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MODELING GENETIC REGULATORY NETWORKS:A DELAY DISCRETE DYNAMICAL MODEL APPROACH

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Journal of Systems Science & Complexity 2012年第6期25卷 1052-1067页

作者： Hao JIANG Wai-Ki CHING Kiyoko F.AOKI-KINOSHITA Dianjing GUO Advanced Modeling and Applied Computing Laboratory Department of MathematicsThe University of Hong Kong Department of Bioinformatics Faculty of EngineeringSoka University Department of Biology The Chinese University of Hong Kong

Modeling genetic regulatory networks is an important research topic in genomic research and computationM systems biology. This paper considers the problem of constructing a genetic regula- tory network （GRN） using the discrete dynamic system （DDS） model approach. Although considerable research has been devoted to building GRNs, many of the works did not consider the time-delay effect. Here, the authors propose a time-delay DDS model composed of linear difference equations to represent temporal interactions among significantly expressed genes. The authors also introduce interpolation scheme and re-sampling method for equalizing the non-uniformity of sampling time points. Statistical significance plays an active role in obtaining the optimal interaction matrix of GRNs. The constructed genetic network using linear multiple regression matches with the original data very well. Simulation results are given to demonstrate the effectiveness of the proposed method and model.

关键词： Delay effect discrete dynamic system model genetic regulatory networks k-means clustering method linear multiple regression.

On Using Physico-Chemical Properties of Amino Acids in String Kernels for Protein Classification via Support Vector Machines

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Journal of Systems Science & Complexity 2015年第2期28卷 504-516页

作者： LI Limin AOKI-KINOSHITA Kiyoko F CHING Wai-Ki JIANG Hao Institute of Information and System Science Xi'an Jiaotong University Department of Bioinformatics Faculty of EngineeringSoka University Advanced Modeling and Applied Computing Laboratory Department of MathematicsThe University of Hong Kong Department of Mathematics School of InformationRenmin University of China

String kernels are popular tools for analyzing protein sequence data and they have been successfully applied to many computational biology problems. The traditional string kernels assume that different substrings are independent. However, substrings can be highly correlated due to their substructure relationship or common physico-chemical properties. This paper proposes two kinds of weighted spectrum kernels： The correlation spectrum kernel and the AA spectrum kernel. We evMuate their performances by predicting glycan-binding proteins of 12 glycans. The results show that the correlation spectrum kernel and the AA spectrum kernel perform significantly better than the spectrum kernel for nearly all the 12 glycans. By comparing the predictive power of AA spectrum kernels constructed by different physico-chemical properties, the authors can also identify the physico- chemical properties which contributes the most to the glycan-protein binding. The results indicate that physico-chemical properties of amino acids in proteins play an important role in the mechanism of glycamprotein binding.

关键词： AAindex AA spectrum kernel correlation spectrum kernel physico-chemical properties string kernel weighted spectrum kernel.

The Role of Integrated English Language Skills and Critical Thinking in the Development of Global Awareness

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Sociology Study 2014年第4期4卷 316-322页

作者： Laurence MacDonald Izumi Kanzaka Richmond Stroupe soka university lapan

The ability to communicate effectively in English is increasingly being viewed as an expectation of individuals who wish to engage with the global community. Mindful of these needs, the goals of the Global Citizenship Program （GCP） at soka university, Tokyo, Japan, focus not only on increasing English proficiency, but also on developing independent study skills, raising awareness of global issues, and enhancing the abilities of students to integrate information from multiple sources in meaningful ways. In the GCP, students enroll in English for Academic Purposes （EAP） courses which focus on developing critical thinking and research skills as well as English fluency. Through activities that require students to critically evaluate and synthesize information, opportunities are provided to engage in independent research focusing on the development process and global initiatives. This paper describes how the GCP curriculum develops academic skills and English proficiency, incorporates critical thinking activities, emphasizes global awareness, and integrates content-knowledge in order to equip students with the skills and knowledge necessary to interact successfully in the global community.

关键词： Global citizenship English education critical thinking

Fostering Global Citizens Through Study Abroad―A Case Study

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Sino-US English Teaching 2020年第5期17卷 158-165页

作者： LIU Xiaoxing soka university of America CaliforniaUnited States

In today’s increasingly globalized world,study abroad programs are receiving unprecedented attention as a significant part of international *** mission of soka university of America(SUA)is in line with the trend of producing *** in higher education who demonstrate intercultural and international *** has joined the academic world in this growing area of interest and requires all its students to study *** from other institutions and exploring its own path,SUA has developed a comprehensive study abroad program that seamlessly integrated in the liberal arts curricular of the university,which positively affected foreign language learning,improved students’abilities to function as global citizens,and opened various opportunities worldwide for the *** insure students’study abroad experiences fruitful,the following aspects need to be considered:*** institutional support;*** staff to work on study abroad affairs;*** students about the courses to take while abroad;*** need support from the entire home institution;and *** study abroad with a given institution’s broader goals.

关键词： study abroad intercultural communication intercultural competence fostering global citizens

A Partial Order in the Knot Table Ⅱ

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Acta Mathematica Sinica,English Series 2008年第11期24卷 1801-1816页

作者： Teruaki KITANO Masaaki SUZUKI Department of Information Systems Science Faculty of Engineering Soka University 1-236 Tangi-cho Hachioji-city Tokyo 192-8577 Japan Department of Mathematics Akita University 1-1 Tegata-Gakuenmachi Akita 010-8502 Japan

A partial order on the set of the prime knots can be defined by the existence of a surjective homomorphism between knot groups. In the previous paper, we determined the partial order in the knot table. In this paper, we prove that 31 and 41 are minimal elements. Further, we study which surjection a pair of a periodic knot and its quotient knot induces, and which surjection a degree one map can induce.

关键词： knot partial order surjective homomorphism period degree one map

Synthesis and mesomorphic properties of 4-(4-bromopropyloxy)-4'-(4-alkyloxybenzylidene)anilines

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Chinese Chemical Letters 2012年第7期23卷 769-772页

作者： Guan-Yeow Yeap Yew-Hong Ooi Kenji Kubo Masato M.Ito Liquid Crystal Research Laboratory School of Chemical SciencesUniversiti Sains Malaysia11800 MindenPenangMalaysia Department of Environmental Engineering for Symbiosis Faculty of EngineeringSoka UniversityTokyo 192-8577Japan

This article describes the preparation and liquid crystalline properties of a new homologous series of 4-（4-bromopropyloxy）-4＇- （4-alkyloxybenzylidene）anilines in which the phenyl ring is armed by a bromopropyloxy *** thermal behavior and mesomorphic properties of the synthesized compounds were studied with particular attention given to the correlation between their phase transition temperatures and anisotropic change influenced by molecular *** the members displayed enantiotropic smectic phase except for the homologue with the longest alkyloxy chain（R = C_（18）H_（37））,exhibiting only monotropic characteristic. The presence of bromine atom from the propyloxy side chain is found to be capable of altering and influencing the mesomorphic properties.

关键词： 4-(4-Bromopropyloxy)-4'-(4-alkyloxybenzylidene)anilines Mesomorphic properties Enantiotropic smectic DSC

Effects of silver nanoparticle size,concentration and coating on soil quality as indicated by arylsulfatase and sulfite oxidase activities

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Pedosphere 2022年第5期32卷 733-743页

作者： Yutong XUE Prashank MISHRA Frieda EIVAZI Zahra AFRASIABI Environmental Studies Concentration Soka University of AmericaAliso Viejo CA 92656(USA) Nicholas School of the Environment Duke UniversityDurham NC 27707(USA) Department of Agriculture and Environmental Sciences Lincoln UniversityJeferson City MO 6510l(USA)

Recently, the nanotechnology industry has seen a growing interest in integrating silver nanoparticles(AgNPs) into agricultural products, which increases soil exposure to these particles. This demands an investigation into the effect of AgNPs on soil health. Changes in soil enzyme activities upon exposure to AgNPs can serve as early indicators of any adverse effects that these particles may have on soil quality. This study aimed to determine the effects of AgNP size, concentration, coating, and exposure time on the activities of two sulfur cycle enzymes, arylsulfatase and sulfite oxidase. To investigate the sensitivity of soil enzyme activity to AgNP contamination, silt loam soil samples were treated with 30, 80, and 200 nm-sized AgNPs coated with citrate, lipoic acid,and polyvinylpyrrolidone at 1, 10, and 100 mg Ag kgsoil, with the changes in enzyme activities monitored at 3 h, 3 d, and 30 d after treatment. For comparison, the effects of silver(Ag) ions on the enzyme activities were studied under similar treatment conditions. For most of the concentrations tested, the inhibitory effects of AgNPs on different enzymes differed, with a much stronger effect on sulfite oxidase activity than on arylsulfatase activity. The AgNP concentration and exposure time played much important roles than coating type and particle size in the effects of AgNPs on soil enzyme activities.

关键词： citrate lipoic acid polyvinylpyrrolidone soil health sulfur cycle enzyme

Can Quality of Content Be a Differentiator for Broadcast Programs？ A Case Study in Japan

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Journalism and Mass Communication 2016年第6期6卷 303-312页

作者： Azusa Tanada Isamu Okada Freelance Toyama Japan soka university Tokyo Japan

This paper discusses the idea that the industry can have a differentiator of program quality by encouraging the activities of the Broadcasting Ethics ＆ Program Improvement Organization （BPO） in Japan. The BPO, a worldwide independent organization, has a mission of a breakwater against state power, and thus can be regarded as a kind of media accountability system, as proposed by Claude-Jean Bertrand. We review some controversial affairs in the TV industry and discuss BPO＇s activities aimed preventing ＂yellow journalism＂ and improving the quality of programming. High-quality content may be a differentiator for viewers faced with a choice of media, and thus, we focus on BPO and its role as a differentiator of the Japanese TV industry among the other, especially, Internet media. We also propose four ideas in response of critiques of BPO. Those are to strengthen transparency of governance of BPO, to improve the conformity of the TV industry to BPO＇s assessments of it, to establish a new committee to examine the whole concept of journalism, and to introduce a new certification institution to guarantee quality.

关键词： TV industry media accountability systems TV journalism BPO (Broadcasting Ethics & ProgramImprovement Organization)

Effectiveness of gelatin solidification for unfrozen preservation and transportation of astrocytes

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Advances in Biological Chemistry 2012年第3期2卷 238-242页

作者： Nobuko Ishibashi Shinichi Sotome Kazuyuki Nakajima Akio Shimizu Department of Bioinformatics Faculty of Engineering Soka University Tokyo Japan Department of Environmental Engineering for Symbiosis Faculty of Engineering Soka University Tokyo Japan

We herein studied a non-cryogenic cell preservation and transportation method. We found that astrocytes can be preserved in an unfrozen state at 4℃ (without medium exchange), while maintaining good condition in comparison with cryopreservation for the periods of 5 - 7 days. The gelatin solidification method can also prevent decreases in survival rate by preventing damage to astrocytes during transportation. Therefore, the gelatin solidification method at 4℃ may be a useful choice for short-term preservation and transportation.

关键词： Cell preservation Gelatin Astrocytes Unfrozen Preservation Transportation