Using radial basis function networks and significance testing to select effective siRNA sequences

Although short interfering RNA (siRNA) has been widely used for studying gene functions in mammalian cells, its gene silencing efficacy varies markedly and there are only a few consistencies among the recently reported design rules/guidelines for selecting siRNA sequences effective for mammalian genes. We propose a method for selecting effective siRNA target sequences by using a radial basis function (RBF) network and statistical significance analysis for a large number of known effective and ineffective siRNAs. The siRNA classification is first carried out by using the RBF network and then the preferred and unpreferred nucleotides for effective siRNAs at individual positions are chosen by significance testing. The gene degradation measure is defined as a score based on the preferred and unpreferred nucleotides. The effectiveness for the proposed method was confirmed by evaluating effective and ineffective siRNAs for the recently reported genes (15 genes, 196 sequences) and comparing the scores thus obtained with those obtained using other scoring methods. Since the score is closely correlated with the degree of gene degradation, it can easily be used for selecting high-potential siRNA candidates. The evaluation results indicate that the proposed method may be applicable for many other genes. It will therefore be useful for selecting siRNA sequences in mammalian genes.     

Improving cache attacks by considering cipher structure

A concrete attack using side channel information from cache memory behaviour was proposed for the first time at ISITA 2002. The attack uses the difference between execution times associated with S-box cache-hits and cache-misses to recover the intermediate key. Recently, a theoretical estimation of the number of messages needed for the attack was proposed and it was reported that the average method obtains key information with fewer messages than maximum threshold or intermediate threshold method. Taking the structure of cipher into account, this paper provided the cache attack in which the average method is embodied, and provides improved key estimation. This paper includes the study on the attack that exploits internal collision. Yukiyasu Tsunoo received his BE degree from Waseda University in 1982, MS degree from JAIST, Dr.Eng from Chuo University. He joined NEC Software Hokuriku, Ltd. in 1985. He is now a research fellow of NEC Internet Systems Research Laboratories. He is engaged in the designing of common key ciphers and the study of evaluation technique. Dr. Tsunoo is a member of the Expert Commission of Information Security Research, The Institute of Electronics, Information and Communication Engineers, the Information Processing Society of Japan, the Japan Society for Security Management and the Atomic Energy Society of Japan. Etsuko Tsujihara received her BS degree from Aoyama Gakuin University in 1983. She joined NEC in 1983. She developed the VLSI automatic layout system. She joined NEC Software Hokuriku Ltd. in 1986 and Y.D.K. Co. Ltd. in 2004. She is engaged in the designing of common key ciphers and the study of evaluation technique. Maki Shigeri received her BE degree from University of Tsukuba in 1992. She joined NEC Software Hokuriku Ltd. in 1992. She is engaged in the designing of common key ciphers and the study of evaluation technique. Hiroyasu Kubo received his BE degree from Kanazawa Institute of Technology in 1990. He joined NEC Software Hokuriku Ltd. in 1990. He is engaged in the designing of common key ciphers and the study of evaluation technique. Kazuhiko Minematsu received his BS degree from Waseda University in 1996, MS degree in 1998 and joined NEC in 1998. He is engaged in the designing of common key ciphers and research on block cipher modes of operations. He is a member of the Information Processing Society of Japan, the Society of Information Theory and Its Applications.     

Computation of high Prandtl number turbulent thermal fields by the analytical wall-function

The extended version of the analytical wall-function (AWF) for rough wall turbulence by Suga et al. [K. Suga, T.J. Craft, H. Iacovides, An analytical wall-function for turbulent flows and heat transfer over rough walls. Int. J. Heat Fluid Flow 27 (2006) 852–866] is improved for high Prandtl number flows. The original AWF assumes a linear profile of turbulent viscosity near a wall though it is widely recognised that a theoretically correct cubic profile of the turbulent viscosity is essential for heat transfer of high Prandtl number flows. In order to predict thermal boundary layer of high Prandtl number fluid flows, the present approach thus employs a correct limiting profile of the turbulent viscosity in the analytical integration process. The presently proposed version of the AWF proves its good performance for predicting turbulent high Prandtl number thermal flows at Pr  4 × 10⁴ for smooth wall cases, and at least at Pr  10 for rough wall cases.     

Aircraft measurement of organic aerosols over China

Lower to middle (0.5-3.0 km altitude) tropospheric aerosols (PM2.5) collected by aircraft over inland and east coastal China were, for the first time, characterized for organic molecular compositions to understand anthropogenic, natural, and photochemical contribution to the air quality. n-Alkanes, fatty acids, sugars, polyacids are detected as major compound classes, whereas lignin and resin products, sterols, polycyclic aromatic hydrocarbons, and phthalic acids are minor species. Average concentrations of all the identified compounds excluding malic acid correspond to 40-50% of those reported on the ground sites. Relative abundances of secondary organic aerosol (SOA) components such as malic acid are much higher in the aircraft samples, suggesting an enhanced photochemical production over China. Organic carbon (OC) concentrations in summer (average, 24.3 microg m(-3)) were equivalent to those reported on the ground sites. Higher OC/EC (elemental carbon) ratios in the summer aircraft samples also support a significant production of SOA over China. High loadings of organic aerosols in the Chinese troposphere may be responsible to an intercontinental transport of the pollutants and potential impact on the regional and global climate changes.     

Exploiting small molecule binding to DNA for the detection of single-nucleotide mismatches and their base environment

Naphthyridine-azaquinolone (Npt-Azq, described previously by Nakatani et al. ( Nakatani, K.; Hagihara, S.; Goto, Y.; Kobori, A.; Hagihara, M.; Hayashi, G.; Kyo, M.; Nomura, M.; Mishima, M.; Kojima, C. Nat. Chem. Biol. 2005, 1, 39-43.), was exploited to detect an adenine-adenine mismatch with a symmetrical G-C flanking sequence (5'-GAC-3'/5'-CAG-3') in a synthetic 20-mer DNA by electrochemical impedance spectroscopy. This innovative strategy enables us to obtain information about the presence of a specific mismatch in addition to sequence information. Npt-Azq binds the G-A region of the mismatch, which causes significant changes in the structure of the DNA, which in turn causes changes in the electrochemical properties of DNA/Npt-Azq films. For a 20-mer DNA containing an A-A mismatch, the electron-transfer resistance (RCT) of the system is significantly different in the presence of bound Npt-Azq, presumably due to the structural differences in the two films. Npt-Azq does not bind to matched DNA, and thus, the presence of Npt-Azq does not affect the electrochemical properties of such films.     

Swelling properties and coefficient of permeability of friction-reducing polymer for pull-out of temporary sheet piles

Harmful cracks and settlements occur after the pull-out removal of temporary sheet piles. This is because a large amount of soil is discharged from the ground due to the significant skin friction at the steel surface. In order to prevent these cracks and settlement problems, a friction-reducing polymer was developed. After a sheet pile coated with the polymer is installed into the ground; the polymer absorbs ground water and transforms to a swollen gel layer which separates the soil and the sheet piles. In this investigation, a newly designed column type test apparatus was used to simulate ground conditions. The swelling test was carried out, followed by a continuous permeability test. Based on the obtained test results, the swelling properties and coefficient of permeability of the friction-reducing polymer in the ground were determined. The main conclusions are as follows. The values of the water-absorbing ratio, Ra_max, decrease with increasing earth pressure, p′, independent of the pore water pressure, u. Equations to determine the values of Ra_max are proposed as functions of p′ only. The maximum swelling pressure, at which the friction-reducing polymer cannot absorb water and swell, is p′_max?=?560?kPa. Even at a depth of approximately 100?m, the polymer absorbs ground water, and the swollen gel layer forms. The approximate range of coefficient of permeability, k, of the swollen gel layer is 10^?13–10^?11 m/s; these are extremely small values. The swollen gel can be considered an impermeable material. Depth distributions of the thickness and the coefficient of permeability of the swollen gel layer are illustrated in practical charts, based on the test results.     

Genome Mining of the Hitachimycin Biosynthetic Gene Cluster: Involvement of a Phenylalanine‐2,3‐aminomutase in Biosynthesis

Hitachimycin is a macrolactam antibiotic with (S)‐β‐phenylalanine (β‐Phe) at the starter position of its polyketide skeleton. To understand the incorporation mechanism of β‐Phe and the modification mechanism of the unique polyketide skeleton, the biosynthetic gene cluster for hitachimycin in Streptomyces scabrisporus was identified by genome mining. The identified gene cluster contains a putative phenylalanine‐2,3‐aminomutase (PAM), five polyketide synthases, four β‐amino‐acid‐carrying enzymes, and a characteristic amidohydrolase. A hitA knockout mutant showed no hitachimycin production, but antibiotic production was restored by feeding with (S)‐β‐Phe. We also confirmed the enzymatic activity of the HitA PAM. The results suggest that the identified gene cluster is responsible for the biosynthesis of hitachimycin. A plausible biosynthetic pathway for hitachimycin, including a unique polyketide skeletal transformation mechanism, is proposed.     

Optimization layout of viscous dampers and its application in retrofitting of a high-rise steel structure

阻尼器优化布置是结构减震设计过程中的重要环节，通常需要通过多次动力响应计算来完成。为此，提出了一种通过结构静力分析确定阻尼器合理布置位置的方法，并能够快速计算出优化方案的附加阻尼比。将该方法应用于一栋位于日本东京都新宿区29层钢结构建筑的减震加固设计中，分析了该建筑的强震观测系统在日本“311地震”中采集到的部分楼层加速度时程数据，并基于分析结果验证了所建立的非线性数值分析模型的可靠性。采用所提方法对结构进行减震加固，得到双向共64个阻尼器的优化布置方案及其附加阻尼比，并通过动力方法对结果进行了验证。同时针对长周期及长持时特性的地震波，对减震结构进行动力弹塑性时程分析，评估其抗震性能。分析结果表明：减震优化方案的减震效果明显，结构整体地震反应和构件损伤较非减震方案都大大减小；减震优化方案有效改善了高层钢结构楼层变形不均匀的情况，层间位移角均满足小于1/100的性能要求；通过减震优化后大部分钢支撑和钢梁的塑性率都降低至小于1。     

Formation of Hexagonal Metastable Phases from an Undercooled LuFeO3 Melt in an Atmosphere with Low Oxygen Partial Pressure

Controlling the oxygen partial pressure ( P _O2) in the ambient atmosphere is an important parameter for material processing because the transition metal ion changes its valence depending on P _O2. In the present study, containerless solidification of the LuFeO₃ melt, where the undercooling level can be treated as another experimental parameter, was carried out in order to explore the unidentified metastable phases under the controlled P _O2 using an aerodynamic levitator. Decreasing P _O2 down to 1 × 10³ Pa, the unidentified phase was solidified from the undercooled melt. The X-ray diffractometry results after annealing at 1 × 10³ Pa showed the peak profile of the stable perovskite LuFeO₃ phase, suggesting that this unidentified phase was thermodynamically metastable. Thermogravimetric analysis showed that the mass of the sample solidified at P _O2= 1 × 10³ Pa significantly increased, suggesting that the formation of the metastable phases might be related to the presence of Fe²⁺ ions.     

Hydrogen production by oxidative methanol reforming with various oxidants over Cu-based catalysts

In order to improve the start-up property of a small hydrogen producer with a micro methanol reformer, oxidative methanol reforming (OMR) with various oxidants over copper-based catalysts was examined. The addition of Fe to a Cu/ZnO/Al₂O₃ catalyst resulted in higher catalyst durability, with a slight improvement in catalytic activity, for OMR with air. However, the addition of larger amounts of Fe inhibited further improvement of catalytic performance, possibly due to the formation of less active CuFe₂O₄ spinel in the catalyst. The production of hydrogen by OMR with hydrogen peroxide as an alternative oxidant, which has the potential to provide concentrated hydrogen without nitrogen dilution, was also considered. It was found that hydrogen peroxide is an effective oxidant for OMR over copper-based catalysts due to its ability to suppress CO formation and its improving effect on methanol conversion.