Optimization of GEMV on Intel AVX Processor

Jun Liang,Yunquan Zhang 보안공학연구지원센터 2016 International Journal of Database Theory and Appli Vol.9 No.2

To improve the performance of BLAS 2 GEMV subroutine under the latest instruction set, Intel AVX, this paper presents a new approach to analyze the new generation instruction set and enhance the efficiency of current data-oriented math subroutines. The whole optimizing process involves memory access optimization, SIMD optimization and parallel optimization. Also, this paper shows the comparison between the traditional SSE instruction set and the AVX instruction set. Experiments show that the optimized GEMV function has obtained considerable increase on performance. Compared with the Intel MKL, GotoBLAS, ATLAS, this optimized GEMV exceeds these BLAS implementations from 5% to 10%.

Exosome-mediated lnc-ABCA12-3 promotes proliferation and glycolysis but inhibits apoptosis by regulating the toll-like receptor 4/nuclear factor kappa-B signaling pathway in esophageal squamous cell carcinoma

Junliang Ma,Yijun Luo,Yingjie Liu,Cheng Chen,Anping Chen,Lubiao Liang,Wenxiang Wang,Yongxiang Song 대한약리학회 2023 The Korean Journal of Physiology & Pharmacology Vol.27 No.1

Esophageal squamous cell carcinoma (ESCC) is a kind of malignant tumor with high incidence and mortality in the digestive system. The aim of this study is to explore the function of lnc-ABCA12-3 in the development of ESCC and its unique mechanisms. RT-PCR was applied to detect gene transcription levels in tissues or cell lines like TE-1, EC9706, and HEEC cells. Western blot was conducted to identify protein expression levels of mitochondrial apoptosis and toll-like receptor 4 (TLR4)/nuclear factor kappa-B (NF-κB) signaling pathway. CCK-8 and EdU assays were carried out to measure cell proliferation, and cell apoptosis was examined by flow cytometry. ELISA was used for checking the changes in glycolysis-related indicators. Lnc-ABCA12-3 was highly expressed in ESCC tissues and cells, which preferred it to be a candidate target. The TE-1 and EC9706 cells proliferation and glycolysis were obviously inhibited with the downregulation of lnc-ABCA12-3, while apoptosis was promoted. TLR4 activator could largely reverse the apoptosis acceleration and relieved the proliferation and glycolysis suppression caused by lnc-ABCA12-3 downregulation. Moreover, the effect of lnc-ABCA12-3 on ESCC cells was actualized by activating the TLR4/NF-κB signaling pathway under the mediation of exosome. Taken together, the lnc-ABCA12-3 could promote the proliferation and glycolysis of ESCC, while repressing its apoptosis probably by regulating the TLR4/NF-κB signaling pathway under the mediation of exosome.

EpiSIM: simulation of multiple epistasis, linkage disequilibrium patterns and haplotype blocks for genome-wide interaction analysis

Junliang Shang,Junying Zhang,Xiujuan Lei,Wenying Zhao,Yafei Dong 한국유전학회 2013 Genes & Genomics Vol.35 No.3

Epistasis is a ubiquitous phenomenon in genetics,and is considered to be one of the main factors in current efforts to detect missing heritability for complex diseases. Simulation is a critical tool in developing methodologies that can more effectively detect and study epistasis. Here we present a simulator, epiSIM (epistasis SIMulator), that can simulate some of the statistical properties of genetic data. EpiSIM is capable of expanding the range of the epistasis models that current simulators offer, including epistasis models that display marginal effects and those that display no marginal effects. One or more of these epistasis models can be embedded simultaneously into a single simulation data set, jointly determining the phenotype. In addition,epiSIM is independent of any outside data source in generating linkage disequilibrium patterns and haplotype blocks. We demonstrate the wide applicability of epiSIM by performing several data simulations, and examine its properties by comparing it with current representative simulators and by comparing the data that it generates with real data. Our experiments demonstrate that epiSIM is a valuable addition and a nice complement to the existing epistasis simulators. The software package is available online at https://sourceforge.net/projects/episimsimulator/files/.

Incorporating heuristic information into ant colony optimization for epistasis detection

Junliang Shang,Junying Zhang,Xiujuan Lei,Yuanyuan Zhang,Baodi Chen 한국유전학회 2012 Genes & Genomics Vol.34 No.3

Epistasis has been receiving increasing attention in understanding the mechanism underlying susceptibility to complex diseases. Though many works have been done for epistasis detection, genome-wide association study remains a challenging task: it makes the search space excessively huge while solution quality is excessively demanded. In this study, we introduce an ant colony optimization based algorithm,AntMiner, by incorporating heuristic information into ant-decision rules. The heuristic information is used to direct ants in the search process for improving computational efficiency and solution accuracy. During iterations, chi-squared test is conducted to measure the association between an interaction and the phenotype. At the completion of the iteration process, statistically significant epistatic interactions are ordered and then screened by a post-procedure. Experiments of AntMiner and its comparison with existing algorithms epiMODE, TEAM and AntEpiSeeker are performed on both simulation data sets and real age-related macular degeneration data set, under the criteria of detection power and sensitivity. Results demonstrate that AntMiner is promising for epistasis detection. In terms of detection power, AntMiner performs best among all the other algorithms on all cases regardless of epistasis models and single nucleotide polymorphism size; compared with AntEpiSeeker, AntMiner can obtain better detection power but with less ants and iterations. In terms of sensitivity, AntMiner is better than AntEpiSeeker in detecting epistasis models displaying marginal effects but it has moderate sensitivity on epistasis models displaying no marginal effects. The study may provide clues on heuristics for further epistasis detection. The software package is available online at https://sourceforge.net/projects/antminer/files/.

The enumeration of rooted cubic c-nets$^{\dag}$

Junliang Cai,Rongxia Hao,Yanpei Liu 한국전산응용수학회 2005 Journal of applied mathematics & informatics Vol.18 No.1-2

This paper is to establish a functional equation satisfied by the generating function for counting rooted cubic c-nets and then to determine the parametric expressions of the equation directly. Meanwhile, the explicit formulae for counting rooted cubic c-nets are derived immediately by employing Lagrangian inversion with one or two parameters. Both of them are summation-free and in which one is just an answer to the open problem (8.6.5) in [1].

A Chinese Restaurant Game for Distributed Cooperative Caching in Small Cell Networks

( Junliang Chen ),( Gang Wang ),( Fuxiang Wang ) 한국인터넷정보학회 2019 KSII Transactions on Internet and Information Syst Vol.13 No.1

Wireless content caching in small cell networks has recently been considered as a promising way to alleviate the congestion of the backhaul in emerging heterogenous cellular network. However, how to select files which are cached in SBSs and how to make SBSs work together is an important issue for cooperative cache research for the propose of reducing file download time. In this paper, a Cooperative-Greedy strategy (CGS) among cache-enabled small base stations (SBSs) in small cell network is proposed, in order to minimize the download time of files. This problem is formulated as a Chinese restaurant game.Using this game model, we can configure file caching schemes based on file popularity and the spectrum resources allocated to several adjacent SBSs. Both the existence and uniquencess of a Nash equilibrium are proved. In the theoretical analysis section, SBSs cooperate with each other in order to cache popular files as many as possible near UEs. Simulation results show that the CGS scheme outperforms other schemes in terms of the file-download time.

The location for eigenvalues of complex matrices by a numerical method

Junliang Wu,Pingping Zhang,Yong Wang 한국전산응용수학회 2011 Journal of applied mathematics & informatics Vol.29 No.1

In this paper, we adopt a numerical method to establish the smallest set to contain all Geršgorin discs of a given complex matrix and its some similar matrices. With the smallest set, a new estimation for all eigenvalues of the matrix is obtained.

Sodium ferulate inhibits high-fat diet-induced inflammatory factors expression in human umbilical vein endothelial cells

Junliang Tao,Dongxian Zhang,Yonghong Man,Weina Wang,Yongyi Bi,Yongyi Bi 대한독성 유전단백체 학회 2016 Molecular & cellular toxicology Vol.12 No.2

Vascular inflammation is an important hallmark of high-fat-induced atherosclerosis. Oxidized low-density lipoprotein (ox-LDL) is a key initiator of inflammation as it induces inflammatory gene expression in vascular endothelial cells. Sodium ferulate (SF), an active component from Chinese medicine, demonstrated anti-atherosclerotic potency. However, the mechanism is unknown. Here we investigated how SF changed the cellular gene expression profile and restored ox-LDL-triggered inflammation in HUVECs. Gene expression profile, inflammatory gene expression and NF-κB activation were investigated in human umbilical vein endothelial cells (HUVECs) with or without SF (5 μM) treatment after precondition with ox-LDL (50 μg/mL). Ox-LDL treatment increased the production of IL-1β, CCL20, IL-6, IL-8 and CXCL1. SF stimulation modulated the translocation of NF-κB between cytoplasm and nucleus, and alleviated the inflammatory response induced by ox-LDL. Collectively, SF could suppress the expression of inflammatory factors in ox-LDL-stimulated endothelial cells, and transcription factor NF-κB might be involved in such process.

비밀키를 이용한 토큰 업데이트 보안 인증 기법

준량(JunLiang),장인주(Jang In Joo),유형선(Hyeong Seon Yoo) 한국전자거래학회 2007 한국전자거래학회지 Vol.12 No.1

최근 들어 OTP를 고려한 스마트카드 환경에서의 많은 인증 기법이 제안되고 있다. 그러나 이러한 인증 기법들이 개인 컴퓨터 환경에서 구현될 경우 개인 컴퓨터상에서는 데이터를 쉽게 읽어 내고, 유출 시킬 수 있기에 위장 공격이나 Stolen-Verifier 공격 등에 대하여 취약점이 노출된다. 본 논문에서는 이러한 취약점을 재선한 인증기법을 제시함으로 스마트카드 상에서 사용되는 인증 기법이 컴퓨터 환경에서도 효율적으로 사용될 수 있도록 하였다. 본 논문이 제안하는 기법은 Stolen-Verifier 공격과 위장 공격에 안전하며, 상호 인증 기능을 부여하고 비밀 키의 생성에 있어 쉽다는 장점을 지니고 있다. Recently, a large number of authentication schemes based on smart cards have been proposed, using the thinking of OTP (one-time password) to withstand replay attack. Unfortunately, if these schemes implement on Pes instead of smart cards, most of them cannot withstand impersonation attack and Stolen-Verifier attack since the data on Pes is easy to read and steal. In this paper, a secure authentication scheme based on a security key and a renewable token is proposed to implement on Pes. A comparison with other schemes demonstrates the proposed scheme has following merits: (1) Withstanding Stolen-Verifier attack (2) Withstanding Impersonation attack (3) Providing mutual authentication; (4) Easy to construct secure session keys.

The role of exosomal miR-181b in the crosstalk between NSCLC cells and tumor-associated macrophages

Ma Junliang,Chen Shaolin,Liu Yingjie,Han Hao,Gong Ming,Song Yongxiang 한국유전학회 2022 Genes & Genomics Vol.44 No.10

Background: It has been reported that tumor-associated macrophages (TAMs) participate in modulating the progression of cancer in the tumor microenvironment. However, the crosstalk between TAMs and non-small cell lung cancer (NSCLC) is still unclear. Objective: We investigated whether NSCLC-derived exosomes could affect TAMs, which feedback modulated progression of NSCLC. Methods: MiR-181b expression was measured by RT-PCR. Human THP-1 monocyte was differentiated into macrophages with phorbol myristate acetate, which were further identified by transmission electron microscopy and western blot. Macrophage M1 and M2 polarizations were detected by flow cytometry, RT-PCR and western blot. Proliferation, migration, and invasion of NSCLC cells treated with conditioned mediums were detected by EdU and Transwell assays. Results: We demonstrated that miR-181b was up-regulated in exosomes derived from NSCLC patients' serum and NSCLC cells. MiR-181b could be transferred to macrophages via exosomes in the co-culture system of macrophages and NSCLC cells, which promoted macrophage M2 polarization. Further examinations revealed that exosomes derived from NSCLC cells could enhanced macrophage M2 polarizations by regulating miR-181b/JAK2/STAT3 axis, and silencing miR-181b in NSCLC cells and JAK2 inhibitor used in macrophages could reverse the effects. Importantly, the conditioned medium of macrophages treated with NSCLC cell-derived exosomes could promote NSCLC cell proliferation, migration, and invasion. Silencing miR-181b in NSCLC cells and JAK2 inhibitor used in macrophages could block the effects. Conclusions: All of these results indicated that exosomal miR-181b participated in the crosstalk between NSCLC cells and TAMs, providing potential therapeutic targets for NSCLC.