• Korean Journal of Agricultural and Forest Meteorology
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• v.12 no.2
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• pp.122-131
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• 2010

This paper introduces the concept of a virtual ecosystem and reports the following three mathematical approaches that could be widely used to construct such an ecosystem, along with examples: (1) a molecular dynamics simulation approach for animal flocking behavior, (2) a stochastic lattice model approach for termite colony behavior, and (3) a rule-based cellular automata approach for biofilm growth. The ecosystem considered in this study consists of artificial organisms and their environment. Each organism in the ecosystem is an agent that interacts autonomously with the dynamic environment, including the other organisms within it. The three types of model were successful to account for each corresponding ecosystem. In order to accurately mimic a natural ecosystem, a virtual ecosystem needs to take many ecological variables into account. However, doing so is likely to introduce excess complexity and nonlinearity in the analysis of the virtual ecosystem's dynamics. Nonetheless, the development of a virtual ecosystem is important, because it can provide possible explanations for various phenomena such as environmental disturbances and disasters, and can also give insights into ecological functions from an individual to a community level from a synthetic viewpoint. As an example of how lower and higher levels in an ecosystem can be connected, this paper also briefly discusses the application of the second model to the simulation of a termite ecosystem and the influence of climate change on the termite ecosystem.

• Journal of the Korea Convergence Society
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• v.9 no.3
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• pp.257-263
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• 2018

Hyperthermia supplies RF high-frequency energy above 1MHz to the tumor tissue through the electrodes. And the temperature of the tumor tissue is increased to $42^{\circ}C$ or more to cause thermal necrosis. A mathematical model can be derived a human body model for absorption and transmission of electromagnetic energy in the human model and It is possible to evaluate the distribution of temperature fields in biological tissues. In this paper, we build the human model based on the adult standard model of the geometric shape of the 3D model and use the FVM code. It is assumed that Joule heat is supplied to the anatomical model to simulate the magnetic field induced by the external electrode and the temperature distribution was analyzed for 0-1,200 seconds. As a result of the simulation, it was confirmed that the transferred energy progressively penetrates from the edge of the electrode to the pulmonary tumors and from the skin surface to the subcutaneous layer.

• Microbiology and Biotechnology Letters
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• v.37 no.3
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• pp.248-257
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• 2009

The inhibitors against Vibrio harveyi quorum sensing (QS) signaling were developed by modifying the molecular structure of the major signal, N-3-hydroxybutanoyl-L-homoserine lactone (3-OH-$C_4$-HSL). A series of structural derivatives, N-(3-hydroxysulfonyl)-L-homoserine lactones (HSHLs) were synthesized by the solid-phase organic synthesis method. The in vivo QS inhibition by these compounds was measured by a bioassay system using the V. harveyi bioluminescence, and all showed significant inhibitory effects. To analyze the interaction between these compounds and LuxN, a 3-OH-$C_4$-HSL receptor protein of V. harveyi, we tentatively determined the putative signal binding domain of LuxN based on the sequence homology with other acyl-HSL binding proteins, and predicted the partial 3-D structure of the putative signal binding domain of LuxN by using ORCHESTRA program, and further estimated the binding poses and energies (docking scores) of 3-OH-$C_4$-HSL and HSHLs within the domain. In comparison of the result from this modeling study with that of in vivo bioassay, we suggest that the in silica interpretation of the interaction between ligands and their receptor proteins can be a valuable way to develop better competitive inhibitors, especially in the case that the structural information of the protein is limited.

• Analytical Science and Technology
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• v.13 no.4
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• pp.494-503
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• 2000

A 21-residue peptide corresponding to amino acids 84-104 of $p16^{INK4A}$, the tumor suppressor, has been synthesized and its structure was studied by Circular Dichroism, $^1H$ NMR spectroscopy and molecular modeling. A p16-derived peptide (84-104 amino acids) forming stable complex with CDK4 and CDK6 inhibits the ability of CDK4/6 to phosphorylate pRb in vitro, and blocks cell-cycle progression through G1/S phase as shown in the function of the full-length p16. Its NMR spectral data including NOEs, $^3J_{NH-H{\alpha}}$ coupling constants, $C_{\alpha}H$ chemical shift, the average amplitude of amide chemical shift oscillation and temperature coefficients indicate that the secondary structure of a p16-derived peptide is similar to that of the same region of full-length p16, which consists of helix-turn-helix structure. The 3-D distance geometry structure based on NOE-hased distance and torsion angle restraints is characterized by ${\gamma}$-turn conformation between residues $Gly^{89}-Leu^{91}$(${\varphi}_{i+1}=-79.8^{\circ}$, ${\varphi}_{i+1}=60.2^{\circ}$) as evidenced in a single crystal structure for the corresponding region of p18 or p19, but is undefined at both the N and C termini. This compact and rigid ${\gamma}$-turn region is considered to stabilize the structure of p16-derived peptide and serve as a site recognizing cyelin dependent kinase, and this well-defined ${\gamma}$-turn structure could be utilized for the design of anti-cancer drug candidates.

• Journal of Chest Surgery
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• v.35 no.6
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• pp.407-419
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• 2002

Atherosclerosis is a chronic inflammatory disease of the arterial wall characterized by progressive accumulation of lipids, cells, and extracellular matrix. Matrix metalloproteinases(MMPs) and tissue inhibitor of metalloproteinases(TIMPS) contribute to vascular matrix remodeling in atherosclerosis, and some cytokines may play role in the synthesis or activation of MMPs or TIMPs. Material and Method： We produced experimental atherosclerotic plaques in 9 rabbits by atherogenic hypercholesterol diet for 12 weeks, and 10 other rabbits were used as control group with standard laboratory chow, At that time, 19 rabbits were sacrificed and aorta, coronary arteries and blood specimens were prepared. The expressions of MMP-9, TIMP-2 and interleukin(IL)-18, and the bioactivity of IL-6 were investigated with H&E stain, immunohistochemical stain, immunoblotting(Western blot analysis), and bioassay. Result： Serum cholesterol in the experimental group increased up to 1258$\pm$262 mg/dL(control group： 41$\pm$7 mg/dL). All experimental group showed well-developed atherosclerotic plaques in aorta and coronary artery. The expression of MMP-9 in aorta and coronary artery of the experimental group showed significant increase than that of the control group by immunohistochemistry. Among the experimental group, complicated lesions with intimal rupture or complete luminal occlusion, demonstrated stronger expression of MMP-9. Interestingly, there was no difference in expression of TIMP-2 between the experimental and the control group. These findings were confirmed by Western blot analysis. The bioassay revealed significant up-regulation of serum bioactivity of IL-6 in the experimental group(4819.60$\pm$2021.25 IU/$m\ell$) compared to that of IL-6 in the control group(27.20 $\pm$ 12.19 IU/$m\ell$). IL-18 was expressed in all atherosclerotic plaques, whereas little or no expression was detected in the control group. Conclusion： The increased MMP-9 expression along with the unchanged TIMP-2 expression seem to be contributory factors in extracellular matrix degradation in atherosclerosis. Focal overexpression of MMP-9 may promote plaque destabilization and cause complications of atherosclerotic plaques such as thrombosis with/without acute coronary syndrome. Elevation of IL-6 and IL-18 may be more than just markers of atherosclerosis but actual participants in lesion development. Identification of critical regulatory pathway is important to improve the understanding of the cellular and molecular basis of atherosclerosis and may open the way for novel therapeutic strategies.