• The Journal of the Korea Contents Association
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• v.14 no.11
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• pp.467-475
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• 2014

With the development of genomics, wearable device and IT/NT, a vast amount of bio-medical data are generated recently. Also, healthcare industries based on big-data are booming and big-data technology based on bio-medical data is rising rapidly as a core technology for improving the national health and aged society. A pathway is the biological deep knowledge that represents the relations of dynamics and interaction among proteins, genes and cells by a network. A pathway is wildly being used as an important part of a bio-medical big-data analysis. However, a pathway analysis requires a lot of time and effort because a pathway is very diverse and high volume. Also, multidimensional analysis systems for various pathways are nonexistent even now. In this paper, we proposed a pathway analysis system that collects user interest pathways from KEGG pathway database that supports the most widely used pathways, constructs a network based on a hierarchy structure of pathways and analyzes the relations of dynamics and interaction among pathways by clustering and selecting core pathways from the network. Finally, to verify the superiority of our pathway analysis system, we evaluate the performance of our system in various experiments.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.26-51
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• 2003

Large scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in thePDB. PSIMAP incorporates both functional and evolutionary information into a single network. It makes it possible to age protein domains in terms of taxonomic diversity, interaction and function. One consequence of it is to predict the most important protein domain structure in evolution. We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: ${\bullet}$ Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. ${\bullet}$ Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. ${\bullet}$ Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. This led to the prediction of the oldest and most important protein domain in evolution of lift. ${\bullet}$ Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level.

• Microbiology and Biotechnology Letters
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• v.47 no.4
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• pp.667-672
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• 2019

We compared two integration systems for stable expression of heterologous genes in Saccharomyces cerevisiae. A Candida glabrata-derived gene was used as the selective marker for the Cre/loxP system, and XYLP, XYLB, GRE3, and XYL2 genes were used as model heterologous genes and ligated into the universal pRS-CMT vector. The resulting pRS-XylP, pRS-XylB, pRS-Gre3, and pRS-Xyl2 plasmids were sequentially integrated into yeast chromosome VII by four integration processes (marker rescue and gene integration). The four introduced genes were successfully expressed. Further, the pRS-PBG2 plasmid harboring expression cassettes for the four genes was constructed for one-step integration. The four genes that were introduced were stably maintained as a gene cluster and were simultaneously expressed. The one-step integration was more effective for the simultaneous integration and expression of the four genes related to xylan/xylose metabolism. This method will enable the generation of a useful biosystem through appropriate use of gene integration methods.

• Journal of Korea Multimedia Society
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• v.1 no.2
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• pp.239-248
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• 1998

Software reengineering is making various research for solutions against problem of maintain existing system. Reengineering has a meaning of development of softwares on existing systems through the reverse-engineering and the forward-engineering. It extracts classes from existing system's softwares to increase the comprehension of the system and enhance the maintenability of softwares. Most of the important concepts used in reengineering is composition that is restructuring of the existing objects from other components. The classes and clusters in storage have structural relationship with system's main components to reuse in the higher level. These are referenced as dynamic informations through structuring an architect for each of them. The classes are created by extractor, searcher and composer through representing existing object-oriented source code. Each of classes and clusters extract refined informations through optimization. New architecture is created from the cluster based on its classes' relationship in storage. This information can be used as an executable code later on. In this paper, we propose the tools, it presented by this thesis presents a new information to users through analysing, based on reengineering, Object-Oriented informations and practicing composition methodology. These composite classes will increase reusability and produce higher comprehension information to consist maintainability for existing codes.

• Journal of KIISE:Computer Systems and Theory
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• v.34 no.9
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• pp.416-424
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• 2007

The Bio-Inspired system is a computing model that emulates the objects in ecosystem which are evolving themselves and cooperate each other to perform some tasks. Since it could be used to solved the complex problems that have been very difficult to resolve with previous algorithms, there have been a lot of researches to develop an application based on the Bio-Inspired system. However, since this computing model requires the process of evolving and cooperating with a lot of objects and this process takes a lot of times, it has been very hard to develop an application based on this computing model. This paper presents a parallel simulator for a Bio-Inspired system that is designed and implemented with OMNeT++ on PC clusters, and proves its usefulness by showing its simulation performance for a couple of applications. In the proposed parallel simulator, the functions required in the ERS platform for evolving and cooperating between objects (called Ecogent) are mapped onto the functions of OMNeT++, and they are simulated on PC clusters simultaneously to reduce the total simulation time. The simulation results could be monitored with a GUI In realtime, and they are also recorded into DBMS for systematic analyses afterward. This paper shows the usefulness of the proposed system by analyzing its performances for simulating various applications based on Bio-Inspired system on PC clusters with 4 PCs.

• Microbiology and Biotechnology Letters
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• v.34 no.2
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• pp.101-108
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• 2006

YNB54 strain which shows inhibitory activities specific to the plant pathogenic Phytophthora sp. on potato dextrose agar medium was screened among lots of strains isolated from Korean soils. To identify taxonomy of the Phytophthora specific antagonistic bacteria YNB54, 165 rDNA sequence, MIDI fatty acid composition, DNA-DNA hybridization, GC content, and commercial multitest systems such as API 20E and Biolog GN were performed. Results of commercial kits including lots of biochemical and physiological reactions showed that this strain was closely related to taxa including Enterobacter cloacae and Enterobacter cancerogenus species than other genera(Citerobacter Klebsiella, Leclercia). Also, analysis of its MIDI, G+C contents, and DNA-DNA hybridization suggests that this strain was more similiar to the Genus Enterobacter than other genera (Citerobacter Klebsiella, Leclercia). This strain was potentially identified as Enterobacter sp. by these results. But our 16S ribosomal DNA sequences (rDNA) analysis confirmed that it was more closely related to the cluster of Citerobacter freundii ATCC 29935 than any other Enterobacter species. In the absence of defined phylogenetic critia for delineating genera, the results observed with Citrobacter and Enterobacter species suggest that further studies are needed to clarify their relationships. This investigation demonstrates that YNB54 strain is genetically diverse and potentially more taxonomically complex than hitherto realized. Further study is necessary to confirm their taxonomic positions.

• Journal of Korea Spatial Information System Society
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• v.10 no.2
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• pp.63-79
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• 2008

With the recent development of advanced GIS and complex spatial analysis technologies, the more sophisticated technologies are being required to support the advanced knowledge for solving geographical or spatial problems in various decision support systems. In addition, necessity for research on scientific crime investigation and forensic science is increasing particularly at law enforcement agencies and investigation institutions for efficient investigation and the prevention of crimes. There are active researches on geographic profiling to predict the base location such as criminals' residence by analyzing the spatial patterns of serial crimes. However, as previous researches on geographic profiling use simply statistical methods for spatial pattern analysis and do not apply a variety of spatial and temporal analysis technologies on serial crimes, they have the low prediction accuracy. Therefore, this paper identifies the typology the spatio-temporal patterns of serial crimes according to spatial distribution of crime sites and temporal distribution on occurrence of crimes and proposes STA-BLP(Spatio-Temporal Analysis based Base Location Prediction) algorithm which predicts the base location of serial crimes more accurately based on the patterns. STA-BLP improves the prediction accuracy by considering of the anisotropic pattern of serial crimes committed by criminals who prefer specific directions on a crime trip and the learning effect of criminals through repeated movement along the same route. In addition, it can predict base location more accurately in the serial crimes from multiple bases with the local prediction for some crime sites included in a cluster and the global prediction for all crime sites. Through a variety of experiments, we proved the superiority of the STA-BLP by comparing it with previous algorithms in terms of prediction accuracy.

• Korean Journal of Social Welfare
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• v.57 no.2
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• pp.205-230
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• 2005

This study empirically examines if there is a certain linkage between the production regimes and welfare systems; and if linked, how they are linked. It also investigates what the different regimes performed in terms of economic growth and redistribution. As a matter of fact, we have a series of studies that explores structural diversity of production and welfare. However, the existing studies are limited in that they consider only specific facets of the structure, although the structure of welfare capitalism should be studied as a comprehensive whole. This is the gap which this study tries to overcome. The study is composed of two major parts. The first one is the cluster analysis that examines if Esping-Andersen's notion about three different welfare regime and the thesis of diversity of capitalism can be dealt within a single research framework. The second is the ANOVA analysis investigating if variables of production and welfare are to be statistically different in the trichotomy framework. According to the result of the analyses, we can find at least two important evidences about institutional complementaries of production and welfare. First, Esping-Andersen's framework is useful to comprehensively deal with production as well as welfare. Secondly, there are statistically different regimes of production and welfare in the context of political economic and social policy variables. What is the most striking conclusion of the study is that there is no difference among the regimes in terms of the level of economic efficiency; while we can find a huge differences in terms of the level of welfare effectiveness. In conclusion, there is no substantive evidence to argue that welfare is innately antithesis of economic growth.

• Journal of Advanced Marine Engineering and Technology
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• v.39 no.7
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• pp.760-764
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• 2015

Wireless sensors, installed on machinery, and Time Division Multiple Access (TDMA) transmission make an ideal system for monitoring machine conditions in industrial plants because there is no need for electronic wiring. However, there has not yet been a successful field application of such a system, capable of continuously transmitting data at sample rates greater than 100 Hz. In this research, a TDMA network protocol capable of acquiring data from multiple sensors at sample rates greater than 100 Hz was developed for field application. The protocol was implemented in a single cluster-star topology network, and the system was evaluated based on the node number and transmission distance. Network simulator 2 (ns-2) was used for a real field simulation. Non-TDMA and TDMA protocol cases were compared using four sensor nodes. In the cases of 20-s and 40-s transmission times, there was little difference between the reception rates of the non-TDMA and TDMA systems. However, the difference was much greater when using a 60-s transmission time.

• Journal of the Korean association of regional geographers
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• v.2 no.2
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• pp.1-8
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• 1996

The purpose of this study is to analyse the regional variation of tenancy system in later Yi-Dynasty in Korea. Materials for the analysis are acquired through materials(韓國土地農産調査報告), published in 1905 and agricultural census published in 1912. For the identification of difference of tenancy system between agricultural region, regionalization are conducted through by crop combination. Crop combination structure, using rank of LQ index, was clustered into five generic lesions through cluster analysis. In these contexts, this study has come to following conclusions. There are three types of tenancy system in materials; (1) Doji(賭地) system of which landrent was 1/3 agricultural products. Tenant healed the land tax and seeds. (2) Byoengjak(竝作) system of which landrent was 1/2 agricultural products. Landlords healed the land tax and seeds (3) Jeongaek(定額法) system of which landrent was fixed without relation to annual products. But through the analysis of relationship between agricultural region and tenancy system, a new tenancy system could be identified : Byeongjak(竝作) II system. In this system, landrent was 1/2 of agricultural products, but landlord and tenant shared the landtax and seed in common. In the distribution of these systems, relationship between tenancy system and agricultural regions could be identified. Doji system was distributed in the regions where rice and double cropping was specialized. But Byoeongjak(竝作) system was distributed in the regions where upland crops are specialized and ratio of Paddy field is comparatively low. Especially new types were emenged where ratio of paddy field was very low. These show that increase of productivity of land didn't induce the development of the right of ownership in land. The development of ownership was emerged only on the rice paddy fields. Barley cultivated through double-cropping passed into tenant's possessions. So nominal landrent in paddy field seemed to be raised, but actual landrent was maintained about 1/3 of Products through double cropping. On the contrary, rights of cultivation is developed through double cropping. As double cropping is developed, competition on paddy field between tenants was intensified. Consequently nominal land rent of Paddy fields should be raised.