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Genome-wide analysis of codon usage bias patterns in an enterotoxigenic Escherichia coli F18 strain
Ri Wei Xia,Wen Bin Bao,Xue Mei Yin,Wei Yun Qin,Guo Qiang Zhu,Sheng Long Wu 한국유전학회 2017 Genes & Genomics Vol.39 No.11
Enterogenic Escherichia coli (ETEC) F18 strains are the main pathogenic bacteria causing severe diarrhea in humans and domestic animals. However, the information about synonymous codon usage pattern of ETEC F18 genome remains unclear. We conducted a genome-wide analysis of synonymous codon usage patterns in the ETEC F18 strain SRA: SAMN02471895. After filtering of the complete genome sequence, 4327 coding sequences were analyzed using multivariate statistical methods to calculate synonymous codon usage patterns and to evaluate the influence of various factors in shaping the codon usage. The mean GC content was 51.38%, with a slight preference for G/C-ending codons. Twenty-two codons were determined as ‘‘optimal codons”. ENC plots showed some of the genes were on or close to the expected curve, while only points with low-ENC values were below the curve. PR2 analysis showed that GC and AT were not used proportionally, suggesting major roles for mutational pressure and natural selection in shaping usage. Neutrality plots showed a significant correlation between GC12 and GC3, suggesting that mutational pressure is responsible for nucleotide composition in shaping the strength of codon usage. Translational selection was the main factor shaping the codon usage pattern of ETEC F18 genome, while other factors such as protein length, GRAVY and ARO values also influenced codon usage to some extent. We analyzed the codon usage pattern systematically and identified the factors shaping codon usage bias in the ETEC F18 genome. Such information further elucidates the mechanisms of synonymous codon usage bias and provides the basis of molecular genetic engineering and evolutionary studies.
Adaptive CVT-Based Reduced-Order Modeling of Burgers Equation
Guang Ri Piao,Qiang Du,Hyung Chun Lee 한국산업응용수학회(구 한국산업정보응용수학회) 2009 한국산업정보응용수학회 Vol.13 No.2
In this article, we consider a weighted CVT-based reduced-order modelling for Burgers equation. Brief review of the CVT (centroidal Voronoi tessellation) approaches to reduced-order bases are provided. In CVT-reduced order modelling, we start with a snapshot set just as is done in a POD (Proper Orthogonal Decomposition)-based setting. So far, the CVT was researched with uniform density (p(y)=1) to determine the basis elements for the approximating subspaces. Here, we shall investigate the technique of CVT with nonuniform density as a procedure to determine the basis elements for the approximating subspaces. Some numerical experiments including comparison of two CVT (CVT-uniform and CVT-nonuniform)-based algorithm with numerical results obtained from FEM(finite element method) and POD-based algorithm are reported.
ADAPTIVE CVT-BASED REDUCED-ORDER MODELING OF BURGERS EQUATION
GUANG-RI PIAO,QIANG DU,HYUNG-CHUN LEE 한국산업응용수학회 2009 Journal of the Korean Society for Industrial and A Vol.13 No.2
In this article, we consider a weighted CVT-based reduced-order modelling for Burgers equation. Brief review of the CVT (centroidal Voronoi tessellation) approaches to reduced-order bases are provided. In CVT-reduced order modelling, we start with a snapshot set just as is done in a POD (Proper Orthogonal Decomposition)-based setting. So far, the CVT was researched with uniform density (p(y) = 1) to determine the basis elements for the approximating subspaces. Here, we shall investigate the technique of CVT with nonuniform density as a procedure to determine the basis elements for the approximating subspaces. Some numerical experiments including comparison of two CVT (CVT-uniform and CVT-nonuniform)-based algorithm with numerical results obtained from FEM(finite element method) and POD-based algorithm are reported.
Robust Digital Image Watermarking Algorithm Using RBF Neural Networks in DWT domain
Cheng-Ri Piao,Qiang Guan,Jun Rim Choi,Seung-Soo Han 한국지능시스템학회 2007 INTERNATIONAL JOURNAL of FUZZY LOGIC and INTELLIGE Vol.7 No.2
This paper proposes a new watermarking scheme in which a logo watermark is embedded into the discrete wavelet transform (DWT) domain of the original image using exact radial basis function neural networks (RBF). RBF will learn the characteristics of the image, and then watermark is embedded and extracted by the trained RBF. A watermark is added to the coefficients at the low frequency band of the DWT of an image and a watermark is embedded into the DWT domain using the trained RBF. The trained RBF also used in watermark extracting process. Experimental results show that the proposed method has good imperceptibility and high robustness to common image processing attacks.
Xiao-Qiang, Shao,Jing-Ji, Wen,Xing-Ri, Jin,Ai-Dong, Zhu,Shou, Zhang,Kyu-Hwang, Yeon Science Press 2007 Chinese physics letters Vol.24 No.10
<P>A scheme for implementing a Fredkin gate with an atom sent through a microwave cavity is proposed. The scheme is based on the resonant atom-cavity interaction so that the gating time is sharply short, which is important in view of decoherence.</P>
Robust Digital Image Watermarking Algorithm Using RBF Neural Networks in DWT domain
Piao, Cheng-Ri,Guan, Qiang,Choi, Jun-Rim,Han, Seung-Soo Korean Institute of Intelligent Systems 2007 INTERNATIONAL JOURNAL of FUZZY LOGIC and INTELLIGE Vol.7 No.2
This paper proposes a new watermarking scheme in which a logo watermark is embedded into the discrete wavelet transform (DWT) domain of the original image using exact radial basis function neural networks (RBF). RBF will learn the characteristics of the image, and then watermark is embedded and extracted by the trained RBF. A watermark is added to the coefficients at the low frequency band of the DWT of an image and a watermark is embedded into the DWT domain using the trained RBF. The trained RBF also used in watermark extracting process. Experimental results show that the proposed method has good imperceptibility and high robustness to common image processing attacks.
Effects of Polymerization and Spinning Conditions on Mechanical Properties of PAN Precursor Fibers
Qi-Feng Qin,Yong-Qiang Dai,Kai Yi,Li Zhang,Seung-Kon Ryu,Ri-Guang Jin 한국탄소학회 2010 Carbon Letters Vol.11 No.3
PAN precursor fibers were produced via wet-spinning process, and effects of polymerization and spinning processes, especially the stretching process, were investigated on mechanical properties and micro-morphologies of precursor fibers. An increase in molecular weight, dope solid and densification and a decrease in surface defects were possible by controlling polymerization temperature, the number of heating rollers for densification and the jet stretch ratio, which improved the mechanical properties of precursor fibers. The curves for strength, modulus, tensile power and diameter as a function of stretch ratio can be divided into three stages: steady change area, little change area and sudden change area. With the increase of stretch ratio, the fiber diameter became smaller, the degree of crystallization increased and the structure of precursor fibers became compact and homogeneous, which resulted in the increase of strength, modulus and tensile power of precursor fibers. Empirical relationship between fiber strength and stretch ratio was studied by using the sub-cluster statistical theory. It was successfully predicted when the strengths were 0.8 GPa and 1.0 GPa under a certain technical condition, the corresponding stretch ratio of the fiber were 11.16 and 12.83 respectively.
Liu, Tian-Hua,Guo, Kun,Liu, Ri-Qiang,Zhang, Shu,Huang, Zhuo-Hui,Liu, Yin-Kun Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.8
Objective: To investigate whether the expression of serum soluble neural cell adhesion molecule (sNCAM) is associated with hepatic encephalopathy (HE) in hepatocelular carcinoma (HCC) patients. Materials and Methods: The Oncomine Cancer Microarray database was used to determine the clinical relevance of NCAM expression in different kinds of human cancers. Sera from 75 HCC cases enrolled in this study were assessed for expression of sNCAM by enzyme linked immunosorbent assay (ELISA). Results: Dependent on the Oncomine Cancer Microarray database analysis, NCAM was down regulated in 10 different kinds of cancer, like bladder cancer, brain and central nervous system cancer, while up-regulated in lung cancer, uterine corpus leiomyoma and sarcoma, compared to normal groups. Puzzlingly, NCAM expression demonstrated no significant difference between normal and HCC groups. However, we found by quantitative ELISA that the level of sNCAM in sera from HCC patients with HE ($347.4{\pm}151.9ng/ml$) was significantly more up-regulated than that in HCC patients without HE ($260.3{\pm}104.2ng/ml$), the p-value being 0.008. sNCAM may be an important risk factor of HE in HCC patients, the correlation coefficients was 0.278 (P<0.05) on rank correlation analysis. Conclusions: This study highlights that up-regulated level of serum sNCAM is associated with HE in HCC patients and suggests that the high expression can be used as an indicator.
Chen, Zhen-Hua,Sun, Liang-Peng,Zhang, Wei,Shen, Qiang,Gao, Li-Xin,Li, Jia,Piao, Hu-Ri Korean Chemical Society 2012 Bulletin of the Korean Chemical Society Vol.33 No.5
Protein tyrosine phosphatase 1B (PTP1B) is a key factor in negative regulation of the insulin pathway, and is a promising target for the treatment of type-II diabetes, obesity and cancer. Herein, compound ($\mathbf{4}$) was first observed to have moderate inhibitory activity against PTP1B with an $IC_{50}$ value of $13.72{\pm}1.53{\mu}M$. To obtain more potent PTP1B inhibitors, we synthesized a series of chalcone derivatives using compound ($\mathbf{4}$) as the lead compound. Compound $\mathbf{4l}$ ($IC_{50}=3.12{\pm}0.18{\mu}M$) was 4.4-fold more potent than the lead compound $\mathbf{4}$ ($IC_{50}=13.72{\pm}1.53{\mu}M$), and more potent than the positive control, ursolic acid ($IC_{50}=3.40{\pm}0.21{\mu}M$). These results may help to provide suitable drug-like lead compounds for the design of inhibitors of PTP1B as well as other PTPs.