined a field factorial manipulation experiment with δ13C natural abundance partitioning and a complementary meta-analysis to quantify responses of Rs and its components in grassland ecosystems.
DOI: 10.6084/m9.figshare.31108639.v2
title: Soil respiration dataset

description: Soil respiration (Rs) is a highly sensitive and consequential process in terrestrial ecosystem carbon (C) cycling under global change scenarios, particularly warming and altered precipitation patterns. However, how warming and delayed rainfall interact to influence Rs and its components remains poorly understood. Here, we combined a field factorial manipulation experiment with δ13C natural abundance partitioning and a complementary meta-analysis to quantify responses of Rs and its components in grassland ecosystems.
DOI: 10.15468/dl.9g2ufk
title: Occurrence Download

description: A dataset containing 308306 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Laridae",
 "Country is France",
 "HasCoordinate is true",
 "Year is greater than or equal to 2024"
 ]
}

 The dataset includes 308306 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002161-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/r52r3tsc3x
title: Black liquor valorization Machine learning model

description: This data set used microbial fermentation system adopting constant initial COD or constant sucrose COD with BL COD supplementation. Each batch have multiple sets with replicate. This data set is used to model COD consumption, biomass, polymer production. The model is further used to optimize the yield.
DOI: 10.17632/r52r3tsc3x.1
title: Black liquor valorization Machine learning model

description: This data set used microbial fermentation system adopting constant initial COD or constant sucrose COD with BL COD supplementation. Each batch have multiple sets with replicate. This data set is used to model COD consumption, biomass, polymer production. The model is further used to optimize the yield.
DOI: 10.17632/gcrz8r25vp
title: Data for "Enhancing the biodegradation of hydrophobic volatile organic compounds: A study on microbial consortia adaptation and the role of surfactants"

description: This dataset contains the experimental data underlying the research study on the biodegradation of hydrophobic Volatile Organic Compounds (VOCs) in a Stirred Tank Bioreactor (STBR). The study evaluates the long-term impact of adding non-ionic surfactants (Tween 80) and biological surfactants (Saponin) on the removal efficiency of Cyclohexane, Toluene, and Hexane, as well as the adaptation of microbial consortia. The dataset is organized into processed files covering continuous bioreactor operation, batch kinetic tests, and carbon balance analysis.
DOI: 10.17632/gcrz8r25vp.1
title: Data for "Enhancing the biodegradation of hydrophobic volatile organic compounds: A study on microbial consortia adaptation and the role of surfactants"

description: This dataset contains the experimental data underlying the research study on the biodegradation of hydrophobic Volatile Organic Compounds (VOCs) in a Stirred Tank Bioreactor (STBR). The study evaluates the long-term impact of adding non-ionic surfactants (Tween 80) and biological surfactants (Saponin) on the removal efficiency of Cyclohexane, Toluene, and Hexane, as well as the adaptation of microbial consortia. The dataset is organized into processed files covering continuous bioreactor operation, batch kinetic tests, and carbon balance analysis.
DOI: 10.15468/dl.ty8a6b
title: Occurrence Download

description: A dataset containing 8690 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Picea glauca)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is Europe"
 ]
}

 The dataset includes 8690 records from 113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002224-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yy8rtb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ClassKey is Chordata",
 "HasCoordinate is true",
 "Continent is Africa"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002225-260120142942310/datasets/export for details.
DOI: 10.15468/dl.6jprc2
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Carex enervis",
 "Year 1970-2000"
 ]
}

 The dataset includes 92 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002226-260120142942310/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.31111253
title: Action mechanism of Qianlie Xiaozheng decoction against prostate cancer: network pharmacology, molecular docking, and molecular dynamics simulations

description: Prostate cancer (PCa) is a leading male malignancy. This study explores the anti-PCa mechanism of Qianlie Xiaozheng decoction (QLXZD) using network pharmacology. From 34 ingredients and 23 potential therapeutic targets, 3 hub ingredients (baicalein, kaempferol, quercetin) and 4 hub targets (CCNB1, CDK1, EGFR, TOP2A) were prioritized. Enrichment analysis of the 23 targets linked them to cell cycle and kinase signaling. Molecular docking confirmed strong binding of the hub ingredients to the hub targets, comparable to known inhibitors. Molecular dynamics simulations supported baicalein-TOP2A complex stability. These findings reveal QLXZD exerts anti-PCa effects <i>via</i> a multi-component, multi-target mechanism, supporting its clinical application.
DOI: 10.6084/m9.figshare.31111253.v1
title: Action mechanism of Qianlie Xiaozheng decoction against prostate cancer: network pharmacology, molecular docking, and molecular dynamics simulations

description: Prostate cancer (PCa) is a leading male malignancy. This study explores the anti-PCa mechanism of Qianlie Xiaozheng decoction (QLXZD) using network pharmacology. From 34 ingredients and 23 potential therapeutic targets, 3 hub ingredients (baicalein, kaempferol, quercetin) and 4 hub targets (CCNB1, CDK1, EGFR, TOP2A) were prioritized. Enrichment analysis of the 23 targets linked them to cell cycle and kinase signaling. Molecular docking confirmed strong binding of the hub ingredients to the hub targets, comparable to known inhibitors. Molecular dynamics simulations supported baicalein-TOP2A complex stability. These findings reveal QLXZD exerts anti-PCa effects <i>via</i> a multi-component, multi-target mechanism, supporting its clinical application.
DOI: 10.60797/geo.2025.2.4.7
title: Месторождения полезных ископаемых черных металлов и элементов группы «Платина» в Бурунди

description: Cifra. Науки о Земле и окружающей среде, Выпуск 1 (2) 2025
DOI: 10.25934/pr00004827.1
title: Available datapackage for study 'A Randomized, Double-Blind, Placebo-Controlled, Parallel-Group, Fixed-Dose, Multicenter Study of JNS010 (Paliperidone Palmitate) in Patients With Schizophrenia'

description: The purpose of this study is to evaluate the efficacy and safety of paliperidone palmitate as compared with placebo in the treatment of participants with schizophrenia (psychiatric disorder with symptoms of emotional instability, detachment from reality, often with delusions [a false belief held in the face of strong differing evidence, especially as a symptom of psychiatric disorder] and hallucinations [imagining things], and withdrawal into the self).
DOI: 10.5281/zenodo.16524193
title: 25 Synthetic TP53 Genomic Datasets for Benchmarking and Method Development

description: This collection contains 25 synthetic genomics datasets generated using NEAT v3, simulating the TP53 gene of Homo sapiens. These datasets are intended for benchmarking somatic variant calling algorithms, especially in tumor-only settings.

Each dataset is composed of paired-end reads and was designed to systematically explore the impact of two intrinsic NGS parameters on variant detection performance:





Sequencing coverage: 300×, 700×, 1000×, 3000×, and 5000×




Read length: 50 bp, 75 bp, 100 bp, 150 bp, and 300 bp



All 25 datasets are labeled using the format {coverage}_{readLength} to reflect their specific configuration. For example, the dataset 1000_150 corresponds to 1000× coverage and 150 bp read length. All combinations are shown in the following table:




 
50bp
75bp
100bp
150bp
300bp


300x
300_50
300_75
300_100
300_150
300_300


700x
700_50
700_75
700_100
700_150
700_300


1000x
1000_50
1000_75
1000_100
1000_150
1000_300


3000x
3000_50
3000_75
3000_100
3000_150
3000_300


5000x
5000_50
5000_75
5000_100
5000_150
5000_300




This expanded set builds upon our previous dataset release, which varied each parameter independently. Here, we provide a grid design, allowing researchers to analyze both individual and combined effects of coverage and read length on somatic variant calling tools. The files included are aligned files with their index (BAM and BAI) along with the VCF files containing the variants for each sample.

For more information about the synthetic data generation framework, please visit the synth4bench GitHub repositoryOur work has been submitted to the bioRxiv preprint repository. If you use synth4bench, or any of our data/scripts/code, please cite doi:10.1101/2024.03.07.582313v2.
DOI: 10.5281/zenodo.16524192
title: 25 Synthetic TP53 Genomic Datasets for Benchmarking and Method Development

description: This collection contains 25 synthetic genomics datasets generated using NEAT v3, simulating the TP53 gene of Homo sapiens. These datasets are intended for benchmarking somatic variant calling algorithms, especially in tumor-only settings.

Each dataset is composed of paired-end reads and was designed to systematically explore the impact of two intrinsic NGS parameters on variant detection performance:





Sequencing coverage: 300×, 700×, 1000×, 3000×, and 5000×




Read length: 50 bp, 75 bp, 100 bp, 150 bp, and 300 bp



All 25 datasets are labeled using the format {coverage}_{readLength} to reflect their specific configuration. For example, the dataset 1000_150 corresponds to 1000× coverage and 150 bp read length. All combinations are shown in the following table:




 
50bp
75bp
100bp
150bp
300bp


300x
300_50
300_75
300_100
300_150
300_300


700x
700_50
700_75
700_100
700_150
700_300


1000x
1000_50
1000_75
1000_100
1000_150
1000_300


3000x
3000_50
3000_75
3000_100
3000_150
3000_300


5000x
5000_50
5000_75
5000_100
5000_150
5000_300




This expanded set builds upon our previous dataset release, which varied each parameter independently. Here, we provide a grid design, allowing researchers to analyze both individual and combined effects of coverage and read length on somatic variant calling tools. The files included are aligned files with their index (BAM and BAI) along with the VCF files containing the variants for each sample.

For more information about the synthetic data generation framework, please visit the synth4bench GitHub repositoryOur work has been submitted to the bioRxiv preprint repository. If you use synth4bench, or any of our data/scripts/code, please cite doi:10.1101/2024.03.07.582313v2.
DOI: 10.60797/geo.2025.2.4.13
title: Месторождения полезных ископаемых черных металлов и элементов группы «Платина» в Бурунди

description: Cifra. Науки о Земле и окружающей среде, Выпуск 1 (2) 2025
DOI: 10.5281/zenodo.18325018
title: Data for "Drone-Imaging Assisted GWAS Reveal Key QTLs for Emergence and Late Blight Resistance in Tetraploid Potato"

description: The data applied in the study includes phenotypic and genotypic information on two panels of breeding clones from Danespo A/S. Due to proprietary rights of the breeding clones, they are masked by IdX numbers in the data. For commercially available clones, the IdX is linked to their commercial name through the Name column. The genotypic data was generated by SNP array using a custom 20k Affymetrix chip. This chip is also proprietary, and the SNP positions on each chromosome are also masked, but retain colinearity along the chromosome. The phenotypic data was computed from image data as a commercial service by Phenoyard AB without preprocessing. The phenotypes submitted here include the 1-9 grading of clone emergence across day 0-20 of the early growth season. 9 denotes early emergence, and 1 denotes late emergence. Late blight resistance is reported as an area-under-disease-progression-curve normalized by total monitoration period, i.e. a single across-season phenotype for each clone. 

File descriptions:SNP_map.csv - .csv file holding the masked marker coordinates on the chromosomes. Chromosome 0 is scaffolds, chromosome 13 is unmapped. The SNPs are based on the v6.1 potato DM reference genome, but positions are masked within chromosome. The colinearity of the SNPs along the chromosomes are conserved relative to the true positions. 

gt_emergence_panel.csv - .csv file holding imputed genotypic data of 8,731 SNPs for 2,576 clones in the emergence panel. The row names are clone IdX. The column names are SNP ID. 

gt_late_blight_resistance_panel.csv - .csv file holding imputed genotypic data of 8,731 SNPs for 1,520 clones in the late blight resistance panel. The row names are clone IdX. The column names are SNP ID. 

pt_emergence.csv - .csv file holding "Emergence" phenotypic data for the emergence panel, including 6,262 observations. Also including metadata such as field location, year of phenotyping, and clone market group.

pt_late_blight_resistance.csv - .csv file holding late blight resistance phenotypic data for the late blight resistance panel at each time point across the infection period for each clone in each testing year with field location metadata, including 6,972 observations. Also including metadata such as year of phenotyping, and clone market group.
DOI: 10.6084/m9.figshare.31109638
title: An Integrated Framework for Global Detection and Quantification of Lunar Pyroclastic Deposits1

description: These are the data products for the published article entitled "<b>An Integrated Framework for Global Detection and Quantification of Lunar Pyroclastic Deposits</b>" by Dibyendu Misra, Megha Bhatt, Marcel Hess, and Christian Wöhler in <i>The </i><i>Planetary Science Journal</i> (https://doi.org/10.3847/PSJ/ae317c).
DOI: 10.6084/m9.figshare.31109638.v1
title: An Integrated Framework for Global Detection and Quantification of Lunar Pyroclastic Deposits1

description: These are the data products for the published article entitled "<b>An Integrated Framework for Global Detection and Quantification of Lunar Pyroclastic Deposits</b>" by Dibyendu Misra, Megha Bhatt, Marcel Hess, and Christian Wöhler in <i>The </i><i>Planetary Science Journal</i> (https://doi.org/10.3847/PSJ/ae317c).
DOI: 10.15468/dl.acfefw
title: Occurrence Download

description: A dataset containing 1638 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Royal Botanic Gardens, Kew - Herbarium Specimens",
 "TaxonKey is Aeschynanthus"
 ]
}

 The dataset includes 1638 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002227-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18324676
title: Real Time Anomaly Detection in Aviation Composites: An Edge Computing Framework for Acoustic Tap Test
DOI: 10.5281/zenodo.18324677
title: Real Time Anomaly Detection in Aviation Composites: An Edge Computing Framework for Acoustic Tap Test
DOI: 10.15468/dl.d62xrq
title: Occurrence Download

description: A dataset containing 1135 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calendulauda burra"
 ]
}

 The dataset includes 1135 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002228-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.va6bpf
title: Occurrence Download

description: A dataset containing 58827 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Myotis myotis)",
 "OccurrenceStatus is Present",
 "SpeciesKey is not null",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2026",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 },
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation)"
 ]
}

 The dataset includes 58827 records from 1208 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002195-260120142942310/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.29181452
title: Raw Data

description: Introduction: Weight misperception (WM) is common and associated with adverse health outcomes. Moreover, it may be associated with anti-obesity medication misuse. Previous studies in other countries report that WM is common among university students. However, its frequency differs between countries, and data regarding university students in Turkey are lacking.
Methodology: We designed and conducted a cross-sectional survey on a university campus in Turkey. Demographic, anthropometric, educational, nutritional, and perceptional data were acquired. Weight misperception was analyzed verbally and visually. Misperceptions were grouped as weight overestimation and underestimation. Factors associated with misperceptions were analyzed using multivariate multinomial logistic regression (LR) analysis.
Results: 748 participants were included in the analysis. Verbal and visually appropriate perceptions were 75% and 65%, respectively. Female participants were more likely to perceive appropriately. Among participants with misperception, the females were more likely to overestimate while the males were more likely to underestimate. LR analysis demonstrated that body mass index, gender, tobacco use, overall health perception, physical self-esteem, and fast-food serving were associated with misperception in different models.
Discussion: Weight misperception is common among university students in Turkey. Lean female students are prone to overestimation and may end up misusing anti-obesity medication. Overweight male students are prone to underestimation and prevented from benefiting from anti-obesity medications.
<br>