The effects of codon usage on the formation of secondary structures of nucleocapsid protein of peste des petits ruminants virus

Xiao‑xia Ma,Yi‑ning Wang,Xiao‑an Cao,Xue‑rui Li,Yong‑sheng Liu,Jian‑hua Zhou,Xue‑peng Cai 한국유전학회 2018 Genes & Genomics Vol.40 No.9

The nucleocapsid (N) protein of peste des petits ruminants virus (PPRV) with a conserved amino acid usage pattern plays an important role in viral replication. The primary objective of this study was to estimate roles of synonymous codon usages of PPRV N gene and tRNA abundances of host in the formation of secondary structure of N protein. The potential effects of synonymous codon usages of N gene and tRNA abundances of host on shaping different folding units (α-helix, β-strand and the coil) in N protein were estimated, based on the information about the modeling secondary structure of PPRV N protein. The synonymous codon usage bias was found in different folding units in PPRV N protein. To better understand the role of translation speed caused by variant tRNA abundances in shaping the specific folding unit in N protein, we modeled the changing trends of tRNA abundance at the transition boundaries from one folding unit to another folding unit (β-strand → coil, coil → β-strand, α-helix → coil, coil → α-helix). The obvious fluctuations of tRNA abundance were identified at the two transition boundaries (β-strand → coil and coil → β-strand) in PPRV N protein. Our findings suggested that viral synonymous codon usage bias and cellular tRNA abundance variation might have potential effects on the formation of secondary structure of PPRV N protein.

Finite-time and Fixed-time Bipartite Consensus Tracking for Second-order Multi-agent Systems via an Integral Sliding-mode Approach

Xiao-Feng Zhao,Tao Han,Bo Xiao,Xi-Sheng Zhan,Huaicheng Yan 제어·로봇·시스템학회 2023 International Journal of Control, Automation, and Vol.21 No.12

This paper investigates the finite-time and fixed-time bipartite consensus tracking (Fin- and Fix-TBCT) problems for second-order multi-agent systems (MASs) under a signed directed communication network, in which both cooperative and competition exist. To achieve bipartite consensus tracking (BCT) within finite time and fixed time, two novel distributed control protocols utilizing integral sliding-mode control concept are presented and discussed, respectively. By virtue of Lyapunov stability and homogeneity with dilation, several sufficient conditions for achieving Fin- and Fix-TBCT for second-order MASs are obtained. Eventually, numerical simulation results are provided to verify the validity of the obtained theoretical results.

Metastatic Axillary Lymph Node Ratio (LNR) is Prognostically Superior to pN Staging in Patients with Breast Cancer -- Results for 804 Chinese Patients from a Single Institution

Xiao, Xiang-Sheng,Tang, Hai-Lin,Xie, Xin-Hua,Li, Lai-Sheng,Kong, Ya-Nan,Wu, Min-Qing,Yang, Lu,Gao, Jie,Wei, Wei-Dong,Xie, Xiaoming Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.9

The number of axillary lymph nodes involved and retrieved are important prognostic factors in breast cancer. The purpose of our study was to investigate whether the lymph node ratio (LNR) is a better prognostic factor in predicting disease-free survival (DFS) for breast cancer patients as compared with pN staging. The analysis was based on 804 breast cancer patients who had underwent axillary lymph node dissection between 1999 and 2008 in Sun Yat-Sen University Cancer Center. Optimal cutoff points of LNR were calculated using X-tile software and validated by bootstrapping. Patients were then divided into three groups (low-, intermediate-, and high-risk) according to the cutoff points. Predicting risk factors for relapse were performed according to Cox proportional hazards analysis. DFS was estimated using the Kaplan-Meier method and compared by the log-rank test. The 5-year DFS rate decreased significantly with increasing LNRs and pN. Univariate analysis found that the pT, pN, LNR, molecule type, HER2, pTNM stage and radiotherapy well classified patients with significantly different prognosis. By multivariate analysis, only LNR classification was retained as an independent prognostic factor. Furthermore, there was a significant prognostic difference among different LNR categories for pN2 category, but no apparent prognostic difference was seen between different pN categories in any LNR category. Therefore, LNR rather than pN staging is preferable in predicting DFS in node positive breast cancer patients, and routine clinical decision-making should take the LNR into consideration.

Functional Characterization of 5-Enopyruvylshikimate-3-Phosphate Synthase from Alkaliphilus metalliredigens in Transgenic Arabidopsis

( Xiao Juan Xing ),( Yong Sheng Tian ),( Ri He Peng ),( Jing Xu ),( Wei Zhao ),( Quan Hong Yao ),( Sheng Sun ) 한국미생물 · 생명공학회 2014 Journal of microbiology and biotechnology Vol.24 No.10

Although a large number of AroA enzymes (EPSPS: 5-enopyruvylshikimate-3-phosphate synthase) have been identified, cloned, and tested for glyphosate resistance, only two AroA variants, derived from Agrobacterium tumefaciens strain CP4 and Zea mays, have been utilized to produce the commercial glyphosate-resistant crops. Here, we have used a PCR-based twostep DNA synthesis method to synthesize an aroA gene (aroAA. metalliredigens) from Alkaliphilus metalliredigens, encoding a new EPSPS. Furthermore, transgenic Arabidopsis with the new aroAA. metalliredigens gene was obtained to confirm the potential of the novel aroA gene in developing glyphosate-resistant crops.

Effect of the Oxygen Flux Ratio on the Structural and the Optical Properties of Silver-oxide Films Deposited by Using the Direct-current Reactive Magnetron Sputtering Method

Xiao-Yong Gao,Hong-Liang Feng,Zeng-Yuan Zhang,Jiao-Min Ma,Meng-Ke Zhao,Chao Chen,Jin-Hua Gu,Shi-E Yang,Yong-Sheng Chen,Jing-Xiao Lu 한국물리학회 2011 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.58 No.2

Using values of the oxygen flux ratio (OFR = [O2]/[Ar]) ranging from 0 to 0.5, authors deposited a series of silver-oxide (Ag_xO) films on glass substrates by direct-current reactive magnetron sputtering (DC sputtering) at a substrate temperature of 150 ℃. The effect of the OFR on the film’s structural and optical properties was systematically investigated by using X-ray diffractometry, scanning electron microscopy and spectrophotometry. The Ag_xO films deposited clearly show an evolution of the film’s phase structure from the biphased (Ag + Ag_2O) structure to the biphased (AgO + Ag_2O) structure and then to the single-phased (Ag_2O) structure as value of the OFR increases. Accordingly, the film’s surface morphology, related to the film’s crystalline structure, clearly changes from a loose and porous surface structure to a compact surface structure and then to a pyramid-like surface structure with increasing value of the OFR. The novel porous structure may be attributed to the interruption of the silver’s growth course by the AgO on the film’s surface. Notably, a single-phased Ag_2O film is deposited by DC-sputtering at OFR = 0.5 due to the dual effects of thermal decomposition of the AgO phase and a combination reaction of AgO and Ag to Ag_2O. The oscillations both in the film’s reflectivity and transmissivity spectra are strengthened with increasing OFR, indicating an evolution from the metallic behavior of the biphased (Ag + Ag_2O) film to the dielectric behavior of the biphased (Ag_2O + AgO) film and the single-phased Ag2O film. The fitted optical absorption edges of the Ag_2O and the Ag_xO films deposited at values of the OFR of 0.5 and 0.33 are approximately 2.43 eV and 2.34 eV, respectively. The absorption edges are closely related to the direct interband transitions.

Counterpoise correction is not useful for short and Van der Waals distances but may be useful at long range

Sheng, Xiao Wei,Mentel, Lukasz,Gritsenko, Oleg V.,Baerends, Evert Jan Wiley Subscription Services, Inc., A Wiley Company 2011 Journal of computational chemistry Vol.32 No.13

<P><B>Abstract</B></P><P>This article investigates the errors in supermolecule calculations for the helium dimer. In a full CI calculation, there are two errors. One is the basis set superposition error (BSSE), the other is the basis set convergence error (BSCE). Both of the errors arise from the incompleteness of the basis set. These two errors make opposite contributions to the interaction energies. The BSCE is by far the largest error in the short range and larger than (but much closer to) BSSE around the Van der Waals minimum. Only at the long range, the BSSE becomes the larger error. The BSCE and BSSE largely cancel each other over the Van der Waals well. Accordingly, it may be recommended to not include the BSSE for the calculation of the potential energy curve from short distance till well beyond the Van der Waals minimum, but it may be recommended to include the BSSE correction if an accurate tail behavior is required. Only if the calculation has used a very large basis set, one can refrain from including the counterpoise correction in the full potential range. These results are based on full CI calculations with the aug‐cc‐pVXZ (<I>X</I> = D, T, Q, 5) basis sets. © 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2896–2901, 2011</P>

Stability of Zirconium Metal Organic Frameworks with 9,10- Dicarboxylic Acid Anthracene as Ligand

Xiao, Sheng-Bao,Chen, Sai-Sai,Liu, Jin,Li, Zhen,Zhang, Feng-Jun,Wang, Xian-Biao,Oh, Won-Chun The Korean Ceramic Society 2016 한국세라믹학회지 Vol.53 No.2

With high specific surface area and pore structural diversity, MOFs show important applications in gas storage, catalysis, sensing, separation, and biomedicine. However, the stability of the structure of MOFs has restricted their application and development. In this study, zirconium metal organic frameworks with 9,10-dicarboxylic acid anthracene as ligand, named UIO-66 ($H_2DCA$), were synthesized and their properties and structures were characterized by XRD, SEM, and $N_2$ adsorption. We focus on the stability of the structure of UIO-66 ($H_2DCA$) under different conditions (acid, alkali, and water). The structural changes or ruins of UIO-66 ($H_2DCA$) were traced by means of XRD, TG, and FT-IR under different conditions. The results show that the UIO-66 ($H_2DCA$) materials are stable at 583 K, and that this structural stability is greatly influenced by different types of acid and alkali compounds. Importantly, we found that the structures maintain their stability in environments of nitric acid, triethylamine, and boiling water.

A LSTM-based method for intelligent prediction on mechanical response of precast nodular piles

Sheng-Liang Lu,Xiao-Xiao Chen,Chang-Sheng Zhan 국제구조공학회 2022 Smart Structures and Systems, An International Jou Vol.30 No.2

The determination for bearing capacity of precast nodular piles is conventionally time-consuming and high-cost by using numerous experiments and empirical methods. This study proposes an intelligent method to evaluate the bearing capacity and shaft resistance of the nodular piles with high efficiency based on long short-term memory (LSTM) approach. A series of field tests are first designed to measure the axial force, shaft resistance and displacement of the combined nodular piles under different loadings, in comparison with the single pre-stressed high-strength concrete piles. The test results confirm that the combined nodular piles could provide larger ultimate bearing capacity (more than 100%) than the single pre-stressed highstrength concrete piles. Both the LSTM-based method and empirical methods are used to calculate the shift resistance of the combined nodular piles. The results show that the LSTM-based method has a high-precision estimation on shaft resistance, not only for the ultimate load but also for the working load.

Calpain-10 SNP43 and SNP19 Polymorphisms and Colorectal Cancer: a Matched Case-control Study

Hu, Xiao-Qin,Yuan, Ping,Luan, Rong-Sheng,Li, Xiao-Ling,Liu, Wen-Hui,Feng, Fei,Yan, Jin,Yang, Yan-Fang Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.11

Objective: Insulin resistance (IR) is an established risk factor for colorectal cancer (CRC). Given that CRC and IR physiologically overlap and the calpain-10 gene (CAPN10) is a candidate for IR, we explored the association between CAPN10 and CRC risk. Methods: Blood samples of 400 case-control pairs were genotyped, and the lifestyle and dietary habits of these pairs were recorded and collected. Unconditional logistic regression (LR) was used to assess the effects of CAPN10 SNP43 and SNP19, and environmental factors. Both generalized multifactor dimensionality reduction (GMDR) and the classification and regression tree (CART) were used to test gene-environment interactions for CRC risk. Results: The GA+AA genotype of SNP43 and the Del/Ins+Ins/Ins genotype of SNP19 were marginally related to CRC risk (GA+AA: OR = 1.35, 95% CI = 0.92-1.99; Del/Ins+Ins/Ins: OR = 1.31, 95% CI = 0.84-2.04). Notably, a high-order interaction was consistently identified by GMDR and CART analyses. In GMDR, the four-factor interaction model of SNP43, SNP19, red meat consumption, and smoked meat consumption was the best model, with a maximum cross-validation consistency of 10/10 and testing balance accuracy of 0.61 (P < 0.01). In LR, subjects with high red and smoked meat consumption and two risk genotypes had a 6.17-fold CRC risk (95% CI = 2.44-15.6) relative to that of subjects with low red and smoked meat consumption and null risk genotypes. In CART, individuals with high smoked and red meat consumption, SNP19 Del/Ins+Ins/Ins, and SNP43 GA+AA had higher CRC risk (OR = 4.56, 95%CI = 1.94-10.75) than those with low smoked and red meat consumption. Conclusions: Though the single loci of CAPN10 SNP43 and SNP19 are not enough to significantly increase the CRC susceptibility, the combination of SNP43, SNP19, red meat consumption, and smoked meat consumption is associated with elevated risk.

Performance Analysis of Power Line Communication Network Model Based on Spider Web

Liu Xiao-sheng,Zhang Liang,ZHOU Yan,Xu Dian-guo 전력전자학회 2011 ICPE(ISPE)논문집 Vol.2011 No.5

To enhance the reliability of narrow band PLC (Power Line Communication) in low-voltage network, inspired by the structure and invulnerability of spider web, a new PLC network model is proposed in this paper. The characteristics of the model and the transformational process of low-voltage distribution network from physical topology to artificially spider web logical topology are thoroughly discussed. New networking algorithm and route-reconstruction algorithm are put forward. A two-state Markov model is used to simulate a terminal node and the time-delay characteristic of the new algorithm is analyzed by modeling. Based on Opnet14.5, simulation and comparison are conducted, which prove that the new network model has advantages in improving the communication reliability of PLC network.