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.

Effect of Different Cooling Rates in High Rheological Rate Forming Process on Mechanical Properties of Zr57Cu20Al10Ni8Ag5 Bulk Metallic Glass

Xiao‑Bo Mei,Bao‑Chuan Liu,Wei Jiang,Quan Xu,Qi‑Dong Zhang,Yu‑Bai Ma,Fang‑Qiu Zu 대한금속·재료학회 2020 METALS AND MATERIALS International Vol.26 No.9

The influence of cooling rates on the mechanical properties of a Zr-based bulk metallic glass prepared with high rheologicalrate forming (HRRF) was investigated and compared with traditional suction cast methods. Amorphous samples of Zr57Cu-20Ni8Al10Ag5 were prepared in copper molds with different sizes in order to obtain different cooling rates for both HRRFand traditional cast methods. These specimens were subjected to compression experiments, including microhardness testing,X-ray diffraction testing and differential scanning calorimetry analysis. The results indicate that the plasticity of the samplesformed by HRRF are higher than that of the as-cast ones at the same cooling rates, while the microhardness manifests theopposite principle. As the cooling rate increases further, the difference in plasticity further increases between two methods,indicating that the plasticity of metallic glasses is more sensitive to cooling rates during the HRRF process. At the core ofthis phenomenon is the fact that HRRF methods can introduce more free volume into glasses than traditional cast methodswith an elevated cooling rate are able to.

Field-controllable injection of virtual magnetic domainwall in discrete magnetic nanodot chains

Xiao-Ping Ma,김선대,PIAO HONGGUANG,김동현 한국물리학회 2018 Current Applied Physics Vol.18 No.1

Periodic injection behaviors of virtual magnetic domain wall (VDW) have been systematically investigated in asymmetrically shaped nanodot chains by means of micromagnetic simulations. Systematic investigation on a controllable VDW injection has been carried out. We demonstrate that precise control of VDW injection is achievable by using different nanodot shapes as well as by changing alternating magnetic field (AC field) profiles. The VDW position can be tuned by adjusting AC field frequency and amplitude. Field-controllable periodic VDW injection phenomenon is found to be sustainable over wide ranges of phase diagram spanned by AC field frequency and amplitude.

ELECTRIC-FIELD DEPENDENCE OF MOLECULAR CONFORMATIONS OBSERVED BY USING SCANNING TUNNELING MICROSCOPY

XIAO JING MA,RUI ZHANG,YONG TAO SHEN,XIAO HUI QIU,YAN LIAN YANG,CHEN WANG 성균관대학교(자연과학캠퍼스) 성균나노과학기술원 2008 NANO Vol.3 No.2

We review the progress in observation of electrically induced conformational changes of a range of single molecules and molecular assemblies using scanning tunneling microscopy (STM). Recent results using species with optical active functional groups and supramolecular structures confirmed the previously observed effects that the cholesterol molecules with soft linkers have the conformational bistability when switching the bias polarity, while no discernable changes were observed for the mesogen molecules, containing rigid linking units. In addition, it was also observed that the linker units could have appreciable impacts on the assembling characteristics.

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.

Position-dependent Spontaneous Motion of the Magnetic Domain Wall in Ferromagnetic Nanowires

Xiao-Ping Ma,Hong-Guang Piao,심제호,주하나 데데,김동현 한국물리학회 2013 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.62 No.2

We have investigated the dependence of the spontaneous dynamics of the magnetic domain wall in ferromagnetic nanowires on the initial position of the domain wall without any external field. Using micromagnetic simulations, we have observed in detail a spontaneous magnetic domain wall motion for various wire widths and thicknesses. We have found that the average speed of the spontaneous domain wall motion significantly depends on the wire width and thickness, as well as the starting position of the domain wall motion. We conclude that the spontaneous magnetic domain wall motion should be considered very carefully in practical design of spintronic devices based on magnetic domain wall motion.

Structural and Optical Properties of RF Magnetron Reactively Sputtered Ag2O Film

Xiao-Yong Gao,Jiao-Min Ma,Chao Chen,Meng-Ke Zhao,Jin-Hua Gu,Jing-Xiao Lu 한국물리학회 2012 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.60 No.5

A series of <111> oriented Ag2O films was deposited onto glass substrates by using RF magnetron reactive sputtering at different flow ratios (FRs) of oxygen to argon. The Ag2O film deposited at FR = 0.667 was the best <111> oriented film due to dual contributions from both lattice strain and film stress. The films’ transmissivity of over 70% in the near-infrared region indicated that Ag2O films are not suitable for applications as transparent conductive films in the visible region. Ag2O films deposited at FRs from 0.467 to 0.800 had optical band gaps ranging from 3.266 eV to 3.107 eV. The redshift in the films’ absorption edge may be attributed to the decrease in the lattice strain with increasing in FR. A series of <111> oriented Ag2O films was deposited onto glass substrates by using RF magnetron reactive sputtering at different flow ratios (FRs) of oxygen to argon. The Ag2O film deposited at FR = 0.667 was the best <111> oriented film due to dual contributions from both lattice strain and film stress. The films’ transmissivity of over 70% in the near-infrared region indicated that Ag2O films are not suitable for applications as transparent conductive films in the visible region. Ag2O films deposited at FRs from 0.467 to 0.800 had optical band gaps ranging from 3.266 eV to 3.107 eV. The redshift in the films’ absorption edge may be attributed to the decrease in the lattice strain with increasing in FR.

Clinical Evaluation of Tumor Markers for Diagnosis in Patients with Non-small Cell Lung Cancer in China

Ma, Li,Xie, Xiao-Wei,Wang, Hai-Yan,Ma, Ling-Yun,Wen, Zhong-Guang Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.12

Background: To evaluate the value of combined detection of serum carcinoembryonic antigen (CEA), cytokeratin 19 fragment (CYFRA21-1), and carbohydrateantigen 125 (CA125) for the clinical diagnosis of nonsmall cell lung cancer (NSCLC). Materials and Methods: Serum CEA, CYFRA21-1 and CA125 were assessed in 140 patients with NSCLC, 90 patients with benign lung disease and 90 normal control subjects, and differences of expression were compared in each group, and joint effects of these tumor markers in the diagnosis of NSCLC were analyzed. Results: Serum CEA, CYFRA21-1 and CA125 in patients with NSCLC were significantly higher than those with benign lung disease and normal controls (P<0.05). The sensitivity of CEA, CYFRA21-1 and CA125 were 49.45%, 59.67%, and 44.87% respectively. As expected, combinations of these tumor markers improved their sensitivity for NSCLC. The combined detection of CEA + CYFRA21-1 was the most cost-effective combination which had higher sensitivity and specificity in NSCLC. Elevation of serum CEA and CYFRA21-1 was significantly associated with pathological types (P<0.05) and elevation of serum CEA, CYFRA21-1 and CA125 was significantly associated with TNM staging (P<0.05). Conclusions: Single measurement of CEA, CYFRA21-1 and CA125 is of diagnostic value in the diagnosis of lung cancer, and a joint detection of these three tumor markers, could greatly improve the sensitivity of diagnosis on NSCLC. Combined detection of CEA + CYFRA21-1 proved to be the most economic and practical strategy in diagnosis of NSCLC, which can be used to screen the high-risk group.

Energy-Aware Virtual Data Center Embedding

( Xiao Ma ),( Zhongbao Zhang ),( Sen Su ) 한국정보처리학회 2020 Journal of information processing systems Vol.16 No.2

As one of the most significant challenges in the virtual data center, the virtual data center embedding has attracted extensive attention from researchers. The existing research works mainly focus on how to design algorithms to increase operating revenue. However, they ignore the energy consumption issue of the physical data center in virtual data center embedding. In this paper, we focus on studying the energy-aware virtual data center embedding problem. Specifically, we first propose an energy consumption model. It includes the energy consumption models of the virtual machine node and the virtual switch node, aiming to quantitatively measure the energy consumption in virtual data center embedding. Based on such a model, we propose two algorithms regarding virtual data center embedding: one is heuristic, and the other is based on particle swarm optimization. The second algorithm provides a better solution to virtual data center embedding by leveraging the evolution process of particle swarm optimization. Finally, experiment results show that our proposed algorithms can effectively save energy while guaranteeing the embedding success rate.

TERM LIMITS AND AUTHORITARIAN POWER SHARING: THEORY AND EVIDENCE FROM CHINA

Xiao Ma 동아시아연구원 2016 Journal of East Asian Studies Vol.16 No.1

Term limits that effectively govern leadership transition play an important role in authoritarian power sharing. A fixed term and a pre-appointed successor – two crucial components of term limits – credibly commit the incumbent ruler to share power with other elites, and also allow the elites to monitor and coordinate against the ruler's transgression of the power-sharing agreement. While the successful adoption of term limits often requires an even balance of power among the ruling elites in the first place, once adopted it initiates an evolving bargain over allocation of political power among multiple generations of leaders that further keeps any one faction from dominating the others. I corroborate this argument using a biographical dataset of elite members of the Chinese Communist Party from 1982 to 2012. The findings suggest that the Party's incumbent leaders and their rivals (i.e., predecessor and heir-apparent) shared equal chances in promoting their associates—which proxy their political influence—and this pattern has become more salient since the 16th party congress, when the term limits that currently govern China's leadership transition became fully fledged. This result also sheds light on the role of informal, patronage-based promotion in the institutionalization of authoritarian politics.