• Journal of the Korean Chemical Society
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• v.56 no.1
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• pp.14-19
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• 2012

We investigate the doublet and quartet potential energy surfaces associated with the gas-phase reaction between $Ti^+$ and $CF_3COCH_3$ for two plausible reaction pathways, $TiF_2^+$ and $TiO^+$ formation pathways by using the density functional theory (DFT) method. The molecular structures of intermediates and transition states involved in these reaction pathways are optimized at the DFT level by using the PBE0 functional. All transition states are identified by using the intrinsic reaction coordinate (IRC) method, and the resulting reaction coordinates describe how $Ti^+$ activates $CF_3COCH_3$ and produces $TiF_2^+$ and $TiO^+$ as products. On the basis of presented results, we propose the most favorable reaction pathway in the reaction between $Ti^+$ and $CF_3COCH_3$.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.383-387
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• 2005

One of the most important issues in post-genome era is identifying functions of genes and understanding the interaction among them. Such interactions from complex biochemical pathways, which are very useful to understand the organism system. We present an integrated biochemical pathway database system with a set of software tools for reconstruction, visualization, and simulation of the pathways from the database. The novel features of the presented system include: (a) automatic integration of the heterogeneous biochemical pathway databases, (b) gene ontology for high quality of database in the integration and query (c) various biochemical simulations on the pathway database, (d) dynamic pathway reconstruction for the gene list or sequence data, (e) graphical tools which enable users to view the reconstructed pathways in a dynamic form, (f) importing/exporting SBML documents, a data exchange standard for systems biology.

• The Plant Pathology Journal
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• v.26 no.2
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• pp.101-109
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• 2010

Protein phosphorylation is one of the major mechanisms for controlling many cellular processes in all living organisms. Mitogen-activated protein kinase (MAPK) cascades are known to transducer extracellular stimuli to several cellular processes, including cell division, differentiation as well as responses to various stresses. In plants, several studies have revealed that MAPK cascade pathways play an important role in responses against biotic and abiotic stresses, including wounding, pathogen infection, temperature, drought, salinity and plant hormones. It is also known that MAPK cascades-mediated signaling is an essential process in the resistance step to pathogens by regulating the activity of transcription factors. Here, the insights into the functions of MAPK cascade pathways in plant defense response signaling from Arabidopsis, tobacco and rice are described.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.8
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• pp.3905-3909
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• 2012

Ovarian cancer is the fifth leading cause of cancer death in women aged 35 to 74 years. Although there are several popular hypothesis of ovarian cancer pathogenesis, the genetic mechanisms are far from being clear. Recently, systems biology approaches such as network-based methods have been successfully applied to elucidate the mechanisms of diseases. In this study, we constructed a crosstalk network among ovarian cancer related pathways by integrating protein-protein interactions and KEGG pathway information. Several significant pathways were identified to crosstalk with each other in ovarian cancer, such as the chemokine, Notch, Wnt and NOD-like receptor signaling pathways. Results from these studies will provide the groundwork for a combination therapy approach targeting multiple pathways which will likely be more effective than targeting one pathway alone.

• Biomolecules & Therapeutics
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• v.19 no.2
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• pp.141-148
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• 2011

Osteoclasts are bone-resorbing cells of monocyte/macrophage origin and are culprits of bone destruction associated with osteoporosis, rheumatoid arthritis, and cancer bone metastasis. Recent advances in osteoclast biology revealed central roles of various cytokines in regulating osteoclastogenesis both in vitro and in vivo. However, exact underlying mechanisms including signaling pathways downstream of receptor ligation are still under pursuit. In the present review, the role of Jak/STAT proteins and their regulators will be discussed in connection with osteoclastogenesis, since growing evidence indicates that a number of cytokines and growth factors utilizing Jak/STAT signaling pathways affect osteoclastogenesis. A better understanding on the role of Jak/STAT pathways in osteoclast differentiation will not only strengthen our knowledge on osteoclast biology but also provide invaluable insights into the development of anti-resorptive strategies for treating bone-lytic diseases.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.2
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• pp.609-617
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• 2013

Renal cell carcinomas make up 3% of all cancers and one in four patients is metastatic at time of diagnosis. This cancer is one of the most resistant to cytotoxic chemotherapy. Studies have shown that the efficiency of interferon-alpha and/or interleukin-2 based immune therapies is limited in patients with metastatic renal cell carcinoma but latest advances in molecular biology and genetic science have resulted in better understanding of its biology. Tumor angiogenesis, tumor proliferation and metastasis develop by the activation of signal message pathways playing a role in the development of renal cell carcinomas. Better definition of these pathways has caused an increase in preclinic and clinical studies into target directed treatment of renal cell carcinoma. Many recent studies have shown that numerous anti-angiogenic agents have marked clinical activity. In this article, the focus is on general characteristics of molecular pathways playing a major role in renal cell carcinoma, reviewing clinical information onagents used in the target directed treatment of metastatic lesions.

• Journal of Chest Surgery
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• v.27 no.3
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• pp.230-233
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• 1994

A 21-year-old man with atrioventricular[AV] reentry tachycardia secondary to concealed accessory AV connection underwent surgical division of two accessory pathways following failure of radiofrequency catheter ablation. pathways were located in the left free wall area.Before cardiopulmonary bypass, the epicardial mapping confirmed the existence and localization of two accessory pathways. The patient was approached through a left atriotomy with a dissection of the left free wall area beginning with an internal mapping was carried out after separation from cardiopulmonary bypass to confirm the absence of retrograde conduction of accessory pathway. Five weeks after surgery, the electrophysiololgic study demonstrated no retrograde conduction through two accessory pathways.

• Genomics & Informatics
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• v.5 no.3
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• pp.124-128
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• 2007

Microarray technology enables us to measure the expression of tens of thousands of genes simultaneously under various experimental conditions. Clustering analysis is one of the most successful methods for analyzing microarray data using the assumption that co-expressed genes may be co-regulated. It is important to extract meaningful clusters from a long unordered list of clusters and to evaluate the functional homogeneity and heterogeneity of clusters. Many quality measures for clustering results have been suggested in different conditions. In the present study, we consider biological pathways as a collection of biological knowledge and used them as a reference for measuring the quality of clustering results and functional homogeneities. PathTalk visualizes and evaluates functional relationships between gene clusters and biological pathways.

• Molecules and Cells
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• v.25 no.3
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• pp.397-406
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• 2008

Computational modeling of signal transduction is currently attracting much attention as it can promote the understanding of complex signal transduction mechanisms. Although several mathematical models have been used to examine signaling pathways, little attention has been given to crosstalk mechanisms. In this study, an attempt was made to develop a computational model for the pathways involving growth-factor-mediated mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3'-kinase/protein kinase B (PI3K/Akt). In addition, the dynamics of the protein activities were analyzed based on a set of kinetic data. The simulation approach integrates the information on several levels and predicts systems behavior. The in-silico analysis conducted revealed that the Raf and Akt pathways act independently.

• The Plant Pathology Journal
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• v.28 no.3
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• pp.227-238
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• 2012

Mitogen-activated protein kinase (MAPK) cascades are conserved signaling modules in the eukaryotic cells. They are involved in many major cell processes in fungi such as stress responses, vegetative growth, pathogenicity, secondary metabolism and cell wall integrity. In this review, we summarized the advances of research on the MAPK signaling pathways in Alternaria species. As major phytopathogenic fungi, Alternaria species reduce crop production. In contrast to the five MAPK pathways known in yeast, only three MAPK pathways as Fus3/Kss1-type, Hog1-type, and Slt2-type have been characterized in Alternaria. The Fus3/Kss1-type MAPK pathway participates in regulation of vegetative growth, conidiation, production of some cell-wall-degrading enzymes and pathogenicity. The Hog1-type pathway is involved in osmotic and oxidative stress, fungicides susceptibility and pathogenicity. The Slt2-type MAP kinases play an important role on maintaining cell wall integrity, pathogenicity and conidiation. Although recent advances on the MAPK pathways in Alternaria spp. reveal many important features on the pathogenicity, there are many unsolved problems regarding to the unknown MAP kinase cascade components and network among other major signal transduction. Considering the economic loss induced by Alternaria spp., more researches on the MAPK pathways will need to control the Alternaria diseases.