cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25282024.v1
title: Lessons on harmonization of scoring criteria for dicentric chromosome assay in South Korea

description: Networking with other biodosimetry laboratories is necessary to assess the radiation exposure of many individuals in large-scale radiological accidents. The Korea biodosimetry network, K-BioDos, prepared harmonized scoring guidelines for dicentric chromosome assay to obtain homogeneous results within the network and investigated the efficiency of the guidelines. Three laboratories in K-BioDos harmonized the scoring guidelines for dicentric chromosome assay. The results of scoring dicentric chromosomes using the harmonized scoring guidelines were compared with the laboratories’ results using their own methods. Feedback was collected from the scorers following the three intercomparison exercises in 3 consecutive years. K-BioDos members showed comparable capacity to score dicentrics in the three exercises. However, the results of the K-BioDos guidelines showed no significant improvement over those of the scorers’ own methods. According to the scorers, our harmonized guidelines led to more rejected metaphases and ultimately decreased the number of scorable metaphases compared with their own methods. Moreover, the scoring time was sometimes longer with the K-BioDos protocol because some scorers were not yet familiar with the guidelines, though most scorers reported that the time decreased or was unchanged. These challenges may cause low adherence to the guidelines. Most scorers expressed willingness to use the guidelines to select scorable metaphases or identify dicentrics for other biodosimetry works, whereas one did not want to use it due to the difference from their calibration curves. We identified potential resistance to following the harmonized guidelines and received requests for more detailed methods. Our findings suggest that the harmonized criteria should be continually updated, and education and training should be provided for all scorers. These changes could allow members within the biodosimetry network to successfully collaborate and support each other in large-scale radiological accidents.
DOI: 10.6084/m9.figshare.25421143
title: Distinguish response of low-dose radiation with different dose-rate on gene expression of human coronary artery endothelial cells: a bioinformatic study based on transcriptomic sequencing

description: People are exposed to low-dose radiation in medical diagnosis, occupational, or life circumstances, but the effect of low-dose radiation on human health is still controversial. The biological effects of radiation below 100 mGy are still unproven. In this study, we observed the effects of low-dose radiation (100 mGy) on gene expression in human coronary artery endothelial cells (HCAECs) and its effect on molecular signaling. HCAECs were exposed to 100 mGy ionizing radiation at 6 mGy/h (low-dose-rate) or 288 mGy/h (high-dose-rate). After 72 h, total RNA was extracted from sham or irradiated cells for Quant-Seq 3'mRNA-Seq, and bioinformatic analyses were performed using Metascape. Gene profiling was validated using qPCR. Compared to the non-irradiated control group, 100 mGy of ionizing radiation at 6 mGy/h altered the expression of 194 genes involved in signaling pathways related to heart contraction, blood circulation, and cardiac myofibril assembly differentially. However, 100 mGy at 288 mGy/h altered expression of 450 genes involved in cell cycle-related signaling pathways, including cell division, nuclear division, and mitosis differentially. Additionally, gene signatures responding to low-dose radiation, including radiation dose-specific gene profiles (HIST1H2AI, RAVER1, and POTEI) and dose-rate-specific gene profiles (MYL2 for the low-dose-rate and DHRS9 and CA14 for the high-dose-rate) were also identified. We demonstrated that 100 mGy low-dose radiation could alter gene expression and molecular signaling pathways at the low-dose-rate and the high-dose-rate differently. Our findings provide evidence for further research on the potential impact of low-dose radiation on cardiovascular function.
DOI: 10.6084/m9.figshare.25282024
title: Lessons on harmonization of scoring criteria for dicentric chromosome assay in South Korea

description: Networking with other biodosimetry laboratories is necessary to assess the radiation exposure of many individuals in large-scale radiological accidents. The Korea biodosimetry network, K-BioDos, prepared harmonized scoring guidelines for dicentric chromosome assay to obtain homogeneous results within the network and investigated the efficiency of the guidelines. Three laboratories in K-BioDos harmonized the scoring guidelines for dicentric chromosome assay. The results of scoring dicentric chromosomes using the harmonized scoring guidelines were compared with the laboratories’ results using their own methods. Feedback was collected from the scorers following the three intercomparison exercises in 3 consecutive years. K-BioDos members showed comparable capacity to score dicentrics in the three exercises. However, the results of the K-BioDos guidelines showed no significant improvement over those of the scorers’ own methods. According to the scorers, our harmonized guidelines led to more rejected metaphases and ultimately decreased the number of scorable metaphases compared with their own methods. Moreover, the scoring time was sometimes longer with the K-BioDos protocol because some scorers were not yet familiar with the guidelines, though most scorers reported that the time decreased or was unchanged. These challenges may cause low adherence to the guidelines. Most scorers expressed willingness to use the guidelines to select scorable metaphases or identify dicentrics for other biodosimetry works, whereas one did not want to use it due to the difference from their calibration curves. We identified potential resistance to following the harmonized guidelines and received requests for more detailed methods. Our findings suggest that the harmonized criteria should be continually updated, and education and training should be provided for all scorers. These changes could allow members within the biodosimetry network to successfully collaborate and support each other in large-scale radiological accidents.
DOI: 10.6084/m9.figshare.25395512
title: Construction of dose prediction model and identification of sensitive genes for space radiation based on single-sample networks under spaceflight conditions

description: To identify sensitive genes for space radiation, we integrated the transcriptomic samples of spaceflight mice from GeneLab and predicted the radiation doses absorbed by individuals in space. A single-sample network (SSN) for each individual sample was constructed. Then, using machine learning and genetic algorithms, we built the regression models to predict the absorbed dose equivalent based on the topological structure of SSNs. Moreover, we analyzed the SSNs from each tissue and compared the similarities and differences among them. Our model exhibited excellent performance with the following metrics: R2=0.980, MSE=6.74e−04, and the Pearson correlation coefficient of 0.990 (<i>p</i> value &lt;.0001) between predicted and actual values. We identified 20 key genes, the majority of which had been proven to be associated with radiation. However, we uniquely established them as space radiation sensitive genes for the first time. Through further analysis of the SSNs, we discovered that the different tissues exhibited distinct mechanisms in response to space stressors. The topology structures of SSNs effectively predicted radiation doses under spaceflight conditions, and the SSNs revealed the gene regulatory patterns within the organisms under space stressors.
DOI: 10.6084/m9.figshare.25395512.v1
title: Construction of dose prediction model and identification of sensitive genes for space radiation based on single-sample networks under spaceflight conditions

description: To identify sensitive genes for space radiation, we integrated the transcriptomic samples of spaceflight mice from GeneLab and predicted the radiation doses absorbed by individuals in space. A single-sample network (SSN) for each individual sample was constructed. Then, using machine learning and genetic algorithms, we built the regression models to predict the absorbed dose equivalent based on the topological structure of SSNs. Moreover, we analyzed the SSNs from each tissue and compared the similarities and differences among them. Our model exhibited excellent performance with the following metrics: R2=0.980, MSE=6.74e−04, and the Pearson correlation coefficient of 0.990 (<i>p</i> value &lt;.0001) between predicted and actual values. We identified 20 key genes, the majority of which had been proven to be associated with radiation. However, we uniquely established them as space radiation sensitive genes for the first time. Through further analysis of the SSNs, we discovered that the different tissues exhibited distinct mechanisms in response to space stressors. The topology structures of SSNs effectively predicted radiation doses under spaceflight conditions, and the SSNs revealed the gene regulatory patterns within the organisms under space stressors.
DOI: 10.25549/pcra-c14-229824
title: Bible study about spiritual gifts = Studiu biblic despre darurile duhovniceşti

description: [description english/roman)] Eugen Bodor (1902-1983), during the period between the wars and after WWII has been one of the two Pentecostal ministers with theological studies. He was marginalized by the Communist regime. For writing candestinely a "Bible study about the spiritual gifts" in 1961 he was sentenced to 5 years in prison and confiscation of personal belongings. He served a year and a few months and was afterwards pardoned by decree. In 1977 he makes this writing available to the students of the Theological Pentecostal Institute.
DOI: 10.15468/dl.3sw8pb
title: Occurrence Download

description: A dataset containing 27914 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phlomis purpurea L."
 ]
}

 The dataset includes 27914 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0056030-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wx7azt
title: Occurrence Download

description: A dataset containing 3232 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Knipolegus poecilurus (P.L.Sclater, 1862)"
 ]
}

 The dataset includes 3232 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0380809-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-229791
title: Bible study about spiritual gifts = Studiu biblic despre darurile duhovniceşti

description: [description english/roman)] Eugen Bodor (1902-1983), during the period between the wars and after WWII has been one of the two Pentecostal ministers with theological studies. He was marginalized by the Communist regime. For writing candestinely a "Bible study about the spiritual gifts" in 1961 he was sentenced to 5 years in prison and confiscation of personal belongings. He served a year and a few months and was afterwards pardoned by decree. In 1977 he makes this writing available to the students of the Theological Pentecostal Institute.
DOI: 10.15468/dl.e6egd9
title: Occurrence Download

description: A dataset containing 1206 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Artemisia dubia Wall. ex Besser"
 ]
}

 The dataset includes 1206 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055990-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-229821
title: Bible study about spiritual gifts = Studiu biblic despre darurile duhovniceşti

description: [description english/roman)] Eugen Bodor (1902-1983), during the period between the wars and after WWII has been one of the two Pentecostal ministers with theological studies. He was marginalized by the Communist regime. For writing candestinely a "Bible study about the spiritual gifts" in 1961 he was sentenced to 5 years in prison and confiscation of personal belongings. He served a year and a few months and was afterwards pardoned by decree. In 1977 he makes this writing available to the students of the Theological Pentecostal Institute.
DOI: 10.15468/dl.4qjpq6
title: Occurrence Download

description: A dataset containing 3080 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gentianella Moench",
 "BasisOfRecord is one of (Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (United States of America, Canada)"
 ]
}

 The dataset includes 3080 records from 97 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0327572-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pm3j85
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Brachymenium leptophyllum (Bruch & Schimp. ex Müll.Hal.) Bruch & Schimp. ex A.Jaeger"
 ]
}

 The dataset includes 68 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004187-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-229802
title: Bible study about spiritual gifts = Studiu biblic despre darurile duhovniceşti

description: [description english/roman)] Eugen Bodor (1902-1983), during the period between the wars and after WWII has been one of the two Pentecostal ministers with theological studies. He was marginalized by the Communist regime. For writing candestinely a "Bible study about the spiritual gifts" in 1961 he was sentenced to 5 years in prison and confiscation of personal belongings. He served a year and a few months and was afterwards pardoned by decree. In 1977 he makes this writing available to the students of the Theological Pentecostal Institute.
DOI: 10.15468/dl.dmspth
title: Occurrence Download

description: A dataset containing 403 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Gaultheria fragrantissima Wall."
 ]
}

 The dataset includes 403 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0380819-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vfyg3k
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-90.6301464000000010 41.5326293000000035, -90.6301464000000010 41.5346614099999982, -90.6301464000000010 41.5361855000000020, -90.6301464000000010 41.5394876800000006, -90.6301464000000010 41.5416468000000023, -90.6301464000000010 41.5431708799999981, -90.6301464000000010 41.5453299999999999, -90.6265776999999986 41.5453299999999999, -90.6246656499999972 41.5453299999999999, -90.6222437200000002 41.5453299999999999, -90.6185470799999990 41.5453299999999999, -90.6156152700000064 41.5453299999999999, -90.6131938000000048 41.5453299999999999, -90.6131938000000048 41.5425358500000002, -90.6131938000000048 41.5410117600000035, -90.6131938000000048 41.5387256400000027, -90.6131938000000048 41.5360584900000021, -90.6131938000000048 41.5344073999999992, -90.6131938000000048 41.5326293000000035, -90.6168899700000026 41.5326293000000035, -90.6185470799999990 41.5326293000000035, -90.6219887799999952 41.5326293000000035, -90.6244107100000065 41.5326293000000035, -90.6275974600000040 41.5326293000000035, -90.6301464000000010 41.5326293000000035))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 151 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094880-210914110416597/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.25679940
title: Native AI-predicted Models

description: The compressed folder includes the AI-predicted models as they were generated by AlphaFold 2 (or downloaded from the AlphaFold database), OpenFold, and ESMFold. Each modeling type is represented by a distinct folder, named by the respective modeling type. These folders include, as individual PDB files, 41,688 AlphaFold 2 models, 41,217 OpenFold models, and 37,673 ESMFold models.
DOI: 10.6084/m9.figshare.25679943
title: Refined AI-predicted Models

description: This record is of the same structure as the relaxed AI-predicted models, however, it contains the refined version of the energy minimized (relaxed) structural models. Refinement includes, as described in the Methods section, the removal of low confidence regions with a pLDDT score below 70, and filtering for models with 10 or more amino acid residues remaining. These folders include, as individual PDB files, 39,484 refined AlphaFold 2 models, 39,748 refined OpenFold models, and 31,870 refined ESMFold models.
DOI: 10.6084/m9.figshare.25679943.v1
title: Refined AI-predicted Models

description: This record is of the same structure as the relaxed AI-predicted models, however, it contains the refined version of the energy minimized (relaxed) structural models. Refinement includes, as described in the Methods section, the removal of low confidence regions with a pLDDT score below 70, and filtering for models with 10 or more amino acid residues remaining. These folders include, as individual PDB files, 39,484 refined AlphaFold 2 models, 39,748 refined OpenFold models, and 31,870 refined ESMFold models.
DOI: 10.6084/m9.figshare.25679952
title: Refined AI-predicted Models with Ligands

description: This data record contains the energy minimized (relaxed) ligand-containing structures which are included in the relaxed AI-predicted models with ligands, but their refined version. Refinement includes, as described in the Methods section, the removal of low confidence regions with a pLDDT score below 70, and filtering for models with 10 or more amino-acid residues remaining. After refinement, ligands which are no longer within 5 Å of any atom in the model were removed. The included subfolders contain, as individual PDB files, 14,973 ligand-containing relaxed and refined AlphaFold 2 models, 15,070 ligand-containing relaxed and refined OpenFold models, and 12,855 ligand-containing relaxed and refined ESMFold models.
DOI: 10.6084/m9.figshare.25679940.v1
title: Native AI-predicted Models

description: The compressed folder includes the AI-predicted models as they were generated by AlphaFold 2 (or downloaded from the AlphaFold database), OpenFold, and ESMFold. Each modeling type is represented by a distinct folder, named by the respective modeling type. These folders include, as individual PDB files, 41,688 AlphaFold 2 models, 41,217 OpenFold models, and 37,673 ESMFold models.
DOI: 10.6084/m9.figshare.25679949
title: Relaxed AI-predicted Models

description: This data record is of the same structure as the native AI-predicted models, however, it contains the energy minimized (relaxed) structural models. The subfolders include, as individual PDB files, 41,688 relaxed AlphaFold 2 models, 41,217 relaxed OpenFold models, and 37,673 relaxed ESMFold models.
DOI: 10.6084/m9.figshare.25679949.v1
title: Relaxed AI-predicted Models

description: This data record is of the same structure as the native AI-predicted models, however, it contains the energy minimized (relaxed) structural models. The subfolders include, as individual PDB files, 41,688 relaxed AlphaFold 2 models, 41,217 relaxed OpenFold models, and 37,673 relaxed ESMFold models.
DOI: 10.6084/m9.figshare.25679958
title: Ramachandran Plots

description: Ramachandran plots are available for native, relaxed and refined versions of the models.
DOI: 10.6084/m9.figshare.25679961
title: RMSD Calculations for Model Comparison

description: Results from a pairwise alignment of models in the form of CSV files for the native and refined models.
DOI: 10.6084/m9.figshare.25679961.v1
title: RMSD Calculations for Model Comparison

description: Results from a pairwise alignment of models in the form of CSV files for the native and refined models.
DOI: 10.6084/m9.figshare.25679964
title: Protein Information and Statistics

description: Further, a compressed CSV file (protein_information_and_statistics.csv) contains valuable information regarding the protein sequences and models. The file comprises 42,158 entries, each corresponding to a protein sequence considered in the modeling process. It includes UniProt accession codes, gene names (and synonyms), amino-acid sequences, details about the model type available for each protein (AlphaFold 2 or downloaded from the AlphaFold database, OpenFold, ESMFold, homology model), and, if applicable, the ligands they include. Additionally, the file provides detailed information about each model's secondary structure as well as a statistical analysis of quality parameters, offering insights into the reliability of each model.
DOI: 10.6084/m9.figshare.25679955
title: Relaxed AI-predicted Models with Ligands

description: The data record includes the native AI-predicted models, in which ligands were incorporated (as described in the Methods section), and which were energy minimized (relaxed) afterwards. The included subfolders contain, as individual PDB files, 15,566 ligand-containing relaxed AlphaFold 2 models, 15,487 ligand-containing relaxed OpenFold models, and 13,914 ligand-containing relaxed ESMFold models.
DOI: 10.6084/m9.figshare.25679955.v1
title: Relaxed AI-predicted Models with Ligands

description: The data record includes the native AI-predicted models, in which ligands were incorporated (as described in the Methods section), and which were energy minimized (relaxed) afterwards. The included subfolders contain, as individual PDB files, 15,566 ligand-containing relaxed AlphaFold 2 models, 15,487 ligand-containing relaxed OpenFold models, and 13,914 ligand-containing relaxed ESMFold models.
DOI: 10.6084/m9.figshare.25679958.v1
title: Ramachandran Plots

description: Ramachandran plots are available for native, relaxed and refined versions of the models.
DOI: 10.6084/m9.figshare.25679964.v1
title: Protein Information and Statistics

description: Further, a compressed CSV file (protein_information_and_statistics.csv) contains valuable information regarding the protein sequences and models. The file comprises 42,158 entries, each corresponding to a protein sequence considered in the modeling process. It includes UniProt accession codes, gene names (and synonyms), amino-acid sequences, details about the model type available for each protein (AlphaFold 2 or downloaded from the AlphaFold database, OpenFold, ESMFold, homology model), and, if applicable, the ligands they include. Additionally, the file provides detailed information about each model's secondary structure as well as a statistical analysis of quality parameters, offering insights into the reliability of each model.