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Search Results: 1 - 10 of 747 matches for " Katsuyuki Tomita "
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A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks
Katsuyuki Yugi, Yoichi Nakayama, Shigen Kojima, Tomoya Kitayama, Masaru Tomita
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-299
Abstract: We present a microarray data-based semi-kinetic (MASK) method which facilitates the prediction of regulatory dynamics of genetic networks composed of recurrently appearing network motifs with reasonable accuracy. The MASK method allows the determination of model parameters representing the contribution of regulators to transcription rate from time-series microarray data. Using a virtual regulatory network and a Saccharomyces cerevisiae ribosomal protein gene module, we confirmed that a MASK model can predict expression profiles for various conditions as accurately as a conventional kinetic model.We have demonstrated the MASK method for the construction of dynamic simulation models of genetic networks from time-series microarray data, initial mRNA copy number and first-order degradation constants of mRNA. The quantitative accuracy of the MASK models has been confirmed, and the results indicated that this method enables the prediction of quantitative dynamics in genetic networks composed of commonly used network motifs, which cover considerable fraction of the whole network.With the advent of high-throughput biotechnologies in the last decade of the 20th century, enormous amounts of data have been generated on intracellular molecules [1-5]. The ongoing accumulation of such large-scale information presents a significant challenge to the scientific community: Namely, to understand the cell-wide molecular network as a living system [6-8]. In particular, modelling the behaviour of genetic regulatory networks has been one of the most significant milestones in systems biology [9-12]. In many previous studies, the dynamic behaviours of genetic networks were quantitatively predicted and analyzed in terms of non-linear ordinary differential equations based on reaction kinetics [13-15]. However, because it is arduous to obtain a complete set of sufficiently accurate kinetic properties of molecular interactions, the application of this method is limited to small regulatory netwo
Hybrid dynamic/static method for large-scale simulation of metabolism
Katsuyuki Yugi, Yoichi Nakayama, Ayako Kinoshita, Masaru Tomita
Theoretical Biology and Medical Modelling , 2005, DOI: 10.1186/1742-4682-2-42
Abstract: Here we describe a simulation method based on cooperation between kinetics-based dynamic models and MFA-based static models. This hybrid method enables quasi-dynamic simulations of large-scale metabolic pathways, while drastically reducing the number of kinetics assays needed for dynamic simulations. The dynamic behaviour of metabolic pathways predicted by our method is almost identical to that determined by dynamic kinetic simulation.The discrepancies between the dynamic and the hybrid models were sufficiently small to prove that an MFA-based static module is capable of performing dynamic simulations as accurately as kinetic models. Our hybrid method reduces the number of biochemical experiments required for dynamic models of large-scale metabolic pathways by replacing suitable enzyme reactions with a static module.Recent progress in high-throughput biotechnology [1-3] has made advances in understanding of cell-wide molecular networks possible at the systems level [4,5]. To reconstruct cellular systems using the high-throughput data that are becoming available on their components, computer simulations are being revisited as an integrative approach to systems biology. Mathematical modelling of biochemical networks has been attempted since the 1960s, and before genome-scale pathway information became available, they mostly employed numerical integration of ordinary differential equations for reaction rates [6-10]. This kind of dynamic simulation model provides the time evolution of pathway properties such as metabolite concentration and reaction rate. To create accurate simulations, dynamic models require kinetic parameters and detailed rate-laws such as the MWC model [11] and those derived using the King-Altman method [12]. However, with few exceptions such as human erythrocyte metabolism [13,14], it is virtually impossible to collect a complete set of kinetic properties for large-scale metabolic pathways. Therefore, the applicability of the dynamic method has been
Cough and asthma diagnosis: physicians’ diagnosis and treatment of patients complaining of acute, subacute and chronic cough in rural areas of Japan
Akira Yamasaki, Keichi Hanaki, Katsuyuki Tomita, et al
International Journal of General Medicine , 2010, DOI: http://dx.doi.org/10.2147/IJGM.S8167
Abstract: ugh and asthma diagnosis: physicians’ diagnosis and treatment of patients complaining of acute, subacute and chronic cough in rural areas of Japan Original Research (4404) Total Article Views Authors: Akira Yamasaki, Keichi Hanaki, Katsuyuki Tomita, et al Published Date March 2010 Volume 2010:3 Pages 101 - 107 DOI: http://dx.doi.org/10.2147/IJGM.S8167 Akira Yamasaki1, Keichi Hanaki2, Katsuyuki Tomita3, Masanari Watanabe1, Yasuyuki Hasagawa1, Ryota Okazaki1, Miki Yamamura1, Kouji Fukutani4, Yuji Sugimoto5, Kazuhiro Kato4, Masahiro Kodani6, Toshikazu Ikeda7, Tatsuya Konishi8, Yuji Kawasaki9, Hirokazu Tokuyasu9, Hiroki Yajima3, Hitoshi Sejima10, Takeshi Isobe11, Eiji Shimizu1, SAN-IN Asthma Research Group 1Third Department of Internal Medicine, 2Department of Pediatrics, Tottori University, Japan; 3Department of Respiratory Medicine, Hakuai Hospital, Japan; 4Department of Respiratory Medicine, San-in Rosai Hospital, Japan; 5Department of Respiratory Medicine, Tottori Prefectural Central Hospital, Japan; 6Department of Respiratory Medicine, Tottori Red Cross Hospital, Japan; 7Department of Respiratory Medicine, National Organization, Matsue Hospital, Japan; 8Department of Respiratory Medicine, Matsue City Hospital, Japan; 9Department of Respiratory Medicine, Matsue Red Cross Hospital, Japan; 10Department of Pediatrics, 11Department of Internal Medicine, Shimane University, Shimane, Japan Background: Cough is one of the most common reasons for visiting a clinic. The causes of cough differ according to the duration of cough. Infectious disease is commonly observed in acute cough while noninfectious disease is commonly observed in chronic cough. On the other hand, cough is frequently observed in patients with asthma/cough variant asthma (CVA). Objective: In this study, we investigated the causes of cough in a rural region in Japan and the clinical examination and treatment for the patients diagnosed as asthma/CVA. Methods: We analyzed 124 patients who complained of cough. Results: The most common reason for acute cough was respiratory tract infection while asthma/CVA is the most common reason for subacute and chronic cough. The diagnostic procedure for asthma/CVA depends on clinical symptoms in asthmatic patients with acute cough. While in asthmatic patients with subacute and chronic cough, diagnosis of asthma depends on clinical examinations including chest radiogram, immunoglobulin E, white blood cells counts, sputum examination or spirometry as well as symptoms. For the treatment of asthma, the use of long-acting β2-stimulant was dominant in asthmatic patients with acute cough while the use of leukotriene receptor and inhaled corticosteroid were dominant in asthmatic patients with subacute or chronic cough. Conclusions: Diagnosis and treatment for asthma differs according to the duration of cough. Simple guidelines for asthma/CVA according to the duration of cough might be necessary for diagnosis and treatment of asthma/CVA for general physicians e
Cough and asthma diagnosis: physicians’ diagnosis and treatment of patients complaining of acute, subacute and chronic cough in rural areas of Japan
Akira Yamasaki,Keichi Hanaki,Katsuyuki Tomita,et al
International Journal of General Medicine , 2010,
Abstract: Akira Yamasaki1, Keichi Hanaki2, Katsuyuki Tomita3, Masanari Watanabe1, Yasuyuki Hasagawa1, Ryota Okazaki1, Miki Yamamura1, Kouji Fukutani4, Yuji Sugimoto5, Kazuhiro Kato4, Masahiro Kodani6, Toshikazu Ikeda7, Tatsuya Konishi8, Yuji Kawasaki9, Hirokazu Tokuyasu9, Hiroki Yajima3, Hitoshi Sejima10, Takeshi Isobe11, Eiji Shimizu1, SAN-IN Asthma Research Group1Third Department of Internal Medicine, 2Department of Pediatrics, Tottori University, Japan; 3Department of Respiratory Medicine, Hakuai Hospital, Japan; 4Department of Respiratory Medicine, San-in Rosai Hospital, Japan; 5Department of Respiratory Medicine, Tottori Prefectural Central Hospital, Japan; 6Department of Respiratory Medicine, Tottori Red Cross Hospital, Japan; 7Department of Respiratory Medicine, National Organization, Matsue Hospital, Japan; 8Department of Respiratory Medicine, Matsue City Hospital, Japan; 9Department of Respiratory Medicine, Matsue Red Cross Hospital, Japan; 10Department of Pediatrics, 11Department of Internal Medicine, Shimane University, Shimane, JapanBackground: Cough is one of the most common reasons for visiting a clinic. The causes of cough differ according to the duration of cough. Infectious disease is commonly observed in acute cough while noninfectious disease is commonly observed in chronic cough. On the other hand, cough is frequently observed in patients with asthma/cough variant asthma (CVA).Objective: In this study, we investigated the causes of cough in a rural region in Japan and the clinical examination and treatment for the patients diagnosed as asthma/CVA.Methods: We analyzed 124 patients who complained of cough.Results: The most common reason for acute cough was respiratory tract infection while asthma/CVA is the most common reason for subacute and chronic cough. The diagnostic procedure for asthma/CVA depends on clinical symptoms in asthmatic patients with acute cough. While in asthmatic patients with subacute and chronic cough, diagnosis of asthma depends on clinical examinations including chest radiogram, immunoglobulin E, white blood cells counts, sputum examination or spirometry as well as symptoms. For the treatment of asthma, the use of long-acting β2-stimulant was dominant in asthmatic patients with acute cough while the use of leukotriene receptor and inhaled corticosteroid were dominant in asthmatic patients with subacute or chronic cough.Conclusions: Diagnosis and treatment for asthma differs according to the duration of cough. Simple guidelines for asthma/CVA according to the duration of cough might be necessary for diagnosis and treatme
Dissociation of DNA damage and mitochondrial injury caused by hydrogen peroxide in SV-40 transformed lung epithelial cells
Yoshihiro Fujii, Katsuyuki Tomita, Hiroyuki Sano, Akira Yamasaki, Yutaka Hitsuda, Ian M Adcock, Eiji Shimizu
Cancer Cell International , 2002, DOI: 10.1186/1475-2867-2-16
Abstract: DNA damage and mitochondrial injury were measured after oxidative stress in the SV-40 transformed lung epithelial cell line challenged with hydrogen peroxide (H2O2). Single cell analysis of DNA damage was determined by assessing the number of 8-oxo-2-deoxyguanosine (8-oxo-dG) positive cells, a marker of DNA modification, and the length of a comet tail. Mitochondrial membrane potential, ΔΨm, was determined using JC-1. A 1 h pulse of H2O2 induced small amounts of apoptosis (3%). 8-oxo-dG-positive cells and the length of the comet tail increased within 1 h of exposure to H2O2. The number of cells with reduced ΔΨm increased after the addition of H2O2 in a concentration-dependent manner. In spite of a continual loss of ΔΨm, DNA fragmentation was reduced 2 h after exposure to H2O2.The data suggest that SV-40 transformed lung epithelial cells are resistant to oxidative stress, showing that DNA damage can be dissociated from mitochondrial injury.Aerobic cells are constantly exposed to reactive oxygen intermediates (ROIs). Increased intracellular levels of the ROIs, superoxide (O2-), hydroxyl radical (·OH), or hydrogen peroxide (H2O2) are referred to as oxidative stress [1,2]. The alveolar surface of the lung is a major target for oxidative stress. Also, cigarette smoking can cause an acute inflammatory reaction in the lung, characterized by the accumulation and activation of leukocytes in vivo, producing ROIs and nitrogen species in high concentrations [3,4]. These different reactive species might be responsible for much of the tissue injuries and disease states associated with inflammation. Increased oxidative DNA damage, such as 8-hydroxyguanine formation in human lung tissue [5], is found in smokers compared with non-smokers. Oxidative stress may play an important role in the pathogenesis of smoking-associated diseases, such as chronic obstructive pulmonary diseases (COPD) [6,7], asthma [8], and carcinogenesis [9-11].ROIs damage DNA, resulting in base modifications, e.g.
Case of an unusual clinical and radiological presentation of pulmonary metastasis from a costal chondrosarcoma after wide surgical resection: A transbronchial biopsy is recommended
Makoto Emori, Ken-ichiro Hamada, Takenori Kozuka, Katsuyuki Nakanishi, Yasuhiko Tomita, Norifumi Naka, Nobuhito Araki
World Journal of Surgical Oncology , 2011, DOI: 10.1186/1477-7819-9-50
Abstract: Chondrosarcomas are the second most frequent primary malignant bone tumors, after osteosarcomas [1,2]. They are also the most common primary malignant chest wall tumors: 5-15% of chondrosarcomas are located in the thoracic wall [3]. Since radiotherapy and chemotherapy are generally ineffective against chondrosarcomas, surgery is the only curative treatment, and the quality of the surgery is an essential prognostic factor [2]. Enneking et al. classified surgical margins into wide, marginal, and intralesional [4]. A wide resection is accomplished by a procedure in which the lesion, its pseudocapsule and/or reactive zone, and a surrounding cuff of normal tissue are taken as a single block. Therefore, resection for chest wall chondrosarcoma should be wide, taking intact pleura internally, intact muscle fascia externally, and transverse rib resection > 2 cm from the tumor on both directions [4,5]. Clinically, the involved rib en bloc should be resected along with the 2 intercostal spaces above and below the tumor.On roentgenograms, pulmonary metastases usually appear as multiple peripheral, round nodules of varying sizes. Here, we describe an atypical presentation of pulmonary metastasis occurring soon after wide surgical resection of a costal chondrosarcoma. In this case, a thoracic computed tomography (CT) scan showed consolidation, predominantly in both the lower lobes, surrounded by ground-glass opacities and air bronchograms, mimicking serious pneumonia.A 62-year-old woman was admitted to our hospital because of a mass that grew gradually in the right lateral chest wall for 1 year. Physical examination revealed a tumor (5 × 3.5 cm) in the right eighth rib. The mass was hard with an unclear border, no mobility, redness, or local heat, but it was tender. An X-ray revealed a mass with coarse calcification located on the right eighth rib, expanding beyond the irregular cortex. Thoracic CT revealed a 70 × 60 × 30 mm low-density mass (CT value, +18 HU) along the right eig
The Effects of Income Inequality on Education Policy and Economic Growth  [PDF]
Katsuyuki Naito, Keigo Nishida
Theoretical Economics Letters (TEL) , 2012, DOI: 10.4236/tel.2012.21020
Abstract: This paper presents a simple model to investigate the relationship among initial income inequality, education and eco- nomic growth. Public expenditure on education is determined through majority voting. Although preferences of individuals are not single-peaked, the individual with the median income becomes the decisive voter. Our model predicts that high initial inequality has a negative impact on education expenditure and therefore retards economic growth.
Cancer-Associated Lymphatic and Venous Vessels in Colonic Carcinomas  [PDF]
Tatsuo Tomita
Open Journal of Pathology (OJPathology) , 2014, DOI: 10.4236/ojpathology.2014.43016
Abstract:

Objective: Colonic carcinomas spread to regional lymph nodes and liver. There are cancer-associated lymphatic and venous vessels at the margin of colonic carcinomas, which facilitate spreading carcinoma through lymphatic and venous vessels. This study aimed to examine cancer-associated lymphatic and venous vessels in TNM T1 to T3 carcinomas using lymphatic vessel hyaluronan receptor for lymphatic vessels and von Willebrand factor for venous vessels by immunocytochemical staining. Materials and Methods: A total of 40 cases of moderately differentiated colonic carcinoma were studied using routinely formalin-fixed and paraffin-embedded sections. The cases consisted of 10 cases of TNM T1, 15 cases each of T2 and T3 cases. Immunocytochemical staining was performed using goat antihuman LYVE-1for lymphatic vessels and rabbit antihuman von Willebrand factor for venous vessels. Results: In TNM T1 carcinoma, increased, irregular and narrow lymphatic and venous vessels were present in the adjacent normal mucosa to the carcinoma, some of which penetrated cancerous lesion. There were no tumor emboli in lymphatic and venous vessels. In TNM T2 carcinoma, there were few lymphatic and venous vessels in midst of the carcinoma whereas numerous small lymphatic and venous vessels were present within muscle layers adjacent to the invading carcinoma. Extramural tumor embolus

Tumor-Associated Lymphatic and Venous Vessels in Medullary Thyroid Carcinomas  [PDF]
Tatsuo Tomita
Open Journal of Pathology (OJPathology) , 2015, DOI: 10.4236/ojpathology.2015.52008
Abstract: Objective: Medullary thyroid carcinomas (MTCs) invade local lymph node through lymphatic vessels and metastasize to distant organs hematogenously and account for a significant mortality. There are possibly increased lymphatic and venous vessels, through which the tumor spreads to lymph nodes and distant organs. Materials and Methods: By immunocytochemical staining for lymphatic and venous vessels, MTC lesions with adjacent normal thyroid and both normal and metastatic lymph nodes were studied for the peritumoral lymphatic and venous vessels, which were morphometrically compared with those of normal thyroid and lymph nodes. Sixteen cases of MTC cases with adjacent thyroid tissues and attached lymph nodes were immunocytochemically stained for lymphatic vessels using lymphatic vessel hyaluronan receptor (LYVE-1) and venous vessels for factor VIII (F-8). The immunostained sections of MTC lesions and metastatic lymph nodes were morphometrically compared for the number and sizes of the vessels with those of normal thyroid tissues and lymph nodes. Results: Significantly increased lymphatic vessels and markedly increased blood vessels were identified in many MTC cases at the peritumoral tissues and metastatic lymph nodes whereas a few lymphatic vessels and no venous vessels were identified in midst of MTCs. The irregular peritumoral lymphatic vessels resembled that of immature lymphatic vessels observed in papillary thyroid carcinomas and increased irregularly, entrapped venous vessels in peritumoral tissues resembled those observed in follicular thyroid carcinomas. Conclusion: The significantly increased lymphatic vessels and markedly increased venous vessels in the peritumoral thyroid tissue support a propensity of MTCs for providing an easy access of tumor cells to both lymphatic spread to the regional lymph nodes and venous spread to distant organs with further tumor spread through metastatic lymph nodes by moderately increased lymphatic and venous vessels.
STAT6 expression in T cells, alveolar macrophages and bronchial biopsies of normal and asthmatic subjects
Katsuyuki Tomita, Gaetano Caramori, Kazuhiro Ito, Hiroyuki Sano, Sam Lim, Timothy Oates, Borja Cosio, K Fan Chung, Yuji Tohda, Peter J Barnes, Ian M Adcock
Journal of Inflammation , 2012, DOI: 10.1186/1476-9255-9-5
Abstract: We have investigated the expression of STAT6 in peripheral blood T-lymphocytes, alveolar macrophages and bronchial biopsies from 17 normal subjects and 18 mild-moderate steroid-na?ve stable asthmatic patients.STAT6 expression was variable and was detected in T-lymphocytes, macrophages and bronchial epithelial cells from all subjects with no difference between normal and stable asthmatic subjects.STAT6 expression in different cells suggests that it may be important in regulating the expression of not only Th2-like cytokines in T cells of man, but may also regulate STAT-inducible genes in alveolar macrophages and airway epithelial cells.Asthma is characterised by chronic airway inflammation, with infiltration of T-lymphocytes, mast cells, eosinophils and monocytes/macrophages. This is associated with the increased expression of several inflammatory proteins, including cytokines, enzymes, receptors and adhesion molecules [1]. The molecular pathways involved in the induction of chronic cytokine expression and recruitment to the airways and activation of inflammatory cells in asthma are not well understood. However, there is increasing recognition that these processes involve increased transcription of inflammatory genes, and that this is regulated by transcription factors [1]. Several transcription factors are involved in asthmatic inflammation including nuclear factor-κB (NF-κB) [2,3] and activator protein-1 (AP-1) [4].CD4+ T helper (Th) cells can be divided into four major subsets termed Th1, Th2, Th17 and Th0 based on the pattern of cytokines they produce. More recently, another two subsets of effector CD4+ Th cells, named Th9 and Th22 cells, have been described, even if their pathophysiological meaning is still unclear [5,6]. Th1 cells produce predominantly interferon gamma (IFNγ) and predominantly promote cell-mediated immune responses, whereas Th2 cells, which produce mainly IL-4, IL-5 and IL-13, provide help for some B cell responses. IL-4 and IL-13 in particular
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