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Search Results: 1 - 10 of 2124 matches for " Masayuki Takeda "
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Development of an Algorithm for Reconstructing a Comprehensive Pathway Model: Application to Saccharomyces cerevisiae  [PDF]
Itaru Takeda, Masayuki Machida, Sachiyo Aburatani
Journal of Biomedical Science and Engineering (JBiSE) , 2015, DOI: 10.4236/jbise.2015.88047
Abstract: The generation of bioactive products by microbial bioprocesses is important for drug discovery, functional food development, and other beneficial purposes. Many pathways contribute to the production of these bioactive compounds, but important knowledge for improving productivity still remains in hidden pathways. Recently, an abundance of knowledge about metabolic pathways has been accumulated in metabolic pathway databases, such as BioCyc and KEGG. Many by-products are chemically transformed and actually used in other enzymatic reactions. In this work, we developed an algorithm for the reconstruction of a comprehensive genetic pathway model from a known metabolic pathway database. This model considers the interactions of the by-products, in addition to the main products. Furthermore, we developed a method for the construction of a comprehensive pathway model in a specific organism. In this study, we reconstructed a Saccharomyces cerevisiae model. From this model, the pathways among enzymes that contributed to galactose metabolism were explored. Using S. cerevisiae DNA microarray data, the activated pathways were found among the explored pathways.
Information Exchange on MANET for Efficient Evacuation  [PDF]
Asuka Ohta, Tomofumi Matsuzawa, Masayuki Takeda
Int'l J. of Communications, Network and System Sciences (IJCNS) , 2017, DOI: 10.4236/ijcns.2017.108010
Abstract: In disaster situations, people need to evacuate from dangerous areas to safe ones. In particular, they must formulate an evacuation plan for themselves when they cannot obtain support. Communicating with other evacuees to obtain information is useful in formulating an evacuation plan, and some studies have used a mobile ad hoc network (MANET) for this purpose, because such a network can be constructed using only wireless devices even when a fatal situation arises. However, we cannot treat a MANET in the same manner as other networks (such as a carrier network or Wi-Fi), and MANETs have several shortcomings in regard to information exchange. It is necessary to investigate the effects of these limitations on creating evacuation support systems on a MANET. We evaluated whether the limited information exchange available using a MANET is sufficient to create evacuation support systems through the use of a multi-agent evacuation simulator. As a result, our simulator showed that limited communication in which people communicate only with neighbors provides substantial efficiency for evacuation. People can continue to evacuate effectively even if they cannot obtain all of the desired information owing to MANET limitations.
Acceleration of Homomorphic Arithmetic Processing Based on the ElGamal Cryptosystem  [PDF]
Takuma Jogan, Tomofumi Matsuzawa, Masayuki Takeda
Communications and Network (CN) , 2019, DOI: 10.4236/cn.2019.111001
Abstract: In recent years, opportunities for using cloud services as computing resources have increased and there is a concern that private information may be leaked when processes data. The data processing while maintaining confidentiality is called secret computation. Cryptosystems can add and multiply plaintext through the manipulation of ciphertexts of homomorphic cryptosystems, but most of them have restrictions on the number of multiplications that can be performed. Among the different types of cryptosystems, fully homomorphic encryption can perform arbitrary homomorphic addition and multiplication, but it takes a long time to eliminate the limitation on the number of homomorphic operations and to carry out homomorphic multiplication. Therefore, in this paper, we propose an arithmetic processing method that can perform an arbitrary number of homomorphic addition and multiplication operations based on ElGamal cryptosystem. The results of experiments comparing with the proposed method with HElib in which the BGV scheme of fully homomorphic encryption is implemented showed that, although the processing time for homomorphic addition per ciphertext increased by about 35%, the processing time for homomorphic multiplication was reduced to about 1.8%, and the processing time to calculate the statistic (variance) had approximately a 15% reduction.
The Lateral Occipital Complex is Activated by Melody with Accompaniment: Foreground and Background Segregation in Auditory Processing  [PDF]
Masayuki Satoh, Katsuhiko Takeda, Ken Nagata, Hidekazu Tomimoto
Journal of Behavioral and Brain Science (JBBS) , 2011, DOI: 10.4236/jbbs.2011.13013
Abstract: Objective: Most of the western music consists of a melody and an accompaniment. The melody is referred to as the foreground, with the accompaniment the background. In visual processing, the lateral occipital complex (LOC) is known to participate in foreground and background segregation. We investigated the role of LOC in music processing with use of positron emission tomography (PET). Method: Musically naïve subjects listened to unfamiliar novel melodies with (accompaniment condition) and without the accompaniment (melodic condition). Using a PET subtraction technique, we studied changes in regional cerebral blood flow (rCBF) during the accompaniment condition compared to the melodic condition. Results: The accompanyment condition was associated with bilateral increase of rCBF at the lateral and medial surfaces of both occipital lobes, medial parts of fusiform gyri, cingulate gyri, precentral gyri, insular cortices, and cerebellum. During the melodic condition, the activation at the anterior and posterior portions of the temporal lobes, medial surface of the frontal lobes, inferior frontal gyri, orbitofrontal cortices, inferior parietal lobules, and cerebellum was observed. Conclusions: The LOC participates in recognition of melody with accompaniment, a phenomenon that can be regarded as foreground and background segregation in auditory processing. The fusiform cortex which was known to participate in the color recognition might be activated by the recognition of flourish sounds by the accompaniment, compared to melodic condition. It is supposed that the LOC and fusiform cortex play similar functions beyond the difference of sensory modalities.
Expression of Large Conductance, Voltage- and Ca2+-Activated K+ (BK) Channels in Human Urinary Bladder: Alteration of Subunit Expression Profile in Association with Bladder Outlet Obstruction  [PDF]
Hidenori Zakoji, Hideki Kobayashi, Mitsuharu Yoshiyama, Masayuki Takeda, Isao Araki
Open Journal of Urology (OJU) , 2013, DOI: 10.4236/oju.2013.32009

Purpose: Large conductance, voltage- and Ca2+-activated K+ (BK) channel is thought to have a central role to regulate urinary bladder smooth muscle functions, and its dysfunction may lead to increase of urination frequency and overactive bladder. The present study aims to investigate the expression pattern of BK channel subunits in the human urinary bladder, and how it changes in association with bladder outlet obstruction (BOO). Materials and Methods: Human bladders were obtained from 7 controls without prostatic enlargement and lower urinary tract symptoms and 4 BPH patients with clinically diagnosed overactive bladder who were verified by the International Prostate Symptom Score (IPSS) and prostate volume. The expression and location of BK channel protein complex was examined using immunohistochemistry with affinity-purified anti-BKα antibodies. A real-time RT-PCR was used to quantify the expression of each BK channel subunit (α and β1 - 4) gene in the mucosal and muscle layers of human urinary bladder. Results: Immunohistochemical staining for BK-α protein complex was localized in the muscle and submucosal regions of urinary bladder. RT-PCR analysis revealed the presence of α-, β1-, and β4-subunit genes of BK channel in the mucosal layer, α- and β1-subunit in the muscle layer. The expressions of α- and β1-subunit genes in the muscle (α: p = 0.0003, β1: p = 0.0003) and mucosal (α: p = 0.03, β1: p = 0.02) layers significantly decreased in BOO bladders compared with controls. The expression levels of α- and β1-subunit in mucosal layer were statistically correlated with storage score of IPSS (α; r = 0.84, p = 0.002, β1; r = 0.84, p = 0.002), and

An Online Algorithm for Lightweight Grammar-Based Compression
Shirou Maruyama,Hiroshi Sakamoto,Masayuki Takeda
Algorithms , 2012, DOI: 10.3390/a5020214
Abstract: Grammar-based compression is a well-studied technique to construct a context-free grammar (CFG) deriving a given text uniquely. In this work, we propose an online algorithm for grammar-based compression. Our algorithm guarantees O(log 2 n)- approximation ratio for the minimum grammar size, where n is an input size, and it runs in input linear time and output linear space. In addition, we propose a practical encoding, which transforms a restricted CFG into a more compact representation. Experimental results by comparison with standard compressors demonstrate that our algorithm is especially effective for highly repetitive text.
Distribution and Possible Function of Cannabinoid Receptor Subtype 1 in the Human Prostate  [PDF]
Manabu Kamiyama, Mizuya Fukasawa, Yoshio Takihana, Norifumi Sawada, Hiroshi Nakagomi, Mitsuharu Yoshiyama, Isao Araki, Masayuki Takeda
Open Journal of Urology (OJU) , 2013, DOI: 10.4236/oju.2013.32020

Background: Cannabinoid receptor subtype 1 (CB1) has a relationship to the proliferation of various cells including malignant tumoral cells. We investigated and compared the expression of CB1 in benign and malignant human prostate tissues and in benign and malignant human prostate cell lines, as well as its function for the proliferation of human prostate cancer cells. Methods: Real-time quantitative PCR was performed to compare its expressions in human prostate tissues (normal, benign hyperplasia, and cancer) and prostate cell lines (3 normal and 3 malignant). For localization of CB1, immunofluorescent staining with rabbit anti-CB1 polyclonal antibodies and tetramethyl isothiocyanate (TRITC)-labeled swine anti-rabbit immunoglobulin (DAKO) were used under fluorescence microscope. To further analyze whether cell death was induced by anandamide (non-selective agonist for CB1/CB2) via a receptor dependent mechanism, the viability of DU145 cells, which is known as androgen-insensitive prostate cancer cell, was measured using MTT assay. Results: CB1mRNA was found to be expressed in the all 3 human prostate tissues, however, CB1 protein was expressed in BPH and low grade malignant PC tissues, but not in high grade malignant PC tissues. CB1 as for cell lines, the expression of CB1 was low in malignant cell lines except for DU145. Anandamide elicited cell death, which was significantly inhibited by AM251 (selective antagonist for CB1), indicating that cell death induced by anandamide in DU145 cells was mediated by CB1. Anandamide time-dependently elicits up-regulation of CB1 in DU145 cells. Conclusions: CB1 may be an inhibitory regulator of androgen-insensitive human prostate cancer epithelial cell growth.

Tailor-Made Mesh for Pelvic Organ Prolapses: Correlation between Patient’s Height and Mesh Size  [PDF]
Hideki Kobayashi, Yaburu Haneda, Satoru Kira, Takayuki Tsuchida, Isao Araki, Masayuki Takeda
Open Journal of Urology (OJU) , 2013, DOI: 10.4236/oju.2013.32023

Tension-free vaginal mesh (TVM) surgery is a common and minimally invasive procedure for pelvic organ prolapses. Since commercial kits are not readily available in Japan, we have planned tailor-made mesh by information of each patient before every TVM surgery. The aim of this report is to inform methods to design mesh for individual patients with pelvic organ prolapses. We also investigated the correlations among mesh size and height, weight, and body mass index (BMI). Before the operation, we obtained a KUB (abdominal X-ray). Three factors were measured from this X-ray: the first was the distance between the bilateral ischial spine, the second was the distance between the obturator foramen, and the third was the length of the arcus tendineus fascia pelvis (ATFP). These three factors always should be considered for designing of mesh. The correlations among the bilateral ischial spine distance, obturator foramen distance, ATFP length, height, weight, and BMI were assessed using the Pearson correlation coefficient. Although these three factors described above are necessary to design a mesh for individual patients, the bilateral ischial spine and obturator foramen distance correlated with the height of the patient. On the other hand, since the length of ATFP differs in each patient and is not correlated with height, we should consider this length when we design the mesh. Well-designed, tailor-made mesh will probably fit each pelvic organ prolapsed patient very well.

Efficient LZ78 factorization of grammar compressed text
Hideo Bannai,Shunsuke Inenaga,Masayuki Takeda
Computer Science , 2012, DOI: 10.1007/978-3-642-34109-0_10
Abstract: We present an efficient algorithm for computing the LZ78 factorization of a text, where the text is represented as a straight line program (SLP), which is a context free grammar in the Chomsky normal form that generates a single string. Given an SLP of size $n$ representing a text $S$ of length $N$, our algorithm computes the LZ78 factorization of $T$ in $O(n\sqrt{N}+m\log N)$ time and $O(n\sqrt{N}+m)$ space, where $m$ is the number of resulting LZ78 factors. We also show how to improve the algorithm so that the $n\sqrt{N}$ term in the time and space complexities becomes either $nL$, where $L$ is the length of the longest LZ78 factor, or $(N - \alpha)$ where $\alpha \geq 0$ is a quantity which depends on the amount of redundancy that the SLP captures with respect to substrings of $S$ of a certain length. Since $m = O(N/\log_\sigma N)$ where $\sigma$ is the alphabet size, the latter is asymptotically at least as fast as a linear time algorithm which runs on the uncompressed string when $\sigma$ is constant, and can be more efficient when the text is compressible, i.e. when $m$ and $n$ are small.
Exploration of Activated Pathways for Improving Antifungal Agent FR901469 Productivity in Fungal Species No.11243 Using Comprehensive Pathway Model  [PDF]
Itaru Takeda, Hiroya Itoh, Makoto Matsui, Takashi Shibata, Masayuki Machida, Sachiyo Aburatani
Journal of Biosciences and Medicines (JBM) , 2017, DOI: 10.4236/jbm.2017.57003
Abstract: Secondary metabolites are important for various industrial applications. The production of secondary metabolites is often improved by the activation of substrate supply pathways for biosynthesis. However, many important pathways have remained unclear. In this study, we explored possible pathways related to substrate supply for the biosynthesis of the antifungal agent FR901469 which is a nonribosomal peptide and a fungal secondary metabolite. To clarify the unknown activated pathways, we utilized the Comprehensive Pathway Model (CPM) which was developed in our previous study. We verified that the overexpression of the hypothetical beta-alanine-aminotransferase (BAL-AT), which was included in the explored pathways, improved the FR901469 productivity. The genes encoding the BAL metabolic enzymes are considered to be important for improving the FR901469 productivity.
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