Search results for: Maenaka Katsumi

Authors: Sundaram Arulmozhiraja, Kanade Shimizu, Yuta Yamamoto, Satoshi Ichikawa, Maenaka Katsumi, Hiroaki Tokiwa

Abstract:

Drug discovery is shifting from small molecule based drugs targeting local active site to middle molecules (MM) targeting large, flat, and groove-shaped binding sites, for example, protein-protein interface because at least half of all targets assumed to be involved in human disease have been classified as “difficult to drug” with traditional small molecules. Hence, MMs such as peptides, natural products, glycans, nucleic acids with various high potent bioactivities become important targets for drug discovery programs in the recent years as they could be used for ‘undruggable” intracellular targets. Cell membrane permeability is one of the key properties of pharmacodynamically active MM drug compounds and so evaluating this property for the potential MMs is crucial. Computational prediction for cell membrane permeability of molecules is very challenging; however, recent advancement in the molecular dynamics simulations help to solve this issue partially. It is expected that MMs with high membrane permeability will enable drug discovery research to expand its borders towards intracellular targets. Further to understand the chemistry behind the permeability of MMs, it is necessary to investigate their conformational changes during the permeation through membrane and for that their interactions with the membrane field should be studied reliably because these interactions involve various non-bonding interactions such as hydrogen bonding, -stacking, charge-transfer, polarization dispersion, and non-classical weak hydrogen bonding. Therefore, parameters-based classical mechanics calculations are hardly sufficient to investigate these interactions rather, quantum mechanical (QM) calculations are essential. Fragment molecular orbital (FMO) method could be used for such purpose as it performs ab initio QM calculations by dividing the system into fragments. The present work is aimed to study the cell permeability of middle molecules using molecular dynamics simulations and FMO-QM calculations. For this purpose, a natural compound syringolin and its analogues were considered in this study. Molecular simulations were performed using NAMD and Gromacs programs with CHARMM force field. FMO calculations were performed using the PAICS program at the correlated Resolution-of-Identity second-order Moller Plesset (RI-MP2) level with the cc-pVDZ basis set. The simulations clearly show that while syringolin could not permeate the membrane, its selected analogues go through the medium in nano second scale. These correlates well with the existing experimental evidences that these syringolin analogues are membrane-permeable compounds. Further analyses indicate that intramolecular -stacking interactions in the syringolin analogues influenced their permeability positively. These intramolecular interactions reduce the polarity of these analogues so that they could permeate the lipophilic cell membrane. Conclusively, the cell membrane permeability of various middle molecules with potent bioactivities is efficiently studied using molecular dynamics simulations. Insight of this behavior is thoroughly investigated using FMO-QM calculations. Results obtained in the present study indicate that non-bonding intramolecular interactions such as hydrogen-bonding and -stacking along with the conformational flexibility of MMs are essential for amicable membrane permeation. These results are interesting and are nice example for this theoretical calculation approach that could be used to study the permeability of other middle molecules. This work was supported by Japan Agency for Medical Research and Development (AMED) under Grant Number 18ae0101047.

Keywords: fragment molecular orbital theory, membrane permeability, middle molecules, molecular dynamics simulation

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Authors: Katsumi Hirata

Abstract:

Certain systems can function well only if they recognize the sound environment as humans do. In this research, we focus on sound classification by adopting a convolutional neural network and aim to develop a method that automatically classifies various environmental sounds. Although the neural network is a powerful technique, the performance depends on the type of input data. Therefore, we propose an approach via a slice bispectrogram, which is a third-order spectrogram and is a slice version of the amplitude for the short-time bispectrum. This paper explains the slice bispectrogram and discusses the effectiveness of the derived method by evaluating the experimental results using the ESC‑50 sound dataset. As a result, the proposed scheme gives high accuracy and stability. Furthermore, some relationship between the accuracy and non-Gaussianity of sound signals was confirmed.

Keywords: environmental sound, bispectrum, spectrogram, slice bispectrogram, convolutional neural network

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Authors: Katsumi Hirata

Abstract:

To develop the useful acoustic environmental recognition system, the method of estimating 3D-position of a stationary random acoustic source using bispectral analysis of 4-point detected signals is proposed. The method uses information about amplitude attenuation and propagation delay extracted from amplitude ratios and angles of auto- and cross-bispectra of the detected signals. It is expected that using bispectral analysis affects less influence of Gaussian noises than using conventional power spectral one. In this paper, the basic principle of the method is mentioned first, and its validity and features are considered from results of the fundamental experiments assumed ideal circumstances.

Keywords: 4-point detection, a stationary random acoustic source, auto- and cross-bispectra, estimation of 3D-position

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Authors: Takahiro Nishigaki, Katsumi Nitta, Takashi Onoda

Abstract:

In this paper, we present a method of applying Independent Topic Analysis (ITA) to increasing the number of document data. The number of document data has been increasing since the spread of the Internet. ITA was presented as one method to analyze the document data. ITA is a method for extracting the independent topics from the document data by using the Independent Component Analysis (ICA). ICA is a technique in the signal processing; however, it is difficult to apply the ITA to increasing number of document data. Because ITA must use the all document data so temporal and spatial cost is very high. Therefore, we present Incremental ITA which extracts the independent topics from increasing number of document data. Incremental ITA is a method of updating the independent topics when the document data is added after extracted the independent topics from a just previous the data. In addition, Incremental ITA updates the independent topics when the document data is added. And we show the result applied Incremental ITA to benchmark datasets.

Keywords: text mining, topic extraction, independent, incremental, independent component analysis

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Authors: Yuhao Jin, Zhou Zhou, Katsumi Yoshida, Zhengcao Li, Tadashi Maruyama, Toyohiko Yano

Abstract:

Four kinds of nuclear graphite, IG-110U, ETP-10, CX-2002U and IG-430U were neutron-irradiated at different fluences and temperatures, ranged from 1.38 x 1024 to 7.4 x 1025 n/m2 (E > 1.0 MeV) at 473K, 573K and 673K. To take into account the disorder in the microstructure, such as stacking faults and anisotropic coherent lengths, the X-ray diffraction patterns were interpreted using a comprehensive structural model and a refinement program CARBONXS. The deduced structural parameters show the changes of lattice parameters, coherent lengths along the c-axis and the basal plane, and the degree of turbostratic disorder as a function of the irradiation dose. Our results reveal neutron irradiation effects on the microstructure and macroscopic dimension, which are consistent with previous work. The methodology used in this work enables the quantification of the damage on the microstructure of nuclear graphite induced by neutron irradiation.

Keywords: nuclear graphite, neutron irradiation, thermal annealing, recovery behavior, dimensional change, CARBONX, XRD analysis

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Authors: Katsumi Hirano, Yusuke Kakuta, Koji Yoshida, Shozo Itagaki, Masahiko Kajioka, Toshihiko Okada

Abstract:

A conversion technology of cellulosic biomass and waste plastics to liquid fuel at low pressure and low temperature has been investigated. This study aims at the production of the liquefied fuel (CPLF) of substituting diesel oil by mixing cellulosic biomass and waste plastics in the presence of solvent. Co-liquefaction of cellulosic biomass (Japan cedar) and polypropylene (PP) using wood tar or mineral oil as solvent at 673K with an autoclave was carried out. It was confirmed that the co-liquefaction gave CPLF in a high yield among the cases of wood or of polypropylene Which was ascribed the acceleration of decomposition of plastics by radicals derived from the decomposition of wood. The co-liquefaction was also conducted by a small twin screw extruder. It was found that CPLF was obtained in the co-liquefaction, And the acceleration of decomposition of plastics in the presence of cellulosic biomass. The engine test of CPLF showed that the engine performances, Compression ignition and combustion　characteristics were almost similar to those of diesel fuel at any mixing ratio of CPLF and any load, Therefore, CPLF could be practically used as alternative fuel for diesel engines.

Keywords: Cellulosic Biomass, Co-liquefaction, Solvent, Waste Plastics

Procedia PDF Downloads 372

Authors: Katsumi Mera

Abstract:

The purpose of this study was to clarify the relationship between strengths/weaknesses on studying and subjective well-being among Japanese working adults. We conducted an online questionnaire survey of Japanese working adults (aged 20-69) and obtained 1,063 valid responses. Subjective well-being was evaluated using the Cantril Self-Anchoring Striving Scale, the method used in the World Happiness Survey, in which the highest possible life is set at 10, and the lowest possible life is set at 0. The mean subjective well-being of all 1,063 respondents was 5.87, which is a very similar value that was obtained in the Japanese World Happiness Survey in 2023. First, we investigated the respondents' strengths/weaknesses in studying and their subjective well-being. The results showed that the subjective well-being of the group who answered that they were good at studying (6.62) was significantly higher than that of the group who answered that they were poor at studying (5.15). Next, we investigated the subjective well-being of students who answered that they were good at Japanese, Math, English, Social studies, and Science, the major subjects in Japan, and found that the subjective well-being of the group that answered that they were good at these subjects was higher than that of the group that answered that they were poor at these subjects. When the correlation between the score of "strengths/weaknesses on studying" and the score of "subjective well-being" was examined, those who answered that they were good at studying had higher subjective well-being (correlation coefficient r = 0.26, p < 0.001). The correlation between the subjective well-being score and the score of "strengths/weaknesses on studying each subject” was examined. Among the subjects, the subjective well-being score was the highest for those who answered that they were good at English (correlation coefficient r = 0.17, p < 0.001). These results indicate a relationship between strengths/weaknesses on studying and subjective well-being among workers in Japan. These findings may provide an important basis for considering what kind of education should be focused on in order to nurture working adults with high levels of well-being.

Keywords: subject well-being, strengths/weaknesses, studying, Japanese working adults

Procedia PDF Downloads 78