• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.267-271
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• 2005

The goal of data mining is to extract new and useful knowledge from large scale datasets. As the amount of available data grows explosively, it became vitally important to develop faster data mining algorithms for various types of data. Recently, an interest in developing data mining algorithms that operate on graphs has been increased. Especially, mining frequent patterns from structured data such as graphs has been concerned by many research groups. A graph is a highly adaptable representation scheme that used in many domains including chemistry, bioinformatics and physics. For example, the chemical structure of a given substance can be modelled by an undirected labelled graph in which each node corresponds to an atom and each edge corresponds to a chemical bond between atoms. Internet can also be modelled as a directed graph in which each node corresponds to an web site and each edge corresponds to a hypertext link between web sites. Notably in bioinformatics area, various kinds of newly discovered data such as gene regulation networks or protein interaction networks could be modelled as graphs. There have been a number of attempts to find useful knowledge from these graph structured data. One of the most powerful analysis tool for graph structured data is frequent subgraph analysis. Recurring patterns in graph data can provide incomparable insights into that graph data. However, to find recurring subgraphs is extremely expensive in computational side. At the core of the problem, there are two computationally challenging problems. 1) Subgraph isomorphism and 2) Enumeration of subgraphs. Problems related to the former are subgraph isomorphism problem (Is graph A contains graph B?) and graph isomorphism problem(Are two graphs A and B the same or not?). Even these simplified versions of the subgraph mining problem are known to be NP-complete or Polymorphism-complete and no polynomial time algorithm has been existed so far. The later is also a difficult problem. We should generate all of 2$^n$ subgraphs if there is no constraint where n is the number of vertices of the input graph. In order to find frequent subgraphs from larger graph database, it is essential to give appropriate constraint to the subgraphs to find. Most of the current approaches are focus on the frequencies of a subgraph: the higher the frequency of a graph is, the more attentions should be given to that graph. Recently, several algorithms which use level by level approaches to find frequent subgraphs have been developed. Some of the recently emerging applications suggest that other constraints such as connectivity also could be useful in mining subgraphs : more strongly connected parts of a graph are more informative. If we restrict the set of subgraphs to mine to more strongly connected parts, its computational complexity could be decreased significantly. In this paper, we present an efficient algorithm to mine frequent subgraphs that are more strongly connected. Experimental study shows that the algorithm is scaling to larger graphs which have more than ten thousand vertices.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.36-36
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• 2017

Out of twenty common protein amino acids, there are many kinds of non protein amino acids (NPAAs) that exist as secondary metabolites and exert ecological functions in plants. Mimosine (Mim), one of those NPAAs derived from L. leucocephala acts as an iron chelator and reversely block mammalian cell cycle at G1/S phases. Cysteine (Cys) is decisive for protein and glutathione that acts as an indispensable sulfur grantor for methionine and many other sulfur-containing secondary products. Cys biosynthesis includes consecutive two steps using two enzymes-serine acetyl transferase (SAT) and O-acetylserine (thiol)lyase (OASTL) and appeared in plant cytosol, chloroplast, and mitochondria. In the first step, the acetylation of the ${\beta}$-hydroxyl of L-serine by acetyl-CoA in the existence of SAT and finally, OASTL triggers ${\alpha}$, ${\beta}$-elimination of acetate from OAS and bind $H_2S$ to catalyze the synthesis of Cys. Mimosine synthase, one of the isozymes of the OASTLs, is able to synthesize Mim with 3-hydroxy-4-pyridone (3H4P) instead of $H_2S$ for Cys in the last step. Thus, the aim of this study was to clone and characterize the cytosolic (Cy) OASTL gene from L. leucocephala, express the recombinant OASTL in Escherichia coli, purify it, do enzyme kinetic analysis, perform docking dynamics simulation analysis between the receptor and the ligands and compare its performance between Cys and Mim synthesis. Cy-OASTL was obtained through both directional degenerate primers corresponding to conserved amino acid region among plant Cys synthase family and the purified protein was 34.3KDa. After cleaving the GST-tag, Cy-OASTL was observed to form mimosine with 3H4P and OAS. The optimum Cys and Mim reaction pH and temperature were 7.5 and $40^{\circ}C$, and 8.0 and $35^{\circ}C$ respectively. Michaelis constant (Km) values of OAS from Cys were higher than the OAS from Mim. Inter fragment interaction energy (IFIE) of substrate OAS-Cy-OASTL complex model showed that Lys, Thr81, Thr77 and Gln150 demonstrated higher attraction force for Cys but 3H4P-mimosine synthase-OAS intermediate complex showed that Gly230, Tyr227, Ala231, Gly228 and Gly232 might provide higher attraction energy for the Mim. It may be concluded that Cy-OASTL demonstrates a dual role in biosynthesis both Cys and Mim and extending the knowledge on the biochemical regulatory mechanism of mimosine and cysteine.

• Journal of Society of Preventive Korean Medicine
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• v.21 no.2
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• pp.1-13
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• 2017

Objectives : This paper serves to explore current trends of systems biology in Traditional Chinese Medicine (TCM) and examine how it may influence the Traditional Korean medicine. Methods : Literature review method was collectively used to classify Introduction to systems biology, diagnosis and syndrome classification of systems biology in TCM perspective, physiotherapy including acupuncture, herbs and formula functions, TCM systems biology, and directions of academic development. Results : The term 'Systems biology' is coined as a combination of systems science and biology. It is a field of study that tries to understand living organism by establishing a theory based on an ideal model that analyzes and predicts the desired output with understanding of interrelationships and dynamics between variables. Systems biology has an integrated and multi-dimensional nature that observes the interaction among the elements constructing the network. The current state of systems biology in TCM is categorized into 4 parts: diagnosis and syndrome, physical therapy, herbs and formulas and academic development of TCM systems biology and its technology. Diagnosis and syndrome field is focusing on developing TCM into personalized medicine by clarifying Kidney yin deficiency patterns and metabolic differences among five patterns of diabetes and analyzing plasma metabolism and biomarkers of coronary heart disease patients. In the field of physical therapy such as acupuncture and moxibustion, researchers discovered the effect of stimulating acupoint ST40 on gene expression and the effects of acupuncture on treating functional dyspepsia and acute ischemic stroke. Herbs and formulas were analyzed with TCM network pharmacology. The therapeutic mechanisms of Si Wu Tang and its series formulas are explained by identifying potential active substances, targets and mechanism of action, including metabolic pathways of amino acid and fatty acid. For the academic development of TCM systems biology and its technology, it is necessary to integrate massive database, integrate pharmacokinetics and pharmacodynamics, as well as systems biology. It is also essential to establish a platform to maximize herbal treatment through accumulation of research data and diseases-specific, or drug-specific network combined with clinical experiences, and identify functions and roles of molecules in herbs and conduct animal-based studies within TCM frame. So far, few literature reviews exist for systems biology in traditional Korean medicine and they merely re-examine known efficacies of simple substances, herbs and formulas. For the future, it is necessary to identify specific mechanisms of working agents and targets to maximize the effects of traditional medicine modalities. Conclusions : Systems biology is widely accepted and studied in TCM and already advanced into a field known as 'TCM systems biology', which calls for the study of incorporating TCM and systems biology. It is time for traditional Korean medicine to acknowledge the importance of systems biology and present scientific basis of traditional medicine and establish the principles of diagnosis, prevention and treatment of diseases. By doing so, traditional Korean medicine would be innovated and further developed into a personalized medicine.

• Science of Emotion and Sensibility
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• v.20 no.4
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• pp.89-100
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• 2017

Since smart devices are able to efficiently provide information without barriers of time and location, they are widely utilized with advent of the hyper-connected society. Especially, the smart devices have been developed in the form of wearable devices for mutual interaction between human and objects. Smart clothing, which embeds smart devices within clothes, measures and obtains a variety of bio-signals as it is in close contact with the human bodies. Conventional smart clothing generated wearers' discomfort because they were developed by simple attachment of electronic devices to clothes. Therefore, it is highly recommended to develop novel smart clothing based on smart textiles which integrate electronic devices as parts of textiles. As smart watches are currently the most available wearable devices in the market, smart watch users were selected in this study, for the purpose of investigating core needs of wearable smart device users based on the user experience and user's sensibility. Qualitative research was performed through semi-structured interview in order to obtain detailed answers about user sensibility based on smart watch user experience. After the in-depth interview, the user's sensibility was categorized into four aspects; functional, aesthetic, social, and empirical. Sensibility adjectives and key words were assigned to each aspect and their frequency was analyzed. It was the functional aspect of sensibility that the wearable device users require the most. The results of this study will be utilized as a fundamental data to develop the smart textiles required for the next generation of smart clothing which is attracting as a future wearable device.

• Journal of Life Science
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• v.27 no.2
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• pp.149-154
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• 2017

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-hodgkin lymphoma. Advances in the chemotherapeutic treatment of this disease have improved the outcomes of DLBCL; nonetheless, many patients still die of DLBCL, and therefore, a better understanding of this disease and identification of novel therapeutic targets are urgently required. In a recent gene expression profiling study, PDE (phosphodiesterase) 4B was found to be overexpressed in chemotherapy-resistant tumors. The major function of PDE4B is to inactivate the second messenger cyclic 3',5' monophosphate (cAMP) by catalyzing the hydrolysis of cAMP to 5'AMP. It is known that cAMP induces cell cycle arrest and/or apoptosis in B cells, and PDE4B abolishes cAMP's effect on B cells. However, the mechanism by which PDE4B is overexpressed remains unclear. Here, we show that the aberrant expression of miRNA may be associated with the overexpression of this gene. The PDE4B 3' untranslated region (UTR) has three functional binding sites of miR-23b, as confirmed by luciferase reporter assays. Interestingly, miR-23b-binding sites were evolutionarily conserved from humans to lizards, implying the critical role of PDE4B-miR-23b interaction in cellular physiology. The ectopic expression of miR-2 3b repressed PDE4B mRNA levels and enhanced intracellular cAMP concentrations. Additionally, miR-23b expression inhibited cell proliferation and survival of DLBCL cells only in the presence of forskolin, an activator of adenylyl cyclase, suggesting that miR-23b's effect is via the downregulation of PDE4B. These results together suggest that miR-23b could be a therapeutic target for overcoming drug resistance by repressing PDE4B in DLBCL.

• Journal of Life Science
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• v.13 no.3
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• pp.314-323
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• 2003

The purpose of this study was to examine the effects of xenobiotic nuclear receptors, CAR, SXR, and PPAR${\gamma}$ on the transcriptional activity of estrogen receptor in human breast cancer cell lines and compare with those in human hepatoma cell line. Two different breast cancer cell lines, MCF-7 and MDA-MB-231 were cultured and effects of CAR, SXR, and PPAR${\gamma}$ on the ER-mediated transcriptional activation of synthetic (4ERE)-tk-luciferase reporter gene were analyzed. Consistent with the previous report, CAR significantly inhibited ER-mediated transactivation and SXR repressed modestly whereas the PPAR${\gamma}$ did not repress the ER-mediated transactivation. However, in breast cancer cells neither of the xenobiotic receptors repressed the ER-mediated transactivation. Instead, they tend to increase the transactivation depending on the cell type and xenobiotic nuclear receptors. In MCF-7, SXR but neither CAR nor PPAR${\gamma}$ slightly increased ER-mediated transactivation whereas in MDA-MB-231, CAR and PPAR${\gamma}$ but not SXR tend to increase the transactivation of the reporter gene. These results indicate that the effects of ER cross-talk by the CAR, SXR, and PPAR${\gamma}$ , are different in breast cancer cells from hepatoma cells. In conclusion, the transcriptional regulation by estrogen can involve different cross-talk interaction between estrogen receptor and xenobiotic nuclear receptors depending on the estrogen target cells.

• Journal of Life Science
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• v.26 no.9
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• pp.1027-1032
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• 2016

Antigen is substance causing disease derived from pathogen. Living organism has the immune system in terms of defense mechanism against antigen. Antigen is processed through several pathways such as phagocytosis, antibody action, complement activation, and cytotoxins by NK or cytotoxic T lymphocyte via MHC molecule. Lymph node (LN) is comprised of the complicated 3 dimensional network and several stromal cells. Fibroblastic reticular cells (FRC) are distributed in T zone for interaction with T cells. FRC produces the extra cellular matrix (ECM) into LN for ECM reorganization against pathogen infections and secretes homing chemokines. However, it has not so much been known about the involvement of the antigen process of FRC. The present report is for the function of FRC on antigen process. For this, FRC was positioned with several infected situations such as co-culture with macrophage, T cell, lipopolysaccharide (LPS) and TNFα stimulation. When co-culture between FRC with macrophage and T cells was performed, morphological change of FRC was observed and empty space between FRCs was made by morphological change. The matrix metallo-proteinase (MMP) activity was up-regulated by Y27632 and T cells onto FRC. Furthermore, inflammatory cytokine, TNFα regulated the expression of adhesion molecules and MHC I antigen transporter in FRC by gene chip assay. NO production was elevated by FRC monolayer co-cultured with macrophage stimulated by LPS. GFP antigen was up-taken by macrophage co-cultured with FRC. Collectively, it suggests that FRC assists of the facilitation of antigen process and LN stroma is implicated into antigen process pathway.

• Molecules and Cells
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• v.38 no.1
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• pp.40-50
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• 2015

In the interaction between plants and pathogens, carbon (C) resources provide energy and C skeletons to maintain, among many functions, the plant immune system. However, variations in C availability on pathogen associated molecular pattern (PAMP) triggered immunity (PTI) have not been systematically examined. Here, three types of starch mutants with enhanced susceptibility to Pseudomonas syringae pv. tomato DC3000 hrcC were examined for PTI. In a dark period-dependent manner, the mutants showed compromised induction of a PTI marker, and callose accumulation in response to the bacterial PAMP flagellin, flg22. In combination with weakened PTI responses in wild type by inhibition of the TCA cycle, the experiments determined the necessity of C-derived energy in establishing PTI. Global gene expression analyses identified flg22 responsive genes displaying C supply-dependent patterns. Nutrient recycling-related genes were regulated similarly by C-limitation and flg22, indicating re-arrangements of expression programs to redirect resources that establish or strengthen PTI. Ethylene and NAC transcription factors appear to play roles in these processes. Under C-limitation, PTI appears compromised based on suppression of genes required for continued biosynthetic capacity and defenses through flg22. Our results provide a foundation for the intuitive perception of the interplay between plant nutrition status and pathogen defense.

• Proceedings of the Korean Society of Medical Physics Conference
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• 2003.09a
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• pp.44-44
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• 2003

As a basic measurement tool in the areas of animal models of human disease, gene expression and therapy, and drug discovery and development, small animal PET imaging is being used increasingly. An ideal small animal PET should have high sensitivity and high and uniform resolution across the field of view to achieve high image quality. However, the combination of long narrow pixellated crystal array and small ring diameter of small animal PET leads to the degradation of spatial resolution for the source located at off center. This degradation of resolution can be improved by determining the depth of interaction (DOI) in the crystal and by taking into account the information in sorting the coincident events. Among a number of 001 identification schemes, dual layer phsowich detector has been widely investigated by many research groups due to its practicability and effectiveness on extracting DOI information. However, the effects of each crystal length composing dual layer phoswich detector on DOI measurements and image qualities were not fully characterized. In order to minimize the DOI effect, the length of each layer of phoswich detector should be optimized. The aim of this study was to perform simulations using a simulation tool, GATE to design the optimum lengths of crystals composing a dual layer phoswich detector. The simulated small PET system employed LSO front layer LuYAP back layer phoswich detector modules and the module consisted of 8${\times}$8 arrays of dual layer crystals with 2 mm ${\times}$ 2 mm sensitive area coupled to a Hamamatsu R7600 00 M64 PSPMT. Sensitivities and variation of radial resolutions were simulated by varying the length of LSO front layer from 0 to 10 mm while the total length (LSO + LuYAP) was fixed to 20 mm for 10 cm diameter ring scanner. The radial resolution uniformity was markedly improved by using DOI information. There existed the optimal lengths of crystal layers to minimize the variation of radial resolutions. In 10 cm ring scanner configuration, the radial resolution was kept below 3.4 mm over 8 cm FOV while the sensitivity was higher than 7.4% for LSO 5 mm : LuYAP 15 mm phoswich detector. In this study, the optimal length of dual layer phoswich detector was derived to achieve high and uniform radial resolution.

• Korean journal of communication and information
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• v.41
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• pp.337-382
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• 2008

This study examined the case of women's conflict experience in small and medium size enterprises. Although the number of women working in business organizations is rapidly growing in Korea, discourse about them is still scarce. Some discourse about them focuses only on the productivity and inequality aspects within the organizations. Therefore, we need to examine their organizational lives through a more dynamic and performance based perspective. Especially, because conflicts experience by women within business organizations involve a variety of organizational interactions, they reveal the vivid reality with which working women face today. The existing conflict research studies focused on communication or interpersonal relationship are limited by the fact that they have primarily dealt with the variables such as conflict management styles. However, conflict research needs a more specific and wholistic interpretation because conflicts usually depend on their contexts and interaction dynamics. Therefore, the phenomenological methodology was employed as a more appropriate method for the current conflict study. Results shows that the two themes were identified regarding the conflict content. The first and second themes were the unfair situations and the hierarchical rank respectively. The three themes were identified regarding the attitudes about conflicts. They were the passive stance toward conflicts, the recognition of the gender difference, and the acknowledgement of the importance of the relational aspect respectively. Finally, three more themes were identified regarding the conflict management styles. The first, second and third themes were the passive responding, the aggressive responding and the positive conflict management respectively. In addition, the implications of the results and the suggestions for future studies were made.