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Search Results: 1 - 10 of 981 matches for " Ryota Nomura "
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Constructing a Coactivation Model for Explaining Humor Elicitation  [PDF]
Ryota Nomura, Shunichi Maruno
Psychology (PSYCH) , 2011, DOI: 10.4236/psych.2011.25074
Abstract: The present study first aimed to construct a coactivation model that integrates cognitive and motivational variables that determine an individual’s conscious humor experience. It then aimed to test the model’s reliability, validity, and generalizability. As part of the study, 16 (out of 48) four-frame cartoons were randomly presented to 201 (42 male and 159 female) high school students and 302 (185 male and 117 female) undergraduate and graduate students (age range was 15 to 23, M = 18.15, SD = 1.79) who were instructed to rate items related to the variable humor. Using structural equation modeling (SEM), the generalizability of the model to predict the humor experience to a great extent within different population samples was shown. Furthermore, the theoretical prediction of the coactivation model was supported. The results are discussed from the viewpoint of future research that could demonstrate the possible application of the coactivation model.
Disorder effects on thermal transport on the surface of topological superconductors by the self-consistent Born approximation
Ryota Nakai,Kentaro Nomura
Physics , 2013, DOI: 10.1103/PhysRevB.89.064503
Abstract: We have studied the longitudinal thermal conductivity of the surface of a three-dimensional time-reversal symmetric topological superconductor with random disorder. Majorana fermions on the surface of topological superconductors have a response to the gravitational field, which is realized as a thermal response to the temperature gradient inside of the material. Because of the presence of both time-reversal symmetry and particle-hole symmetry, disorder on the surface emerges in the Hamiltonian only as spatial deformations of the pair potential. In terms of the gravitational field, the disorder results in spatial fluctuations of the metric. We consider disorder effects on the thermal conductivity perturbatively within the self-consistent Born approximation. The density of states is calculated with the Green's function technique and the thermal conductivity of the surface modes is derived through the electronic conductivity using Wiedemann-Franz law for the Majorana fermions.
DFT Calculations on the Effect of Solvation on the Tautomeric Reactions for Wobble Gua-Thy and Canonical Gua-Cyt Base-Pairs  [PDF]
Kazuya Nomura, Ryota Hoshino, Eisuke Shimizu, Yasuhiro Hoshiba, Victor I. Danilov, Noriyuki Kurita
Journal of Modern Physics (JMP) , 2013, DOI: 10.4236/jmp.2013.43A059
Abstract:

To elucidate the reaction mechanism from wobble Guanine-Thymine (wG-T) to tautomeric G-T base-pairs, we investigate its transition state (TS) by density functional theory (DFT) calculations, in vacuum and in water approximated by continuum solvation model. From the comparison of these results, we attempt to elucidate the effect of solvation on the tautomeric reaction for wG-T. In addition, the same DFT calculations are performed for the canonical G-C base-pair, in order to reveal the difference in the activation energy for the reactions involving wG-T and G-C. The obtained TS structures between wG-T and G*-T/G-T* (asterisk is an enol-form of base) are almost the same in vacuum and in water. However, the activation energy is 16.6 and 19.1 kcal/mol in vacuum and in water, respectively, indicating that the effect of solvation enlarges the energy barrier for the reactions from wG-T to G-T*/G*-T. The activation energy for the tautomeric reaction from G-C to G*-C* is also evaluated to be 15.8 and 12.9 kcal/mol in vacuum and in water, respectively. Therefore, it is expected that the tautomeric reaction from wG-T to G*-T/G-T* can occur in vacuum with a similar probability as that from G-C to G*-C*. We furthermore investigate the TS structure for wG-BrU to reveal the effect of the BrU introduction into wG-T. The activation energy is 14.5 and 16.7 kcal/mol in vacuum and in water, respectively. Accordingly, the BrU introduction is found to increase the probability of the tautomeric reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G bases is accelerated by the introduction of wG-BrU base-pair.

DFT Study on Reaction Mechanism of DNA Base Pair with Hydroxyl Radical  [PDF]
Eisuke Shimizu, Ryota Hoshino, Kazuya Nomura, Victor I. Danilov, Noriyuki Kurita
Journal of Modern Physics (JMP) , 2013, DOI: 10.4236/jmp.2013.43A062
Abstract:

In order to elucidate the indirect effect by radiation on DNA base pairs, we investigate the mechanism for the attacking reaction of a hydroxyl radical (·OH-radical) to the G-C and A-T base pairs, by the density functional theory (DFT) calculations. The effect of solvation on the mechanism is also revealed by performing the same DFT calculations under the continuum solvation approximation. We find the stable structures for the dehydrogenated G-C and A-T base pairs, in which the hydrogen atom of NH2 group of G or A base is abstracted by the ·OH-radical. The solvation around the base pairs stabilizes the dehydrogenated structures significantly, indicating the acceleration of the attacking reaction by ·OH-radical to the base pairs in water. Therefore, we conclude that the hydrogen atom of the NH2 group of G or A base in the G-C and A-T base pairs is the most preferably abstracted by the ·OH-radical in living cells.

Finite-temperature effective field theory of the quantized thermal Hall effect
Ryota Nakai,Shinsei Ryu,Kentaro Nomura
Physics , 2015,
Abstract: A finite-temperature effective free energy of a quantized thermal Hall system is derived microscopically from the two-dimensional Dirac fermion coupled with a gravitational field. In two spatial dimensions, the thermal Hall conductivity of fully gapped insulators and superconductors is quantized and given by the bulk Chern number, in analogy to the quantized electric Hall conductivity in quantum Hall systems. From the perspective of effective action functionals, two distinct types of the field theory have been proposed to describe the quantized thermal Hall effect. One of these, known as the gravitational Chern-Simons action, is a kind of topological field theory, and the other is a phenomenological theory relevant to the Str\v{e}da formula. In this paper, we consider the two-dimensional Dirac fermion under a static background gravitational field in equilibrium at a finite temperature, and derive microscopically an effective free energy functional of the gravitational field of a Lorentz invariant system by tracing out the Dirac fermionic degrees of freedom. The bulk effective theory is consistently determined via the boundary effective theory of the chiral boundary mode. This bulk effective free energy generates an energy current flowing perpendicular and proportional to the gradient of the gravitational potential, which turns out to represent the quantized thermal Hall effect using Luttinger's argument.
Distribution of periodontopathic bacterial species in Japanese children with developmental disabilities
Shuhei Naka, Aki Yamana, Kazuhiko Nakano, Rena Okawa, Kazuyo Fujita, Ayuchi Kojima, Hirotoshi Nemoto, Ryota Nomura, Michiyo Matsumoto, Takashi Ooshima
BMC Oral Health , 2009, DOI: 10.1186/1472-6831-9-24
Abstract: A total of 187 children (136 boys, 51 girls) aged 1-6 years old and diagnosed with such disabilities as mental retardation, cerebral palsy, and autism, participated in the study. Subgingival dental plaque specimens were collected from the buccal side of the maxillary left second primary molar after a clinical examination. Bacterial DNA was extracted from the specimens and PCR analyses were carried out to detect 10 selected periodontopathic species using specific primers for each. In addition, statistical analyses were performed to analyze the correlations among clinical parameters and the detected species.The most frequently detected species was Capnocytophaga sputigena (28.3%), followed by Aggregatibacter actinomycetemcomitans (20.9%) and Campylobacter rectus (18.2%). Eikenella corrodens, Capnocytophaga ochracea, and Prevotella nigrescence were detected in approximately 10% of the specimens, whereas Treponema denticola, Tannerella forsythia, and Prevotella intermedia were rarely found, and Porphyromonas gingivalis was not detected in any of the subjects. The total numbers of detected species were positively correlated with the age of the subjects. There were 10 subjects with positive reactions for T. denticola and/or T. forsythia, in whom the total number of bacterial species was significantly higher as compared to the other subjects. Furthermore, subjects possessing C. rectus showed significantly greater values for periodontal pocket depth, gingival index, and total number of species.We found that approximately one-fourth of the present subjects with disabilities who possessed at least one of T. denticola, T. forsythia, and C. rectus were at possible risk for periodontitis. Follow-up examinations as well as preventive approaches should be utilized for such individuals.Gingivitis is the most common periodontal disease among children and its primary etiological factor is considered to be bacterial plaque [1]. Studies of bacterial profiles in dental plaque specimens
Rapid Algorithm for Independent Component Analysis  [PDF]
Ryota Yokote, Yasuo Matsuyama
Journal of Signal and Information Processing (JSIP) , 2012, DOI: 10.4236/jsip.2012.33037
Abstract: A class of rapid algorithms for independent component analysis (ICA) is presented. This method utilizes multi-step past information with respect to an existing fixed-point style for increasing the non-Gaussianity. This can be viewed as the addition of a variable-size momentum term. The use of past information comes from the idea of surrogate optimization. There is little additional cost for either software design or runtime execution when past information is included. The speed of the algorithm is evaluated on both simulated and real-world data. The real-world data includes color images and electroencephalograms (EEGs), which are an important source of data on human-computer interactions. From these experiments, it is found that the method we present here, the RapidICA, performs quickly, especially for the demixing of super-Gaussian signals.
Blackening of the Surfaces of Mesopotamian Clay Tablets Due to Manganese Precipitation  [PDF]
Etsuo Uchida, Ryota Watanabe
Archaeological Discovery (AD) , 2014, DOI: 10.4236/ad.2014.24012
Abstract: Blackening was observed on the surfaces of Mesopotamian clay tablets from Umma, Dilbat, Larsa, Ur, Babylon, Uruk, Sippar, and Nippur produced between the Third Dynasty of Ur and the Early Achaemenid Dynasty. Portable X-ray fluorescence analysis revealed that manganese was concentrated on the blackened surfaces. Rod-shaped materials with a length of 100 - 200 nm and a width of 30 nm were observed using a field emission scanning electron microscope. Distinct peaks were not necessarily obtained by micro-X-ray diffractometer analysis, but several samples of the black material showed peaks identifiable as buserite. These results may suggest that blackening on the surfaces of the clay tablets can be ascribed to the activity of manganese-oxidizing microbe. However, the size of the rod-shaped materials is too small compared to common bacteria.
Code Clone Detection Method Based on the Combination of Tree-Based and Token-Based Methods  [PDF]
Ryota Ami, Hirohide Haga
Journal of Software Engineering and Applications (JSEA) , 2017, DOI: 10.4236/jsea.2017.1013051
Abstract: This article proposes the high-speed and high-accuracy code clone detection method based on the combination of tree-based and token-based methods. Existence of duplicated program codes, called code clone, is one of the main factors that reduces the quality and maintainability of software. If one code fragment contains faults (bugs) and they are copied and modified to other locations, it is necessary to correct all of them. But it is not easy to find all code clones in large and complex software. Much research efforts have been done for code clone detection. There are mainly two methods for code clone detection. One is token-based and the other is tree-based method. Token-based method is fast and requires less resources. However it cannot detect all kinds of code clones. Tree-based method can detect all kinds of code clones, but it is slow and requires much computing resources. In this paper combination of these two methods was proposed to improve the efficiency and accuracy of detecting code clones. Firstly some candidates of code clones will be extracted by token-based method that is fast and lightweight. Then selected candidates will be checked more precisely by using tree-based method that can find all kinds of code clones. The prototype system was developed. This system accepts source code and tokenizes it in the first step. Then token-based method is applied to this token sequence to find candidates of code clones. After extracting several candidates, selected source codes will be converted into abstract syntax tree (AST) for applying tree-based method. Some sample source codes were used to evaluate the proposed method. This evaluation proved the improvement of efficiency and precision of code clones detecting.
Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content
Fumito Maruyama, Mitsuhiko Kobata, Ken Kurokawa, Keishin Nishida, Atsuo Sakurai, Kazuhiko Nakano, Ryota Nomura, Shigetada Kawabata, Takashi Ooshima, Kenta Nakai, Masahira Hattori, Shigeyuki Hamada, Ichiro Nakagawa
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-358
Abstract: We have sequenced the complete genome of S. mutans serotype c strain NN2025, and compared it with the genome of UA159. The NN2025 genome is composed of 2,013,587 bp, and the two strains show highly conserved core-genome. However, comparison of the two S. mutans strains showed a large genomic inversion across the replication axis producing an X-shaped symmetrical DNA dot plot. This phenomenon was also observed between other streptococcal species, indicating that streptococcal genetic rearrangements across the replication axis play an important role in Streptococcus genetic shuffling. We further confirmed the genomic diversity among 95 clinical isolates using long-PCR analysis. Genomic diversity in S. mutans appears to occur frequently between insertion sequence (IS) elements and transposons, and these diversity regions consist of restriction/modification systems, antimicrobial peptide synthesis systems, and transporters. S. mutans may preferentially reject the phage infection by clustered regularly interspaced short palindromic repeats (CRISPRs). In particular, the CRISPR-2 region, which is highly divergent between strains, in NN2025 has long repeated spacer sequences corresponding to the streptococcal phage genome.These observations suggest that S. mutans strains evolve through chromosomal shuffling and that phage infection is not needed for gene acquisition. In contrast, S. pyogenes tolerates phage infection for acquisition of virulence determinants for niche adaptation.The genomic heterogeneity within a bacterial species reflects its lifestyle, the niche it occupies, and its exposure to mobile elements, such as bacteriophages and plasmids [1]. Even though organisms belonging to the same genus/species have a common gene set (the core genome), individual organisms differ (strain-specific genes) in ways representative of the physiological and virulence properties of an organism [2,3]. Although not all genetic differences between strains are important for niche adapta
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