Chiba Institute of Technology

About: Chiba Institute of Technology is a education organization based out in Narashino, Japan. It is known for research contribution in the topics: RNA & Magnet. The organization has 2663 authors who have published 4999 publications receiving 56870 citations. The organization is also known as: Chiba kōgyō daigaku & Kōa Institute of Technology.

A new entropy model for RNA: part III. Is the folding free energy landscape of RNA funnel shaped?

Abstract: The concept of a free energy (FE) landscape, in which the conformations of a polymer progressively take on the structure of the native state while spiraling down a FE surface that resembles the shape of a funnel, has long been viewed as the reason why a complex protein structure forms so rapidly compared to the number of conformations available to it. On the other hand, this landscape picture is less clear with RNA due to the multiplicity of conformations and the uncertainties in the current thermodynamics. It is therefore sometimes proposed that within the ensemble of suboptimal states of the RNA molecule, the vast majority of those states all closely resemble the native state and therefore simply overwhelm the few states that represent the global minimum FE. However, calculations of the free energy of observed structures often suggest that the most frequently observed cluster of structures are far from the minimum FE, particularly in the case of long sequences. If so, then such a FE surface is unlikely to be funnel shaped. We have been developing a version of vsfold that can evaluate the suboptimal structures of the FE surface (through a modified version called vs_subopt ). Here we show that the ensemble of suboptimal structures for a number of known RNA structures can actually be both close to the minimum FE and also be the dominant observed structure when a proper Kuhn length is selected. Two state aptamers known as riboswitches can show neighboring FE states in the suboptimal structures that match the observed structures and their relative difference in FE is well within the range of the binding free energy of the metabolite. For the riboswitches and other short RNA sequences (less than 250 nt), the flow of the suboptimal structures (including pseudoknots) tended to resemble a rock rolling down a hill along the reaction coordinate axis. An important insight yielded by the cross-linking entropy (CLE) model is that the global entropy limits the size of domains. Hence, based on the CLE model, Levinthal’s paradox is overcome by the funnel shape in the FE, by a reduction in the number of degrees of freedom due to Kuhn length, and by limits on the size of the domains that can form. These concepts are also applicable to calculating transition rates between different suboptimal structures.

Additional harmonic losses of induction motors by PWM inverters: Comparison between result of finite element method and IEC/TS 60034

Abstract: In this study, we investigate the additional harmonic losses of induction motors driven by PWM inverters from both results of experiments and calculations. In the experiments, the additional loss caused by the inverter carrier is obtained by subtracting the total input of the motor driven by a sinusoidal power supply from that of the motor driven by the inverter. In the calculation, a combined 2-D and 1-D finite element method is applied in order to take into account the skin effect in electrical steel sheets used for the core. Then, the components of the additional motor loss are individually calculated according to their origins. Both the experimental and calculated results show that the total additional loss caused by the inverter decreases with an increase in the switching frequency and that the total additional loss does not depend on load conditions. These tendencies are exactly the same as that described in IEC/TS 60034. On the other hand, the finite element method reveals the variation in each loss component with switching frequency and load conditions. It is concluded that the variation in the additional loss with the switching frequency is mainly attributed to the variation in the core loss. In addition, the ratio of harmonic copper and rotor cage losses increase whereas that of harmonic core loss decreases with load because of an increase in the magnetic saturation at the rotor surface.

Nuclear electric dipole moments for the lowest 1 / 2 + states in Xe and Ba isotopes

Abstract: The electric dipole moments for the lowest $1/{2}^{+}$ states of Xe and Ba isotopes are calculated in terms of the nuclear shell model, which includes two-body nucleon interactions violating parity and time-reversal invariance. Using the wave functions thus obtained, the nuclear electric dipole moments arising from the intrinsic nucleon electric dipole moments and also from asymmetric charge distribution are calculated. The upper limits for the nuclear electric dipole moments of Xe and Ba isotopes are estimated.

Hot spot of structural ambivalence in prion protein revealed by secondary structure principal component analysis.

Abstract: The conformational conversion of proteins into an aggregation-prone form is a common feature of various neurodegenerative disorders including Alzheimer’s, Huntington’s, Parkinson’s, and prion diseases. In the early stage of prion diseases, secondary structure conversion in prion protein (PrP) causing β-sheet expansion facilitates the formation of a pathogenic isoform with a high content of β-sheets and strong aggregation tendency to form amyloid fibrils. Herein, we propose a straightforward method to extract essential information regarding the secondary structure conversion of proteins from molecular simulations, named secondary structure principal component analysis (SSPCA). The definite existence of a PrP isoform with an increased β-sheet structure was confirmed in a free-energy landscape constructed by mapping protein structural data into a reduced space according to the principal components determined by the SSPCA. We suggest a “spot” of structural ambivalence in PrP—the C-terminal part of helix 2—tha...

Fair news reader: recommending news articles with different sentiments based on user preference

Abstract: We have developed a news portal site called Fair News Reader (FNR) that recommends news articles with different sentiments for a user in each of the topics in which the user is interested FNR can detect various sentiments of news articles, and determine the sentimetal preferences of a user based on the sentiments of previously read articles by the user While there are many news portal sites on the Web, such as GoogleNews, Yahoo!, and MSN News, they can not recommend and present news articles based on the sentiments they are likely to create since they simply select articles based on whether they contain user-specified keywords FNR collects and recommends news articles based on the topics in which the user is interested and the sentiments the articles are likely to create Eight of the sentiments each article is likely to create are represented by an "article vector" with four elements Each element corresponds to a measure consisting of two symmetrical sentiments The sentiments of the articles previously read with respect to a topic are then extracted and represented as a "user vector" Finally, based on a comparison between the user and article vectors in each topic, FNR recommends articles that have symmetric sentiments against the sentiments of read articles by the user for fair reading about the topic Evaluation of FNR using two experiments showed that the user vectors can be determined by FNR based on the sentiments of the read articles about a topic and that it can provide a unique interface with categories containing the recommended articles