cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60732/0f8a1418
title: CA-9_BR_validation

description: Binning-random configurations from CA-9 dataset used during validation step for NNP_BR potential. CA-9 consists of configurations of carbon with curated subsets chosen to test the effects of intentionally choosing dissimilar configurations when training neural network potentials
DOI: 10.60732/40d9f4e8
title: HO_LiMoNiTi_NPJCM_2020_LiMoNiTi_validation

description: Validation configurations of Li8Mo2Ni7Ti7O32 from HO_LiMoNiTi_NPJCM_2020 used in the training of an ANN, whereby total energy is extrapolated by a Taylor expansion as a means of reducing computational costs.
DOI: 10.15468/dl.nuuhkk
title: Occurrence Download

description: A dataset containing 224 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingCountry is Canada",
 "TaxonKey is one of (Eleocharis macrostachya Britton)"
 ]
}

 The dataset includes 224 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050782-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/831d1c4a
title: HPt_NC_2022

description: A training dataset of 90,000 configurations with interaction properties between H2 and Pt(111) surfaces.
DOI: 10.15468/dl.k56jh2
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ligularia macrodonta Y.Ling"
 ]
}

 The dataset includes 24 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050783-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/07b7d297
title: CA-9_BR_training

description: Binning-random configurations from CA-9 dataset used for training NNP_BR potential. CA-9 consists of configurations of carbon with curated subsets chosen to test the effects of intentionally choosing dissimilar configurations when training neural network potentials
DOI: 10.15468/dl.u54pzm
title: Occurrence Download

description: A dataset containing 208 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lyonia doyonensis (Hand.-Mazz.) Hand.-Mazz."
 ]
}

 The dataset includes 208 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050785-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/8d5bdb05
title: 23-Single-Element-DNPs_RSCDD_2023-Pd

description: Configurations of Pd from Andolina & Saidi, 2023. One of 23 minimalist, curated sets of DFT-calculated properties for individual elements for the purpose of providing input to machine learning of deep neural network potentials (DNPs). Each element set contains on average ~4000 structures with 27 atoms per structure. Configuration metadata includes Materials Project ID where available, as well as temperatures at which MD trajectories were calculated.These temperatures correspond to the melting temperature (MT) and 0.25*MT for elements with MT &lt; 2000K, and MT, 0.6*MT and 0.25*MT for elements with MT &gt; 2000K.
DOI: 10.15468/dl.bmpgju
title: Occurrence Download

description: A dataset containing 3010 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mauranthemum paludosum (Poir.) Vogt & Oberpr."
 ]
}

 The dataset includes 3010 records from 139 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050784-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/f3f6ad68
title: JARVIS_mlearn

description: The JARVIS_mlearn dataset is part of the joint automated repository for various integrated simulations (JARVIS) database. This dataset contains configurations from the Organic Materials Database (OMDB): a dataset of 12,500 crystal materials for the purpose of training models for the prediction of properties for complex and lattice-periodic organic crystals with large numbers of atoms per unit cell. Dataset covers 69 space groups, 65 elements; averages 82 atoms per unit cell. This dataset also includes classical force-field inspired descriptors (CFID) for each configuration. JARVIS is a set of tools and collected datasets built to meet current materials design challenges.
DOI: 10.60732/bfdb46b7
title: 3BPA_isolated_atoms

description: Reference C, H, O, and N atoms from 3BPA, used to showcase the performance of linear atomic cluster expansion (ACE) force fields in a machine learning model to predict the potential energy surfaces of organic molecules.
DOI: 10.15468/dl.vzsnfd
title: Occurrence Download

description: A dataset containing 108 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macrosolen melintangensis (Korth.) Miq."
 ]
}

 The dataset includes 108 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050786-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/57c54149
title: 23-Single-Element-DNPs_RSCDD_2023-I

description: Configurations of I from Andolina & Saidi, 2023. One of 23 minimalist, curated sets of DFT-calculated properties for individual elements for the purpose of providing input to machine learning of deep neural network potentials (DNPs). Each element set contains on average ~4000 structures with 27 atoms per structure. Configuration metadata includes Materials Project ID where available, as well as temperatures at which MD trajectories were calculated.These temperatures correspond to the melting temperature (MT) and 0.25*MT for elements with MT &lt; 2000K, and MT, 0.6*MT and 0.25*MT for elements with MT &gt; 2000K.
DOI: 10.60732/6367ea51
title: W_PRB2019

description: This dataset was originally designed to fit a GAP potential with a specific focus on properties relevant for simulations of radiation-induced collision cascades and the damage they produce, including a realistic repulsive potential for short-range many-body cascade dynamics and a good description of the liquid phase.
DOI: 10.60732/d4e67cf8
title: ANI-2x-B973c-def2mTZVP

description: ANI-2x-B973c-def2mTZVP is a portion of the ANI-2x dataset, which includes DFT-calculated energies for structures from 2 to 63 atoms in size containing H, C, N, O, S, F, and Cl. This portion of ANI-2x was calculated in ORCA at the B973c level of theory using the def2m-TZVP basis set. Configuration sets are divided by number of atoms per structure. Force corrections and dipoles are recorded in the metadata.
DOI: 10.60732/eb6e9ead
title: CGM-MLP_natcomm2023_screening_carbon-cluster@Cu_test

description: 192 structures were uniformly selected from the AIMD simulation, excluding any structures that are part of the training set. This dataset was one of the datasets used in testing screening parameters during the process of producing an active learning dataset for Cu-C interactions for the purposes of exploring substrate-catalyzed deposition as a means of controllable synthesis of carbon nanomaterials. The combined dataset includes structures from the Carbon_GAP_20 dataset and additional configurations of carbon clusters on a Cu(111) surface.
DOI: 10.60732/8122ca50
title: JARVIS_Materials_Project_2020

description: The JARVIS_Materials_Project_2020 dataset is part of the joint automated repository for various integrated simulations (JARVIS) DFT database. This subset contains 127,000 configurations of 3D materials from the Materials Project database. JARVIS is a set of tools and datasets built to meet current materials design challenges.
DOI: 10.60732/9ed20baf
title: BOTnet_ACAC_2022_test_300K_MD

description: Test set of decorrelated geometries sampled from 300 K xTB MD. Acetylacetone dataset generated from a long molecular dynamics simulation at 300 K using a Langevin thermostat at the semi-empirical GFN2-xTB level of theory. Configurations were sampled at an interval of 1 ps and the resulting set of configurations were recomputed with density functional theory using the PBE exchange-correlation functional with D3 dispersion correction and def2-SVP basis set and VeryTightSCF convergence settings using the ORCA electronic structure package.
DOI: 10.60732/1e0997f8
title: 23-Single-Element-DNPs_RSCDD_2023-Re

description: Configurations of Re from Andolina & Saidi, 2023. One of 23 minimalist, curated sets of DFT-calculated properties for individual elements for the purpose of providing input to machine learning of deep neural network potentials (DNPs). Each element set contains on average ~4000 structures with 27 atoms per structure. Configuration metadata includes Materials Project ID where available, as well as temperatures at which MD trajectories were calculated.These temperatures correspond to the melting temperature (MT) and 0.25*MT for elements with MT &lt; 2000K, and MT, 0.6*MT and 0.25*MT for elements with MT &gt; 2000K.
DOI: 10.15468/dl.su65jn
title: Occurrence Download

description: A dataset containing 644 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Maianthemum dahuricum (Turcz. ex Fisch. & C.A.Mey.) LaFrankie"
 ]
}

 The dataset includes 644 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050787-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/5a57f6ad
title: CA-9_test

description: Test configurations from CA-9 dataset used to evaluate trained NNPs.CA-9 consists of configurations of carbon with curated subsets chosen to test the effects of intentionally choosing dissimilar configurations when training neural network potentials
DOI: 10.60732/7d8a06fe
title: Sn-SCAN_PRM_2023

description: Approximately 6,500 configurations of Sn, including Sn8, Sn16 and Sn32, used in developing a deep potential that predicts the phase diagram of Sn.
DOI: 10.60732/a85ea3a9
title: DFT_polymorphs_PNAS_2022_PBE0_MBD_glycine_test

description: Glycine test PBE0-MBD dataset from "Semi-local and hybrid functional DFT data for thermalised snapshots of polymorphs of benzene, succinic acid, and glycine". DFT reference energies and forces were calculated using Quantum Espresso v6.3. The calculations were performed with the semi-local PBE xc functional, Tkatchenko-Scheffler dispersion correction, optimised norm-conserving Vanderbilt pseudopotentials, a Monkhorst-Pack k-point grid with a maximum spacing of 0.06 x 2π A^-1, and a plane-wave energy cut-off of 100 Ry for the wavefunction.
DOI: 10.60732/63ab9206
title: mlearn_Li_train

description: A comprehensive DFT data set was generated for six elements - Li, Mo, Ni, Cu, Si, and Ge. These elements were chosen to span a variety of chemistries (main group metal, transition metal, and semiconductor), crystal structures (bcc, fcc, and diamond) and bonding types (metallic and covalent). This dataset comprises only the Li configurations
DOI: 10.60732/efb626b6
title: 23-Single-Element-DNPs_RSCDD_2023-Zr

description: Configurations of Zr from Andolina & Saidi, 2023. One of 23 minimalist, curated sets of DFT-calculated properties for individual elements for the purpose of providing input to machine learning of deep neural network potentials (DNPs). Each element set contains on average ~4000 structures with 27 atoms per structure. Configuration metadata includes Materials Project ID where available, as well as temperatures at which MD trajectories were calculated.These temperatures correspond to the melting temperature (MT) and 0.25*MT for elements with MT &lt; 2000K, and MT, 0.6*MT and 0.25*MT for elements with MT &gt; 2000K.
DOI: 10.15468/dl.bmu8gd
title: Occurrence Download

description: A dataset containing 173 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ligularia macrophylla (Ledeb.) DC."
 ]
}

 The dataset includes 173 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050788-240321170329656/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.13142518.v1
title: Morroniside protects HT-22 cells against oxygen-glucose deprivation/reperfusion through activating the Nrf2/HO-1 signaling pathway

description: Neonatal hypoxic-ischemic encephalopathy (HIE) is a devastating condition that affects neurodevelopment and results in brain injury in infants. Morroniside (MOR), a natural secoiridoid glycoside, has been found to possess neuroprotective effect. However, the effects of MOR on neonatal HIE are unclear. An <i>in vitro</i> HIE model was established in murine hippocampal neurons HT-22 cells using oxygen-glucose deprivation/reoxygenation (OGD/R) stimulation. Our results showed that MOR improved OGD/R-caused cell viability reduction in HT-22 cells. MOR suppressed the production of reactive oxygen species (ROS) and malondialdehyde (MDA) in OGD/R-induced HT-22 cells in a dose-dependent manner. The activities of superoxide dismutase (SOD) and glutathione peroxidase (GP<sub>X</sub>) were significantly elevated by MOR. Moreover, MOR treatment caused a significant increase in bcl-2 expression, and obvious decreases in the expression levels of bax, cleaved caspase-3, and cleaved caspase-9 expression. Furthermore, MOR significantly upregulated the expression levels of nuclear Nrf2 and HO-1 in OGD/R-treated HT-22 cells. Additionally, knockdown of Nrf2 or HO-1 abrogated the effects of MOR on OGD/R-induced oxidative stress and apoptosis in HT-22 cells. In conclusion, these findings suggested that MOR protects HT-22 cells against OGD/R <i>via</i> regulating the Nrf2/HO-1 signaling pathway.
DOI: 10.6084/m9.figshare.14715170
title: Additional file 7 of Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation

description: Additional file 7: Table S6. CBS promoter methylation levels and gene expression in expanded GC cell line cohort.
DOI: 10.6084/m9.figshare.13142363
title: Additional file 2 of Metabolomics analysis reveals Embden Meyerhof Parnas pathway activation and flavonoids accumulation during dormancy transition in tree peony

description: Additional file 2: Table S2. KEGG pathway enrichment of dormancy release related DMs.
DOI: 10.6084/m9.figshare.13142128.v1
title: Additional file 1 of Investigating effects of preoperative inflammatory biomarkers on predicting survival outcomes of intrahepatic cholangiocarcinoma after curative resection

description: Additional file 1.
DOI: 10.6084/m9.figshare.13142372.v1
title: Additional file 5 of Metabolomics analysis reveals Embden Meyerhof Parnas pathway activation and flavonoids accumulation during dormancy transition in tree peony

description: Additional file 5: Table S5. The accession number of protein used in phylogenetic analysis.
DOI: 10.6084/m9.figshare.8948138.v1
title: Additional file 4: of Effects of short-time exposure to atrazine on miRNA expression profiles in the gonad of common carp (Cyprinus carpio)

description: Differentially expressed mRNAs of PGC stage after exposed to atrazine for 24â h. (XLS 13978 kb)
DOI: 10.6084/m9.figshare.14715143
title: Additional file 23 of Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation

description: Additional file 23: Table S22. List of upregulated genes and pathways in CBS-deficient mouse stomachs (FDR &lt; 0.05).
DOI: 10.6084/m9.figshare.8948147.v1
title: Additional file 5: of Effects of short-time exposure to atrazine on miRNA expression profiles in the gonad of common carp (Cyprinus carpio)

description: Differentially expressed mRNAs of juvenile ovary after exposed to atrazine for 8â h. (XLS 20365 kb)
DOI: 10.6084/m9.figshare.14715032
title: Additional file 2 of Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids

description: Additional file 2: Table S1. Body fluid samples from patients positive for malignancy by cytology and/or flow cytometry.
DOI: 10.6084/m9.figshare.12617885
title: Additional file 1 of Rapid exacerbation featuring acute leukemoid reaction after retrolaparoscopic nephrectomy: a rare case report of renal cell carcinoma with postoperative comprehensive genomic profiling

description: Additional file 1: Supplemental 1
DOI: 10.6084/m9.figshare.12618162.v1
title: Additional file 1 of Maternal obesity alters C19MC microRNAs expression profile in fetal umbilical cord blood

description: Additional file 1: Table S1. Differentially expressed known miRNAs in overweight/obese and control groups.
DOI: 10.6084/m9.figshare.14715152
title: Additional file 2 of Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation

description: Additional file 2: Table S1. List of hypermethylated gene promoters in the discovery set of CIMP vs non-CIMP cell lines identified by MeDIP-sequencing (P &lt; 0.05).
DOI: 10.6084/m9.figshare.14715158.v1
title: Additional file 3 of Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation

description: Additional file 3: Table S2. List of downregulated genes at RNA level in the discovery set of CIMP vs non-CIMP cell lines (P &lt; 0.05).
DOI: 10.6084/m9.figshare.8948159.v1
title: Additional file 6: of Effects of short-time exposure to atrazine on miRNA expression profiles in the gonad of common carp (Cyprinus carpio)

description: Differentially expressed mRNAs of juvenile ovary after exposed to atrazine for 24â h. (XLS 20271 kb)
DOI: 10.6084/m9.figshare.8948165
title: Additional file 7: of Effects of short-time exposure to atrazine on miRNA expression profiles in the gonad of common carp (Cyprinus carpio)

description: Differentially expressed mRNAs of juvenile testis after exposed to atrazine for 8â h. (XLS 24312 kb)
DOI: 10.6084/m9.figshare.14715134.v1
title: Additional file 20 of Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation

description: Additional file 20: Table S19. Overlap of negatively correlated genes to CBS in various TCGA cancers (q-value &lt; 0.05) with MSigDB hallmark gene sets (q-value &lt; 0.01).
DOI: 10.6084/m9.figshare.14715173.v1
title: Additional file 8 of Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation

description: Additional file 8: Table S7. Overlap of genes with promoter hypermethylation (β-value difference ≥ 0.3), and significant downregulation at the RNA (q-value &lt; 0.05) level in CIMP compared to non-CIMP tumours in TCGA and Singapore cohorts.
DOI: 10.6084/m9.figshare.13142363.v1
title: Additional file 2 of Metabolomics analysis reveals Embden Meyerhof Parnas pathway activation and flavonoids accumulation during dormancy transition in tree peony

description: Additional file 2: Table S2. KEGG pathway enrichment of dormancy release related DMs.
DOI: 10.6084/m9.figshare.13142372
title: Additional file 5 of Metabolomics analysis reveals Embden Meyerhof Parnas pathway activation and flavonoids accumulation during dormancy transition in tree peony

description: Additional file 5: Table S5. The accession number of protein used in phylogenetic analysis.
DOI: 10.6084/m9.figshare.14715032.v1
title: Additional file 2 of Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids

description: Additional file 2: Table S1. Body fluid samples from patients positive for malignancy by cytology and/or flow cytometry.
DOI: 10.6084/m9.figshare.14715035.v1
title: Additional file 3 of Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids

description: Additional file 3: Table S2. Select microbiological cases that have overlapping features with cancer presentations.
DOI: 10.6084/m9.figshare.13142107.v1
title: Additional file 1 of Exosomal PD-L1 and N-cadherin predict pulmonary metastasis progression for osteosarcoma patients

description: Additional file 1: Table S1. OS patient Sr-exosome vs healthy donor Sr-exosome DEG mRNA.
DOI: 10.6084/m9.figshare.14715173.v2
title: Additional file 8 of Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation

description: Additional file 8: Table S7. Overlap of genes with promoter hypermethylation (β-value difference ≥ 0.3), and significant downregulation at the RNA (q-value &lt; 0.05) level in CIMP compared to non-CIMP tumours in TCGA and Singapore cohorts.
DOI: 10.6084/m9.figshare.7375490.v2
title: Table S6 from The histone deacetylase NlHDAC1 regulates both female and male fertility in the brown planthopper, <i>Nilaparvata lugens</i>.

description: Histone acetylation is a specific type of chromatin modification that serves as a key regulatory mechanism for many cellular processes in mammals. However, little is known about its biological function in invertebrates. Here, we identified 12 members of histone deacetylases (NlHDACs) in the brown planthopper (BPH), <i>Nilaparvata lugens</i>. RNAi-mediated silencing assay showed that <i>NlHdac1</i>, <i>NlHdac3</i> and <i>NlHdac4</i> played critical roles in female fertility via regulating ovary maturation or ovipositor development. Silencing of <i>NlHdac1</i> substantially increased acetylation level of histones H3 and H4 in ovaries, indicating NlHDAC1 is the main histone deacetylase in ovaries of BPH. RNA sequencing (RNA-seq) analysis showed that knockdown of <i>NlHdac1</i> impaired ovary development via multiple signalling pathways including the TOR pathway. Acoustic recording showed that males with <i>NlHdac1</i> knockdown failed to make courtship songs, and thus were unacceptable to wild-type females, resulting in unfertilized eggs. Competition mating assay showed that wild-type females overwhelmingly preferred to mate with control males over <i>NlHdac1</i>-knockdown males. These findings improve our understanding of reproductive strategies controlled by HDACs in insects and provide a potential target for pest control.
DOI: 10.6084/m9.figshare.14715038.v1
title: Additional file 4 of Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids

description: Additional file 4: Table S3. Microbiological cases - all other cases.
DOI: 10.6084/m9.figshare.22619702.v1
title: Additional file 6 of Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton

description: Additional file 6: Table S5. Statistics for the fiber length dynamics.