• KIPS Transactions on Software and Data Engineering
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• v.3 no.12
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• pp.523-530
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• 2014

Ontology alignment is the way to share and reuse of ontology knowledge. Because of the ambiguity of concept, most ontology alignment systems combine a set of various measures and complete enumeration to provide the satisfactory result. However, calculating process becomes more complex and required time increases exponentially since the number of concept increases, more errors can appear at the same time. Lately the focus is on meta-matching using the heuristic algorithm. Existing meta-matching system tune extra parameter and it causes complex calculating, as a consequence, the results in the various data of specific domain are not good performed. In this paper, we propose a high performance algorithm by using DCS that can solve ontology alignment through simple process. It provides an efficient search strategy according to distribution of Levy Flight. In order to evaluate the approach, benchmark data from the OAEI 2012 is employed. Through the comparison of the quality of the alignments which uses DCS with state of the art ontology matching systems.

• Journal of Pharmacopuncture
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• v.11 no.2
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• pp.5-12
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• 2008

Objective In this article, we report on the intradermal Alcian blue staining method for tracing the meridians of acupuncture. Methods 1% Alcian blue solution was injected into acupoints by using a 0.5mL insulin syringe with a 31-gauge needle, then the skin was incised and was observed under a stereoscopic microscope. The specimens were examined by using immunohistochemical methods and were observed under a confocal laser scanning microscope. Results A threadlike structure, which was visualized with Alcian blue, existed in dermis layer and proceeded to hypodermis. In this structure, characteristic alignments of rod- shaped nuclei and $1-2{\mu}m$ sized DNA granules were observed. Furthermore, abundant blood capillary plexuses, peripheral nerve endings, and a corpuscle-like structure(about $300{\mu}m$ in diameter) were visualized in the skin tissues of acupoints. Conclusion It was concluded that the specific threadlike and corpuscle-like structures corresponded to superficial Bonghan duct and corpuscle, respectively.

• Journal of Microbiology and Biotechnology
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• v.11 no.6
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• pp.1046-1054
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• 2001

Bioleaching is the process in which insoluble metal sulfide is oxidized by specialized iron- and/or sulfur-oxidizing lithotrophic bacteria in acidic, metal-rich environments. Most of these processes are carried out by the genus Thiobacillus. Three novel Thiobacillus strains (Thiobacillus thiooxidans AZ11, Thiobacillus thiooxidans MET, and thiobacillus thiooxidans TAS) associated with bioleaching have been isolated from soil and sludge (Korean patent No. 1999-0073060 for T. thiooxidans AZ11, Korean patent No. 1999-0005798 for T. thiooxidans MET, and Korean patent No. 1999-0073059 for T. thiooxidans TAS). A partial sequence of 16S ribosomal RNA gene (16S rDNA) and the entire sequence of 16S/23S intergenic spacer region (ISR) were determined in the three above novel strains and in Thiobacillus ferrooxidans ATCC19859 as a reference strain. When phylogenetic analysis was performed based on G+C contents and sequence alignments, T. ferroxidans ATCC19859 was found to be closely related to previously registered T. ferrooxidans strains in a monophyletic manner, while the three novel T. thiooxidans strains were classified in a paraphyletic manner. Close examination on the base composition of 16S/23S ISR revealed that the 5\` part (nucleotide residues 21-200) was specific for the genus Thiobacillus. On the other end, the 3\` part (nucleotide residues 201-520) showed specificity in T. ferrooxidans strains, but not in T. thiooxidans strains. These results suggest that the proximal and distal halves of 16S/23S could be used as a genetic marker for the identification of the genus Thiobacillus and the species T. ferrooxidans, respectively.

• Journal of Microbiology and Biotechnology
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• v.14 no.3
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• pp.620-627
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• 2004

On the foundation of a database of genome sequences and protein analyses, the ability to clone a gene based on a peptide analysis is becoming more feasible and effective for identifying a specific gene and its protein product of interest. As such, the current study conducted a protein analysis using 2-D PAGE followed by MALDI- TOF and ESI-MS to identify a highly expressed gene product of C. parasitica. A distinctive and highly expressed protein spot with a molecular size of 47.2 kDa was randomly selected and MALDI-TOF MS analysis was conducted. A homology search indicated that the protein appeared to be a fungal enolase (enol). Meanwhile, multiple alignments of fungal enolases revealed a conserved amino acid sequence, from which degenerated primers were designed. A screening of the genomic $\lambda$ library of C. parasitica, using the PCR amplicon as a probe, was conducted to obtain the full-length gene, while RT-PCR was performed for the cDNA. The E. coli-expressed eno 1 exhibited enolase enzymatic activity, indicating that the cloned gene encoded the C. parasitica enolase. Moreover, ESI-MS of two of the separated peptides resolved from the protein spot on 2-D PAGE revealed sequences identical to the deduced sequences, suggesting that the cloned gene indeed encoded the resolved protein spot. Northern blot analysis indicated a consistent accumulation of an eno1 transcript during the cultivation.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.5
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• pp.615-621
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• 2007

AMP-activated protein kinase alpha 2 (PRKAA2) plays a key role in regulation of fatty acid and cholesterol metabolism. This study investigated the porcine PRKAA2 gene as a positional candidate for intramuscular fat and backfat thickness traits in pig chromosome 6. A partial fragment of the porcine PRKAA2 gene, amplified by PCR, contained a putative intron 3 including a part of exon 3 and 4, comparable with that of human PRKAA2 gene. Within the fragment, several single nucleotide polymorphisms were identified using multiple sequence alignments. Of these, TaqI restriction enzyme polymorphism was used for genotyping various pig breeds including Korean reference family. Using linkage and physical mapping, the porcine PRKAA2 gene was mapped in the region between microsatellite markers SW1881 and SW1680 on chromosome 6. Allele frequencies were quite different among pig breeds. The full length cDNA of the porcine PRKAA2 (2,145 bp) obtained by RACE containing 1,656 bp open reading frame of deduced 552 amino acids, had sequence identities with PRKAA2 of human (98.2%), rat (97.8%), and mouse (97.5%). These results suggested that the porcine PRKAA2 is a positional candidate gene for fat deposition trait at near telomeric region of the long arm of SSC 6.

• The KIPS Transactions:PartA
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• v.16A no.3
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• pp.143-152
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• 2009

One of the main issues in comparative genomics is to study chromosomal gene order in one or more related species. For this purpose, the whole genome alignment is usually applied to find the horizontal gene transfer, gene duplication, and gene loss between two related genomes. Also it is well known that the novel visualization tool with whole genome alignment is greatly useful for us to understand genome organization and evolution process. There are a lot of algorithms and visualization tools already proposed to find the "gene clusters" on genome alignments. But due to the huge size of whole genome, the previous visualization tools are not convenient to discover the relationship between two genomes. In this paper, we propose AlignScope, a novel visualization system for whole genome alignment, especially useful to find gene clusters between two aligned genomes. This AlignScope not only provides the simplified structure of genome alignment at any simplified level, but also helps us to find gene clusters. In experiment, we show the performance of AlignScope with several microbial genomes such as B. subtilis, B.halodurans, E. coli K12, and M. tuberculosis H37Rv, which have more than 5000 alignment pairs (matched DNA subsequence).

• International Journal of Highway Engineering
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• v.13 no.1
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• pp.59-67
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• 2011

It can prevent traffic accidents in a way as taking precautionary measures for road safety at signalized intersection in advance. Particularly, traffic accidents can be reduced at relatively low cost without redesigning alignments. That is 'Positive Guidance method' which can help prevent traffic accidents through improvement of road facilities at signalized intersection. In this study, potentially higher hazardous signalized intersection due to speeding was selected through site investigation. Field analysis at designated section was conducted and devised a plan for improvements of road facilities. Subjects drove in driving simulator in 3-D virtual reality of designated intersection. Based on data from simulator, statistical analysis(t-verification) was conducted for 'Before and After effectiveness' of speed reduction. As a result, it indicates that speed reduction was effective after improvements at each spot in driving simulator. In the future, hazardous signalized intersections which can be applied for PG method will be effective for road safety based on this research.

• Proceedings of the Polymer Society of Korea Conference
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• 2006.10a
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• pp.239-239
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• 2006

In the present study, we synthesized CBDA-FDA and its analogue, poly(4,4' -(9,9-fluorenyl)diphenylene pyromellitimide) (PMDA-FDA), and then investigated quantitatively the orientational distributions of the polymer chain segments in the surfaces of their films by using linearly polarized Fourier transform infrared (FTIR) spectroscopy and optical retardation analysis. We also examined the films' surface topographies using high spatial resolution atomic force microscopy (AFM). Further, rubbed films were used to assemble antiparallel and $90^{\circ}-twisted$ nematic (TN) LC cells, and the alignment behaviors, pretilt angles and anchoring energies of the LC molecules in the cells were determined. The films were found to have very interesting surface morphologies and LC alignment behaviors, which have not previously been reported. The observed LC alignments, pretilt angles and anchoring energies are discussed by taking into account the interactions of the LC molecules with the oriented polymer chain segments and the surface morphologies.

• The Korean Journal of Malacology
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• v.31 no.3
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• pp.233-241
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• 2015

Toll-like receptors (TLRs) are a major pattern recognition receptor that recognize the structure of invading pathogen and play key roles by triggering immune response. In this study, we identified a sequence of TLR homolog and characterized at molecular level from the abalone (Haliotis discus hannai). Multiple alignments and phylogenetic analysis of abalone TLR protein belongs to the TLR 2/6. Expression level of abalone TLR 2/6 in the tissue was comparatively high in the mantle, gill, digestive duct, and hemocytes, but lowest in the muscle. Expression level of abalone TLR 2/6 mRNA in the mantle, gill, digestive duct, and hemocytes was 20-fold, 60-fold, 115-fold, 112-fold higher than in the muscle, respectively. Expression level of abalone TLR 2/6 mRNA in the mantle was steadily increased until 12 h and decreased post-infection with Vibrio parahemolyticus. While the expression level of abalone TLR 2/6 mRNA in the gill and hemocytes was drastically increased at 6 and 9 h post-infection with Vibrio parahemolyticus, respectively. These results suggest that abalone TLR 2/6 is conserved through evolution and may play roles similar to its mammalian counterparts.

• Journal of the Korean Society of Tobacco Science
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• v.28 no.2
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• pp.100-110
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• 2006

A mutant of Potato vims Y (PVY) was occurred in PVY resistance flue-cured tobacco breeding line KF0402 $(TC1146{\times}KF117)$ showing vein necrosis at Suwon in Korea. This isolate, PVY-SWM, was differentiated from other PVY based on biological properties and nucleotide sequence analyses of coat protein gene. PVY-SWM caused typical symptoms on 21 indicator plants as compared to the PVY-TOJC37. Remarkably, the PVY-SWM induced distinctly different symptom of systemic vein necrosis on tobacco cultivars V.SCR, PBD6, TN86, TN90, Virgin A Mutant (VAM), Wislica, NC744, KB108 and KB111, which were reported to have the recessive potyvirus resistance gene va. In RT-PCR assays with specific primers for detection of PVY, a single band of about 800bp in length was produced. The amplified DNA was cloned and the nucleotide sequence was determined. The coat protein gene of PVY-SWM showed 88.4%-99.0% and 92.5%-98.5% identities to the 12 different PVY isolates of Genbank Database at the nucleotide and amino acidi respectively. Multiple alignments as well as cluster dendrograms of PVY-SWM isolate revealed close phylogenetic relationship to the $PVY^{NTN}$ subgroup.