An Iterative Space Alternative Tiling Parallel Algorithm for 3D Finite Difference Stencil Computations

Jing Shen,Jilin Zhang,Jian Wan,Li Zhou,Ming Jiang 보안공학연구지원센터 2014 International Journal of Database Theory and Appli Vol.7 No.6

Stencils are finite-difference algorithms for solving large-scale and high-dimension partial differential equations. Due to the data dependences among the iterative statements in Stencils, traditional Stencil computations are be executed serially, rather than in parallel. It’s challenging to design an effective and scalable Stencil parallelized method. To address the issue of 3D data space computing, we present a serial execution model based on multi-layers symmetric Stencil method and time skewing techniques. Within this model, the iteration space is divided to multiple tiles based on time skewing, where the executive process is ordered by the sequence of tiles, and the nodes in each individual tile can be swept repeatedly to improve the data locality. In addition, we propose a novel 3D iterative space alternate tiling Stencil parallel method, which subdivides the iteration space along high dimension, and changes the execution sequence of tiles to reduce the data dependency and communication cost, where the partial order of tiles is still guaranteed. Experimental results demonstrate our proposed alternative tiling parallel method achieves better parallel efficiency and scalability compared with the domain-decomposition methods.

Transcriptome profiling identifies immune response genes against porcine reproductive and respiratory syndrome virus and Haemophilus parasuis co-infection in the lungs of piglets

Jing Zhang,Jing Wang,Xiong Zhang,Chunping Zhao,Sixuan Zhou,Chunlin Du,Ya Tan,Yu Zhang,Kaizhi Shi 대한수의학회 2022 Journal of Veterinary Science Vol.23 No.1

Background: Co-infections of the porcine reproductive and respiratory syndrome virus (PRRSV) and the Haemophilus parasuis (HPS) are severe in Chinese pigs, but the immune response genes against co-infected with 2 pathogens in the lungs have not been reported. Objectives: To understand the effect of PRRSV and/or HPS infection on the genes expression associated with lung immune function. Methods: The expression of the immune-related genes was analyzed using RNA-sequencing and bioinformatics. Differentially expressed genes (DEGs) were detected and identified by quantitative real-time polymerase chain reaction (qRT-PCR), immunohistochemistry (IHC) and western blotting assays. Results: All experimental pigs showed clinical symptoms and lung lesions. RNA-seq analysis showed that 922 DEGs in co-challenged pigs were more than in the HPS group (709 DEGs) and the PRRSV group (676 DEGs). Eleven DEGs validated by qRT-PCR were consistent with the RNA sequencing results. Eleven common Kyoto Encyclopedia of Genes and Genomes pathways related to infection and immune were found in single-infected and co-challenged pigs, including autophagy, cytokine-cytokine receptor interaction, and antigen processing and presentation, involving different DEGs. A model of immune response to infection with PRRSV and HPS was predicted among the DEGs in the co-challenged pigs. Dual oxidase 1 (DUOX1) and interleukin-21 (IL21) were detected by IHC and western blot and showed significant differences between the co-challenged pigs and the controls. Conclusions: These findings elucidated the transcriptome changes in the lungs after PRRSV and/or HPS infections, providing ideas for further study to inhibit ROS production and promote pulmonary fibrosis caused by co-challenging with PRRSV and HPS.

Overexpression of NDRG2 Can Inhibit Neuroblastoma Cell Proliferation through Negative Regulation by CYR61

Zhang, Zhi-Guo,Li, Gang,Feng, Da-Yun,Zhang, Jian,Zhang, Jing,Qin, Huai-Zhou,Ma, Lian-Ting,Gao, Guo-Dong,Wu, Lin Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.1

Several recent studies have showed that the n-myc downstream regulated gene 2 (NDRG2) is a new tumor suppressor gene, and that it plays an important role in tumor suppression in several cancers or cancer cell lines. However, few studies focused on its function in neuroblastoma cells. In the present investigation, we demonstrated that NDRG2 overexpression inhibited their proliferation. Using a cDNA microarray, we found that overexpression of NDRG2 inhibited the expression of cysteine-rich protein 61 (CYR61), a proliferation related gene. From our research, CYR61 may partially hinder NDRG2-mediated inhibition of cell proliferation. Overexpression of NDRG2 resulted in accumulation of cells in the G1 phase, which was accompanied by upregulation of p21 and p27 and downregulation of CDK4 and cyclin D1. Taken together, these data indicate that NDRG2 inhibits the proliferation of neuroblastoma cells partially through suppression of CYR61. Our findings offer novel insights into the physiological roles of NDRG2 in neuroblastoma cell proliferation, and NDRG2 may prove to be effective candidate for the treatment of children with neuroblastoma.

Potential Therapeutic Targets for the Primary Gallbladder Carcinoma: Estrogen Receptors

Zhang, Ling-Qiang,Zhang, Xiu-De,Xu, Jia,Wan, Yong,Qu, Kai,Zhang, Jing-Yao,Wang, Zhi-Xin,Wei, Ji-Chao,Meng, Fan-Di,Tai, Ming-Hui,Zhou, Lei,Liu, Chang Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.4

Gallbladder carcinoma, the most frequent malignant neoplasm of the biliary tract system, has always been considered to feature late clinical presentation and diagnosis, limited treatment options and an extremely poor prognosis. In recent years, while the incidence of gallbladder cancer has appeared to be on the increase, the available treatment methods have not greatly improved survival of the affected patients. Thus, exploring new therapeutic targets for this devastating disease is an urgent matter at present. Epidemical studies have demonstrated that the incidence of gallbladder carcinoma exhibits a distinct gender bias, affecting females two to three times more than males, pointing to crucial roles of estrogen. It is well known that estrogen acts on target tissues by binding to estrogen receptors (ERs), which are mainly divided into three subtypes, $ER{\alpha}$, $ER{\beta}$ and $ER{\gamma}$. $ER{\alpha}$ and $ER{\beta}$ appear to have overlapping but also unique even opposite biological effects. As important pathogenic mediators, ERs have been considered to relate to several kinds of tumors. In gallbladder carcinoma tissue, ERs have been shown to be positively expressed, and ERs expression levels are associated with differentiation and prognosis of this cancer. Nevertheless, the exact mechanisms of estrogen inducing growth of gallbladder carcinoma remain poorly understood. On the base of the current investigations, we deduce that estrogen participates in promotion of gallbladder carcinoma by influencing the formation of gallstones, stimulating angiogenesis, and promoting abnormal proliferation. Since ERs mediate the carcinogenic actions of estrogen in gallbladder, and therapy targeting ERs may provide new directions for gallbladder carcinoma. Therefore, it should be stressed that ERs are potential therapeutic targets for gallbladder carcinoma.

Prognostic Values of Various Clinical Factors and Genetic Subtypes for Diffuse Large B-cell lymphoma Patients: A Retrospective Analysis of 227 Cases

Zhou, De,Xie, Wan-Zhuo,Hu, Ke-Yue,Huang, Wei-Jia,Wei, Guo-Qing,He, Jing-Song,Shi, Ji-Min,Luo, Yi,Li, Li,Zhu, Jing-Jing,Zhang, Jie,Lin, Mao-Fang,Ye, Xiu-Jin,Cai, Zhen,Huang, He Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.2

Aim: To analyze the significance of different clinical factors for prognostic prediction in diffuse large B-cell lymphoma (DLBCL) patients. Methods: Two hundred and twenty-seven DLBCL patients were retrospectively reviewed. Patients were managed with cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) regimen or rituximab plus the CHOP (RCHOP) regimen. Results: Lactate dehydrogenase (LDH), ${\beta}2$-microglobulin (${\beta}2$-M), B symptoms, Ann Arbor stage and genetic subtypes were statistically relevant in predicting the prognosis of the overall survival (OS). In the CHOP group, the OS in patients with germinal center B-cell-like (GCB)(76.2%) was significantly higher than that of the non-GCB group (51.9%, P=0.032). With RCHOP management, there was no statistical difference in OS between the GCB (88.4%) and non-GCB groups (81.9%, P=0.288). Conclusion: Elevated LDH and ${\beta}2$-M levels, positive B symptoms, Ann Arbor stage III/IV, and primary nodal lymphoma indicate an unfavorable prognosis of DLBCL patients. Patients with GCB-like DLBCL have a better prognosis than those with non-GCB when treated with the CHOP regimen. The RCHOP treatment with the addition of rituximab can improve the prognosis of patients with DLBCL.

Comprehensive Expression Analysis Suggests Functional Overlapping of Human FOX Transcription Factors in Cancer

Zhang, Ya-Li,Sun, Feng-Ting,Zhang, Ze,Chen, Xiao-Xu,Liu, Ai-Xiang,Pan, Jing-Jing,Peng, Fei,Zhou, Shuai,Sun, Li-Jun Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.23

Forkhead-box (FOX) transcription factors comprise a large gene family that contains more than 50 members in man. Extensive studies have revealed that they not only have functions in control of growth and development, but also play important roles in different diseases, especially in cancer. However, biological functions for most of the members in the FOX family remain unknown. In the present study, the expression of 39 FOX genes in 48 kinds of cancer was mined from the Gene Expression Atlas database of European Bioinformatics Institute. The analysis results showed that some FOX genes demonstrate overlapping expression in various cancers, which suggests particular biological functions. The pleiotropic features of the FOX genes make them excellent candidates in efforts aimed to give medical treatment for cancers at the genetic level. The results also indicated that different FOX genes may have the synergy or antagonistics effects in the same cancers. The study provides clues for further functional analysis of FOX genes, especially for the pleiotropic biological functions and crosstalk of FOX genes in human cancers.

Effects of Insect Hormones on the Replication of Nucleopolyhedrovirus

( Ya Jing Zhou ),( Yong Zhu Yi ),( Qing Li Xiao ),( Zhi Fang Zhang ),( Jia Lu He ),( Yuan Xing Zhang ) 한국잠사학회 2002 International Journal of Industrial Entomology Vol.4 No.2

Kinetics and Modeling for Extraction of Chrysin from Oroxylum indicum Seeds

Li Zhou,Ting Jing,Peipei Zhang,Liqin Zhang,Shaona Cai,Tingting Liu,Huihui Fan,Guangde Yang,Rong Lin,Jiye Zhang 한국식품과학회 2015 Food Science and Biotechnology Vol.24 No.6

Research on extraction of chrysin is crucial for theoretical purposes and for food industrial bioprocesses. Optimization and kinetics of chrysin extraction from seeds of Oroxylum indicum (L.) Vent. were analyzed using agitated solid-liquid extractions with ethanol and water mixtures. The influence of extraction process parameters was investigated. Optimized conditions for chrysin extraction were a 0.2 mole fraction of ethanol as an extraction solvent, a temperature of 318 K, an agitation speed 1,400 rpm, and a solid to solvent ratio of 1:30. The extraction kinetic behavior of chrysin followed first order kinetics. The kinetic expression developed by Spiro and Siddique was used and the model was in agreement with experimental results. The diffusion coefficient ranged from 1.38×10−11 to 19.43×10−11 m2·s−1 and the activation energy for extraction kinetics was 21.85 kJ·mol−1.

An Accurate Isotope Dilution Liquid Chromatography-Tandem Mass Spectrometry Method for Serum C-Peptide and Its Use in Harmonization in China

Deng Yuhang,Zhang Chao,Wang Jing,Zeng Jie,Zhang Jiangtao,Zhang Tianjiao,Zhao Haijian,Zhou Weiyan,Zhang Chuanbao 대한진단검사의학회 2023 Annals of Laboratory Medicine Vol.43 No.4

Background: Serum C-peptide results from various routine methods used in China are highly variable, warranting well-performing methods to serve as an accuracy base to improve the harmonization of C-peptide measurements in China. We developed an accurate isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC–MS/MS) method for serum C-peptide measurement and explored its use in harmonization. Methods: After protein precipitation with ZnSO4 solution, C-peptide was extracted from serum samples by anion-exchange solid-phase extraction and quantified by ID-LC–MS/MS in positive ion mode. The precision and analytical recovery of the ID-LC–MS/MS method were assessed. Seventy-six serum samples were analyzed using the ID-LC–MS/MS method and six routine immunoassays. Ordinary linear regression (OLR) and Bland-Altman (BA) analyses were conducted to evaluate the relationship between the ID-LC–MS/MS method and routine immunoassays. Five serum pool samples assigned using the ID-LC–MS/MS method were used to recalibrate the routine assays. OLR and BA analyses were re-conducted after recalibration. Results: The within-run, between-run, and total precision for the ID-LC–MS/MS method at four concentrations were 1.0%–2.1%, 0.6%–1.2%, and 1.3%–2.2%, respectively. The analytical recoveries for the ID-LC–MS/MS method at three concentrations were 100.3%–100.7%, 100.4%–101.0%, and 99.6%–100.7%. The developed method and the immunoassays were strongly correlated, with all R2 >0.98. The comparability among the immunoassays was substantially improved after recalibration. Conclusions: The performance of the ID-LC–MS/MS method was carefully validated, and this method can be used to improve the harmonization of serum C-peptide measurements in China.

Superluminescent diode integrated with monitor photodiode

Zhou Shuai,Liu Kun,Li Peng,Pang Fu-Bin,Zhang Jing,Kong Xiang-Ping,Duan Li-Hua,Zhang Chang-Chun 한국물리학회 2023 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.82 No.2

Ridge-waveguide superluminescent diodes with integrated rear-side monitoring photodiode have been fabricated. When electrical isolation trench is not etched to active layer, the leakage current of monitoring photodiode is determined by the resistance between active region electrode and monitoring photodiode electrode, i.e. the resistance multiplied by the leakage current approximately equals to 0.8 V. In order to reduce the leakage current of monitoring photodiode, the electrical isolation trench must be etched into substrate layer. In addition, the electrical isolation trench has to be far enough away from the active region so that the superluminescent diode could achieve small spectral ripple.