• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.66-72
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• 2003

Toxicogenomics is now emerging as one of the most important genomics application because the toxicity test based on gene expression profiles is expected more precise and efficient than current histopathological approach in pre-clinical phase. One of the challenging points in Toxicogenomics is the construction of intelligent database management system which can deal with very heterogeneous and complex data from many different experimental and information sources. Here we present a new Toxicogenomics database developed as a part of 'Toxicogenomics for Efficient Safety Test (TEST) project'. The TEST database is especially focused on the connectivity of heterogeneous data and intelligent query system which enables users to get inspiration from the complex data sets. The database deals with four kinds of information; compound information, histopathological information, gene expression information, and annotation information. Currently, TEST database has Toxicogenomics information fer 12 molecules with 4 efficacy classes; anti cancer, antibiotic, hypotension, and gastric ulcer. Users can easily access all kinds of detailed information about there compounds and simultaneously, users can also check the confidence of retrieved information by browsing the quality of experimental data and toxicity grade of gene generated from our toxicology annotation system. Intelligent query system is designed for multiple comparisons of experimental data because the comparison of experimental data according to histopathological toxicity, compounds, efficacy, and individual variation is crucial to find common genetic characteristics .Our presented system can be a good information source for the study of toxicology mechanism in the genome-wide level and also can be utilized fur the design of toxicity test chip.

• Journal of Plant Biotechnology
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• v.35 no.2
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• pp.133-140
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• 2008

The modification of DNA and histone plays an important role for gene expression in plant development. The objective of this research is to observe the effects of methylation on the gene expression during dedifferentiation from rice mature seeds to callus and differentiation from callus to shoots. The embryogenic callus with ability to shoot regeneration was not induced on the N6A medium supplemented with 5-azacytidine and abnormal callus with brown color was formed. When the normal rice callus was placed on the regeneration MSRA medium supplemented with 5-azacytidine, the shoot regeneration was inhibited. The results showed that 5-azacytidine, DNA demethylating agent, had negative effects on normal embryogenic callus formation and shoot regeneration. This suggested that DNA methylation of some genes was required for normal cell dedifferentiation and differentiation in tissue culture. The microarray and $GeneFishig^{TM}$ DEG screening were used to observe the gene transcript profile in callus induction and regeneration on N6A (N6 medium + 5-azaC) and MSRA (MS regeneration medium + 5-azaC). Subsets of genes were up-regulated or down-regulated in response to 5-azaC treatments. The genes related with epigenetic regulation, electron transport, nucleic acid metabolism and response to stress were up and down regulated. The different expression of some genes (germin like protein etc.) during callus induction and shoot regeneration was confirmed using RT-PCR and northern blot analysis.

• Journal of the Korean Vacuum Society
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• v.21 no.3
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• pp.164-170
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• 2012

The dependance of degradation on the blue-peak wavelength is investigated with the blue light-emitting diode (LED) of InGaN/GaN with respect to the optical and the electrical characteristics of the devices. The LED devices emitting the blue-peak wavelength ranging from 437 nm to 452 nm is prepared to be stressed for a long aging time with three different currents of 60 mA, 75 mA and 90 mA, respectively. The degradation of optical intensity is observed with and without phosphor in the devices. The device without phosphor has been degraded significantly as the wavelength of blue-peak is decreased while the optical intensity of LED device with phosphor become less sensitive than that of device without phosphor. The electrical property does not depend on the emission peak wavelength. However, the series-resistance of LED device is slowly increased as the aging time is increased. The deformation of device is observed severely the short wavelength of blue-peak even with the same current since the short wavelength is absorbed substantially at the materials of device during the aging time. Consequently, in order to enhance the lifetime of LED devices, it is important to understand the optical degradation property of the materials against the specific wavelengths emitted from the blue chip.

• Journal of Applied Biological Chemistry
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• v.60 no.2
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• pp.149-153
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• 2017

Contamination and growth of Trichoderma, a green mold, on the oak log and wooden chip or sawdust media can severely inhibit the growth of oak mushroom. Chemicals including pesticides and antibiotics are generally not allowed for the control of green mold disease during mushroom cultivation. In this study, bacterial pathogens causing blotch disease on the oyster mushrooms were isolated and their peptide toxins were purified for the control of green mold disease. Strains of Pseudomonas tolaasii secret various peptide toxins, tolaasin and its structural analogues, having antifungal activities. These peptides have shown no effects on the growth of oak mushrooms. When the peptide toxins were applied to the green mold, Trichoderma harzianum H1, they inhibited the growth of green molds. Among the 20 strains of peptide-forming P. tolaasii, strong, moderate, and weak antifungal activities were measured from 8, 5, and 7 strains, respectively. During oak mushroom cultivation, bacterial culture supernatants containing the peptide toxins were sprayed on the aerial mycelia of green molds grown on the surface of sawdust media. The culture supernatants were able to suppress the fungal growth of green molds while no effect was observed on the mushroom growth and production. They changed the color of molds from white aerial mycelium into yellowish dried scab, representing the powerful anti-fungal and sterilization activities of peptide toxins.

• Journal of Animal Science and Technology
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• v.52 no.4
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• pp.329-336
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• 2010

Myogenic satellite cells (MSCs) are mononuclear, multipotent progenitors of adult skeletal muscle possessing a capacity of forming adipocyte-like cells (ALC). To identify the skeletal muscle type-specific myogenic and adipogenic genes during MSCs differentiation, total RNA was extracted from bovine MSCs, myotube-formed cell (MFC), and ALC from each of Beef shank, Longissimus dorsi, Deep pectoral, and Semitendinosus. DNA microarray analysis (24,000 oligo chip) comparing MSCs with MFC and ALC, respectively, revealed 135 differentially expressed genes (> 4 fold) among four cuts. Real-time PCR confirmed expression of 29 genes. Furthermore, the whole tissue sample RNAs analysis showed 6 differentially expressed genes in Beef shank. Among which, 1 gene in MSCs, 4 in MFC, and 1 in ALCs were highly expressed. This study will provide an insight for better understanding the molecular mechanism of differentiation of skeletal muscle type-specific MSCs. The identified genes may be used as marker to distinguish skeletal muscle types.

• Horticultural Science & Technology
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• v.32 no.2
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• pp.171-177
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• 2014

In an effort to investigate special distribution of glucose content of potato tuber of a cultivar 'Superior' after harvest, a whole tuber was longitudinally cut into halves and cut-surface was divided into 11 regions. Approximate glucose concentration of each section was determined using a commercial blood glucose meter. Higher level of glucose was detected in the outer layers of tissue than inner part of tuber although there were lower coefficients of variation value, 37.4% and 34.1% among individual tubers and among defined sections, respectively. A positive correlation between the whole tuber and individual section was existed in glucose content, where the central pith tissue gave the highest coefficient (r = 0.921) and bud end tissue did the lowest (r = 0.544). Glucose content of the tubers stored for 4 months at $2.0^{\circ}C$ was 5.5 fold higher compared to the tubers kept in ambient temperature. The chip color of the former tubers was much brighter than those of the latter tubers. The result obtained in the present study suggests that the blood glucose meter can be used to a rapid and simple evaluation of glucose content and therein be applied to estimate the processing quality of potato tubers during postharvest handling.

• The Journal of the Korea Contents Association
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• v.8 no.6
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• pp.1-7
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• 2008

The paper is to solve the problem of existing sound system, which has difficulties of system organization and the increase of additional install cost and unfriendly interior. To solve the existing system, we drew the new sound system based on PLC and studied it. A transmitter and a receiver were designed using the PLC chip INT5500CS. Sound system was configured with a CD player that sound signals are sent from the transmitter and a speaker connected to the receiver. For analysis of characteristics of this system, a USBPre external sound card and Smaart Live 5 which is a PC-based sound measuring program were added. As a result of our experiment, the measured signal level is $2{\sim}3$[dB] lower than reference signal, latency is 16.69[ms] and the specific character of coherency is bad in high frequency band. Otherwise, this system transmits and receives signals over 90[%] in good condition as a result of measuring pink noise, frequency(1kHz), and phase, magnitude. In view of the result so far achieved, the system designed our team has excellent performance, it resolves defect of existing audio signal transmition system.

• Journal of KIISE:Computer Systems and Theory
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• v.31 no.9
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• pp.514-526
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• 2004

Microarray is a new technique for gene expression experiment, which has gained biologist's attention for recent years. This technology enables us to obtain hundreds and thousands of expression of gene or genotype at once using microarray Since it requires manual work to analyze patterns of gene expression, we want to develop an effective and automated tools to analyze microarray image. However it is difficult to analyze DNA chip images automatically due to several problems such as the variation of spot position, the irregularity of spot shape and size, and sample contamination. Especially, one of the most difficult problems in microarray analysis is the block and spot addressing, which is performed by manual or semi automated work in all the commercial tools. In this paper we propose a new algorithm to address the position of spot and block using a new concept of regular structure grid searching. In our algorithm, first we construct maximal I-regular sequences from the set of input points. Secondly we calculate the rotational angle and unit distance. Finally, we construct I-regularity graph by allowing pseudo points and then we compute the spot/block address using this graph. Experiment results showed that our algorithm is highly robust and reliable. Supplement information is available on http://jade.cs.pusan.ac.kr/~autogrid.

• Proceedings of the Korean Information Science Society Conference
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• 2001.04a
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• pp.37-39
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• 2001

반도체 설계는 급속한 기능 추가와 기가 헬쯔에 육박하는 고속 동작에 부응하는 제품의 설계와 빠른 출시를 위하여 다방면의 연구를 거듭하고 있다. 하지만, 인터넷과 정보 가전의 모바일 기기에서 요구하는 폭발적인 기능의 추가와 가전기기의 최소화를 위하여서는 그 요구를 감당하지 못하고 있다. 이를 위한 방안으로 설계 재활용과 System-On-Chip의 설계가 수년 전부터 대두되었으나 아직 큰 실효를 거두지 못하고 있다. SoC설계는 다기능을 한 칩에 구성하는 방법을 시도하고 있고, 설계 재활용은 기존의 설계(IP)를 다른 것과 혼합하여 필요한 기능을 제공하는 방법이 시도되고 있다. 이 두가지의 VLSI 설계 방식 흐름을 가능하도록 하기 위한 연구로써, 레이아웃 이식에 관한 연구를 진행하였다. IP 재활용을 위하여서는 다양한 공정변화에 신속히 대응하고, 기존의 설계 설계규칙으로 설계된 면을 현재의 공정인 0.25um, 0.18um 테크놀러지에 맞도록 변환하는 VLSI 소프트웨어 시스템을 필요로 한다. 레이아웃 설계도면을 분석하여 소자 및 배선을 인식하는 알고리즘을 연구와 개발하고, 도면을 첨단 테크놀러지의 설계 규칙에 부응하도록 타이밍, 소비 전력, 수율을 고려한 최적의 소자 및 배선의 크기를 조절하는 방법을 고안하며, 칩 면적을 최적화할 수 있는 컴팩션 알고리즘을 개발하여 레이아웃 설계 도면을 이식할 수 있는 자동화 소프트웨어 시스템을 연구하였다. 더불어, 현재 반도체 소프트웨어 시스템의 최대 문제점에 해당하는 처리 속도와 도면의 처리 능력을 비교, 검토하여 본 연구가 속도면에서 평균 27배 효율면에서 3배 이상의 상대우위를 점하였다.전송과 복원이 이루어질 것이다.하지 않은 경우 단어 인식률이 43.21%인 반면 표제어간 음운변화 현상을 반영한 1-Best 사전의 경우 48.99%, Multi 사전의 경우 50.19%로 인식률이 5~6%정도 향상되었음을 볼 수 있었고, 수작업에 의한 표준발음사전의 단어 인식률 45.90% 보다도 약 3~4% 좋은 성능을 보였다.으로서 hemicellulose구조가 polyuronic acid의 형태인 것으로 사료된다. 추출획분의 구성단당은 여러 곡물연구의 보고와 유사하게 glucose, arabinose, xylose 함량이 대체로 높게 나타났다. 점미가 수가용성분에서 goucose대비 용출함량이 고르게 나타나는 경향을 보였고 흑미는 알칼리가용분에서 glucose가 상당량(0.68%) 포함되고 있음을 보여주었고 arabinose(0.68%), xylose(0.05%)도 다른 종류에 비해서 다량 함유한 것으로 나타났다. 흑미는 총식이섬유 함량이 높고 pectic substances, hemicellulose, uronic acid 함량이 높아서 콜레스테롤 저하 등의 효과가 기대되며 고섬유식품으로서 조리 특성 연구가 필요한 것으로 사료된다.리하였다. 얻어진 소견(所見)은 다음과 같았다. 1. 모년령(母年齡), 임신회수(姙娠回數), 임신기간(姙娠其間), 출산시체중등(出産時體重等)의 제요인(諸要因)은 주산기사망(周産基死亡)에 대(對)하여 통계적(統計的)으로 유의(有意)한 영향을 미치고 있어 $25{\sim}29$세(歲)의 연령군에서, 2번째 임신과 2번째의 출산에서 그리고 만삭의 임신 기간에, 출산시체중(出産時體重) $

• The Korean Journal of Physiology and Pharmacology
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• v.12 no.2
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• pp.83-87
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• 2008

The fyn-related kinase (FRK) belongs to the tyrosine kinase family of protein kinases. Recent studies have shown that Frk affects pancreatic beta cell number during embryogenesis and promotes beta cell cytotoxic signals in response to streptozotocin. To investigate the genetic association between FRK polymorphisms and the risk of obesity in Korean population, single nucleotide polymorphisms (SNPs) in the FRK gene region were selected and analyzed. The body mass index (BMI) was calculated, and biochemical data (systolic blood pressure, diastolic blood pressure, hemoglobin A1C, triglyceride, total cholesterol, high density lipoprotein, and low density lipoprotein) of blood sample from each subject were also measured. One hundred fifty five healthy control and 204 overweight/obesity subjects were recruited. Genotype frequencies of six SNPs [rs6568920 (+8391G>A), rs3756772 (+56780A>G), rs3798234 (+75687C>T), rs9384970 (+68506G>A), rs1933739 (+72978G>A), and rs9400883 (+75809A>G)] in the FRK gene were determined by Affymetrix Targeted Genotyping Chip data. According to the classification of Korean Society for the Study of Obesity, control (BMI 18 to < 23) and overweight/obesity (BMI$\geq$23) subjects were recruited. For the analysis of genetic data, EM algorithm, SNPStats, Haploview, HapAnalyzer, SNPAnalyzer, and Helixtree programs were used. Multiple logistic regression analysis (codominant, dominant, and recessive models) was performed. Age and gender as covariates were adjusted. For biochemical data, Student's t test was used. The mean value of BMI in the control and overweigh/obesity groups was 21.1${\pm}$1.2 (mean${\pm}$SD) and 25.6${\pm}$2.0, respectively. All biochemical data of the overweight/obesity group were statistically significance, compared with the control group. Among six SNPs, two linkage disequilibrium (LD) blocks were discovered. One block consisted of rs1933739 and rs9400883, and the other comprised rs3756772 and rs3798234. One SNP (rs9384970, +68506G>A) showed an association with overweight/obesity in the codominant model (p=0.03). Interestingly, the AA genotype distribution in the overweight/obesity group (n=7, 3.5%) was higher than those in the control group (n=1, 0.6%), which is not found in either Japanese or Chinese subjects. Therefore, the AA genotype of rs9384970 may be a risk factor for development of obesity in Korean population. The results suggest that FRK may be associated with overweight/obesity in Korean population.