• 한국염색가공학회:학술대회논문집
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• 한국염색가공학회 2011년도 제44차 학술발표회
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• pp.36-36
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• 2011

We synthesized new dye sensor based on indole compound. Through the UV-vis absorptions, we analyzed chemosensing properties to explain metal binding properties. The peak absorptions increased at 472 nm when added metal cations($Cd^{2+}$, $Cu^{2+}$, $Hg^{2+}$, $Fe^{2+}$, $Zn^{2+}$, $Ni^{2+}$ and $Cr^{3+}$) and gradually decreased the peak at 516 nm. Thus, this UV-Vis absorption behavior clearly showed the metal binding reaction. To measure energy level of used dye sensor, HOMO/LUMO energy value was calculated with cyclovaltagramm(CV) and using computational calculation method, in which we estimated the optimum structure of dye sensor. CV and computational calculation method, both compared to find suitable geometric structure. (with almost same energy values.) From the computational calculation, dye sensor has plane structure. So, Amine and ketone in the dye sensor faced each other and makes position to bind metal cations. In addition, these positions was supported pull-push electron system and generated MLCT process, when the dye sensor was bonded with the metal cations and resulted chemosensing properties. Through the electrochemical and computational calculation method analyze, we proposed the chemosensing principles that the dye sensor bind the metal cation between ketone and amine. Finally, the formation type of metal ion bindings was determined by Job's plot measurements.

• 한국정보과학회논문지:소프트웨어및응용
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• 제31권8호
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• pp.991-998
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• 2004

생물 정보학 등 많은 응용 분야에서 데이타 분석을 할 때는 적은 수의 분류표시된 데이터 (labeled data)와 많은 수의 비분류표시된 데이타(unlabeled data)가 있을 수 있다 분류표시된 자료는 사람의 노력이 요구되기 때문에 얻기가 어렵고 비용이 많이 들지만, 비분류표시된 자료는 별 어려움 없이 쉽게 얻을 수 있다. 이때 비분류표시된 자료를 이용하여 자료를 분류하고 분석하는데 널리 이용되고 있는 방법이 co-training 알고리즘이다. 이 방법은 적은 수의 분류표시된 자료에서 두 가지 뷰(view)로 각 분류자를 학습한다. 그리고 각 분류자는 분석하고자 하는 모든 비분류표시된 자료에서 가장 만족할만한 예측자들을 만들어 나간다. 이렇게 훈련 데이타 셋에서 실험을 여러 번 반복적으로 하게 되면 각 뷰에서 새로운 분류자가 학습되어 분류표시된 자료의 수가 증가한다. 본 논문에서는 비분류표시된 데이타를 이용하여 새로운 co-training 방법을 제시한다. 이 방법은 두 가지 분류자와 WebKB 및 BIND XML의 2가지 실험 데이타를 가지고 평가하였다. 실험 결과로서, 이 논문에서 제안한 co-training 방법이 분류표시된 자료의 수가 매우 적을 때 분류정확성을 효과적으로 향상시킬 수 있음을 보였다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.277-287
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• 2003

Acetolactate synthase (ALS, EC 4.1.3.18; also referred to as acetohydroxy acid synthase) catalyzes the first common step in the biosynthesis of valine, leucine, and isoleucine in microorganisms and plants. Recently X-ray structure of yeast ALS was available. Pair-wise alignment of yeast and tobacco ALS sequences revealed 63% sequence similarity. Using Deep View and automatic modeling on Swiss model server, we have generated reliable models of tobacco ALS based on yeast ALS template with a calculated pair-wise RMSD of 0.86 Angstrom. Functional roles of four residues located on the subunit interface (H142, El43, M350, and R376) were examined by site-directed mutagenesis. Seven mutants were generated and purified, of which three mutants (H142T, M350V, and R376F) were found to be inactivated under various assay conditions. The H142k mutant showed moderately altered kinetic properties. The E143A mutant increased 10-fold in K$_m$ value while other parameters remained unchanged. The M350C mutant was strongly resistant to three tested herbicides, while the R376k mutant can bind with herbicide carder at similar affinity to that of wild type enzyme, as determined by tryptophan quenching study. Except M350V mutant, all other mutants were ate to bind with cofactor FAD. Taken together, it is likely that residues H142 and E143 are located at the active site, while residues M350 and R376 are possibly located at the overlapping region of active site and herbicide binding site of the enzyme. Our data also allows us to hypothesize that the interaction between side chains of residues M350 and R376 are probably essential for the correct conformation of the active site. It remains to be elucidated that, whether the herbicide, upon binding with enzyme, inactivates the enzyme by causing change in the active site allosterically, which is unfavorable for catalytic activity.

• BMB Reports
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• 제31권4호
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• pp.370-376
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• 1998

Src-Homology 2 (SH2) domains have a capacity to bind phosphotyrosine-containing sequence context and play essential roles in various cellular signaling pathways. Due to the specific nature of the binding between SH2 domains and their counterpart proteins, inhibitors of SID domain binding have drawn extensive attention as a potential candidate for therapeutic agents. Here, we describe the binding assay system to screen for the ligands or blockers of the SH2 domains with an emphasis on the $p56^{lck}$ SH2 domain. In our assay system, SID domains expressed and purified as fusion proteins to Glutathione-S-transferase (GST) were covalently attached to 96-well microtitre plates through amide bond formation, which were subsequently allowed to bind the biotinylated phosphotyrosine (pY)containing synthetic pep tides. The binding of biotinylated pY peptides was detected by the horseradish peroxidase (HRP)-conjugated streptavidin. Using the various combinations of SH2 domain-pY peptides, we observed that: (1) The binding of pY-peptides to its counterpart SH2 domain is concentration-dependent and saturable; (2) The binding is highly specific for a particular combination of SH2 domain-pY peptide pair; and (3) The binding of Lck SH2-cognate pY-peptides is specifically competed by the nonbiotinylated peptides with expected relative affinity. These results indicate that the established assay system detects the SH2-pY peptide interaction with reproducible sensitivity and specificity and is suitable for screening the specific inhibitors of $p56^{lck}$ SH2 function.

• Journal of Microbiology and Biotechnology
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• 제16권11호
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• pp.1713-1719
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• 2006

A method for the simple, rapid, specific, and accurate detection of Bacillus anthracis spores was developed by employing specific capture peptides conjugated with fluorescent quantum dots (QDs). It was possible to distinguish B. anthracis spores from the spores of B. thuringiensis and B. cereus using these peptide-QD conjugates by flow cytometric and confocal laser scanning microscopic analyses. For more convenient high-throughput detection of B. anthracis spores, spectrofluorometric analysis of spore-peptide-QD conjugates was performed. B. anthracis spores could be detected in less than 1 h using this method. In order to avoid any minor yet false-positive signal caused by the presence of B. thuringiensis spores, the B-Negative peptide, which can only bind to B. thuringiensis, conjugated with another type of QD that fluoresces at different wavelength was also developed. In the presence of mixed B. anthracis and B. thuringiensis spores, the BABA peptide conjugated with QD525 and the B-Negative peptide conjugated with QD585 were able to bind to the former and the latter, specifically and respectively, thus allowing the clear detection of B. anthracis spores against B. thuringiensis spores by using two QD-labeling systems. This capture peptide-conjugated QD system should be useful for the detection of B. anthracis spores.

• Reproductive and Developmental Biology
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• 제42권1호
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• pp.1-6
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• 2018

In this study, we analyzed signal transduction by equine follicle-stimulating hormone receptor (eFSHR) on sti- mulation with recombinant $eelFSH{\beta}/{\alpha}$ ($rec-eelFSH{\beta}/{\alpha}$), natural porcine FSH (pFSH), and natural human FSH (hFSH). cAMP stimulation in CHO-K1 cells expressing eFSHR was determined upon exposure to different doses (0-1450 ng/mL) of these hormones. The $EC_{50}$ value of $rec-eelFSH{\beta}/{\alpha}$ was 53.35 ng/mL. The Rmax values of $rec-eelFSH{\beta}/{\alpha}$ and pFSH were 28.12 and 2.88 ng/mL, respectively. The activity of $rec-eelFSH{\beta}/{\alpha}$ was much higher than that of natural pFSH. However, signal transduction in CHO PathHunter Parental cells expressing eFSHR was not enhanced by stimulation with natural hFSH. Thus, $rec-eelFSH{\beta}/{\alpha}$ was completely active in cells expressing eFSHR. However, natural hFSH did not invoke a signal response in cells expressing eFSHR. Particularly, natural pFSH was weakly active in the same cells. These results showed that $eelFSH{\beta}/{\alpha}$ has potent activity in cells expressing eFSHR. Thus, $rec-eelFSH{\beta}/{\alpha}$ may efficiently bind to eFSHR, where as natural hFSH does not bind to eFSHR.

• Journal of Microbiology and Biotechnology
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• 제25권3호
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• pp.393-398
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• 2015

Aptamers are composed of single-stranded oilgonucleotides that can selectively bind desired molecules. It has been reported that RNA or DNA could act as not only a genetic messenger but also a catalyst in metabolic pathways. RNA aptamers (average sizes 40-50 bp) are smaller than antibodies and have strong binding capacities to target molecules, similar to antigenantibody interactions. Once an aptamer was selected, it can be readily produced in large quantities at low cost. The objectives of this study are to screen and develop aptamers specific to oral pathogens such as Porphyromonas gingivalis, Treponema denticola, and Streptococcus mutans. The bacterial cell pellet was fixed with formaldehyde as a target molecule for the screening of aptamers. The SELEX method was used for the screening of aptamers and a modified western blot analysis was used to verify their specificities. Through SELEX, 40 kinds of aptamers were selected and the specificity of the aptamers to the bacterial cells was confirmed by modified western blot analysis. Through the SELEX method, 40 aptamers that specifically bind to oral pathogens were screened and isolated. The aptamers showed possibility as effective candidates for the detection agents of oral infections.

• JSTS:Journal of Semiconductor Technology and Science
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• 제2권2호
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• pp.132-140
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• 2002

This paper presents an ARM-based SOC bus transaction verification IP and the usage experiences in SOC designs. The verification IP is an AMBA AHB protocol checker, which captures legal AHB transactions in FSM-style signal sequence checking routines. This checker can be considered as a reusable verification IP since it does not change unless the bus protocol changes. Our AHB protocol checker is designed to be scalable to any number of AHB masters and reusable for various AMBA-based SOC designs. The keys to the scalability and the reusability are Object-Oriented Programming (OOP), virtual port, and bind operation. This paper describes how OOP, virtual port, and bind features are used to implement AHB protocol checker. Using the AHB protocol checker, an AHB simulation monitor is constructed. The monitor checks the legal bus arbitration and detects the first cycle of an AHB transaction. Then it calls AHB protocol checker to check the expected AHB signal sequences. We integrate the AHB bus monitor into Verilog simulation environment to replace time-consuming visual waveform inspection, and it allows us to find design bugs quickly. This paper also discusses AMBA AHB bus transaction coverage metrics and AHB transaction coverage analysis. Test programs for five AHB masters of an SOC, four channel DMAs and a host interface unit are executed and transaction coverage for DMA verification is collected during simulation. These coverage results can be used to determine the weak point of test programs in terms of the number of bus transactions occurred and guide to improve the quality of the test programs. Also, the coverage results can be used to obtain bus utilization statistics since the bus cycles occupied by each AHB master can be obtained.

• Bulletin of the Korean Chemical Society
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• 제34권12호
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• pp.3695-3702
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• 2013

A nickel(II) complex $[Ni(H_2biim)_2(H_2O)_2](ClO_4)_2{\cdot}H_2O$ (1) of biimidazole ligand has been synthesized and characterized (Where $H_2biim$ = 2,2'-biimidazole). The single crystal X-ray diffraction of the complex shows a dimeric structure with six coordinated psudo-octahedral geometry. The cyclic voltammograms of complex exhibited one quasireversible reduction wave ($E_{pc}=-0.61V$) and an irreversible oxidation wave ($E_{pa}=1.28V$) in DMF solution. The interaction of the complex with Calf-Thymus DNA (CT-DNA) has been investigated by absorption and fluorescence spectroscopy. The complex is an avid DNA binder with a binding constant value of $1.03{\times}10^5M^{-1}$. The results suggest that the nickel(II) complex bind to CT-DNA via intercalative mode and can quench the fluorescence intensity of EB bind to CT-DNA with $K_{app}$ value of $3.2{\times}10^5M^{-1}$. The complex also shown efficient oxidative cleavage of supercoiled pBR322 DNA in the presence of hydrogen peroxide as oxidizing agent. The DNA cleavage by complex in presence of quenchers; viz. DMSO, KI, $NaN_3$ and EDTA reveals that hydroxyl radical or singlet oxygen mechanism is involved. The complex showed invitro antimicrobial activity against four bacteria and two fungi. The antimicrobial activity was nearer to that of standard drugs and greater than that of the free ligand.

• 대한전자공학회논문지TC
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• 제46권5호
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• pp.36-47
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• 2009

RFID의 리더와 태그간의 비가역성으로 인해 리더들이 밀집한 경우 리더간에 서로 간섭을 일으켜서 태그로부터 오는 신호의 SIR을 낮게 만들어 수신단에서 태그를 식별하지 못하는 RFID 주파수 간섭문제가 존재한다. 현재 이에 대한 해결 방법으로서 서로 다른 시간자원을 할당하는 TDM 기반의 방법들이 제안되고 있다. 그러나 대부분 리더들 간에 최적의 시간 할당을 구하는 것이 아닌 heuristic 스케줄링 알고리즘을 제안하고 있다. 이에 본 논문에서는 리더들 간의 주파수 간섭문제를 게임의 참여자간에 발생되는 이해관계를 해결하는 게임이론을 주파수 간섭문제에 적용함으로써 TDM을 사용하는 RFID 리더간에 발생되는 시간 자원 할당 문제를 사전 협약이 존재하는 협조 게임의과 협약이 존재하지 않는 비협조 게임의 내쉬 협상 해와 내쉬 균형 관점에서 해석해 보았다. 게임이론을 적용한 결과는 밀집리더환경에서는 협조게임의 내쉬 협상 해가 비협조게임의 내쉬 균형보다 더 큰 이득을 만들어 내는 것을 보여주고, 밀집 리더 환경에서의 최적의 시간할당량을 보여준다.