• Journal of the Korean Society for Aeronautical & Space Sciences
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• v.42 no.2
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• pp.108-118
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• 2014

On the optimization design problem using surrogate model, it requires considerable number of sampling points to construct a surrogate model which retains the accuracy. As an alternative to reduce construction cost of the surrogate model, Variable-Fidelity Modeling(VFM) technique, where correct high fidelity model based on the low fidelity surrogate model is introduced. In this study, hierarchical kriging model for variable-fidelity surrogate modeling is used and an optimization framework with multi-objective genetic algorithm(MOGA) is presented. To prove the feasibility of this framework, airfoil design optimization process is performed for the transonic region. The parameters of PARSEC are used to design variables and the optimization process is performed in case of varying number of grid and varying fidelity. The results showed that pareto front of all variable-fidelity models are similar with its single-level of fidelity model and calculation time is considerably reduced. Based on computational results, it is shown that VFM is a more efficient way and has an accuracy as high as that single-level of fidelity model optimization.

• BMB Reports
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• v.37 no.2
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• pp.167-176
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• 2004

Although efficient antiviral lamivudine is used for HBV-infected patients, a prolonged treatment with nucleoside analogs often results in lamivudine-resistant variants. In this study, we evaluated the fidelity of the lamivudine-resistant variants. The FLAG-tagged wild-type (FPolE) and Met550 variants (FPolE/M550A, M550V, and M550I) of HBV DNA polymerases were expressed in insect cells then purified. Like many other reverse transcriptases, no $3'{\rightarrow}5'$ exonuclease activity was detected in the HBV DNA polymerase. Since there is no proofreading activity, then the use of the site-specific nucleotide misincorporation method is beneficial. From the $f_{ins}$ value analysis, it is evident that M550I and M550V exhibit higher fidelity values than the wild-type HBV DNA polymerase, while M550A exhibits similar fidelity values. It is therefore suggested that lamivudine resistance comes from the stringency to dNTP binding and the discrimination of dCTP and lamivudine in M550V and M550I.

• BMB Reports
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• v.37 no.3
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• pp.269-274
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• 2004

DNA polymerases without the 3' exonuclease function ($exo^-$ pol) have been widely used in sequencing and SNP genotyping. As a major player that expedited the coming of the postgenomic era, $exo^-$ polymerases worked remarkably well in the Human Genome Sequencing Project. However, it has become a challenge for this class of polymerases to efficiently screen the large number of SNPs that are found in the human genome. For more than three decades it has been recognized that polymerase fidelity varied according to the presence of proofreading activity that is mediated by its internal 3' exonuclease. Polymerases with proofreading function are famous for their high fidelity in DNA replication both in vivo and in vitro, but this well-known class of polymerases has been almost completely neglected in genetic analysis in the postgenomic era. We speculate that $exo^+$ polymerases may exhibit higher nucleotide identification ability when compared to $exo^-$ polymerases for an in vitro genetic analysis. With the application of $exo^+$ polymerases in SNP assays, a novel mechanism for the maintenance of DNA replication, the on/off switch, was discovered. Two new SNP assays have been developed to carry out genome-wide genotyping, taking advantage of the enzymatic properties of $exo^+$ polymerases. Furthermore, the on/off switch mechanism embodies a powerful nucleotide identification ability, which can be used to discriminate the bases that are upstream of the 3' terminus, and thus defines a new concept in de novo sequencing technology. Application of $exo^+$ polymerases to genetic analysis, and especially SNP assays, will greatly accelerate the pace to personalized medicine.

• Journal of Forest and Environmental Science
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• v.38 no.3
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• pp.152-158
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• 2022

A cryopreservation is an essential tool for preservation of germplasm. In this study, the possibility for cryopreservation of embryogenic cells of Siberian ginseng (Eleutherococcus senticosus) in liquid nitrogen (-196℃) was evaluated. The effects of glycerol and dimethyl sulfoxide (DMSO) at different concentrations (5%, 10% and 20%) as cryoprotectants on regrowth of cryopreserved E. senticosus embryogenic cells were tested. There was significant effect of cryoprotectants on regrowth of embryogenic cells (p=0.0019). The highest and lowest fresh mass gain were achieved when embryogenic cells were frozen with 10% DMSO and 5% glycerol (138.2±5.9 and 61.3±14.6, respectively). The effect of the cryoprotectants on the frequency embryo germination was tested. There was no significant difference between glycerol and DMSO (p=0.846). Three different concentrations of cryoprotectants did not significantly affect the frequency embryo germination (p=0.534). Finally, the genetic fidelity of the plantlets regenerated from non-cryopreserved and cryopreserved embryogenic cells was tested by random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analysis. RAPD and ISSR analysises showed that there was no genetic variation among regenerants.

• Journal of Plant Biotechnology
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• v.6 no.2
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• pp.119-124
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• 2004

For long-term conservation of germ plasm, somatic embryos of sweet potato are important because shoot tips are not amenable to liquid nitrogen storage. Somatic embryos from different genotypes were used for induction of somatic embryogenesis in a large number of genotypes. Somatic embryogenesis was induced on 2,4-D medium in all the 11 genotypes, collected from geographically distinct locations. Genetic fidelity of the regenerated plants was confirmed by morphological and RAPD markers.

• Journal of computational fluids engineering
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• v.17 no.4
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• pp.56-68
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• 2012

Nowadays, Unmanned Combat Air Vehicle(UCAV) has become an important aircraft system for the national defense. For its efficiency and survivability, shape optimization of UCAV is an essential part of its design process. In this paper, shape optimization of UCAV was processed for aerodynamic performance improvement and Radar Cross Section(RCS) reduction using Multi Objective Genetic Algorithm(MOGA). Lift and induced drag, friction drag, RCS were calculated using panel method, boundary layer theory, Physical Optics(PO) approximation respectively. In particular, calculation applied Radar Absorbing Material(RAM) was performed for the additional RCS reduction. Results are indicated that shape optimization is performed well for improving aerodynamic performance, reducing RCS. Further study will be performed with higher fidelity tools and consider other design segments including structure.

• Journal of computational fluids engineering
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• v.14 no.1
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• pp.53-61
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• 2009

The objective of this research is to design blade planform to reduce high speed impulsive(HSI) noise from a non-lifting helicopter rotor using CFD method and optimization techniques. As for the aero-acoustic analysis, CFD technique for aerodynamic analysis and Kirchhoff's method for the acoustic analysis were used. As for the optimization method, Kriging-based genetic algorithm(GA) model as a high-fidelity optimization method was chosen. Design variables and constraints are determined for arbitrary blade planform. The result shows that the optimized blade planform with high swept-back and taper ratio can reduce HSI noise by suppressing generation of the strong shock wave on blade surface and propagation of the noise to the farfield flow region.

• Journal of Microbiology and Biotechnology
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• v.17 no.7
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• pp.1090-1097
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• 2007

Genomic analysis of Thermococcus sp. NA1 revealed the presence of a 3,927-base-pair (bp) family B-type DNA polymerase gene, TNA1_pol. TNA1_pol, without its intein, was overexpressed in Escherichia coli, purified using metal affinity chromatography, and characterized. TNA1_pol activity was optimal at pH 7.5 and $75^{\circ}C$. TNA1_pol was highly thermostable, with a half-life of 3.5h at $100^{\circ}C$ and 12.5h at $95^{\circ}C$. Polymerase chain reaction parameters of TNA1_pol such as error-rate, processivity, and extension rate were measured in comparison with rTaq, Pfu, and KOD DNA polymerases. TNA1_pol averaged one incorrect bp every 4.45 kilobases (kb), and had a processivity of 150 nucleotides (nt) and an extension rate of 60 bases/s. Thus, TNA1_pol has a much faster elongation rate than Pfu DNA polymerase with 7-fold higher fidelity than that of rTaq.

• Plant Biotechnology Reports
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• v.2 no.3
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• pp.213-218
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• 2008

Swertia chirata is an endangered gentian species that prefers to grow at higher altitudes. This ethnomedicinal herb is known primarily for its bitter taste caused by the presence of important phytochemicals that are directly associated with human health benefits. Due to a continuous loss of habitat and inherent problems of seed viability and seed germination, alternative strategies for propagation and conservation are urgently required to prevent the possible extinction of this species. We have formulated a reproducible protocol for the rapid propagation and conservation of this plant using leaves taken from in vitro shoot cultures. Direct induction of more than seven shoot buds per explant was achieved for the first time when the explants were placed on MS medium supplemented with $2.22{\mu}M$ N-6-benzyladenine, $11.6{\mu}M$ kinetin, and $0.5{\mu}M$ ${\alpha}-naphthalene$ acetic acid. Direct organogenesis was noted exclusively from the adaxial surface of the basal segments of leaves. Leaves closer to the apical meristem were more responsive than those farther away from the meristem. Plants raised through direct organogenesis were evaluated for their clonal fidelity by chromosomal analysis and DNA fingerprinting. Complete plants were successfully transferred to the field condition and produced viable seeds. Given the enormous potential of this age-old medicinal plant in terms of potential health-benefitting drugs, this protocol can be used for commercial propagation purposes and to initiate future genetic improvement studies.

• Journal of Plant Biotechnology
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• v.8 no.1
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• pp.27-35
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• 2006

Plantlet regeneration in Asteracantha longifolia(L.) Nees (Acanthaceae), a medicinal herb has been achieved from seedling explants on basal MS medium. Three different seedling explants including node, internode and leaf segments on used. Of these three explant, leaf explants gave better response for both callus mediated organogenesis and direct multiple shoot induction. Number of explants showing differentiation of shout buds was higher on MS media supplemented with BA compared to kinetin. MS medium fortified with BA ($2.0mgl^{-1}$) and NAA ($0.5mgl^{-1}$) was found to be most suitable for both callus mediated organogenesis and elongation of shouts. The elongated shoots were successfully routed on MS medium fortified with NAA or IBA. Among them $0.1mgl^{-1}$ NAA or $0.2mgl^{-1}$ IBA provides better response for rhizogenesis. Regenerated plantlets were successfully established in soil where 85.4% or them developed into morphologically normal and fertile plants. RAPD profiling using four decamer primers confirmed the genetic uniformity of the regenerated plantlets and substantiated the efficacy and suitability of this protocol for in vitro propagation of A. longifolia.