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Open access

Jinwei Luan, Xianglan Li, Rutao Guo, Shanshan Liu, Hongyu Luo and Qingshan You

Abstract

Background

Next generation sequencing and bio-informatic analyses were conducted to investigate the mechanism of reactivation of p53 and induction of tumor cell apoptosis (RITA)-enhancing X-ray susceptibility in FaDu cells.

Materials and methods

The cDNA was isolated from FaDu cells treated with 0 X-ray, 8 Gy X-ray, or 8 Gy X-ray + RITA. Then, cDNA libraries were created and sequenced using next generation sequencing, and each assay was repeated twice. Subsequently, differentially expressed genes (DEGs) were identified using Cuffdiff in Cufflinks and their functions were predicted by pathway enrichment analyses. Genes that were constantly up- or down-regulated in 8 Gy X-ray-treated FaDu cells and 8 Gy X-ray + RITA-treated FaDu cells were obtained as RITA genes. Afterward, the protein-protein interaction (PPI) relationships were obtained from the STRING database and a PPI network was constructed using Cytoscape. Furthermore, ClueGO was used for pathway enrichment analysis of genes in the PPI network.

Results

Total 2,040 and 297 DEGs were identified in FaDu cells treated with 8 Gy X-ray or 8 Gy X-ray + RITA, respectively. PARP3 and NEIL1 were enriched in base excision repair, and CDK1 was enriched in p53 signaling pathway. RFC2 and EZH2 were identified as RITA genes. In the PPI network, many interaction relationships were identified (e.g., RFC2-CDK1, EZH2-CDK1 and PARP3-EZH2). ClueGO analysis showed that RFC2 and EZH2 were related to cell cycle.

Conclusions

RFC2, EZH2, CDK1, PARP3 and NEIL1 may be associated, and together enhance the susceptibility of FaDu cells treated with RITA to the deleterious effects of X-ray.

Open access

Jiao Li, Si Zheng, Hongyu Kang, Zhen Hou and Qing Qian

Abstract

Purpose

In the open science era, it is typical to share project-generated scientific data by depositing it in an open and accessible database. Moreover, scientific publications are preserved in a digital library archive. It is challenging to identify the data usage that is mentioned in literature and associate it with its source. Here, we investigated the data usage of a government-funded cancer genomics project, The Cancer Genome Atlas (TCGA), via a full-text literature analysis.

Design/methodology/approach

We focused on identifying articles using the TCGA dataset and constructing linkages between the articles and the specific TCGA dataset. First, we collected 5,372 TCGA-related articles from PubMed Central (PMC). Second, we constructed a benchmark set with 25 full-text articles that truly used the TCGA data in their studies, and we summarized the key features of the benchmark set. Third, the key features were applied to the remaining PMC full-text articles that were collected from PMC.

Findings

The amount of publications that use TCGA data has increased significantly since 2011, although the TCGA project was launched in 2005. Additionally, we found that the critical areas of focus in the studies that use the TCGA data were glioblastoma multiforme, lung cancer, and breast cancer; meanwhile, data from the RNA-sequencing (RNA-seq) platform is the most preferable for use.

Research limitations

The current workflow to identify articles that truly used TCGA data is labor-intensive. An automatic method is expected to improve the performance.

Practical implications

This study will help cancer genomics researchers determine the latest advancements in cancer molecular therapy, and it will promote data sharing and data-intensive scientific discovery.

Originality/value

Few studies have been conducted to investigate data usage by government-funded projects/programs since their launch. In this preliminary study, we extracted articles that use TCGA data from PMC, and we created a link between the full-text articles and the source data.

Open access

Taichao Su, Hongyu Zhu, Hongan Ma, Shangsheng Li, Meihua Hu, Xiaolei Li, Fengrong Yu, Yongjun Tian and Xiaopeng Jia

Abstract

In this paper, crack-free bulk thermoelectric material Zn4Sb3 was prepared rapidly by high pressure and high temperature (HPHT) method. Near a single-phase Zn4Sb3 specimen was obtained using nominal stoichiometric powder mixtures, which were indexed by powder X-ray diffraction. The temperature-dependent thermoelectric properties including the Seebeck coefficient and electrical resistivity were studied. The maximum power factor of Zn4Sb3 specimen prepared by HPHT reaches 10.8 μW/(cmK2) at 637 K, which is comparable to the published data. The results show that the HPHT offers potential processing route to produce the thermoelectric material Zn4Sb3 quickly and effectively.

Open access

He Zhang, Haiyan Wang, Hongyu Zhu, Hongtao Li, Taichao Su, Shangsheng Li, Meihua Hu and Haotian Fan

Abstract

In this paper, hydrothermal approach combined with high pressure sintering method was employed to synthesize PbS. The X-ray diffraction results show that single phase PbS can be obtained by a simple hydrothermal method. The scanning electron microscope results show that the PbS sample has nearly cubic shape and preserves well crystallized and coarse grains after high pressure sintering. The thermoelectric performance of PbS obtained in this study is comparable to that of a PbS sample prepared by conventional method. The carrier type and concentration of PbS can be tuned effectively by doping with Bi. The maximum figure of merit for PbS doped with 1 mol% Bi reaches 0.44 at 550 K, which is about 30 % higher than that of undoped PbS. These results indicate that hydrothermal method provides a viable and controllable way of tuning the electrical transport and thermoelectric properties for PbS.

Open access

Xingshun Qi, Hongyu Li, Xiaodong Shao, Zhendong Liang, Xia Zhang, Ji Feng, Hao Lin and Xiaozhong Guo

Abstract

Varices manifest as a major etiology of upper gastrointestinal bleeding in patients with chronic liver diseases, such as liver cirrhosis and hepatocellular carcinoma. By contrast, non-variceal upper gastrointestinal bleeding is rare. Pharmacological treatment differs between patients with variceal and non-variceal bleeding. Vasoconstrictors are recommended for the treatment of variceal bleeding, rather than non-variceal bleeding. In contrast, pump proton inhibitors are recommended for the treatment of non-variceal bleeding, rather than variceal bleeding. Herein, we present a case with liver cirrhosis and acute upper gastrointestinal bleeding who had a high risk of rebleeding (i.e., Child–Pugh class C, hepatocellular carcinoma, portal vein thrombosis, low albumin, and high international normalized ratio and D-dimer). As the source of bleeding was obscure, only terlipressin without pump proton inhibitors was initially administered. Acute bleeding episode was effectively controlled. After that, an elective endoscopic examination confirmed that the source of bleeding was attributed to peptic ulcer, rather than varices. Based on this preliminary case report, we further discussed the potential role of vasoconstrictors in a patient with cirrhosis with acute non-variceal upper gastrointestinal bleeding.

Open access

Xiangbo Xu, Zhaohui Bai, Qingchun Zhao, Hongyu Li, Qiang Shi, Jiao Deng, Jingqiao Zhang, Xiaozhong Guo and Xingshun Qi

Abstract

Acute-on-chronic liver failure (ACLF) is a potentially lethal syndrome, which is characterized by an acute deterioration of liver function in patients with chronic liver diseases. The present paper reported that an alcoholic cirrhotic patient with ACLF developed septic shock, hydrothorax, ascites, hepatic encephalopathy, acute kidney injury, and acute upper gastrointestinal bleeding at the same hospitalization and was successfully rescued by pharmacotherapy alone without any invasive intervention.