• Applied Biological Chemistry
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• v.48 no.4
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• pp.345-351
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• 2005

To access the natural products of uncultured microorganisms, we constructed and screened the metagenomic DNA libraries by using a cosmid vector and DNA inserts isolated directly from soil. Initial screening of the libraries in Escherichia coli resulted in the isolation of several clones that produce a dark brown color when grown in LB medium. One of the positive clones, designed pYS85C, was transposon mutagenized and the DNA surrounding the transposon insertions in cosmids that no longer conferred the production of brown pigment to E. coli was sequenced. Annotation of the pYS85C sequence obtained from the transposon mutagenesis experiment indicated a single 393 amino acid open reading frame (ORF) with a molecular mass of about 44.5 kDa, predicted to be a 4-hydroxyphenylpyruvate dioxygenases (HPPDs), was responsible for the observed brown pigment. In a BLAST search against deposited sequence, the translated protein from this ORF showed moderate-level identity (>60%) to the other known HPPDs and was most conserved in the C-terminal region of the protein. These results show that genes involved in natural product synthesis can be cloned directly from soil DNA and expressed in a heterologous host, supporting the idea that this technology has the potential to provide novel natural products from the wealth of environmental microbial diversity and is a potentially important new tool for drug discovery.

• Journal of KIISE:Databases
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• v.34 no.4
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• pp.304-314
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• 2007

Content Based Image Retrieval (CBIR) is to store and retrieve images using the feature description of image contents. In order to support more accurate image retrieval, it has become necessary to develop features that can effectively describe image contents. The commonly used low-level features, such as color, texture, and shape features may not be directly mapped to human visual perception. In addition, such features cannot effectively describe a single image that contains multiple objects of interest. As a result, the research on feature descriptions has shifted to focus on higher-level features, which support representations more similar to human visual perception like spatial relationships between objects. Nevertheless, the prior works on the representation of spatial relations still have shortcomings, particularly with respect to supporting rotational invariance, Rotational invariance is a key requirement for a feature description to provide robust and accurate retrieval of images. This paper proposes a high-level feature named 8AB (8 Angular Bin) that effectively describes the spatial relations of objects in an image while providing rotational invariance. With this representation, a similarity calculation and a retrieval technique are also proposed. In addition, this paper proposes a search-space pruning technique, which supports efficient image retrieval using the 8AB feature. The 8AB feature is incorporated into a CBIR system, and the experiments over both real and synthetic image sets show the effectiveness of 8AB as a high-level feature and the efficiency of the pruning technique.

• Journal of KIISE:Databases
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• v.34 no.4
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• pp.283-303
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• 2007

Recently, the study of efficient way to store and retrieve enormous music data is becoming the one of important issues in the multimedia database. Most general method of MIR (Music Information Retrieval) includes a text-based approach using text information to search a desired music. However, if users did not remember the keyword about the music, it can not give them correct answers. Moreover, since these types of systems are implemented only for exact matching between the query and music data, it can not mine any information on similar music data. Thus, these systems are inappropriate to achieve similarity matching of music data. In order to solve the problem, we propose an Efficient Query-By-Humming System (EQBHS) with a content-based indexing method that efficiently retrieve and store music when a user inquires with his incorrect humming. For the purpose of accelerating query processing in EQBHS, we design indices for significant melodies, which are 1) frequent melodies occurring many times in a single music, on the assumption that users are to hum what they can easily remember and 2) melodies partitioned by rests. In addition, we propose an error tolerated mapping method from a note to a character to make searching efficient, and the frequent melody extraction algorithm. We verified the assumption for frequent melodies by making up questions and compared the performance of the proposed EQBHS with N-gram by executing various experiments with a number of music data.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.2
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• pp.187-196
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• 2020

Objective: Porcine respiratory disease is one of the most important health problems causing significant economic losses. To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 single nucleotide polymorphisms in a total of 249 individuals based on genome-wide sequencing data. Methods: Genome comparison of susceptibility to swine EP in three pig breeds (Jinhua, Erhualian, and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using cross-population extended haplotype homozygosity and F-statistic (F_ST) statistical approaches identified 691 positively selected genes. Based on quantitative trait loci, gene ontology terms and literature search, we selected 14 candidate genes that have convincible biological functions associated with swine EP or human asthma. Results: Most of these genes were tested by several methods including transcription analysis and candidate genes association study. Among these genes: cytochrome P450 1A1 and catenin beta 1 (CTNNB1) are involved in fertility; transforming growth factor beta receptor 3 plays a role in meat quality traits; Wnt family member 2, CTNNB1 and transcription factor 7 take part in adipogenesis and fat deposition simultaneously; plasminogen activator, urokinase receptor (completely linked to AXL receptor tyrosine kinase, r² = 1) plays an essential role in the successful ovulation of matured oocytes in pigs; colipase like 2 (strongly linked to SAM pointed domain containing ETS transcription factor, r² = 0.848) is involved in male fertility. Conclusion: These adverse genes susceptible to swine EP may be selected while selecting for economic traits (especially reproduction traits) due to pleiotropic and hitchhiking effect of linked genes. Our study provided a completely new point of view to understand the genetic basis for susceptibility or resistance to swine EP in pigs thereby, provides insight for designing sustainable breed selection programs. Finally, the candidate genes are crucial due to their potential roles in respiratory diseases in a large number of species, including human.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.1
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• pp.145-150
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• 2014

MicroRNAs (miRNAs) negatively regulate gene expression and act as tumor suppressors or oncogenes in oncogenesis. The association between a single nucleotide polymorphism (SNP) in miR-146a rs2910164 and susceptibility to digestive system cancers was inconsistent in previous studies. In this study, we conducted a literature search of PubMed to identify all relevant studies published before August 31, 2013. A total of 21 independent case-control studies were included in this updated meta-analysis with 9,558 cases and 10,614 controls. We found that the miR-146a rs2910164 polymorphism was significantly associated with decreased risk of digestive system cancers in an allele model (OR=0.90, 95%CI 0.87-0.94), homozygote model (OR=0.84, 95%CI 0.77-0.91), dominant model (OR=0.90, 95%CI 0.84-0.96), and recessive model (OR=0.85, 95%CI 0.79-0.91), while in a heterozygous model (OR = 0.99, 95% CI 0.89-1.11) the association showed marginal significance. Subgroup analysis by cancer site revealed decreased risk in colorectal cancer above allele model (OR=0.90, 95%CI 0.83-0.97) and homozygote model (OR=0.85, 95%CI 0.72-1.00). Similarly, decreased cancer risk was observed when compared with allele model (OR=0.87, 95%CI 0.81-0.93) and recessive model (OR=0.81, 95%CI 0.72-0.90) in gastric cancer. When stratified by ethnicity, genotyping methods and quality score, decreased cancer risks were also observed. This current meta-analysis indicated that miR-146a rs2910164 polymorphism may decrease the susceptibility to digestive system cancers, especially in Asian populations.

• Journal of KIISE
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• v.41 no.9
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• pp.674-685
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• 2014

The Knowledge service system needs to infer a new knowledge from indicated knowledge to provide its effective service. Most of the Knowledge service system is expressed in terms of ontology. The volume of knowledge information in a real world is getting massive, so effective technique for massive data of ontology is drawing attention. This paper is to provide the method to infer massive data-ontology to the extent of RDFS, based on cloud computing environment, and evaluate its capability. RDFS inference suggested in this paper is focused on both the method applying MapReduce based on RDFS meta table, and the method of single use of cloud computing memory without using MapReduce under distributed file computing environment. Therefore, this paper explains basically the inference system structure of each technique, the meta table set-up according to RDFS inference rule, and the algorithm of inference strategy. In order to evaluate suggested method in this paper, we perform experiment with LUBM set which is formal data to evaluate ontology inference and search speed. In case LUBM6000, the RDFS inference technique based on meta table had required 13.75 minutes(inferring 1,042 triples per second) to conduct total inference, whereas the method applying the cloud computing memory had needed 7.24 minutes(inferring 1,979 triples per second) showing its speed twice faster.

• Journal of Microbiology and Biotechnology
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• v.23 no.11
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• pp.1519-1528
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• 2013

Bacillus pumilus SG2, a halotolerant strain, expresses two major chitinases designated ChiS and ChiL that were induced by chitin and secreted into the supernatant. The present work aimed to obtain a mutant with higher chitinolytic activity through mutagenesis of Bacillus pumilus SG2 using a combination of UV irradiation and nitrous acid treatment. Following mutagenesis and screening on chitin agar and subsequent formation of halos, the mutated strains were examined for degradation of chitin under different conditions. A mutant designated AV2-9 was selected owing to its higher chitinase activity. To search for possible mutations in the whole operon including ChiS and ChiL, the entire chitinase operon, including the intergenic region, promoter, and two areas corresponding to the ChiS and ChiL ORF, was suquenced. Nucleotide sequence analysis of the complete chitinase operon from the SG2 and AV2-9 strains showed the presence of a mutation in the catalytic domain (GH18) of chitinase (ChiL). The results demonstrated that a single base change had occurred in the ChiL sequence in AV2-9. The wild-type chitinase, ChiL, and the mutant (designated ChiLm) were cloned, expressed, and purified in E. coli. Both enzymes showed similar profiles of activity at different ranges of pH, NaCl concentration, and temperature, but the mutant enzyme showed approximately 30% higher catalytic activity under all the conditions tested. The results obtained in this study showed that the thermal stability of chitinase increased in the mutant strain. Bioinformatics analysis was performed to predict changes in the stability of proteins caused by mutation.

• KIPS Transactions on Computer and Communication Systems
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• v.6 no.9
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• pp.377-384
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• 2017

The performance improvement of a single core processor has reached its limit since the circuit density cannot be increased any longer due to overheating. Therefore, the multicore and manycore architectures have emerged as viable approaches and parallel programming becomes more important. Haskell, a purely functional language, is getting popular in this situation since it naturally supports parallel programming owing to its beneficial features including the implicit parallelism in evaluating expressions and the monadic tools supporting parallel constructs. However, the performance of Haskell parallel programs is strongly influenced by the performance of the run-time system including the garbage collector. Though a memory profiling tool namely GC-tune has been suggested, we need a more systematic way to use this tool. Since GC-tune finds the optimal memory size by executing the target program with all the different possible GC options, the GC-tuning time takes too long. This paper suggests a basic divide-and-conquer method to reduce the number of GC-tune executions by reducing the search area by one-quarter for every searching step. Applying this method to two parallel programs, a maximally independent set and a K-means programs, the memory tuning time is reduced by 7.78 times with accuracy 98% on average.

• Journal of Korea Water Resources Association
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• v.47 no.4
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• pp.343-356
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• 2014

The SWMM (storm water management model) has been widely used in the world and is a watershed runoff simulation model used for a single event or a continuous simulation of runoff quantity and quality. However, there are many uncertain parameters in the watershed runoff continuous simulation module and the water quality module, which make it difficult to use the SWMM. The purpose of the study is to develop an automatic calibration module of the SWMM not only for watershed runoff continuous simulation, but also water quality simulation. The automatic calibration module was developed by linking the SWMM with the SCE-UA (shuffled complex evolution-University of Arizona) that is a global optimization algorithm. Estimation parameters of the SWMM were selected and search ranges of them were reasonably configured. The module was validated by calibration and verification of the watershed runoff continuous simulation model and the water quality model for the Donghyang Stage Station Basin. The calibration results for watershed runoff continuous simulation model were excellent and those for water quality simulation model were generally satisfactory. The module could be used in various studies and designs for watershed runoff and water quality analyses.

• Journal of Global Scholars of Marketing Science
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• v.16 no.3
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• pp.169-189
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• 2006

The product categories that can be sold on-line are expanding. It is interesting to see which product categories have more sales possibilities on internet. Small-sized firms' products have low distribution coverage, low brand recognition, bigger dispersion in the perception on the values which consist of quality vs. price, and higher possibilities of perceived purchase risks. Since on-line shopping is supposed to provide opportunities to small-sized firms that have low distribution and brand power, it is quite necessary to evaluate the fitness of on-line sales for small-sized firms' product categories. There are virtually no research studies on the on-line sales for small-sized firms' product categories. In this study, based on the integration of SEC, FCB, and related concepts, we develop new theoretical framework and test the fitness of on-line sales for small-sized firms' product categories by conducting empirical analysis. The empirical results on 17 product categories show that SEC, FCB, purchase risks, brand factors are somewhat related. Unlike previous studies, since the fitness of SEC and on-line sales are not clearly shown, we need to consider those problems within inter-related multiple frameworks. That is, it is necessary to evaluate the fitness of on-line sales after defining the product categories within the integrated multiple frameworks rather than within the single framework.