cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60732/4ca1927e
title: aC_JCP_2023_test

description: Test split from the 216-atom amorphous portion of the aC_JCP_2023 dataset. The amorphous carbon dataset was generated using ab initio calculations with VASP software. We utilized the LDA exchange-correlation functional and the PAW potential for carbon. Melt-quench simulations were performed to create amorphous and liquid-state structures. A simple cubic lattice of 216 carbon atoms was chosen as the initial state. Simulations were conducted at densities of 1.5, 1.7, 2.0, 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, and 3.5 g/cm3 to produce a variety of structures. The NVT ensemble was employed for all melt-quench simulations, and the density was adjusted by modifying the size of the simulation cell. A time step of 1 fs was used for the simulations. For all densities, only the Γ points were sampled in the k-space. To increase structural diversity, six independent simulations were performed.In the melt-quench simulations, the temperature was raised from 300 K to 9000 K over 2 ps to melt carbon. Equilibrium molecular dynamics (MD) was conducted at 9000 K for 3 ps to create a liquid state, followed by a decrease in temperature to 5000 K over 2 ps, with the system equilibrating at that temperature for 2 ps. Finally, the temperature was lowered from 5000 K to 300 K over 2 ps to generate an amorphous structure.During the melt-quench simulation, 30 snapshots were taken from the equilibrium MD trajectory at 9000 K, 100 from the cooling process between 9000 and 5000 K, 25 from the equilibrium MD trajectory at 5000 K, and 100 from the cooling process between 5000 and 300 K. This yielded a total of 16,830 data points.Data for diamond structures containing 216 atoms at densities of 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, and 3.5 g/cm3 were also prepared. Further data on the diamond structure were obtained from 80 snapshots taken from the 2 ps equilibrium MD trajectory at 300 K, resulting in 560 data points.To validate predictions for larger structures, we generated data for 512-atom systems using the same procedure as for the 216-atom systems. A single simulation was conducted for each density. The number of data points was 2,805 for amorphous and liquid states
DOI: 10.15468/dl.ny24w6
title: Occurrence Download

description: A dataset containing 3762 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Meniocus linifolius (Stephan ex Willd.) DC."
 ]
}

 The dataset includes 3762 records from 140 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050833-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/a6b0da5e
title: ZIF-4_Amorphous_Zeolitic_Imidazolate_Frameworks_2023

description: This dataset contains four trajectories of amorphous zeolitic imidazolate frameworks (ZIF-4), liquids calculated at four different volumes and at temperatures of 1500K and 1750K; and three trajectories of the ZIF-4 crystal: one at 300K and two at 1500K. Data was generated at the DFT-PBE-D3 level of theory.
DOI: 10.60732/c2d25b5f
title: Matbench_perovskites

description: The Matbench_perovskites dataset is a Matbench v0.1 test dataset for predicting formation energy from crystal structure. Adapted from an original dataset generated by Castelli et al. Refer to the Automatminer/Matbench publication for more details. This dataset contains the energy of formation of the entire 5-atom perovskite cell in eV as calculated by RPBE GGA-DFT. Note the reference state for oxygen was computed from oxygen's chemical potential in water vapor, not as oxygen molecules, to reflect the application for which these perovskites were studied. Matbench is an automated leaderboard for benchmarking state of the art ML algorithms predicting a diverse range of solid materials' properties. It is hosted and maintained by the Materials Project.
DOI: 10.60732/b1104cc5
title: Transition1x_train

description: The training split of the Transition1x dataset. Transition1x is a benchmark dataset containing 9.6 million Density Functional Theory (DFT) calculations of forces and energies of molecular configurations on and around reaction pathways at the ωB97x/6-31 G(d) level of theory. The configurations contained in this dataset allow a better representation of features in transition state regions when compared to other benchmark datasets -- in particular QM9 and ANI1x.
DOI: 10.15468/dl.dhaj3k
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingCountry is Canada",
 {
 "or" : [
 "VerbatimScientificName ~Eleocharis mamillata",
 "VerbatimScientificName is eleocharis mamillata (lindb.fil.) lindb.fil.",
 "VerbatimScientificName is eleocharis mamillata (h. lindberg) h. lindberg",
 "VerbatimScientificName is eleocharis mamillata h. lindb.",
 "VerbatimScientificName is eleocharis mamillata auct. non lindb. f.",
 "VerbatimScientificName is eleocharis mamillata subsp. mamillata (lindberg) h. lindberg"
 ]
 }
 ]
}

 The dataset includes 12 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050835-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/f2c623f1
title: CoNbV_CMS2019

description: This dataset was generated using the following active learning scheme: 1) candidate structures were relaxed by a partially-trained MTP model, 2) structures for which the MTP had to perform extrapolation were passed to DFT to be re-computed, 3) the MTP was retrained, including the structures that were re-computed with DFT, 4) steps 1-3 were repeated until the MTP no longer extrapolated on any of the original candidate structures. The original candidate structures for this dataset included about 27,000 configurations that were bcc-like and close-packed (fcc, hcp, etc.) with 8 or fewer atoms in the unit cell and different concentrations of Co, Nb, and V.
DOI: 10.60732/a9dd64f6
title: JARVIS_DFT_3D_8_18_2021

description: The JARVIS_DFT_3D_8_18_2021 dataset is part of the joint automated repository for various integrated simulations (JARVIS) DFT database. This subset contains configurations of 3D materials. JARVIS is a set of tools and datasets built to meet current materials design challenges.
DOI: 10.60732/ad4e82a6
title: WS22_dmabn

description: Configurations of dmabn from WS22. The WS22 database combines Wigner sampling with geometry interpolation to generate 1.18 million molecular geometries equally distributed into 10 independent datasets of flexible organic molecules with varying sizes and chemical complexity. In addition to the potential energy and forces required to construct potential energy surfaces, the WS22 database provides several other quantum chemical properties, all obtained via single-point calculations for each molecular geometry. All quantum chemical calculations were performed with the Gaussian 09 program.
DOI: 10.60732/861da1bc
title: Al_Cu_Mg_GSFE_JMPS2019

description: Dataset from "Stress-dependence of generalized stacking fault energies":DFT calculations of generalized stacking fault energies (GSFE) for Al, Cu, and Mg.
DOI: 10.15468/dl.acdn4x
title: Occurrence Download

description: A dataset containing 552 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lyperia tristis (L.fil.) Benth."
 ]
}

 The dataset includes 552 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050836-240321170329656/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.12618374
title: Additional file 2 of Mapping regulatory variants controlling gene expression in drought response and tolerance in maize

description: Additional file 2: Table S1. The SNP concordant rate between the previous and present studies. Table S2. Information on static and dynamic eQTLs identified in the present study. Table S3. 3733 eQTLs directly located in TF genes. Table S4. Detail information on the eQTL network. Table S5. Detail information on 97 candidate genes identified by Mendelian Randomization analysis. Table S6. Primers used in the present study.
DOI: 10.6084/m9.figshare.14715140.v2
title: Additional file 22 of Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation

description: Additional file 22: Table S21. Gene expression analysis of Cbs+/+ vs. Cbs-/- mice.
DOI: 10.6084/m9.figshare.8948381
title: Additional file 16: of A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis

description: Table S2. Relative abundances of species determined by the metagenomic sequencing. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.14715158
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.14715170.v1
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.7375556.v2
title: Table S4 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.8948381.v1
title: Additional file 16: of A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis

description: Table S2. Relative abundances of species determined by the metagenomic sequencing. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.13142132
title: Additional file 1 of QTL mapping for soybean (Glycine max L.) leaf chlorophyll-content traits in a genotyped RIL population by using RAD-seq based high-density linkage map

description: Additional file 1: Table S1: The pairwise correlation coefficients between different chlorophyll-content traits in the ZH RILs across environments; Table S2: Correlation coefficients between different environments for leaf chlorophyll-content traits in the ZH RILs; Table S3: Number of SNPs in the bin markers; Table S4: Description of characteristics of 20 chromosomes in the ZH RIL population high-density genetic map; Table S5: Segregation distortions of 2639 bin markers among the ZH RIL population; Table S6: The 78 QTLs and 70 loci for leaf chlorophyll-content traits in the ZH RIL population across different environments; Table S7: Information of Soybase published leaf chlorophyll-content traits QTLs; Table S8: Comparisons of the detected chlorophyll-content QTLs with the previously published ones; Table S9: Five important chlorophyll-content traits QTL hotspots are associated with several reported yield-related QTLs on SoyBase; Table S10: Genes in the hereditary intervals of the 13 major chlorophyll-content trait QTLs; Table S11: Genes in the hereditary intervals of the five important QTL hotspots; Table S12: Gene Ontology (GO) enrichment analysis of the genes in genetic blocks of the major QTLs and important QTL hotspots; Table S13: Filtered GO enrichment terms of the genes in genetic blocks of the major QTLs and important QTL hotspots; Table S14: Gene annotations from SoyBase; Table S15: Details of field trails, meteorological conditions and soybean growth stages used to determine the soybean leaf chlorophyll-content traits.
DOI: 10.6084/m9.figshare.7375517.v2
title: Table S3 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.7375517
title: Table S3 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.7375538
title: Table S1 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.7375538.v1
title: Table S1 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 modifications 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 the <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. 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.7375556
title: Table S4 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.7899854
title: Tea polyphenols induce S phase arrest and apoptosis in gallbladder cancer cells

description: Gallbladder cancer (GBC) is the most common malignancy in the biliary tract. Without effective treatment, its prognosis is notoriously poor. Tea polyphenols (TPs) have many pharmacological and health benefits, including antioxidant, anti-inflammatory, anti-tumor, anti-thrombotic, antibacterial, and vasodilatory properties. However, the anti-cancer effect of TPs in human gallbladder cancer has not yet been determined. Cell viability and colony formation assay were used to investigate the cell growth. Cell cycle and apoptosis were evaluated by flow cytometry analysis. Western blot assay was used to detect the expression of proteins related to cell cycle and apoptosis. Human tumor xenografts were used to examine the effect of TPs on gallbladder cancer cells in vivo. TPs significantly inhibited cell growth of gallbladder cancer cell lines in a dose- and time-dependent manner. Cell cycle progression in GBC cells was blocked at the S phase by TPs. TPs also induced mitochondrial-related apoptosis in GBC cells by upregulating Bax, cleaved caspase-3, and cleaved PARP expressions and downregulating Bcl-2, cyclin A, and Cdk2 expressions. The effects of TPs on GBC were further proven in vivo in a mouse xenograft model. Our study is the first to report that TPs inhibit GBC cell growth and these compounds may have potential as novel therapeutic agents for treating gallbladder cancer.
DOI: 10.6084/m9.figshare.13142557.v1
title: Establishment of a survey method to determine rice stigma length from preparation, sampling, and preservation to measurement

description: The lack of a unified standard for sampling stage, preservation and measurement of stigma length is the main restriction factor for the study of stigma length trait in rice. In this study, stigma lengths were compared among four different developmental stages (T1-T4) of 30 rice materials under two environments (years) and in 10 measurement periods (D1-D120) of 3 rice materials after treatment with 6 fixatives (S1–S6), and finally the results revealed that the T3 were the best sampling stage and the S6 was the most suitable fixative for stigma length. This study thoroughly describes the process for surveying and measuring stigma length in 6 steps: preparation before sampling, flower sampling, focusing, flower dissection and imaging, obtaining measurements, and data analysis. These findings provide an outline of the methodology for the discovery, fine mapping, and functional analysis of the genes that control the stigma length trait.