• KSBB Journal
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• v.25 no.5
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• pp.490-496
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• 2010

As sequencing technologies are steadily improving, massive sequence data have been accumulated in public databases. Thereby, programs based on various algorithms are developed to mine useful information, such as genes, operons and regulatory factors,from these sequences. However, despite its usefulness in a wide range of applications, comprehensive analyses of metagenome using these programs have some drawbacks, thereby yielding inaccurate or complex results. We here provide a possibility of signature sequences (cis-acting transcriptional and translational factors of metagenome) as a hallmark of ORFs finding from metagenome.

• Journal of Microbiology and Biotechnology
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• v.10 no.5
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• pp.620-627
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• 2000

To determine the prevalence of genetic polymorphisms in Epstein-Barr virus (EBV) strains in the Korean population, the restriction site polymorphisms for BamHI and XhoI enzymes were analyzed with 16 EBV isolates from cancer patients and 7 EBV isolates from healthy carriers, using polymerase chain reaction techniques. None of the 23 isolates were found to carry an extra BamHI site in the BamHI F-fragment (f-variant). Of the 12 type-1 isolates from the cancer patients, 10 lost both the LMP1 XhoI site and the BamHI site between the BamHi W1* and I1* fragments (a W1*I1* fusion variant or type C). The latter W1*I1* fusion variant was due to a mutation of thymidine to adenine, as evidenced by a sequence analysis. The remaining two type-1 isolates showed either no variation at both sites or the loss of only the XhoI site. In contrast, two type-2 isolates and two intertypic recombinants with a type-1 allele at the EBNA2 locus and type-2 alleles at all or some of the EBNA3 loci retained both enzyme sites. In similar analyses of the 7 isolates from the healthy carriers, five of six type-1 isolates lost these two sites, however, one type-2 isolate did not. These results clearly indicate a strong association of both the LMP1 XhoI site loss and the W1*I1* fusion variant with the type-1 rather than the type-2 EBV strains circulating in the immunocompetent Korean carriers.

• Smart Structures and Systems
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• v.4 no.6
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• pp.727-740
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• 2008

A down hole vertical seismic array is a sequence of instruments installed at various depths in the earth to record the ground motion at multiple points during an earthquake. Numerous studies demonstrate the unique utility of vertical seismic arrays for studying in situ site response and soil behavior. Examples are given of analyses made at two sites to show the value of data from vertical seismic arrays. The sites examined are the Lotung, Taiwan SMART1 array and a new site installed at Jingliao, Taiwan. Details of the installation of the Jingliao array are given. ARX models are theoretically the correct process models for vertical wave propagation in the layered earth, and are used to linearly map deeper sensor input signals to shallower sensor output signals. An example of Event 16 at the Lotung array is given. This same data, when examined in detail with a Bayesian inference model, can also be explained by nonlinear filters yielding commonly accepted soil degradation curves. Results from applying an ARMAX model to data from the Jingliao vertical seismic array are presented. Estimates of inter-transducer soil increment resonant frequency, shear modulus, and damping ratio are presented. The shear modulus varied from 50 to 150 MPa, and damping ratio between 8% and 15%. A new hardware monitoring system - TerraScope - is an affordable 4-D down-hole seismic monitoring system based on independent, microprocessor-controlled sensor Pods. The Pods are nominally 50 mm in diameter, and about 120 mm long. An internal 16-bit micro-controller oversees all aspects of instrumentation, eight programmable gain amplifiers, and local signal storage.

• Journal of the Korean Society of Safety
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• v.29 no.4
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• pp.116-122
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• 2014

This study proposes a system reliability analysis of rack storage facilities subjected to forklift colliding events. The proposed system reliability analysis consists of two steps: the first step is to identify dominant failure modes that most contribute to the failure of the whole rack facilities, and the second step is to evaluate the system failure probability. In the first step, dominant failure modes are identified by using a simulation-based selective searching technique where the contribution of a failure mode to the system failure is roughly estimated based on the distance from the origin in the space of the random variables. In the second step, the multi-scale system reliability method is used to compute the system reliability where the first-order reliability method (FORM) is initially used to evaluate the component failure probability (failure probability of one member), and then the probabilities of the identified failure modes and their statistical dependence are evaluated, which is called as the lower-scale reliability analysis. Since the system failure probability is comprised of the probabilities of the failure modes, a higher-scale reliability analysis is performed again based on the results of the lower-scale analyses, and the system failure probability is finally evaluated. The illustrative example demonstrates the results of the system reliability analysis of the rack storage facilities subjected to forklift impact loadings. The numerical efficiency and accuracy of the approach are compared with the Monte Carlo simulations. The results show that the proposed two-step approach is able to provide accurate reliability assessment as well as significant saving of computational time. The results of the identified failure modes additionally let us know the most-critical members and their failure sequence under the complicated configuration of the member connections.

• Journal of the Korean Institute of Landscape Architecture
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• v.34 no.5 s.118
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• pp.24-31
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• 2006

The tourism sites and attractions of South Korea in many ways have little specialties in their image due to the local development plan's uniformed way of designing and improving landscape. The lack of specialties in tourist sites and attractions have caused displeasure from the local residents, as the sites don't characterize the locals as attractively and appealingly as is the potential. There have been no research or studies on the scenic effect on tourism or resort development thus producing an urgent call for local authorities to develop planned landscapes of local sites. This study compares Bugok Onchon (hot spring), whose image hardly differentiates itself from the others, with Kinosaki Onsen (hot spring). Bugok Hot Spring, which is the case study of this report, has recorded a steady decline of visitors due to a result of uniformed development planning. In the case of Kinosaki Hot Spring, scenery development, however, has made a breakthrough in tourist increase despite its no-so-easily-accessible location. The study assumes that scenery effects changes in promoting local tourism, thus analyzing and comparing the two hot springs to unearth critical factors in tourist site development, as well as viewing the present state of Bugok Hot Spring for further study. Furthermore, the study provides tourist site developers with a guideline of the two comparative Hot Spring cases. Investigations and analyses are mainly focused on colors, which are important factors in making underlying images of tourist sites, and the comparison of Bugok Hot Spring with Kinosaki Hot Suing. Bugok Hot Spring shows the influences of accent colors as well as a variety of color combinations and similarities of color tones. Kinosaki Hot Spring shows a combination of naturally-generated colors its own scenic beauty by trimming the landscape. Through the comparative study of the two hot springs, Bugok (boulevard) uncovers a typical case of Korean local landscape planning, even with the well-known tourist attraction 'Bugok-Hawaii', and calls upon a new, serious landscape-improvement plan to increase visitors.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.17 no.1
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• pp.284-289
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• 2016

In recent years, the earthquake sequence in Christchurch, New Zealand (NZ) was unprecedented in terms of repeated earthquake shocks with substantial levels of ground motion affecting modern infrastructure, and in particular, broad and precise reports for liquefaction-induced permanent ground deformation (PGD) and repairs of wastewater (WW) pipelines were collected. In this study, a geographical information system (GIS) and linear regression analysis were performed using data for the length and repair points of earthenware (EW) and concrete (CONC) wastewater pipelines acquired after the MW 6.2 February 22, 2011 earthquake. The repair rates (repairs/km) for the EW and CONC wastewater pipelines were evaluated inside the areas of PGD, and both angular distortion of ground and lateral ground strain were calculated from the high resolution LiDAR data acquired before and after the seismic event. The research results showed that both pipelines have similar trends of damage but the CONC wastewater pipeline with higher stiffness showed less damage. The results of linear regression analyses can be used to predict the repair rates for EW and CONC wastewater pipelines inside the areas of PGD induced by future earthquakes.

• Journal of Microbiology and Biotechnology
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• v.16 no.10
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• pp.1570-1576
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• 2006

An encephalomyocarditis virus (EMCV-CBNU) was isolated from an aborted swine fetus in October 2005. To investigate the genetic origin and virulence of the EMCV-CBNU strain, we determined the complete sequence of the virus and tested its virulence in mice. Genetic characterization revealed that the RNA genome was composed of 7,713 nucleotides with a single open reading frame (2,292 amino acids), coding 12 proteins. The EMCV-CBNU had the shortest poly(C) tract, consisting of 10 C's ($C_{10}$), compared with all the other EMCV strains reported in GenBank. Amino acid and phylogenetic analyses showed that EMCV-CBNU had the highest genetic identity with strain 2887A (99.7%), which was originally isolated from a fetus in a pig breeding farm that had a history of reproductive failure. Because rodents are the natural host of EMCV, we investigated the virulence of EMCV-CBNU in mice. Surprisingly, all mice inoculated with more than $1{\times}10^2\;TCID_{50}/0.1ml$ of EMCV-CBNU showed symptoms of hind limb paralysis and eventually died during 3 and 8 days postinoculation (DPI). Furthermore, when we inoculated the virus into pregnant mice, all dams and their fetuses died in 6 DPI. This is the first report on a full genomic analysis of swine EMCV in Korea, which exhibits high virulence in mice.

• Journal of Microbiology and Biotechnology
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• v.25 no.8
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• pp.1349-1360
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• 2015

The rhizospheric zone abutting plant roots usually clutches a wealth of microbes. In the recent past, enormous genetic resources have been excavated with potential applications in host plant interaction and ancillary aspects. Two Pseudomonas strains were isolated and identified through 16S rRNA and rpoD sequence analyses as P. fluorescens QAU67 and P. putida QAU90. Initial biochemical characterization and their root-colonizing traits indicated their potential role in plant growth promotion. Such aerobic systems, involved in gluconic acid production and phosphate solubilization, essentially require the pyrroloquinoline quinine (PQQ)-dependent glucose dehydrogenase (GDH) in the genome. The PCR screening and amplification of GDH and PQQ and subsequent induction of mutagenesis characterized their possible role as antioxidants as well as in growth promotion, as probed in vitro in lettuce and in vivo in rice, bean, and tomato plants. The results showed significant differences (p ≤ 0.05) in parameters of plant height, fresh weight, and dry weight, etc., deciphering a clear and in fact complementary role of GDH and PQQ in plant growth promotion. Our study not only provides direct evidence of the in vivo role of GDH and PQQ in host plants but also reveals their functional inadequacy in the event of mutation at either of these loci.

• The Plant Pathology Journal
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• v.33 no.4
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• pp.370-381
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• 2017

Rathayibacter tritici, which is a Gram positive, plant pathogenic, non-motile, and rod-shaped bacterium, causes spike blight in wheat and barley. For successful pathogenesis, R. tritici is associated with Anguina tritici, a nematode, which produces seed galls (ear cockles) in certain plant varieties and facilitates spread of infection. Despite significant efforts, little research is available on the mechanism of disease or bacteria-nematode association of this bacterium due to lack of genomic information. Here, we report the first complete genome sequence of R. tritici NCPPB 1953 with diverse features of this strain. The whole genome consists of one circular chromosome of 3,354,681 bp with a GC content of 69.48%. A total of 2,979 genes were predicted, comprising 2,866 protein coding genes and 49 RNA genes. The comparative genomic analyses between R. tritici NCPPB 1953 and R. toxicus strains identified 1,052 specific genes in R. tritici NCPPB 1953. Using the BlastKOALA database, we revealed that the flexible genome of R. tritici NCPPB 1953 is highly enriched in 'Environmental Information Processing' system and metabolic processes for diverse substrates. Furthermore, many specific genes of R. tritici NCPPB 1953 are distributed in substrate-binding proteins for extracellular signals including saccharides, lipids, phosphates, amino acids and metallic cations. These data provides clues on rapid and stable colonization of R. tritici for disease mechanism and nematode association.

• Animal Systematics, Evolution and Diversity
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• v.16 no.2
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• pp.169-176
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• 2000

As one of researches to clarify the taxonomic status of roe deer from Jeju island (C. pygargus tianschanicus), we analyzed partial sequences of mtDNA cytochrome b gene from six roe deers at Jeju island in Korea. Maximum nucleotide Tamura & Nei's distance among three haplotypes was 0.005, and this distance was comparable to the diversity within other roe deer subspecies: it is suggested that roe deers from the mainland dispersed rarely to Jejudo Island, although further analyses are ne-cessary to decide whether or not it was occurred by human introduction. Furthermore, nucleotide distance between cytochrome b sequences of roe deers from Jeju (C. pygargus tianschanicus) and the sequence of roe deer from west Siberia(C. p. pygargus), obtained from GenBank, was average 0.013, and it is suggested that C. p. tianschanicus diverged from C. p. pygargus of west Siberia 0.65 Myr ago.