cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13487381
title: Global insights to drought stress perturbed genes in oat (<i>Avena sativa L</i>.) seedlings using RNA sequencing

description: Oat (<i>Avena sativa</i> L.) is an important crop in northwestern China. Drought stress is the most significant factor affecting oat yield. In the present study, we explored the changes that occur in oats under drought stress conditions at a global genomic level. RNA sequencing was performed using 15-day-old oat seedlings. The differentially expressed transcripts were identified, and their related functions and pathways were investigated. In total, 1,065 unigenes were differentially expressed in oats under drought stress conditions. Of these, 386 unigenes were upregulated and 679 were downregulated. The perturbed transcripts were closely related to the biosynthesis of secondary metabolites, plant hormone signal transduction, and biosynthesis of antibiotics. DN50483_c0_g1_i3, which was annotated as acetyl-CoA carboxylase, was a significant node in the protein-protein interaction network. Biosynthesis of antibiotics and secondary metabolites may be involved in the drought stress response mechanisms of oats. The perturbed transcripts may provide targets for improving plant stress responses.
DOI: 10.6084/m9.figshare.14536000
title: Circ_0017956 promotes the proliferation and metastasis of non-small cell lung cancer through regulating miR-515-5p/ITGB8 axis

description: Circular RNAs (circRNAs) have been reported to exert vital roles in the tumorigenesis of non-small cell lung cancer (NSCLC). The study aimed to probe the function of circ_0017956 in NSCLC development. The expression of circ_0017956, microRNA (miR)-515-5p and integrin subunit beta 8 (ITGB8) was gauged by quantitative real-time polymerase chain reaction (qRT-PCR) or western blot. The proliferation detection was conducted employing Cell Counting Kit-8 (CCK-8) and colony formation assays. Transwell assay was performed to determine cell migratory and invasive abilities. Western blot was implemented for the measurement of related proteins. The targeted interactions among circ_0017956, miR-515-5p and ITGB8 were affirmed by dual-luciferase reporter assay, RNA immunoprecipitation (RIP) assay and RNA pull-down assay. The role of circ_0017956 in NSCLC tumor growth <i>in vivo</i> was studied by xenograft mice model. Circ_0017956 and ITGB8 abundances were overtly raised whereas miR-515-5p was low expressed in NSCLC tissues and cells. Circ_0017956 knockdown caused inhibitory effects on the proliferative and metastasizing capacities of NSCLC cells. Mechanistically, circ_0017956 could sponge miR-515-5p, and circ_0017956 depletion blocked NSCLC cell malignant behaviors by increasing miR-515-5p expression. Furthermore, miR-515-5p targeted ITGB8 and ITGB8 overexpression also neutralized the miR-515-5p-triggered inhibition effects on NSCLC cell progression. Moreover, circ_0017956 could regulate ITGB8 expression through sponging miR-515-5p. In addition, circ_0017956 knockdown repressed NSCLC tumorigenesis by targeting miR-515-5p/ITGB8 axis <i>in vivo</i>. Circ_0017956 could promote NSCLC carcinogenesis at least partly through sponging miR-515-5p and upregulating ITGB8 level, providing a novel theoretical basis for NSCLC treatment.
DOI: 10.6084/m9.figshare.19254555
title: Additional file 1 of LAP2α preserves genome integrity through assisting RPA deposition on damaged chromatin

description: Additional file 1: Table S1. SILAC-based quantitative mass spectrometry analysis of RPA1-containing protein complexes.
DOI: 10.6084/m9.figshare.19254555.v1
title: Additional file 1 of LAP2α preserves genome integrity through assisting RPA deposition on damaged chromatin

description: Additional file 1: Table S1. SILAC-based quantitative mass spectrometry analysis of RPA1-containing protein complexes.
DOI: 10.6084/m9.figshare.14536000.v1
title: Circ_0017956 promotes the proliferation and metastasis of non-small cell lung cancer through regulating miR-515-5p/ITGB8 axis

description: Circular RNAs (circRNAs) have been reported to exert vital roles in the tumorigenesis of non-small cell lung cancer (NSCLC). The study aimed to probe the function of circ_0017956 in NSCLC development. The expression of circ_0017956, microRNA (miR)-515-5p and integrin subunit beta 8 (ITGB8) was gauged by quantitative real-time polymerase chain reaction (qRT-PCR) or western blot. The proliferation detection was conducted employing Cell Counting Kit-8 (CCK-8) and colony formation assays. Transwell assay was performed to determine cell migratory and invasive abilities. Western blot was implemented for the measurement of related proteins. The targeted interactions among circ_0017956, miR-515-5p and ITGB8 were affirmed by dual-luciferase reporter assay, RNA immunoprecipitation (RIP) assay and RNA pull-down assay. The role of circ_0017956 in NSCLC tumor growth <i>in vivo</i> was studied by xenograft mice model. Circ_0017956 and ITGB8 abundances were overtly raised whereas miR-515-5p was low expressed in NSCLC tissues and cells. Circ_0017956 knockdown caused inhibitory effects on the proliferative and metastasizing capacities of NSCLC cells. Mechanistically, circ_0017956 could sponge miR-515-5p, and circ_0017956 depletion blocked NSCLC cell malignant behaviors by increasing miR-515-5p expression. Furthermore, miR-515-5p targeted ITGB8 and ITGB8 overexpression also neutralized the miR-515-5p-triggered inhibition effects on NSCLC cell progression. Moreover, circ_0017956 could regulate ITGB8 expression through sponging miR-515-5p. In addition, circ_0017956 knockdown repressed NSCLC tumorigenesis by targeting miR-515-5p/ITGB8 axis <i>in vivo</i>. Circ_0017956 could promote NSCLC carcinogenesis at least partly through sponging miR-515-5p and upregulating ITGB8 level, providing a novel theoretical basis for NSCLC treatment.
DOI: 10.6084/m9.figshare.19254561
title: Additional file 3 of LAP2α preserves genome integrity through assisting RPA deposition on damaged chromatin

description: Additional file 3: Table S2. Mass spectrometry analysis of LAP2α-containing protein complexes.
DOI: 10.6084/m9.figshare.19254561.v1
title: Additional file 3 of LAP2α preserves genome integrity through assisting RPA deposition on damaged chromatin

description: Additional file 3: Table S2. Mass spectrometry analysis of LAP2α-containing protein complexes.
DOI: 10.6084/m9.figshare.16625444
title: Additional file 1 of Dexamethasone enhances the efficacy of atorvastatin in inhibiting excessively inflammation-induced abnormal angiogenesis by regulating macrophages

description: Additional file 1: File S1. The inclusion and exclusion criteria. Table S1. RT-PCR Primers used in this study. Table S2. Baseline characteristics and outcome of CSDH patients treated with a combination regimen or ATO monotherapy. Table S3. Baseline characteristics and outcomes of conservatively treated patients who have good efficacy or switched to surgery. Table S4. The functions of these proteins identified, but not specifically discussed in the manuscript. Figure S1. o-ATO and p-ATO in CSDH patients. Figure S2. Concentrations of ATO and DEX in HUVEC. Figure S3. Effects of ATO and DEX on expression of drug transport and catabolism-related proteins in macrophages. Figure S4. Monocytes and macrophages in the haematoma of CSDH patients. Figure S5. The differentiation of THP-1 cells into macrophages stimulated by PMA. Figure S6. LPS can effectively simulate the effect of haematoma on THP-1 macrophages. Figure S7. Regulation of ATO and DEX on the morphological changes of THP-1 macrophages. Figure S8. The effect of ATO and DEX on the MFI of CD86 and CD163 in macrophages. Figure S9. The concentrations of ET-1 in the haematoma, serum and medium supernatant quantified by ELISA.
DOI: 10.6084/m9.figshare.19254666.v1
title: Additional file 1 of ZNF498 promotes hepatocellular carcinogenesis by suppressing p53-mediated apoptosis and ferroptosis via the attenuation of p53 Ser46 phosphorylation

description: Additional file 1: Supplementary Figure S1. Anti-ZNF498 antibody specifically recognizes ZNF498. Supplementary Figure S2. ZNF498 promotes the initiation of DEN-induced HCC. Supplementary Figure S3. ZNF498 interacts with p53, represses p53 transcriptional activity and inhibits p53 Ser46 phosphorylation under DNA damage conditions. Supplementary Figure S4. ZNF498 has no effect on p53 Ser46 phosphorylation in HCC cells with knockdown of DYRK2, ATM, HIPK1 and p38. Supplementary Figure S5. ZNF498 does not interact with p53INP1. Supplementary Figure S6. ZNF498 promotes HCC cell growth in vitro. Supplementary Figure S7. p53 expression was identified in HepG2 cells with stable knockout of p53. Supplementary Figure S8. The correlation between ZNF498 overexpression and different p53 statuses in HCC tissues. Supplementary Figure S9. ZNF498 represses p53-mediated apoptosis. Supplementary Figure S10. ZNF498 represses ferroptosis. Supplementary Figure S11. ZNF498 represses p53 activity and apoptosis by inhibiting p53 Ser46 phosphorylation.
DOI: 10.6084/m9.figshare.19254721.v1
title: Additional file 4 of HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples

description: Additional file 4: Table S4. Class-specific regulators identified from the TCGA pan-cancer ATAC-seq data set.
DOI: 10.6084/m9.figshare.19254666
title: Additional file 1 of ZNF498 promotes hepatocellular carcinogenesis by suppressing p53-mediated apoptosis and ferroptosis via the attenuation of p53 Ser46 phosphorylation

description: Additional file 1: Supplementary Figure S1. Anti-ZNF498 antibody specifically recognizes ZNF498. Supplementary Figure S2. ZNF498 promotes the initiation of DEN-induced HCC. Supplementary Figure S3. ZNF498 interacts with p53, represses p53 transcriptional activity and inhibits p53 Ser46 phosphorylation under DNA damage conditions. Supplementary Figure S4. ZNF498 has no effect on p53 Ser46 phosphorylation in HCC cells with knockdown of DYRK2, ATM, HIPK1 and p38. Supplementary Figure S5. ZNF498 does not interact with p53INP1. Supplementary Figure S6. ZNF498 promotes HCC cell growth in vitro. Supplementary Figure S7. p53 expression was identified in HepG2 cells with stable knockout of p53. Supplementary Figure S8. The correlation between ZNF498 overexpression and different p53 statuses in HCC tissues. Supplementary Figure S9. ZNF498 represses p53-mediated apoptosis. Supplementary Figure S10. ZNF498 represses ferroptosis. Supplementary Figure S11. ZNF498 represses p53 activity and apoptosis by inhibiting p53 Ser46 phosphorylation.
DOI: 10.6084/m9.figshare.19254727.v1
title: Additional file 6 of HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples

description: Additional file 6: Table S6. Significant HVRs and LVRs (BH-adjusted p-value&lt;0.1) identified by HyperChIP for each of the data sets in Table 1.
DOI: 10.6084/m9.figshare.12443378
title: Complete chloroplast genome sequence of Stachys japonica (Labiatae)

description: The complete chloroplast genome of <i>Stachys japonica</i> was reconstructed by reference-based assembly using Illumina paired-end data. The assembled plastome is 150,599 base pairs (bp) in length, including a pair of inverted repeat regions (IRs) of 25,654 bp each, a large single-copy region (LSC) of 81,701 bp and a small single-copy region (SSC) of 17,590 bp. A total of 131 genes were predicted from the chloroplast genome, including 86 protein coding genes, 37 tRNA genes and 8 rRNA genes. The overall GC content of <i>S. japonica</i> chloroplast genome was 38.5%. Phylogenetic analysis with several reported chloroplast genomes showed that <i>S. japonica</i> is closely clustered with <i>S. sylvatica</i>. The complete chloroplast genome of <i>S. japonica</i> provides new insight into Labiatae evolutionary and genomic studies.
DOI: 10.6084/m9.figshare.16633041.v1
title: Additional file 5 of Potential mechanism of Ziyin Tongluo Formula in the treatment of postmenopausal osteoporosis: based on network pharmacology and ovariectomized rat model

description: Additional file 5: Table S5. The binding energies of ten core compounds and fifty key proteins.
DOI: 10.6084/m9.figshare.16633035
title: Additional file 3 of Potential mechanism of Ziyin Tongluo Formula in the treatment of postmenopausal osteoporosis: based on network pharmacology and ovariectomized rat model

description: Additional file 3: Table S3. Detail information of "Herb-Active ingredient-Overlapping gene" network.
DOI: 10.6084/m9.figshare.16633038.v1
title: Additional file 4 of Potential mechanism of Ziyin Tongluo Formula in the treatment of postmenopausal osteoporosis: based on network pharmacology and ovariectomized rat model

description: Additional file 4: Table S4. Results of Gene Ontology (GO) terms and pathways.
DOI: 10.6084/m9.figshare.16633041
title: Additional file 5 of Potential mechanism of Ziyin Tongluo Formula in the treatment of postmenopausal osteoporosis: based on network pharmacology and ovariectomized rat model

description: Additional file 5: Table S5. The binding energies of ten core compounds and fifty key proteins.
DOI: 10.6084/m9.figshare.16633035.v1
title: Additional file 3 of Potential mechanism of Ziyin Tongluo Formula in the treatment of postmenopausal osteoporosis: based on network pharmacology and ovariectomized rat model

description: Additional file 3: Table S3. Detail information of "Herb-Active ingredient-Overlapping gene" network.
DOI: 10.6084/m9.figshare.19783498
title: A comprehensive genomic and transcriptomic dataset of triple-negative breast cancers

description: Molecular subtyping of triple-negative breast cancer (TNBC) is essential for understanding the mechanisms and discovering actionable targets of this highly heterogeneous type of breast cancer. We previously performed a large single-center and multiomics study consisting of genomics, transcriptomics, and clinical information from 465 patients with primary TNBC. To facilitate reusing this unique dataset, we provided a detailed description of the dataset with special attention to data quality in this study. The multiomics data were generally of high quality, but a few sequencing data had quality issues and should be noted in subsequent data reuse. Furthermore, we reconduct data analyses with updated pipelines and the updated version of the human reference genome from hg19 to hg38. The updated profiles were in good concordance with those previously published in terms of gene quantification, variant calling, and copy number alteration. Additionally, we developed a user-friendly web-based database for convenient access and interactive exploration of the dataset. Our work will facilitate reusing the dataset, maximize the values of data and further accelerate cancer research.
DOI: 10.6084/m9.figshare.17162283
title: Cyclic tensile strain facilitates proliferation and migration of human aortic smooth muscle cells and reduces their apoptosis via miRNA-187-3p

description: The cardiovascular is a system that contains extremely complex mechanical factors, in which the circulatory flow of blood has rich mechanical laws. Many studies have revealed that mechanical factors play a very important role in the process of revascularization. Hence, it is essential to investigate the mechanical factors in the process of revascularization in depth. A cyclic tensile strain (CTS) was applied to human aortic smooth muscle cells (HASMCs) at a frequency of 1 Hz and amplitudes of 5%, 10% and 15%, respectively. SmallRNA-seq was used to identify differentially expressed miRNAs (DE-miRNAs) responding to CTS in HASMCs. Starbase database predicted the target genes of DE-miRNAs. Metascape was applied for GO and KEGG pathway enrichment analysis and protein–protein interaction network construction. The proliferation and migration of CTS-treated HASMCs were significantly enhanced, and apoptosis were significantly reduced compared to the control group. SmallRNA-seq results demonstrated that 55, 16 and 16 DE-miRNAs were present in 5%, 10% and 15% CTS-treated HASMCs, respectively. Compared to controls, with miR-26a-2-3p and miR-187-3p being the intersection of these DE-miRNAs. Starbase database identified 189 common target genes for miR-26a-2-3p and miR-187-3p. Common target genes are mainly enriched in the basolateral plasma membrane and endocytosis. Further, <i>in vitro</i> experiments exhibited that CTS upregulated miR-187-3p expression, and miR-187-3p enhanced the proliferation and migration of HASMCs and reduced their apoptosis. It is suggested that miR-187-3p may be an important target for CTS participate in the process of cardiovascular disease.
DOI: 10.6084/m9.figshare.19254579
title: Additional file 1 of The association between continuous renal replacement therapy as treatment for sepsis-associated acute kidney injury and trend of lactate trajectory as risk factor of 28-day mortality in intensive care units

description: Additional file 1: Supplementary Table 1. The full result of the Joint Model.
DOI: 10.6084/m9.figshare.19254579.v1
title: Additional file 1 of The association between continuous renal replacement therapy as treatment for sepsis-associated acute kidney injury and trend of lactate trajectory as risk factor of 28-day mortality in intensive care units

description: Additional file 1: Supplementary Table 1. The full result of the Joint Model.
DOI: 10.6084/m9.figshare.19254675.v1
title: Additional file 4 of ZNF498 promotes hepatocellular carcinogenesis by suppressing p53-mediated apoptosis and ferroptosis via the attenuation of p53 Ser46 phosphorylation

description: Additional file 4: Table S3. ZNF498 mRNA level and TP53 mutational status in HCC patients from TCGA datasets.
DOI: 10.6084/m9.figshare.20295600.v1
title: Additional file 1 of Associations of visceral adipose tissue with bone mineral density and fracture: observational and Mendelian randomization studies

description: Additional file 1: Table 1. Baseline characteristics of the final application datasets by quartiles of VAT^ mass. Table 2. Baseline characteristics of the final application datasets by sex. Table 3. ICD-10 codes for fracture definition in the UK biobank. Table 4. Associations of VAT^ with heel BMD in men and women by BMI categories. Table 5. Associations of VAT^ with heel BMD in men and women by BMI categories after excluding participants with T2D, CVD or cancer at baseline. Table 6. Association of DXA-derived VAT mass with DXA-derived BMD among participants by BMI categories. Table 7. Associations of VAT^ with incident fractures in men and women by BMI categories. Table 8. Associations of VAT^ with incident fractures in men and women by BMI categories after excluding participants with T2D, CVD or cancer at baseline. Table 9. Schoenfeld residuals test of the Cox models. Table 10. Genetic variants associated with VAT^ in the UK Biobank. Table 11. MR estimates of the causal effects of VAT^ on DXA-derived BMD without excluding LM-associated SNPs. Table 12. MR estimates of the causal effects of VAT^ on fractures without excluding LM-associated SNPs. Table 13. MR Egger test of directional horizontal pleiotropy.
DOI: 10.6084/m9.figshare.19254679
title: Additional file 1 of Atheroprotective mechanism by which folic acid regulates monocyte subsets and function through DNA methylation

description: Additional file 1: Original datasets.
DOI: 10.6084/m9.figshare.6152351.v1
title: Experimental study on the self-suspending proppant-laden flow in a single fracture

description: Abstract The flow of proppant-laden fluid (PLF) in the fracture is a typical problem of solid-liquid two phase flow, and the transportation and deposition of proppants are essential to determine the flow conductivity of hydraulic fracturing. The self-suspending proppant with a water soluble surface coating is a newly presented supporting material and has great potential for hydraulic fracturing. The purpose of this paper is to understand the physical process, and investigate the effect of the self-suspending proppant on particle placement and transportation in the fracture. Two experiments of the PLF flow were conducted in a fracture, using the common ceramic proppant and self-suspending proppant, respectively. The fracture was formed by two parallel plexiglass planes, and was 4000 mm in length, 10 mm in width and 600 mm in height. It was found that four different zones developed when proppants were injected into the fracture continuously, which were the proppant bank zone, tumbling zone, suspending zone, and free zone. Compared with the common proppant, the self-suspending proppant changes the particle distribution in the fracture, and increases the thickness of proppant suspending and bank zone. The motion behavior of self-suspending proppants in the fracture is described. The conclusion is that appropriate reduction in the proppant concentration and density is beneficial to the good distribution and transportation of proppants in the fracture, and the self-suspending proppant favors the effective supporting of fracture.
DOI: 10.6084/m9.figshare.19254679.v1
title: Additional file 1 of Atheroprotective mechanism by which folic acid regulates monocyte subsets and function through DNA methylation

description: Additional file 1: Original datasets.
DOI: 10.6084/m9.figshare.14541039
title: Real-world comparison of direct-acting oral anticoagulants and vitamin K antagonists in chronic kidney disease: a systematic review and meta-analysis

description: <b>Background</b>: No clear clinical guidelines exist on anticoagulant use for chronic kidney disease (CKD) patients. We compared the efficacy and safety of direct-acting oral anticoagulants (DOACs) vs. vitamin K antagonists (VKA) in patients with CKD by pooling data from real-world observational studies. <b>Research design & methods</b>: This systematic review searched PubMed, Embase, and CENTRAL databases and pooled multivariable-adjusted hazard ratios (HR) of outcomes. <b>Results</b>: Fifteen studies were included. Our results indicated a small but significant reduction in the risk of all-cause mortality (p = 0.01), stroke or systemic embolism (p = 0.03), and major bleeding (p = 0.01) with DOAC as compared to VKA. In subgroup analysis based on the severity of CKD, no difference in the risk of stroke or systemic embolism was noted in any subgroups. The risk of mortality was reduced only in patients with moderate-severe or severe CKD and the risk of major bleeding was reduced only in patients with moderate-severe or moderate CKD. <b>Conclusion</b>: DOACs are associated with only a modest reduction in stroke or systemic embolism, major bleeding, and mortality when compared to VKA in CKD patients. Reduction in mortality and major bleeding with DOAC may only be seen in moderate-to-severe CKD patients.
DOI: 10.6084/m9.figshare.19254724
title: Additional file 5 of HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples

description: Additional file 5: Table S5. Stage-specific regulators identified from the mouse ATAC-seq data set.
DOI: 10.6084/m9.figshare.19254628
title: Additional file 2 of Abundant expression of ferroptosis-related SAT1 is related to unfavorable outcome and immune cell infiltration in low-grade glioma

description: Additional file 2: Table S2. The correlation between SAT1 gene expression levels and immune cell infiltration.
DOI: 10.6084/m9.figshare.19254675
title: Additional file 4 of ZNF498 promotes hepatocellular carcinogenesis by suppressing p53-mediated apoptosis and ferroptosis via the attenuation of p53 Ser46 phosphorylation

description: Additional file 4: Table S3. ZNF498 mRNA level and TP53 mutational status in HCC patients from TCGA datasets.
DOI: 10.6084/m9.figshare.20295613
title: Additional file 1 of A novel nitidine chloride nanoparticle overcomes the stemness of CD133+EPCAM+ Huh7 hepatocellular carcinoma cells for liver cancer therapy

description: Additional file 1.
DOI: 10.6084/m9.figshare.19254724.v1
title: Additional file 5 of HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples

description: Additional file 5: Table S5. Stage-specific regulators identified from the mouse ATAC-seq data set.