• Interdisciplinary Bio Central
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• v.6 no.4
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• pp.3.1-3.10
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• 2014

Amino acid substitution matrices are essential tools for protein sequence analysis, homology sequence search in protein databases and multiple sequence alignment. The PAM matrix was the first widely used amino acid substitution matrix. The BLOSUM series then succeeded the PAM matrix. Most substitution matrixes were developed by using the statistical frequency of substitution between each amino acid at blocks representing groups of protein families or related proteins. However, substitution of amino acids is based on the similarity of physiochemical properties of each amino acid. In this study, a new approach was used to obtain major physiochemical properties in multiple sequence alignment. Frequency of amino acid substitution in multiple sequence alignment database and selected attributes of amino acids in physiochemical properties database were merged. This merged data showed the major physiochemical properties through principle components analysis. Using factor analysis, these four principle components were interpreted as flexibility of electronic movement, polarity, negative charge and structural flexibility. Applying these four components, BAPS was constructed and validated for accuracy. When comparing receiver operated characteristic ($ROC_{50}$) values, BAPS scored slightly lower than BLOSUM and PAM. However, when evaluating for accuracy by comparing results from multiple sequence alignment with the structural alignment results of two test data sets with known three-dimensional structure in the homologous structure alignment database, the result of the test for BAPS was comparatively equivalent or better than results for prior matrices including PAM, Gonnet, Identity and Genetic code matrix.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.15 no.4
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• pp.765-772
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• 2011

In this paper, a simulation-based method is presented to dispose direction finders in three dimensional space for locating targets using the directional data. A direction finder(DF) is a military weapon that is used to find locations of targets that emit radio frequencies by operating two or more DFs simultaneously. If one or more DFs are operated in the air, the accuracy of location estimation can be enhanced by disposing them in a better configuration. By extending the line method, which is a well-known algorithm for 2-D location estimation, into 3-D space, the problem of 3-D location estimation is defined as an nonlinear programming form and solved analytically. Then the optimal disposition of DFs is considered with the presented method in which methods of simulation and search technique are combined. With the suggested algorithm for 3-D disposition of DFs, regions in which targets exist can be effectively covered so that the operation effect of DF be increased.

• BMB Reports
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• v.45 no.2
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• pp.102-107
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• 2012

The aim of this study was to investigate protein profiles related to the induction of adipogenesis within the bovine longissimus dorsi muscle (BLDM) by proteomic analysis. We analyzed BLDM proteins at different growth stages to clarify the physiological mechanisms of marbled muscle development in 20 head of Korean native cattle (11 month: 10 head, 17 month: 10 head). BLDM proteins were analyzed by two-dimensional electrophoresis and image analysis. Villin 2 was specifically identified by mass spectrometry and a protein search engine. Villin 2 protein expression in BLDM decreased during the fat development stage in test steers. In a Western blot cell culture study of spontaneously immortal bovine muscle fibroblasts, the abundance of Villin 2 was shown to be down-regulated during differentiation into muscle. In 3T3-L1 mouse embryonic fibroblasts, Villin 2 was decreased during differentiation into adipocytes. The results suggest that Villin 2 may be related to the induction of transdifferentiation and adipogenesis in bovine longissimus dorsi muscle.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.29 no.3B
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• pp.339-348
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• 2004

Packet classification is an important factor to support various services such as QoS guarantee and VPN for users in Internet. Packet classification is a searching process for best matching rule on rule tables by employing multi-field such as source address, protocol, and port number as well as destination address in If header. In this paper, we propose hardware based packet classification algorithm by employing tree bitmap of multi-bit trio. We divided prefixes of searching fields and rule into multi-bit stride, and perform a rule searching with multi-bit of fixed size. The proposed scheme can reduce the access times taking for rule search by employing indexing key in a fixed size of upper bits of rule prefixes. We also employ a marker prefixes in order to remove backtracking during searching a rule. In this paper, we generate two dimensional random rule set of source address and destination address using routing tables provided by IPMA Project, and compare its memory usages and performance.

• Journal of the Korean Geotechnical Society
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• v.16 no.1
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• pp.51-64
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• 2000

This paper presents a procedure of calculating a safety factor of the unsaturated slope suffering from the rainfall infiltration. The process of infiltration into a slope due to rainfall and its effect on the behavior of the soil slope are examined by using a two dimensional finite element flow-deformation coupled analysis. A factor of safety is calculated at various elapsed times after the commencement of rainfall as in the following procedure. First, stresses are estimated at each Gaussian point from the coupled finite element analysis. Then, the global stress smoothing method is applied to get a continuous stress field. Based on this stress field, a factor of safety is calculated for a specified slip surface by a stress integration scheme. Then, a search strategy is used to find out a critical slip surface which is associated with the minimum factor of safety. Some numerical examples are analyzed in order to study the effect of hydraulic conductivity on the slope stability during rain-induced infiltration. According to the results, local failure zone can be formed near the slope surface due to inhomogeneous distribution of hydraulic conductivity If the failure zone is once formed, then the region extends until a large amount of slide activates. Therefore the local failure can be neglected no longer in the stability analysis.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.131-131
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• 2017

Though the Platycodon grandiflorum, has a broad range of pharmacologic properties, but the mechanisms underlying these effects remain unclear. In order to profile proteins from the nodal segment, callus, root and shoot, high throughput proteome approach was executed in the present study. Two-dimensional gels stained with CBB, a total of 84 differential expressed proteins were confirmed out of 839 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 58 differential expressed protein spots (${\geq}2-fold$) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Out of 58 differential expressed protein, 32 protein spots were up-regulated such as ribulose-1,5-bisphosphate carboxylase, endoplasmic oxidoreductin-1, heat stress transcription factor A3, RNA pseudourine synthase 4, cysteine proteinase, GntR family transcriptional regulator, E3 xyloglucan 6-xylosyltransferase, while 26 differential protein spots were down-regulated such as L-ascorbate oxidase precursor, late embryogenesis abundant protein D-34, putative SCO1 protein, oxygen-evolving enhancer protein 3. However, the frequency distribution of identified proteins using iProClass databases, and assignment by function based on gene ontology revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding (17%), transferase activity (14%) and ion binding (12%). Taken together, the protein profile may provide insight clues for better understanding the characteristics of proteins and its metabolic activities in various explants of this essential medicinal plant P. grandiflorum.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.7
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• pp.922-926
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• 2005

The present study was aimed to investigate proteome affected by Panax ginseng extracts in chicken muscles. The whole muscle proteins from chicken fed boiled extracts of 0% (control), 1%, 3%, and 5% Panax ginseng in water were separated by two-dimensional electrophoresis (2-DE) gels using immobilized non-linear gradient (pH 3-10) strips. More than 300 protein spots were detected on silver staining gels. Among them, four protein spots were distinctively up-regulated by Panax ginseng treatments and further investigated by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The obtained MS data were searched against SwissProt database using the Mascot search engine. The up-regulated proteins were finally identified as $\alpha$-tropomyosin (2 spots), triosephosphate isomerase, and one unknown protein. Based on the known functions of the identified proteins, they are highly related to muscle development and enhanced immunity in chickens. These proteins can give valuable information of biochemical roles for Panax ginseng in chicken meats.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.1
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• pp.97-106
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• 2015

Platycodon grandiflorum, commonly known as Doraji in Korea, has a wide range of pharmacologic properties, such as reducing adiposity and hyperlipidemia, and antiatherosclerotic effects. However, the mechanisms underlying these effects remain unclear. In order to profile proteins from the nodal segment, callus, root and shoot, high throughput proteome approach was executed in the present study. Two dimensional gels stained with CBB, a total of 84 differential expressed proteins were confirmed out of 839 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 58 differential expressed protein spots (${\geq}$ 2-fold) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Out of 58 differential expressed protein, 32 protein spots were up-regulated such as ribulose-1,5-bisphosphate carboxylase, endoplasmic oxidoreductin-1, heat stress transcription factor A3, RNA pseudourine synthase 4, cysteine proteinase, GntR family transcriptional regulator, E3 xyloglucan 6-xylosyltransferase, while 26 differential protein spots were down-regulated such as L-ascorbate oxidase precursor, late embryogenesis abundant protein D-34, putative SCO1 protein, oxygen-evolving enhancer protein 3. However, frequency distribution of identified proteins using iProClass databases, and assignment by function based on gene ontology revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding (17%), transferase activity (14%) and ion binding (12%). In that way, the exclusive protein profile may provide insight clues for better understanding the characteristics of proteins and metabolic activity in various explants of the economically important medicinal plant Platycodon grandiflorum.

• Journal of Korean Society for Quality Management
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• v.48 no.2
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• pp.269-282
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• 2020

Purpose: The practical design for experiments with mixtures of q components is consisted in the four types of design points, vertex, center of edge, axial, and center points in a (q-1)-dimensional simplex space. We propose a sequential method for the successful construction of the design space in Quality by Design (QbD) by allowing the different number of replicates at the four types of design points in the practical design when the quadratic canonical polynomial model is assumed. Methods: To compare the mixture designs efficiency, fraction of design space (FDS) plot is used. We search for the practical mixture designs whose the minimal half-width of the tolerance interval per a standard deviation, which is denoted as d₂, is less than 4.5 at 0.8 fraction of the design space. They are found by adding the different number of replicates at the four types of the design points in the practical design. Results: The practical efficient mixture designs for the number of components between three and five are listed. The sequential method to establish a design space is illustrated with the two examples based on the simulated data. Conclusion: The designs with the center of edge points replications are more efficient than those with the vertex points replication. We propose the sample size of at least 23 for three components, 28 for four components, and 33 for the five components based on the list of efficient mixture designs.

• Science of Emotion and Sensibility
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• v.12 no.1
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• pp.129-136
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• 2009

Unlike former researches, this study for developing the caricature generator began observing the methods that other caricature experts have adopted. According to the observation, it seemed that experts tried to exaggerate characteristics of the target shape from other similar objects. When we are saying "This is similar to that," we give salience to their difference among the identical form groups. This study was to find the most similar geometry form to the target shape and then to transform its form through exaggeration. The research scope was restricted to exaggerate the outline shape of two-dimensional looped curve as a caricature form. For this, the author discussed the following: (a) organization method of four kinds of similar geometry form database, (b) search method to find the pertinent similar geometry form, (c) arrangement method for those searched data, and (d) method to exaggerate the target shape. Human faces and cars were selected as research categories to make the database. According to the survey over the transformed results, it was proved its possibility.