cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17031708.v2
title: Cyclin-Dependent Kinase 4 is expected to be a therapeutic target for hepatocellular carcinoma metastasis using integrated bioinformatic analysis

description: Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related mortality worldwide. HCC cells possess biological characteristics of high invasion and metastasis. In this respect, to prevent cancer cell invasion and metastasis and early active intervention, we herein screened through the TCGA database for further prognostic analysis including overall survival and disease-free survival . The Kaplan-Meier curve suggested that Cyclin-Dependent Kinase 4 (CDK4) might be an independent prognostic factor for HCC. Moreover, we performed mRNA expression analysis to measure CDK4 levels in normal liver tissues and HCC tissues, and immunohistochemistry analysis to detect protein level of CDK4 in Non-tumor tissue and HCC tissues . Our findings indicated that the expression of CDK4 was significantly higher in tumor tissues compared with Non-tumor tissue in HCC, which increased from HCC stage 1 to 3. Furthermore, the results of transwell-assay indicated that knocking down CDK4 significantly suppresses the invasion and migration of HCC cells, and the results of bioinformatics analysis revealed that genes closely associated with CDK4 are potentially worthy of further investigation. Additionally, the results of Western Blot indicated CDK4 regulates epithelial mesenchymal transition in HCC,and CDK4 appears to regulate EMT and HCC progression via the Wnt/β-catenin pathway. Collectively, this study found the key target gene through bioinformatic analysis and further functional validation through cell experiments. In particular, CDK4 is anticipated to become a crucial hub gene to snipe the metastasis of cancer cells in HCC. <b>Abbreviations</b>: Hepatocellular carcinoma (HCC);Cyclin-Dependent Kinase 4(CDK4);Genomic Data Commons (GDC); genes; EC, Endometrial cancer; GEO, gene expression omnibus; GO, Gene Ontology; GSEA, Gene set enrichment analysis; KEGG, Database; TCGA, The Cancer Genome Atlas; TSGs, tumor suppressor genes;epithelial mesenchymal transition (EMT).
DOI: 10.6084/m9.figshare.19128793.v1
title: Additional file 5 of CENPF/CDK1 signaling pathway enhances the progression of adrenocortical carcinoma by regulating the G2/M-phase cell cycle

description: Additional file 5: Table S5. GSEA analysis of KEGG pathway.
DOI: 10.6084/m9.figshare.19128799
title: Additional file 6 of CENPF/CDK1 signaling pathway enhances the progression of adrenocortical carcinoma by regulating the G2/M-phase cell cycle

description: Additional file 6: Table S6. GSEA enrichment analyses of Biocarta pathway.
DOI: 10.6084/m9.figshare.19128830
title: Additional file 9 of Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma

description: Additional file 9. MEturquiose DAVID. DAVID enrichment of MEturquiose.
DOI: 10.6084/m9.figshare.19128782
title: Additional file 12 of Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma

description: Additional file 12. 10 hub genes. The location and function for 10 hub genes.
DOI: 10.6084/m9.figshare.13346364
title: Additional file 2 of Transcriptome profiles of sturgeon lateral line electroreceptor and mechanoreceptor during regeneration

description: Additional file 2.
DOI: 10.6084/m9.figshare.19128797
title: Additional file 3 of Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma

description: Additional file 3. Up-lncRNA. Up reglation of lncRNA.
DOI: 10.6084/m9.figshare.7070246
title: Single-molecule long-read transcriptome profiling of <i>Platysternon megacephalum</i> mitochondrial genome with gene rearrangement and control region duplication

description: <i>Platysternon megacephalum</i> is the sole living representative of the poorly studied turtle lineage Platysternidae. Their mitochondrial genome has been subject to gene rearrangement and control region duplication, resulting in a unique mitochondrial gene order in vertebrates. In this study, we sequenced the first full-length turtle (<i>P. megacephalum</i>) liver transcriptome using single-molecule real-time sequencing to study the transcriptional mechanisms of its mitochondrial genome. ND5 and ND6 anti-sense (ND6AS) forms a single transcript with the same expression in the human mitochondrial genome, but here we demonstrated differential expression of the rearranged ND5 and ND6AS genes in <i>P. megacephalum</i>. And some polycistronic transcripts were also reported in this study. Notably, we detected some novel long non-coding RNAs with alternative polyadenylation from the duplicated control region, and a novel ND6AS transcript composed of a long non-coding sequence, ND6AS, and tRNA-GluAS. These results provide the first description of a mtDNA transcriptome with gene rearrangement and control region duplication. These findings further our understanding of the fundamental concepts of mitochondrial gene transcription and RNA processing, and provide a new insight into the mechanism of transcription regulation of the mitochondrial genome.
DOI: 10.6084/m9.figshare.19128794.v1
title: Additional file 2 of Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma

description: Additional file 2. Down-mRNA. Down regulation of mRNA.
DOI: 10.6084/m9.figshare.22274671.v2
title: Clustered Coefficient Regression Models for Poisson Process with an Application to Seasonal Warranty Claim Data

description: Motivated by a product warranty claims dataset, we propose clustered coefficient regression models in a nonhomogeneous Poisson process for recurrent event data. The proposed method, referred as CLUPP, can estimate the group structure and parameters simultaneously. In our proposed method, a penalized regression approach is used to identify the group structure. Numerical studies show that the proposed approach can identify the group structure well, and outperforms traditional methods such as hierarchical clustering and <i>K</i>-means. We also establish theoretical properties, which show that the proposed estimators can converge to true parameters in high probability. In the end, we apply our proposed methods to the product warranty claims dataset, which achieve better prediction than the state-of-the-art methods.
DOI: 10.6084/m9.figshare.22274686.v1
title: Fixed-domain Posterior Contraction Rates for Spatial Gaussian Process Model with Nugget

description: Spatial Gaussian process regression models typically contain finite dimensional covariance parameters that need to be estimated from the data. We study the Bayesian estimation of covariance parameters including the nugget parameter in a general class of stationary covariance functions under fixed-domain asymptotics, which is theoretically challenging due to the increasingly strong dependence among spatial observations. We propose a novel adaptation of the Schwartz’s consistency theorem for showing posterior contraction rates of the covariance parameters including the nugget. We derive a new polynomial evidence lower bound, and propose consistent higher-order quadratic variation estimators that satisfy concentration inequalities with exponentially small tails. Our Bayesian fixed-domain asymptotics theory leads to explicit posterior contraction rates for the microergodic and nugget parameters in the isotropic Matérn covariance function under a general stratified sampling design. We verify our theory and the Bayesian predictive performance in simulation studies and an application to sea surface temperature data.
DOI: 10.6084/m9.figshare.19128797.v1
title: Additional file 3 of Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma

description: Additional file 3. Up-lncRNA. Up reglation of lncRNA.
DOI: 10.6084/m9.figshare.19128803
title: Additional file 4 of Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma

description: Additional file 4. Down-lncRNA. Down regulation of lncRNA.
DOI: 10.6084/m9.figshare.19128815
title: Additional file 6 of Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma

description: Additional file 6. Down-miRNA. Down regulation miRNA.
DOI: 10.6084/m9.figshare.19128901
title: Additional file 3 of Clinical utility of cerebrospinal fluid-derived circular RNAs in lung adenocarcinoma patients with brain metastases

description: Additional file 3: Table S3. circRNA-miRNA-mRNA.
DOI: 10.25380/iastate.7070216.v1
title: Reverse-Engineering of Graphene on Metal Surfaces: A Case Study of Embedded Ruthenium

description: Using scanning tunneling microscopy, X-ray photoelectron spectroscopy, and X-ray absorption spectroscopy, we show that Ru forms metallic nanoislands on graphite, covered by a graphene monolayer. These islands are air-stable, contain 2-4 layers of Ru, and have diameters on the order of 10 nm. To produce these nanoislands two conditions must be met during synthesis. The graphite surface must be ion bombarded, and subsequently held at elevated temperature (1000-1180 K) during Ru deposition. A coincidence lattice forms between the graphene overlayer and the Ru island top. Its characteristics – coincidence lattice constant, corrugation amplitude, and variation of carbon lattice appearance within the unit cell – closely resemble the well-established characteristics of single-layer graphene on the (0001) surface of bulk Ru. Quantitative analysis of the graphene lattice in relation to the coincidence lattice on the island tops shows that the two-dimensional lattice constant of the underlying metal equals that of bulk Ru(0001), within experimental error. The embedded Ru islands are energetically favored over on-top (adsorbed) islands, based on density-functional-theory calculations for Ru films with 1-3 Ru layers. We propose a formation mechanism in which Ru atoms intercalate via defects that act as entry portals to the carbon galleries, followed by nucleation and growth in the galleries. In this model, high deposition temperature is necessary to prevent blockage of entry portals.<br>The file contains raw scanning tunneling microscopy (STM) images and x-ray photoelectron spectroscopy (XPS) spectra. To view and process STM images, the user can use a software called WSxM. To view XPS spectra, the program CASA XPS is recommended. The STM and XPS data uploaded herein are used to generate figures in the paper, which will be published by Nanotechnology soon.<br>
DOI: 10.6084/m9.figshare.19128815.v1
title: Additional file 6 of Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma

description: Additional file 6. Down-miRNA. Down regulation miRNA.
DOI: 10.6084/m9.figshare.19128901.v1
title: Additional file 3 of Clinical utility of cerebrospinal fluid-derived circular RNAs in lung adenocarcinoma patients with brain metastases

description: Additional file 3: Table S3. circRNA-miRNA-mRNA.
DOI: 10.6084/m9.figshare.19128809.v1
title: Additional file 5 of Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma

description: Additional file 5. Up-miRNA. Up regulation of miRNA.
DOI: 10.6084/m9.figshare.19128824.v1
title: Additional file 8 of Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma

description: Additional file 8. MEbrown DAVID. DAVID enrichment of MEbrown.
DOI: 10.6084/m9.figshare.19120316
title: Additional file 7 of RNA-Seq with a novel glabrous-ZM24fl reveals some key lncRNAs and the associated targets in fiber initiation of cotton

description: Additional file 7. Differentially expressed lncRNA and their targets in all comparisons.
DOI: 10.6084/m9.figshare.19120316.v1
title: Additional file 7 of RNA-Seq with a novel glabrous-ZM24fl reveals some key lncRNAs and the associated targets in fiber initiation of cotton

description: Additional file 7. Differentially expressed lncRNA and their targets in all comparisons.
DOI: 10.6084/m9.figshare.7070246.v1
title: Single-molecule long-read transcriptome profiling of <i>Platysternon megacephalum</i> mitochondrial genome with gene rearrangement and control region duplication

description: <i>Platysternon megacephalum</i> is the sole living representative of the poorly studied turtle lineage Platysternidae. Their mitochondrial genome has been subject to gene rearrangement and control region duplication, resulting in a unique mitochondrial gene order in vertebrates. In this study, we sequenced the first full-length turtle (<i>P. megacephalum</i>) liver transcriptome using single-molecule real-time sequencing to study the transcriptional mechanisms of its mitochondrial genome. ND5 and ND6 anti-sense (ND6AS) forms a single transcript with the same expression in the human mitochondrial genome, but here we demonstrated differential expression of the rearranged ND5 and ND6AS genes in <i>P. megacephalum</i>. And some polycistronic transcripts were also reported in this study. Notably, we detected some novel long non-coding RNAs with alternative polyadenylation from the duplicated control region, and a novel ND6AS transcript composed of a long non-coding sequence, ND6AS, and tRNA-GluAS. These results provide the first description of a mtDNA transcriptome with gene rearrangement and control region duplication. These findings further our understanding of the fundamental concepts of mitochondrial gene transcription and RNA processing, and provide a new insight into the mechanism of transcription regulation of the mitochondrial genome.
DOI: 10.6084/m9.figshare.19128892
title: Additional file 1 of Clinical utility of cerebrospinal fluid-derived circular RNAs in lung adenocarcinoma patients with brain metastases

description: Additional file 1: Table S1. QC information.
DOI: 10.6084/m9.figshare.19128898
title: Additional file 2 of Clinical utility of cerebrospinal fluid-derived circular RNAs in lung adenocarcinoma patients with brain metastases

description: Additional file 2: Table S2. FPKM of all samples.
DOI: 10.6084/m9.figshare.19128904
title: Additional file 4 of Clinical utility of cerebrospinal fluid-derived circular RNAs in lung adenocarcinoma patients with brain metastases

description: Additional file 4: Table S4. circRNA-coexpressed mRNA symbol.
DOI: 10.6084/m9.figshare.19128904.v1
title: Additional file 4 of Clinical utility of cerebrospinal fluid-derived circular RNAs in lung adenocarcinoma patients with brain metastases

description: Additional file 4: Table S4. circRNA-coexpressed mRNA symbol.
DOI: 10.6084/m9.figshare.19120319
title: Additional file 8 of RNA-Seq with a novel glabrous-ZM24fl reveals some key lncRNAs and the associated targets in fiber initiation of cotton

description: Additional file 8. The KEGG pathways of differentially expressed targeted genes of DELs.
DOI: 10.6084/m9.figshare.19128898.v1
title: Additional file 2 of Clinical utility of cerebrospinal fluid-derived circular RNAs in lung adenocarcinoma patients with brain metastases

description: Additional file 2: Table S2. FPKM of all samples.
DOI: 10.6084/m9.figshare.17031708.v1
title: Cyclin-Dependent Kinase 4 is expected to be a therapeutic target for hepatocellular carcinoma metastasis using integrated bioinformatic analysis

description: Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related mortality worldwide. Currently, the definitive treatment modality for HCC is radical resection. However, HCC cells possess biological characteristics of high invasion and metastasis. In this respect, to prevent cancer cell invasion and metastasis and early active intervention, we herein screened through the TCGA database for further prognostic analysis including overall survival (OS) and disease-free survival (DFS). The Kaplan-Meier curve suggested that Cyclin-Dependent Kinase 4 (CDK4) might be an independent prognostic factor for HCC. Moreover, we performed mRNA expression analysis to measure CDK4 levels in normal liver tissues and HCC tissues, and immunohistochemistry (IHC) analysis to detect protein level of CDK4 in Non-tumor tissue and HCC tissues collected from patients. Our findings indicated that the expression of CDK4 was significantly higher in tumor tissues compared with Non-tumor tissue in HCC, which increased from HCC stage 1 to 3. Furthermore, the results of transwell-assay indicated that knocking down CDK4 significantly suppresses the invasion and migration of HCC cells, and the results of bioinformatics analysis revealed that genes closely associated with CDK4 are potentially worthy of further investigation. Additionally, the results of Western Blot indicated CDK4 regulates epithelial mesenchymal transition (EMT) in HCC,and CDK4 appears to regulate EMT and HCC progression via the Wnt/β-catenin pathway. Collectively, this study found the key target gene through bioinformatic analysis and further functional validation through cell experiments. In particular, CDK4 is anticipated to become a crucial hub gene to snipe the metastasis of cancer cells in HCC.
DOI: 10.6084/m9.figshare.19120322
title: Additional file 9 of RNA-Seq with a novel glabrous-ZM24fl reveals some key lncRNAs and the associated targets in fiber initiation of cotton

description: Additional file 9. List of primers used in this research.
DOI: 10.6084/m9.figshare.19120322.v1
title: Additional file 9 of RNA-Seq with a novel glabrous-ZM24fl reveals some key lncRNAs and the associated targets in fiber initiation of cotton

description: Additional file 9. List of primers used in this research.
DOI: 10.25380/iastate.7070216
title: Data for: Reverse-Engineering of Graphene on Metal Surfaces: A Case Study of Embedded Ruthenium

description: Using scanning tunneling microscopy, X-ray photoelectron spectroscopy, and X-ray absorption spectroscopy, we show that Ru forms metallic nanoislands on graphite, covered by a graphene monolayer. These islands are air-stable, contain 2-4 layers of Ru, and have diameters on the order of 10 nm. To produce these nanoislands two conditions must be met during synthesis. The graphite surface must be ion bombarded, and subsequently held at elevated temperature (1000-1180 K) during Ru deposition. A coincidence lattice forms between the graphene overlayer and the Ru island top. Its characteristics – coincidence lattice constant, corrugation amplitude, and variation of carbon lattice appearance within the unit cell – closely resemble the well-established characteristics of single-layer graphene on the (0001) surface of bulk Ru. Quantitative analysis of the graphene lattice in relation to the coincidence lattice on the island tops shows that the two-dimensional lattice constant of the underlying metal equals that of bulk Ru(0001), within experimental error. The embedded Ru islands are energetically favored over on-top (adsorbed) islands, based on density-functional-theory calculations for Ru films with 1-3 Ru layers. We propose a formation mechanism in which Ru atoms intercalate via defects that act as entry portals to the carbon galleries, followed by nucleation and growth in the galleries. In this model, high deposition temperature is necessary to prevent blockage of entry portals.<br><br>The file contains raw scanning tunneling microscopy (STM) images and x-ray photoelectron spectroscopy (XPS) spectra. To view and process STM images, the user can use a software called WSxM. To view XPS spectra, the program CASA XPS is recommended. The STM and XPS data uploaded herein are used to generate figures in the paper, which will be published by Nanotechnology soon.<br><b>curation change log:</b> added link to paper; updated title to distinguish from paper; updated funding metadata - MNO<br>
DOI: 10.25380/iastate.7070216.v2
title: Data for: Reverse-Engineering of Graphene on Metal Surfaces: A Case Study of Embedded Ruthenium

description: Using scanning tunneling microscopy, X-ray photoelectron spectroscopy, and X-ray absorption spectroscopy, we show that Ru forms metallic nanoislands on graphite, covered by a graphene monolayer. These islands are air-stable, contain 2-4 layers of Ru, and have diameters on the order of 10 nm. To produce these nanoislands two conditions must be met during synthesis. The graphite surface must be ion bombarded, and subsequently held at elevated temperature (1000-1180 K) during Ru deposition. A coincidence lattice forms between the graphene overlayer and the Ru island top. Its characteristics – coincidence lattice constant, corrugation amplitude, and variation of carbon lattice appearance within the unit cell – closely resemble the well-established characteristics of single-layer graphene on the (0001) surface of bulk Ru. Quantitative analysis of the graphene lattice in relation to the coincidence lattice on the island tops shows that the two-dimensional lattice constant of the underlying metal equals that of bulk Ru(0001), within experimental error. The embedded Ru islands are energetically favored over on-top (adsorbed) islands, based on density-functional-theory calculations for Ru films with 1-3 Ru layers. We propose a formation mechanism in which Ru atoms intercalate via defects that act as entry portals to the carbon galleries, followed by nucleation and growth in the galleries. In this model, high deposition temperature is necessary to prevent blockage of entry portals.<br><br>The file contains raw scanning tunneling microscopy (STM) images and x-ray photoelectron spectroscopy (XPS) spectra. To view and process STM images, the user can use a software called WSxM. To view XPS spectra, the program CASA XPS is recommended. The STM and XPS data uploaded herein are used to generate figures in the paper, which will be published by Nanotechnology soon.<br><b>curation change log:</b> added link to paper; updated title to distinguish from paper; updated funding metadata - MNO<br>
DOI: 10.6084/m9.figshare.19128892.v1
title: Additional file 1 of Clinical utility of cerebrospinal fluid-derived circular RNAs in lung adenocarcinoma patients with brain metastases

description: Additional file 1: Table S1. QC information.
DOI: 10.6084/m9.figshare.8119016
title: Evaluating the impact of criminalizing drunk driving on years of life lost due to road traffic deaths in one megacity, China

description: <b>Objective:</b> Road safety is an important public health issue worldwide. However, few studies have analyzed the association between criminalizing drunk driving and years of life lost (YLL) due to road traffic deaths (RTDs). Our study can provide useful information about this policy. <b>Methods:</b> We used interrupted time-series analysis to find the changes in monthly YLL and RTD before and after law enforcement began using RTD data from 2008 to 2014 in Tianjin. <b>Results:</b> After adjustment for seasonality, months, holidays, and the number of people in each district, criminalizing drunk driving was followed by a 11.1% (95% confidence interval [CI], 1.1–21.1%) reduction in risk of RTDs and a corresponding 778.1-year (95% CI, 200–1,355.1) reduction in monthly YLL. The reduction in YLL was especially significant among males, those aged 16–64 years old, and suburban residents. <b>Conclusions:</b> This study highlights that the law can lead to a reduction in YLL due to RTDs in Tianjin, China. Large immediate public health benefits resulted from the new road traffic law in China. YLL provides a complementary measure for examining the effect of criminalization on drunk driving RTDs.
DOI: 10.6084/m9.figshare.13346388
title: Additional file 2 of Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining

description: Additional file 2: Supplementary Table 2. The SSR primers used in molecular-marker assisted backcrossing (MAB). FAM and HEX are different fluorescent label.