• ETRI Journal
• /
• 제38권3호
• /
• pp.518-528
• /
• 2016

The searching of an extensive document database for documents that are locally similar to a given query document, and the subsequent detection of similar regions between such documents, is considered as an essential task in the fields of information retrieval and data management. In this paper, we present a framework for such a task. The proposed framework employs the method of short-read mapping, which is used in bioinformatics to reveal similarities between genomic sequences. In this paper, documents are considered biological objects; consequently, edit operations between locally similar documents are viewed as an evolutionary process. Accordingly, we are able to apply the method of evolution tracing in the detection of similar regions between documents. In addition, we propose heuristic methods to address issues associated with the different stages of the proposed framework, for example, a frequency-based fragment ordering method and a locality-aware interval aggregation method. Extensive experiments covering various scenarios related to the search of an extensive document database for documents that are locally similar to a given query document are considered, and the results indicate that the proposed framework outperforms existing methods.

• 약학회지
• /
• 제48권2호
• /
• pp.153-158
• /
• 2004

Paecilomyces tenuipes is one of the famous Chinese medicinal entomopathogenic fungi that parasite in the lavae of silkworm. A cytotoxic compound, 4$\beta$-acetoxyscirpendiol (ASD) was isolated from a methanolic extracts of Paecilomyces tenuipes. The ASD compound belongs to scirpenol subfamily of trichothecene mycotoxin. In a continuation of the elucidation of the mechanism of ASD, we report here the evidences of induction of apoptosis by ASD in human Jurkat T cell line. In MTT reduction assay for monitoring cell viability, ASD showed strong toxicity. The 50 percent inhibitory concentrations of ASD against human T lymphoid Jurkat cell was 59.5 ng/$m\ell$. Phosphatidylserine externalization was increased by ASD at 3 and 6 hrs when compared with that of 6 hrs in the cell line showing in a time-dependent manner. When whole lysates of cells treated with ASD were subjected to western blot assay, 113 kDa poly(ADP-ribose) polymerase (PARP) was significantly cleaved to 89 kDa fragment. Time-dependent DNA fragmentation was also observed when Jurkat T cells were treated with ASD at 100 ng/$m\ell$ for 6 hrs and 18 hrs at the ratios of 8.5% and 15.0%, respectively. From these data, Jurkat T lymphocytes treated with ASD from Paecilomyces tenuipes underwent typical cascades of apoptotic cell death.

• Journal of Plant Biotechnology
• /
• 제40권1호
• /
• pp.27-36
• /
• 2013

We isolated and functionally characterized a Dendrobium Actin1 (DmACT1) promoter that drives strong gene expression in the orchid genus Dendrobium. A genomic fragment containing the region 3227 bp upstream of the coding region of DmACT1 was obtained by inverse PCR. Detailed comparison of the full-length cDNA and genomic sequences revealed that DmACT1 has a 1374 bp first intron in the 5' UTR. However, the 5' flanking sequences upstream of the coding region showed no obvious sequence similarities compared to those of known promoters, including plant actin promoters. Serial deletion constructs of the 5' flanking region from the translation initiation codon were fused to the coding sequence of a GUS/luciferase fusion reporter to identify the regulatory elements necessary for promoter activity. Transient assays in the flowers of Dendrobium revealed that the 5' UTR-intron greatly enhanced promoter activity. Moreover, the DmACT1 promoter with its 5' UTR-intron yielded approximately 10-fold higher reporter activity than the rice Act1 promoter-intron. Our data suggest that the DmACT1 promoter with its 5' UTR-intron is a useful tool for strong expression of transgenes in Dendrobium orchids.

• Molecular & Cellular Toxicology
• /
• 제3권3호
• /
• pp.159-164
• /
• 2007

Stimulation of epidermal growth factor receptor (EGFR) is essential in signaling pathway of tumor cells. Thus, EGFR has intensely studied as an anticancer target. We developed hologram quantitative structure activity relationship (HQSAR) models for data set which consists of tricyclic azepine derivatives showing inhibitory activities for EGFR. The optimal HQSAR model was generated with fragment size of 6 to 7 while differentiating fragments having different atom and connectivity. The model showed cross-validated $q^2$ value of 0.61 and non-cross-validated $r^2$ value of 0.93. When the model was validated with an external set excluding one outlier, it gave predictive $r^2$ value of 0.43. The contribution maps generated from this model were used to interpret the atomic contribution of each atom to the overall inhibition activity. This can be used to find more efficient EGFR inhibitors.

• 한국축산식품학회지
• /
• 제25권3호
• /
• pp.328-332
• /
• 2005

The effect of k-casein (k-CN) variant on milk production traits (milk yield, fat yield, protein yield, fat percentage and protein percentage) was estimated for 568 Holstein cows in the first lactation. The k-CN valiant were determined by PCR-RFLP (restriction fragment length polymorphism) technique at the DNA level. Single trait linear model was used for the statistical analysis of the data. Result of this study indicated that k-CN variant affected significantly milk yield (P<0.05) and protein yield (P<0.01). Animals with the BB variant produced 622kg milk more and had protein yield higher by 32kg compared with animals with the AA variant No associations between the k-CN variants and other milk production trait were found. Therefore, milk and protein yield may be improved through milk protein typing by increasing the frequencies of k-CN B variant in dairy cattle population. In cheese making, it will be also preferable to have milk with the B variant of k-CN, which gives higher yield having a better quality than the A variant milk.

• 동의생리병리학회지
• /
• 제18권1호
• /
• pp.254-259
• /
• 2004

Jeongshin-tang (JST) is a Korean herbal prescription, which has been successfully applied for the various neuronal diseases. However, it's effect remains unknown in experimental models. To investigate the biological effect of JST in Alzheimer's disease (AD) in vitro model, we analized the production of interleukin (IL)-6 and IL-8, and expression of cyclooxygenase (COX)-2 in IL-1β plus β-amyloid [25-35] fragment (A)-stimulated human astrocytoma cell line U373MG. JST alone had no effect on the cell viability. The production of IL-6 and IL-8 was significantly inhibited by pretreatment with JST (1mg/㎖) on IL-1β plus A-stimulated U373MG cells. Maximal inhibition rate of IL-6 and IL-8 production by JST was about 41.22% (P<0.01) and 34.45% (P<0.05), respectively. The expression level of COX-2 protein was up-regulated by IL-1β plus A but the increased level of COX-2 was inhibited by pretreatment with JST (1 mg/㎖). These data indicate that JST has a regulatory effect on cytokine production and COX-2 expression, which might explain it's beneficial effect in the treatment of AD.

• Food Science and Biotechnology
• /
• 제18권5호
• /
• pp.1237-1242
• /
• 2009

Polymethoxylated flavones (PMFs) extracted from Citrus sinensis 'Jincheng' peel were characterized by chromatographic and spectroscopic techniques. Seven individual PMF were identified. 3, 3', 4', 5, 6, 7-hexamethoxyflavone (HEX), nobiletin (NOB), heptamethoxyflavone (HEP), 5-demethylnobiletin (DN), and tangeretin (TAN) were characterized through electrospray ionization mass spectrometry (ESI-MS) in positive mode of protonated molecular ions $[M+H]^+$, the diagnostic fragment ions, together with the UV-Vis spectra and high performance liquid chromatography (HPLC) elution order from literature data. Sinensetin (SIN) and tetramethyl-O-scutellarein (SCU) were isolated and identified through their MS, $^1H$ nuclear magnetic resonance (NMR) and UV-Vis spectral studies. The levels of PMFs in peels from different cultivars of citrus fruits grown in China were determined for the first time. The results showed that C. aurantium 'Bitter orange' peel was the most promising variety for HEP. C. sinensis peel was a good source for SIN and SCU.

• 한국해양바이오학회지
• /
• 제2권4호
• /
• pp.263-266
• /
• 2007

Vibrio vulnificusis a causative agent of serious diseases in humans resulting from the contact of wound with seawater or consumption of raw seafood. Several studies aimed at detecting V. vulnificus have targeted vvh as a representative virulence toxin gene belonging to the bacterium. In this study, we targeted the rpoS gene, a general stress regulator, to detect V. vulnificus. PCR specificity was identified by amplification of 8 V. vulnificus templates and by the loss of a PCR product with 36 non-V. vulnificus strains. The PCR assay had the 273-bp fragment and the sensitivity of 10 pg DNA from V. vulnificus. SYBR Green I-based real-time PCR assay targeting the rpoS gene showed a melting temperature of approximately $84^{\circ}C$ for V. vulnificus strains. The minimum level of detection by real-time PCR was 2 pg of purified genomic DNA, or $10^3$ V. vulnificus cells from pure cultured broth and $10^3$ cells in 1g of oyster tissue homogenates. These data indicate that real-time PCR is a sensitive, species-specific, and rapid method for detecting this bacterium using the rpoS gene in pure cultures and in infected oyster tissues.

• 한국약용작물학회지
• /
• 제21권6호
• /
• pp.455-460
• /
• 2013

Collected germplasms of five representative species belonging to Curcuma genus (C. longa, C. aromatica, C. zedoaria, C. phaeocaulis and C. kwangsiensis) were 52 samples from different farmhouse in Korea and China. To elucidate the genetic diversity among the species, 52 samples were analyzed by genomic fingerprinting method using amplified fragment length polymorphism (AFLP). AFLP results of 6 primer combinations were revealed 643 total DNA fragments and 349 polymorphic bands with the 54.3% ratio of polymorphism. In the analysis of coefficient similarity using unweight pair group method with arithmetic averages (UPGMA), 52 Curcuma germplasm lines were ranged from 0.60 to 0.99 and clustered distinct five groups according to the species and collected geographical levels. However, the result of principal coordinate analysis (PCA) by multi-variate analysis was shown significantly greater differences among species than geographical origins based on AFLP profiling data of these samples.

• 정보처리학회논문지B
• /
• 제16B권2호
• /
• pp.141-150
• /
• 2009

본 논문에서는 사람의 노랫소리를 자동으로 채보할 수 있는 시스템을 제안한다. 먼저 입력된 음성으로부터 추출된 피치 정보를 안정화된 역확산 방정식(Stabilized Inverse Diffusion Equation : SIDE)을 이용하여 음절 단위로 분할한다. 이를 바탕으로 유전자 알고리즘에 기반한 클러스터링을 통해 음길이 인식을 수행하였다. 또한 시창자의 음 높이에 강인한 음정 인식을 위하여 상대 음정이라는 개념을 도입하였다. 그리고 휴지기 정보를 이용한 마디 추출 알고리즘을 적용하여 보다 정확한 노래의 채보를 가능하게 하였다. 제안된 시스템을 통하여 동요 16곡을 채보한 결과 마디 인식률은 91.5%였으며, DMOS 방법으로 측정한 악곡 전체 유사도는 3.82로써 시스템 성능의 유효성을 확인할 수 있었다.