• BMB Reports
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• 제37권6호
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• pp.648-656
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• 2004

This paper deals with the development of a predictive probabilistic model, a composite dependency-reflecting model (CDRM), which was designed to detect core promoter regions and transcription start sites (TSS) in vertebrate genomic DNA sequences, an issue of some importance for genome annotation. The model actually represents a combination of first-, second-, third- and much higher order or long-range dependencies obtained using the expanded maximal dependency decomposition (EMDD) procedure, which iteratively decomposes data sets into subsets on the basis of dependency degree and patterns inherent in the target promoter region to be modeled. In addition, decomposed subsets are modeled by using a first-order Markov model, allowing the predictive model to reflect dependency between adjacent positions explicitly. In this way, the CDRM allows for potentially complex dependencies between positions in the core promoter region. Such complex dependencies may be closely related to the biological and structural contexts since promoter elements are present in various combinations separated by various distances in the sequence. Thus, CDRM may be appropriate for recognizing core promoter regions and TSSs in vertebrate genomic contig. To demonstrate the effectiveness of our algorithm, we tested it using standardized data and real core promoters, and compared it with some current representative promoter-finding algorithms. The developed algorithm showed better accuracy in terms of specificity and sensitivity than the promoter-finding ones used in performance comparison.

• 대한음성학회지:말소리
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• 제31_32호
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• pp.51-82
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• 1996

The purpose of this paper is to gather pairs of heteronyms in Modem Korean and to propose that all of them should be differentiated in both the Hanngul orthography and Romanization as well as in the IPA transcription. More than a quarter of the whole Korean vocabulary consists of words with a long vowel and the number of minimal pairs distinguished only by the chroneme reaches nearly ten thousand (ie. twenty thousand words). It is suggested here that the letter s in Hanngul and the letter 'h' in the Roman alphabet be used to represent the long vowel. Another factor which brings forth lots of heteronyms in Korean is the lacking of enough indication as to non-automatic reinforcement in the initial consonant o( a word (or a morpheme) when following another within a phrase (or a word). It is proposed here that the non-automatincally rienforced word-initial consonant should be written with the letter h (like ㅺ, ㅼ, ㅽ, ㅾ) and an apostrophe (like 물'새 or 밭'이랑, 물'약) in Hanngul, and with the letter c and an apostrophe (like c'g-, c'd-, c'b-, c'j- ) in the Roman alphabet The morpheme-initial reinforced consonant within a word is written with the letters k, 1, p and cz for ㅺ, ㅼ, ㅽ, and ㅾ respectively. The contrasted pronunciations of pairs of heteronyms beginning with ㅁ/m sound are transcribed here for exemplification in the IPA, Roman alphabet and Hanngul.

• 한국축산식품학회지
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• 제33권3호
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• pp.395-402
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• 2013

Sodium chloride is used to improve various properties of processed meat products, e.g., taste, preservation, water binding capacity, texture, meat batter viscosity, safety, and flavor; however, many studies have shown that sodium chloride increases the resistance of many foodborne pathogens to heat and acid. Listeria monocytogenes has been isolated from various readyto- eat (RTE) meat and dairy products formulated with sodium chloride; therefore, the objective of this paper was to review the effects of sodium chloride on the physiological characteristics of L. monocytogenes. The exposure of L. monocytogenes to sodium chloride may increase biofilm formation on foods or food contact surfaces, virulence gene transcription, invasion of Caco-2 cells, and bacteriocin production, depending on L. monocytogenes strain and serotype as well as sodium chloride concentration. When L. monocytogenes cells were exposed to sodium chloride, their resistance to UV-C irradiation and freezing temperatures increased, but sodium chloride had no effect on their resistance to gamma irradiation. The morphological properties of L. monocytogenes, especially cell elongation and filament formation, also change in response to sodium chloride. These findings indicate that sodium chloride affects various physiological responses of L. monocytogenes and thus, the effect of sodium chloride on L. monocytogenes in RTE meat and dairy products needs to be considered with respect to food safety. Moreover, further studies of microbial risk assessment should be conducted to suggest an appropriate sodium chloride concentration in animal origin foods.

• 정보관리연구
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• 제19권1호
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• pp.95-122
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• 1988

지금까지 데이터베이스를 만들 때에 일정한 표기기준(表記基準)이 없어서 정보교환(情報交換)이 불가능하였으며, 검색(檢索)에 있어서도 어려움이 있었다. 이 자료(資料)에서는 검색(檢索)을 위한 데이터베이스를 제작(製作)할 때에 사용하는 기호(記號)와 용어(用語)의 표기법(表記法)을 제시하고 있다. 학술논문(學術論文)을 기술(記述)할 때에 사용되고 있는 기호(記號)와 문자(文字) 가운데 컴퓨터 단말기(端末機)를 통하여 입력(入力) 및 검색(檢索)이 곤란한 경우가 있으므로 이러한 기호(記號)와 문자(文字)를 입력(入力) 검색(檢索)이 가능한 형태(形態)로 표현하는 방법(方法)을 고안했으며, 문교부(文敎部)가 고시한 "한글 맞춤법"과 "외래어 표기법"을 검토하여 2가지 이상으로 표기(表記)가 가능한 부분에 대해 검색효율(檢索效率)이 높아지는 쪽을 택해 일정하게 용어(用語)를 표기(表記)하도록 규정(規定)했다.

• Journal of Life Science
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• 제11권2호
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• pp.94-98
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• 2001

Type I signal peptidase cleaves the signal sequence from the amino terminus of membrane and secreted proteins afters these protein insert across the membrane. This enzyme serves as a potential target for the development of novel antibacterial agents due to its unique physiological and biochemical properties. Despite considerable research, the signal peptidase assay still remains improvement to provide further understanding of the mechanism and high-throughput inhibitor screening of this enzyme. In this paper, three known signal peptidase assays are tested with an E. coli D276A mutant signal peptidase to distinguish the sensitivity of each assays. In vitro assay using the procoat synthesized by in vitro transcription translation shows that the D276A signal peptidase I was inactive while in vivo processing of pro-OmpA expressed in the temperature-sensitive E. coli strain IT41 as well as in vitro assay using pro-OmpA nuclease A substrate show that D276A signal peptidase I has activity like wild-type signal peptidase. These results suggest that in vitro assay using the pro-OmpA nuclease A and in vivo pro-OmpA processing assay are more sensitive monitors than in vitro assay using the pro-coat. In conculsion, caution should be used when interpreting the in vitro results using the procoat.

• Bulletin of the Korean Chemical Society
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• 제34권11호
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• pp.3405-3409
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• 2013

The activation of heat shock factor 1 (HSF1) can be induced by the changes in environmental pH, but the mechanism of HSF1 activation by acidification is not completely understood. This paper reports that a low pH (pH~6.0) can trigger human HSF1 activation. Considering the involvement of the imidazole group of histidine residues under acid pH stress, an in vitro EMSA experiment, Trp-fluorescence spectroscopy, and protein structural analysis showed that the residue, His83, is the essential for pH-dependent human HSF1-activation. To determine the roles of His83 in the HSF1-mediated stress response affecting the cellular acid resistance, mouse embryo fibroblasts with normal wild-type or mutant mouse HSF1 expression were preconditioned by heating or pH stress. The results suggest that His83 is essential for HSF1 activation or the HSF1-mediated transcription of heat shock proteins, in protecting cells from acid pH stress.

• The Journal of the Acoustical Society of Korea
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• 제22권4E호
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• pp.141-149
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• 2003

As music of digital form has been widely used, many people have been interested in the automatic extraction of natural information of music itself, such as key of a music, chord progression, melody progression, tempo, etc. Although some studies have been tried, consistent and reliable results of musical information extraction had not been achieved. In this paper, we propose a method to extract chord and tempo information from general polyphonic music signals. Chord can be expressed by combination of some musical notes and those notes also consist of some frequency components individually. Thus, it is necessary to analyze the frequency components included in musical signal for the extraction of chord information. In this study, we utilize a sinusoidal modeling, which uses sinusoids corresponding to frequencies of musical tones, and show reliable chord extraction results of sinusoidal modeling. We could also find that the tempo of music, which is the one of remarkable feature of music signal, interactively supports the chord extraction idea, if used together. The proposed scheme of musical feature extraction is able to be used in many application fields, such as digital music services using queries of musical features, the operation of music database, and music players mounting chord displaying function, etc.

• Bulletin of the Korean Chemical Society
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• 제33권11호
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• pp.3719-3726
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• 2012

Formation of Z-DNA, a left-handed double helix, from B-DNA, the canonical right-handed double helix, occurs during important biological processes such as gene expression and DNA transcription. Such B-Z transitions can also be induced by high salt concentration in vitro, but the changes in the relative stability of B-DNA and Z-DNA with salt concentration have not been fully explained despite numerous attempts. For example, electrostatic effects alone could not account for salt-induced B-Z transitions in previous studies. In this paper, we propose that the B-Z transition can be explained if counterion entropy is considered along with the electrostatic interactions. This can be achieved by conducting all-atom, explicit-solvent MD simulations followed by MM-PBSA and molecular DFT calculations. Our MD simulations show that counterions tend to bind at specific sites in B-DNA and Z-DNA, and that more ions cluster near Z-DNA than near B-DNA. Moreover, the difference in counterion ordering near B-DNA and Z-DNA is larger at a low salt concentration than at a high concentration. The results imply that the exclusion of counterions by Z-DNA-binding proteins may facilitate Z-DNA formation under physiological conditions.

• Journal of Microbiology
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• 제43권5호
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• pp.411-416
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• 2005

The high-throughput sequencing of microbial genomes has resulted in the relatively rapid accumulation of an enormous amount of genomic sequence data. In this context, the problem posed by the detection of promoters in genomic DNA sequences via computational methods has attracted considerable research attention in recent years. This paper addresses the development of a predictive model, known as the dependence decomposition weight matrix model (DDWMM), which was designed to detect the core promoter region, including the -10 region and the transcription start sites (TSSs), in prokaryotic genomic DNA sequences. This is an issue of some importance with regard to genome annotation efforts. Our predictive model captures the most significant dependencies between positions (allowing for non­adjacent as well as adjacent dependencies) via the maximal dependence decomposition (MDD) procedure, which iteratively decomposes data sets into subsets, based on the significant dependence between positions in the promoter region to be modeled. Such dependencies may be intimately related to biological and structural concerns, since promoter elements are present in a variety of combinations, which are separated by various distances. In this respect, the DDWMM may prove to be appropriate with regard to the detection of core promoter regions and TSSs in long microbial genomic contigs. In order to demonstrate the effectiveness of our predictive model, we applied 10-fold cross-validation experiments on the 607 experimentally-verified promoter sequences, which evidenced good performance in terms of sensitivity.

• 한국정밀공학회지
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• 제22권6호
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• pp.55-60
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• 2005

This paper has been focused in developing of plastic lens with ultra-precision and low birefringence ability using by injection molding simulation tools. The simulation tools, $3D-Timon^{TM}\;and\;Asu-Mold^{TM}$ were applied to visualize indirectly the flow pattern of melted polymer enter the mould and the simulation results are verified as compared with the experimental results. Birefringence and polarized light generated in injection molding process was also calculated for each injection conditions and compared with .the pictures of experimented optical lens go through the polarized light plates device. A spherical radius of plastic optical lens transcribed from profile of mould core surface was measured to estimate the geometrical accuracy fer the each injection conditions. It is confirmed that the simulation results about flow pattern and polarized light area coincided in experimental results. It is known that increasing in thickness shrinkage at center of lens, the spherical radius is larger from comparing the graph measured spherical radius and the thickness shrinkage at center of lens